[ { "id": "https://authors.library.caltech.edu/records/6b26e-8v344", "eprint_id": 118051, "eprint_status": "archive", "datestamp": "2023-11-20 19:08:14", "lastmod": "2024-01-09 22:21:17", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Salahshoor-Hossein", "name": { "family": "Salahshoor", "given": "Hossein" }, "orcid": "0000-0002-7264-7650" }, { "id": "Yao-Yuxing", "name": { "family": "Yao", "given": "Yuxing" }, "orcid": "0000-0003-0337-6372" }, { "id": "Dutka-Przemys\u0142aw", "name": { "family": "Dutka", "given": "Przemys\u0142aw" }, "orcid": "0000-0003-3819-1618" }, { "id": "Nystr\u00f6m-Nivin-N", "name": { "family": "Nystr\u00f6m", "given": "Nivin N." }, "orcid": "0000-0001-6288-6060" }, { "id": "Jin-Zhiyang", "name": { "family": "Jin", "given": "Zhiyang" }, "orcid": "0000-0002-4411-6991" }, { "id": "Min-Ellen", "name": { "family": "Min", "given": "Ellen" } }, { "id": "Malounda-Dina", "name": { "family": "Malounda", "given": "Dina" }, "orcid": "0000-0001-7086-9877" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Ortiz-M", "name": { "family": "Ortiz", "given": "Michael" }, "orcid": "0000-0001-5877-4824" }, { "id": "Shapiro-M-G", "name": { "family": "Shapiro", "given": "Mikhail G." }, "orcid": "0000-0002-0291-4215" } ] }, "title": "Geometric effects in gas vesicle buckling under ultrasound", "ispublished": "pub", "full_text_status": "public", "keywords": "Biophysics", "note": "The authors are grateful to Ngozi A. Eze for the helpful editorial comments. The authors are also grateful to Dr. Di Wu for insightful discussions and input. This research was supported by the National Institutes of Health grant R01-EB018975. Related research in the Shapiro lab is supported by the Packard Foundation, The Pew Charitable Trusts, and the Chan Zuckerberg Initiative. Cryo-EM was performed at the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech. M.G.S. is an investigator of the Howard Hughes Medical Institute (HHMI). This article is subject to HHMI's Open Access to Publications policy. HHMI Investigators have previously granted a nonexclusive CC BY 4.0 license to the public and a sublicensable license to HHMI in their research articles. Pursuant to those licenses, the author-accepted manuscript of this article can be made freely available under a CC BY 4.0 license immediately upon publication.\n\n
\u00a9 2022 Biophysical Society. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
\n\nH.S., Y.Y., P.D., and M.G.S. conceived and designed the study and wrote and edited the manuscript. H.S. and E.M. developed the computational models, performed the simulations, and analyzed the simulation data. Y.Y., P.D., Z.J., and D.M. conducted in vitro experiments and analyzed the experimental data. N.N.N. was involved in planning experiments and data analysis. M.G.S., M.O., and G.J.J. supervised the research. All authors read, edited, and confirmed the content of the manuscript.
", "abstract": "Acoustic reporter genes based on gas vesicles (GVs) have enabled the use of ultrasound to noninvasively visualize cellular function in vivo. The specific detection of GV signals relative to background acoustic scattering in tissues is facilitated by nonlinear ultrasound imaging techniques taking advantage of the sonomechanical buckling of GVs. However, the effect of geometry on the buckling behavior of GVs under exposure to ultrasound has not been studied. To understand such geometric effects, we developed computational models of GVs of various lengths and diameters and used finite element simulations to predict their threshold buckling pressures and postbuckling deformations. We demonstrated that the GV diameter has an inverse cubic relation to the threshold buckling pressure, whereas length has no substantial effect. To complement these simulations, we experimentally probed the effect of geometry on the mechanical properties of GVs and the corresponding nonlinear ultrasound signals. The results of these experiments corroborate our computational predictions. This study provides fundamental insights into how geometry affects the sonomechanical properties of GVs, which, in turn, can inform further engineering of these nanostructures for high-contrast, nonlinear ultrasound imaging.", "date": "2023-11-01", "date_type": "published", "publication": "Biophysical Journal", "volume": "121", "number": "21", "publisher": "Biophysical Society", "pagerange": "4221-4228", "id_number": "CaltechAUTHORS:20221128-494241100.5", "issn": "0006-3495", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20221128-494241100.5", "funders": { "items": [ { "agency": "David and Lucile Packard Foundation" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "R01-EB018975" }, { "agency": "Pew Charitable Trusts" }, { "agency": "Chan Zuckerberg Initiative" } ] }, "local_group": { "items": [ { "id": "GALCIT" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.bpj.2022.09.004", "pmcid": "PMC9674984", "primary_object": { "basename": "main.pdf", "url": "https://authors.library.caltech.edu/records/6b26e-8v344/files/main.pdf" }, "related_objects": [ { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/6b26e-8v344/files/mmc1.pdf" } ], "resource_type": "article", "pub_year": "2023", "author_list": "Salahshoor, Hossein; Yao, Yuxing; et el." }, { "id": "https://authors.library.caltech.edu/records/me61v-mhy57", "eprint_id": 122033, "eprint_status": "archive", "datestamp": "2023-08-22 20:53:20", "lastmod": "2023-12-22 23:34:57", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Dutka-Przemys\u0142aw", "name": { "family": "Dutka", "given": "Przemys\u0142aw" }, "orcid": "0000-0003-3819-1618" }, { "id": "Metskas-Lauren-Ann", "name": { "family": "Metskas", "given": "Lauren Ann" }, "orcid": "0000-0002-8073-6960" }, { "id": "Hurt-Robert-C", "name": { "family": "Hurt", "given": "Robert C." }, "orcid": "0000-0002-4347-6901" }, { "id": "Salahshoor-Hossein", "name": { "family": "Salahshoor", "given": "Hossein" }, "orcid": "0000-0002-7264-7650" }, { "id": "Wang-Ting-Yu", "name": { "family": "Wang", "given": "Ting-Yu" } }, { "id": "Malounda-Dina", "name": { "family": "Malounda", "given": "Dina" }, "orcid": "0000-0001-7086-9877" }, { "id": "Lu-George-Jiaozhi", "name": { "family": "Lu", "given": "George J." }, "orcid": "0000-0002-4689-9686" }, { "id": "Chou-Tsui-Fen", "name": { "family": "Chou", "given": "Tsui-Fen" }, "orcid": "0000-0003-2410-2186" }, { "id": "Shapiro-M-G", "name": { "family": "Shapiro", "given": "Mikhail G." }, "orcid": "0000-0002-0291-4215" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Structure of Anabaena flos-aquae gas vesicles revealed by cryo-ET", "ispublished": "pub", "full_text_status": "public", "keywords": "Molecular Biology; Structural Biology", "note": "\u00a9 2023 The Author(s). Published by Elsevier. Under a Creative Commons license. Attribution 4.0 International (CC BY 4.0).\n\nThe authors are grateful to Catherine Oikonomou for helpful editorial comments. We thank Songye Chen for assistance with tomography data collection. Electron microscopy was performed in the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech. The Proteome Exploration Laboratory (PEL) is supported by the Beckman Institute and National Institutes of Health 1S10OD02001301. This work was supported by the National Institutes of Health (R01-AI127401 to G.J.J. and R01-EB018975 to M.G.S.) and the Caltech Center for Environmental Microbial Interactions (CEMI). Related research in the Shapiro Laboratory is supported by the Packard Foundation, the Chan Zuckerberg Initiative, and the Heritage Medical Research Institute. M.G.S. is a Howard Hughes Medical Institute Investigator. \n\nAuthor contributions. P.D. conceived experiments, prepared samples, acquired and analyzed data, performed data exploration, drafted the manuscript, and prepared the figures. L.A.M. initiated the project and collected data for Mega GVs. R.C.H. performed mutation screening for GvpA and participated in initial sample preparation and optimization for Mega GVs. H.S. performed finite element simulation and analyzed data. T.-Y.W. performed XLMS experiments and analyzed the data. D.M. expressed and purified GV samples. G.L. participated in initial sample preparation and optimization for Mega GVs. T.-F.C. supervised XLMS experiments. All authors participated in correction of the manuscript. M.G.S. participated in guidance, experimental design, funding, and correction/advising on writing the manuscript. G.J.J. participated in guidance, experimental design, funding, and correction/advising on writing the manuscript. \n\nData and code availability:\nThe unprocessed tilt series used for the data analysis are available upon request. Representative tomograms for Ana, Mega, and Halo GVs have been deposited in the Electron Microscopy Data Bank under accession codes EMDB: EMD-29922, EMD-29925, EMD-29924, EMD-29923. Subtomogram averages for native Ana and AnaS GV shell have been deposited in EMDB under accession codes EMD-29921 and EMD-29916, respectively. The integrative model of Ana GvpA/GvpC has been deposited in the Protein Data Bank (PDB): 8GBS. The XLMS data have been deposited to the ProteomeXchange Consortium with the dataset identifier PXD038631. The code for ultrasound data collection and processing is available upon request. \n\nThe authors declare no competing interests.\n\nPublished - 1-s2.0-S0969212623000941-main.pdf
Supplemental Material - 1-s2.0-S0969212623000941-mmc1.pdf
", "abstract": "Gas vesicles (GVs) are gas-filled protein nanostructures employed by several species of bacteria and archaea as flotation devices to enable access to optimal light and nutrients. The unique physical properties of GVs have led to their use as genetically encodable contrast agents for ultrasound and MRI. Currently, however, the structure and assembly mechanism of GVs remain unknown. Here we employ cryoelectron tomography to reveal how the GV shell is formed by a helical filament of highly conserved GvpA subunits. This filament changes polarity at the center of the GV cylinder, a site that may act as an elongation center. Subtomogram averaging reveals a corrugated pattern of the shell arising from polymerization of GvpA into a \u03b2 sheet. The accessory protein GvpC forms a helical cage around the GvpA shell, providing structural reinforcement. Together, our results help explain the remarkable mechanical properties of GVs and their ability to adopt different diameters and shapes.", "date": "2023-05-04", "date_type": "published", "publication": "Structure", "volume": "31", "number": "5", "publisher": "Cell Press", "pagerange": "518-528", "id_number": "CaltechAUTHORS:20230628-257245000.39", "issn": "0969-2126", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230628-257245000.39", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "1S10OD02001301" }, { "agency": "NIH", "grant_number": "R01 AI127401" }, { "agency": "NIH", "grant_number": "R01 EB018975" }, { "agency": "Caltech Center for Environmental Microbial Interactions (CEMI)" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "Chan Zuckerberg Initiative" }, { "agency": "Heritage Medical Research Institute" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "local_group": { "items": [ { "id": "Caltech-Center-for-Environmental-Microbial-Interactions-(CEMI)" }, { "id": "Heritage-Medical-Research-Institute" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.str.2023.03.011", "pmcid": "PMC10185304", "primary_object": { "basename": "1-s2.0-S0969212623000941-main.pdf", "url": "https://authors.library.caltech.edu/records/me61v-mhy57/files/1-s2.0-S0969212623000941-main.pdf" }, "related_objects": [ { "basename": "1-s2.0-S0969212623000941-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/me61v-mhy57/files/1-s2.0-S0969212623000941-mmc1.pdf" } ], "resource_type": "article", "pub_year": "2023", "author_list": "Dutka, Przemys\u0142aw; Metskas, Lauren Ann; et el." }, { "id": "https://authors.library.caltech.edu/records/a0qff-47g29", "eprint_id": 121452, "eprint_status": "archive", "datestamp": "2023-08-22 20:48:05", "lastmod": "2023-12-22 23:11:00", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kaplan-Mohammed", "name": { "family": "Kaplan", "given": "Mohammed" }, "orcid": "0000-0002-0759-0459" }, { "id": "Yao-Qing", "name": { "family": "Yao", "given": "Qing" }, "orcid": "0000-0003-3575-9909" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Structure and Assembly of the Proteus mirabilis Flagellar Motor by Cryo-Electron Tomography", "ispublished": "pub", "full_text_status": "public", "keywords": "Inorganic Chemistry; Organic Chemistry; Physical and Theoretical Chemistry; Computer Science Applications; Spectroscopy; Molecular Biology; General Medicine; Catalysis", "note": "\u00a9 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). \n\n(This article belongs to the Special Issue Flagella 2.0) \n\nWe thank Douglas Weibel at the University of Wisconsin\u2013Madison for providing the Proteus mirabilis strain. We are grateful to George Auer from the University of Wisconsin\u2013Madison for his help in preparing the swarmer cells. \n\nThis project was funded by the National Institutes of Health (grant R01 AI127401 to G.J.J). \n\nAuthor Contributions. Conceptualization, M.K. and G.J.J.; methodology, M.K. and Q.Y.; software, M.K. and Q.Y.; validation, M.K., Q.Y. and G.J.J.; formal analysis, M.K. and G.J.J.; investigation, M.K.; resources, M.K. and G.J.J.; data curation, M.K. and Q.Y.; writing\u2014original draft preparation, M.K.; writing\u2014review and editing, M.K., Q.Y. and G.J.J.; visualization, M.K. and Q.Y.; supervision, G.J.J.; project administration, M.K. and G.J.J.; funding acquisition, G.J.J. All authors have read and agreed to the published version of the manuscript. \n\nData Availability Statement. All tomograms are available upon request. \n\nThe authors declare no conflict of interest.\n\nPublished - ijms-24-08292.pdf
Supplemental Material - ijms-24-08292-s001.zip
", "abstract": "Proteus mirabilis is a Gram-negative Gammaproteobacterium and a major causative agent of urinary tract infections in humans. It is characterized by its ability to switch between swimming motility in liquid media and swarming on solid surfaces. Here, we used cryo-electron tomography and subtomogram averaging to reveal the structure of the flagellar motor of P. mirabilis at nanometer resolution in intact cells. We found that P. mirabilis has a motor that is structurally similar to those of Escherichia coli and Salmonella enterica, lacking the periplasmic elaborations that characterize other more specialized gammaproteobacterial motors. In addition, no density corresponding to stators was present in the subtomogram average suggesting that the stators are dynamic. Finally, several assembly intermediates of the motor were seen that support the inside-out assembly pathway.", "date": "2023-05", "date_type": "published", "publication": "International Journal of Molecular Sciences", "volume": "24", "number": "9", "publisher": "MDPI", "pagerange": "Art. No. 8292", "id_number": "CaltechAUTHORS:20230519-1595000.11", "issn": "1422-0067", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230519-1595000.11", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 AI127401" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.3390/ijms24098292", "pmcid": "PMC10179241", "primary_object": { "basename": "ijms-24-08292.pdf", "url": "https://authors.library.caltech.edu/records/a0qff-47g29/files/ijms-24-08292.pdf" }, "related_objects": [ { "basename": "ijms-24-08292-s001.zip", "url": "https://authors.library.caltech.edu/records/a0qff-47g29/files/ijms-24-08292-s001.zip" } ], "resource_type": "article", "pub_year": "2023", "author_list": "Kaplan, Mohammed; Yao, Qing; et el." }, { "id": "https://authors.library.caltech.edu/records/htxbn-bhm86", "eprint_id": 120363, "eprint_status": "archive", "datestamp": "2023-08-22 20:37:50", "lastmod": "2023-12-22 23:10:35", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kreida-Stefan", "name": { "family": "Kreida", "given": "Stefan" }, "orcid": "0000-0003-1593-8360" }, { "id": "Narita-Akihiro", "name": { "family": "Narita", "given": "Akihiro" }, "orcid": "0000-0003-1504-9352" }, { "id": "Johnson-Matthew-D", "name": { "family": "Johnson", "given": "Matthew D." }, "orcid": "0000-0002-0808-3336" }, { "id": "Tocheva-Elitza-I", "name": { "family": "Tocheva", "given": "Elitza I." }, "orcid": "0000-0002-4869-8319" }, { "id": "Das-Anath", "name": { "family": "Das", "given": "Anath" }, "orcid": "0000-0002-2803-2018" }, { "id": "Ghosal-Debnath", "name": { "family": "Ghosal", "given": "Debnath" }, "orcid": "0000-0002-2227-0330" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Cryo-EM structure of the Agrobacterium tumefaciens T4SS-associated T-pilus reveals stoichiometric protein-phospholipid assembly", "ispublished": "pub", "full_text_status": "public", "keywords": "Molecular Biology; Structural Biology", "note": "\u00a9 2023 Elsevier Ltd.\n\nWe thank Dr. Songye Chen, Caltech cryo-EM facility, for assistance during data collection; Dr. Tsui-Fen Chou, Dr. Brett Lomenick, and Dr. Jeff Jones from the Caltech Proteome Exploration Laboratory for conducting the protein mass spectrometry analysis. We also thank Dr. Kevin Williams and UCLA Lipidomics for performing lipid extraction and lipid data collection and giving valuable advice in lipidomic experimental design and data interpretation. This project was funded by a National Institutes of Health grant (R01 AI127401 to G.J.J.), a National Health and Medical Research Council grant (APP1196924 to D.G.), and a Natural Sciences and Engineering Research Council of Canada Discovery grant (RGPIN 04345 to E.I.T.). S.K. is supported by the Swedish Research Council (2019-06293).\n\nAuthor contributions:\nConceptualization, G.J.J. and D.G.; methodology, S.K., A.N., A.D., E.I.T., M.D.J., and D.G.; investigation, S.K., A.N., AD., M.D.J., and D.G.; formal analysis, S.K., A.N., and D.G.; writing \u2013 original draft, S.K., D.G., and A.N.; writing \u2013 review & editing, S.K., A.N., M.D.J., E.I.T., A.D., D.G., and G.J.J.; visualization, A.N., D.G., and S.K.; supervision, A.D., G.J.J., and D.G.; funding acquisition, A.D., G.J.J., and D.G.\n\nThe authors declare no competing interests.\n\nData and code availability:\nThe Cryo-EM map and model have been deposited to EMBD (ID: EMD-28957) and RCSB (PDB ID: 8FAI), respectively. The raw data is available upon request.\n\nThis paper does not report original code.\n \nAny additional information required to reanalyze the data, including lipidomics raw data, presented in this study is available from the lead contact upon request.\n\nSupplemental Material - 1-s2.0-S0969212623000394-mmc1.pdf
", "abstract": "Agrobacterium tumefaciens causes crown gall disease in plants by the horizontal transfer of oncogenic DNA. The conjugation is mediated by the VirB/D4 type 4 secretion system (T4SS) that assembles an extracellular filament, the T-pilus, and is involved in mating pair formation between A. tumefaciens and the recipient plant cell. Here, we present a 3 \u00c5 cryoelectron microscopy (cryo-EM) structure of the T-pilus solved by helical reconstruction. Our structure reveals that the T-pilus is a stoichiometric assembly of the VirB2 major pilin and phosphatidylglycerol (PG) phospholipid with 5-start helical symmetry. We show that PG head groups and the positively charged Arg 91 residues of VirB2 protomers form extensive electrostatic interactions in the lumen of the T-pilus. Mutagenesis of Arg 91 abolished pilus formation. While our T-pilus structure is architecturally similar to previously published conjugative pili structures, the T-pilus lumen is narrower and positively charged, raising questions of whether the T-pilus is a conduit for ssDNA transfer.", "date": "2023-04-06", "date_type": "published", "publication": "Structure", "volume": "31", "number": "4", "publisher": "Cell Press", "pagerange": "385-394", "id_number": "CaltechAUTHORS:20230323-670848000.1", "issn": "0969-2126", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230323-670848000.1", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 AI127401" }, { "agency": "National Health and Medical Research Council (Australia)", "grant_number": "APP1196924" }, { "agency": "Natural Sciences and Engineering Research Council of Canada (NSERC)", "grant_number": "RGPIN 04345" }, { "agency": "Swedish Research Council", "grant_number": "2019-06293" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.str.2023.02.005", "primary_object": { "basename": "1-s2.0-S0969212623000394-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/htxbn-bhm86/files/1-s2.0-S0969212623000394-mmc1.pdf" }, "resource_type": "article", "pub_year": "2023", "author_list": "Kreida, Stefan; Narita, Akihiro; et el." }, { "id": "https://authors.library.caltech.edu/records/mcr2b-n1w85", "eprint_id": 122531, "eprint_status": "archive", "datestamp": "2023-08-22 18:25:32", "lastmod": "2023-12-22 23:08:56", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Nicolas-William-J", "name": { "family": "Nicolas", "given": "William J." }, "orcid": "0000-0001-5970-8626" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Meyerowitz-E-M", "name": { "family": "Meyerowitz", "given": "Elliot M." }, "orcid": "0000-0003-4798-5153" } ] }, "title": "Focused Ion Beam Milling and Cryo-electron Tomography Methods to Study the Structure of the Primary Cell Wall in Allium cepa", "ispublished": "pub", "full_text_status": "public", "keywords": "Plant Science; General Immunology and Microbiology; General Biochemistry, Genetics and Molecular Biology; General Neuroscience", "note": "\u00a9 2022 The Authors; exclusive licensee Bio-protocol LLC. \n\nThe work related to this protocol was supported by the Howard Hughes Medical Institute (HHMI) and grant R35 GM122588 to Grant J Jensen, and Austrian Science Fund (FWF): P33367 to Florian KM Schur. Cryo-EM work was done in the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech. \n\nThis article is subject to HHMI's Open Access to Publications policy. HHMI lab heads have previously granted a nonexclusive CC BY 4.0 license to the public and a sublicensable license to HHMI in their research articles. Pursuant to those licenses, the author-accepted manuscript of this article can be made freely available under a CC BY 4.0 license immediately upon publication. \n\nThere are no conflicts of interest or competing interests.\n\nPublished - Bio-protocol4559.pdf
", "abstract": "Cryo-electron tomography (cryo-ET) is a formidable technique to observe the inner workings of vitrified cells at a nanometric resolution in near-native conditions and in three-dimensions. One consequent drawback of this technique is the sample thickness, for two reasons: i) achieving proper vitrification of the sample gets increasingly difficult with sample thickness, and ii) cryo-ET relies on transmission electron microscopy (TEM), requiring thin samples for proper electron transmittance (<500 nm). For samples exceeding this thickness limit, thinning methods can be used to render the sample amenable for cryo-ET. Cryo-focused ion beam (cryo-FIB) milling is one of them and despite having hugely benefitted the fields of animal cell biology, virology, microbiology, and even crystallography, plant cells are still virtually unexplored by cryo-ET, in particular because they are generally orders of magnitude bigger than bacteria, viruses, or animal cells (at least 10 \u03bcm thick) and difficult to process by cryo-FIB milling. Here, we detail a preparation method where abaxial epidermal onion cell wall peels are separated from the epidermal cells and subsequently plunge frozen, cryo-FIB milled, and screened by cryo-ET in order to acquire high resolution tomographic data for analyzing the organization of the cell wall.", "date": "2022-12-05", "date_type": "published", "publication": "Bio-protocol", "volume": "12", "number": "23", "publisher": "Bio-Protocol", "pagerange": "Art. No. e4559", "id_number": "CaltechAUTHORS:20230725-706516000.44", "issn": "2331-8325", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230725-706516000.44", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "R35 GM122588" }, { "agency": "FWF Der Wissenschaftsfonds", "grant_number": "P33367" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.21769/bioprotoc.4559", "pmcid": "PMC9729855", "primary_object": { "basename": "Bio-protocol4559.pdf", "url": "https://authors.library.caltech.edu/records/mcr2b-n1w85/files/Bio-protocol4559.pdf" }, "resource_type": "article", "pub_year": "2022", "author_list": "Nicolas, William J.; Jensen, Grant J.; et el." }, { "id": "https://authors.library.caltech.edu/records/xkgq6-j7r79", "eprint_id": 120345, "eprint_status": "archive", "datestamp": "2023-08-22 18:00:17", "lastmod": "2023-12-22 23:14:53", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Boltje-Daan-B", "name": { "family": "Boltje", "given": "Daan B." }, "orcid": "0000-0003-4881-4700" }, { "id": "Hoogenboom-Jacob-P", "name": { "family": "Hoogenboom", "given": "Jacob P." }, "orcid": "0000-0003-4539-8772" }, { "id": "Jakobi-Arjen-J", "name": { "family": "Jakobi", "given": "Arjen J." }, "orcid": "0000-0002-7761-2027" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Jonker-Caspar-T-H", "name": { "family": "Jonker", "given": "Caspar T. H." } }, { "id": "Kaag-Max-J", "name": { "family": "Kaag", "given": "Max J." } }, { "id": "Koster-Abraham-J", "name": { "family": "Koster", "given": "Abraham J." }, "orcid": "0000-0003-1717-2549" }, { "id": "Last-Mart-G-F", "name": { "family": "Last", "given": "Mart G. F." }, "orcid": "0000-0002-3739-8863" }, { "id": "de-Agrela-Pinto-Cecilia", "name": { "family": "de Agrela Pinto", "given": "Cecilia" } }, { "id": "Plitzko-J\u00fcrgen-M", "name": { "family": "Plitzko", "given": "J\u00fcrgen M." }, "orcid": "0000-0002-6402-8315" }, { "id": "Raunser-Stefan", "name": { "family": "Raunser", "given": "Stefan" }, "orcid": "0000-0001-9373-3016" }, { "id": "Tacke-Sebastian", "name": { "family": "Tacke", "given": "Sebastian" }, "orcid": "0000-0002-4503-367X" }, { "id": "Wang-Zhexin", "name": { "family": "Wang", "given": "Zhexin" }, "orcid": "0000-0002-4256-1143" }, { "id": "van-der-Wee-Ernest-B", "name": { "family": "van der Wee", "given": "Ernest B." }, "orcid": "0000-0002-0139-4019" }, { "id": "Wepf-Roger-A", "name": { "family": "Wepf", "given": "Roger" }, "orcid": "0000-0003-2203-3674" }, { "id": "den-Hoedt-Sander", "name": { "family": "den Hoedt", "given": "Sander" } } ] }, "title": "A cryogenic, coincident fluorescence, electron, and ion beam microscope", "ispublished": "pub", "full_text_status": "public", "keywords": "General Immunology and Microbiology; General Biochemistry, Genetics and Molecular Biology; General Medicine; General Neuroscience", "note": "\u00a9 2022, Boltje et al. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited. \n\nDrosophila flight muscle myofibrils were kindly provided by EH Chan and F Schnorrer (Institut de Biologie du D\u00e9veloppement de Marseille), and zebrafish myofibrils by Y Hinits and M Gautel (King's College London). We express our gratitude to Fulvio Reggiori (University of Groningen, Netherlands) for providing the HeLa cells and are thankful to Mingjun Xu for help during sample preparation. We thank Andries Effting (Delmic BV) for helpful discussions, and we would like to thank Ryan Lane (TU Delft) for his contribution in various Python developments. The majority of the 3D CAD design was done by Thomas van der Heijden (Delmic BV), for which we are grateful. This work was financially supported by NWO-TTW project no. 17152 to JPH, NIH grant RO1 AI127401 to GJJ, European SME2 grant no. 879673 to Delmic BV, Eurostars grant no. E13008 to SH & SR, and ERC grant ERC-StG-852880 to AJJ. \n\nThe funders had no role in study design, data collection, and interpretation, or the decision to submit the work for publication.\n\nPublished - elife-82891.pdf
", "abstract": "Cryogenic electron tomography (cryo-ET) combined with subtomogram averaging, allows in situ visualization and structure determination of macromolecular complexes at subnanometre resolution. Cryogenic focused ion beam (cryo-FIB) micromachining is used to prepare a thin lamella-shaped sample out of a frozen-hydrated cell for cryo-ET imaging, but standard cryo-FIB fabrication is blind to the precise location of the structure or proteins of interest. Fluorescence-guided focused ion beam (FIB) milling at target locations requires multiple sample transfers prone to contamination, and relocation and registration accuracy is often insufficient for 3D targeting. Here, we present in situ fluorescence microscopy-guided FIB fabrication of a frozen-hydrated lamella to address this problem: we built a coincident three-beam cryogenic correlative microscope by retrofitting a compact cryogenic microcooler, custom positioning stage, and an inverted widefield fluorescence microscope (FM) on an existing FIB scanning electron microscope. We show FM controlled targeting at every milling step in the lamella fabrication process, validated with transmission electron microscope tomogram reconstructions of the target regions. The ability to check the lamella during and after the milling process results in a higher success rate in the fabrication process and will increase the throughput of fabrication for lamellae suitable for high-resolution imaging.", "date": "2022-10-28", "date_type": "published", "publication": "eLife", "volume": "11", "publisher": "eLife Sciences Publications", "pagerange": "Art. No. e82891", "id_number": "CaltechAUTHORS:20230322-367800000.31", "issn": "2050-084X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230322-367800000.31", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)", "grant_number": "17152" }, { "agency": "NIH", "grant_number": "RO1 AI127401" }, { "agency": "European Research Council (ERC)", "grant_number": "879673" }, { "agency": "Eurostars", "grant_number": "E13008" }, { "agency": "European Research Council (ERC)", "grant_number": "852880" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.7554/elife.82891", "pmcid": "PMC9714966", "primary_object": { "basename": "elife-82891.pdf", "url": "https://authors.library.caltech.edu/records/xkgq6-j7r79/files/elife-82891.pdf" }, "resource_type": "article", "pub_year": "2022", "author_list": "Boltje, Daan B.; Hoogenboom, Jacob P.; et el." }, { "id": "https://authors.library.caltech.edu/records/83chr-xfe88", "eprint_id": 117862, "eprint_status": "archive", "datestamp": "2023-08-22 17:57:00", "lastmod": "2023-12-22 23:15:10", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Metskas-Lauren-Ann", "name": { "family": "Metskas", "given": "Lauren Ann" }, "orcid": "0000-0002-8073-6960" }, { "id": "Wilfong-Rosalie", "name": { "family": "Wilfong", "given": "Rosalie" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Subtomogram averaging for biophysical analysis and supramolecular context", "ispublished": "pub", "full_text_status": "public", "keywords": "Structural Biology", "note": "We thank S. Chen and A. Malyutin for assistance with the tomography data collection script, and A. Burt for pseudocode to transition between Dynamo and Relion software packages. This work was supported by a Ruth L. Kirschstein NRSA Individual Postdoctoral Fellowship F32 1F32GM135994-01 to LAM, NIAID New Innovators Award 1DP2AI164293-01 to LAM, and NIH R01 AI127401 to GJJ.", "abstract": "Recent advances in hardware, software and computing power have led to increasingly ambitious applications of cryo-electron tomography and subtomogram averaging. It is now possible to reveal both structures and biophysical relationships like protein binding partners and small molecule occupancy in these experiments. However, some data processing choices require the user to prioritize structure or biophysical context. Here, we present a modified subtomogram averaging approach that preserves both capabilities. By increasing the accuracy of particle-picking, performing alignment and averaging on all subtomograms, and decreasing reliance on symmetry and tight masks, the usability of tomography and subtomogram averaging data for biophysical analyses is greatly increased without negatively impacting structural refinements.", "date": "2022-10-18", "date_type": "published", "publication": "Journal of Structural Biology: X", "volume": "6", "publisher": "Elsevier BV", "pagerange": "Art. No. 100076", "id_number": "CaltechAUTHORS:20221114-805533100.17", "issn": "2590-1524", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20221114-805533100.17", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "1DP2AI164293-01" }, { "agency": "NIH Postdoctoral Fellowship", "grant_number": "1F32GM135994-01" }, { "agency": "NIH", "grant_number": "R01 AI127401" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.yjsbx.2022.100076", "pmcid": "PMC9596874", "resource_type": "article", "pub_year": "2022", "author_list": "Metskas, Lauren Ann; Wilfong, Rosalie; et el." }, { "id": "https://authors.library.caltech.edu/records/wvpk5-f6j05", "eprint_id": 116664, "eprint_status": "archive", "datestamp": "2023-08-22 17:39:33", "lastmod": "2023-12-22 23:15:12", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Pakharukova-Natalia", "name": { "family": "Pakharukova", "given": "Natalia" }, "orcid": "0000-0002-8363-6105" }, { "id": "Malmi-Henri", "name": { "family": "Malmi", "given": "Henri" }, "orcid": "0000-0001-9872-8523" }, { "id": "Tuittila-Minna", "name": { "family": "Tuittila", "given": "Minna" } }, { "id": "Dahlberg-Tobias", "name": { "family": "Dahlberg", "given": "Tobias" } }, { "id": "Ghosal-Debnath", "name": { "family": "Ghosal", "given": "Debnath" }, "orcid": "0000-0002-2227-0330" }, { "id": "Chang-Yi-Wei", "name": { "family": "Chang", "given": "Yi-Wei" }, "orcid": "0000-0003-2391-473X" }, { "id": "Myint-Si-Lhyam", "name": { "family": "Myint", "given": "Si Lhyam" } }, { "id": "Paavilainen-Sari", "name": { "family": "Paavilainen", "given": "Sari" } }, { "id": "Knight-Stefan-David", "name": { "family": "Knight", "given": "Stefan David" }, "orcid": "0000-0002-7180-8758" }, { "id": "Lamminm\u00e4ki-Urpo", "name": { "family": "Lamminm\u00e4ki", "given": "Urpo" } }, { "id": "Uhlin-Bernt-Eric", "name": { "family": "Uhlin", "given": "Bernt Eric" }, "orcid": "0000-0002-2991-8072" }, { "id": "Andersson-Magnus", "name": { "family": "Andersson", "given": "Magnus" }, "orcid": "0000-0002-9835-3263" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant" }, "orcid": "0000-0003-1556-4864" }, { "id": "Zavialov-Anton-V", "name": { "family": "Zavialov", "given": "Anton V." }, "orcid": "0000-0001-6191-5931" } ] }, "title": "Archaic chaperone-usher pili self-secrete into superelastic zigzag springs", "ispublished": "pub", "full_text_status": "public", "keywords": "Multidisciplinary", "note": "We thank the staff of the Cryo-EM Swedish National Facility at SciLifeLab, Stockholm and the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech, Pasadena for their assistance during data collection; and C. Sachse, J. Huiskonen and S. Huber for their suggestions on helical reconstruction. This work was supported by grants from the Academy of Finland (321762) and S. Juselius Foundation (2019) to A.V.Z.; the National Institutes of Health (RO1 AI127401) to G.J.; the Swedish Research Council (SRC) (2019-04016) to M.A.; SRC (2019-01720) and The Kempe Foundations (JCK-1724) to B.E.U.; and SRC (2016-04451) to S.D.K.\n\nOpen access funding provided by University of Turku (UTU) including Turku University Central Hospital.", "abstract": "Adhesive pili assembled through the chaperone\u2013usher pathway are hair-like appendages that mediate host tissue colonization and biofilm formation of Gram-negative bacteria. Archaic chaperone\u2013usher pathway pili, the most diverse and widespread chaperone\u2013usher pathway adhesins, are promising vaccine and drug targets owing to their prevalence in the most troublesome multidrug-resistant pathogens. However, their architecture and assembly\u2013secretion process remain unknown. Here, we present the cryo-electron microscopy structure of the prototypical archaic Csu pilus that mediates biofilm formation of Acinetobacter baumannii\u2014a notorious multidrug-resistant nosocomial pathogen. In contrast to the thick helical tubes of the classical type 1 and P pili, archaic pili assemble into an ultrathin zigzag architecture secured by an elegant clinch mechanism. The molecular clinch provides the pilus with high mechanical stability as well as superelasticity, a property observed\u00a0for the first time,\u00a0to our knowledge, in biomolecules, while enabling a more economical and faster pilus production. Furthermore, we demonstrate that clinch formation at the cell surface drives pilus secretion through the outer membrane. These findings suggest that clinch-formation inhibitors might represent a new strategy to fight multidrug-resistant bacterial infections.", "date": "2022-09-08", "date_type": "published", "publication": "Nature", "volume": "609", "publisher": "Nature Publishing Group", "pagerange": "335-340", "id_number": "CaltechAUTHORS:20220901-478558800.783", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220901-478558800.783", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Academy of Finland", "grant_number": "321762" }, { "agency": "S. Juselius Foundation" }, { "agency": "NIH", "grant_number": "RO1 AI127401" }, { "agency": "Swedish Research Council", "grant_number": "2019-04016" }, { "agency": "Swedish Research Council", "grant_number": "2019-01720" }, { "agency": "Kempe Foundation", "grant_number": "JCK-1724" }, { "agency": "Swedish Research Council", "grant_number": "2016-04451" }, { "agency": "University of Turku" }, { "agency": "Turku University Central Hospital" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1038/s41586-022-05095-0", "resource_type": "article", "pub_year": "2022", "author_list": "Pakharukova, Natalia; Malmi, Henri; et el." }, { "id": "https://authors.library.caltech.edu/records/wxejd-3sm32", "eprint_id": 116620, "eprint_status": "archive", "datestamp": "2023-08-22 17:24:28", "lastmod": "2023-12-22 23:15:19", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Metskas-Lauren-Ann", "name": { "family": "Metskas", "given": "Lauren Ann" }, "orcid": "0000-0002-8073-6960" }, { "id": "Ortega-Davi-R", "name": { "family": "Ortega", "given": "Davi" }, "orcid": "0000-0002-8344-2335" }, { "id": "Oltrogge-Luke-M", "name": { "family": "Oltrogge", "given": "Luke M." }, "orcid": "0000-0001-5716-9980" }, { "id": "Blikstad-Cecilia", "name": { "family": "Blikstad", "given": "Cecilia" }, "orcid": "0000-0001-5740-926X" }, { "id": "Lovejoy-Derik-R", "name": { "family": "Lovejoy", "given": "Derik R." } }, { "id": "Laughlin-Thomas-G", "name": { "family": "Laughlin", "given": "Thomas G." }, "orcid": "0000-0001-8943-1330" }, { "id": "Savage-David-F", "name": { "family": "Savage", "given": "David F." }, "orcid": "0000-0003-0042-2257" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Rubisco forms a lattice inside alpha-carboxysomes", "ispublished": "pub", "full_text_status": "public", "keywords": "General Physics and Astronomy; General Biochemistry, Genetics and Molecular Biology; General Chemistry; Multidisciplinary", "note": "Cryo-electron microscopy was done in the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech, and subtomogram alignment and averaging used the Caltech Resnick High Performance Computing Center. We thank S. Chen and A. Malyutin for assistance with tomography data collection, A. Burt for pseudocode to transition between Dynamo and Relion software packages, and A. Pranger for assistance reconstructing cellular tomograms. This work was supported by a Ruth L. Kirschstein NRSA Individual Postdoctoral Fellowship F32 1F32GM135994-01 to L.A.M., NIH R01GM129241 to D.F.S., and NIH R01 AI127401 to G.J.J.", "abstract": "Despite the importance of microcompartments in prokaryotic biology and bioengineering, structural heterogeneity has prevented a complete understanding of their architecture, ultrastructure, and spatial organization. Here, we employ cryo-electron tomography to image \u03b1-carboxysomes, a pseudo-icosahedral microcompartment responsible for carbon fixation. We have solved a high-resolution subtomogram average of the Rubisco cargo inside the carboxysome, and determined the arrangement of the enzyme. We find that the H. neapolitanus Rubisco polymerizes in vivo, mediated by the small Rubisco subunit. These fibrils can further pack to form a lattice with six-fold pseudo-symmetry. This arrangement preserves freedom of motion and accessibility around the Rubisco active site and the binding sites for two other carboxysome proteins, CsoSCA (a carbonic anhydrase) and the disordered CsoS2, even at Rubisco concentrations exceeding 800 \u03bcM. This characterization of Rubisco cargo inside the \u03b1-carboxysome provides insight into the balance between order and disorder in microcompartment organization.", "date": "2022-08-18", "date_type": "published", "publication": "Nature Communications", "volume": "13", "number": "1", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 4863", "id_number": "CaltechAUTHORS:20220829-467858200.777", "issn": "2041-1723", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220829-467858200.777", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "F32 1F32GM135994-01" }, { "agency": "NIH", "grant_number": "R01GM129241" }, { "agency": "NIH", "grant_number": "R01 AI127401" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1038/s41467-022-32584-7", "resource_type": "article", "pub_year": "2022", "author_list": "Metskas, Lauren Ann; Ortega, Davi; et el." }, { "id": "https://authors.library.caltech.edu/records/3wpcj-x8704", "eprint_id": 115975, "eprint_status": "archive", "datestamp": "2023-10-24 19:34:06", "lastmod": "2024-01-09 22:18:45", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kaplan-Mohammed", "name": { "family": "Kaplan", "given": "Mohammed" } }, { "id": "Oikonomou-Catherine-M", "name": { "family": "Oikonomou", "given": "Catherine M." } }, { "id": "Wood-Cecily-R", "name": { "family": "Wood", "given": "Cecily R." } }, { "id": "Chreifi-Georges", "name": { "family": "Chreifi", "given": "Georges" } }, { "id": "Ghosal-Debnath", "name": { "family": "Ghosal", "given": "Debnath" } }, { "id": "Dobro-Megan-J", "name": { "family": "Dobro", "given": "Megan J." } }, { "id": "Yao-Qing", "name": { "family": "Yao", "given": "Qing" } }, { "id": "Pal-Ritesh-Ranjan", "name": { "family": "Pal", "given": "Ritesh Ranjan" } }, { "id": "Baidya-Amit-K", "name": { "family": "Baidya", "given": "Amit K." } }, { "id": "Liu-Yuxi", "name": { "family": "Liu", "given": "Yuxi" } }, { "id": "Maggi-Stefano", "name": { "family": "Maggi", "given": "Stefano" } }, { "id": "McDowall-Alasdair-W", "name": { "family": "McDowall", "given": "Alasdair W." } }, { "id": "Ben-Yehuda-Sigal", "name": { "family": "Ben-Yehuda", "given": "Sigal" } }, { "id": "Rosenshine-Ilan", "name": { "family": "Rosenshine", "given": "Ilan" } }, { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" } }, { "id": "Beeby-Morgan-D", "name": { "family": "Beeby", "given": "Morgan" } }, { "id": "Chang-Yi-Wei", "name": { "family": "Chang", "given": "Yi-Wei" } }, { "id": "Shaffer-Carrie-L", "name": { "family": "Shaffer", "given": "Carrie L." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." } } ] }, "title": "Discovery of a Novel Inner Membrane-Associated Bacterial Structure Related to the Flagellar Type III Secretion System", "ispublished": "pub", "full_text_status": "public", "keywords": "bacteria; cryo-ET; flagella; secretion systems; Molecular Biology; Microbiology", "note": "\u00a9 2022 Kaplan et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. \n\nReceived: 19 April 2022. Accepted: 30 May 2022. Published online: 18 July 2022. \n\nThis project was funded by the NIH (grant R01 AI127401 to G.J.J., and grant P20 GM130456 to C.L.S.) and the European Research Council (ERC) Synergy grant (no. 810186 awarded to S.B.Y. and I.R.). M.K. acknowledges a Baxter postdoctoral fellowship from Caltech. Cryo-ET work was done in the Beckman Institute Resource Center for Transmission Electron Microscopy at the California Institute of Technology. We are grateful to Marc Erhardt (Humboldt-Universit\u00e4t zu Berlin) for critically reading an initial version of this work. We thank Elitza I. Tocheva for collecting the A. tumefaciens data, Jian Shi for collecting the H. neptunium data, and Martin Pilhofer for collecting the P. luteoviolacea data. We thank Dianne Newman's lab for providing the P. aeruginosa transposon mutant. We are grateful to the lab of Robert Heinzen at the National Institute of Allergy and Infectious Diseases in Montana for growing the Coxiella burnetii cells.\n\nThe authors declare no conflict of interest.\n\nSupplemental Material - jb.00144-22-s0001.pdf
Supplemental Material - jb.00144-22-s0002.mov
Published - jb.00144-22.pdf
", "abstract": "The bacterial flagellar type III secretion system (fT3SS) is a suite of membrane-embedded and cytoplasmic proteins responsible for building the flagellar motility machinery. Homologous nonflagellar (NF-T3SS) proteins form the injectisome machinery that bacteria use to deliver effector proteins into eukaryotic cells, and other family members were recently reported to be involved in the formation of membrane nanotubes. Here, we describe a novel, evolutionarily widespread, hat-shaped structure embedded in the inner membranes of bacteria, of yet-unidentified function, that is present in species containing fT3SS. Mutant analysis suggests a relationship between this novel structure and the fT3SS, but not the NF-T3SS. While the function of this novel structure remains unknown, we hypothesize that either some of the fT3SS proteins assemble within the hat-like structure, perhaps including the fT3SS core complex, or that fT3SS components regulate other proteins that form part of this novel structure.", "date": "2022-08-16", "date_type": "published", "publication": "Journal of Bacteriology", "volume": "204", "number": "8", "publisher": "American Society for Microbiology", "pagerange": "e0014422", "id_number": "CaltechAUTHORS:20220729-894327000", "issn": "0021-9193", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220729-894327000", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 AI127401" }, { "agency": "NIH", "grant_number": "P20 GM130456" }, { "agency": "European Research Council (ERC)", "grant_number": "810186" }, { "agency": "Baxter Foundation" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1128/jb.00144-22", "pmcid": "PMC9380563", "primary_object": { "basename": "kaplan-et-al-2022-discovery-of-a-novel-inner-membrane-associated-bacterial-structure-related-to-the-flagellar-type-iii.pdf", "url": "https://authors.library.caltech.edu/records/3wpcj-x8704/files/kaplan-et-al-2022-discovery-of-a-novel-inner-membrane-associated-bacterial-structure-related-to-the-flagellar-type-iii.pdf" }, "related_objects": [ { "basename": "jb.00144-22-s0001.pdf", "url": "https://authors.library.caltech.edu/records/3wpcj-x8704/files/jb.00144-22-s0001.pdf" }, { "basename": "jb.00144-22-s0002.mov", "url": "https://authors.library.caltech.edu/records/3wpcj-x8704/files/jb.00144-22-s0002.mov" } ], "resource_type": "article", "pub_year": "2022", "author_list": "Kaplan, Mohammed; Oikonomou, Catherine M.; et el." }, { "id": "https://authors.library.caltech.edu/records/k8aqv-xe524", "eprint_id": 113213, "eprint_status": "archive", "datestamp": "2023-08-22 16:13:46", "lastmod": "2023-12-22 23:08:54", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Nicolas-William-J", "name": { "family": "Nicolas", "given": "William J." }, "orcid": "0000-0001-5970-8626" }, { "id": "F\u00e4\u00dfler-Florian", "name": { "family": "F\u00e4\u00dfler", "given": "Florian" }, "orcid": "0000-0001-7149-769X" }, { "id": "Dutka-Przemyslaw", "name": { "family": "Dutka", "given": "Przemyslaw" }, "orcid": "0000-0003-3819-1618" }, { "id": "Schur-Florian-K-M", "name": { "family": "Schur", "given": "Florian K. M." }, "orcid": "0000-0003-4790-8078" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant" }, "orcid": "0000-0003-1556-4864" }, { "id": "Meyerowitz-E-M", "name": { "family": "Meyerowitz", "given": "Elliot" }, "orcid": "0000-0003-4798-5153" } ] }, "title": "Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks", "ispublished": "pub", "full_text_status": "public", "keywords": "onion; cryo-tomography; cell wall; cellulose; pectins", "note": "\u00a9 2022 The Author(s). Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). \n\nReceived 10 February 2022, Revised 17 March 2022, Accepted 8 April 2022, Available online 3 May 2022. \n\nThis work was supported by the Howard Hughes Medical Institute (HHMI) and grant R35 GM122588 to G.J. and the Austrian Science Fund (FWF) P33367 to F.K.M.S. We thank No\u00e9 Cochetel for his guidance and great help in data analysis, discovery, and representation with the R software. We thank Hans-Ulrich Endress for graciously providing us with the purified citrus pectin and Jozef Mravec for generating and providing the COS488 probe. Cryo-EM work was done in the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech. This article is subject to HHMI's Open Access to Publications policy. HHMI lab heads have previously granted a nonexclusive CC BY 4.0 license to the public and a sublicensable license to HHMI in their research articles. Pursuant to those licenses, the author accepted manuscript of this article can be made freely available under a CC BY 4.0 license immediately upon publication. \n\nAuthor contributions: W.J.N. conceived the experiments, prepared the samples, acquired and analyzed the data, performed the data exploration, wrote the manuscript, and drew the figures. F.F. wrote the custom scripts that allowed collection of the per-fiber parameters, helped in data analysis, and participated in writing/correction of the manuscript. P.D. performed the fiber averages, helped in the data analysis relative to the fiber averages, and participated in the correction of the manuscript. F.K.M.S. participated in experimental design of the data analysis, funding, and the correction of the manuscript. G.J. participated in guidance, experimental design, funding, and correction/advising on writing the manuscript. E.M. participated in guidance, experimental design, funding, and correction/advising on writing the manuscript. \n\nThe authors declare no competing interests. \n\nData and code availability: The tilt series, tomograms,.mdoc and.rawtlt used for the data analysis are available upon request. Representative tomograms have been deposited in the Electron Microscopy Data Bank (EMDB) under accession codes EMDB: EMD-26564, EMD-26569, EMD-26568, and EMD-26570. The three cellulose fiber averages have been deposited in EMDB under accession codes EMD-26571, EMD-26572, and EMD-26573. See key resources table for individual description. The bash script used to generate the meshing subtracted maps and quantify the fiber/meshing ratios was deposited on ResearchGate (https://doi.org/10.13140/RG.2.2.17904.53764). DOIs are lister in the key resources table.\n\nPublished - 1-s2.0-S0960982222005930-main.pdf
Submitted - 2022.01.31.478342v1.full.pdf
Supplemental Material - 1-s2.0-S0960982222005930-mmc1.pdf
Supplemental Material - 1-s2.0-S0960982222005930-mmc2.mp4
Supplemental Material - 1-s2.0-S0960982222005930-mmc3.mp4
Supplemental Material - 1-s2.0-S0960982222005930-mmc4.mp4
", "abstract": "One hallmark of plant cells is their cell wall. They protect cells against the environment and high turgor and mediate morphogenesis through the dynamics of their mechanical and chemical properties. The walls are a complex polysaccharidic structure. Although their biochemical composition is well known, how the different components organize in the volume of the cell wall and interact with each other is not well understood and yet is key to the wall's mechanical properties. To investigate the ultrastructure of the plant cell wall, we imaged the walls of onion (Allium cepa) bulbs in a near-native state via cryo-focused ion beam milling (cryo-FIB milling) and cryo-electron tomography (cryo-ET). This allowed the high-resolution visualization of cellulose fibers in situ. We reveal the coexistence of dense fiber fields bathed in a reticulated matrix we termed \"meshing,\" which is more abundant at the inner surface of the cell wall. The fibers adopted a regular bimodal angular distribution at all depths in the cell wall and bundled according to their orientation, creating layers within the cell wall. Concomitantly, employing homogalacturonan (HG)-specific enzymatic digestion, we observed changes in the meshing, suggesting that it is\u2014at least in part\u2014composed of HG pectins. We propose the following model for the construction of the abaxial epidermal primary cell wall: the cell deposits successive layers of cellulose fibers at \u221245\u00b0 and +45\u00b0 relative to the cell's long axis and secretes the surrounding HG-rich meshing proximal to the plasma membrane, which then migrates to more distal regions of the cell wall.", "date": "2022-06-06", "date_type": "published", "publication": "Current Biology", "volume": "32", "number": "11", "publisher": "Cell Press", "pagerange": "2375-2389", "id_number": "CaltechAUTHORS:20220202-980591000", "issn": "0960-9822", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220202-980591000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "R35 GM122588" }, { "agency": "FWF Der Wissenschaftsfonds", "grant_number": "P33367" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.cub.2022.04.024", "pmcid": "PMC9240970", "primary_object": { "basename": "2022.01.31.478342v1.full.pdf", "url": "https://authors.library.caltech.edu/records/k8aqv-xe524/files/2022.01.31.478342v1.full.pdf" }, "related_objects": [ { "basename": "1-s2.0-S0960982222005930-main.pdf", "url": "https://authors.library.caltech.edu/records/k8aqv-xe524/files/1-s2.0-S0960982222005930-main.pdf" }, { "basename": "1-s2.0-S0960982222005930-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/k8aqv-xe524/files/1-s2.0-S0960982222005930-mmc1.pdf" }, { "basename": "1-s2.0-S0960982222005930-mmc2.mp4", "url": "https://authors.library.caltech.edu/records/k8aqv-xe524/files/1-s2.0-S0960982222005930-mmc2.mp4" }, { "basename": "1-s2.0-S0960982222005930-mmc3.mp4", "url": "https://authors.library.caltech.edu/records/k8aqv-xe524/files/1-s2.0-S0960982222005930-mmc3.mp4" }, { "basename": "1-s2.0-S0960982222005930-mmc4.mp4", "url": "https://authors.library.caltech.edu/records/k8aqv-xe524/files/1-s2.0-S0960982222005930-mmc4.mp4" } ], "resource_type": "article", "pub_year": "2022", "author_list": "Nicolas, William J.; F\u00e4\u00dfler, Florian; et el." }, { "id": "https://authors.library.caltech.edu/records/yzjs7-1cv55", "eprint_id": 111774, "eprint_status": "archive", "datestamp": "2023-08-22 15:47:56", "lastmod": "2023-12-22 23:30:30", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Peck-Ariana", "name": { "family": "Peck", "given": "Ariana" }, "orcid": "0000-0002-5940-3897" }, { "id": "Carter-Stephen-D", "name": { "family": "Carter", "given": "Stephen D." }, "orcid": "0000-0002-4237-4276" }, { "id": "Mai-Huanghao", "name": { "family": "Mai", "given": "Huanghao" }, "orcid": "0000-0003-2278-0768" }, { "id": "Chen-Songye", "name": { "family": "Chen", "given": "Songye" }, "orcid": "0000-0001-5407-5049" }, { "id": "Burt-Alister", "name": { "family": "Burt", "given": "Alister" }, "orcid": "0000-0002-9341-2295" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Montage electron tomography of vitrified specimens", "ispublished": "pub", "full_text_status": "public", "keywords": "Cryo-electron microscopy; Montage tomography; Image processing; Ultrastructural analysis; Cellular biology", "note": "\u00a9 2022 Elsevier Inc. \n\nReceived 15 November 2021, Revised 25 March 2022, Accepted 20 April 2022, Available online 26 April 2022, Version of Record 6 May 2022. \n\nData collection and analysis were respectively performed at the Beckman Institute Resource Center for Transmission Electron Microscopy and the Resnick High Performance Computing Center at Caltech. We thank Wei Zhao for preliminary samples, David Mastronarde for valuable discussions, and Tom Morrell for help with the Caltech Data Repository. A.P. is The Mark Foundation for Cancer Research Fellow of the Damon Runyon Cancer Research Foundation (DRG 2361-19). This work was supported by NIH grant AI127401 to G.J.J. \n\nData and code availability: Raw data are available at the Caltech Data Repository (https://data.caltech.edu) under accession IDs 2096, 2099, and 2103. The processed tilt-series binned to 5.3 \u00c5 can be found in the Caltech Electron Tomography Database (https://etdb.caltech.edu/). The code developed for data collection and processing is available at https://github.com/apeck12/montage.\n\nCRediT authorship contribution statement:\nAriana Peck: Methodology, Software, Writing \u2013 original draft, Writing \u2013 review & editing. Stephen D. Carter: Conceptualization, Methodology, Investigation. Huanghao Mai: Methodology, Software. Songye Chen: Software, Methodology, Investigation. Alister Burt: Formal analysis, Writing \u2013 review & editing. Grant J. Jensen: Conceptualization, Writing \u2013 original draft, Writing \u2013 review & editing, Funding acquisition, Supervision.\n\nDeclaration of Competing Interest:\nThe authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.\n\nAccepted Version - 1-s2.0-S1047847722000302-main-1.pdf
Accepted Version - nihms-1871136.pdf
Submitted - 2021.11.02.466666v1.full.pdf
Supplemental Material - 1-s2.0-S1047847722000302-mmc1.pdf
Supplemental Material - 1-s2.0-S1047847722000302-mmc2.mp4
Supplemental Material - 1-s2.0-S1047847722000302-mmc3.mp4
Supplemental Material - 1-s2.0-S1047847722000302-mmc4.mp4
Supplemental Material - 1-s2.0-S1047847722000302-mmc5.mp4
Supplemental Material - 1-s2.0-S1047847722000302-mmc6.mp4
Supplemental Material - 1-s2.0-S1047847722000302-mmc7.mp4
", "abstract": "Cryo-electron tomography provides detailed views of macromolecules in situ. However, imaging a large field of view to provide more cellular context requires reducing magnification during data collection, which in turn restricts the resolution. To circumvent this trade-off between field of view and resolution, we have developed a montage data collection scheme that uniformly distributes the dose throughout the specimen. In this approach, sets of slightly overlapping circular tiles are collected at high magnification and stitched to form a composite projection image at each tilt angle. These montage tilt-series are then reconstructed into massive tomograms with a small pixel size but a large field of view. For proof-of-principle, we applied this method to the thin edge of HeLa cells. Thon rings to better than 10 \u00c5 were detected in the montaged tilt-series, and diverse cellular features were observed in the resulting tomograms. These results indicate that the additional dose required by this technique is not prohibitive to performing structural analysis to intermediate resolution across a large field of view. We anticipate that montage tomography will prove particularly useful for lamellae, increase the likelihood of imaging rare cellular events, and facilitate visual proteomics.", "date": "2022-06", "date_type": "published", "publication": "Journal of Structural Biology", "volume": "214", "number": "2", "publisher": "Elsevier", "pagerange": "107860", "id_number": "CaltechAUTHORS:20211105-210618923", "issn": "1047-8477", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211105-210618923", "funders": { "items": [ { "agency": "Damon Runyon Cancer Research Foundation", "grant_number": "DRG 2361-19" }, { "agency": "NIH", "grant_number": "AI150464" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.jsb.2022.107860", "pmcid": "PMC10081539", "primary_object": { "basename": "nihms-1871136.pdf", "url": "https://authors.library.caltech.edu/records/yzjs7-1cv55/files/nihms-1871136.pdf" }, "related_objects": [ { "basename": "1-s2.0-S1047847722000302-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/yzjs7-1cv55/files/1-s2.0-S1047847722000302-mmc1.pdf" }, { "basename": "1-s2.0-S1047847722000302-mmc2.mp4", "url": "https://authors.library.caltech.edu/records/yzjs7-1cv55/files/1-s2.0-S1047847722000302-mmc2.mp4" }, { "basename": "2021.11.02.466666v1.full.pdf", "url": "https://authors.library.caltech.edu/records/yzjs7-1cv55/files/2021.11.02.466666v1.full.pdf" }, { "basename": "1-s2.0-S1047847722000302-mmc7.mp4", "url": "https://authors.library.caltech.edu/records/yzjs7-1cv55/files/1-s2.0-S1047847722000302-mmc7.mp4" }, { "basename": "1-s2.0-S1047847722000302-main-1.pdf", "url": "https://authors.library.caltech.edu/records/yzjs7-1cv55/files/1-s2.0-S1047847722000302-main-1.pdf" }, { "basename": "1-s2.0-S1047847722000302-mmc3.mp4", "url": "https://authors.library.caltech.edu/records/yzjs7-1cv55/files/1-s2.0-S1047847722000302-mmc3.mp4" }, { "basename": "1-s2.0-S1047847722000302-mmc4.mp4", "url": "https://authors.library.caltech.edu/records/yzjs7-1cv55/files/1-s2.0-S1047847722000302-mmc4.mp4" }, { "basename": "1-s2.0-S1047847722000302-mmc5.mp4", "url": "https://authors.library.caltech.edu/records/yzjs7-1cv55/files/1-s2.0-S1047847722000302-mmc5.mp4" }, { "basename": "1-s2.0-S1047847722000302-mmc6.mp4", "url": "https://authors.library.caltech.edu/records/yzjs7-1cv55/files/1-s2.0-S1047847722000302-mmc6.mp4" } ], "resource_type": "article", "pub_year": "2022", "author_list": "Peck, Ariana; Carter, Stephen D.; et el." }, { "id": "https://authors.library.caltech.edu/records/vs382-6pm08", "eprint_id": 114403, "eprint_status": "archive", "datestamp": "2023-08-22 15:38:00", "lastmod": "2023-12-22 23:14:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kaplan-Mohammed", "name": { "family": "Kaplan", "given": "Mohammed" }, "orcid": "0000-0002-0759-0459" }, { "id": "Oikonomou-Catherine-M", "name": { "family": "Oikonomou", "given": "Catherine M." }, "orcid": "0000-0003-2312-4746" }, { "id": "Wood-Cecily-R", "name": { "family": "Wood", "given": "Cecily R." }, "orcid": "0000-0003-1259-3862" }, { "id": "Chreifi-Georges", "name": { "family": "Chreifi", "given": "Georges" }, "orcid": "0000-0003-4194-1694" }, { "id": "Subramanian-Poorna", "name": { "family": "Subramanian", "given": "Poorna" } }, { "id": "Ortega-Davi-R", "name": { "family": "Ortega", "given": "Davi R." }, "orcid": "0000-0002-8344-2335" }, { "id": "Chang-Yi-Wei", "name": { "family": "Chang", "given": "Yi-Wei" }, "orcid": "0000-0003-2391-473X" }, { "id": "Beeby-Morgan-D", "name": { "family": "Beeby", "given": "Morgan" }, "orcid": "0000-0001-6413-9835" }, { "id": "Shaffer-Carrie-L", "name": { "family": "Shaffer", "given": "Carrie L." }, "orcid": "0000-0002-7457-7422" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Novel transient cytoplasmic rings stabilize assembling bacterial flagellar motors", "ispublished": "pub", "full_text_status": "public", "keywords": "assembly; bacterial flagellar motor; cryo-ET; high-torque; tomography; General Immunology and Microbiology; General Biochemistry, Genetics and Molecular Biology; Molecular Biology; General Neuroscience", "note": "\u00a9 2022 The Authors. \n\nReceived 22 August 2021; Revised 31 January 2022; Accepted 16 February 2022. \n\nThis project was funded by the NIH (grant R01 AI127401 to G.J.J and NIH P20 GM130456 to C.L.S.) and a Baxter postdoctoral fellowship from Caltech to M.K. Cryo-ET work was performed in the Beckman Institute Resource Center for Transmission Electron Microscopy at the California Institute of Technology. We are grateful to Prof. Marc Erhardt (Humboldt-Universit\u00e4t zu Berlin) for critically reading an initial version of this work. \n\nAuthor contributions: Grant J Jensen: Conceptualization; Resources; Formal analysis; Funding acquisition; Writing\u2014review and editing. Mohammed Kaplan: Conceptualization; Data curation; Formal analysis; Funding acquisition; Investigation; Methodology; Writing\u2014original draft; Writing\u2014review and editing. Catherine M Oikonomou: Formal analysis; Writing\u2014review and editing. Cecily R Wood: Data curation; Methodology; Writing\u2014review and editing. Georges Chreifi: Data curation; Writing\u2014review and editing. Poorna Subramanian: Data curation; Writing\u2014review and editing. Davi R Ortega: Data curation; Writing\u2014review & editing. Yi-Wei Chang: Data curation; Writing\u2014review and editing. Morgan Beeby: Data curation; Writing\u2014review and editing. Carrie Shaffer: Data curation; Funding acquisition; Methodology; Writing\u2014review and editing. \n\nIn addition to the CRediT author contributions listed above, the contributions in detail are: \n\nMK and GJJ designed research. MK, CRW, PS, YWC, MB, and CLS prepared samples. MK, GC, PS, YWC, and MB collected data. MK, CMO, DRO, CLS, and GJJ analyzed data. MK wrote the manuscript and all authors edited it.\n\nThe authors declare that they have no conflict of interest. \n\nData availability: The following subtomogram averages have been deposited in the Electron Microscopy Data Bank (https://www.ebi.ac.uk/emdb/) under the following accession codes: fully assembled flagellar motor of H.\u2009gracilis (EMD-25702; https://www.ebi.ac.uk/emdb/EMD-25702), the MS-complex of H.\u2009pylori \u0394fliM fliP* (EMD-25703; http://www.ebi.ac.uk/pdbe/entry/EMD-25703), the MS-complex of H.\u2009pylori fliP* (EMD-25704; http://www.ebi.ac.uk/pdbe/entry/EMD-25704), the MS-complex of H.\u2009pylori \u0394fliQ fliP*, (EMD-25705; http://www.ebi.ac.uk/pdbe/entry/EMD-25705).\n\nSupplemental Material - embj2021109523-sup-0001-appendix.pdf
Supplemental Material - embj2021109523-sup-0002-evfigs.pdf
Supplemental Material - embj2021109523-sup-0003-tableev1.docx
Supplemental Material - embj2021109523-sup-0004-movieev1.zip
Supplemental Material - embj2021109523-sup-0005-movieev2.zip
Supplemental Material - embj2021109523-sup-0006-movieev3.zip
Supplemental Material - embj2021109523-sup-0007-movieev4.zip
Supplemental Material - embj2021109523-sup-0008-movieev5.zip
", "abstract": "The process by which bacterial cells build their intricate flagellar motility apparatuses has long fascinated scientists. Our understanding of this process comes mainly from studies of purified flagella from two species, Escherichia coli and Salmonella enterica. Here, we used electron cryo-tomography (cryo-ET) to image the assembly of the flagellar motor in situ in diverse Proteobacteria: Hylemonella gracilis, Helicobacter pylori, Campylobacter jejuni, Pseudomonas aeruginosa, Pseudomonas fluorescens, and Shewanella oneidensis. Our results reveal the in situ structures of flagellar intermediates, beginning with the earliest flagellar type III secretion system core complex (fT3SScc) and MS-ring. In high-torque motors of Beta-, Gamma-, and Epsilon-proteobacteria, we discovered novel cytoplasmic rings that interact with the cytoplasmic torque ring formed by FliG. These rings, associated with the MS-ring, assemble very early and persist until the stators are recruited into their periplasmic ring; in their absence the stator ring does not assemble. By imaging mutants in Helicobacter pylori, we found that the fT3SScc proteins FliO and FliQ are required for the assembly of these novel cytoplasmic rings. Our results show that rather than a simple accretion of components, flagellar motor assembly is a dynamic process in which accessory components interact transiently to assist in building the complex nanomachine.", "date": "2022-05-16", "date_type": "published", "publication": "EMBO Journal", "volume": "41", "number": "10", "publisher": "European Molecular Biology Organization", "pagerange": "Art. No. e109523", "id_number": "CaltechAUTHORS:20220421-311275900", "issn": "0261-4189", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220421-311275900", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 AI127401" }, { "agency": "NIH", "grant_number": "P20 GM130456" }, { "agency": "Baxter Foundation" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.15252/embj.2021109523", "pmcid": "PMC9108667", "primary_object": { "basename": "embj2021109523-sup-0002-evfigs.pdf", "url": "https://authors.library.caltech.edu/records/vs382-6pm08/files/embj2021109523-sup-0002-evfigs.pdf" }, "related_objects": [ { "basename": "embj2021109523-sup-0003-tableev1.docx", "url": "https://authors.library.caltech.edu/records/vs382-6pm08/files/embj2021109523-sup-0003-tableev1.docx" }, { "basename": "embj2021109523-sup-0004-movieev1.zip", "url": "https://authors.library.caltech.edu/records/vs382-6pm08/files/embj2021109523-sup-0004-movieev1.zip" }, { "basename": "embj2021109523-sup-0005-movieev2.zip", "url": "https://authors.library.caltech.edu/records/vs382-6pm08/files/embj2021109523-sup-0005-movieev2.zip" }, { "basename": "embj2021109523-sup-0006-movieev3.zip", "url": "https://authors.library.caltech.edu/records/vs382-6pm08/files/embj2021109523-sup-0006-movieev3.zip" }, { "basename": "embj2021109523-sup-0007-movieev4.zip", "url": "https://authors.library.caltech.edu/records/vs382-6pm08/files/embj2021109523-sup-0007-movieev4.zip" }, { "basename": "embj2021109523-sup-0008-movieev5.zip", "url": "https://authors.library.caltech.edu/records/vs382-6pm08/files/embj2021109523-sup-0008-movieev5.zip" }, { "basename": "embj2021109523-sup-0001-appendix.pdf", "url": "https://authors.library.caltech.edu/records/vs382-6pm08/files/embj2021109523-sup-0001-appendix.pdf" } ], "resource_type": "article", "pub_year": "2022", "author_list": "Kaplan, Mohammed; Oikonomou, Catherine M.; et el." }, { "id": "https://authors.library.caltech.edu/records/htkht-z4a69", "eprint_id": 114447, "eprint_status": "archive", "datestamp": "2023-08-22 13:59:35", "lastmod": "2023-12-22 23:15:14", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Metskas-Lauren-Ann", "name": { "family": "Metskas", "given": "Lauren Ann" }, "orcid": "0000-0002-8073-6960" }, { "id": "Ortega-Davi-R", "name": { "family": "Ortega", "given": "Davi" }, "orcid": "0000-0002-8344-2335" }, { "id": "Oltrogge-Luke-M", "name": { "family": "Oltrogge", "given": "Luke M." }, "orcid": "0000-0001-5716-9980" }, { "id": "Blikstad-Cecilia", "name": { "family": "Blikstad", "given": "Cecilia" }, "orcid": "0000-0001-5740-926X" }, { "id": "Savage-David-F", "name": { "family": "Savage", "given": "David" }, "orcid": "0000-0003-0042-2257" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Bacterial microcompartment organization by cryo electron tomography and high-resolution subtomogram averaging", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Biophysics", "note": "\u00a9 2021 Biophysical Society. Published by Elsevier Inc. \n\nAvailable online 11 February 2022, Version of Record 11 February 2022.", "abstract": "Roughly 20% of bacteria employ bacterial microcompartments (BMCs) to sequester dangerous or inefficient enzymatic processes. In these structures, a cargo of enzymes and accessory proteins is encased within a semi-permeable protein shell that permits passage of substrates and products but restricts movement of intermediates. In addition to their importance as a component of many bacterial species' metabolisms, BMCs have become a target of protein engineering due to their potential for alternative pharmacological and biotechnological applications.\nDespite the importance of BMCs in prokaryotic biology and bioengineering, structural heterogeneity has prevented a complete understanding of the architecture, ultrastructure, and spatial organization of both the shell proteins and the cargo. Here, we employ cryo electron tomography to image intact alpha-carboxysomes, a model BMC responsible for carbon fixation in cyanobacteria and chemoautotrophs. We have identified novel arrangements of the enzymatic cargo, RuBisCO, characterized states of known protein-protein interactions, and solved a high-resolution subtomogram average of the enzyme in situ. Efforts are underway to identify and resolve additional cargo components and the lattice-like arrangement of the shell proteins to build a complete model of the entire assembly. Taken together, these data offer new insights into conserved BMC organization and heterogeneity, and characterize arrangements that were unresolved in previous in vitro and low-resolution in situ studies.", "date": "2022-02-11", "date_type": "published", "publication": "Biophysical Journal", "volume": "121", "number": "3", "publisher": "Biophysical Society", "pagerange": "168a", "id_number": "CaltechAUTHORS:20220425-145423351", "issn": "0006-3495", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220425-145423351", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.bpj.2021.11.1892", "resource_type": "article", "pub_year": "2022", "author_list": "Metskas, Lauren Ann; Ortega, Davi; et el." }, { "id": "https://authors.library.caltech.edu/records/x6mmr-rf360", "eprint_id": 109830, "eprint_status": "archive", "datestamp": "2023-09-15 07:05:02", "lastmod": "2023-12-22 23:15:07", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Depelteau-Jamie-S", "name": { "family": "Depelteau", "given": "Jamie S." }, "orcid": "0000-0001-8983-2855" }, { "id": "Renault-Ludovic", "name": { "family": "Renault", "given": "Ludovic" }, "orcid": "0000-0001-6464-8808" }, { "id": "Althof-Nynke", "name": { "family": "Althof", "given": "Nynke" } }, { "id": "Cassidy-C-Keith", "name": { "family": "Cassidy", "given": "C. Keith" }, "orcid": "0000-0001-8106-1187" }, { "id": "Mendon\u00e7a-Luiza-M", "name": { "family": "Mendon\u00e7a", "given": "Luiza M." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Resch-Guenter-P", "name": { "family": "Resch", "given": "Guenter P." } }, { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" } ] }, "title": "UVC inactivation of pathogenic samples suitable for cryo-EM analysis", "ispublished": "pub", "full_text_status": "public", "keywords": "Cryoelectron microscopy; Microbiology", "note": "\u00a9 The Author(s) 2022. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. \n\nReceived 24 July 2021; Accepted 07 December 2021; Published 11 January 2022. \n\nWe are grateful to Davi Ortega for helpful discussions. We also wish to thank Weng Yang and Willem Noteborn of NeCEN for assistance during data collection, and Gert Koning (Department of Fine Mechanicsl) for assistance with the construction of the prototype UVC inactivation box. This work was funded in part by the Building Blocks of Life Grant 737.016.004 from the Netherlands Organization for Scientific Research (A.B.) and Instruct-ULTRA (Horizon 2020 Coordination and Support action Number ID: 731005 (A.B. and NeCEN). Funding was also provided to C.K.C. by UK Biotechnology and Biological Sciences Research Council grant number BB/S003339/1. G.J.J. and L.M.M. was funded by NIH grant AI150464. \n\nData availability: The structures resulting from single particle analysis of the untreated and UVC-treated ICP1 bacteriophage data (EMD-13403, EMD-13402), and the UVC-treated ApoF (EMD-13364; PDB ID: 7PF1) data have been deposited in the EMDB. \n\nAuthor Contributions: J.S.D., L.M.M., G.J.J., G.P.R., and A.B. designed the research, J.S.D., L.R., N.A., performed experiments, J.S.D., L.R., N.A., and C.K.C. analyzed data. J.S.D., L.R., N.A., C.K.C., and A.B. wrote the manuscript. All authors read and commented on the manuscript. \n\nThe authors declare no competing interests. \n\nPeer review information: Communications Biology thanks Koji Yonekura, Andreas Boland and the other, anonymous, reviewer for their contribution to the peer review of this work. Primary Handling Editors: Janesh Kumar and Caitlin Karniski.\n\nPublished - s42003-021-02962-w.pdf
Submitted - 2021.07.06.451241v1.full.pdf
Supplemental Material - 42003_2021_2962_MOESM1_ESM.pdf
Supplemental Material - 42003_2021_2962_MOESM2_ESM.pdf
", "abstract": "Cryo-electron microscopy has become an essential tool to understand structure and function of biological samples. Especially for pathogens, such as disease-causing bacteria and viruses, insights gained by cryo-EM can aid in developing cures. However, due to the biosafety restrictions of pathogens, samples are often treated by chemical fixation to render the pathogen inert, affecting the ultrastructure of the sample. Alternatively, researchers use in vitro or ex vivo models, which are non-pathogenic but lack the complexity of the pathogen of interest. Here we show that ultraviolet-C (UVC) radiation applied at cryogenic temperatures can be used to eliminate or dramatically reduce the infectivity of Vibrio cholerae and the bacterial virus, the ICP1 bacteriophage. We show no discernable structural impact of this treatment of either sample using two cryo-EM methods: cryo-electron tomography followed by sub-tomogram averaging, and single particle analysis (SPA). Additionally, we applied the UVC irradiation to the protein apoferritin (ApoF), which is a widely used test sample for high-resolution SPA studies. The UVC-treated ApoF sample resulted in a 2.1\u2009\u00c5 structure indistinguishable from an untreated published map. This research demonstrates that UVC treatment is an effective and inexpensive addition to the cryo-EM sample preparation toolbox.", "date": "2022-01-11", "date_type": "published", "publication": "Communications Biology", "volume": "5", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 29", "id_number": "CaltechAUTHORS:20210715-140139799", "issn": "2399-3642", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210715-140139799", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)", "grant_number": "737.016.004" }, { "agency": "European Research Council (ERC)", "grant_number": "731005" }, { "agency": "Biotechnology and Biological Sciences Research Council (BBSRC)", "grant_number": "BB/S003339/1" }, { "agency": "NIH", "grant_number": "AI150464" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1038/s42003-021-02962-w", "primary_object": { "basename": "2021.07.06.451241v1.full.pdf", "url": "https://authors.library.caltech.edu/records/x6mmr-rf360/files/2021.07.06.451241v1.full.pdf" }, "related_objects": [ { "basename": "42003_2021_2962_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/x6mmr-rf360/files/42003_2021_2962_MOESM1_ESM.pdf" }, { "basename": "42003_2021_2962_MOESM2_ESM.pdf", "url": "https://authors.library.caltech.edu/records/x6mmr-rf360/files/42003_2021_2962_MOESM2_ESM.pdf" }, { "basename": "s42003-021-02962-w.pdf", "url": "https://authors.library.caltech.edu/records/x6mmr-rf360/files/s42003-021-02962-w.pdf" } ], "resource_type": "article", "pub_year": "2022", "author_list": "Depelteau, Jamie S.; Renault, Ludovic; et el." }, { "id": "https://authors.library.caltech.edu/records/ey475-5s465", "eprint_id": 101068, "eprint_status": "archive", "datestamp": "2023-08-20 05:35:04", "lastmod": "2023-12-22 23:14:35", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Phillips-Daniel-A", "name": { "family": "Phillips", "given": "Daniel A." }, "orcid": "0000-0003-2759-5246" }, { "id": "Zacharoff-Lori-A", "name": { "family": "Zacharoff", "given": "Lori A." }, "orcid": "0000-0001-8657-0968" }, { "id": "Hampton-Cheri-M", "name": { "family": "Hampton", "given": "Cheri M." }, "orcid": "0000-0003-0069-8712" }, { "id": "Chong-Grace-W", "name": { "family": "Chong", "given": "Grace W." }, "orcid": "0000-0003-1369-1405" }, { "id": "Malanoski-Anthony-P", "name": { "family": "Malanoski", "given": "Anthony P." }, "orcid": "0000-0001-6192-888X" }, { "id": "Metskas-Lauren-Ann", "name": { "family": "Metskas", "given": "Lauren Ann" }, "orcid": "0000-0002-8073-6960" }, { "id": "Xu-Shuai", "name": { "family": "Xu", "given": "Shuai" }, "orcid": "0000-0001-8849-7506" }, { "id": "Bird-Lina-J", "name": { "family": "Bird", "given": "Lina J." }, "orcid": "0000-0003-4127-4756" }, { "id": "Eddie-Brian-J", "name": { "family": "Eddie", "given": "Brian J." }, "orcid": "0000-0002-3559-3892" }, { "id": "Miklos-Aleksandr-E", "name": { "family": "Miklos", "given": "Aleksandr E." }, "orcid": "0000-0001-6375-2304" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Drummy-Lawrence-F", "name": { "family": "Drummy", "given": "Lawrence F." }, "orcid": "0000-0002-6452-5768" }, { "id": "El-Naggar-M=Mohamed-Y", "name": { "family": "El-Naggar", "given": "Mohamed Y." }, "orcid": "0000-0001-5599-6309" }, { "id": "Glaven-Sarah-M", "name": { "family": "Glaven", "given": "Sarah M." }, "orcid": "0000-0003-0857-3391" } ] }, "title": "A bacterial membrane sculpting protein with BAR domain-like activity", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2021 Phillips et al. This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. \n\nPreprint posted: January 31, 2020 (view preprint); Received: June 15, 2020; Accepted: October 12, 2021; Accepted Manuscript published: October 13, 2021 (version 1); Version of Record published: December 20, 2021 (version 2). \n\nWe thank Dr Jeffrey Gralnick for helpful discussions and advice, as well as the S. oneidensis JG1194 strain; Dr Adam Meyer and Dr Chris Voigt for the DAPG-inducible Marionette promoter; Dr Annie Moradian and Dr Mike Sweredoski and the California Institute of Technology Proteome Exploration Lab for useful discussions on the preparation and analysis of proteomics data. Some of the cryo-TEM work was done in the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech. This work was supported by the United States Department of Defense Synthetic Biology for Military Environments (SBME) Applied Research for the Advancement of Science and Technology Priorities (ARAP) program. DP and AEM were partially supported by the U.S. Army via the Surface Science Initiative Program (PE 0601102 A Project VR9) at the Combat Capabilities Development Command (CCDC) Chemical Biological Center. Work in ME-N's lab was supported by the U.S. Office of Naval Research Multidisciplinary University Research Initiative Grant No. N00014-18-1-2632. LAZ was partially supported by the National Science Foundation grant DEB-1542527. GWC was also supported by the National Science Foundation Graduate Research Fellowship Program (grant DGE1418060). SX was supported by the Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences of the U.S. Department of Energy through grant DE-FG02-13ER16415. Work in GJJ's lab was supported by the National Institute of Health (GM122588 to GJJ). \n\nThe funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication. \n\nAuthor contributions: Daniel A Phillips, Conceptualization, DP and LZ conceived the study independently then combined projects when complementary data on BdpA was discovered., Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Supervision, Validation, Visualization, Writing \u2013 original draft, Writing \u2013 review and editing; Lori A Zacharoff, Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Supervision, Validation, Visualization, Writing \u2013 original draft, Writing \u2013 review and editing; Cheri M Hampton, Formal analysis, Investigation, Methodology, Visualization, Writing \u2013 review and editing; Grace W Chong, Data curation, Formal analysis, Investigation, Methodology, Visualization, Writing \u2013 review and editing; Anthony P Malanoski, Data curation, Formal analysis, Investigation, Methodology, Visualization, Writing \u2013 original draft, Writing \u2013 review and editing; Lauren Ann Metskas, Investigation, Methodology, Visualization, Writing \u2013 review and editing; Shuai Xu, Lina J Bird, Resources, Writing \u2013 review and editing; Brian J Eddie, Data curation, Formal analysis, Investigation, Validation, Writing \u2013 original draft, Writing \u2013 review and editing; Aleksandr E Miklos, Funding acquisition, Investigation, Software, Visualization; Grant J Jensen, Funding acquisition, Supervision, Writing \u2013 review and editing; Lawrence F Drummy, Investigation, Methodology, Supervision, Validation, Visualization, Writing \u2013 review and editing; Mohamed Y El-Naggar, Sarah M Glaven, Formal analysis, Funding acquisition, Project administration, Resources, Supervision, Writing \u2013 original draft, Writing \u2013 review and editing. \n\nCompeting interests: Daniel A Phillips: along with SG holds the patent US10793865B2 on \"Transferrable mechanism of generating inducible, BAR domain protein-mediated bacterial outer membrane extensions\". Sarah M Glaven: along with DP holds the patent US10793865B2 on \"Transferrable mechanism of generating inducible, BAR domain protein-mediated bacterial outer membrane extensions\". The other authors declare that no competing interests exist. \n\nData availability: The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [1] partner repository with the dataset identifier PXD020577.\n\nPublished - elife-60049-v2.pdf
Submitted - 2020.01.30.926147v3.full.pdf
Supplemental Material - elife-60049-supp1-v2.xlsx
Supplemental Material - elife-60049-supp2-v2.docx
Supplemental Material - elife-60049-transrepform1-v2.docx
Supplemental Material - elife-60049-video1.mp4
Supplemental Material - elife-60049-video2.mp4
Supplemental Material - elife-60049-video3.mp4
Supplemental Material - elife-60049-video4.mp4
Supplemental Material - elife-60049-video5.mp4
Supplemental Material - elife-60049-video6.mp4
", "abstract": "Bin/Amphiphysin/RVS (BAR) domain proteins belong to a superfamily of coiled-coil proteins influencing membrane curvature in eukaryotes and are associated with vesicle biogenesis, vesicle-mediated protein trafficking, and intracellular signaling. Here, we report a bacterial protein with BAR domain-like activity, BdpA, from Shewanella oneidensis MR-1, known to produce redox-active membrane vesicles and micrometer-scale outer membrane extensions (OMEs). BdpA is required for uniform size distribution of membrane vesicles and influences scaffolding of OMEs into a consistent diameter and curvature. Cryo-TEM reveals that a strain lacking BdpA produces lobed, disordered OMEs rather than membrane tubules or narrow chains produced by the wild-type strain. Overexpression of BdpA promotes OME formation during planktonic growth of S. oneidensis where they are not typically observed. Heterologous expression results in OME production in Marinobacter atlanticus and Escherichia coli. Based on the ability of BdpA to alter membrane architecture in vivo, we propose that BdpA and its homologs comprise a newly identified class of bacterial BAR domain-like proteins.", "date": "2021-10-13", "date_type": "published", "publication": "eLife", "volume": "10", "publisher": "eLife Sciences Publications", "pagerange": "Art. No. e60049", "id_number": "CaltechAUTHORS:20200203-093321992", "issn": "2050-084X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200203-093321992", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Department of Defense" }, { "agency": "Army Research Office (ARO)", "grant_number": "PE 0601102" }, { "agency": "Office of Naval Research (ONR)", "grant_number": "N00014-18-1-2632" }, { "agency": "NSF", "grant_number": "DEB-1542527" }, { "agency": "NSF Graduate Research Fellowship", "grant_number": "DGE-1418060" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02-13ER16415" }, { "agency": "NIH", "grant_number": "GM122588" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.7554/elife.60049", "pmcid": "PMC8687657", "primary_object": { "basename": "2020.01.30.926147v3.full.pdf", "url": "https://authors.library.caltech.edu/records/ey475-5s465/files/2020.01.30.926147v3.full.pdf" }, "related_objects": [ { "basename": "elife-60049-transrepform1-v2.docx", "url": "https://authors.library.caltech.edu/records/ey475-5s465/files/elife-60049-transrepform1-v2.docx" }, { "basename": "elife-60049-video1.mp4", "url": "https://authors.library.caltech.edu/records/ey475-5s465/files/elife-60049-video1.mp4" }, { "basename": "elife-60049-video4.mp4", "url": "https://authors.library.caltech.edu/records/ey475-5s465/files/elife-60049-video4.mp4" }, { "basename": "elife-60049-video5.mp4", "url": "https://authors.library.caltech.edu/records/ey475-5s465/files/elife-60049-video5.mp4" }, { "basename": "elife-60049-video6.mp4", "url": "https://authors.library.caltech.edu/records/ey475-5s465/files/elife-60049-video6.mp4" }, { "basename": "elife-60049-supp1-v2.xlsx", "url": "https://authors.library.caltech.edu/records/ey475-5s465/files/elife-60049-supp1-v2.xlsx" }, { "basename": "elife-60049-supp2-v2.docx", "url": "https://authors.library.caltech.edu/records/ey475-5s465/files/elife-60049-supp2-v2.docx" }, { "basename": "elife-60049-v2.pdf", "url": "https://authors.library.caltech.edu/records/ey475-5s465/files/elife-60049-v2.pdf" }, { "basename": "elife-60049-video2.mp4", "url": "https://authors.library.caltech.edu/records/ey475-5s465/files/elife-60049-video2.mp4" }, { "basename": "elife-60049-video3.mp4", "url": "https://authors.library.caltech.edu/records/ey475-5s465/files/elife-60049-video3.mp4" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Phillips, Daniel A.; Zacharoff, Lori A.; et el." }, { "id": "https://authors.library.caltech.edu/records/5pshx-a3497", "eprint_id": 108215, "eprint_status": "archive", "datestamp": "2023-08-20 05:27:13", "lastmod": "2023-12-22 23:14:47", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Tran-Ngoc-Han", "name": { "family": "Tran", "given": "Ngoc-Han" }, "orcid": "0000-0003-0638-2583" }, { "id": "Carter-Stephen-D", "name": { "family": "Carter", "given": "Stephen D." }, "orcid": "0000-0002-4237-4276" }, { "id": "De-Maziere-Ann", "name": { "family": "De Maziere", "given": "Ann" }, "orcid": "0000-0001-8070-5104" }, { "id": "Ashkenazi-Avi", "name": { "family": "Ashkenazi", "given": "Avi" }, "orcid": "0000-0002-6890-4589" }, { "id": "Klumperman-Judith", "name": { "family": "Klumperman", "given": "Judith" }, "orcid": "0000-0003-4835-6228" }, { "id": "Walter-Peter", "name": { "family": "Walter", "given": "Peter" }, "orcid": "0000-0002-6849-708X" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "The stress-sensing domain of activated IRE1\u03b1 forms helical filaments in narrow ER membrane tubes", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2021 American Association for the Advancement of Science. \n\nReceived 24 February 2021; accepted 11 August 2021. \n\nWe thank E. Karagoz, S. Niekamp, V. Belyy, M. Elvekrog, D. Acosta-Alvear, R. Fetter, and S. van Dijk for their advice and technical assistance and G. Huber, R. Ernst, A. Frost, and J. Nunnari for insightful discussions. \n\nThis work was supported in part by NWO NEMI (grant 184.034.014 to J.K.) and the NIH (grants P50 AI150464 and R35 GM122588 to G.J.J. and R01-GM032384 to P.W.). N.-H.T. is supported by the NSF GRFP. P.W. is an Investigator of the Howard Hughes Medical Institute. \n\nAuthor contributions: Methodology: N.-H.T., S.D.C., A.D.M.; Formal analysis: N.-H.T., S.D.C., A.D.M. Visualization: N.-H.T., S.D.C.; Writing \u2013 original draft & editing: N.-H.T., S.D.C.; Conceptualization: A.A., J.K., P.W., G.J.J.; Resources: A.A., J.K., P.W., G.J.J.; Supervision: A.A., J.K., P.W., G.J.J.; Funding acquisition: A.A., J.K., P.W., G.J.J.; Writing \u2013 review & editing: P.W., G.J.J. \n\nCompeting interests: A.D.M. received a salary from Genentech, Inc. The authors declare no other competing interests. \n\nData and materials availability: The codes used for analyses are available through Zenodo (38). The subtomogram-averaged maps can be accessed at EMDB (EMD-23058). Raw and processed data, cell lines, and reagents are available upon request.\n\nSubmitted - 2021.02.24.432779v1.full.pdf
Supplemental Material - science.abh2474_mdar_reproducibility_checklist.pdf
Supplemental Material - science.abh2474_movies_s1_to_s3.zip
Supplemental Material - science.abh2474_sm.pdf
", "abstract": "The signaling network of the unfolded protein response (UPR) adjusts the protein-folding capacity of the endoplasmic reticulum (ER) according to need. The most conserved UPR sensor, IRE1\u03b1, spans the ER membrane and activates through oligomerization. IRE1\u03b1 oligomers accumulate in dynamic foci. We determined the in situ structure of IRE1\u03b1 foci by cryogenic correlated light and electron microscopy combined with electron cryo-tomography and complementary immuno\u2013electron microscopy in mammalian cell lines. IRE1\u03b1 foci localized to a network of narrow anastomosing ER tubes (diameter, ~28 nm) with complex branching. The lumen of the tubes contained protein filaments, which were likely composed of arrays of IRE1\u03b1 lumenal domain dimers that were arranged in two intertwined, left-handed helices. This specialized ER subdomain may play a role in modulating IRE1\u03b1 signaling.", "date": "2021-10-01", "date_type": "published", "publication": "Science", "volume": "374", "number": "6563", "publisher": "American Association for the Advancement of Science", "pagerange": "52-57", "id_number": "CaltechAUTHORS:20210225-141123693", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210225-141123693", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)", "grant_number": "184.034.014" }, { "agency": "NIH", "grant_number": "P50 AI150464" }, { "agency": "NIH", "grant_number": "R35 GM122588" }, { "agency": "NIH", "grant_number": "R01-GM032384" }, { "agency": "NSF Graduate Research Fellowship" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1126/science.abh2474", "primary_object": { "basename": "2021.02.24.432779v1.full.pdf", "url": "https://authors.library.caltech.edu/records/5pshx-a3497/files/2021.02.24.432779v1.full.pdf" }, "related_objects": [ { "basename": "science.abh2474_mdar_reproducibility_checklist.pdf", "url": "https://authors.library.caltech.edu/records/5pshx-a3497/files/science.abh2474_mdar_reproducibility_checklist.pdf" }, { "basename": "science.abh2474_movies_s1_to_s3.zip", "url": "https://authors.library.caltech.edu/records/5pshx-a3497/files/science.abh2474_movies_s1_to_s3.zip" }, { "basename": "science.abh2474_sm.pdf", "url": "https://authors.library.caltech.edu/records/5pshx-a3497/files/science.abh2474_sm.pdf" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Tran, Ngoc-Han; Carter, Stephen D.; et el." }, { "id": "https://authors.library.caltech.edu/records/tbsj0-r0g25", "eprint_id": 109850, "eprint_status": "archive", "datestamp": "2023-08-20 04:58:27", "lastmod": "2023-12-22 23:10:49", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kaplan-Mohammed", "name": { "family": "Kaplan", "given": "Mohammed" }, "orcid": "0000-0002-0759-0459" }, { "id": "Chreifi-Georges", "name": { "family": "Chreifi", "given": "Georges" }, "orcid": "0000-0003-4194-1694" }, { "id": "Metskas-Lauren-Ann", "name": { "family": "Metskas", "given": "Lauren Ann" }, "orcid": "0000-0002-8073-6960" }, { "id": "Liedtke-Janine", "name": { "family": "Liedtke", "given": "Janine" }, "orcid": "0000-0003-2680-4130" }, { "id": "Wood-Cecily-R", "name": { "family": "Wood", "given": "Cecily R." } }, { "id": "Oikonomou-Catherine-M", "name": { "family": "Oikonomou", "given": "Catherine M." }, "orcid": "0000-0003-2312-4746" }, { "id": "Nicolas-William-J", "name": { "family": "Nicolas", "given": "William J." }, "orcid": "0000-0001-5970-8626" }, { "id": "Subramanian-Poorna", "name": { "family": "Subramanian", "given": "Poorna" } }, { "id": "Zacharoff-Lori-A", "name": { "family": "Zacharoff", "given": "Lori A." }, "orcid": "0000-0001-8657-0968" }, { "id": "Wang-Yuhang", "name": { "family": "Wang", "given": "Yuhang" }, "orcid": "0000-0003-3715-8349" }, { "id": "Chang-Yi-Wei", "name": { "family": "Chang", "given": "Yi-Wei" }, "orcid": "0000-0003-2391-473X" }, { "id": "Beeby-Morgan-D", "name": { "family": "Beeby", "given": "Morgan" }, "orcid": "0000-0001-6413-9835" }, { "id": "Dobro-Megan-J", "name": { "family": "Dobro", "given": "Megan J." }, "orcid": "0000-0002-6464-3932" }, { "id": "Zhu-Yongtao", "name": { "family": "Zhu", "given": "Yongtao" }, "orcid": "0000-0002-3069-6518" }, { "id": "McBride-Mark-J", "name": { "family": "McBride", "given": "Mark J." }, "orcid": "0000-0002-3798-6761" }, { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Shaffer-Carrie-L", "name": { "family": "Shaffer", "given": "Carrie L." }, "orcid": "0000-0002-7457-7422" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "In situ imaging of bacterial outer membrane projections and associated protein complexes using electron cryo-tomography", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2021 Kaplan et al. This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited. \n\nPreprinted: 13 July 2021; Received: 17 August 2021; Accepted: 23 August 2021; Published: 01 September 2021. \n\nThis project was funded by the NIH (grant R35 GM122588 to GJJ, and P20 GM130456 to CLS) and a Baxter postdoctoral fellowship from Caltech to MK. Cryo-ET work was done in the Beckman Institute Resource Center for Transmission Electron Microscopy at the California Institute of Technology. We are grateful to Prof. Martin Pilhofer for collecting the P. luteoviolacea data and for critically reading the manuscript. We thank Prof. Elitza I Tocheva for collecting the D. acidovorans data. We thank Prof. Mohamed El-Naggar for insights into preparing S. oneidensis samples and Dr. Yuxi Liu for discussions. Briegel lab data was collected at the Netherlands Center for Electron Nanoscopy with support from Dr Wen Yang. This data was collected with support from the National Roadmap for Large-Scale Research Infrastructure 2017\u20132018 with project number 184.034.014, which is financed in part by the Dutch Research Council (NWO). This work was also supported by the NWO OCENW.GROOT.2019.063 grant. \n\nThe funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication. \n\nAuthor Contributions: Mohammed Kaplan, Conceptualization, Data curation, Formal analysis, Funding acquisition, Writing - original draft; Georges Chreifi, Lauren Ann Metskas, Cecily R Wood, Poorna Subramanian, Lori A Zacharoff, Yuhang Wang, Yi-Wei Chang, Morgan Beeby, Megan J Dobro, Yongtao Zhu, Mark J McBride, Data curation, Writing \u2013 review and editing; Janine Liedtke, Data curation, Formal analysis, Writing \u2013 review and editing; Catherine M Oikonomou, William J Nicolas, Formal analysis, Writing \u2013 review and editing; Ariane Briegel, Formal analysis, Funding acquisition, Writing \u2013 review and editing; Carrie L Shaffer, Data curation, Formal analysis, Funding acquisition, Writing \u2013 review and editing; Grant J Jensen, Conceptualization, Formal analysis, Funding acquisition, Investigation, Supervision, Writing \u2013 review and editing. \n\nThe authors declare that no competing interests exist. \n\nData availability: All data generated or analysed during this study are included in the manuscript and supporting files and movies.\n\nPublished - elife-73099-v2.pdf
Submitted - 2021.07.13.452161v1.full.pdf
Supplemental Material - elife-73099-transrepform1-v2.docx
Supplemental Material - elife-73099-video1.mp4
Supplemental Material - elife-73099-video2.mp4
Supplemental Material - elife-73099-video3.mp4
Supplemental Material - elife-73099-video4.mp4
Supplemental Material - elife-73099-video5.mp4
Supplemental Material - elife-73099-video6.mp4
", "abstract": "The ability to produce outer membrane projections in the form of tubular membrane extensions (MEs) and membrane vesicles (MVs) is a widespread phenomenon among diderm bacteria. Despite this, our knowledge of the ultrastructure of these extensions and their associated protein complexes remains limited. Here, we surveyed the ultrastructure and formation of MEs and MVs, and their associated protein complexes, in tens of thousands of electron cryo-tomograms of ~90 bacterial species that we have collected for various projects over the past 15 years (Jensen lab database), in addition to data generated in the Briegel lab. We identified outer MEs and MVs in 13 diderm bacterial species and classified several major ultrastructures: (1) tubes with a uniform diameter (with or without an internal scaffold), (2) tubes with irregular diameter, (3) tubes with a vesicular dilation at their tip, (4) pearling tubes, (5) connected chains of vesicles (with or without neck-like connectors), (6) budding vesicles and nanopods. We also identified several protein complexes associated with these MEs and MVs which were distributed either randomly or exclusively at the tip. These complexes include a secretin-like structure and a novel crown-shaped structure observed primarily in vesicles from lysed cells. In total, this work helps to characterize the diversity of bacterial membrane projections and lays the groundwork for future research in this field.", "date": "2021-09-01", "date_type": "published", "publication": "eLife", "volume": "10", "publisher": "eLife Sciences Publications", "pagerange": "Art. No. e73099", "id_number": "CaltechAUTHORS:20210715-193000687", "issn": "2050-084X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210715-193000687", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R35 GM122588" }, { "agency": "NIH", "grant_number": "P20 GM130456" }, { "agency": "Baxter Foundation" }, { "agency": "Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)", "grant_number": "184.034.014" }, { "agency": "Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)", "grant_number": "OCENW.GROOT.2019.063" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.7554/eLife.73099", "primary_object": { "basename": "elife-73099-video2.mp4", "url": "https://authors.library.caltech.edu/records/tbsj0-r0g25/files/elife-73099-video2.mp4" }, "related_objects": [ { "basename": "2021.07.13.452161v1.full.pdf", "url": "https://authors.library.caltech.edu/records/tbsj0-r0g25/files/2021.07.13.452161v1.full.pdf" }, { "basename": "elife-73099-transrepform1-v2.docx", "url": "https://authors.library.caltech.edu/records/tbsj0-r0g25/files/elife-73099-transrepform1-v2.docx" }, { "basename": "elife-73099-v2.pdf", "url": "https://authors.library.caltech.edu/records/tbsj0-r0g25/files/elife-73099-v2.pdf" }, { "basename": "elife-73099-video5.mp4", "url": "https://authors.library.caltech.edu/records/tbsj0-r0g25/files/elife-73099-video5.mp4" }, { "basename": "elife-73099-video6.mp4", "url": "https://authors.library.caltech.edu/records/tbsj0-r0g25/files/elife-73099-video6.mp4" }, { "basename": "elife-73099-video1.mp4", "url": "https://authors.library.caltech.edu/records/tbsj0-r0g25/files/elife-73099-video1.mp4" }, { "basename": "elife-73099-video3.mp4", "url": "https://authors.library.caltech.edu/records/tbsj0-r0g25/files/elife-73099-video3.mp4" }, { "basename": "elife-73099-video4.mp4", "url": "https://authors.library.caltech.edu/records/tbsj0-r0g25/files/elife-73099-video4.mp4" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Kaplan, Mohammed; Chreifi, Georges; et el." }, { "id": "https://authors.library.caltech.edu/records/n7cz7-km327", "eprint_id": 111990, "eprint_status": "archive", "datestamp": "2023-08-22 11:05:55", "lastmod": "2023-12-22 23:15:09", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Oikonomou-Catherine-M", "name": { "family": "Oikonomou", "given": "Catherine M." }, "orcid": "0000-0003-2312-4746" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "The Atlas of Bacterial & Archaeal Cell Structure: an Interactive Open-Access Microbiology Textbook", "ispublished": "pub", "full_text_status": "public", "keywords": "bacteria, archaea, cryo-EM, cryo-electron tomography, microbiology, educational resource, open access, online, textbook; General Agricultural and Biological Sciences; General Immunology and Microbiology; General Biochemistry, Genetics and Molecular Biology; Education", "note": "\u00a9 2021 Oikonomou and Jensen. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International license. \n\nReceived: 12 January 2021, Accepted: 22 July 2021, Published: 31 August 2021. \n\nThis work was supported by the National Institutes of Health (NIH) (grant R01 AI127401 to G.J.J.). Imaging data shown in the described textbook were acquired in the course of research projects conducted in the Jensen laboratory at the California Institute of Technology. Major funding for those projects came from the NIH, the Howard Hughes Medical Institute (HHMI), the Beckman Institute, the Gordon and Betty Moore Foundation, the Agouron Institute, and the John Templeton Foundation. Cryo-EM was performed in the Beckman Institute Resource Center for Transmission Electron Microscopy at the California Institute of Technology and the HHMI Janelia Farm CryoEM Facility.\n\nPublished - jmbe.00128-21.pdf
", "abstract": "Here, we describe a new open-access digital textbook for microbiology, The Atlas of Bacterial & Archaeal Cell Structure (available at cellstructureatlas.org). The book addresses a fundamental gap in existing textbooks, namely, what bacterial and archaeal cells look like and how the macromolecular structures they contain give rise to their diverse and complex functions. The interactive, multimedia resource features real data from more than 150 cells belonging to approximately 70 different species, imaged by cutting-edge cryogenic electron microscopy (cryo-EM). Complementary animations show the cellular machinery in action. Only a basic familiarity with fundamental biology concepts is required to understand the material, which targets a wide range of students in courses from general biology for nonmajors to specialized graduate-level microbiology. The content can be digested in several hours, making it well suited to be assigned as a supplemental resource for a course covering either more diverse topics in cell biology or a more specialized topic such as medical microbiology. By making this resource freely available online, we hope it will serve students in diverse educational settings, including self-directed learners.", "date": "2021-09", "date_type": "published", "publication": "Journal of Microbiology & Biology Education", "volume": "22", "number": "2", "publisher": "American Society for Microbiology", "pagerange": "Art. No. e00128-21", "id_number": "CaltechAUTHORS:20211122-231810071", "issn": "1935-7877", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211122-231810071", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 AI127401" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Agouron Institute" }, { "agency": "John Templeton Foundation" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1128/jmbe.00128-21", "pmcid": "PMC8442016", "primary_object": { "basename": "jmbe.00128-21.pdf", "url": "https://authors.library.caltech.edu/records/n7cz7-km327/files/jmbe.00128-21.pdf" }, "resource_type": "article", "pub_year": "2021", "author_list": "Oikonomou, Catherine M. and Jensen, Grant J." }, { "id": "https://authors.library.caltech.edu/records/095s1-gqc19", "eprint_id": 108827, "eprint_status": "archive", "datestamp": "2023-08-22 10:16:02", "lastmod": "2023-12-22 23:14:40", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kaplan-Mohammed", "name": { "family": "Kaplan", "given": "Mohammed" }, "orcid": "0000-0002-0759-0459" }, { "id": "Wang-Yuhang", "name": { "family": "Wang", "given": "Yuhang" }, "orcid": "0000-0003-3715-8349" }, { "id": "Chreifi-Georges", "name": { "family": "Chreifi", "given": "Georges" }, "orcid": "0000-0003-4194-1694" }, { "id": "Zhang-Lujia", "name": { "family": "Zhang", "given": "Lujia" }, "orcid": "0000-0003-3566-917X" }, { "id": "Chang-Yi-Wei", "name": { "family": "Chang", "given": "Yi-Wei" }, "orcid": "0000-0003-2391-473X" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Programmed Flagellar Ejection in Caulobacter crescentus Leaves PL-subcomplexes", "ispublished": "pub", "full_text_status": "public", "keywords": "bacterial flagellar motor; flagellar ejection; disassembly; PL-subcomplexes; electron cryo-tomography", "note": "\u00a9 2021 Elsevier. \n\nReceived 11 December 2020, Revised 12 April 2021, Accepted 13 April 2021, Available online 20 April 2021. \n\nThis project was funded by the NIH (grant RO1 AI127401 to G.J.J.) and a Baxter postdoctoral fellowship from Caltech to M.K. Cryo-ET work was done in the Beckman Institute Resource Center for Transmission Electron Microscopy at the California Institute of Technology. We are grateful to Catherine Oikonomou for critically reading the manuscript. We thank Prof. Ariane Briegel for collecting some of the data and Songye Chen for technical support. We are grateful to the lab of Prof. Patrick Viollier (University of Geneva) for sending wild type and delta CapF strains. The C. crescentus DpleD strain (UJ4450) was kindly sent to us from the lab of Prof. Urs Jenal (University of Basel), and we also thank Prof. Urs Jenal for critically reading our manuscript. \n\nCRediT authorship contribution statement: Mohammed Kaplan: Conceptualization, Data curation, Data analysis, writing original draft and editing, Funding acquisition. Yuhang Wang: Data curation, Writing - review & editing. Georges Chreifi: Data curation, Writing - review & editing. Lujia Zhang: Data curation, Writing - review & editing. Yi-Wei Chang: Data curation, Writing - review & editing. Grant J. Jensen: Conceptualization, Data analysis, Writing - review & editing, Funding acquisition. \n\nThe authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.\n\nAccepted Version - nihms-1862485.pdf
Supplemental Material - 1-s2.0-S0022283621002059-mmc1.docx
", "abstract": "The bacterial flagellum consists of a long extracellular filament that is rotated by a motor embedded in the cell envelope. While flagellar assembly has been extensively studied, the disassembly process remains less well understood. In addition to the programmed flagellar ejection that occurs during the life cycle of Caulobacter crescentus, we and others have recently shown that many bacterial species lose their flagella under starvation conditions, leaving relic structures in the outer membrane. However, it remains unknown whether the programmed flagellar ejection of C. crescentus leaves similar relics or not. Here, we imaged the various stages of the C. crescentus life cycle using electron cryo-tomography (cryo-ET) and found that flagellar relic subcomplexes, akin to those produced in the starvation-induced process, remain as a result of flagellar ejection during cell development. This similarity suggests that the programmed flagellar ejection of C. crescentus might share a common evolutionary path with the more general, and likely more ancient (Kaplan et al., 2020), starvation-related flagellar loss.", "date": "2021-06-25", "date_type": "published", "publication": "Journal of Molecular Biology", "volume": "433", "number": "13", "publisher": "Elsevier", "pagerange": "Art. No. 167004", "id_number": "CaltechAUTHORS:20210423-164854049", "issn": "0022-2836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210423-164854049", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "RO1 AI127401" }, { "agency": "Caltech" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.jmb.2021.167004", "pmcid": "PMC9843737", "primary_object": { "basename": "1-s2.0-S0022283621002059-mmc1.docx", "url": "https://authors.library.caltech.edu/records/095s1-gqc19/files/1-s2.0-S0022283621002059-mmc1.docx" }, "related_objects": [ { "basename": "nihms-1862485.pdf", "url": "https://authors.library.caltech.edu/records/095s1-gqc19/files/nihms-1862485.pdf" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Kaplan, Mohammed; Wang, Yuhang; et el." }, { "id": "https://authors.library.caltech.edu/records/1y0cj-ek324", "eprint_id": 104448, "eprint_status": "archive", "datestamp": "2023-08-22 10:08:56", "lastmod": "2023-12-22 23:10:54", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Vulovic-Ivan", "name": { "family": "Vulovic", "given": "Ivan" }, "orcid": "0000-0003-4208-6183" }, { "id": "Yao-Qing", "name": { "family": "Yao", "given": "Qing" }, "orcid": "0000-0003-3575-9909" }, { "id": "Park-Young-Jun", "name": { "family": "Park", "given": "Young-Jun" }, "orcid": "0000-0003-2901-6949" }, { "id": "Courbet-Alexis", "name": { "family": "Courbet", "given": "Alexis" }, "orcid": "0000-0003-0539-7011" }, { "id": "Norris-Andrew", "name": { "family": "Norris", "given": "Andrew" }, "orcid": "0000-0002-0121-5922" }, { "id": "Busch-Florian", "name": { "family": "Busch", "given": "Florian" }, "orcid": "0000-0002-4324-6065" }, { "id": "Sahasrabuddhe-Aniruddha", "name": { "family": "Sahasrabuddhe", "given": "Aniruddha" }, "orcid": "0000-0002-3980-0035" }, { "id": "Merten-Hannes", "name": { "family": "Merten", "given": "Hannes" }, "orcid": "0000-0003-2150-0867" }, { "id": "Sahtoe-Danny-D", "name": { "family": "Sahtoe", "given": "Danny D." }, "orcid": "0000-0001-9095-0744" }, { "id": "Ueda-George", "name": { "family": "Ueda", "given": "George" }, "orcid": "0000-0002-9792-7149" }, { "id": "Fallas-Jorge-A", "name": { "family": "Fallas", "given": "Jorge A." }, "orcid": "0000-0002-1431-820X" }, { "id": "Weaver-Sara-J", "name": { "family": "Weaver", "given": "Sara J." }, "orcid": "0000-0001-7753-6215" }, { "id": "Hsia-Yang", "name": { "family": "Hsia", "given": "Yang" }, "orcid": "0000-0001-7467-8373" }, { "id": "Langan-Robert-A", "name": { "family": "Langan", "given": "Robert A." }, "orcid": "0000-0003-3319-3016" }, { "id": "Pl\u00fcckthun-Andreas", "name": { "family": "Pl\u00fcckthun", "given": "Andreas" }, "orcid": "0000-0003-4191-5306" }, { "id": "Wysocki-Vicki-H", "name": { "family": "Wysocki", "given": "Vicki H." }, "orcid": "0000-0003-0495-2538" }, { "id": "Veesler-David", "name": { "family": "Veesler", "given": "David" }, "orcid": "0000-0002-6019-8675" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Baker-David", "name": { "family": "Baker", "given": "David" }, "orcid": "0000-0001-7896-6217" } ] }, "title": "Generation of ordered protein assemblies using rigid three-body fusion", "ispublished": "pub", "full_text_status": "public", "keywords": "protein design; cryo-EM; DARPin; protein fusion; nanomaterials", "note": "\u00a9 2021 National Academy of Sciences. Published under the PNAS license. \n\nEdited by Shane Gonen, University of California, Irvine, CA, and accepted by Editorial Board Member William F. DeGrado April 18, 2021 (received for review July 21, 2020). \n\nResearch reported in this publication was supported by the National Institute of General Medical Sciences (NIGMS) under the NIH under Award Number T32GM008268 to I.V., and the Open Philanthropy Project, HHMI, and NSF grant CHE-1629214 to D.B. NIH grant under award AI150464 provided support to G.J.J. Cryo-EM work under G.J.J. was performed in the Caltech Beckman Institute Resource Center for Transmission Electron Microscopy. We also thank Dr. Songye Chen and Dr. Andrey Malyutin at Caltech for technical assistance. This work was also supported by the National Institute of Allergy and Infectious Diseases (NIAID) grant DP1AI158186, NIH grant HHSN272201700059C, NIGMS grant R01GM120553, a Pew Biomedical Scholars Award, and a Burroughs Wellcome Investigators in the Pathogenesis of Infectious Diseases award to D.V. This work was also supported by NIH grant P41GM128577 to V.H.W. and Swiss National Science Foundation grant 310030_192689 to A.P. In addition, we thank Kathryn Burnett and Greg Hura for SAXS data collection through the SIBYLS mail-in SAXS program at the Advanced Light Source (ALS), a national user facility operated by Lawrence Berkeley National Laboratory on behalf of the Department of Energy, Office of Basic Energy Sciences, through the Integrated Diffraction Analysis Technologies program, supported by the Department of Energy (DOE) Office of Biological and Environmental Research. Additional support comes from the NIH project ALS-ENABLE (grant P30 GM124169) and High-End Instrumentation Grant S10OD018483. A.C. is a recipient of the Human Frontiers Science Program Long Term Fellowship. A.C. and D.D.S. received Washington Research Foundation fellowships. We thank Albumedix for providing high-quality Veltis-grade HSA. I.V. thanks Shane Caldwell (University of Washington) for discussion on SAXS analysis and Vikram Mulligan (Flatiron Institute) for answering questions on RosettaScripts. \n\nData Availability: Cryo-EM maps have been deposited in the Electron Microscopy Data Bank (see SI Appendix for details), and the fusion method implementation is available on GitHub (archived with Zenodo at https://zenodo.org/record/4771121) (58). Additional supporting data is deposited with Zenodo (https://zenodo.org/record/4771103) (59) and all other data is included in the article or supporting information. \n\nQ.Y. and Y.-J.P. contributed equally to this work. \n\nAuthor contributions: I.V., Q.Y., G.J.J., and D.B. designed research; I.V. developed software; I.V., Q.Y., Y.-J.P., A.C., A.N., F.B., A.S., D.D.S., G.U., J.A.F., S.J.W., Y.H., V.H.W., D.V., and G.J.J. performed research; H.M., R.A.L., and A.P. contributed new reagents/analytic tools; I.V., Q.Y., Y.-J.P., A.C., A.N., F.B., A.S., and S.J.W. analyzed data; and I.V., Q.Y., Y.-J.P., A.C., A.N., F.B., H.M., D.D.S., A.P., V.H.W., D.V., G.J.J., and D.B. wrote the paper. \n\nThe authors declare no competing interest. \n\nThis article is a PNAS Direct Submission. S.G. is a guest editor invited by the Editorial Board. \n\nThis article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.2015037118/-/DCSupplemental.\n\nPublished - e2015037118.full.pdf
Submitted - 2020.07.18.210294v1.full.pdf
Supplemental Material - pnas.2015037118.sapp.pdf
", "abstract": "Protein nanomaterial design is an emerging discipline with applications in medicine and beyond. A long-standing design approach uses genetic fusion to join protein homo-oligomer subunits via \u03b1-helical linkers to form more complex symmetric assemblies, but this method is hampered by linker flexibility and a dearth of geometric solutions. Here, we describe a general computational method for rigidly fusing homo-oligomer and spacer building blocks to generate user-defined architectures that generates far more geometric solutions than previous approaches. The fusion junctions are then optimized using Rosetta to minimize flexibility. We apply this method to design and test 92 dihedral symmetric protein assemblies using a set of designed homodimers and repeat protein building blocks. Experimental validation by native mass spectrometry, small-angle X-ray scattering, and negative-stain single-particle electron microscopy confirms the assembly states for 11 designs. Most of these assemblies are constructed from designed ankyrin repeat proteins (DARPins), held in place on one end by \u03b1-helical fusion and on the other by a designed homodimer interface, and we explored their use for cryogenic electron microscopy (cryo-EM) structure determination by incorporating DARPin variants selected to bind targets of interest. Although the target resolution was limited by preferred orientation effects and small scaffold size, we found that the dual anchoring strategy reduced the flexibility of the target-DARPIN complex with respect to the overall assembly, suggesting that multipoint anchoring of binding domains could contribute to cryo-EM structure determination of small proteins.", "date": "2021-06-08", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "118", "number": "23", "publisher": "National Academy of Sciences", "pagerange": "Art. No. e2015037118", "id_number": "CaltechAUTHORS:20200720-122329527", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200720-122329527", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "T32GM008268" }, { "agency": "Open Philanthropy Project" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NSF", "grant_number": "CHE-1629214" }, { "agency": "NIH", "grant_number": "AI150464" }, { "agency": "NIH", "grant_number": "DP1AI158186" }, { "agency": "NIH", "grant_number": "HHSN272201700059C" }, { "agency": "NIH", "grant_number": "R01GM120553" }, { "agency": "Pew Charitable Trust" }, { "agency": "Burroughs Wellcome Fund" }, { "agency": "NIH", "grant_number": "P41GM128577" }, { "agency": "Swiss National Science Foundation (SNSF)", "grant_number": "310030_192689" }, { "agency": "Department of Energy (DOE)" }, { "agency": "NIH", "grant_number": "P30 GM124169" }, { "agency": "NIH", "grant_number": "S10OD018483" }, { "agency": "Human Frontier Science Program" }, { "agency": "Washington Research Foundation" }, { "agency": "National Institute of Allergy and Infectious Diseases" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1073/pnas.2015037118", "pmcid": "PMC8201882", "primary_object": { "basename": "2020.07.18.210294v1.full.pdf", "url": "https://authors.library.caltech.edu/records/1y0cj-ek324/files/2020.07.18.210294v1.full.pdf" }, "related_objects": [ { "basename": "e2015037118.full.pdf", "url": "https://authors.library.caltech.edu/records/1y0cj-ek324/files/e2015037118.full.pdf" }, { "basename": "pnas.2015037118.sapp.pdf", "url": "https://authors.library.caltech.edu/records/1y0cj-ek324/files/pnas.2015037118.sapp.pdf" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Vulovic, Ivan; Yao, Qing; et el." }, { "id": "https://authors.library.caltech.edu/records/78rfd-e6179", "eprint_id": 111237, "eprint_status": "archive", "datestamp": "2023-08-20 03:33:40", "lastmod": "2023-12-22 23:14:54", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kaplan-Mohammed", "name": { "family": "Kaplan", "given": "Mohammed" }, "orcid": "0000-0002-0759-0459" }, { "id": "Tocheva-Elitza-I", "name": { "family": "Tocheva", "given": "Elitza I." }, "orcid": "0000-0002-4869-8319" }, { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Dobro-Megan-J", "name": { "family": "Dobro", "given": "Megan J." }, "orcid": "0000-0002-6464-3932" }, { "id": "Chang-Yi-Wei", "name": { "family": "Chang", "given": "Yi-Wei" }, "orcid": "0000-0003-2391-473X" }, { "id": "Subramanian-Poorna", "name": { "family": "Subramanian", "given": "Poorna" } }, { "id": "McDowall-Alasdair-W", "name": { "family": "McDowall", "given": "Alasdair" } }, { "id": "Beeby-Morgan-D", "name": { "family": "Beeby", "given": "Morgan" }, "orcid": "0000-0001-6413-9835" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Loss of the Bacterial Flagellar Motor Switch Complex upon Cell Lysis", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2021 Kaplan et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. \n\nReceived 5 February 2021; Accepted 26 April 2021; Published 8 June 2021. \n\nThis project was funded by the NIH (grant RO1 AI127401 to G.J.J.) and a Baxter postdoctoral fellowship from Caltech to M.K. Cryo-ET work was done in the Beckman Institute Resource Center for Transmission Electron Microscopy at the California Institute of Technology. \n\nWe are grateful to Catherine Oikonomou for critically reading the manuscript. We thank Cristina Iancu for collecting H. crunogenus data.\n\nPublished - mBio.00298-21.pdf
", "abstract": "The bacterial flagellar motor is a complex macromolecular machine whose function and self-assembly present a fascinating puzzle for structural biologists. Here, we report that in diverse bacterial species, cell lysis leads to loss of the cytoplasmic switch complex and associated ATPase before other components of the motor. This loss may be prevented by the formation of a cytoplasmic vesicle around the complex. These observations suggest a relatively loose association of the switch complex with the rest of the flagellar machinery.", "date": "2021-06", "date_type": "published", "publication": "mBio", "volume": "12", "number": "3", "publisher": "American Society for Microbiology", "pagerange": "Art. No. mBio.00298-21", "id_number": "CaltechAUTHORS:20211006-155256213", "issn": "2150-7511", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211006-155256213", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "RO1 AI127401" }, { "agency": "Baxter Foundation" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1128/mBio.00298-21", "pmcid": "PMC8263016", "primary_object": { "basename": "mBio.00298-21.pdf", "url": "https://authors.library.caltech.edu/records/78rfd-e6179/files/mBio.00298-21.pdf" }, "resource_type": "article", "pub_year": "2021", "author_list": "Kaplan, Mohammed; Tocheva, Elitza I.; et el." }, { "id": "https://authors.library.caltech.edu/records/n3w6m-k5b80", "eprint_id": 103403, "eprint_status": "archive", "datestamp": "2023-08-22 09:57:13", "lastmod": "2023-12-22 23:10:58", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chreifi-Georges", "name": { "family": "Chreifi", "given": "Georges" }, "orcid": "0000-0003-4194-1694" }, { "id": "Chen-Songye", "name": { "family": "Chen", "given": "Songye" }, "orcid": "0000-0001-5407-5049" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Rapid tilt-series method for cryo-electron tomography: Characterizing stage behavior during FISE acquisition", "ispublished": "pub", "full_text_status": "public", "keywords": "Cryo-ET; Cryo-EM; Tomography; Tilt series; K3; FISE", "note": "\u00a9 2021 Published by Elsevier Inc. \n\nReceived 22 May 2020, Revised 2 March 2021, Accepted 5 March 2021, Available online 11 March 2021. \n\nThis work was supported by NIH grant GM122588 (to G.J.J.). Electron cryomicroscopy was done in the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech. \n\nCRediT authorship contribution statement: Georges Chreifi: Conceptualization, Methodology, Software, Investigation, Writing - review & editing. Songye Chen: Supervision, Methodology. Grant J. Jensen: Conceptualization, Methodology, Writing - review & editing. \n\nThe authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.\n\nAccepted Version - nihms-1690820.pdf
Submitted - 2020.05.19.104828v1.full.pdf
", "abstract": "We and others recently developed rapid tilt-series acquisition methods for cryo-electron tomography on a Titan Krios G3i equipped with a single axis holder and a K-series direct electron detector and showed that one of these, the fast-incremental single exposure (FISE) method, significantly accelerates tilt-series acquisition when compared to traditional methods while preserving the quality of the images. Here, we characterize the behavior of our single axis holder in detail during a FISE experiment to optimally balance data quality with speed. We explain our methodology in detail so others can characterize their own stages, and conclude with recommendations for projects with different resolution goals.", "date": "2021-06", "date_type": "published", "publication": "Journal of Structural Biology", "volume": "213", "number": "2", "publisher": "Elsevier", "pagerange": "Art. No. 107716", "id_number": "CaltechAUTHORS:20200522-113331410", "issn": "1047-8477", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200522-113331410", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM122588" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.jsb.2021.107716", "pmcid": "PMC8217199", "primary_object": { "basename": "2020.05.19.104828v1.full.pdf", "url": "https://authors.library.caltech.edu/records/n3w6m-k5b80/files/2020.05.19.104828v1.full.pdf" }, "related_objects": [ { "basename": "nihms-1690820.pdf", "url": "https://authors.library.caltech.edu/records/n3w6m-k5b80/files/nihms-1690820.pdf" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Chreifi, Georges; Chen, Songye; et el." }, { "id": "https://authors.library.caltech.edu/records/8bjsm-pz940", "eprint_id": 107983, "eprint_status": "archive", "datestamp": "2023-08-20 03:21:27", "lastmod": "2023-12-22 23:14:44", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Jewett-Andrew-I", "name": { "family": "Jewett", "given": "Andrew I." }, "orcid": "0000-0002-6252-9888" }, { "id": "Stelter-David", "name": { "family": "Stelter", "given": "David" }, "orcid": "0000-0001-8493-5118" }, { "id": "Lambert-Jason", "name": { "family": "Lambert", "given": "Jason" }, "orcid": "0000-0003-0608-4332" }, { "id": "Saladi-Shyam-M", "name": { "family": "Saladi", "given": "Shyam M." }, "orcid": "0000-0001-9701-3059" }, { "id": "Roscioni-Otello-M", "name": { "family": "Roscioni", "given": "Otello M." }, "orcid": "0000-0001-7815-6636" }, { "id": "Ricci-Matteo", "name": { "family": "Ricci", "given": "Matteo" }, "orcid": "0000-0002-4534-6318" }, { "id": "Autin-Ludovic", "name": { "family": "Autin", "given": "Ludovic" }, "orcid": "0000-0002-2197-191X" }, { "id": "Maritan-Martina", "name": { "family": "Maritan", "given": "Martina" }, "orcid": "0000-0001-9901-1153" }, { "id": "Bashusqeh-Saeed-M", "name": { "family": "Bashusqeh", "given": "Saeed M." } }, { "id": "Keyes-Tom", "name": { "family": "Keyes", "given": "Tom" } }, { "id": "Dame-Remus-T", "name": { "family": "Dame", "given": "Remus T." }, "orcid": "0000-0001-9863-1692" }, { "id": "Shea-Joan-Emma", "name": { "family": "Shea", "given": "Joan-Emma" }, "orcid": "0000-0002-9801-9273" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Goodsell-David-S", "name": { "family": "Goodsell", "given": "David S." }, "orcid": "0000-0002-5932-2130" } ] }, "title": "Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics", "ispublished": "pub", "full_text_status": "public", "keywords": "coarse-grained simulation, molecular modeling, LAMMPS, molecular dynamics", "note": "\u00a9 2021 Elsevier Ltd. \n\nReceived 22 September 2020, Revised 19 January 2021, Accepted 20 January 2021, Available online 2 February 2021. \n\nMoltemplate was supported by NIH grants T32-AI007354-29, GM120604 and GM122588, NSF-MCB-1158577 and NSF-MCB-1716956, and HFSP RGP0014/2014. We thank Valeria Molinero, Yandong Zhang, Nathaniel Charest, William M. Clemons Jr., David Keffer, Marcus Martin, Paul Saxe and Robert Compton for support and useful discussions. \n\nCode availability: Moltemplate (available at http://moltemplate.org) is free open-source software. It is distributed under the MIT and PSF licenses. Moltemplate uses modern tools for public collaborative development and has many contributors. Users contribute suggestions, bug-reports, code, force-fields, examples, and documentation using GitHub. TravisCI is used for continuous-integration. \n\nAuthor contributions: AJ conceived, developed the original software, and carried out simulations. DS, JL, SMS, and OMR, contributed code improvements. OMR and MR contributed the MOLC example. SMB contributed the MARTINI example. MM, LA, and DSG created the mycoplasma models. AJ and DSG drafted the manuscript. DSG, GJJ, JES, TK, and RTD, planned and supervised the work. \n\nCRediT authorship contribution statement: Andrew I. Jewett: Conceptualization, Software, Investigation, Writing - original draft, Writing - review & editing. David Stelter: Investigation, Software, Writing - review & editing. Jason Lambert: Software, Writing - review & editing. Shyam M. Saladi: Software, Writing - review & editing. Otello M. Roscioni: Software, Investigation, Writing - review & editing. Matteo Ricci: Investigation, Writing - review & editing. Ludovic Autin: Investigation, Writing - review & editing. Martina Saeed M. Maritan Bashusqeh: Investigation, Writing - review & editing, Investigation, Writing - review & editing. Tom Keyes: Supervision, Writing - review & editing. Remus T. Dame: Supervision, Writing - review & editing. Joan-Emma Shea: Supervision, Writing - review & editing. Grant J. Jensen: Supervision, Writing - review & editing. David S. Goodsell: Supervision, Writing - original draft, Writing - review & editing. \n\nThe authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.\n\nSupplemental Material - 1-s2.0-S0022283621000358-mmc1.pdf
", "abstract": "Coarse-grained models have long been considered indispensable tools in the investigation of biomolecular dynamics and assembly. However, the process of simulating such models is arduous because unconventional force fields and particle attributes are often needed, and some systems are not in thermal equilibrium. Although modern molecular dynamics programs are highly adaptable, software designed for preparing all-atom simulations typically makes restrictive assumptions about the nature of the particles and the forces acting on them. Consequently, the use of coarse-grained models has remained challenging. Moltemplate is a file format for storing coarse-grained molecular models and the forces that act on them, as well as a program that converts moltemplate files into input files for LAMMPS, a popular molecular dynamics engine. Moltemplate has broad scope and an emphasis on generality. It accommodates new kinds of forces as they are developed for LAMMPS, making moltemplate a popular tool with thousands of users in computational chemistry, materials science, and structural biology. To demonstrate its wide functionality, we provide examples of using moltemplate to prepare simulations of fluids using many-body forces, coarse-grained organic semiconductors, and the motor-driven supercoiling and condensation of an entire bacterial chromosome.", "date": "2021-05-28", "date_type": "published", "publication": "Journal of Molecular Biology", "volume": "433", "number": "11", "publisher": "Elsevier", "pagerange": "Art. No. 166841", "id_number": "CaltechAUTHORS:20210210-100826621", "issn": "0022-2836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210210-100826621", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32-AI007354-29" }, { "agency": "NIH", "grant_number": "GM120604" }, { "agency": "NIH", "grant_number": "GM122588" }, { "agency": "NSF", "grant_number": "MCB-1158577" }, { "agency": "NSF", "grant_number": "MCB-1716956" }, { "agency": "Human Frontier Science Program", "grant_number": "RGP0014/2014" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.jmb.2021.166841", "primary_object": { "basename": "1-s2.0-S0022283621000358-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/8bjsm-pz940/files/1-s2.0-S0022283621000358-mmc1.pdf" }, "resource_type": "article", "pub_year": "2021", "author_list": "Jewett, Andrew I.; Stelter, David; et el." }, { "id": "https://authors.library.caltech.edu/records/f4cvf-d5r69", "eprint_id": 105468, "eprint_status": "archive", "datestamp": "2023-08-22 09:40:04", "lastmod": "2023-12-22 23:10:56", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Peck-Ariana", "name": { "family": "Peck", "given": "Ariana" }, "orcid": "0000-0002-5940-3897" }, { "id": "Yao-Qing", "name": { "family": "Yao", "given": "Qing" }, "orcid": "0000-0003-3575-9909" }, { "id": "Brewster-Aaron-S", "name": { "family": "Brewster", "given": "Aaron S." }, "orcid": "0000-0002-0908-7822" }, { "id": "Zwart-Petrus-H", "name": { "family": "Zwart", "given": "Petrus H." }, "orcid": "0000-0003-3315-4092" }, { "id": "Heumann-John-M", "name": { "family": "Heumann", "given": "John M." }, "orcid": "0000-0001-6751-3028" }, { "id": "Sauter-Nicholas-K", "name": { "family": "Sauter", "given": "Nicholas K." }, "orcid": "0000-0003-2786-6552" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Challenges in solving structures from radiation-damaged tomograms of protein nanocrystals assessed by simulation", "ispublished": "pub", "full_text_status": "public", "keywords": "cryo-electron tomography; diffraction methods; nanocrystals; radiation damage", "note": "\u00a9 2021 International Union of Crystallography. This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited. \n\nReceived 19 September 2020; Accepted 2 March 2021. \n\nWe thank Lauren Ann Metskas and Florian Schur for valuable discussions, in addition to David Stokes and Steven Ludtke for advice on the phase-splitting phenomenon. \n\nAP is The Mark Foundation for Cancer Research Fellow of\nthe Damon Runyon Cancer Research Foundation (DRG\n2361-19). This work was supported by NIH grants R35\nGM122588 (to GJJ), AI150464 (to GJJ) and GM117126 (to\nNKS). \n\nCode availability: The code developed to process tomograms of nanocrystals is available at https://github.com/apeck12/cryoetX.\n\nPublished - S2059798321002369.pdf
Submitted - 2020.09.18.298562v1.full.pdf
Supplemental Material - qh5069sup1.pdf
", "abstract": "Structure-determination methods are needed to resolve the atomic details that underlie protein function. X-ray crystallography has provided most of our knowledge of protein structure, but is constrained by the need for large, well ordered crystals and the loss of phase information. The rapidly developing methods of serial femtosecond crystallography, micro-electron diffraction and single-particle reconstruction circumvent the first of these limitations by enabling data collection from nanocrystals or purified proteins. However, the first two methods also suffer from the phase problem, while many proteins fall below the molecular-weight threshold required for single-particle reconstruction. Cryo-electron tomography of protein nanocrystals has the potential to overcome these obstacles of mainstream structure-determination methods. Here, a data-processing scheme is presented that combines routines from X-ray crystallography and new algorithms that have been developed to solve structures from tomograms of nanocrystals. This pipeline handles image-processing challenges specific to tomographic sampling of periodic specimens and is validated using simulated crystals. The tolerance of this workflow to the effects of radiation damage is also assessed. The simulations indicate a trade-off between a wider tilt range to facilitate merging data from multiple tomograms and a smaller tilt increment to improve phase accuracy. Since phase errors, but not merging errors, can be overcome with additional data sets, these results recommend distributing the dose over a wide angular range rather than using a finer sampling interval to solve the protein structure.", "date": "2021-05", "date_type": "published", "publication": "Acta Crystallographica Section D: Biological Crystallography", "volume": "D77", "number": "5", "publisher": "International Union of Crystallography", "pagerange": "572-586", "id_number": "CaltechAUTHORS:20200922-102800972", "issn": "0907-4449", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200922-102800972", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Damon Runyon Cancer Research Foundation", "grant_number": "DRG 2361-19" }, { "agency": "NIH", "grant_number": "R35 GM122588" }, { "agency": "NIH", "grant_number": "AI150464" }, { "agency": "NIH", "grant_number": "GM117126" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1107/S2059798321002369", "pmcid": "PMC8098477", "primary_object": { "basename": "2020.09.18.298562v1.full.pdf", "url": "https://authors.library.caltech.edu/records/f4cvf-d5r69/files/2020.09.18.298562v1.full.pdf" }, "related_objects": [ { "basename": "S2059798321002369.pdf", "url": "https://authors.library.caltech.edu/records/f4cvf-d5r69/files/S2059798321002369.pdf" }, { "basename": "qh5069sup1.pdf", "url": "https://authors.library.caltech.edu/records/f4cvf-d5r69/files/qh5069sup1.pdf" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Peck, Ariana; Yao, Qing; et el." }, { "id": "https://authors.library.caltech.edu/records/3r2p1-tan16", "eprint_id": 107703, "eprint_status": "archive", "datestamp": "2023-08-22 09:41:28", "lastmod": "2023-12-22 23:43:54", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Dutka-Przemys\u0142aw", "name": { "family": "Dutka", "given": "Przemys\u0142aw" }, "orcid": "0000-0003-3819-1618" }, { "id": "Malounda-Dina", "name": { "family": "Malounda", "given": "Dina" }, "orcid": "0000-0001-7086-9877" }, { "id": "Metskas-Lauren-Ann", "name": { "family": "Metskas", "given": "Lauren Ann" }, "orcid": "0000-0002-8073-6960" }, { "id": "Chen-Songye", "name": { "family": "Chen", "given": "Songye" }, "orcid": "0000-0001-5407-5049" }, { "id": "Hurt-Robert-C", "name": { "family": "Hurt", "given": "Robert C." }, "orcid": "0000-0002-4347-6901" }, { "id": "Lu-George-Jiaozhi", "name": { "family": "Lu", "given": "George J." }, "orcid": "0000-0002-4689-9686" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Shapiro-M-G", "name": { "family": "Shapiro", "given": "Mikhail G." }, "orcid": "0000-0002-0291-4215" } ] }, "title": "Measuring gas vesicle dimensions by electron microscopy", "ispublished": "pub", "full_text_status": "public", "keywords": "critical collapse pressure; cryo\u2010electron microscopy; diameter; electron microscopy; gas vesicles; negative staining", "note": "\u00a9 2021 The Protein Society. \n\nIssue Online:\n12 April 2021;\nVersion of Record online:\n11 March 2021;\nAccepted manuscript online:\n27 February 2021;\nManuscript accepted:\n22 February 2021;\nManuscript received:\n22 January 2021.\n\nThis work was supported by the National Institutes of Health (grant R35-GM122588 to G.J.J. and R01-EB018975 to M.G.S.) and the Caltech Center for Environmental Microbial Interactions (CEMI). Electron microscopy was performed in the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech. Related research in the Shapiro Laboratory is also supported by the Heritage Medical Research Institute, the Pew Scholarship in the Biomedical Sciences, and the Packard Fellowship for Science and Engineering. \n\nAuthor Contributions: Przemys\u0142aw Dutka: Conceptualization; methodology; investigation; formal analysis; visualization; writing \u2013 original draft preparation; writing \u2013 review editing. Dina Malounda: Investigation. Lauren Ann Metskas: Investigation. Songye Chen: Investigation. Robert C. Hurt: Investigation. George J. Lu: Investigation. Grant J. Jensen: Conceptualization; writing \u2013 review editing; supervision; funding acquisition. Mikhail G. Shapiro: Conceptualization; writing \u2013 review editing; supervision; funding acquisition. \n\nThe authors declare no competing interests.\n\nSubmitted - 2021.01.22.427725v1.full.pdf
", "abstract": "Gas vesicles (GVs) are cylindrical or spindle\u2010shaped protein nanostructures filled with air and used for flotation by various cyanobacteria, heterotrophic bacteria, and Archaea. Recently, GVs have gained interest in biotechnology applications due to their ability to serve as imaging agents and actuators for ultrasound, magnetic resonance and several optical techniques. The diameter of GVs is a crucial parameter contributing to their mechanical stability, buoyancy function and evolution in host cells, as well as their properties in imaging applications. Despite its importance, reported diameters for the same types of GV differ depending on the method used for its assessment. Here, we provide an explanation for these discrepancies and utilize electron microscopy (EM) techniques to accurately estimate the diameter of the most commonly studied types of GVs. We show that during air drying on the EM grid, GVs flatten, leading to a ~1.5\u2010fold increase in their apparent diameter. We demonstrate that GVs' diameter can be accurately determined by direct measurements from cryo\u2010EM samples or alternatively indirectly derived from widths of flat collapsed and negatively stained GVs. Our findings help explain the inconsistency in previously reported data and provide accurate methods to measure GVs dimensions.", "date": "2021-05", "date_type": "published", "publication": "Protein Science", "volume": "30", "number": "5", "publisher": "Wiley", "pagerange": "1081-1086", "id_number": "CaltechAUTHORS:20210125-082358436", "issn": "0961-8368", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210125-082358436", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R35-GM122588" }, { "agency": "NIH", "grant_number": "R01-EB018975" }, { "agency": "Caltech Center for Environmental Microbial Interactions (CEMI)" }, { "agency": "Heritage Medical Research Institute" }, { "agency": "Pew Charitable Trust" }, { "agency": "David and Lucile Packard Foundation" } ] }, "local_group": { "items": [ { "id": "Caltech-Center-for-Environmental-Microbial-Interactions-(CEMI)" }, { "id": "Heritage-Medical-Research-Institute" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1002/pro.4056", "pmcid": "PMC8040859", "primary_object": { "basename": "2021.01.22.427725v1.full.pdf", "url": "https://authors.library.caltech.edu/records/3r2p1-tan16/files/2021.01.22.427725v1.full.pdf" }, "resource_type": "article", "pub_year": "2021", "author_list": "Dutka, Przemys\u0142aw; Malounda, Dina; et el." }, { "id": "https://authors.library.caltech.edu/records/apc3h-m6s48", "eprint_id": 100447, "eprint_status": "archive", "datestamp": "2023-08-20 02:24:21", "lastmod": "2023-12-22 23:10:38", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Mageswaran-Shrawan-Kumar", "name": { "family": "Mageswaran", "given": "Shrawan Kumar" }, "orcid": "0000-0002-0803-7129" }, { "id": "Yang-Wei-Yuan", "name": { "family": "Yang", "given": "Wei Yuan" }, "orcid": "0000-0002-8939-651X" }, { "id": "Chakrabarty-Yogaditya", "name": { "family": "Chakrabarty", "given": "Yogaditya" }, "orcid": "0000-0002-3230-9251" }, { "id": "Oikonomou-C-M", "name": { "family": "Oikonomou", "given": "Catherine M." }, "orcid": "0000-0003-2312-4746" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "A cryo\u2013electron tomography workflow reveals protrusion-mediated shedding on injured plasma membrane", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC). \n\nSubmitted 5 May 2020; Accepted 9 February 2021; Published 26 March 2021. \n\nWe thank A. A. Hyman and I. Poser for providing the HeLa cell line stably expressing CHMP4B-EGFP. We thank A. Collazo and S. Wilbert for technical assistance with confocal microscopy. We also thank S. Chen and A. Malyutin for technical assistance with cryo-EM. The bulk of the confocal imaging was performed at the Biological Imaging Facility, and EM was performed at the Beckman Institute Resource Center for Transmission Electron Microscopy, both at Caltech. \n\nThis work was supported by funding from the NIH (P50 AI150464 awarded to G.J.J.). \n\nAuthor contributions: W.Y.Y. performed light microscopy experiments and prepared sample for cryo-ET with help from S.K.M. S.K.M. performed CLEM, cryo-ET, and data analyses. S.K.M. prepared the manuscript with help from W.Y.Y., C.M.O., and G.J.J. Y.C. performed the Western blot assays for Myo1a and Vps4B knockdowns. \n\nThe authors declare that they have no competing interests. \n\nData and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. Additional data related to this paper may be requested from the first and corresponding authors.\n\nPublished - eabc6345.full.pdf
Submitted - 2019.12.23.887638v1.full.pdf
Supplemental Material - abc6345_Movie_S1.mp4
Supplemental Material - abc6345_Movie_S2.mp4
Supplemental Material - abc6345_Movie_S3.mp4
Supplemental Material - abc6345_SM.pdf
", "abstract": "Cryo\u2013electron tomography (cryo-ET) provides structural context to molecular mechanisms underlying biological processes. Although straightforward to implement for studying stable macromolecular complexes, using it to locate short-lived structures and events can be impractical. A combination of live-cell microscopy, correlative light and electron microscopy, and cryo-ET will alleviate this issue. We developed a workflow combining the three to study the ubiquitous and dynamic process of shedding in response to plasma membrane damage in HeLa cells. We found filopodia-like protrusions enriched at damage sites and acting as scaffolds for shedding, which involves F-actin dynamics, myosin-1a, and vacuolar protein sorting 4B (a component of the 'endosomal sorting complex required for transport' machinery). Overall, shedding is more complex than current models of vesiculation from flat membranes. Its similarities to constitutive shedding in enterocytes argue for a conserved mechanism. Our workflow can also be adapted to study other damage response pathways and dynamic cellular events.", "date": "2021-03-26", "date_type": "published", "publication": "Science Advances", "volume": "7", "number": "13", "publisher": "American Association for the Advancement of Science", "pagerange": "Art. No. eabc6345", "id_number": "CaltechAUTHORS:20200102-095248499", "issn": "2375-2548", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200102-095248499", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P50 AI150464" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1126/sciadv.abc6345", "pmcid": "PMC7997517", "primary_object": { "basename": "abc6345_Movie_S2.mp4", "url": "https://authors.library.caltech.edu/records/apc3h-m6s48/files/abc6345_Movie_S2.mp4" }, "related_objects": [ { "basename": "abc6345_Movie_S3.mp4", "url": "https://authors.library.caltech.edu/records/apc3h-m6s48/files/abc6345_Movie_S3.mp4" }, { "basename": "abc6345_SM.pdf", "url": "https://authors.library.caltech.edu/records/apc3h-m6s48/files/abc6345_SM.pdf" }, { "basename": "eabc6345.full.pdf", "url": "https://authors.library.caltech.edu/records/apc3h-m6s48/files/eabc6345.full.pdf" }, { "basename": "2019.12.23.887638v1.full.pdf", "url": "https://authors.library.caltech.edu/records/apc3h-m6s48/files/2019.12.23.887638v1.full.pdf" }, { "basename": "abc6345_Movie_S1.mp4", "url": "https://authors.library.caltech.edu/records/apc3h-m6s48/files/abc6345_Movie_S1.mp4" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Mageswaran, Shrawan Kumar; Yang, Wei Yuan; et el." }, { "id": "https://authors.library.caltech.edu/records/dkj5k-c1v91", "eprint_id": 108077, "eprint_status": "archive", "datestamp": "2023-08-20 01:50:07", "lastmod": "2023-12-22 23:14:48", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant" }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Imaging Biopolymers In Vivo Directly with Cryo-ET: Trim5 Nets and IRE-1 Helices", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2021 Biophysical Society.", "abstract": "In the last ten years electron cryotomography (cryo-ET) has made it possible to visualize large macromolecular assemblies inside intact cells in a near-native, \"frozen-hydrated\" state in 3-D to a few nanometers resolution. increasingly, atomic models of individual proteins and smaller complexes obtained by X-ray crystallography, NMR spectroscopy, or other methods can be fit into cryotomograms to reveal how the various pieces work together inside cells. A few good pictures is therefore sometimes all that is really needed to distinguish between competing models. To illustrate these points, I will present examples of current results from our recent work on the HIV-restriction protein Trim5\u03b1 and the unfolded protein response sensor IRE1\u03b1, both of which form polymers inside cells. Trim5\u03b1 polymerizes into hexagonal lattices near sites of macroautophagy. IRE1\u03b1 polymerizes into left-handed double helices inside thin ER tubules. Time permitting, I will also describe ongoing technology development efforts that promise to dramatically expand the applicability of cryo-ET.", "date": "2021-02-12", "date_type": "published", "publication": "Biophysical Journal", "volume": "120", "number": "3, Supp. 1", "publisher": "Biophysical Society", "pagerange": "1a", "id_number": "CaltechAUTHORS:20210216-140505110", "issn": "0006-3495", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210216-140505110", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.bpj.2020.11.046", "resource_type": "article", "pub_year": "2021", "author_list": "Jensen, Grant" }, { "id": "https://authors.library.caltech.edu/records/f8aha-fmx23", "eprint_id": 97936, "eprint_status": "archive", "datestamp": "2023-08-20 01:37:12", "lastmod": "2023-12-22 23:10:47", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Nguyen-Lam-Thanh", "name": { "family": "Nguyen", "given": "Lam T." }, "orcid": "0000-0002-0756-0911" }, { "id": "Oikonomou-Catherine-M", "name": { "family": "Oikonomou", "given": "Catherine M." }, "orcid": "0000-0003-2312-4746" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Simulations of Proposed Mechanisms of FtsZ-Driven Cell Constriction", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2021 Nguyen et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. \n\nReceived 16 October 2020; Accepted 26 October 2020; Accepted manuscript posted online 16 November 2020; Published 11 January 2021. \n\nWe thank Debnath Ghosal and Andrew Jewett for their helpful discussions and Jane Ding for help setting up simulations on clusters. This work was supported by the NIH (grant R35 GM122588 to G.J.J.).\n\nPublished - Journal_of_Bacteriology-2021-Nguyen-e00576-20.full.pdf
Submitted - 737189.full.pdf
Supplemental Material - supp_data_source_00576-20.pdf
", "abstract": "To divide, bacteria must constrict their membranes against significant force from turgor pressure. A tubulin homolog, FtsZ, is thought to drive constriction, but how FtsZ filaments might generate constrictive force in the absence of motor proteins is not well understood. There are two predominant models in the field. In one, FtsZ filaments overlap to form complete rings around the circumference of the cell, and attractive forces cause filaments to slide past each other to maximize lateral contact. In the other, filaments exert force on the membrane by a GTP-hydrolysis-induced switch in conformation from straight to bent. Here, we developed software, ZCONSTRICT, for quantitative three-dimensional (3D) simulations of Gram-negative bacterial cell division to test these two models and identify critical conditions required for them to work. We find that the avidity of any kind of lateral interactions quickly halts the sliding of filaments, so a mechanism such as depolymerization or treadmilling is required to sustain constriction by filament sliding. For filament bending, we find that a mechanism such as the presence of a rigid linker is required to constrain bending to within the division plane and maintain the distance observed in vivo between the filaments and the membrane. Of these two models, only the filament bending model is consistent with our lab's recent observation of constriction associated with a single, short FtsZ filament.", "date": "2021-02", "date_type": "published", "publication": "Journal of Bacteriology", "volume": "203", "number": "3", "publisher": "American Society for Microbiology", "pagerange": "Art. No. e00576-20", "id_number": "CaltechAUTHORS:20190816-081257805", "issn": "0021-9193", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190816-081257805", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R35 GM122588" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1128/JB.00576-20", "pmcid": "PMC7886793", "primary_object": { "basename": "737189.full.pdf", "url": "https://authors.library.caltech.edu/records/f8aha-fmx23/files/737189.full.pdf" }, "related_objects": [ { "basename": "Journal_of_Bacteriology-2021-Nguyen-e00576-20.full.pdf", "url": "https://authors.library.caltech.edu/records/f8aha-fmx23/files/Journal_of_Bacteriology-2021-Nguyen-e00576-20.full.pdf" }, { "basename": "supp_data_source_00576-20.pdf", "url": "https://authors.library.caltech.edu/records/f8aha-fmx23/files/supp_data_source_00576-20.pdf" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Nguyen, Lam T.; Oikonomou, Catherine M.; et el." }, { "id": "https://authors.library.caltech.edu/records/dw7sg-enw51", "eprint_id": 102640, "eprint_status": "archive", "datestamp": "2023-08-20 01:38:10", "lastmod": "2023-12-22 23:32:53", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Nicolas-William-J", "name": { "family": "Nicolas", "given": "William J." }, "orcid": "0000-0001-5970-8626" }, { "id": "Ghosal-Debnath", "name": { "family": "Ghosal", "given": "Debnath" }, "orcid": "0000-0002-2227-0330" }, { "id": "Tocheva-Elitza-I", "name": { "family": "Tocheva", "given": "Elitza I." }, "orcid": "0000-0002-4869-8319" }, { "id": "Meyerowitz-E-M", "name": { "family": "Meyerowitz", "given": "Elliot M." }, "orcid": "0000-0003-4798-5153" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Structure of the Bacterial Cellulose Ribbon and Its Assembly-Guiding Cytoskeleton by Electron Cryotomography", "ispublished": "pub", "full_text_status": "public", "keywords": "cellulose, Gluconacetobacter, electron cryotomography", "note": "\u00a9 2020 Nicolas et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. \n\nReceived 29 June 2020; Accepted 26 October 2020; Accepted manuscript posted online 16 November 2020; Published 11 January 2021. \n\nThis work was supported by NIH grant R35-GM122588 to G.J.J., the Howard Hughes Medical Institute (HHMI), and the Center for Environmental Microbial Interactions (CEMI) pilot grant program. \n\nCryo-electron microscopy was performed in the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech. We thank Jean Marc Ghigo for kindly providing us the E. coli 1094 strain. Special acknowledgments go to Catherine Oikonomou for all the help and scientific advice given during this study and also to Candace Haigler for sharing her thoughts and her precious experience on the not so common Gluconacetobacter spp. \n\nWe declare that there are no conflicts of interest.\n\nPublished - Journal_of_Bacteriology-2021-Nicolas-e00371-20.full.pdf
Submitted - 2020.04.16.045534v2.full.pdf
Supplemental Material - JB.00371-20-s0001.pdf
Supplemental Material - media-2.mp4
Supplemental Material - media-3.mp4
Supplemental Material - media-4.mp4
Supplemental Material - media-5.mp4
", "abstract": "Cellulose is a widespread component of bacterial biofilms, where its properties of exceptional water retention, high tensile strength, and stiffness prevent dehydration and mechanical disruption of the biofilm. Bacteria in the genus Gluconacetobacter secrete crystalline cellulose, with a structure very similar to that found in plant cell walls. How this higher-order structure is produced is poorly understood. We used cryo-electron tomography and focused-ion-beam milling of native bacterial biofilms to image cellulose-synthesizing Gluconacetobacter hansenii and Gluconacetobacter xylinus bacteria in a frozen-hydrated, near-native state. We confirm previous results suggesting that cellulose crystallization occurs serially following its secretion along one side of the cell, leading to a cellulose ribbon that can reach several micrometers in length and combine with ribbons from other cells to form a robust biofilm matrix. We were able to take direct measurements in a near-native state of the cellulose sheets. Our results also reveal a novel cytoskeletal structure, which we have named the cortical belt, adjacent to the inner membrane and underlying the sites where cellulose is seen emerging from the cell. We found that this structure is not present in other cellulose-synthesizing bacterial species, Agrobacterium tumefaciens and Escherichia coli 1094, which do not produce organized cellulose ribbons. We therefore propose that the cortical belt holds the cellulose synthase complexes in a line to form higher-order cellulose structures, such as sheets and ribbons.", "date": "2021-02", "date_type": "published", "publication": "Journal of Bacteriology", "volume": "203", "number": "3", "publisher": "American Society for Microbiology", "pagerange": "Art. No. e00371-20", "id_number": "CaltechAUTHORS:20200417-145045074", "issn": "0021-9193", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200417-145045074", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R35-GM122588" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Caltech Center for Environmental Microbial Interactions (CEMI)" } ] }, "local_group": { "items": [ { "id": "Caltech-Center-for-Environmental-Microbial-Interactions-(CEMI)" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1128/JB.00371-20", "pmcid": "PMC7811197", "primary_object": { "basename": "media-5.mp4", "url": "https://authors.library.caltech.edu/records/dw7sg-enw51/files/media-5.mp4" }, "related_objects": [ { "basename": "2020.04.16.045534v2.full.pdf", "url": "https://authors.library.caltech.edu/records/dw7sg-enw51/files/2020.04.16.045534v2.full.pdf" }, { "basename": "JB.00371-20-s0001.pdf", "url": "https://authors.library.caltech.edu/records/dw7sg-enw51/files/JB.00371-20-s0001.pdf" }, { "basename": "Journal_of_Bacteriology-2021-Nicolas-e00371-20.full.pdf", "url": "https://authors.library.caltech.edu/records/dw7sg-enw51/files/Journal_of_Bacteriology-2021-Nicolas-e00371-20.full.pdf" }, { "basename": "media-2.mp4", "url": "https://authors.library.caltech.edu/records/dw7sg-enw51/files/media-2.mp4" }, { "basename": "media-3.mp4", "url": "https://authors.library.caltech.edu/records/dw7sg-enw51/files/media-3.mp4" }, { "basename": "media-4.mp4", "url": "https://authors.library.caltech.edu/records/dw7sg-enw51/files/media-4.mp4" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Nicolas, William J.; Ghosal, Debnath; et el." }, { "id": "https://authors.library.caltech.edu/records/n4h8t-mnm30", "eprint_id": 106975, "eprint_status": "archive", "datestamp": "2023-08-20 00:49:57", "lastmod": "2023-12-22 23:14:38", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zhang-Xianjun", "name": { "family": "Zhang", "given": "Xianjun" } }, { "id": "Carter-Stephen-D", "name": { "family": "Carter", "given": "Stephen D." }, "orcid": "0000-0002-4237-4276" }, { "id": "Singla-Jitin", "name": { "family": "Singla", "given": "Jitin" }, "orcid": "0000-0001-6225-0783" }, { "id": "White-Kate-L", "name": { "family": "White", "given": "Kate L." } }, { "id": "Butler-Peter-C", "name": { "family": "Butler", "given": "Peter C." }, "orcid": "0000-0002-2981-8979" }, { "id": "Stevens-Raymond-C", "name": { "family": "Stevens", "given": "Raymond C." }, "orcid": "0000-0002-4522-8725" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Visualizing insulin vesicle neighborhoods in \u03b2 cells by cryo-electron tomography", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License 4.0 (CC BY). \n\nSubmitted 16 May 2020; Accepted 22 October 2020; Published 9 December 2020. \n\nWe thank S. Chen and A. Malyutin for technical assistance with cryo\u2013electron microscopy. Cryo\u2013electron microscopy was performed in the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech. We thank K. Villers and C. Hanson for cell culture; W. Zhao for help with FIB milling; and C. Cato, A. Walker, and C. Oikonomou for assistance with manuscript preparation. We thank the members of the Pancreatic Beta Cell Consortium for their feedback and inspiring discussions. \n\nThis work was supported by the USC Bridge Institute (R.C.S.) and NIH grant R35GM122588 to G.J.J. \n\nAuthor contributions: R.C.S. and G.J.J. designed the project. X.Z. prepared samples, collected and processed electron tomography data, and prepared figures and supplementary videos with help from S.D.C. J.S. helped with data analysis and prepared statistical graphs in Fig. 3. K.L.W. initiated the INS-1E cell studies and helped with the design of INS-1E experiments and biological data analysis. P.C.B. provided scientific input and helped with INS-1E cell data analysis. The manuscript was written by X.Z., J.S., R.C.S., and G.J.J. with contributions from all authors. \n\nCompeting interests: R.C.S. is a founder of ShouTi, a biotech company focused on G protein\u2013coupled receptor small-molecule drug discovery including diabetes research. R.C.S. acknowledges that his primary affiliation is with USC; he holds a secondary appointment at ShanghaiTech University/iHuman Institute. The other authors declare that they have no competing interests. \n\nData and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. Additional data related to this paper may be requested from the authors.\n\nPublished - eabc8258.full.pdf
Supplemental Material - abc8258_Movie_S1.mp4
Supplemental Material - abc8258_Movie_S2.mov
Supplemental Material - abc8258_Movie_S3.mov
Supplemental Material - abc8258_Movie_S4.mov
Supplemental Material - abc8258_Movie_S5.mov
Supplemental Material - abc8258_Movie_S6.mov
Supplemental Material - abc8258_SM.pdf
", "abstract": "Subcellular neighborhoods, comprising specific ratios of organelles and proteins, serve a multitude of biological functions and are of particular importance in secretory cells. However, the role of subcellular neighborhoods in insulin vesicle maturation is poorly understood. Here, we present single-cell multiple distinct tomogram acquisitions of \u03b2 cells for in situ visualization of distinct subcellular neighborhoods that are involved in the insulin vesicle secretory pathway. We propose that these neighborhoods play an essential role in the specific function of cellular material. In the regions where we observed insulin vesicles, a measurable increase in both the fraction of cellular volume occupied by vesicles and the average size (diameter) of the vesicles was apparent as sampling moved from the area near the nucleus toward the plasma membrane. These findings describe the important role of the nanometer-scale organization of subcellular neighborhoods on insulin vesicle maturation.", "date": "2020-12-09", "date_type": "published", "publication": "Science Advances", "volume": "6", "number": "50", "publisher": "American Association for the Advancement of Science", "pagerange": "Art. No. eabc8258", "id_number": "CaltechAUTHORS:20201209-113043013", "issn": "2375-2548", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201209-113043013", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "University of Southern California" }, { "agency": "NIH", "grant_number": "R35GM122588" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1126/sciadv.abc8258", "pmcid": "PMC7725471", "primary_object": { "basename": "eabc8258.full.pdf", "url": "https://authors.library.caltech.edu/records/n4h8t-mnm30/files/eabc8258.full.pdf" }, "related_objects": [ { "basename": "abc8258_Movie_S3.mov", "url": "https://authors.library.caltech.edu/records/n4h8t-mnm30/files/abc8258_Movie_S3.mov" }, { "basename": "abc8258_Movie_S4.mov", "url": "https://authors.library.caltech.edu/records/n4h8t-mnm30/files/abc8258_Movie_S4.mov" }, { "basename": "abc8258_Movie_S5.mov", "url": "https://authors.library.caltech.edu/records/n4h8t-mnm30/files/abc8258_Movie_S5.mov" }, { "basename": "abc8258_Movie_S6.mov", "url": "https://authors.library.caltech.edu/records/n4h8t-mnm30/files/abc8258_Movie_S6.mov" }, { "basename": "abc8258_SM.pdf", "url": "https://authors.library.caltech.edu/records/n4h8t-mnm30/files/abc8258_SM.pdf" }, { "basename": "abc8258_Movie_S1.mp4", "url": "https://authors.library.caltech.edu/records/n4h8t-mnm30/files/abc8258_Movie_S1.mp4" }, { "basename": "abc8258_Movie_S2.mov", "url": "https://authors.library.caltech.edu/records/n4h8t-mnm30/files/abc8258_Movie_S2.mov" } ], "resource_type": "article", "pub_year": "2020", "author_list": "Zhang, Xianjun; Carter, Stephen D.; et el." }, { "id": "https://authors.library.caltech.edu/records/q9dfe-cyc35", "eprint_id": 105806, "eprint_status": "archive", "datestamp": "2023-08-22 07:45:25", "lastmod": "2023-12-22 23:10:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Garcez-A-S", "name": { "family": "Garcez", "given": "Aguinaldo S." }, "orcid": "0000-0003-2037-7211" }, { "id": "Kaplan-Mohammed", "name": { "family": "Kaplan", "given": "Mohammed" }, "orcid": "0000-0002-0759-0459" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Scheidt-F-R", "name": { "family": "Scheidt", "given": "F\u00e1bio R." } }, { "id": "Oliveira-E-M", "name": { "family": "Oliveira", "given": "Eduardo M." } }, { "id": "Suzuki-Selly-S", "name": { "family": "Suzuki", "given": "Selly S." } } ] }, "title": "Effects of antimicrobial photodynamic therapy on antibiotic-resistant Escherichia coli", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Electron Cryo-tomography; methylene blue; PDT; antibiotics", "note": "\u00a9 2020 Elsevier B.V. \n\nReceived 5 May 2020, Revised 16 September 2020, Accepted 18 September 2020, Available online 24 September 2020. \n\nThis work was supported in part by NIH grant R35 GM122588 (to G.J.J.). M.K. acknowledges a Rubicon postdoctoral fellowship from the Nederlandse Organisatie voor Wetenschappelijk Onderzoek. Cryo-ET work was performed in the Beckman Institute Resource Center for Transmission Electron Microscopy at the California Institute of Technology. \n\nAuthors' contribution: Garcez AS and Kaplan M \u2013 wrote the paper and participate in the experiments. Oliveira EM, Scheidt F R - participate in the experiments. Suzuki SS and Jensen G \u2013 Data interpretation and revision of the text. \n\nThe authors report no declarations of interest.", "abstract": "This study used Electron Cryo-tomography (ECT) and fluorescent images to evaluate antimicrobial photodynamic therapy (aPDT) on the envelope architecture of a Gram-negative bacteria and the effects of combined therapy of aPDT and antibiotics. Standard and clinical suspension of Escherichia coli were submitted to photodynamic treatment with methylene blue solution (100\u03bcM) and a 100\u2009mW LED emitting at 660\u2009nm with 3 and 18\u2009J of energy. As a control group, a suspension of E. coli was submitted to penicillin V for 60\u2009min at 30\u2009\u00b0C, to compare the damage in cell wall structure. After treatment, ECT images were collected and E. coli biofilms were grown in glass-cover slides and stained with live/dead staining for fluorescence analysis before and after treatments. Bacteria were also submitted to disc diffusion and MIC50 tests with Ampicillin, Amoxicillin\u2009+\u2009Clavulanic acid, Clindamycin and Erythromycin. For in vivo experiment Galleria mellonella larvae were infected with E. coli and treated with antibiotics, aPDT or combined therapy. ECT images presented damage to cell walls and vesicles structures inside and outside the bacteria and fluorescent images showed dose dependent effect of aPDT. Antibiotic or aPDT alone did not improve the survival of caterpillars, but the combined therapy significantly increased survival curve. ECT and fluorescent images shows that aPDT seems to promote micro-damages to cell envelope and causes the production of membrane vesicles permeabilizing cell membranes. The results showed that pre-treating bacterial cells with a photosensitizer and light make them more susceptible to antibiotics and could be an alternative to local infection treatment by resistant bacteria.", "date": "2020-12", "date_type": "published", "publication": "Photodiagnosis and Photodynamic Therapy", "volume": "32", "publisher": "Elsevier", "pagerange": "Art. No. 102029", "id_number": "CaltechAUTHORS:20201005-131934069", "issn": "1572-1000", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201005-131934069", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R35 GM122588" }, { "agency": "Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.pdpdt.2020.102029", "pmcid": "PMC7744317", "resource_type": "article", "pub_year": "2020", "author_list": "Garcez, Aguinaldo S.; Kaplan, Mohammed; et el." }, { "id": "https://authors.library.caltech.edu/records/dpqk7-jxk41", "eprint_id": 99748, "eprint_status": "archive", "datestamp": "2023-08-22 07:41:01", "lastmod": "2023-12-22 23:15:17", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Carter-Stephen-D", "name": { "family": "Carter", "given": "Stephen D." }, "orcid": "0000-0002-4237-4276" }, { "id": "Mamede-Jo\u00e3o-I", "name": { "family": "Mamede", "given": "Jo\u00e3o I." }, "orcid": "0000-0002-6048-1876" }, { "id": "Hope-Thomas-J", "name": { "family": "Hope", "given": "Thomas J." }, "orcid": "0000-0001-7183-8319" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Correlated cryogenic fluorescence microscopy and electron cryo-tomography shows that exogenous TRIM5\u03b1 can form hexagonal lattices or autophagy aggregates in vivo", "ispublished": "pub", "full_text_status": "public", "keywords": "cryo-CLEM/ECT; TRIM5\u03b1-body; hexagonal nets; autophagy; endoplasmic reticulum", "note": "\u00a9 2020 the Author(s). Published by PNAS. This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND). \n\nEdited by John M. Coffin, Tufts University, Boston, MA, and approved September 23, 2020 (received for review November 19, 2019). PNAS first published November 5, 2020. \n\nWe thank Sarah Speed (Division of Biology and Biological Engineering, California Institute of Technology) for valuable help in segmenting cryo-tomograms and Catherine Oikonomou (Division of Biology and Biological Engineering, California Institute of Technology) for insights and comments on the manuscript. This work was supported in part by NIH Grant AI150464 (to G.J.J. and T.J.H.). \n\nData Availability: All study data are included in the article and SI Appendix. Author contributions: S.D.C., J.I.M., T.J.H., and G.J.J. designed research; S.D.C. and J.I.M. performed research; S.D.C., J.I.M., T.J.H., and G.J.J. contributed new reagents/analytic tools; S.D.C., J.I.M., T.J.H., and G.J.J. analyzed data; and S.D.C. and G.J.J. wrote the paper. \n\nThe authors declare no competing interest. \n\nThis article is a PNAS Direct Submission. \n\nThis article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.1920323117/-/DCSupplemental.\n\nPublished - 29702.full.pdf
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", "abstract": "Members of the tripartite motif (TRIM) protein family have been shown to assemble into structures in both the nucleus and cytoplasm. One TRIM protein family member, TRIM5\u03b1, has been shown to form cytoplasmic bodies involved in restricting retroviruses such as HIV-1. Here we applied cryogenic correlated light and electron microscopy, combined with electron cryo-tomography, to intact mammalian cells expressing YFP-rhTRIM5\u03b1 and found the presence of hexagonal nets whose arm lengths were similar to those of the hexagonal nets formed by purified TRIM5\u03b1 in vitro. We also observed YFP-rhTRIM5\u03b1 within a diversity of structures with characteristics expected for organelles involved in different stages of macroautophagy, including disorganized protein aggregations (sequestosomes), sequestosomes flanked by flat double-membraned vesicles (sequestosome:phagophore complexes), sequestosomes within double-membraned vesicles (autophagosomes), and sequestosomes within multivesicular autophagic vacuoles (amphisomes or autolysosomes). Vaults were also seen in these structures, consistent with their role in autophagy. Our data 1) support recent reports that TRIM5\u03b1 can form both well-organized signaling complexes and nonsignaling aggregates, 2) offer images of the macroautophagy pathway in a near-native state, and 3) reveal that vaults arrive early in macroautophagy.", "date": "2020-11-24", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "117", "number": "47", "publisher": "National Academy of Sciences", "pagerange": "29702-29711", "id_number": "CaltechAUTHORS:20191108-075710149", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20191108-075710149", "funders": { "items": [ { "agency": "NIH", "grant_number": "AI150464" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1073/pnas.1920323117", "pmcid": "PMC7703684", "primary_object": { "basename": "29702.full.pdf", "url": "https://authors.library.caltech.edu/records/dpqk7-jxk41/files/29702.full.pdf" }, "related_objects": [ { "basename": "pnas.1920323117.sapp.pdf", "url": "https://authors.library.caltech.edu/records/dpqk7-jxk41/files/pnas.1920323117.sapp.pdf" }, { "basename": "pnas.1920323117.sm04.mp4", "url": "https://authors.library.caltech.edu/records/dpqk7-jxk41/files/pnas.1920323117.sm04.mp4" }, { "basename": "pnas.1920323117.sm05.mp4", "url": "https://authors.library.caltech.edu/records/dpqk7-jxk41/files/pnas.1920323117.sm05.mp4" }, { "basename": "pnas.1920323117.sm08.mp4", "url": "https://authors.library.caltech.edu/records/dpqk7-jxk41/files/pnas.1920323117.sm08.mp4" }, { "basename": "pnas.1920323117.sm09.mp4", "url": "https://authors.library.caltech.edu/records/dpqk7-jxk41/files/pnas.1920323117.sm09.mp4" }, { "basename": "pnas.1920323117.sm02.mp4", "url": "https://authors.library.caltech.edu/records/dpqk7-jxk41/files/pnas.1920323117.sm02.mp4" }, { "basename": "pnas.1920323117.sm10.mp4", "url": "https://authors.library.caltech.edu/records/dpqk7-jxk41/files/pnas.1920323117.sm10.mp4" }, { "basename": "pnas.1920323117.sm01.mp4", "url": "https://authors.library.caltech.edu/records/dpqk7-jxk41/files/pnas.1920323117.sm01.mp4" }, { "basename": "pnas.1920323117.sm03.mp4", "url": "https://authors.library.caltech.edu/records/dpqk7-jxk41/files/pnas.1920323117.sm03.mp4" }, { "basename": "pnas.1920323117.sm07.mp4", "url": "https://authors.library.caltech.edu/records/dpqk7-jxk41/files/pnas.1920323117.sm07.mp4" }, { "basename": "835322.full.pdf", "url": "https://authors.library.caltech.edu/records/dpqk7-jxk41/files/835322.full.pdf" }, { "basename": "pnas.1920323117.sm06.mp4", "url": "https://authors.library.caltech.edu/records/dpqk7-jxk41/files/pnas.1920323117.sm06.mp4" }, { "basename": "pnas.1920323117.sm11.mp4", "url": "https://authors.library.caltech.edu/records/dpqk7-jxk41/files/pnas.1920323117.sm11.mp4" } ], "resource_type": "article", "pub_year": "2020", "author_list": "Carter, Stephen D.; Mamede, Jo\u00e3o I.; et el." }, { "id": "https://authors.library.caltech.edu/records/a7kkt-w2v79", "eprint_id": 105918, "eprint_status": "archive", "datestamp": "2023-08-19 23:49:28", "lastmod": "2023-12-22 23:10:42", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Weaver-Sara-J", "name": { "family": "Weaver", "given": "Sara J." }, "orcid": "0000-0001-7753-6215" }, { "id": "Ortega-Davi-R", "name": { "family": "Ortega", "given": "Davi R." }, "orcid": "0000-0002-8344-2335" }, { "id": "Sazinsky-Matthew-H", "name": { "family": "Sazinsky", "given": "Matthew H." }, "orcid": "0000-0001-7550-5116" }, { "id": "Dalia-Triana-N", "name": { "family": "Dalia", "given": "Triana N." }, "orcid": "0000-0001-7614-1377" }, { "id": "Dalia-Ankur-B", "name": { "family": "Dalia", "given": "Ankur B." }, "orcid": "0000-0003-2203-1230" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "CryoEM structure of the type IVa pilus secretin required for natural competence in Vibrio cholerae", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 The Author(s) 2020. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. \n\nReceived 06 March 2020. Accepted 15 September 2020. Published 08 October 2020. \n\nCryo Electron microscopy was performed in the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech. Dr. Songye Chen and Dr. Andrey Malyutin assisted with data collection. Dr. Spiros D. Garbis, Dr. Annie Moradian, Dr. Michael Sweredoski, and Dr. Brett Lomenick at the Caltech Proteome Exploration Laboratory (PEL) performed and analyzed mass spectrometry results. Dr. Naima Sharaf, Jeffery Lai, and Prof. Doug Rees provided invaluable advice on membrane protein biochemistry and instrumentation. Jane Ding and Welison Floriano provided computational support. Dr. Debnath Ghosal, Dr. Mohammed Kaplan, Dr. Catherine Oikonomou, Dr. Lauren Ann Metskas, Dr. Christopher Barnes, Claudia Jette, and Andrew Schacht provided feedback and advice. This work was supported in part by National Institutes of Health grant AI127401 to G.J.J. and National Institutes of Health grant R35GM128674 to A.B.D. \n\nAuthor Contributions. S.J.W. conceptualized the project, expressed and purified the protein, prepared samples for cryoEM, collected cryoEM data, processed cryoEM data, assisted in atomic model building, interpreted results, designed figures, and wrote the paper. D.R.O. designed research, performed sequence analyses, wrote software, collected sequence data, interpreted results, designed figures, and contributed text to the paper. M.H.S. purified protein, assisted with cryoEM sample prep and data collection, built the atomic model, interpreted results, and provided feedback on the paper. T.N.D. engineered the V. cholerae constructs, performed microbial assays, and interpreted results. A.B.D. conceptualized the project, obtained funding, engineered the V. cholerae constructs, performed microbial assays, interpreted results, designed figures, and provided feedback on the paper. G.J.J. conceptualized the project, obtained funding, interpreted results, and provided feedback on the paper. \n\nData availability. Data supporting the findings of this paper are available from the corresponding author upon reasonable request. The cryoEM reconstruction and model have been deposited in the Electron Microscopy Data Bank (https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-21559) and the Protein Data Bank (PDB 6W6M). \n\nCode availability. The scripts underlying the bioinformatics analysis are available at https://gitlab.com/jensenlab/seccomp. The alignment and the phylogenetic tree are available in Supplementary Data 2, while the thresholds used in the genehood.io analysis are in Supplementary Data 3. Other data are available from the corresponding author upon reasonable request. \n\nThe authors declare no competing interests. \n\nPeer review information. Nature Communications thanks the anonymous reviewers for their contributions to the peer review of this work. Peer review reports are available.\n\nWeaver, S.J., Ortega, D.R., Sazinsky, M.H. et al. Publisher Correction: CryoEM structure of the type IVa pilus secretin required for natural competence in Vibrio cholera. Nat Commun 11, 5533 (2020). https://doi.org/10.1038/s41467-020-19389-2\n\nPublished - s41467-020-18866-y.pdf
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", "abstract": "Natural transformation is the process by which bacteria take up genetic material from their environment and integrate it into their genome by homologous recombination. It represents one mode of horizontal gene transfer and contributes to the spread of traits like antibiotic resistance. In Vibrio cholerae, a type IVa pilus (T4aP) is thought to facilitate natural transformation by extending from the cell surface, binding to exogenous DNA, and retracting to thread this DNA through the outer membrane secretin, PilQ. Here, we use a functional tagged allele of VcPilQ purified from native V. cholerae cells to determine the cryoEM structure of the VcPilQ secretin in amphipol to ~2.7\u2009\u00c5. We use bioinformatics to examine the domain architecture and gene neighborhood of T4aP secretins in Proteobacteria in comparison with VcPilQ. This structure highlights differences in the architecture of the T4aP secretin from the type II and type III secretion system secretins. Based on our cryoEM structure, we design a series of mutants to reversibly regulate VcPilQ gate dynamics. These experiments support the idea of VcPilQ as a potential druggable target and provide insight into the channel that DNA likely traverses to promote the spread of antibiotic resistance via horizontal gene transfer by natural transformation.", "date": "2020-10-08", "date_type": "published", "publication": "Nature Communications", "volume": "11", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 5080", "id_number": "CaltechAUTHORS:20201008-083809896", "issn": "2041-1723", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201008-083809896", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "AI127401" }, { "agency": "NIH", "grant_number": "R35GM128674" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1038/s41467-020-18866-y", "pmcid": "PMC7545093", "primary_object": { "basename": "41467_2020_18866_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/a7kkt-w2v79/files/41467_2020_18866_MOESM1_ESM.pdf" }, "related_objects": [ { "basename": "41467_2020_18866_MOESM3_ESM.zip", "url": "https://authors.library.caltech.edu/records/a7kkt-w2v79/files/41467_2020_18866_MOESM3_ESM.zip" }, { "basename": "41467_2020_18866_MOESM4_ESM.zip", "url": "https://authors.library.caltech.edu/records/a7kkt-w2v79/files/41467_2020_18866_MOESM4_ESM.zip" }, { "basename": "41467_2020_18866_MOESM5_ESM.gz", "url": "https://authors.library.caltech.edu/records/a7kkt-w2v79/files/41467_2020_18866_MOESM5_ESM.gz" }, { "basename": "s41467-020-18866-y.pdf", "url": "https://authors.library.caltech.edu/records/a7kkt-w2v79/files/s41467-020-18866-y.pdf" }, { "basename": "41467_2020_18866_MOESM2_ESM.pdf", "url": "https://authors.library.caltech.edu/records/a7kkt-w2v79/files/41467_2020_18866_MOESM2_ESM.pdf" }, { "basename": "41467_2020_18866_MOESM6_ESM.mp4", "url": "https://authors.library.caltech.edu/records/a7kkt-w2v79/files/41467_2020_18866_MOESM6_ESM.mp4" }, { "basename": "41467_2020_18866_MOESM7_ESM.pdf", "url": "https://authors.library.caltech.edu/records/a7kkt-w2v79/files/41467_2020_18866_MOESM7_ESM.pdf" }, { "basename": "s41467-020-19389-2.pdf", "url": "https://authors.library.caltech.edu/records/a7kkt-w2v79/files/s41467-020-19389-2.pdf" } ], "resource_type": "article", "pub_year": "2020", "author_list": "Weaver, Sara J.; Ortega, Davi R.; et el." }, { "id": "https://authors.library.caltech.edu/records/z6ae5-arr04", "eprint_id": 105912, "eprint_status": "archive", "datestamp": "2023-08-19 23:48:16", "lastmod": "2023-12-22 23:10:44", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Treuner-Lange-Anka", "name": { "family": "Treuner-Lange", "given": "Anke" }, "orcid": "0000-0001-6435-5642" }, { "id": "Chang-Yi-Wei", "name": { "family": "Chang", "given": "Yi-Wei" }, "orcid": "0000-0003-2391-473X" }, { "id": "Glatter-Timo", "name": { "family": "Glatter", "given": "Timo" } }, { "id": "Herfurth-Marco", "name": { "family": "Herfurth", "given": "Marco" } }, { "id": "Lindow-Steffi", "name": { "family": "Lindow", "given": "Steffi" } }, { "id": "Chreifi-Georges", "name": { "family": "Chreifi", "given": "Georges" }, "orcid": "0000-0003-4194-1694" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "S\u00f8gaard-Andersen-Lotte", "name": { "family": "S\u00f8gaard-Andersen", "given": "Lotte" }, "orcid": "0000-0002-0674-0013" } ] }, "title": "PilY1 and minor pilins form a complex priming the type IVa pilus in Myxococcus xanthus", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 The Author(s) 2020. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. \n\nReceived 30 September 2019. Accepted 14 September 2020. Published 07 October 2020. \n\nWe thank Ahmet Tekin for strains and plasmids and Magdalena Anna \u015awi\u0105tek-Po\u0142aty\u0144ska for LonD antibodies. Cryo-ET work was done in the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech. This work was supported by the Deutsche Forschungsgemeinschaft (DFG) within the framework of the SFB987 \"Microbial Diversity in Environmental Signal response\" (to L.S.-A.), the Max Planck Society (to L.S.-A.), and NIH grant RO1 AI27401 (to G.J.J.). \n\nData availability. The proteomics datasets are available via the PRIDE database (ProteomeXchange accession: PXD021163). We also used the following publicly available datasets: Uniprot (https://www.uniprot.org/) and KEGG (https://www.genome.jp/kegg/), including the KEGG SSDB database (https://www.kegg.jp/kegg/ssdb/). Source data are provided with this paper. \n\nOpen Access funding enabled and organized by Projekt DEAL. \n\nAuthor Contributions. A.T.-L.: designed and conceived the study and performed most of the experiments. Y.-W.C.: performed the cryo-electron tomographic experiments and the modeling of the priming complex. T.G.: performed purification and analysis of pull-down samples and label-free mass spectrometry-based quantitative proteomics. S.L.: generated plasmids and strains and performed motility assays. M.H.: generated plasmids and strains and helped with transmission electron microscopy and bioinformatics. G.C.: helped with cryo-electron tomography data acquisition. G.J.J. and L.S.-A.: conceived the study, supervised research and provided funding. A.T.-L., Y.-W.C., T.G., G.J.J., and L.S.-A.: analyzed and interpreted data and wrote the manuscript. All authors approved the final manuscript. \n\nThe authors declare no competing interests. \n\nReporting summary. Further information on research design is available in the Nature Research Reporting Summary linked to this article. \n\nPeer review information. Nature Communications thanks Lisa Craig and the other anonymous reviewers for their contribution to the peer review of this work. Peer reviewer reports are available.\n\nPublished - s41467-020-18803-z.pdf
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", "abstract": "Type IVa pili are ubiquitous and versatile bacterial cell surface filaments that undergo cycles of extension, adhesion and retraction powered by the cell-envelope spanning type IVa pilus machine (T4aPM). The overall architecture of the T4aPM and the location of 10 conserved core proteins within this architecture have been elucidated. Here, using genetics, cell biology, proteomics and cryo-electron tomography, we demonstrate that the PilY1 protein and four minor pilins, which are widely conserved in T4aP systems, are essential for pilus extension in Myxococcus xanthus and form a complex that is an integral part of the T4aPM. Moreover, these proteins are part of the extended pilus. Our data support a model whereby the PilY1/minor pilin complex functions as a priming complex in T4aPM for pilus extension, a tip complex in the extended pilus for adhesion, and a cork for terminating retraction to maintain a priming complex for the next round of extension.", "date": "2020-10-07", "date_type": "published", "publication": "Nature Communications", "volume": "11", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 5054", "id_number": "CaltechAUTHORS:20201008-083808921", "issn": "2041-1723", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201008-083808921", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Deutsche Forschungsgemeinschaft (DFG)", "grant_number": "SFB987" }, { "agency": "Max-Planck-Gesellschaft" }, { "agency": "NIH", "grant_number": "R01 AI27401" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1038/s41467-020-18803-z", "pmcid": "PMC7541494", "primary_object": { "basename": "41467_2020_18803_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/z6ae5-arr04/files/41467_2020_18803_MOESM1_ESM.pdf" }, "related_objects": [ { "basename": "41467_2020_18803_MOESM2_ESM.pdf", "url": "https://authors.library.caltech.edu/records/z6ae5-arr04/files/41467_2020_18803_MOESM2_ESM.pdf" }, { "basename": "41467_2020_18803_MOESM3_ESM.pdf", "url": "https://authors.library.caltech.edu/records/z6ae5-arr04/files/41467_2020_18803_MOESM3_ESM.pdf" }, { "basename": "41467_2020_18803_MOESM4_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/z6ae5-arr04/files/41467_2020_18803_MOESM4_ESM.xlsx" }, { "basename": "s41467-020-18803-z.pdf", "url": "https://authors.library.caltech.edu/records/z6ae5-arr04/files/s41467-020-18803-z.pdf" } ], "resource_type": "article", "pub_year": "2020", "author_list": "Treuner-Lange, Anke; Chang, Yi-Wei; et el." }, { "id": "https://authors.library.caltech.edu/records/nptj8-m3102", "eprint_id": 96000, "eprint_status": "archive", "datestamp": "2023-08-19 21:04:54", "lastmod": "2023-12-22 23:10:40", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ortega-Davi-R", "name": { "family": "Ortega", "given": "Davi R." }, "orcid": "0000-0002-8344-2335" }, { "id": "Yang-Wen", "name": { "family": "Yang", "given": "Wen" } }, { "id": "Subramanian-Poorna", "name": { "family": "Subramanian", "given": "Poorna" } }, { "id": "Mann-Petra", "name": { "family": "Mann", "given": "Petra" } }, { "id": "Kj\u00e6r-Andreas", "name": { "family": "Kjaer", "given": "Andreas" }, "orcid": "0000-0002-0096-5764" }, { "id": "Chen-Songye", "name": { "family": "Chen", "given": "Songye" }, "orcid": "0000-0001-5407-5049" }, { "id": "Watta-Kylie-J", "name": { "family": "Watts", "given": "Kylie J." }, "orcid": "0000-0002-8072-2745" }, { "id": "Pirbadian-Sahand", "name": { "family": "Pirbadian", "given": "Sahand" } }, { "id": "Collins-David-A", "name": { "family": "Collins", "given": "David A." } }, { "id": "Kooger-Romain", "name": { "family": "Kooger", "given": "Romain" }, "orcid": "0000-0001-8768-1870" }, { "id": "Kalyuzhnaya-Marina-G", "name": { "family": "Kalyuzhnaya", "given": "Marina G." }, "orcid": "0000-0002-9058-7794" }, { "id": "Ringgaard-Simon", "name": { "family": "Ringgaard", "given": "Simon" } }, { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Repurposing a chemosensory macromolecular machine", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2020 The Author(s). This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. \n\nReceived 13 July 2019; Accepted 23 March 2020; Published 27 April 2020. \n\nThe authors wish to thank Drs. Zhiheng Yu, Jason de la Cruz, Chuan Hong, and Rick Huang for microscopy support at HHMI Janelia Farms; Dr. Mohamed Y. El-Naggar for insights into the culturing of S. oneidensis, Dr. Kristin Wuichet for discussions about the evolutionary interpretation of the bioinformatics data and Dr. Keith Cassidy for discussions on homology model building and for providing the Tar model used in Fig. 5. We also thank Dr. Catherine M. Oikonomou for helpful discussion and suggestions on the paper. This work was supported by the John Templeton Foundation as part of the Boundaries of Life Initiative (grants 51250 and 60973), NIGMS grant R35 GM122588 (to G.J.J.), NIGMS grant R01 GM108655 (to K.J.W.), the Max-Planck-Gesellschaft (to S.R.), the National Science Foundation grant CBET-1605031 (to M.G.K.), the Swiss National Science Foundation (R.K.), and the Air Force Office of Scientific Research Presidential Early Career Award for Scientists and Engineers grant FA955014-1-0294 (S.P.). P. aeruginosa strains were acquired from the transposon mutant collection that was made possible by NIH grant P30 DK089507. \n\nData availability: Tomograms are available in the Electron Tomography Database\u2014Caltech at https://etdb.caltech.edu and their identifiers are listed in the Supplementary Table 6. Phylogenetic trees in Fig. 4, Supplementary Figs. 1, 2, and 4 are available in Supplementary Data 1. The homology models in Fig. 2D are available in Supplementary Data 2. Other data are available from the corresponding authors upon reasonable request. \n\nAuthor Contributions: Conceptualization: D.R.O., A.B., and G.J.J.; Formal analysis: D.R.O.; Funding acquisition: K.J.W., M.G.K., S.R., A.B., and G.J.J.; Investigation: D.R.O., P.S., P.M., A.K., S.C., K.J.W., S.P., S.A.C., R.K., and A.B.; Methodology: D.R.O., W.Y., P.S., P.M., K.J.W., S.P., D.A.C., M.G.K., S.R., and A.B. Project administration: G.J.J.; Software: D.R.O.; Supervision: M.G.K., S.R., A.B., and G.J.J. Validation: D.R.O., W.Y., P.S., P.M., A.K., S.C., K.J.W., S.P., S.A.C., R.K., and A.B.; Visualization: D.R.O., W.Y., P.S., S.P., and A.B.; Writing\u2014original draft: D.R.O., P.S., A.B., and G.J.J. Writing\u2014review and editing: D.R.O., W.Y., P.S., K.J.W., S.P., D.A.C., M.G.K., S.R., A.B., and G.J.J. \n\nThe authors declare no competing interests.\n\nPublished - s41467-020-15736-5.pdf
Submitted - 653600.1.full.pdf
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", "abstract": "How complex, multi-component macromolecular machines evolved remains poorly understood. Here we reveal the evolutionary origins of the chemosensory machinery that controls flagellar motility in Escherichia coli. We first identify ancestral forms still present in Vibrio cholerae, Pseudomonas aeruginosa, Shewanella oneidensis and Methylomicrobium alcaliphilum, characterizing their structures by electron cryotomography and finding evidence that they function in a stress response pathway. Using bioinformatics, we trace the evolution of the system through \u03b3-Proteobacteria, pinpointing key evolutionary events that led to the machine now seen in E. coli. Our results suggest that two ancient chemosensory systems with different inputs and outputs (F6 and F7) existed contemporaneously, with one (F7) ultimately taking over the inputs and outputs of the other (F6), which was subsequently lost.", "date": "2020-04-27", "date_type": "published", "publication": "Nature Communications", "volume": "11", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 2041", "id_number": "CaltechAUTHORS:20190531-091859930", "issn": "2041-1723", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190531-091859930", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "John Templeton Foundation", "grant_number": "51250" }, { "agency": "John Templeton Foundation", "grant_number": "60973" }, { "agency": "NIH", "grant_number": "R35 GM122588" }, { "agency": "NIH", "grant_number": "R01 GM108655" }, { "agency": "Max-Planck-Gesellschaft" }, { "agency": "NSF", "grant_number": "CBET-1605031" }, { "agency": "Swiss National Science Foundation (SNSF)" }, { "agency": "Air Force Office of Scientific Research (AFOSR)", "grant_number": "FA955014-1-0294" }, { "agency": "NIH", "grant_number": "P30 DK089507" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1038/s41467-020-15736-5", "pmcid": "PMC7184735", "primary_object": { "basename": "41467_2020_15736_MOESM5_ESM.gz", "url": "https://authors.library.caltech.edu/records/nptj8-m3102/files/41467_2020_15736_MOESM5_ESM.gz" }, "related_objects": [ { "basename": "41467_2020_15736_MOESM6_ESM.pdf", "url": "https://authors.library.caltech.edu/records/nptj8-m3102/files/41467_2020_15736_MOESM6_ESM.pdf" }, { "basename": "653600.1.full.pdf", "url": "https://authors.library.caltech.edu/records/nptj8-m3102/files/653600.1.full.pdf" }, { "basename": "s41467-020-15736-5.pdf", "url": "https://authors.library.caltech.edu/records/nptj8-m3102/files/s41467-020-15736-5.pdf" }, { "basename": "41467_2020_15736_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/nptj8-m3102/files/41467_2020_15736_MOESM1_ESM.pdf" }, { "basename": "41467_2020_15736_MOESM2_ESM.pdf", "url": "https://authors.library.caltech.edu/records/nptj8-m3102/files/41467_2020_15736_MOESM2_ESM.pdf" }, { "basename": "41467_2020_15736_MOESM3_ESM.pdf", "url": "https://authors.library.caltech.edu/records/nptj8-m3102/files/41467_2020_15736_MOESM3_ESM.pdf" }, { "basename": "41467_2020_15736_MOESM4_ESM.gz", "url": "https://authors.library.caltech.edu/records/nptj8-m3102/files/41467_2020_15736_MOESM4_ESM.gz" } ], "resource_type": "article", "pub_year": "2020", "author_list": "Ortega, Davi R.; Yang, Wen; et el." }, { "id": "https://authors.library.caltech.edu/records/3pake-7s682", "eprint_id": 102314, "eprint_status": "archive", "datestamp": "2023-08-22 04:44:11", "lastmod": "2023-12-22 23:15:04", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kaplan-Mohammed", "name": { "family": "Kaplan", "given": "Mohammed" }, "orcid": "0000-0002-0759-0459" }, { "id": "Sweredoski-Michael-J", "name": { "family": "Sweredoski", "given": "Michael J." }, "orcid": "0000-0003-0878-3831" }, { "id": "Rodrigues-Jo\u00e3o-P-G-L-M", "name": { "family": "Rodrigues", "given": "Jo\u00e3o P. G. L. M." } }, { "id": "Tocheva-Elitza-I", "name": { "family": "Tocheva", "given": "Elitza I." }, "orcid": "0000-0002-4869-8319" }, { "id": "Chang-Yi-Wei", "name": { "family": "Chang", "given": "Yi-Wei" }, "orcid": "0000-0003-2391-473X" }, { "id": "Ortega-Davi-R", "name": { "family": "Ortega", "given": "Davi R." }, "orcid": "0000-0002-8344-2335" }, { "id": "Beeby-Morgan-D", "name": { "family": "Beeby", "given": "Morgan" }, "orcid": "0000-0001-6413-9835" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Bacterial flagellar motor PL-ring disassembly subcomplexes are widespread and ancient", "ispublished": "pub", "full_text_status": "public", "keywords": "cryo-electron tomography; flagellar motor; evolution", "note": "\u00a9 2020 the Author(s). Published by PNAS. This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND). \n\nEdited by Jody W. Deming, University of Washington, Seattle, WA, and approved February 24, 2020 (received for review September 28, 2019). PNAS first published April 2, 2020. \n\nThis work was supported by NIH Grant R35 GM122588 (to G.J.J.). Cryo-ET work was done in the Beckman Institute Resource Center for Transmission Electron Microscopy at the California Institute of Technology. M.K. was supported by a Rubicon postdoctoral fellowship from De Nederlandse Organisatie voor Wetenschappelijk Onderzoek. J.P.G.L.M.R. was supported by NIH Grant R35GM122543. Ariane Briegel kindly helped in collecting part of the data. We thank Catherine M. Oikonomou for reading the manuscript and for the insightful discussions; and Dr. Pat Zambryski from the University of California, Berkeley for providing us with the A. longum strain used in this study. \n\nData Availability: Some of the data used in this study are available in the Electron Tomography Database (ETDB)-Caltech (48). All of the data are available upon request from the corresponding author. \n\nAuthor contributions: M.K. and G.J.J. designed research; M.K., M.J.S., J.P.G.L.M.R., E.I.T., Y.-W.C., D.R.O., and M.B. performed research; M.K. and G.J.J. contributed new reagents/analytic tools; M.K., M.J.S., and G.J.J. analyzed data; and M.K. and G.J.J. wrote the paper. \n\nThe authors declare no competing interest. \n\nThis article is a PNAS Direct Submission. \n\nThis article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.1916935117/-/DCSupplemental.\n\nPublished - 8941.full.pdf
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", "abstract": "The bacterial flagellum is an amazing nanomachine. Understanding how such complex structures arose is crucial to our understanding of cellular evolution. We and others recently reported that in several Gammaproteobacterial species, a relic subcomplex comprising the decorated P and L rings persists in the outer membrane after flagellum disassembly. Imaging nine additional species with cryo-electron tomography, here, we show that this subcomplex persists after flagellum disassembly in other phyla as well. Bioinformatic analyses fail to show evidence of any recent horizontal transfers of the P- and L-ring genes, suggesting that this subcomplex and its persistence is an ancient and conserved feature of the flagellar motor. We hypothesize that one function of the P and L rings is to seal the outer membrane after motor disassembly.", "date": "2020-04-21", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "117", "number": "16", "publisher": "National Academy of Sciences", "pagerange": "8941-8947", "id_number": "CaltechAUTHORS:20200403-104455365", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200403-104455365", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R35 GM122588" }, { "agency": "Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)" }, { "agency": "NIH", "grant_number": "R35GM122543" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1073/pnas.1916935117", "pmcid": "PMC7183148", "primary_object": { "basename": "pnas.1916935117.sapp.pdf", "url": "https://authors.library.caltech.edu/records/3pake-7s682/files/pnas.1916935117.sapp.pdf" }, "related_objects": [ { "basename": "pnas.1916935117.sd07.xlsx", "url": "https://authors.library.caltech.edu/records/3pake-7s682/files/pnas.1916935117.sd07.xlsx" }, { "basename": "pnas.1916935117.sm01.mov", "url": "https://authors.library.caltech.edu/records/3pake-7s682/files/pnas.1916935117.sm01.mov" }, { "basename": "8941.full.pdf", "url": "https://authors.library.caltech.edu/records/3pake-7s682/files/8941.full.pdf" }, { "basename": "pnas.1916935117.sd02.xlsx", "url": "https://authors.library.caltech.edu/records/3pake-7s682/files/pnas.1916935117.sd02.xlsx" }, { "basename": "pnas.1916935117.sd03.xlsx", "url": "https://authors.library.caltech.edu/records/3pake-7s682/files/pnas.1916935117.sd03.xlsx" }, { "basename": "pnas.1916935117.sd04.xlsx", "url": "https://authors.library.caltech.edu/records/3pake-7s682/files/pnas.1916935117.sd04.xlsx" }, { "basename": "pnas.1916935117.sd05.xlsx", "url": "https://authors.library.caltech.edu/records/3pake-7s682/files/pnas.1916935117.sd05.xlsx" }, { "basename": "pnas.1916935117.sd06.xlsx", "url": "https://authors.library.caltech.edu/records/3pake-7s682/files/pnas.1916935117.sd06.xlsx" }, { "basename": "pnas.1916935117.sd01.xlsx", "url": "https://authors.library.caltech.edu/records/3pake-7s682/files/pnas.1916935117.sd01.xlsx" } ], "resource_type": "article", "pub_year": "2020", "author_list": "Kaplan, Mohammed; Sweredoski, Michael J.; et el." }, { "id": "https://authors.library.caltech.edu/records/t8kh2-rfv06", "eprint_id": 102253, "eprint_status": "archive", "datestamp": "2023-08-19 20:50:05", "lastmod": "2023-12-22 23:14:58", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Carter-Stepehn-D", "name": { "family": "Carter", "given": "Stephen D." }, "orcid": "0000-0002-4237-4276" }, { "name": { "family": "Hampton", "given": "Cheri M." } }, { "name": { "family": "Langlois", "given": "Robert" } }, { "name": { "family": "Melero", "given": "Roberto" } }, { "name": { "family": "Farino", "given": "Zachary J." } }, { "name": { "family": "Calderon", "given": "Michael J." } }, { "name": { "family": "Li", "given": "Wen" } }, { "name": { "family": "Wallace", "given": "Callen T." } }, { "name": { "family": "Tran", "given": "Ngoc Han" } }, { "name": { "family": "Grassucci", "given": "Robert A." } }, { "name": { "family": "Siegmund", "given": "Stephanie E." } }, { "name": { "family": "Pemberton", "given": "Joshua" } }, { "name": { "family": "Morgenstern", "given": "Travis J." } }, { "name": { "family": "Eisenman", "given": "Leanna" } }, { "name": { "family": "Aguilar", "given": "Jenny I." } }, { "name": { "family": "Greenberg", "given": "Nili L." } }, { "name": { "family": "Levy", "given": "Elana S." } }, { "name": { "family": "Yi", "given": "Edward" } }, { "name": { "family": "Mitchell", "given": "William G." } }, { "name": { "family": "Rice", "given": "William J." } }, { "name": { "family": "Wigge", "given": "Christoph" } }, { "name": { "family": "Pilli", "given": "Jyotsna" } }, { "name": { "family": "George", "given": "Emily W." } }, { "name": { "family": "Aslanoglou", "given": "Despoina" } }, { "name": { "family": "Courel", "given": "Ma\u00eft\u00e9" } }, { "name": { "family": "Freyberg", "given": "Robin J." } }, { "name": { "family": "Javitch", "given": "Jonathan A." } }, { "name": { "family": "Wills", "given": "Zachary P." } }, { "name": { "family": "Area-Gomez", "given": "Estela" } }, { "name": { "family": "Shiva", "given": "Sruti" } }, { "name": { "family": "Bartolini", "given": "Francesca" } }, { "name": { "family": "Volchuk", "given": "Allen" } }, { "name": { "family": "Murray", "given": "Sandra A." } }, { "name": { "family": "Aridor", "given": "Meir" } }, { "name": { "family": "Fish", "given": "Kenneth N." } }, { "name": { "family": "Walter", "given": "Peter" } }, { "name": { "family": "Balla", "given": "Tamas" } }, { "name": { "family": "Fass", "given": "Deborah" } }, { "id": "Wolf-Sharon-G", "name": { "family": "Wolf", "given": "Sharon G." } }, { "name": { "family": "Watkins", "given": "Simon C." } }, { "name": { "family": "Carazo", "given": "Jos\u00e9 Mar\u00eda" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "name": { "family": "Frank", "given": "Joachim" } }, { "name": { "family": "Freyberg", "given": "Zachary" } } ] }, "title": "Ribosome-associated vesicles: A dynamic subcompartment of the endoplasmic reticulum in secretory cells", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License 4.0 (CC BY). This is an open-access article distributed under the terms of the Creative Commons Attribution license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nSubmitted 1 August 2019; Accepted 13 January 2020; Published 1 April 2020. \n\nWe thank B. Carragher, C. Potter, E. Eng, P. De Camilli, L. Lavis, C. St. Croix, P. Maechler, J. Bewersdorf, M. Thomas-Baum, S. Weiss, M. Solimena, L. Taupenot, E. Schon, S. Mahata, T. Swayne, E. Munteanu, M. Hirano, C. G. Laguarta, R. Leibel, D. Accili, L. C. Burnett, M. Akabas, and P. Arvan for helpful guidance, suggestions, and reagents; Y.H. Kao for computing assistance; and the staffs of the New York Structural Biology Center (NYSBC) and the Confocal and Specialized Microscopy core facility of Columbia University for technical help. This work is dedicated to the memory of D. Shields. Funding: Support for this study was provided by the L. V. Gerstner Jr., Scholars Program (to Z.F.), the Leon Levy Foundation (to Z.F.), the John F. and Nancy A. Emmerling Fund of the Pittsburgh Foundation (to Z.F.), the Department of Defense PR141292 (to Z.F.), NIH K08DA031241 (to Z.F.), NSF MCB-1408986 (to S.A.M.), the National Science Foundation Graduate Research Fellowship (to N.H.T.), NIH K01AG045335 (to E.A.G.), NIH 1S10RR019003 (to S.C.W.), NIH 1S10RR025488 (to S.C.W.), NIH 1S10RR016236 (to S.C.W.), NIH F30NS093798 (to S.E.S.), NIH R56AG058593 (to Z.P.W.), the Howard Hughes Medical Institute (to P.W., N.H.T., J.F., and G.J.J.), NIH GM29169 (to J.F.), NIH GM122588 (to G.J.J.), NIH AI150464 (to G.J.J.), the Israel Science Foundation Grant 1285/14 (to S.G.W.), the European Research Council under the European Union's Seventh Framework Programme (grant number 310649) (to D.F.), MINECO AIC-A-2011-0638 (to J.M.C.), the Spanish Ministry of Economy and Competitiveness grant BIO2016-76400-R AEI/FEDER, UE (to J.M.C.), and Comunidad Aut\u00f3noma de Madrid grant S2017/BMD-3817 (to J.M.C.). Some of the cryo-ET was performed in the Beckman Institute Resource Center for Transmission EM at Caltech. Additional work was also performed at the Simons Electron Microscopy Center and National Resource for Automated Molecular Microscopy located at the New York Structural Biology Center, supported by grants from the Simons Foundation (349247), NYSTAR, and the NIH National Institute of General Medical Sciences (GM103310) with added support from NIH S10 RR029300-01. CSTET data acquisition was partially supported by the Irving and Cherna Moskowitz Center for Nano and Bio-Nano Imaging at the Weizmann Institute of Science. Some of the live confocal images were collected and processed in the Confocal and Specialized Microscopy Shared Resource of the Herbert Irving Comprehensive Cancer Center at Columbia University and supported by NIH P30 CA013696. Part of the cryo-EM image processing was conducted as an Instruct-ERIC collaboration project PD1222 at the Instruct Image Processing Center. \n\nAuthor contributions: S.D.C., C.M.H., R.L., G.J.J., J.F., and Z.F. designed the experiments. C.M.H., Z.F., T.J.M., N.H.T., S.G.W., D.F., E.W.G., D.A., S.E.S., L.E., and Z.J.F. prepared the samples. S.D.C., C.M.H., W.J.R., C.W., R.A.G., S.E.S., and Z.F. performed the cryo-EM and cryo-ET microscopy experiments. S.G.W. and D.F. performed the CSTET experiments. S.D.C. performed the cryo-CLEM and the cryo-FIB milling experiments. C.M.H., R.L., W.L., R.M., and J.M.C. performed the subtomogram averaging. D.F., S.G.W., S.A.M., M.A., and K.N.F. performed the TEM experiments. M.J.C., C.T.W., Z.F., Z.J.F., D.A., S.C.W., J.Pe., and T.B. performed the light microscopy experiments. J.Pi., E.W.G., and S.S. performed the cell metabolism experiments. A.V. performed the ER stress assay experiments. S.D.C., C.M.H., R.L., R.M., Z.J.F., W.L., M.J.C., C.T.W., N.H.T., R.A.G., S.E.S., J.Pe., T.J.M., J.I.A., N.L.G., E.S.L., E.Y., W.G.M., W.J.R., C.W., J.Pi., E.W.G., R.J.F., J.A.J., E.A.G., Z.P.W., S.S., F.B., A.V., S.A.M., M.A., K.N.F., P.W., T.B., D.F., S.G.W., S.C.W., J.M.C., G.J.J., J.F., and Z.F. interpreted the data. R.J.F. performed statistical analyses. S.D.C., G.J.J., J.F., and Z.F. wrote the manuscript, and the other co-authors edited and provided critical comments. S.D.C., C.M.H., and R.L. share co-first authorship given their contributions as indicated above. Z.F., J.F., and G.J.J. directed the research and are co-senior authors. \n\nThe authors declare that they have no competing interests. \n\nData and materials availability: All data needed to evaluate conclusions in the paper are present in the paper and/or the Supplementary Materials. Any additional data related to the paper may be requested from the authors.\n\nPublished - eaay9572.full.pdf
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", "abstract": "The endoplasmic reticulum (ER) is a highly dynamic network of membranes. Here, we combine live-cell microscopy with in situ cryo\u2013electron tomography to directly visualize ER dynamics in several secretory cell types including pancreatic \u03b2-cells and neurons under near-native conditions. Using these imaging approaches, we identify a novel, mobile form of ER, ribosome-associated vesicles (RAVs), found primarily in the cell periphery, which is conserved across different cell types and species. We show that RAVs exist as distinct, highly dynamic structures separate from the intact ER reticular architecture that interact with mitochondria via direct intermembrane contacts. These findings describe a new ER subcompartment within cells.", "date": "2020-04-01", "date_type": "published", "publication": "Science Advances", "volume": "6", "number": "14", "publisher": "American Association for the Advancement of Science", "pagerange": "Art. No. eaay9572", "id_number": "CaltechAUTHORS:20200401-144536810", "issn": "2375-2548", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200401-144536810", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "L. V. Gerstner Jr., Scholars Program" }, { "agency": "Leon Levy Foundation" }, { "agency": "Pittsburgh Foundation" }, { "agency": "Department of Defense", "grant_number": "PR141292" }, { "agency": "NIH", "grant_number": "K08DA031241" }, { "agency": "NSF", "grant_number": "MCB-1408986" }, { "agency": "NSF Graduate Research Fellowship" }, { "agency": "NIH", "grant_number": "K01AG045335" }, { "agency": "NIH", "grant_number": "1S10RR019003" }, { "agency": "NIH", "grant_number": "1S10RR025488" }, { "agency": "NIH", "grant_number": "1S10RR016236" }, { "agency": "NIH", "grant_number": "F30NS093798" }, { "agency": "NIH", "grant_number": "R56AG058593" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "GM29169" }, { "agency": "NIH", "grant_number": "GM122588" }, { "agency": "NIH", "grant_number": "AI150464" }, { "agency": "Israel Science Foundation", "grant_number": "1285/14" }, { "agency": "European Research Council (ERC)", "grant_number": "310649" }, { "agency": "Ministerio de Econom\u00eda, Industria y Competitividad (MINECO)", "grant_number": "AIC-A-2011-0638" }, { "agency": "Ministerio de Econom\u00eda, Industria y Competitividad (MINECO)", "grant_number": "BIO2016-76400-R" }, { "agency": "Comunidad Aut\u00f3noma de Madrid", "grant_number": "S2017/BMD-3817" }, { "agency": "Simons Foundation", "grant_number": "349247" }, { "agency": "NYSTAR" }, { "agency": "NIH", "grant_number": "GM103310" }, { "agency": "NIH", "grant_number": "S10 RR029300-01" }, { "agency": "Weizmann Institute of Science" }, { "agency": "NIH", "grant_number": "P30 CA013696" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1126/sciadv.aay9572", "pmcid": "PMC7112762", "primary_object": { "basename": "aay9572_Movie_S1.mp4", "url": "https://authors.library.caltech.edu/records/t8kh2-rfv06/files/aay9572_Movie_S1.mp4" }, "related_objects": [ { "basename": "aay9572_Movie_S2.mp4", "url": "https://authors.library.caltech.edu/records/t8kh2-rfv06/files/aay9572_Movie_S2.mp4" }, { "basename": "aay9572_Movie_S4.mp4", "url": "https://authors.library.caltech.edu/records/t8kh2-rfv06/files/aay9572_Movie_S4.mp4" }, { "basename": "aay9572_Movie_S5.mp4", "url": "https://authors.library.caltech.edu/records/t8kh2-rfv06/files/aay9572_Movie_S5.mp4" }, { "basename": "aay9572_SM.pdf", "url": "https://authors.library.caltech.edu/records/t8kh2-rfv06/files/aay9572_SM.pdf" }, { "basename": "aay9572_Movie_S11.mp4", "url": "https://authors.library.caltech.edu/records/t8kh2-rfv06/files/aay9572_Movie_S11.mp4" }, { "basename": "aay9572_Movie_S12.avi", "url": "https://authors.library.caltech.edu/records/t8kh2-rfv06/files/aay9572_Movie_S12.avi" }, { "basename": "aay9572_Movie_S13.avi", "url": "https://authors.library.caltech.edu/records/t8kh2-rfv06/files/aay9572_Movie_S13.avi" }, { "basename": "eaay9572.full.pdf", "url": "https://authors.library.caltech.edu/records/t8kh2-rfv06/files/eaay9572.full.pdf" }, { "basename": "aay9572_Movie_S3.mp4", "url": "https://authors.library.caltech.edu/records/t8kh2-rfv06/files/aay9572_Movie_S3.mp4" }, { "basename": "aay9572_Movie_S8.mov", "url": "https://authors.library.caltech.edu/records/t8kh2-rfv06/files/aay9572_Movie_S8.mov" }, { "basename": "aay9572_Movie_S9.mov", "url": "https://authors.library.caltech.edu/records/t8kh2-rfv06/files/aay9572_Movie_S9.mov" }, { "basename": "aay9572_Movie_S10.mov", "url": "https://authors.library.caltech.edu/records/t8kh2-rfv06/files/aay9572_Movie_S10.mov" }, { "basename": "aay9572_Movie_S6.mp4", "url": "https://authors.library.caltech.edu/records/t8kh2-rfv06/files/aay9572_Movie_S6.mp4" }, { "basename": "aay9572_Movie_S7.mp4", "url": "https://authors.library.caltech.edu/records/t8kh2-rfv06/files/aay9572_Movie_S7.mp4" } ], "resource_type": "article", "pub_year": "2020", "author_list": "Carter, Stephen D.; Hampton, Cheri M.; et el." }, { "id": "https://authors.library.caltech.edu/records/5a1c2-3n064", "eprint_id": 101192, "eprint_status": "archive", "datestamp": "2023-08-19 19:54:12", "lastmod": "2023-12-22 23:15:00", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Weaver-S-J", "name": { "family": "Weaver", "given": "Sara J." }, "orcid": "0000-0001-7753-6215" }, { "id": "Sazinsky-M-H", "name": { "family": "Sazinsky", "given": "Matthew H." }, "orcid": "0000-0001-7550-5116" }, { "id": "Dalia-T-N", "name": { "family": "Dalia", "given": "Triana N." }, "orcid": "0000-0001-7614-1377" }, { "id": "Dalia-A-B", "name": { "family": "Dalia", "given": "Ankur B." }, "orcid": "0000-0003-2203-1230" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "CryoEM Structure of the Vibrio cholerae Type IV Pilus Secretin PilQ", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2020 Biophysical Society. \n\nAvailable online 7 February 2020.", "abstract": "Natural competence is the process by which bacteria take up genetic material from their environment and integrate it into their genome using homologous recombination. In Vibrio cholerae, the Type IV pilus (T4P) is thought to mediate DNA uptake by binding DNA and retracting back toward the cell. How the DNA enters the periplasm is unclear. One hypothesis suggests that the DNA-bound T4P retracts completely so that the DNA would pass through the outer membrane secretin pore (PilQ). PilQ is a 870 kDa outer membrane pore with C14 symmetry. Here, we purify the V. cholerae PilQ secretin from V. cholerae cells in amphipols for single particle cryogenic electron microscopy (cryoEM). We solve the structure to 3.5 \u00c5 and provide insight on the channel DNA may traverse through during uptake.", "date": "2020-02-07", "date_type": "published", "publication": "Biophysical Journal", "volume": "118", "number": "3", "publisher": "Biophysical Society", "pagerange": "12a", "id_number": "CaltechAUTHORS:20200210-091000513", "issn": "0006-3495", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200210-091000513", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.bpj.2019.11.247", "resource_type": "article", "pub_year": "2020", "author_list": "Weaver, Sara J.; Sazinsky, Matthew H.; et el." }, { "id": "https://authors.library.caltech.edu/records/1bz5d-s3r86", "eprint_id": 101199, "eprint_status": "archive", "datestamp": "2023-08-19 19:54:56", "lastmod": "2023-12-22 23:15:02", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Metskas-L-A", "name": { "family": "Metskas", "given": "Lauren Ann" }, "orcid": "0000-0002-8073-6960" }, { "id": "Ho-Samuel-H", "name": { "family": "Ho", "given": "Samuel" }, "orcid": "0000-0001-7647-0752" }, { "id": "Weaver-S-J", "name": { "family": "Weaver", "given": "Sara J." }, "orcid": "0000-0001-7753-6215" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Tirrell-D-A", "name": { "family": "Tirrell", "given": "David A." }, "orcid": "0000-0003-3175-4596" } ] }, "title": "The Effect of Cryo Temperature on Commonly used Fluorophores", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2020 Biophysical Society. \n\nAvailable online 7 February 2020.", "abstract": "Correlated cryo-fluorescence and cryo-electron microscopy (cryo-CLEM) has become an increasingly popular method for combining the resolving power of cryo-EM with the specificity of fluorescence. Although cryo-fluorescence microscopy suffers from optical limitations, it is a powerful way to target the resolving power of cryo-EM toward proteins of interest in heterogeneous cellular environments. Super-resolution microscopy at cryo temperatures has also been established using several different approaches.\nWhile fluorescence-derived localization is a key benefit of cryo-CLEM, fluorescence can also be used to bring orthogonal information into cryo-EM images. We recently developed a fusion assay compatible with cryo-CLEM equipment and conditions (Metskas and Briggs, Microscopy & Microanalysis 2019). This development employs auto-quenching by resonant energy transfer to specifically target a function rather than a protein in cryo-CLEM - in this case, adding information on lipid mixing to morphologies from micrographs of influenza virus fusion. However, further methods developments, particularly those involving FRET, are currently hampered by limited characterization of modern fluorophores at cryo-CLEM temperatures (77-100 K).\nHere, we present a study of commonly used synthetic fluorophores and fluorescent proteins, characterizing excitation and emission spectra, singlet state lifetime, and quantum yield at 77 K. We note that 10 nm shifts of the modes are common for both excitation and emission spectra, but are fluorophore specific in magnitude and even in direction. Vibronic coupling and spectral narrowing are visible in all cases characterized, and singlet state lifetimes increase or decrease in a fluorophore-specific manner. Taken together, these data suggest guidelines for choosing cryo-CLEM fluorophores and filter sets, and demonstrate promise for techniques such as FRET in carefully-adapted applications.", "date": "2020-02-07", "date_type": "published", "publication": "Biophysical Journal", "volume": "118", "number": "3", "publisher": "Biophysical Society", "pagerange": "150a-151a", "id_number": "CaltechAUTHORS:20200210-110813112", "issn": "0006-3495", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200210-110813112", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.bpj.2019.11.942", "resource_type": "article", "pub_year": "2020", "author_list": "Metskas, Lauren Ann; Ho, Samuel; et el." }, { "id": "https://authors.library.caltech.edu/records/1akpj-hx598", "eprint_id": 92431, "eprint_status": "archive", "datestamp": "2023-08-22 03:05:26", "lastmod": "2023-12-22 23:41:23", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ghosal-Debnath", "name": { "family": "Ghosal", "given": "Debnath" }, "orcid": "0000-0002-2227-0330" }, { "id": "Kim-Ki-Woo", "name": { "family": "Kim", "given": "Ki Woo" }, "orcid": "0000-0002-7010-0336" }, { "id": "Zheng-Huaixin", "name": { "family": "Zheng", "given": "Huaixin" }, "orcid": "0000-0002-2529-7176" }, { "id": "Kaplan-Mohammed", "name": { "family": "Kaplan", "given": "Mohammed" }, "orcid": "0000-0002-0759-0459" }, { "id": "Truchan-Hilary-K", "name": { "family": "Truchan", "given": "Hilary K." } }, { "id": "Lopez-Alberto-E", "name": { "family": "Lopez", "given": "Alberto E." }, "orcid": "0000-0002-6218-5587" }, { "id": "McIntire-Ian-E", "name": { "family": "McIntire", "given": "Ian E." } }, { "id": "Vogel-Joseph-P", "name": { "family": "Vogel", "given": "Joseph P." }, "orcid": "0000-0002-8054-5021" }, { "id": "Cianciotto-Nicholas-P", "name": { "family": "Cianciotto", "given": "Nicholas P." }, "orcid": "0000-0002-9572-8322" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "In vivo structure of the Legionella type II secretion system by electron cryotomography", "ispublished": "pub", "full_text_status": "public", "keywords": "Bacteriology; Cryoelectron tomography; Pathogens", "note": "\u00a9 2019 Springer Nature Limited. \n\nReceived 19 January 2019; Accepted 07 October 2019; Published 21 November 2019. \n\nData availability: The subtomogram averages of the L. pneumophila T2SS have been deposited in the Electron Microscopy Data Bank under the following accession codes: EMD-20713 (wild type, aligned on the OM part) and EMD-20712 (wild type, aligned on the IM part). All additional data/information are available from the authors upon request. The authors declare that all data supporting the findings of this study, including source data for Fig. 1, are available within the paper and its Supplementary Information. \n\nThis work was supported by National Institutes of Health grants AI127401 to G.J.J. and AI043987 to N.P.C. ECT data were recorded at the Beckman Institute Resource Center for Transmission Electron Microcopy at Caltech and the cryo-EM facility at Janelia Research Campus. We thank D. Ortega, Y.-W. Chang and R.C. White for helpful discussions. M.K. is supported by a postdoctoral Rubicon fellowship from De Nederlandse Organisatie voor Wetenschappelijk Onderzoek. \n\nAuthor Contributions: D.G. and G.J.J. conceived the project. D.G. prepared samples and recorded and processed tomography data. D.G., K.W.K. and G.J.J. analysed data. H.Z., H.K.T., A.E.L., I.E.M., N.P.C. and J.P.V. generated and characterized L. pneumophila mutants. M.K. helped in model building. D.G., K.W.K., N.P.C. and G.J.J. wrote the manuscript with input from all the authors. \n\nThe authors declare no competing interests.\n\nIn the version of this Letter originally published, the author Grant J. Jensen was mistakenly affiliated with Zhengzhou University. His affiliation has now been corrected to: Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA and Howard Hughes Medical Institute, Pasadena, CA, USA.\n\nAccepted Version - nihms-1541075.pdf
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Supplemental Material - 41564_2019_603_MOESM3_ESM.pdf
", "abstract": "The type II secretion system (T2SS) is a multiprotein envelope-spanning assembly that translocates a wide range of virulence factors, enzymes and effectors through the outer membrane of many Gram-negative bacteria. Here, using electron cryotomography and subtomogram averaging methods, we reveal the in vivo structure of an intact T2SS imaged within the human pathogen Legionella pneumophila. Although the T2SS has only limited sequence and component homology with the evolutionarily related type IV pilus (T4P) system, we show that their overall architectures are remarkably similar. Despite similarities, there are also differences, including, for example, that the T2SS\u2013ATPase complex is usually present but disengaged from the inner membrane, the T2SS has a much longer periplasmic vestibule and it has a short-lived flexible pseudopilus. Placing atomic models of the components into our electron cryotomography map produced a complete architectural model of the intact T2SS that provides insights into the structure and function of its components, its position within the cell envelope and the interactions between its different subcomplexes.", "date": "2019-12", "date_type": "published", "publication": "Nature Microbiology", "volume": "4", "number": "12", "publisher": "Nature Publishing Group", "pagerange": "2101-2108", "id_number": "CaltechAUTHORS:20190123-125316052", "issn": "2058-5276", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190123-125316052", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "AI127401" }, { "agency": "NIH", "grant_number": "AI043987" }, { "agency": "Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)" } ] }, "doi": "10.1038/s41564-019-0603-6", "pmcid": "PMC6879910", "primary_object": { "basename": "525063.full.pdf", "url": "https://authors.library.caltech.edu/records/1akpj-hx598/files/525063.full.pdf" }, "related_objects": [ { "basename": "41564_2019_603_Fig6_ESM.jpg", "url": "https://authors.library.caltech.edu/records/1akpj-hx598/files/41564_2019_603_Fig6_ESM.jpg" }, { "basename": "41564_2019_603_Fig8_ESM.jpg", "url": "https://authors.library.caltech.edu/records/1akpj-hx598/files/41564_2019_603_Fig8_ESM.jpg" }, { "basename": "41564_2019_603_Fig7_ESM.jpg", "url": "https://authors.library.caltech.edu/records/1akpj-hx598/files/41564_2019_603_Fig7_ESM.jpg" }, { "basename": "41564_2019_603_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/1akpj-hx598/files/41564_2019_603_MOESM1_ESM.pdf" }, { "basename": "41564_2019_603_MOESM2_ESM.pdf", "url": "https://authors.library.caltech.edu/records/1akpj-hx598/files/41564_2019_603_MOESM2_ESM.pdf" }, { "basename": "41564_2019_603_MOESM3_ESM.pdf", "url": "https://authors.library.caltech.edu/records/1akpj-hx598/files/41564_2019_603_MOESM3_ESM.pdf" }, { "basename": "nihms-1541075.pdf", "url": "https://authors.library.caltech.edu/records/1akpj-hx598/files/nihms-1541075.pdf" }, { "basename": "41564_2019_603_Fig4_ESM.jpg", "url": "https://authors.library.caltech.edu/records/1akpj-hx598/files/41564_2019_603_Fig4_ESM.jpg" }, { "basename": "41564_2019_603_Fig5_ESM.jpg", "url": "https://authors.library.caltech.edu/records/1akpj-hx598/files/41564_2019_603_Fig5_ESM.jpg" } ], "resource_type": "article", "pub_year": "2019", "author_list": "Ghosal, Debnath; Kim, Ki Woo; et el." }, { "id": "https://authors.library.caltech.edu/records/zfkf4-5d063", "eprint_id": 94790, "eprint_status": "archive", "datestamp": "2023-08-22 02:38:22", "lastmod": "2023-10-23 17:00:54", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Martynowycz-M-W", "name": { "family": "Martynowycz", "given": "Michael W." }, "orcid": "0000-0003-0055-230X" }, { "id": "Zhao-Wei", "name": { "family": "Zhao", "given": "Wei" } }, { "id": "Hattne-J", "name": { "family": "Hattne", "given": "Johan" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Gonen-T", "name": { "family": "Gonen", "given": "Tamir" }, "orcid": "0000-0002-9254-4069" } ] }, "title": "Qualitative Analyses of Polishing and Precoating FIB Milled Crystals for MicroED", "ispublished": "pub", "full_text_status": "public", "keywords": "cryoelectron microscopy; cryo-EM; MicroED; FIB-SEM; electron diffraction; electron crystallography", "note": "\u00a9 2019 Elsevier Ltd. \n\nReceived 17 April 2019, Revised 12 June 2019, Accepted 15 July 2019, Available online 15 August 2019. \n\nThe Gonen lab and the Jensen lab are supported by funds from the Howard Hughes Medical Institute. This study was supported grants from the US National Institutes of Health nos. 2P50GM082545 and R35 GM122588 to G.J.J. Author Contributions: M.W.M. prepared the protein crystals. W.Z. and M.W.M. collected the FIB-SEM data and milled the crystals. M.W.M. collected the MicroED data. M.W.M. and J.H. processed the data. The manuscript was written by M.W.M. and T.G. with contributions from all authors. M.W.M., G.J.J., and T.G. designed the experiments. Figures were prepared by M.W.M. and T.G. The authors declare no competing interests.\n\nAccepted Version - nihms-1578161.pdf
Submitted - 613042.full.pdf
", "abstract": "Microcrystal electron diffraction (MicroED) leverages the strong interaction between matter and electrons to determine protein structures from vanishingly small crystals. This strong interaction limits the thickness of crystals that can be investigated by MicroED, mainly due to absorption. Recent studies have demonstrated that focused ion-beam (FIB) milling can thin crystals into ideal-sized lamellae; however, it is not clear how to best apply FIB milling for MicroED. Here, the effects of polishing the lamellae, whereby the last few nanometers are milled away using a low-current gallium beam, are explored in both the platinum-precoated and uncoated samples. Our results suggest that precoating samples with a thin layer of platinum followed by polishing the crystal surfaces prior to data collection consistently led to superior results as indicated by higher signal-to-noise ratio, higher resolution, and better refinement statistics. This study lays the foundation for routine and reproducible methodology for sample preparation in MicroED.", "date": "2019-10-01", "date_type": "published", "publication": "Structure", "volume": "27", "number": "10", "publisher": "Cell Press", "pagerange": "1594-1600", "id_number": "CaltechAUTHORS:20190418-123951811", "issn": "0969-2126", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190418-123951811", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "2P50GM082545" }, { "agency": "NIH", "grant_number": "R35 GM122588" } ] }, "doi": "10.1016/j.str.2019.07.004", "pmcid": "PMC7145226", "primary_object": { "basename": "nihms-1578161.pdf", "url": "https://authors.library.caltech.edu/records/zfkf4-5d063/files/nihms-1578161.pdf" }, "related_objects": [ { "basename": "613042.full.pdf", "url": "https://authors.library.caltech.edu/records/zfkf4-5d063/files/613042.full.pdf" } ], "resource_type": "article", "pub_year": "2019", "author_list": "Martynowycz, Michael W.; Zhao, Wei; et el." }, { "id": "https://authors.library.caltech.edu/records/zvefc-wps44", "eprint_id": 99337, "eprint_status": "archive", "datestamp": "2023-08-19 18:06:15", "lastmod": "2023-10-18 18:14:20", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Anikeeva-P", "name": { "family": "Anikeeva", "given": "Polina" } }, { "id": "Ciss\u00e9-I-I", "name": { "family": "Ciss\u00e9", "given": "Ibrahim I." }, "orcid": "0000-0002-8764-1809" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant Jay" }, "orcid": "0000-0003-1556-4864" }, { "id": "Van-Valen-D", "name": { "family": "Van Valen", "given": "David" }, "orcid": "0000-0001-7534-7621" }, { "id": "Zernicka-Goetz-M", "name": { "family": "Zernicka-Goetz", "given": "Magdalena" }, "orcid": "0000-0002-7004-2471" } ] }, "title": "Voices in methods development", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2019 Springer Nature Limited. \n\nPublished online: 27 September 2019.\n\nAccepted Version - nihms-1552528.pdf
", "abstract": "To mark the 15th anniversary of Nature Methods, we asked scientists from across diverse fields of basic biology research for their views on the most exciting and essential methodological challenges that their communities are poised to tackle in the near future.", "date": "2019-10", "date_type": "published", "publication": "Nature Methods", "volume": "16", "number": "10", "publisher": "Nature Publishing Group", "pagerange": "945-951", "id_number": "CaltechAUTHORS:20191017-144439188", "issn": "1548-7091", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20191017-144439188", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1038/s41592-019-0585-6", "pmcid": "PMC7075469", "primary_object": { "basename": "nihms-1552528.pdf", "url": "https://authors.library.caltech.edu/records/zvefc-wps44/files/nihms-1552528.pdf" }, "resource_type": "article", "pub_year": "2019", "author_list": "Anikeeva, Polina; Ciss\u00e9, Ibrahim I.; et el." }, { "id": "https://authors.library.caltech.edu/records/17j3w-s5h12", "eprint_id": 90533, "eprint_status": "archive", "datestamp": "2023-08-19 17:31:08", "lastmod": "2023-10-20 22:13:36", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Auer-George-K", "name": { "family": "Auer", "given": "George K." } }, { "id": "Oliver-Piercen-M", "name": { "family": "Oliver", "given": "Piercen M." } }, { "id": "Rajendram-Manohary", "name": { "family": "Rajendram", "given": "Manohary" } }, { "id": "Lin-Ti-Yu", "name": { "family": "Lin", "given": "Ti-Yu" } }, { "id": "Yao-Qing", "name": { "family": "Yao", "given": "Qing" }, "orcid": "0000-0003-3575-9909" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Weibel-Douglas-B", "name": { "family": "Weibel", "given": "Douglas B." }, "orcid": "0000-0001-7797-2017" } ] }, "title": "Bacterial swarming reduces Proteus mirabilis and Vibrio parahaemolyticus cell stiffness and increases \u03b2-lactam susceptibility", "ispublished": "pub", "full_text_status": "public", "keywords": "antibiotics, bacterial cell mechanics, bacterial swarming, osmotic pressure, peptidoglycan", "note": "\u00a9 2019 Auer et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. \n\nReceived 4 February 2019; Accepted 14 August 2019; Published 8 October 2019. \n\nWe thank Linda McCarter for V. parahaemolyticus LM5674, Suckjoon Jun for plasmid psulA, Cameron Scarlett and Molly Pellitteri-Hahn for mass spectrometry support, and Julie Last for technical assistance with AFM measurements. \n\nThis research was supported by the Bill and Melinda Gates Foundation (grant OPP1068092), NIH grant 1DP2OD008735-01, National Science Foundation (NSF) grant DMR-1121288, a Mao Wisconsin Distinguished Graduate Fellowship (to M.R.), an NSF postdoctoral fellowship (no. 1202622 to P.M.O.), and the Howard Hughes Medical Institute.\n\nPublished - mBio-2019-Auer-e00210-19.full.pdf
Submitted - 275941.full.pdf
Supplemental Material - 275941-1.pdf
", "abstract": "Swarmer cells of the gram-negative pathogenic bacteria Proteus mirabilis and Vibrio parahaemolyticus become long (>10-100 microns) and multinucleate during their growth and motility on polymer surfaces. We demonstrate increasing cell length is accompanied by a large increase in flexibility. Using a microfluidic assay to measure single-cell mechanics, we identified large differences in swarmer cell stiffness of (bending rigidity of P. mirabilis, 9.6 x 10^(-22) N m^2; V. parahaemolyticus, 9.7 x 10^(-23) N m^2) compared to vegetative cells (1.4 x 10^(-20) N m^2 and 3.2 x 10^(-22) N m^2, respectively). The reduction in bending rigidity (~3-15 fold) was accompanied by a decrease in the average polysaccharide strand length of the peptidoglycan layer of the cell wall from 28-30 to 19-22 disaccharides. Atomic force microscopy revealed a reduction in P. mirabilis peptidoglycan thickness from 1.5 nm (vegetative) to 1.0 nm (swarmer) and electron cryotomography indicated changes in swarmer cell wall morphology. P. mirabilis and V. parahaemolyticus swarmer cells became increasingly sensitive to osmotic pressure and susceptible to cell wall-modifying antibiotics (compared to vegetative cells)--they were ~30% more likely to die after 3 h of treatment with minimum inhibitory concentrations of the beta-lactams cephalexin and penicillin G. Long, flexible swarmer cells enables these pathogenic bacteria to form multicellular structures and promotes community motility. The adaptive cost of swarming is offset by a fitness cost in which cells are more susceptible to physical and chemical changes in their environment, thereby suggesting the development of new chemotherapies for bacteria that leverage swarming for survival.", "date": "2019-09", "date_type": "published", "publication": "mBio", "volume": "10", "number": "5", "publisher": "American Society for Microbiology", "pagerange": "Art. No. e00210-19", "id_number": "CaltechAUTHORS:20181031-082235074", "issn": "2150-7511", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181031-082235074", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Bill and Melinda Gates Foundation", "grant_number": "OPP1068092" }, { "agency": "NIH", "grant_number": "1DP2OD008735-01" }, { "agency": "NSF", "grant_number": "DMR-1121288" }, { "agency": "University of Wisconsin-Madison" }, { "agency": "NSF Postdoctoral Fellowship", "grant_number": "DBI-1202622" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1128/mBio.00210-19", "pmcid": "PMC6786863", "primary_object": { "basename": "275941-1.pdf", "url": "https://authors.library.caltech.edu/records/17j3w-s5h12/files/275941-1.pdf" }, "related_objects": [ { "basename": "275941.full.pdf", "url": "https://authors.library.caltech.edu/records/17j3w-s5h12/files/275941.full.pdf" }, { "basename": "mBio-2019-Auer-e00210-19.full.pdf", "url": "https://authors.library.caltech.edu/records/17j3w-s5h12/files/mBio-2019-Auer-e00210-19.full.pdf" } ], "resource_type": "article", "pub_year": "2019", "author_list": "Auer, George K.; Oliver, Piercen M.; et el." }, { "id": "https://authors.library.caltech.edu/records/x4kps-q9y54", "eprint_id": 98828, "eprint_status": "archive", "datestamp": "2023-10-03 17:00:07", "lastmod": "2023-10-24 15:29:11", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "O'Neal-Lindsey", "name": { "family": "O'Neal", "given": "Lindsey" }, "orcid": "0000-0003-1942-6135" }, { "id": "Gullett-Jessica-M", "name": { "family": "Gullett", "given": "Jessica M." }, "orcid": "0000-0003-3996-9110" }, { "id": "Aksenova-Anastasia", "name": { "family": "Aksenova", "given": "Anastasia" } }, { "id": "Hubler-Adam", "name": { "family": "Hubler", "given": "Adam" } }, { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Ortega-Davi-R", "name": { "family": "Ortega", "given": "Davi" }, "orcid": "0000-0002-8344-2335" }, { "id": "Kj\u00e6r-Andreas", "name": { "family": "Kj\u00e6r", "given": "Andreas" }, "orcid": "0000-0002-0096-5764" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant" }, "orcid": "0000-0003-1556-4864" }, { "id": "Alexandre-Gladys", "name": { "family": "Alexandre", "given": "Gladys" }, "orcid": "0000-0002-9238-4640" } ] }, "title": "Distinct Chemotaxis Protein Paralogs Assemble into Chemoreceptor Signaling Arrays To Coordinate Signaling Output", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2019 O'Neal et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. \n\nReceived 9 July 2019; Accepted 27 August 2019; Published 24 September 2019. \n\nWe thank Lam Vo for excellent technical assistance. \n\nThis research was supported by National Science Foundation grants NSF-MCB 1330344 and NSF-MCB 1715185 (to G.A.). Any opinions, findings, conclusions, or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation.\n\nPublished - mBio-2019-ONeal-e01757-19full.pdf
Supplemental Material - inline-supplementary-material-1.eps
Supplemental Material - inline-supplementary-material-10.docx
Supplemental Material - inline-supplementary-material-2.pdf
Supplemental Material - inline-supplementary-material-3.tif
Supplemental Material - inline-supplementary-material-4.tif
Supplemental Material - inline-supplementary-material-5.pdf
Supplemental Material - inline-supplementary-material-6.docx
Supplemental Material - inline-supplementary-material-7.eps
Supplemental Material - inline-supplementary-material-8.docx
Supplemental Material - inline-supplementary-material-9.docx
", "abstract": "Most chemotactic motile bacteria possess multiple chemotaxis signaling systems, the functions of which are not well characterized. Chemotaxis signaling is initiated by chemoreceptors that assemble as large arrays, together with chemotaxis coupling proteins (CheW) and histidine kinase proteins (CheA), which form a baseplate with the cytoplasmic tips of receptors. These cell pole-localized arrays mediate sensing, signaling, and signal amplification during chemotaxis responses. Membrane-bound chemoreceptors with different cytoplasmic domain lengths segregate into distinct arrays. Here, we show that a bacterium, Azospirillum brasilense, which utilizes two chemotaxis signaling systems controlling distinct motility parameters, coordinates its chemotactic responses through the production of two separate membrane-bound chemoreceptor arrays by mixing paralogs within chemotaxis baseplates. The polar localization of chemoreceptors of different length classes is maintained in strains that had baseplate signaling proteins from either chemotaxis system but was lost when both systems were deleted. Chemotaxis proteins (CheA and CheW) from each of the chemotaxis signaling systems (Che1 and Che4) could physically interact with one another, and chemoreceptors from both classes present in A. brasilense could interact with Che1 and Che4 proteins. The assembly of paralogs from distinct chemotaxis pathways into baseplates provides a straightforward mechanism for coordinating signaling from distinct pathways, which we predict is not unique to this system given the propensity of chemotaxis systems for horizontal gene transfer.", "date": "2019-09", "date_type": "published", "publication": "mBio", "volume": "10", "number": "5", "publisher": "American Society for Microbiology", "pagerange": "Art. No. e01757-19", "id_number": "CaltechAUTHORS:20190924-095952844", "issn": "2150-7511", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190924-095952844", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "MCB-1330344" }, { "agency": "NSF", "grant_number": "MCB-1715185" } ] }, "doi": "10.1128/mbio.01757-19", "pmcid": "PMC6759762", "primary_object": { "basename": "inline-supplementary-material-1.eps", "url": "https://authors.library.caltech.edu/records/x4kps-q9y54/files/inline-supplementary-material-1.eps" }, "related_objects": [ { "basename": "inline-supplementary-material-6.docx", "url": "https://authors.library.caltech.edu/records/x4kps-q9y54/files/inline-supplementary-material-6.docx" }, { "basename": "inline-supplementary-material-7.eps", "url": "https://authors.library.caltech.edu/records/x4kps-q9y54/files/inline-supplementary-material-7.eps" }, { "basename": "inline-supplementary-material-9.docx", "url": "https://authors.library.caltech.edu/records/x4kps-q9y54/files/inline-supplementary-material-9.docx" }, { "basename": "mBio-2019-ONeal-e01757-19full.pdf", "url": "https://authors.library.caltech.edu/records/x4kps-q9y54/files/mBio-2019-ONeal-e01757-19full.pdf" }, { "basename": "inline-supplementary-material-10.docx", "url": "https://authors.library.caltech.edu/records/x4kps-q9y54/files/inline-supplementary-material-10.docx" }, { "basename": "inline-supplementary-material-2.pdf", "url": "https://authors.library.caltech.edu/records/x4kps-q9y54/files/inline-supplementary-material-2.pdf" }, { "basename": "inline-supplementary-material-3.tif", "url": "https://authors.library.caltech.edu/records/x4kps-q9y54/files/inline-supplementary-material-3.tif" }, { "basename": "inline-supplementary-material-4.tif", "url": "https://authors.library.caltech.edu/records/x4kps-q9y54/files/inline-supplementary-material-4.tif" }, { "basename": "inline-supplementary-material-5.pdf", "url": "https://authors.library.caltech.edu/records/x4kps-q9y54/files/inline-supplementary-material-5.pdf" }, { "basename": "inline-supplementary-material-8.docx", "url": "https://authors.library.caltech.edu/records/x4kps-q9y54/files/inline-supplementary-material-8.docx" } ], "resource_type": "article", "pub_year": "2019", "author_list": "O'Neal, Lindsey; Gullett, Jessica M.; et el." }, { "id": "https://authors.library.caltech.edu/records/zydv7-syt37", "eprint_id": 90172, "eprint_status": "archive", "datestamp": "2023-08-22 02:03:54", "lastmod": "2023-10-23 16:11:32", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kaplan-Mohammed", "name": { "family": "Kaplan", "given": "Mohammed" }, "orcid": "0000-0002-0759-0459" }, { "id": "Subramanian-Poorna", "name": { "family": "Subramanian", "given": "Poorna" } }, { "id": "Ghosal-Debnath", "name": { "family": "Ghosal", "given": "Debnath" }, "orcid": "0000-0002-2227-0330" }, { "id": "Oikonomou-Catherine-M", "name": { "family": "Oikonomou", "given": "Catherine M." }, "orcid": "0000-0003-2312-4746" }, { "id": "Pirbadian-Sahand", "name": { "family": "Pirbadian", "given": "Sahand" } }, { "id": "Starwalt-Lee-Ruth", "name": { "family": "Starwalt-Lee", "given": "Ruth" } }, { "id": "Mageswaran-Shrawan-Kumar", "name": { "family": "Mageswaran", "given": "Shrawan Kumar" } }, { "id": "Ortega-Davi-R", "name": { "family": "Ortega", "given": "Davi R." }, "orcid": "0000-0002-8344-2335" }, { "id": "Gralnick-Jeffrey-A", "name": { "family": "Gralnick", "given": "Jeffrey A." }, "orcid": "0000-0001-9250-7770" }, { "id": "El-Naggar-Mohamed-Y", "name": { "family": "El-Naggar", "given": "Mohamed Y." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "In situ imaging of the bacterial flagellar motor disassembly and assembly processes", "ispublished": "pub", "full_text_status": "public", "keywords": "assembly; bacterial flagellar motor; disassembly; electron\ncryo-tomography; in situ imaging", "note": "\u00a9 2019 The Authors. \n\nReceived 18 October 2018; Revised 11 April 2019; Accepted 18 April 2019. \n\nThis work was supported by the National Institutes of Health (NIH, grant R01 AI127401 to G.J.J.). M.K. is supported by a postdoctoral Rubicon fellowship from De Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO). S.P. and M.Y.E.\u2010N. are supported by the Air Force Office of Scientific Research Presidential Early Career Award for Scientists and Engineers (FA955014\u20101\u20100294, to M.Y.E.\u2010N.). R.S.L. and J.A.G acknowledge support from the Office of Naval Research (N00014\u201018\u20101\u20102632 to J.A.G.). We would like to thank Dr. Spiros Garbis, Dr. Annie Moradian, Dr. Michael Sweredoski, and Dr. Brett Lomenick from the Caltech Proteome Exploration Laboratory for their help in mass spectrometry experiments and data analysis. All P. aeruginosa mutants were kindly supplied by Dianne Newman's laboratory at Caltech. ECT was performed in the Beckman Institute Resource Center for Cryo\u2010EM. \n\nAuthor contributions:\nMK and GJJ designed research. MK, PS, DG, and RS-L prepared samples. MK, PS,\nand DG recorded ECT data. MK performed MS experiments. MK and DRO\nperformed bioinformatics analysis. SP, SKM, JAG, and MYE-N supplied reagents.\nMK, CMO, and GJJ analyzed data. MK, CMO, and GJJ wrote the manuscript, and\nall authors edited it.\n\nThe authors declare that they have no conflict of interest.\n\nAccepted Version - embj.2018100957-2.pdf
Submitted - 369405.full.pdf
Supplemental Material - embj.2018100957.reviewer-comments.pdf
Supplemental Material - inline-supplementary-material-1.docx
Supplemental Material - inline-supplementary-material-2.xlsx
Supplemental Material - inline-supplementary-material-3.xlsx
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Supplemental Material - inline-supplementary-material-5.zip
Supplemental Material - inline-supplementary-material-6.zip
Supplemental Material - inline-supplementary-material-7.zip
", "abstract": "The self\u2010assembly of cellular macromolecular machines such as the bacterial flagellar motor requires the spatio\u2010temporal synchronization of gene expression with proper protein localization and association of dozens of protein components. In Salmonella and Escherichia coli, a sequential, outward assembly mechanism has been proposed for the flagellar motor starting from the inner membrane, with the addition of each new component stabilizing the previous one. However, very little is known about flagellar disassembly. Here, using electron cryo\u2010tomography and sub\u2010tomogram averaging of intact Legionella pneumophila, Pseudomonas aeruginosa, and Shewanella oneidensis cells, we study flagellar motor disassembly and assembly in situ. We first show that motor disassembly results in stable outer membrane\u2010embedded sub\u2010complexes. These sub\u2010complexes consist of the periplasmic embellished P\u2010 and L\u2010rings, and bend the membrane inward while it remains apparently sealed. Additionally, we also observe various intermediates of the assembly process including an inner\u2010membrane sub\u2010complex consisting of the C\u2010ring, MS\u2010ring, and export apparatus. Finally, we show that the L\u2010ring is responsible for reshaping the outer membrane, a crucial step in the flagellar assembly process.", "date": "2019-07-15", "date_type": "published", "publication": "EMBO Journal", "volume": "38", "number": "14", "publisher": "European Molecular Biology Organization", "pagerange": "Art. No. e100957", "id_number": "CaltechAUTHORS:20181008-162020064", "issn": "0261-4189", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181008-162020064", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 AI127401" }, { "agency": "Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)" }, { "agency": "Air Force Office of Scientific Research (AFOSR)", "grant_number": "FA955014-1-0294" }, { "agency": "Office of Naval Research (ONR)", "grant_number": "N00014-18-1-2632" } ] }, "doi": "10.15252/embj.2018100957", "pmcid": "PMC6627242", "primary_object": { "basename": "embj.2018100957.reviewer-comments.pdf", "url": "https://authors.library.caltech.edu/records/zydv7-syt37/files/embj.2018100957.reviewer-comments.pdf" }, "related_objects": [ { "basename": "inline-supplementary-material-2.xlsx", "url": "https://authors.library.caltech.edu/records/zydv7-syt37/files/inline-supplementary-material-2.xlsx" }, { "basename": "inline-supplementary-material-4.xlsx", "url": "https://authors.library.caltech.edu/records/zydv7-syt37/files/inline-supplementary-material-4.xlsx" }, { "basename": "inline-supplementary-material-5.zip", "url": "https://authors.library.caltech.edu/records/zydv7-syt37/files/inline-supplementary-material-5.zip" }, { "basename": "369405.full.pdf", "url": "https://authors.library.caltech.edu/records/zydv7-syt37/files/369405.full.pdf" }, { "basename": "embj.2018100957-2.pdf", "url": "https://authors.library.caltech.edu/records/zydv7-syt37/files/embj.2018100957-2.pdf" }, { "basename": "inline-supplementary-material-1.docx", "url": "https://authors.library.caltech.edu/records/zydv7-syt37/files/inline-supplementary-material-1.docx" }, { "basename": "inline-supplementary-material-3.xlsx", "url": "https://authors.library.caltech.edu/records/zydv7-syt37/files/inline-supplementary-material-3.xlsx" }, { "basename": "inline-supplementary-material-6.zip", "url": "https://authors.library.caltech.edu/records/zydv7-syt37/files/inline-supplementary-material-6.zip" }, { "basename": "inline-supplementary-material-7.zip", "url": "https://authors.library.caltech.edu/records/zydv7-syt37/files/inline-supplementary-material-7.zip" } ], "resource_type": "article", "pub_year": "2019", "author_list": "Kaplan, Mohammed; Subramanian, Poorna; et el." }, { "id": "https://authors.library.caltech.edu/records/sc8sh-x1307", "eprint_id": 90702, "eprint_status": "archive", "datestamp": "2023-08-22 02:01:47", "lastmod": "2023-10-23 16:11:11", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Yao-Qing", "name": { "family": "Yao", "given": "Qing" }, "orcid": "0000-0003-3575-9909" }, { "id": "Weaver-Sara-J", "name": { "family": "Weaver", "given": "Sara J." }, "orcid": "0000-0001-7753-6215" }, { "id": "Mock-Jee-Young", "name": { "family": "Mock", "given": "Jee-Young" }, "orcid": "0000-0002-4656-3357" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Fusion of DARPin to Aldolase Enables Visualization of Small Protein by Cryo-EM", "ispublished": "pub", "full_text_status": "public", "keywords": "CryoEM; DARPin; Single-particle analysis; platform; aldolase; artificial protein; Electron cryo-microscopy; cryo-electron microscopy; protein design", "note": "\u00a9 2019 Elsevier Ltd. \n\nReceived 2 December 2018, Revised 4 March 2019, Accepted 5 April 2019, Available online 9 May 2019. \n\nWe thank Dr. Mark Herzik Jr. and Mengyu Wu at The Scripps Research Institute for help with sample preparation. We also thank Dr. Songye Chen, Dr. Andrey Malyutin, Dr. Rebecca Voorhees, and Dr. Bil Clemons at Caltech for technical assistance. We are also grateful to all members of the Jensen laboratory for discussion and technical assistance. In particular, we thank Dr. Lauren Ann Metskas and Dr. Ariana Peck. This work was supported by funds from NIH NIGMS P50 082545. Cryo-EM work was performed in the Caltech Beckman Institute Resource Center for Transmission Electron Microscopy. \n\nAuthor Contributions: Conceptualization, Q.Y., S.J.W., and G.J.J.; Methodology, Q.Y., S.J.W., and J.-Y.M.; Investigation, Q.Y., S.J.W., and J.-Y.M.; Data Curation, S.J.W.; Writing \u2013 Original Draft, S.J.W.; Writing \u2013 Review & Editing, S.J.W., Q.Y., and G.J.J.; Visualization, S.J.W. and Q.Y.; Supervision, G.J.J.; Funding Acquisition, G.J.J. \n\nThe authors declare no competing interests.\n\nAccepted Version - nihms-1528032.pdf
Submitted - 455063.full.pdf
Supplemental Material - 1-s2.0-S096921261930125X-mmc1.pdf
Supplemental Material - 1-s2.0-S096921261930125X-mmc5.pdf
", "abstract": "Solving protein structures by single-particle cryoelectron microscopy (cryo-EM) has become a crucial tool in structural biology. While exciting progress is being made toward the visualization of small macromolecules, the median protein size in both eukaryotes and bacteria is still beyond the reach of cryo-EM. To overcome this problem, we implemented a platform strategy in which a small protein target was rigidly attached to a large, symmetric base via a selectable adapter. Of our seven designs, the best construct used a designed ankyrin repeat protein (DARPin) rigidly fused to tetrameric rabbit muscle aldolase through a helical linker. The DARPin retained its ability to bind its target: GFP. We solved the structure of this complex to 3.0 \u00c5 resolution overall, with 5\u20138 \u00c5 resolution in the GFP region. As flexibility in the DARPin position limited the overall resolution of the target, we describe strategies to rigidify this element.", "date": "2019-07-02", "date_type": "published", "publication": "Structure", "volume": "27", "number": "7", "publisher": "Cell Press", "pagerange": "1148-1155", "id_number": "CaltechAUTHORS:20181107-101625710", "issn": "0969-2126", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181107-101625710", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P50 082545" }, { "agency": "Caltech Beckman Institute" } ] }, "doi": "10.1016/j.str.2019.04.003", "pmcid": "PMC6610650", "primary_object": { "basename": "1-s2.0-S096921261930125X-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/sc8sh-x1307/files/1-s2.0-S096921261930125X-mmc1.pdf" }, "related_objects": [ { "basename": "1-s2.0-S096921261930125X-mmc5.pdf", "url": "https://authors.library.caltech.edu/records/sc8sh-x1307/files/1-s2.0-S096921261930125X-mmc5.pdf" }, { "basename": "455063.full.pdf", "url": "https://authors.library.caltech.edu/records/sc8sh-x1307/files/455063.full.pdf" }, { "basename": "nihms-1528032.pdf", "url": "https://authors.library.caltech.edu/records/sc8sh-x1307/files/nihms-1528032.pdf" } ], "resource_type": "article", "pub_year": "2019", "author_list": "Yao, Qing; Weaver, Sara J.; et el." }, { "id": "https://authors.library.caltech.edu/records/vsczb-9xt25", "eprint_id": 90527, "eprint_status": "archive", "datestamp": "2023-08-19 16:25:43", "lastmod": "2023-10-20 22:02:45", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ghosal-Debnath", "name": { "family": "Ghosal", "given": "Debnath" }, "orcid": "0000-0002-2227-0330" }, { "id": "Jeong-Kwangcheol-C", "name": { "family": "Jeong", "given": "Kwangcheol C." }, "orcid": "0000-0003-4337-0426" }, { "id": "Chang-Yi-Wei", "name": { "family": "Chang", "given": "Yi-Wei" }, "orcid": "0000-0003-2391-473X" }, { "id": "Gyore-Jacob", "name": { "family": "Gyore", "given": "Jacob" } }, { "id": "Teng-Lin", "name": { "family": "Teng", "given": "Lin" } }, { "id": "Gardner-Adam", "name": { "family": "Gardner", "given": "Adam" } }, { "id": "Vogel-Joseph-P", "name": { "family": "Vogel", "given": "Joseph P." }, "orcid": "0000-0002-8054-5021" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Molecular architecture, polar targeting and biogenesis of the Legionella Dot/Icm T4SS", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2019 The Author(s), under exclusive licence to Springer Nature Limited. \n\nReceived 13 July 2018. Accepted 12 March 2019. Published 22 April 2019. \n\nWe thank R. Isberg (Tufts University, Medford, MA, USA) for antibodies that recognize DotF and DotH, E. Buford for technical assistance and P. Levin (Washington University, St Louis, MO, USA) for assistance with deconvolution microscopy. ECT data were recorded at the Beckman Institute Resource Center for Transmission Electron Microcopy at Caltech and the cryo-EM facility at Janelia Research Campus. We thank C. Oikonomou for the creation of the domain maps and for help structuring and revising the text. We also recognize E. Darwin for key suggestions and critical appraisal of this manuscript. This work was funded by the NIH grant R01AI127401 to G.J.J. and the NIH grant R01AI48052 to J.P.V. \n\nThese authors contributed equally: Debnath Ghosal, Kwangcheol C. Jeong. \n\nAuthor Contributions: D.G., K.C.C.J., J.P.V. and G.J.J. conceived the project. K.C.C.J., J.P.V. and J.G. constructed and characterized the L.\u2009pneumophila expression plasmids and strains. K.C.J. and J.P.V. collected the immunofluorescence data. D.G. collected the tomography data. D.G., K.C.C.J., J.P.V., G.J.J., Y.-W.C. and L.T. analysed the data. A.G. made Supplementary Video 1. D.G., J.P.V., K.C.C.J. and G.J.J. wrote the manuscript with input from other authors. \n\nData availability: The subtomogram average of the Dot/Icm (DotF-sfGFP) complex that supports the findings of this study has been deposited in the Electron Microscopy Data Bank (EMDB) under the accession code: EMD-0566. All other density maps are available from the corresponding authors on request. The authors declare that all data supporting the findings of this study are available within the paper and its Supplementary Information documents.\n\nThe authors declare no competing interests.\n\nAccepted Version - nihms-1523869.pdf
Submitted - 312009.full.pdf
Supplemental Material - 312009-1.pdf
Supplemental Material - 41564_2019_427_MOESM1_ESM.pdf
Supplemental Material - 41564_2019_427_MOESM2_ESM.pdf
Supplemental Material - 41564_2019_427_MOESM3_ESM.mov
", "abstract": "Legionella pneumophila survives and replicates inside host cells by secreting ~300 effectors through the defective in organelle trafficking (Dot)/intracellular multiplication (Icm) type IVB secretion system (T4BSS). Here, we used complementary electron cryotomography and immunofluorescence microscopy to investigate the molecular architecture and biogenesis of the Dot/Icm secretion apparatus. Electron cryotomography mapped the location of the core and accessory components of the Legionella core transmembrane subcomplex, revealing a well-ordered central channel that opens into a large, windowed secretion chamber with an unusual 13-fold symmetry. Immunofluorescence microscopy deciphered an early-stage assembly process that begins with the targeting of Dot/Icm components to the bacterial poles. Polar targeting of this T4BSS is mediated by two Dot/Icm proteins, DotU and IcmF, that, interestingly, are homologues of the T6SS membrane complex components TssL and TssM, suggesting that the Dot/Icm T4BSS is a hybrid system. Together, these results revealed that the Dot/Icm complex assembles in an 'axial-to-peripheral' pattern.", "date": "2019-07", "date_type": "published", "publication": "Nature Microbiology", "volume": "4", "number": "7", "publisher": "Nature Publishing Group", "pagerange": "1173-1182", "id_number": "CaltechAUTHORS:20181030-153432354", "issn": "2058-5276", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181030-153432354", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01AI127401" }, { "agency": "NIH", "grant_number": "R01AI48052" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1038/s41564-019-0427-4", "pmcid": "PMC6588468", "primary_object": { "basename": "312009-1.pdf", "url": "https://authors.library.caltech.edu/records/vsczb-9xt25/files/312009-1.pdf" }, "related_objects": [ { "basename": "312009.full.pdf", "url": "https://authors.library.caltech.edu/records/vsczb-9xt25/files/312009.full.pdf" }, { "basename": "41564_2019_427_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/vsczb-9xt25/files/41564_2019_427_MOESM1_ESM.pdf" }, { "basename": "41564_2019_427_MOESM2_ESM.pdf", "url": "https://authors.library.caltech.edu/records/vsczb-9xt25/files/41564_2019_427_MOESM2_ESM.pdf" }, { "basename": "41564_2019_427_MOESM3_ESM.mov", "url": "https://authors.library.caltech.edu/records/vsczb-9xt25/files/41564_2019_427_MOESM3_ESM.mov" }, { "basename": "nihms-1523869.pdf", "url": "https://authors.library.caltech.edu/records/vsczb-9xt25/files/nihms-1523869.pdf" } ], "resource_type": "article", "pub_year": "2019", "author_list": "Ghosal, Debnath; Jeong, Kwangcheol C.; et el." }, { "id": "https://authors.library.caltech.edu/records/kphx1-wxk19", "eprint_id": 95886, "eprint_status": "archive", "datestamp": "2023-08-19 16:02:43", "lastmod": "2023-10-20 20:40:30", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant" }, "orcid": "0000-0003-1556-4864" }, { "id": "Merrikh-H", "name": { "family": "Merrikh", "given": "Houra" } }, { "id": "Monack-D", "name": { "family": "Monack", "given": "Denise" } }, { "id": "Veening-J-W", "name": { "family": "Veening", "given": "Jan-Willem" } } ] }, "title": "What career advice do you give your grad students or postdocs?", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2019 Elsevier Ltd. \n\nAvailable online 25 April 2019.", "abstract": "Advice from a mentor can be an invaluable in terms of seeing yourself better or starting you down a path that you might not have thought about. In this TrendsTalk article we ask four professors about the best piece of advice that they give to their trainees.", "date": "2019-06", "date_type": "published", "publication": "Trends in Microbiology", "volume": "27", "number": "6", "publisher": "Elsevier", "pagerange": "471-472", "id_number": "CaltechAUTHORS:20190529-151054936", "issn": "0966-842X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190529-151054936", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.tim.2019.03.009", "resource_type": "article", "pub_year": "2019", "author_list": "Jensen, Grant; Merrikh, Houra; et el." }, { "id": "https://authors.library.caltech.edu/records/692cz-3jx29", "eprint_id": 90481, "eprint_status": "archive", "datestamp": "2023-08-19 15:24:53", "lastmod": "2023-10-20 21:59:42", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ortega-D-R", "name": { "family": "Ortega", "given": "Davi R." }, "orcid": "0000-0002-8344-2335" }, { "id": "Oikonomou-C-M", "name": { "family": "Oikonomou", "given": "Catherine M." }, "orcid": "0000-0003-2312-4746" }, { "id": "Ding-H-Jane", "name": { "family": "Ding", "given": "H. Jane" } }, { "id": "Rees-Lee-P", "name": { "family": "Rees-Lee", "given": "Prudence" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "ETDB-Caltech: a blockchain-based distributed public database for electron tomography", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2019 Ortega et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived: October 17, 2018; Accepted: April 3, 2019; Published: April 15, 2019. \n\nWe thank members of the Jensen lab for helpful comments on the ETDB interface, as well as past and present lab members (Morgan Beeby, Ariane Briegel, Yi-Wei Chang, Songye Chen, Megan Dobro, Lu Gan, Gregory Henderson, Cristina Iancu, Andreas Kj\u00e6r, Zhuo Li, Alasdair McDowall, Gavin Murphy, Martin Pilhofer, Rasika Ramdasi, Jian Shi, Poorna Subramanian, Matthew Swulius, William Tivol, Elitza Tocheva, Cora Woodward, Qing Yao, Zhiheng Yu, and Elizabeth Wright) who generously allowed data they collected to be made public. We also thank other lab members whose data will be published in the future. The Alexandria team is composed of Devon Read James, Amy James, Jeremiah Buddenhagen, Sky Young, Ryan Chacon, Joseph Fiscella and Anthony Stewart. Thanks also to past Alexandria contributors Ryan Jordan, Robert English and Ryan Taylor for their work on the Open Index Protocol specification. \n\nThis work was supported by grants to GJJ from the National Institute of General Medical Sciences (R35 GM122588) and the John Templeton Foundation as part of the Boundaries of Life Project (51250). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. \n\nData Availability: All relevant data are within the manuscript, Supporting Information files, and on Github at the following links: https://github.com/theJensenLab/go-etdb https://github.com/theJensenLab/etdb-downloads/blob/master/userManual.md https://github.com/oipwg/oip-js https://github.com/floblockchain/flo https://github.com/theJensenLab/etdb-react. \n\nCompeting interests: Alexandria and its contributors hold various cryptocurrency tokens, including FLO. DRO and Alexandria contributed to FLO blockchain development.\n\nPublished - journal.pone.0215531.pdf
Submitted - 453662.full.pdf
", "abstract": "Three-dimensional electron microscopy techniques like electron tomography provide valuable insights into cellular structures, and present significant challenges for data storage and dissemination. Here we explored a novel method to publicly release more than 11,000 such datasets, more than 30 TB in total, collected by our group. Our method, based on a peer-to-peer file sharing network built around a blockchain ledger, offers a distributed solution to data storage. In addition, we offer a user-friendly browser-based interface, https://etdb.caltech.edu, for anyone interested to explore and download our data. We discuss the relative advantages and disadvantages of this system and provide tools for other groups to mine our data and/or use the same approach to share their own imaging datasets.", "date": "2019-04-15", "date_type": "published", "publication": "PLoS ONE", "volume": "14", "number": "4", "publisher": "Public Library of Science", "pagerange": "Art. No. e0215531", "id_number": "CaltechAUTHORS:20181029-160304278", "issn": "1932-6203", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181029-160304278", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R35 GM122588" }, { "agency": "John Templeton Foundation", "grant_number": "51250" } ] }, "doi": "10.1371/journal.pone.0215531", "pmcid": "PMC6464211", "primary_object": { "basename": "453662.full.pdf", "url": "https://authors.library.caltech.edu/records/692cz-3jx29/files/453662.full.pdf" }, "related_objects": [ { "basename": "journal.pone.0215531.pdf", "url": "https://authors.library.caltech.edu/records/692cz-3jx29/files/journal.pone.0215531.pdf" } ], "resource_type": "article", "pub_year": "2019", "author_list": "Ortega, Davi R.; Oikonomou, Catherine M.; et el." }, { "id": "https://authors.library.caltech.edu/records/sge8a-fp515", "eprint_id": 92768, "eprint_status": "archive", "datestamp": "2023-08-22 01:18:56", "lastmod": "2023-10-20 16:25:01", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Xu-Min", "name": { "family": "Xu", "given": "Min" } }, { "id": "Singla-Jitin", "name": { "family": "Singla", "given": "Jitin" } }, { "id": "Tocheva-Elitza-I", "name": { "family": "Tocheva", "given": "Elitza I." }, "orcid": "0000-0002-4869-8319" }, { "id": "Chang-Yi-Wei", "name": { "family": "Chang", "given": "Yi-Wei" }, "orcid": "0000-0003-2391-473X" }, { "id": "Stevens-Raymond-C", "name": { "family": "Stevens", "given": "Raymond C." }, "orcid": "0000-0002-4522-8725" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Alber-Frank", "name": { "family": "Alber", "given": "Frank" } } ] }, "title": "De Novo Structural Pattern Mining in Cellular Electron Cryotomograms", "ispublished": "pub", "full_text_status": "public", "keywords": "electron cryotomography; pattern mining; template-free; unsupervised", "note": "\u00a9 2019 Published by Elsevier Ltd. \n\nReceived 7 February 2018, Revised 27 July 2018, Accepted 14 January 2019, Available online 7 February 2019. \n\nWe thank Z. Frazier, T. Zeev-Ben-Mordehai, L. Pei, T. Jiang, M. Beck, X.J. Zhou, and H. Zhou for assistance and discussions. We also thank Angela Walker for helping in revising the manuscript. This work was supported by NIH R01GM096089, Arnold and Mabel Beckman Foundation (BYI), NSF career 1150287 to F.A., funding from the Howard Hughes Medical Institute to G.J.J., and funding from NIH P41GM103712 to M.X. \n\nAuthor Contributions: F.A. conceived the study. M.X. proposed MPP pattern mining, designed and implemented methods, and ran analysis with input from F.A. J.S. tested the methods using simulated data with high resolution. M.X., F.A., and J.S. analyzed the results. G.J.J., E.I.T., and Y.-W.C. generated experimental tomograms. F.A., M.X., and J.S. wrote the paper with comments and data suggestions from G.J.J., E.I.T., Y.-W.C., and R.C.S. \n\nThe authors declare no competing interests.\n\nAccepted Version - nihms-1047530.pdf
Supplemental Material - 1-s2.0-S096921261930005X-mmc1.pdf
Supplemental Material - 1-s2.0-S096921261930005X-mmc2.xlsx
Supplemental Material - 1-s2.0-S096921261930005X-mmc3.xlsx
Supplemental Material - 1-s2.0-S096921261930005X-mmc4.xlsx
Supplemental Material - 1-s2.0-S096921261930005X-mmc5.xlsx
", "abstract": "Electron cryotomography enables 3D visualization of cells in a near-native state at molecular resolution. The produced cellular tomograms contain detailed information about a plethora of macromolecular complexes, their structures, abundances, and specific spatial locations in the cell. However, extracting this information in a systematic way is very challenging, and current methods usually rely on individual templates of known structures. Here, we propose a framework called \"Multi-Pattern Pursuit\" for de novo discovery of different complexes from highly heterogeneous sets of particles extracted from entire cellular tomograms without using information of known structures. These initially detected structures can then serve as input for more targeted refinement efforts. Our tests on simulated and experimental tomograms show that our automated method is a promising tool for supporting large-scale template-free visual proteomics analysis.", "date": "2019-04-02", "date_type": "published", "publication": "Structure", "volume": "27", "number": "4", "publisher": "Cell Press", "pagerange": "679-691", "id_number": "CaltechAUTHORS:20190207-144006642", "issn": "0969-2126", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190207-144006642", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01GM096089" }, { "agency": "Arnold and Mabel Beckman Foundation" }, { "agency": "NSF", "grant_number": "DBI-1150287" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "P41GM103712" } ] }, "doi": "10.1016/j.str.2019.01.005", "pmcid": "PMC7542605", "primary_object": { "basename": "1-s2.0-S096921261930005X-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/sge8a-fp515/files/1-s2.0-S096921261930005X-mmc1.pdf" }, "related_objects": [ { "basename": "1-s2.0-S096921261930005X-mmc2.xlsx", "url": "https://authors.library.caltech.edu/records/sge8a-fp515/files/1-s2.0-S096921261930005X-mmc2.xlsx" }, { "basename": "1-s2.0-S096921261930005X-mmc3.xlsx", "url": "https://authors.library.caltech.edu/records/sge8a-fp515/files/1-s2.0-S096921261930005X-mmc3.xlsx" }, { "basename": "1-s2.0-S096921261930005X-mmc4.xlsx", "url": "https://authors.library.caltech.edu/records/sge8a-fp515/files/1-s2.0-S096921261930005X-mmc4.xlsx" }, { "basename": "1-s2.0-S096921261930005X-mmc5.xlsx", "url": "https://authors.library.caltech.edu/records/sge8a-fp515/files/1-s2.0-S096921261930005X-mmc5.xlsx" }, { "basename": "nihms-1047530.pdf", "url": "https://authors.library.caltech.edu/records/sge8a-fp515/files/nihms-1047530.pdf" } ], "resource_type": "article", "pub_year": "2019", "author_list": "Xu, Min; Singla, Jitin; et el." }, { "id": "https://authors.library.caltech.edu/records/rxh9k-fbk98", "eprint_id": 90002, "eprint_status": "archive", "datestamp": "2023-08-22 01:10:42", "lastmod": "2023-10-23 16:07:06", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Nguyen-Lam-Thanh", "name": { "family": "Nguyen", "given": "Lam Thanh" }, "orcid": "0000-0002-0756-0911" }, { "id": "Oikonomou-Catherine-M", "name": { "family": "Oikonomou", "given": "Catherine M." }, "orcid": "0000-0003-2312-4746" }, { "id": "Ding-H-Jane", "name": { "family": "Ding", "given": "H. Jane" } }, { "id": "Kaplan-Mohammed", "name": { "family": "Kaplan", "given": "Mohammed" }, "orcid": "0000-0002-0759-0459" }, { "id": "Yao-Qing", "name": { "family": "Yao", "given": "Qing" }, "orcid": "0000-0003-3575-9909" }, { "id": "Chang-Yi-Wei", "name": { "family": "Chang", "given": "Yi-Wei" }, "orcid": "0000-0003-2391-473X" }, { "id": "Beeby-Morgan-D", "name": { "family": "Beeby", "given": "Morgan" }, "orcid": "0000-0001-6413-9835" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Simulations suggest a constrictive force is required for Gram-negative bacterial cell division", "ispublished": "pub", "full_text_status": "public", "keywords": "Bacteria; Cell growth; Cellular microbiology; Computational biophysics", "note": "\u00a9 2019 The Author(s). This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. \n\nReceived 01 September 2018; Accepted 28 February 2019; Published 19 March 2019. \n\nCode availability: The source code of our simulations is provided as Supplementary Software. \n\nData availability: The data supporting the findings of this study are available within the paper and its Supplementary Information files. \n\nWe thank Martin Pilhofer for sharing the electron cryotomogram of an E. coli cell shown in Fig. 4, Debnath Ghosal for helpful discussions, and Andrew Jewett for assisting with membrane-tracing software. This work was supported by the National Institutes of Health (grant R35 GM122588 to G.J.J.). \n\nAuthor Contributions: L.T.N. designed and ran simulations and wrote the manuscript. C.M.O. wrote the manuscript. H.J.D. ran simulations and did analysis of electron cryotomograms. M.K., Q.Y., Y.-W.C. and M.B. performed electron cryotomography. G.J.J. designed simulations and wrote the manuscript. \n\nThe authors declare no competing interests.\n\nPublished - s41467-019-09264-0.pdf
Submitted - 406389.full.pdf
Supplemental Material - 41467_2019_9264_MOESM1_ESM.pdf
Supplemental Material - 41467_2019_9264_MOESM2_ESM.pdf
Supplemental Material - 41467_2019_9264_MOESM3_ESM.pdf
Supplemental Material - 41467_2019_9264_MOESM4_ESM.mp4
Supplemental Material - 41467_2019_9264_MOESM5_ESM.zip
Supplemental Material - 41467_2019_9264_MOESM6_ESM.pdf
", "abstract": "To divide, Gram-negative bacterial cells must remodel cell wall at the division site. It remains debated, however, whether this cell wall remodeling alone can drive membrane constriction, or if a constrictive force from the tubulin homolog FtsZ is required. Previously, we constructed software (REMODELER 1) to simulate cell wall remodeling during growth. Here, we expanded this software to explore cell wall division (REMODELER 2). We found that simply organizing cell wall synthesis complexes at the midcell is not sufficient to cause invagination, even with the implementation of a make-before-break mechanism, in which new hoops of cell wall are made inside the existing hoops before bonds are cleaved. Division can occur, however, when a constrictive force brings the midcell into a compressed state before new hoops of relaxed cell wall are incorporated between existing hoops. Adding a make-before-break mechanism drives division with a smaller constrictive force sufficient to bring the midcell into a relaxed, but not necessarily compressed, state.", "date": "2019-03-19", "date_type": "published", "publication": "Nature Communications", "volume": "10", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 1259", "id_number": "CaltechAUTHORS:20180927-114224004", "issn": "2041-1723", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180927-114224004", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R35 GM122588" } ] }, "doi": "10.1038/s41467-019-09264-0", "pmcid": "PMC6425016", "primary_object": { "basename": "41467_2019_9264_MOESM6_ESM.pdf", "url": "https://authors.library.caltech.edu/records/rxh9k-fbk98/files/41467_2019_9264_MOESM6_ESM.pdf" }, "related_objects": [ { "basename": "s41467-019-09264-0.pdf", "url": "https://authors.library.caltech.edu/records/rxh9k-fbk98/files/s41467-019-09264-0.pdf" }, { "basename": "406389.full.pdf", "url": "https://authors.library.caltech.edu/records/rxh9k-fbk98/files/406389.full.pdf" }, { "basename": "41467_2019_9264_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/rxh9k-fbk98/files/41467_2019_9264_MOESM1_ESM.pdf" }, { "basename": "41467_2019_9264_MOESM2_ESM.pdf", "url": "https://authors.library.caltech.edu/records/rxh9k-fbk98/files/41467_2019_9264_MOESM2_ESM.pdf" }, { "basename": "41467_2019_9264_MOESM3_ESM.pdf", "url": "https://authors.library.caltech.edu/records/rxh9k-fbk98/files/41467_2019_9264_MOESM3_ESM.pdf" }, { "basename": "41467_2019_9264_MOESM4_ESM.mp4", "url": "https://authors.library.caltech.edu/records/rxh9k-fbk98/files/41467_2019_9264_MOESM4_ESM.mp4" }, { "basename": "41467_2019_9264_MOESM5_ESM.zip", "url": "https://authors.library.caltech.edu/records/rxh9k-fbk98/files/41467_2019_9264_MOESM5_ESM.zip" } ], "resource_type": "article", "pub_year": "2019", "author_list": "Nguyen, Lam Thanh; Oikonomou, Catherine M.; et el." }, { "id": "https://authors.library.caltech.edu/records/295fm-40f02", "eprint_id": 90014, "eprint_status": "archive", "datestamp": "2023-08-22 01:04:49", "lastmod": "2023-10-23 16:07:17", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Martynowycz-M-W", "name": { "family": "Martynowycz", "given": "Michael W." }, "orcid": "0000-0003-0055-230X" }, { "id": "Zhao-Wei", "name": { "family": "Zhao", "given": "Wei" } }, { "id": "Hattne-J", "name": { "family": "Hattne", "given": "Johan" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Gonen-T", "name": { "family": "Gonen", "given": "Tamir" }, "orcid": "0000-0002-9254-4069" } ] }, "title": "Collection of continuous rotation MicroED Data from Ion Beam Milled Crystals of Any Size", "ispublished": "pub", "full_text_status": "public", "keywords": "Electron cryo-microscopy (cryoEM); MicroED; FIB-SEM; electron diffraction; electron crystallography", "note": "\u00a9 2018 Elsevier Ltd. \n\nReceived 5 October 2018, Revised 19 November 2018, Accepted 5 December 2018, Available online 17 January 2019. \n\nThe Gonen lab is supported by funds from the Howard Hughes Medical Institute. Work done in the Jensen lab was supported by NIH grant R35 GM122588. We would like to thank Ikaasa Suri (UCLA) for the help with sample preparation. \n\nAuthor Contributions: T.G. and G.J.J. conceived the project. M.W.M. prepared the protein crystals. W.Z. and M.W.M. collected the FIB/SEM data and milled the crystals. M.W.M. collected the MicroED data. M.W.M. and J.H. processed the data. The manuscript was written by M.W.M. and T.G. with contributions from all authors. M.W.M., G.J., and T.G. designed the experiments. Figures were prepared by M.W.M. and T.G. \n\nThe authors declare no conflict of interests.\n\nAccepted Version - nihms-1022710.pdf
Submitted - 425611.full.pdf
", "abstract": "Microcrystal electron diffraction (MicroED) allows for macromolecular structure solution from nanocrystals. To create crystals of suitable size for MicroED data collection, sample preparation typically involves sonication or pipetting a slurry of crystals from a crystallization drop. The resultant crystal fragments are fragile and the quality of the data that can be obtained from them is sensitive to subsequent sample preparation for cryoelectron microscopy as interactions in the water-air interface can damage crystals during blotting. Here, we demonstrate the use of a focused ion beam to generate lamellae of macromolecular protein crystals for continuous rotation MicroED that are of ideal thickness, easy to locate, and require no blotting optimization. In this manner, crystals of nearly any size may be scooped and milled to desired dimensions prior to data collection, thus streamlining the methodology for sample preparation for MicroED.", "date": "2019-03-05", "date_type": "published", "publication": "Structure", "volume": "27", "number": "3", "publisher": "Cell Press", "pagerange": "545-548", "id_number": "CaltechAUTHORS:20180927-114225333", "issn": "0969-2126", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180927-114225333", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "R35 GM122588" } ] }, "doi": "10.1016/j.str.2018.12.003", "pmcid": "PMC6476546", "primary_object": { "basename": "nihms-1022710.pdf", "url": "https://authors.library.caltech.edu/records/295fm-40f02/files/nihms-1022710.pdf" }, "related_objects": [ { "basename": "425611.full.pdf", "url": "https://authors.library.caltech.edu/records/295fm-40f02/files/425611.full.pdf" } ], "resource_type": "article", "pub_year": "2019", "author_list": "Martynowycz, Michael W.; Zhao, Wei; et el." }, { "id": "https://authors.library.caltech.edu/records/dzfre-jdm50", "eprint_id": 94711, "eprint_status": "archive", "datestamp": "2023-08-19 14:36:01", "lastmod": "2023-10-20 18:11:56", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Oikonomou-Catherine-M", "name": { "family": "Oikonomou", "given": "Catherine M." }, "orcid": "0000-0003-2312-4746" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Electron Cryotomography of Bacterial Secretion Systems", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2019 American Society for Microbiology. \n\nReceived: 19 October 2018, Accepted: 11 February 2019, Published: 5 April 2019. \n\nWe apologize to our colleagues whose work we could not discuss due to limited space, and we thank members of the Jensen lab for helpful discussions. \n\nWork on bacterial secretion systems in the lab is supported by the NIH (grant R01 AI127401 to G.J.J.).\n\nPublished - PSIB-0019-2018.pdf
", "abstract": "In biology, function arises from form. For bacterial secretion systems, which often span two membranes, avidly bind to the cell wall, and contain hundreds of individual proteins, studying form is a daunting task, made possible by electron cryotomography (ECT). ECT is the highest-resolution imaging technique currently available to visualize unique objects inside cells, providing a three-dimensional view of the shapes and locations of large macromolecular complexes in their native environment. Over the past 15 years, ECT has contributed to the study of bacterial secretion systems in two main ways: by revealing intact forms for the first time and by mapping components into these forms. Here we highlight some of these contributions, revealing structural convergence in type II secretion systems, structural divergence in type III secretion systems, unexpected structures in type IV secretion systems, and unexpected mechanisms in types V and VI secretion systems. Together, they offer a glimpse into a world of fantastic forms\u2014nanoscale rotors, needles, pumps, and dart guns\u2014much of which remains to be explored.", "date": "2019-03", "date_type": "published", "publication": "Microbiology Spectrum", "volume": "7", "number": "2", "publisher": "American Society for Microbiology", "pagerange": "Art. No. PSIB-0019", "id_number": "CaltechAUTHORS:20190415-141326985", "issn": "2165-0497", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190415-141326985", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 AI127401" } ] }, "doi": "10.1128/microbiolspec.PSIB-0019-2018", "pmcid": "PMC6452891", "primary_object": { "basename": "PSIB-0019-2018.pdf", "url": "https://authors.library.caltech.edu/records/dzfre-jdm50/files/PSIB-0019-2018.pdf" }, "resource_type": "article", "pub_year": "2019", "author_list": "Oikonomou, Catherine M. and Jensen, Grant J." }, { "id": "https://authors.library.caltech.edu/records/mtxf5-4e634", "eprint_id": 92969, "eprint_status": "archive", "datestamp": "2023-08-19 14:20:17", "lastmod": "2023-10-20 16:41:21", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chreifi-G", "name": { "family": "Chreifi", "given": "Georges" } }, { "id": "Chen-Songye", "name": { "family": "Chen", "given": "Songye" }, "orcid": "0000-0001-5407-5049" }, { "id": "Metskas-L-A", "name": { "family": "Metskas", "given": "Lauren Ann" }, "orcid": "0000-0002-8073-6960" }, { "id": "Mastronarde-D-N", "name": { "family": "Mastronarde", "given": "David" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Cryo-Electron Tomography, Faster: Development of a Fast-Incremental Tilting Scheme for Rapid Tomogram Acquisition", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2019 Biophysical Society. \n\nAvailable online 15 February 2019.", "abstract": "Cryo-electron microscopy enables high-resolution imaging for both protein structure determination and cellular imaging studies. When a sample's ultrastructure is unique, cryo-electron tomography can generate a volume image from a single sample, allowing the study of cellular architecture or polymorphic viruses. This technique requires tilting the microscope stage between each exposure, such that a collection of exposures is built into a stack that can be reconstructed into a three-dimensional volume. Proteins within these volumes can be averaged, with sub-tomogram averaged structures capable of reaching high resolution. However, each tomogram can require between 20-60 minutes of data collection time, restricting the number of tomograms that a user can collect in time-limited microscopy sessions. As the final resolution of sub-tomogram averages is dependent upon the number of particles in the dataset, the number of tomograms collected is severely limiting in cases where protein copy number is low.\n\nThe Jensen lab has developed a \"fast-incremental\" tilt scheme, whereby a single tomogram can be collected in 3-10 minutes. An FEI Titan Krios cryo-electron microscope and Gatan K2 camera are operated in continuous acquisition mode, using SerialEM software to blank the electron beam during stage movement; the resulting acquisition is similar in geometry and exposure to a conventional tomogram. We find that the precision of a single-tilt stage and a camera with fast frame capture rates and high sensitivity compensate for the lack of time-consuming stage tracking and adjustments during data collection, to a resolution of roughly 2.5 nm. Further hardware and software development will improve the resolution and utility of this method.", "date": "2019-02-15", "date_type": "published", "publication": "Biophysical Journal", "volume": "116", "number": "3", "publisher": "Biophysical Society", "pagerange": "575a", "id_number": "CaltechAUTHORS:20190219-101505920", "issn": "0006-3495", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190219-101505920", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.bpj.2018.11.3091", "resource_type": "article", "pub_year": "2019", "author_list": "Chreifi, Georges; Chen, Songye; et el." }, { "id": "https://authors.library.caltech.edu/records/vk9w8-sn881", "eprint_id": 90701, "eprint_status": "archive", "datestamp": "2023-08-19 14:11:08", "lastmod": "2023-10-20 22:08:25", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chreifi-Georges", "name": { "family": "Chreifi", "given": "Georges" }, "orcid": "0000-0003-4194-1694" }, { "id": "Chen-Songye", "name": { "family": "Chen", "given": "Songye" }, "orcid": "0000-0001-5407-5049" }, { "id": "Metskas-Lauren-Ann", "name": { "family": "Metskas", "given": "Lauren Ann" }, "orcid": "0000-0002-8073-6960" }, { "id": "Kaplan-Mohammed", "name": { "family": "Kaplan", "given": "Mohammed" }, "orcid": "0000-0002-0759-0459" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Rapid Tilt-Series Acquisition for Electron Cryotomography", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2019 Elsevier Inc. \n\nReceived 28 October 2018, Revised 18 December 2018, Accepted 20 December 2018, Available online 11 January 2019. \n\nWe thank David N. Mastronarde for helpful suggestions and for providing comments on this manuscript. This work was supported by NIH grant GM122588 (to G.J.J.). Electron cryomicroscopy was done in the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech. M.K. is supported by a postdoctoral Rubicon fellowship from De Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO).\n\nAccepted Version - nihms-1519590.pdf
Submitted - 454587.full.pdf
", "abstract": "Using a new Titan Krios stage equipped with a single-axis holder, we developed two methods to accelerate the collection of tilt-series. We demonstrate a continuous-tilting method that can record a tilt-series in seconds, but with loss of details finer than \u223c4\u202fnm. We also demonstrate a fast-incremental method that can record a tilt-series several-fold faster than current methods and with similar resolution. We characterize the utility of both methods in real biological electron cryotomography workflows. We identify opportunities for further improvements in hardware and software and speculate on the impact such advances could have on structural biology.", "date": "2019-02-01", "date_type": "published", "publication": "Journal of Structural Biology", "volume": "205", "number": "2", "publisher": "Elsevier", "pagerange": "163-169", "id_number": "CaltechAUTHORS:20181107-100852395", "issn": "1047-8477", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181107-100852395", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM122588" }, { "agency": "Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)" } ] }, "doi": "10.1016/j.jsb.2018.12.008", "pmcid": "PMC6389375", "primary_object": { "basename": "454587.full.pdf", "url": "https://authors.library.caltech.edu/records/vk9w8-sn881/files/454587.full.pdf" }, "related_objects": [ { "basename": "nihms-1519590.pdf", "url": "https://authors.library.caltech.edu/records/vk9w8-sn881/files/nihms-1519590.pdf" } ], "resource_type": "article", "pub_year": "2019", "author_list": "Chreifi, Georges; Chen, Songye; et el." }, { "id": "https://authors.library.caltech.edu/records/ajgf8-xsn85", "eprint_id": 92767, "eprint_status": "archive", "datestamp": "2023-08-19 14:01:06", "lastmod": "2023-10-20 21:59:04", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Azubel-M", "name": { "family": "Azubel", "given": "Maia" }, "orcid": "0000-0002-1584-2695" }, { "id": "Carter-S-D", "name": { "family": "Carter", "given": "Stephen D." }, "orcid": "0000-0002-4237-4276" }, { "id": "Weiszmann-J", "name": { "family": "Weiszmann", "given": "Jennifer" } }, { "id": "Zhang-Jun", "name": { "family": "Zhang", "given": "Jun" }, "orcid": "0000-0003-4154-3741" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Li-Yang", "name": { "family": "Li", "given": "Yang" }, "orcid": "0000-0002-4939-8174" }, { "id": "Kornberg-R-D", "name": { "family": "Kornberg", "given": "Roger D." } } ] }, "title": "FGF21 trafficking in intact human cells revealed by cryo-electron tomography with gold nanoparticles", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2019 Azubel et al. This article is distributed under the\nterms of the Creative Commons Attribution License, which\npermits unrestricted use and redistribution provided that the original author and source are credited. \n\nReceived: 26 October 2018; Accepted: 07 January 2019; Published: 28 January 2019. \n\nData availability: All data is provided in the manuscript and supporting files. \n\nThis research was supported by NIH grants AI 21144 to RDK and R35 122588 to GJJ. We thank Amgen Department of Protein Sciences for providing some of the reagents used in this study. We thank Dr. E P Geiduschek for discussion and comments on the manuscript. \n\nThe funders had role in study design, and the decision to submit the work for publication. \n\nCompeting interests: Jennifer Weiszmann, Jun Zhang, Yang Li: Employee of Amgen at the time the study was conducted. There are no other competing financial interests to declare. The other authors declare that no competing interests exist.\n\nAuthor contributions: Maia Azubel, Conceptualization, Data curation, Formal analysis, Supervision, Validation, Investigation, Visualization, Methodology, Writing\u2014original draft, Project administration, Writing\u2014review and editing; Stephen D Carter, Investigation, Methodology, Writing\u2014review and editing; Jennifer Weiszmann, Resources, Investigation, Visualization, Methodology, Writing\u2014review and editing; Jun Zhang, Resources, Writing\u2014review and editing; Grant J Jensen, Conceptualization, Resources, Funding acquisition, Writing\u2014review and editing; Yang Li, Conceptualization, Resources, Supervision, Funding acquisition, Methodology, Writing\u2014review and editing; Roger D Kornberg, Conceptualization, Resources, Supervision, Writing\u2014original draft, Writing\u2014review and editing.\n\nPublished - elife-43146-v1.pdf
Supplemental Material - elife-43146-transrepform-v1.docx
", "abstract": "The fibroblast growth factor FGF21 was labeled with molecularly defined gold nanoparticles (AuNPs), applied to human adipocytes, and imaged by cryo-electron tomography (cryo-ET). Most AuNPs were in pairs about 80 \u00c5 apart, on the outer cell surface. Pairs of AuNPs were also abundant inside the cells in clathrin-coated vesicles and endosomes. AuNPs were present but no longer paired in multivesicular bodies. FGF21 could thus be tracked along the endocytotic pathway. The methods developed here to visualize signaling coupled to endocytosis can be applied to a wide variety of cargo and may be extended to studies of other intracellular transactions.", "date": "2019-01-28", "date_type": "published", "publication": "eLife", "volume": "8", "publisher": "eLife Sciences Publications", "pagerange": "Art. No. e43146", "id_number": "CaltechAUTHORS:20190207-143318376", "issn": "2050-084X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190207-143318376", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "AI 21144" }, { "agency": "NIH", "grant_number": "R35 122588" } ] }, "doi": "10.7554/elife.43146", "pmcid": "PMC6349402", "primary_object": { "basename": "elife-43146-transrepform-v1.docx", "url": "https://authors.library.caltech.edu/records/ajgf8-xsn85/files/elife-43146-transrepform-v1.docx" }, "related_objects": [ { "basename": "elife-43146-v1.pdf", "url": "https://authors.library.caltech.edu/records/ajgf8-xsn85/files/elife-43146-v1.pdf" } ], "resource_type": "article", "pub_year": "2019", "author_list": "Azubel, Maia; Carter, Stephen D.; et el." }, { "id": "https://authors.library.caltech.edu/records/p20d8-gaj31", "eprint_id": 92398, "eprint_status": "archive", "datestamp": "2023-08-19 13:55:41", "lastmod": "2023-10-20 00:15:34", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kaplan-Mohammed", "name": { "family": "Kaplan", "given": "Mohammed" }, "orcid": "0000-0002-0759-0459" }, { "id": "Ghosal-Debnath", "name": { "family": "Ghosal", "given": "Debnath" }, "orcid": "0000-0002-2227-0330" }, { "id": "Subramanian-Poorna", "name": { "family": "Subramanian", "given": "Poorna" } }, { "id": "Oikonomou-C-M", "name": { "family": "Oikonomou", "given": "Catherine M." }, "orcid": "0000-0003-2312-4746" }, { "id": "Kj\u00e6r-Andreas", "name": { "family": "Kj\u00e6r", "given": "Andreas" }, "orcid": "0000-0002-0096-5764" }, { "id": "Pirbadian-Sahand", "name": { "family": "Pirbadian", "given": "Sahand" } }, { "id": "Ortega-D-R", "name": { "family": "Ortega", "given": "Davi R." }, "orcid": "0000-0002-8344-2335" }, { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "El-Naggar-M-Y", "name": { "family": "El-Naggar", "given": "Mohamed Y." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "The presence and absence of periplasmic rings in bacterial flagellar motors correlates with stator type", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2019, Kaplan et al. This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited. \n\nReceived: November 8, 2018; Accepted: December 19, 2018; Accepted Manuscript published: January 16, 2019 (version 1). \n\nWe thank Dr. Songye Chen for technical support. This work is supported by the National Institutes of Health (NIH, grant R01 AI127401 to G.J.J.). M.K. is supported by a postdoctoral Rubicon fellowship from De Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO). S.P. and M.Y.E.-N. are supported by the Air Force Office of Scientific Research Presidential Early Career Award for Scientists and Engineers (FA955014-1-0294, to M.Y.E.-N.). \n\nData availability: All data generated or analysed during this study are included in the manuscript and supporting files.The ECT structures have been deposited in the EMDB under the following accession numbers, EMD-0464 for Legionella pneumophila motor, EMD-0465 for Pseudomonas aeruginosa motor and EMD-0467 for Shewanella oneidensis MR-1 motor\n\nPublished - elife-43487-v2.pdf
Supplemental Material - elife-43487-supp1-v2.docx
Supplemental Material - elife-43487-supp2-v2.docx
Supplemental Material - elife-43487-supp3-v2.docx
Supplemental Material - elife-43487-transrepform-v2.docx
", "abstract": "The bacterial flagellar motor, a cell-envelope-embedded macromolecular machine that functions as a cellular propeller, exhibits significant structural variability between species. Different torque-generating stator modules allow motors to operate in different pH, salt or viscosity levels. How such diversity evolved is unknown. Here, we use electron cryo-tomography to determine the in situ macromolecular structures of three Gammaproteobacteria motors: Legionella pneumophila, Pseudomonas aeruginosa, and Shewanella oneidensis, providing the first views of intact motors with dual stator systems. Complementing our imaging with bioinformatics analysis, we find a correlation between the motor's stator system and its structural elaboration. Motors with a single H+-driven stator have only the core periplasmic P- and L-rings; those with dual H^+-driven stators have an elaborated P-ring; and motors with Na^+ or Na^+/H^+-driven stators have both their P- and L-rings embellished. Our results suggest an evolution of structural elaboration that may have enabled pathogenic bacteria to colonize higher-viscosity environments in animal hosts.", "date": "2019-01-16", "date_type": "published", "publication": "eLife", "volume": "8", "publisher": "eLife Sciences Publications", "pagerange": "Art. No. e43487", "id_number": "CaltechAUTHORS:20190122-131221284", "issn": "2050-084X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190122-131221284", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 AI127401" }, { "agency": "Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)" }, { "agency": "Air Force Office of Scientific Research (AFOSR)", "grant_number": "FA955014-1-0294" } ] }, "doi": "10.7554/eLife.43487", "pmcid": "PMC6375700", "primary_object": { "basename": "elife-43487-supp1-v2.docx", "url": "https://authors.library.caltech.edu/records/p20d8-gaj31/files/elife-43487-supp1-v2.docx" }, "related_objects": [ { "basename": "elife-43487-supp2-v2.docx", "url": "https://authors.library.caltech.edu/records/p20d8-gaj31/files/elife-43487-supp2-v2.docx" }, { "basename": "elife-43487-supp3-v2.docx", "url": "https://authors.library.caltech.edu/records/p20d8-gaj31/files/elife-43487-supp3-v2.docx" }, { "basename": "elife-43487-transrepform-v2.docx", "url": "https://authors.library.caltech.edu/records/p20d8-gaj31/files/elife-43487-transrepform-v2.docx" }, { "basename": "elife-43487-v2.pdf", "url": "https://authors.library.caltech.edu/records/p20d8-gaj31/files/elife-43487-v2.pdf" } ], "resource_type": "article", "pub_year": "2019", "author_list": "Kaplan, Mohammed; Ghosal, Debnath; et el." }, { "id": "https://authors.library.caltech.edu/records/kqett-kyb73", "eprint_id": 90585, "eprint_status": "archive", "datestamp": "2023-08-22 00:16:25", "lastmod": "2023-10-19 14:36:20", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ruhe-Zachary-C", "name": { "family": "Ruhe", "given": "Zachary C." } }, { "id": "Subramanian-Poorna", "name": { "family": "Subramanian", "given": "Poorna" } }, { "id": "Song-Kiho", "name": { "family": "Song", "given": "Kiho" } }, { "id": "Nguyen-Josephine-Y", "name": { "family": "Nguyen", "given": "Josephine Y." } }, { "id": "Stevens-Taylor-A", "name": { "family": "Stevens", "given": "Taylor A." } }, { "id": "Low-David-A", "name": { "family": "Low", "given": "David A." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Hayes-Christopher-S", "name": { "family": "Hayes", "given": "Christopher S." } } ] }, "title": "Programmed Secretion Arrest and Receptor-Triggered Toxin Export during Antibacterial Contact-Dependent Growth Inhibition", "ispublished": "pub", "full_text_status": "public", "keywords": "bacterial competition; BamA; \u03b2-barrel protein; outer membrane; self-nonself discrimination; toxin-immunity proteins; Tsx; two-partner secretion; type V secretion system", "note": "\u00a9 2018 Elsevier. \n\nReceived 2 May 2018, Revised 31 July 2018, Accepted 5 September 2018, Available online 1 November 2018. \n\nWe thank Chuan Hong, Rick Huang, and Zhiheng Yu at the HHMI Janelia CryoEM Facility for help with the Titan Krios microscope operation and data collection and Thomas Silhavy for providing antisera. This work was supported by grants GM117930 (C.S.H.) and GM122588 (G.J.J.) from National Institutes of Health and grant MCB 1545720 (C.S.H. and D.A.L.) from the National Science Foundation. \n\nAuthor Contributions: Conceptualization, Z.C.R. and C.S.H.; Methodology, Z.C.R., K.S., and P.S.; Validation, K.S., J.Y.N., and T.A.S.; Investigation, Z.C.R., P.S., K.S., and J.Y.N.; Writing \u2013 Original Draft, Z.C.R. and C.S.H.; Writing \u2013 Review & Editing, D.A.L., G.J.J., and C.S.H.; Visualization, Z.C.R., K.S., P.S., and C.S.H.; Funding Acquisition, D.A.L., G.J.J., and C.S.H.; Supervision, D.A.L., G.J.J., and C.S.H. \n\nData and Software Availability: Individual fluorescent channel data for all immunoblots and the I-TASSER server output for FHA-2 structure predictions are available at https://doi.org/10.17632/hrbmtfv754.1. \n\nThe authors declare no competing interests.\n\nAccepted Version - nihms-1510034.pdf
Supplemental Material - 1-s2.0-S0092867418313862-mmc1.pdf
", "abstract": "Contact-dependent growth inhibition (CDI) entails receptor-mediated delivery of CdiA-derived toxins into Gram-negative target bacteria. Using electron cryotomography, we show that each CdiA effector protein forms a filament extending \u223c33 nm from the cell surface. Remarkably, the extracellular filament represents only the N-terminal half of the effector. A programmed secretion arrest sequesters the C-terminal half of CdiA, including the toxin domain, in the periplasm prior to target-cell recognition. Upon binding receptor, CdiA secretion resumes, and the periplasmic FHA-2 domain is transferred to the target-cell outer membrane. The C-terminal toxin region of CdiA then penetrates into the target-cell periplasm, where it is cleaved for subsequent translocation into the cytoplasm. Our findings suggest that the FHA-2 domain assembles into a transmembrane conduit for toxin transport into the periplasm of target bacteria. We propose that receptor-triggered secretion ensures that FHA-2 export is closely coordinated with integration into the target-cell outer membrane.", "date": "2018-11-01", "date_type": "published", "publication": "Cell", "volume": "175", "number": "4", "publisher": "Cell Press", "pagerange": "921-933", "id_number": "CaltechAUTHORS:20181101-152903489", "issn": "0092-8674", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181101-152903489", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM117930" }, { "agency": "NIH", "grant_number": "GM122588" }, { "agency": "NSF", "grant_number": "MCB-1545720" } ] }, "doi": "10.1016/j.cell.2018.10.033", "pmcid": "PMC6333426", "primary_object": { "basename": "1-s2.0-S0092867418313862-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/kqett-kyb73/files/1-s2.0-S0092867418313862-mmc1.pdf" }, "related_objects": [ { "basename": "nihms-1510034.pdf", "url": "https://authors.library.caltech.edu/records/kqett-kyb73/files/nihms-1510034.pdf" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Ruhe, Zachary C.; Subramanian, Poorna; et el." }, { "id": "https://authors.library.caltech.edu/records/5fvhf-zkt86", "eprint_id": 90146, "eprint_status": "archive", "datestamp": "2023-08-19 11:52:53", "lastmod": "2023-10-23 15:46:49", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Mahinthichaichan-P", "name": { "family": "Mahinthichaichan", "given": "Paween" }, "orcid": "0000-0002-2216-4482" }, { "id": "Morris-D-M", "name": { "family": "Morris", "given": "Dylan M." } }, { "id": "Wang-Yi", "name": { "family": "Wang", "given": "Yi" }, "orcid": "0000-0002-4174-8790" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Tajkhorshid-E", "name": { "family": "Tajkhorshid", "given": "Emad" }, "orcid": "0000-0001-8434-1010" } ] }, "title": "Selective Permeability of Carboxysome Shell Pores to Anionic Molecules", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2018 American Chemical Society. \n\nReceived: July 16, 2018; Revised: September 7, 2018; Published: September 7, 2018. \n\nWe thank Dr. Catherine Oikonomou for help revising the manuscript. This work was supported in part by the National Institutes of Health (NIH P41-GM104601, U01-GM111251, and U54-GM087519 to E.T., and R35 GM122588 to G.J.J.) and the Office of Naval Research (ONR N00014-16-1-2535 to E.T.). P.M. gratefully acknowledges previous support as a trainee of the Molecular Biophysics Training Program by the NIH (T32-GM008276) during his graduate study. \n\nAuthor Contributions: P.M. and D.M.M. contributed equally to this work. \n\nThe authors declare no competing financial interest.\n\nAccepted Version - nihms-1000802.pdf
Submitted - 367714.full.pdf
Supplemental Material - jp8b06822_si_001.pdf
", "abstract": "Carboxysomes are closed polyhedral cellular microcompartments that increase the efficiency of carbon fixation in autotrophic bacteria. Carboxysome shells consist of small proteins that form hexameric units with semipermeable central pores containing binding sites for anions. This feature is thought to selectively allow access to RuBisCO enzymes inside the carboxysome by HCO_3\u2013 (the dominant form of CO_2 in the aqueous solution at pH 7.4) but not O_2, which leads to a nonproductive reaction. To test this hypothesis, here we use molecular dynamics simulations to characterize the energetics and permeability of CO_2, O_2, and HCO_3\u2013 through the central pores of two different shell proteins, namely, CsoS1A of \u03b1-carboxysome and CcmK4 of \u03b2-carboxysome shells. We find that the central pores are in fact selectively permeable to anions such as HCO_3\u2013, as predicted by the model.", "date": "2018-10-04", "date_type": "published", "publication": "Journal of Physical Chemistry B", "volume": "122", "number": "39", "publisher": "American Chemical Society", "pagerange": "9110-9118", "id_number": "CaltechAUTHORS:20181008-085459056", "issn": "1520-6106", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181008-085459056", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P41-GM104601" }, { "agency": "NIH", "grant_number": "U01-GM111251" }, { "agency": "NIH", "grant_number": "U54-GM087519" }, { "agency": "NIH", "grant_number": "R35 GM122588" }, { "agency": "Office of Naval Research (ONR)", "grant_number": "N00014-16-1-2535" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32-GM008276" } ] }, "doi": "10.1021/acs.jpcb.8b06822", "pmcid": "PMC6311388", "primary_object": { "basename": "nihms-1000802.pdf", "url": "https://authors.library.caltech.edu/records/5fvhf-zkt86/files/nihms-1000802.pdf" }, "related_objects": [ { "basename": "367714.full.pdf", "url": "https://authors.library.caltech.edu/records/5fvhf-zkt86/files/367714.full.pdf" }, { "basename": "jp8b06822_si_001.pdf", "url": "https://authors.library.caltech.edu/records/5fvhf-zkt86/files/jp8b06822_si_001.pdf" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Mahinthichaichan, Paween; Morris, Dylan M.; et el." }, { "id": "https://authors.library.caltech.edu/records/e3yj9-zcs79", "eprint_id": 87184, "eprint_status": "archive", "datestamp": "2023-08-19 11:39:05", "lastmod": "2023-10-18 20:55:55", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Li-Po-Nan", "name": { "family": "Li", "given": "Po-Nan" }, "orcid": "0000-0002-7917-7444" }, { "id": "Herrmann-J-R", "name": { "family": "Herrmann", "given": "Jonathan" } }, { "id": "Tolar-B-B", "name": { "family": "Tolar", "given": "Bradley B." }, "orcid": "0000-0003-0493-1470" }, { "id": "Poitevin-F-P-B", "name": { "family": "Poitevin", "given": "Fr\u00e9d\u00e9ric" } }, { "id": "Ramdasi-R", "name": { "family": "Ramdasi", "given": "Rasika" } }, { "id": "Bargar-J-R", "name": { "family": "Bargar", "given": "John R." } }, { "id": "Stahl-D-A", "name": { "family": "Stahl", "given": "David A." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Francis-C-A", "name": { "family": "Francis", "given": "Christopher A." } }, { "id": "Wakatsuki-Soichi", "name": { "family": "Wakatsuki", "given": "Soichi" } }, { "id": "van-den-Bedem-H", "name": { "family": "van den Bedem", "given": "Henry" }, "orcid": "0000-0003-2358-841X" } ] }, "title": "Nutrient transport suggests an evolutionary basis for charged archaeal surface layer proteins", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2018 International Society for Microbial Ecology. \n\nReceived: 30 November 2017; Revised: 11 April 2018; Accepted: 14 April 2018; Published online 13 June 2018. \n\nThis work was partially supported by the US Department of Energy, Laboratory Directed Research and Development under contract No. DE-AC02-76SF00515. JH was supported by the National Science Foundation Graduate Research Fellowship Program (NSF-GRFP), as well as the US Department of Energy Office of Science Graduate Student Research Program (DOE-SCGSR). FP acknowledges support from the National Institutes of Health (NIH), grant No. R35GM122543. DAS was funded in part by the United States National Science Foundation Grants MCB-092074 and OCE-1046017. HvdB acknowledges support from the U.S. Department of Energy, Office of Science, Office of Advanced Scientific Computing Research, Scientific Discovery through Advanced Computing (SciDAC) program. Computations were performed at the Stanford Research Computing Center. Glycosylation analysis by mass spectrometry was possible with assistance from C Adams and R Lieb (Stanford University Mass Spectrometry). \n\nThe authors declare that they have no conflict of interest.\n\nSupplemental Material - 41396_2018_191_MOESM1_ESM.pdf
", "abstract": "Surface layers (S-layers) are two-dimensional, proteinaceous, porous lattices that form the outermost cell envelope component of virtually all archaea and many bacteria. Despite exceptional sequence diversity, S-layer proteins (SLPs) share important characteristics such as their ability to form crystalline sheets punctuated with nano-scale pores, and their propensity for charged amino acids, leading to acidic or basic isoelectric points. However, the precise function of S-layers, or the role of charged SLPs and how they relate to cellular metabolism is unknown. Nano-scale lattices affect the diffusion behavior of low-concentration solutes, even if they are significantly smaller than the pore size. Here, we offer a rationale for charged S-layer proteins in the context of the structural evolution of S-layers. Using the ammonia-oxidizing archaea (AOA) as a model for S-layer geometry, and a 2D electrodiffusion reaction computational framework to simulate diffusion and consumption of the charged solute ammonium (NH_4^+), we find that the characteristic length scales of nanoporous S-layers elevate the concentration of NH_4^+ in the pseudo-periplasmic space. Our simulations suggest an evolutionary, mechanistic basis for S-layer charge and shed light on the unique ability of some AOA to oxidize ammonia in environments with nanomolar NH_4^+ availability, with broad implications for comparisons of ecologically distinct populations.", "date": "2018-10", "date_type": "published", "publication": "ISME Journal", "volume": "12", "number": "10", "publisher": "Nature Publishing Group", "pagerange": "2389-2402", "id_number": "CaltechAUTHORS:20180618-091246320", "issn": "1751-7362", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180618-091246320", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Department of Energy (DOE)", "grant_number": "DE-AC02-76SF00515" }, { "agency": "NSF Graduate Research Fellowship" }, { "agency": "NIH", "grant_number": "R35GM122543" }, { "agency": "NSF", "grant_number": "MCB-0920741" }, { "agency": "NSF", "grant_number": "OCE-1046017" } ] }, "doi": "10.1038/s41396-018-0191-0", "pmcid": "PMC6155111", "primary_object": { "basename": "41396_2018_191_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/e3yj9-zcs79/files/41396_2018_191_MOESM1_ESM.pdf" }, "resource_type": "article", "pub_year": "2018", "author_list": "Li, Po-Nan; Herrmann, Jonathan; et el." }, { "id": "https://authors.library.caltech.edu/records/nmkeb-hen53", "eprint_id": 86773, "eprint_status": "archive", "datestamp": "2023-08-19 09:40:52", "lastmod": "2023-10-20 21:56:00", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Nguyen-Lam-T", "name": { "family": "Nguyen", "given": "Lam T." } }, { "id": "Swulius-Matthew-T", "name": { "family": "Swulius", "given": "Matthew T." } }, { "id": "Aich-Samya", "name": { "family": "Aich", "given": "Samya" } }, { "id": "Mishra-Mithilesh", "name": { "family": "Mishra", "given": "Mithilesh" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Coarse-grained simulations of actomyosin rings point to a nodeless model involving both unipolar and bipolar myosins", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2018 Nguyen et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution\u2013Noncommercial\u2013Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0). \n\nReceived: Dec 19, 2017; Revised: Mar 26, 2018; Accepted: Apr 4, 2018; Published Online:31 May 2018. \n\nWe thank Catherine Oikonomou for helping revise the manuscript for clarity. M.M. is an Intermediate Fellow of the Wellcome Trust\u2212Department of Biotechnology India Alliance (IA/I/14/1/501317). M.M. acknowledges the India Alliance and the Department of Atomic Energy/Tata Institute of Fundamental Research for funds. This work was supported in part by National Institutes of Health Grant GM122588 to G.J.J.\n\nPublished - mbc.e17-12-0736.pdf
Submitted - 194910.full.pdf
Supplemental Material - combinedsupmats.pdf
Supplemental Material - e17-12-0736_zipfile.gz
", "abstract": "Cytokinesis in many eukaryotic cells is orchestrated by a contractile actomyosin ring. While many of the proteins involved are known, the mechanism of constriction remains unclear. Informed by the existing literature and new three-dimensional (3D) molecular details from electron cryotomography, here we develop 3D coarse-grained models of actin filaments, unipolar and bipolar myosins, actin cross-linkers, and membranes and simulate their interactions. Assuming that local force on the membrane results in inward growth of the cell wall, we explored a matrix of possible actomyosin configurations and found that node-based architectures like those presently described for ring assembly result in membrane puckers not seen in electron microscope images of real cells. Instead, the model that best matches data from fluorescence microscopy, electron cryotomography, and biochemical experiments is one in which actin filaments transmit force to the membrane through evenly distributed, membrane-attached, unipolar myosins, with bipolar myosins in the ring driving contraction. While at this point this model is only favored (not proven), the work highlights the power of coarse-grained biophysical simulations to compare complex mechanistic hypotheses.", "date": "2018-06-01", "date_type": "published", "publication": "Molecular Biology of the Cell", "volume": "29", "number": "11", "publisher": "American Society for Cell Biology", "pagerange": "1318-1331", "id_number": "CaltechAUTHORS:20180604-082905260", "issn": "1059-1524", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180604-082905260", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Wellcome Trust\u2212Department of Biotechnology India Alliance", "grant_number": "IA/I/14/1/501317" }, { "agency": "Department of Atomic Energy (India)" }, { "agency": "Tata Institute of Fundamental Research" }, { "agency": "NIH", "grant_number": "GM122588" } ] }, "doi": "10.1091/mbc.E17-12-0736", "pmcid": "PMC5994903", "primary_object": { "basename": "194910.full.pdf", "url": "https://authors.library.caltech.edu/records/nmkeb-hen53/files/194910.full.pdf" }, "related_objects": [ { "basename": "combinedsupmats.pdf", "url": "https://authors.library.caltech.edu/records/nmkeb-hen53/files/combinedsupmats.pdf" }, { "basename": "e17-12-0736_zipfile.gz", "url": "https://authors.library.caltech.edu/records/nmkeb-hen53/files/e17-12-0736_zipfile.gz" }, { "basename": "mbc.e17-12-0736.pdf", "url": "https://authors.library.caltech.edu/records/nmkeb-hen53/files/mbc.e17-12-0736.pdf" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Nguyen, Lam T.; Swulius, Matthew T.; et el." }, { "id": "https://authors.library.caltech.edu/records/6h5mv-2eg62", "eprint_id": 84961, "eprint_status": "archive", "datestamp": "2023-08-21 23:15:51", "lastmod": "2023-10-18 17:00:56", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Krause-D-C", "name": { "family": "Krause", "given": "Duncan C." }, "orcid": "0000-0003-3548-0422" }, { "id": "Chen-Songye", "name": { "family": "Chen", "given": "Songye" }, "orcid": "0000-0001-5407-5049" }, { "id": "Shi-Jian-CELLBIO", "name": { "family": "Shi", "given": "Jian" }, "orcid": "0000-0003-3810-5302" }, { "id": "Jensen-A-J", "name": { "family": "Jensen", "given": "Ashley" } }, { "id": "Sheppard-E-S", "name": { "family": "Sheppard", "given": "Edward S." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Electron Cryotomography of Mycoplasma pneumoniae Mutants Correlates Terminal Organelle Architectural Features and Function", "ispublished": "pub", "full_text_status": "public", "keywords": "Mycoplasma pneumoniae; terminal organelle; electron cryotomography; mutants; bacterial ultrastructure", "note": "\u00a9 2018 John Wiley & Sons Ltd. \n\nAccepted manuscript online: 22 Feb 2018. Manuscript Accepted: 20 Feb 2018. Manuscript Revised: 19 Feb 2018. Manuscript Received: 24 Oct 2017. Issue Online 23 April 2018. \n\nThis work was supported by Public Health Service research grants AI49194 and AI110098 from the National Institute of Allergy and Infectious Diseases to D.C.K. We acknowledge Mitch Balish for helpful discussions. We declare no competing interests. \n\nAUTHOR CONTRIBUTIONS: Study conception and design: D.C.K. and G.J.J.; data acquisition and analysis: D.C.K., S.C., J.S., A.J., E.S.S., and G.J.J.; writing the manuscript: D.C.K., S.C., and G.J.J.\n\nAccepted Version - mmi13937.pdf
Accepted Version - nihms948652.pdf
Supplemental Material - mmi13937-sup-0001-SuppInfo01.docx
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Supplemental Material - mmi13937-sup-00012-Video11.avi
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Supplemental Material - mmi13937-sup-0009-Video8.avi
", "abstract": "The Mycoplasma pneumoniae terminal organelle functions in adherence and gliding motility and is comprised of at least eleven substructures. We used electron cryotomography to correlate impaired gliding and adherence function with changes in architecture in diverse terminal organelle mutants. All eleven substructures were accounted for in the prkC, prpC, and P200 mutants, and variably so for the HMW3 mutant. Conversely, no terminal organelle substructures were evident in HMW1 and HMW2 mutants. The P41 mutant exhibits a terminal organelle detachment phenotype and lacked the bowl element normally present at the terminal organelle base. Complementation restored this substructure, establishing P41 as either a component of the bowl element or required for its assembly or stability, and that this bowl element is essential to anchor the terminal organelle but not for leverage in gliding. Mutants II-3, III-4, and topJ exhibited a visibly lower density of protein knobs on the terminal organelle surface. Mutants II-3 and III-4 lack accessory proteins required for a functional adhesin complex, while the topJ mutant lacks a DnaJ-like co-chaperone essential for its assembly. Taken together, these observations expand our understanding of the roles of certain terminal organelle proteins in the architecture and function of this complex structure.", "date": "2018-05", "date_type": "published", "publication": "Molecular Microbiology", "volume": "108", "number": "3", "publisher": "Wiley", "pagerange": "306-318", "id_number": "CaltechAUTHORS:20180227-074921090", "issn": "0950-382X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180227-074921090", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "AI49194" }, { "agency": "NIH", "grant_number": "AI110098" }, { "agency": "National Institute of Allergy and Infectious Diseases" } ] }, "doi": "10.1111/mmi.13937", "pmcid": "PMC5912986", "primary_object": { "basename": "mmi13937.pdf", "url": "https://authors.library.caltech.edu/records/6h5mv-2eg62/files/mmi13937.pdf" }, "related_objects": [ { "basename": "mmi13937-sup-0007-Video6.avi", "url": "https://authors.library.caltech.edu/records/6h5mv-2eg62/files/mmi13937-sup-0007-Video6.avi" }, { "basename": "mmi13937-sup-0009-Video8.avi", "url": "https://authors.library.caltech.edu/records/6h5mv-2eg62/files/mmi13937-sup-0009-Video8.avi" }, { "basename": "nihms948652.pdf", "url": "https://authors.library.caltech.edu/records/6h5mv-2eg62/files/nihms948652.pdf" }, { "basename": "mmi13937-sup-00012-Video11.avi", "url": "https://authors.library.caltech.edu/records/6h5mv-2eg62/files/mmi13937-sup-00012-Video11.avi" }, { "basename": "mmi13937-sup-0003-Video2.avi", "url": "https://authors.library.caltech.edu/records/6h5mv-2eg62/files/mmi13937-sup-0003-Video2.avi" }, { "basename": "mmi13937-sup-0005-Video4.avi", "url": "https://authors.library.caltech.edu/records/6h5mv-2eg62/files/mmi13937-sup-0005-Video4.avi" }, { "basename": "mmi13937-sup-0006-Video5.avi", "url": "https://authors.library.caltech.edu/records/6h5mv-2eg62/files/mmi13937-sup-0006-Video5.avi" }, { "basename": "mmi13937-sup-0008-Video7.avi", "url": "https://authors.library.caltech.edu/records/6h5mv-2eg62/files/mmi13937-sup-0008-Video7.avi" }, { "basename": "mmi13937-sup-00011-Video10.avi", "url": "https://authors.library.caltech.edu/records/6h5mv-2eg62/files/mmi13937-sup-00011-Video10.avi" }, { "basename": "mmi13937-sup-00013-Video12.avi", "url": "https://authors.library.caltech.edu/records/6h5mv-2eg62/files/mmi13937-sup-00013-Video12.avi" }, { "basename": "mmi13937-sup-0004-Video3.avi", "url": "https://authors.library.caltech.edu/records/6h5mv-2eg62/files/mmi13937-sup-0004-Video3.avi" }, { "basename": "mmi13937-sup-0001-SuppInfo01.docx", "url": "https://authors.library.caltech.edu/records/6h5mv-2eg62/files/mmi13937-sup-0001-SuppInfo01.docx" }, { "basename": "mmi13937-sup-00010-Video9.avi", "url": "https://authors.library.caltech.edu/records/6h5mv-2eg62/files/mmi13937-sup-00010-Video9.avi" }, { "basename": "mmi13937-sup-0002-Video1.avi", "url": "https://authors.library.caltech.edu/records/6h5mv-2eg62/files/mmi13937-sup-0002-Video1.avi" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Krause, Duncan C.; Chen, Songye; et el." }, { "id": "https://authors.library.caltech.edu/records/sd7wb-bpt64", "eprint_id": 85906, "eprint_status": "archive", "datestamp": "2023-08-21 23:11:50", "lastmod": "2023-10-23 15:57:20", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chang-Yi-Wei", "name": { "family": "Chang", "given": "Yi-Wei" }, "orcid": "0000-0003-2391-473X" }, { "id": "Shaffer-Carrie-L", "name": { "family": "Shaffer", "given": "Carrie L." }, "orcid": "0000-0002-7457-7422" }, { "id": "Rettberg-Lee-A", "name": { "family": "Rettberg", "given": "Lee A." } }, { "id": "Ghosal-Debnath", "name": { "family": "Ghosal", "given": "Debnath" }, "orcid": "0000-0002-2227-0330" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "In Vivo Structures of the Helicobacter pylori cag Type IV Secretion System", "ispublished": "pub", "full_text_status": "public", "keywords": "Helicobacter pylori; type IV secretion system; electron cryotomography; cryo-ET; subtomogram averaging; host-pathogen interaction; CagA; gastric cancer; bacterial molecular machines", "note": "\u00a9 2018 The Authors. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). \n\nReceived 16 October 2017, Revised 16 January 2018, Accepted 19 March 2018, Available online 17 April 2018. \n\nWe thank Dr. Tim Cover for providing H. pylori strains and Dr. Joseph Vogel and Dr. Maria Hadjifrangiskou for helpful discussions. This work was supported by NIH grant R01 AI127401 to G.J.J., NIH grant F32 DK105720 to C.L.S., NIH grant T32 A1007474 to C.L.S., and the Burroughs Wellcome Fund 2016 Collaborative Research Travel Grant1016383 to C.L.S. \n\nAuthor Contributions: Y.-W.C., C.L.S., and L.A.R. prepared the samples. Y.-W.C. collected and processed the electron cryotomography data and generated the sub-tomogram averages. All authors analyzed and interpreted the electron cryotomography data. G.J.J. supervised the project. Y.-W.C., C.L.S., and G.J.J. wrote the paper, with input from all authors. \n\nData and Software Availability: The accession numbers for the sub-tomogram averages of cag T4SS machinery that support the findings of this study are EMDB: 7474 (aligned on the periplasmic region) and EMDB: 7475 (aligned on the cytoplasmic region). \n\nThe authors declare no competing interests.\n\nPublished - 1-s2.0-S2211124718304467-main.pdf
Accepted Version - nihms962086.pdf
Submitted - 195685.full.pdf
Supplemental Material - mmc1.pdf
", "abstract": "The type IV secretion system (T4SS) is a versatile nanomachine that translocates diverse effector molecules between microbes and into eukaryotic cells. Here, using electron cryotomography, we reveal the molecular architecture of the Helicobacter pylori cag T4SS. Although most components are unique to H. pylori, the cag T4SS exhibits remarkable architectural similarity to other T4SSs. Our images revealed that, when H. pylori encounters host cells, the bacterium elaborates membranous tubes perforated by lateral ports. Sub-tomogram averaging of the cag T4SS machinery revealed periplasmic densities associated with the outer membrane, a central stalk, and peripheral wing-like densities. Additionally, we resolved pilus-like rod structures extending from the cag T4SS into the inner membrane, as well as densities within the cytoplasmic apparatus corresponding to a short central barrel surrounded by four longer barrels. Collectively, these studies reveal the structure of a dynamic molecular machine that evolved to function in the human gastric niche.", "date": "2018-04-17", "date_type": "published", "publication": "Cell Reports", "volume": "23", "number": "3", "publisher": "Cell Press", "pagerange": "673-681", "id_number": "CaltechAUTHORS:20180417-152641769", "issn": "2211-1247", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180417-152641769", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 AI127401" }, { "agency": "NIH Postdoctoral Fellowship", "grant_number": "F32 DK105720" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32 A1007474" }, { "agency": "Burroughs Wellcome Fund", "grant_number": "1016383" } ] }, "doi": "10.1016/j.celrep.2018.03.085", "pmcid": "PMC5931392", "primary_object": { "basename": "1-s2.0-S2211124718304467-main.pdf", "url": "https://authors.library.caltech.edu/records/sd7wb-bpt64/files/1-s2.0-S2211124718304467-main.pdf" }, "related_objects": [ { "basename": "195685.full.pdf", "url": "https://authors.library.caltech.edu/records/sd7wb-bpt64/files/195685.full.pdf" }, { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/sd7wb-bpt64/files/mmc1.pdf" }, { "basename": "nihms962086.pdf", "url": "https://authors.library.caltech.edu/records/sd7wb-bpt64/files/nihms962086.pdf" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Chang, Yi-Wei; Shaffer, Carrie L.; et el." }, { "id": "https://authors.library.caltech.edu/records/wqa1t-zfc95", "eprint_id": 78333, "eprint_status": "archive", "datestamp": "2023-08-21 23:08:18", "lastmod": "2023-10-23 15:57:12", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Subramanian-Poorna", "name": { "family": "Subramanian", "given": "Poorna" } }, { "id": "Pirbadian-Sahand", "name": { "family": "Pirbadian", "given": "Sahand" } }, { "id": "El-Naggar-Mohamed-Y", "name": { "family": "El-Naggar", "given": "Mohamed Y." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Ultrastructure of Shewanella oneidensis MR-1 nanowires revealed by electron cryotomography", "ispublished": "pub", "full_text_status": "public", "keywords": "extracellular electron transport; electron cryotomography; membrane cytochromes; bacterial nanowires; Shewanella", "note": "\u00a9 2018 National Academy of Sciences. Published under the PNAS license. Edited by E. Peter Greenberg, University of Washington, Seattle, WA, and approved February 21, 2018 (received for review November 6, 2017). We thank Dr. Yi-Wei Chang and Dr. Matthew Swulius for help with preparing Fig. 7 B and C, respectively. We are grateful to Dr. Sean J. Elliott for providing the SAXS model file for MtrA (41) used in Fig. 7B and to Dr. Jeffrey A. Gralnick for providing the cytochrome mutant strain. We thank Dr. Catherine Oikonomou for helping edit the manuscript. P.S. acknowledges support by the Caltech Center for Environmental Microbial Interactions. Work in the laboratory of G.J.J. is supported by the Howard Hughes Medical Institute. The in vivo OM extension imaging platform and mapping of EET proteins are funded by the Air Force Office of Scientific Research Presidential Early Career Award for Scientists and Engineers (FA955014-1-0294, to M.Y.E.-N.). Modeling of ET kinetics and partial support for S.P. are funded by the Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences of the US Department of Energy through Grant DE-FG02-13ER16415 (to M.Y.E.-N.). Author contributions: P.S., S.P., M.Y.E.-N., and G.J.J. designed research; P.S. and S.P. performed research; P.S. and S.P. analyzed data; and P.S., S.P., M.Y.E.-N., and G.J.J. wrote the paper. The authors declare no conflict of interest. This article is a PNAS Direct Submission. This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1718810115/-/DCSupplemental.\n\nPublished - E3246.full.pdf
Submitted - 103242.full.pdf
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Supplemental Material - pnas.201718810SI.pdf
", "abstract": "Bacterial nanowires have garnered recent interest as a proposed extracellular electron transfer (EET) pathway that links the bacterial electron transport chain to solid-phase electron acceptors away from the cell. Recent studies showed that Shewanella oneidensis MR-1 produces outer membrane (OM) and periplasmic extensions that contain EET components and hinted at their possible role as bacterial nanowires. However, their fine structure and distribution of cytochrome electron carriers under native conditions remained unclear, making it difficult to evaluate the potential electron transport (ET) mechanism along OM extensions. Here, we report high-resolution images of S. oneidensis OM extensions, using electron cryotomography (ECT). We developed a robust method for fluorescence light microscopy imaging of OM extension growth on electron microscopy grids and used correlative light and electron microscopy to identify and image the same structures by ECT. Our results reveal that S. oneidensis OM extensions are dynamic chains of interconnected outer membrane vesicles (OMVs) with variable dimensions, curvature, and extent of tubulation. Junction densities that potentially stabilize OMV chains are seen between neighboring vesicles in cryotomograms. By comparing wild type and a cytochrome gene deletion mutant, our ECT results provide the likely positions and packing of periplasmic and outer membrane proteins consistent with cytochromes. Based on the observed cytochrome packing density, we propose a plausible ET path along the OM extensions involving a combination of direct hopping and cytochrome diffusion. A mean-field calculation, informed by the observed ECT cytochrome density, supports this proposal by revealing ET rates on par with a fully packed cytochrome network.", "date": "2018-04-03", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "115", "number": "14", "publisher": "National Academy of Sciences", "pagerange": "E3246-E3255", "id_number": "CaltechAUTHORS:20170619-134442390", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170619-134442390", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Caltech Center for Environmental Microbial Interactions (CEMI)" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Air Force Office of Scientific Research (AFOSR)", "grant_number": "FA955014-1-0294" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02-13ER16415" } ] }, "local_group": { "items": [ { "id": "Caltech-Center-for-Environmental-Microbial-Interactions-(CEMI)" } ] }, "doi": "10.1073/pnas.1718810115", "pmcid": "PMC5889646", "primary_object": { "basename": "pnas.1718810115.sm06.mp4", "url": "https://authors.library.caltech.edu/records/wqa1t-zfc95/files/pnas.1718810115.sm06.mp4" }, "related_objects": [ { "basename": "pnas.1718810115.sm10.mp4", "url": "https://authors.library.caltech.edu/records/wqa1t-zfc95/files/pnas.1718810115.sm10.mp4" }, { "basename": "pnas.1718810115.sm03.mp4", "url": "https://authors.library.caltech.edu/records/wqa1t-zfc95/files/pnas.1718810115.sm03.mp4" }, { "basename": "pnas.1718810115.sm05.mp4", "url": "https://authors.library.caltech.edu/records/wqa1t-zfc95/files/pnas.1718810115.sm05.mp4" }, { "basename": "pnas.1718810115.sm07.mp4", "url": "https://authors.library.caltech.edu/records/wqa1t-zfc95/files/pnas.1718810115.sm07.mp4" }, { "basename": "pnas.1718810115.sm04.mp4", "url": "https://authors.library.caltech.edu/records/wqa1t-zfc95/files/pnas.1718810115.sm04.mp4" }, { "basename": "pnas.1718810115.sm09.mp4", "url": "https://authors.library.caltech.edu/records/wqa1t-zfc95/files/pnas.1718810115.sm09.mp4" }, { "basename": "pnas.1718810115.sm11.mp4", "url": "https://authors.library.caltech.edu/records/wqa1t-zfc95/files/pnas.1718810115.sm11.mp4" }, { "basename": "pnas.201718810SI.pdf", "url": "https://authors.library.caltech.edu/records/wqa1t-zfc95/files/pnas.201718810SI.pdf" }, { "basename": "pnas.1718810115.sm08.mp4", "url": "https://authors.library.caltech.edu/records/wqa1t-zfc95/files/pnas.1718810115.sm08.mp4" }, { "basename": "pnas.1718810115.sm12.mp4", "url": "https://authors.library.caltech.edu/records/wqa1t-zfc95/files/pnas.1718810115.sm12.mp4" }, { "basename": "pnas.1718810115.sm13.mp4", "url": "https://authors.library.caltech.edu/records/wqa1t-zfc95/files/pnas.1718810115.sm13.mp4" }, { "basename": "103242.full.pdf", "url": "https://authors.library.caltech.edu/records/wqa1t-zfc95/files/103242.full.pdf" }, { "basename": "E3246.full.pdf", "url": "https://authors.library.caltech.edu/records/wqa1t-zfc95/files/E3246.full.pdf" }, { "basename": "pnas.1718810115.sm01.mp4", "url": "https://authors.library.caltech.edu/records/wqa1t-zfc95/files/pnas.1718810115.sm01.mp4" }, { "basename": "pnas.1718810115.sm02.mp4", "url": "https://authors.library.caltech.edu/records/wqa1t-zfc95/files/pnas.1718810115.sm02.mp4" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Subramanian, Poorna; Pirbadian, Sahand; et el." }, { "id": "https://authors.library.caltech.edu/records/whqrd-mdx22", "eprint_id": 84419, "eprint_status": "archive", "datestamp": "2023-08-21 22:47:12", "lastmod": "2023-10-23 15:53:31", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Swulius-Matthew-T", "name": { "family": "Swulius", "given": "Matthew T." } }, { "id": "Nguyen-Lam-Thanh", "name": { "family": "Nguyen", "given": "Lam T." }, "orcid": "0000-0002-0756-0911" }, { "id": "Ladinsky-Mark-S", "name": { "family": "Ladinsky", "given": "Mark S." }, "orcid": "0000-0002-1036-3513" }, { "id": "Ortega-Davi-R", "name": { "family": "Ortega", "given": "Davi R." }, "orcid": "0000-0002-8344-2335" }, { "id": "Aich-Samya", "name": { "family": "Aich", "given": "Samya" } }, { "id": "Mishra-Mithilesh", "name": { "family": "Mishra", "given": "Mithilesh" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Structure of the fission yeast actomyosin ring during constriction", "ispublished": "pub", "full_text_status": "public", "keywords": "cell division; cytokinesis; actomyosin ring; cryoEM; FIB mill", "note": "\u00a9 2018 National Academy of Sciences. Published under the PNAS license. \n\nEdited by Thomas D. Pollard, Yale University, New Haven, CT, and approved December 13, 2017 (received for review June 23, 2017). Published online before print January 18, 2018. \n\nWe thank Catherine Oikonomou for revising the manuscript for clarity and Frances Allen for initial training and guidance in cryo-FIB milling. We would also like to thank the reviewers for all of their critical feedback during the refinement of the manuscript. M.M. is an Intermediate Fellow of the Wellcome Trust\u2212Department of Biotechnology India Alliance (IA/I/14/1/501317). M.M. acknowledges the India Alliance and the Department of Atomic Energy/Tata Institute of Fundamental Research for funds. This work was supported in part by National Institutes of Heath Grants GM122588 and GM082545 (to G.J.J.). \n\nAuthor contributions: M.T.S., L.T.N., M.M., and G.J.J. designed research; M.T.S., L.T.N., and M.S.L. performed research; D.R.O. and S.A. contributed new reagents/analytic tools; M.T.S., L.T.N., M.M., and G.J.J. analyzed data; and M.T.S., L.T.N., M.M., and G.J.J. wrote the paper. \n\nThe authors declare no conflict of interest. \n\nThis article is a PNAS Direct Submission. \n\nThis article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1711218115/-/DCSupplemental.\n\nPublished - E1455.full.pdf
Submitted - 194902.full.pdf
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", "abstract": "Cell division in many eukaryotes is driven by a ring containing actin and myosin. While much is known about the main proteins involved, the precise arrangement of actin filaments within the contractile machinery, and how force is transmitted to the membrane, remains unclear. Here we use cryosectioning and cryofocused ion beam milling to gain access to cryopreserved actomyosin rings in Schizosaccharomyces pombe for direct 3D imaging by electron cryotomography. Our results show that straight, overlapping actin filaments, running nearly parallel to each other and to the membrane, form a loose bundle of \u223c150 nm in diameter that \"saddles\" the inward-bending membrane at the leading edge of the division septum. The filaments do not make direct contact with the membrane. Our analysis of the actin filaments reveals the variability in filament number, nearest-neighbor distances between filaments within the bundle, their distance from the membrane, and angular distribution with respect to the membrane.", "date": "2018-02-13", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "115", "number": "7", "publisher": "National Academy of Sciences", "pagerange": "E1455-E1464", "id_number": "CaltechAUTHORS:20180119-110411055", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180119-110411055", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Wellcome Trust\u2212Department of Biotechnology India Alliance", "grant_number": "IA/I/14/1/501317" }, { "agency": "Department of Atomic Energy (India)" }, { "agency": "Tata Institute of Fundamental Research" }, { "agency": "NIH", "grant_number": "GM122588" }, { "agency": "NIH", "grant_number": "GM082545" } ] }, "doi": "10.1073/pnas.1711218115", "pmcid": "PMC5816141", "primary_object": { "basename": "E1455.full.pdf", "url": "https://authors.library.caltech.edu/records/whqrd-mdx22/files/E1455.full.pdf" }, "related_objects": [ { "basename": "pnas.1711218115.sapp.pdf", "url": "https://authors.library.caltech.edu/records/whqrd-mdx22/files/pnas.1711218115.sapp.pdf" }, { "basename": "pnas.1711218115.sm01.mov", "url": "https://authors.library.caltech.edu/records/whqrd-mdx22/files/pnas.1711218115.sm01.mov" }, { "basename": "pnas.1711218115.sm02.mov", "url": "https://authors.library.caltech.edu/records/whqrd-mdx22/files/pnas.1711218115.sm02.mov" }, { "basename": "pnas.1711218115.sm03.mov", "url": "https://authors.library.caltech.edu/records/whqrd-mdx22/files/pnas.1711218115.sm03.mov" }, { "basename": "pnas.1711218115.sm04.mov", "url": "https://authors.library.caltech.edu/records/whqrd-mdx22/files/pnas.1711218115.sm04.mov" }, { "basename": "pnas.201711218SI.pdf", "url": "https://authors.library.caltech.edu/records/whqrd-mdx22/files/pnas.201711218SI.pdf" }, { "basename": "194902.full.pdf", "url": "https://authors.library.caltech.edu/records/whqrd-mdx22/files/194902.full.pdf" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Swulius, Matthew T.; Nguyen, Lam T.; et el." }, { "id": "https://authors.library.caltech.edu/records/7ckth-tjf25", "eprint_id": 86338, "eprint_status": "archive", "datestamp": "2023-08-19 07:43:19", "lastmod": "2023-10-18 19:29:07", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Li-Po-Nan", "name": { "family": "Li", "given": "Po-Nan" }, "orcid": "0000-0002-7917-7444" }, { "id": "Herrmann-J-R", "name": { "family": "Herrmann", "given": "Jonathan R." } }, { "id": "Poitevin-F-P-B", "name": { "family": "Poitevin", "given": "Frederic P. B." } }, { "id": "Ramdasi-R", "name": { "family": "Ramdasi", "given": "Rasika" } }, { "id": "Tolar-B-B", "name": { "family": "Tolar", "given": "Bradley B." }, "orcid": "0000-0003-0493-1470" }, { "id": "Barger-J", "name": { "family": "Barger", "given": "John" } }, { "id": "Stahl-D-A", "name": { "family": "Stahl", "given": "David" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant" }, "orcid": "0000-0003-1556-4864" }, { "id": "Wakatsuki-Soichi", "name": { "family": "Wakatsuki", "given": "Soichi" } }, { "id": "van-den-Bedem-H", "name": { "family": "van den Bedem", "given": "Henry" }, "orcid": "0000-0003-2358-841X" } ] }, "title": "Cryo Electron Tomography and Reaction-Diffusion Simulations Reveal a Molecular and Evolutionary Basis for Charged Archaeal Surface Layer Proteins", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2018 Elsevier Inc. \n\nAvailable online 6 February 2018.", "abstract": "Surface layers (S-layers) are 2D, proteinaceous lattices that form the outermost cell envelope component of many microbes. S-layers, which exhibit exceptional sequence diversity, are found in nearly all archaea and numerous bacteria. Despite their variation, S-layer proteins display several unifying characteristics such as their ability to form crystalline sheets punctuated with nano-scale pores, and their propensity for charged amino acids. However, the precise role of these charged functional groups and how they relate to cellular function is unknown. Here, we offer a rationale for charged S-layer proteins in the context of the structural evolution of S-layers. We have chosen ammonia-oxidizing archaea (AOA) as a model system for S-layer and used the cryo electron tomographic reconstruction of the AOA to develop a 2D electro-diffusion reaction computational framework to simulate diffusion and consumption of the charged solute ammonium. The AOA create energy directly from electrons evolved during ammonia oxidation by ammonia monooxygenase (AMO). While the specific location of the archaeal AMO active site is unknown, a bacterial homologue indicates a location underneath the S-layer in pseudo periplasmic space (PPS). Our simulations suggest that charged S-layers and nanopores expedite diffusion of charged solutes into the PPS when the electro-diffusion-reaction system is driven away from equilibrium, replenishing reacted NH_4^+ in PPS. By contrast, a neutral S-layer would inhibit diffusion of charged molecules, while removing the S-layer altogether dramatically reduced ammonium concentration throughout the PPS. Strikingly, analysis of annotated S-layer amino acid sequences from all known archaeal clades indicated a clear dearth of sequences in the neutral regime. Our simulations suggest that charged S-layers and nanopores impart a potential fitness advantage. Thus, S-layer charge may have emerged by convergent evolution to enhance metabolic function in diverse ecosystems.", "date": "2018-02-02", "date_type": "published", "publication": "Biophysical Journal", "volume": "114", "number": "3", "publisher": "Biophysical Society", "pagerange": "495a", "id_number": "CaltechAUTHORS:20180510-130507276", "issn": "0006-3495", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180510-130507276", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.bpj.2017.11.2710", "resource_type": "article", "pub_year": "2018", "author_list": "Li, Po-Nan; Herrmann, Jonathan R.; et el." }, { "id": "https://authors.library.caltech.edu/records/pf7rb-meq31", "eprint_id": 86329, "eprint_status": "archive", "datestamp": "2023-08-19 07:42:42", "lastmod": "2023-10-18 19:28:29", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Nguyen-Lam-T", "name": { "family": "Nguyen", "given": "Lam T." } }, { "id": "Swulius-M-T", "name": { "family": "Swulius", "given": "Matthew" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Structure and Constriction Mechanism of the Actomyosin Ring", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2018 Elsevier Inc. \n\nAvailable online 6 February 2018.", "abstract": "Cytokinesis is orchestrated by a contractile actomyosin ring, but its structure and mechanism remain elusive. We visualized the 3D structure of the ring in frozen-hydrated dividing yeast cells by electron cryotomography (ECT). Detailed arrangements of actin filaments within the ring and with respect to the membrane were seen for the first time, providing a crucial spatial constraint for the constriction mechanism of the ring. Using the ECT data and input from the literature we then explored sixteen mechanistic models by coarse-grained simulations at the 3D molecular details, revealing plausible mechanisms for preventing membrane distortion and protein aggregation. We found that, in the model that best fits experimental data, both bipolar and membrane-attached unipolar myosins exist in the ring, reconciling two different views in the field regarding the myosin configuration. In this model, ring tension is generated primarily by interactions between bipolar myosins and actin, and transmitted to the membrane via unipolar myosins. This model recapitulates a broad distribution of distances from actin filaments to the membrane observed in our tomograms and separation of two different myosin isoforms into the outer and inner subdomains of the ring reported in a previous fluorescence microscopy study. Further, it rationalizes how bundles of actomyosin were able to separate from the membrane in fluorescence microscopy experiments of the same previous study.", "date": "2018-02-02", "date_type": "published", "publication": "Biophysical Journal", "volume": "114", "number": "3", "publisher": "Biophysical Society", "pagerange": "17A", "id_number": "CaltechAUTHORS:20180510-091232190", "issn": "0006-3495", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180510-091232190", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.bpj.2017.11.135", "resource_type": "article", "pub_year": "2018", "author_list": "Nguyen, Lam T.; Swulius, Matthew; et el." }, { "id": "https://authors.library.caltech.edu/records/057mk-f0112", "eprint_id": 78754, "eprint_status": "archive", "datestamp": "2023-08-23 20:15:33", "lastmod": "2023-10-26 00:21:29", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Carter-Stephen-D", "name": { "family": "Carter", "given": "Stephen D." }, "orcid": "0000-0002-4237-4276" }, { "id": "Mageswaran-Shrawan-K", "name": { "family": "Mageswaran", "given": "Shrawan K." } }, { "id": "Farino-Zachary-J", "name": { "family": "Farino", "given": "Zachary J." } }, { "id": "Mamede-Jo\u00e3o-I", "name": { "family": "Mamede", "given": "Jo\u00e3o I." }, "orcid": "0000-0002-6048-1876" }, { "id": "Oikonomou-C-M", "name": { "family": "Oikonomou", "given": "Catherine M." }, "orcid": "0000-0003-2312-4746" }, { "id": "Hope-Thomas-J", "name": { "family": "Hope", "given": "Thomas J." }, "orcid": "0000-0001-7183-8319" }, { "id": "Freyberg-Zachary", "name": { "family": "Freyberg", "given": "Zachary" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Distinguishing Signal From Autofluorescence In Cryogenic Correlated Light And Electron Microscopy Of Mammalian Cells", "ispublished": "pub", "full_text_status": "public", "keywords": "Cryo-clem; Autofluorescence; Mammalian cells; Electron cryotomography; Fluorescent proteins", "note": "\u00a9 2017 Elsevier Inc. \n\nReceived 12 April 2017, Revised 21 October 2017, Accepted 23 October 2017, Available online 25 October 2017. \n\nThis work was supported by the NIH (grant GM082545 to G.J.J., grant GM082545-6935 to T.J.H., grant K08 DA031241 to Z.F.), the Department of Defense (grant PR141292 to Z.F.), and the John F. and Nancy A. Emmerling Fund of The Pittsburgh Foundation (to Z.F.). We thank Dr. Joachim Frank, Dr. Ma\u00eft\u00e9 Courel, Dr. Hans Breunig, Dr. Estela Area-Gomez, Robert Grassucci and Stephanie Siegmund for guidance, suggestions and reagents. We thank Dr. Pierre Maechler for generously providing INS-1E cells for our studies. We would like to thank Steven Wilbert for technical assistance. Confocal imaging was performed in the Biological Imaging Facility, with the support of the Caltech Beckman Institute and the Arnold and Mabel Beckman Foundation.\n\nAccepted Version - nihms928141.pdf
Submitted - 120642.full.pdf
Supplemental Material - 1-s2.0-S1047847717301776-mmc1.docx
", "abstract": "In cryogenic correlated light and electron microscopy (cryo-CLEM), frozen targets of interest are identified and located on EM grids by fluorescence microscopy and then imaged at higher resolution by cryo-EM. Whilst working with these methods, we discovered that a variety of mammalian cells exhibit strong punctate autofluorescence when imaged under cryogenic conditions (80K). Autofluorescence originated from multilamellar bodies (MLBs) and secretory granules. Here we describe a method to distinguish fluorescent protein tags from these autofluorescent sources based on the narrower emission spectrum of the former. The method is first tested on mitochondria and then applied to examine the ultrastructural variability of secretory granules within insulin-secreting pancreatic beta-cell-derived INS-1E cells.", "date": "2018-01", "date_type": "published", "publication": "Journal of Structural Biology", "volume": "201", "number": "1", "publisher": "Elsevier", "pagerange": "15-25", "id_number": "CaltechAUTHORS:20170705-091308246", "issn": "1047-8477", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170705-091308246", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM082545" }, { "agency": "NIH", "grant_number": "GM082545-6935" }, { "agency": "NIH", "grant_number": "K08 DA031241" }, { "agency": "Department of Defense", "grant_number": "PR141292" }, { "agency": "Pittsburgh Foundation" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Arnold and Mabel Beckman Foundation" } ] }, "doi": "10.1016/j.jsb.2017.10.009", "pmcid": "PMC5771259", "primary_object": { "basename": "1-s2.0-S1047847717301776-mmc1.docx", "url": "https://authors.library.caltech.edu/records/057mk-f0112/files/1-s2.0-S1047847717301776-mmc1.docx" }, "related_objects": [ { "basename": "120642.full.pdf", "url": "https://authors.library.caltech.edu/records/057mk-f0112/files/120642.full.pdf" }, { "basename": "nihms928141.pdf", "url": "https://authors.library.caltech.edu/records/057mk-f0112/files/nihms928141.pdf" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Carter, Stephen D.; Mageswaran, Shrawan K.; et el." }, { "id": "https://authors.library.caltech.edu/records/8xdh0-jbj27", "eprint_id": 85408, "eprint_status": "archive", "datestamp": "2023-08-19 06:55:01", "lastmod": "2023-10-18 18:11:41", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Nguyen-Lam-T", "name": { "family": "Nguyen", "given": "L. T." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "G. J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Structure and constriction mechanism of the actomyosin ring", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2017 American Society for Cell Biology. Free via Creative Commons 2 months after publication.\n\nPublished - Nguyen_2017pM175.pdf
", "abstract": "Cytokinesis is orchestrated by a contractile actomyosin ring, but its structure and mechanism remain elusive. We visualized the 3D structure of the ring in frozen\u2010hydrated dividing yeast cells by electron cryotomography (ECT). Detailed arrangements of actin filaments within the ring and with respect to the membrane were seen for the first time, providing a crucial spatial constraint for the constriction mechanism of the ring. Using the ECT data and input from the current literature we then explored\nsixteen mechanistic models by coarse\u2010grained simulations at the 3D molecular details, revealing plausible mechanisms for preventing membrane distortion and protein aggregation. We found that, in the model that best fits experimental data, both bipolar and membrane\u2010attached unipolar myosins exist in the ring, reconciling two different views in the field regarding the myosin configuration. In this model,\nring tension is generated primarily by interactions between bipolar myosins and actin, and transmitted to the membrane via unipolar myosins. This model recapitulates a broad distribution of distances from actin filaments to the membrane observed in our tomograms and separation of two different myosin isoforms into the outer and inner subdomains of the ring reported in a previous fluorescence\nmicroscopy study. Further, it rationalizes how bundles of actomyosin were able to separate from the membrane in fluorescence microscopy experiments of the same previous study.", "date": "2017-12-15", "date_type": "published", "publication": "Molecular Biology of the Cell", "volume": "28", "number": "26", "publisher": "American Society for Cell Biology", "pagerange": "Art. No. M175", "id_number": "CaltechAUTHORS:20180321-152351149", "issn": "1059-1524", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180321-152351149", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1091/mbc.E17-10-0618", "primary_object": { "basename": "Nguyen_2017pM175.pdf", "url": "https://authors.library.caltech.edu/records/8xdh0-jbj27/files/Nguyen_2017pM175.pdf" }, "resource_type": "article", "pub_year": "2017", "author_list": "Nguyen, L. T. and Jensen, G. J." }, { "id": "https://authors.library.caltech.edu/records/bnyd5-6jk12", "eprint_id": 85410, "eprint_status": "archive", "datestamp": "2023-08-19 06:55:10", "lastmod": "2023-10-18 18:12:05", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Tran-N-T", "name": { "family": "Tran", "given": "N. T." } }, { "id": "Carter-Stephen-D", "name": { "family": "Carter", "given": "S. D." }, "orcid": "0000-0002-4237-4276" }, { "id": "Belyy-V", "name": { "family": "Belyy", "given": "V." } }, { "id": "Acosta-Alvear-D", "name": { "family": "Acosta-Alvear", "given": "D." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "G. J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Walter-Peter", "name": { "family": "Walter", "given": "P." } } ] }, "title": "The activated endoplasmic reticulum stress sensor IRE1 oligomerizes into filaments contained in 30 nm membrane tubes of complex topology", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2017 American Society for Cell Biology. Free via Creative Commons 2 months after publication.\n\nPublished - Tran_2017pP2562.pdf
", "abstract": "The unfolded protein response (UPR) is an intracellular signaling network that adjusts the abundance and protein folding capacity of the endoplasmic reticulum (ER) according to need. The most conversed branch of the UPR is mediated by the ER\u2010resident transmembrane kinase/endoribonuclease IRE1. It senses unfolded protein accumulation within the ER and transduces the signal via a non\u2010conventional mRNA splicing mechanism. In response to direct binding of unfolded proteins in the ER lumen, IRE1\nactivates by oligomerization and accumulates in dynamic foci. IRE1 foci are not autophagosomes as they did not colocalize with the autophagosomal marker LC3. Fluorescence recovery after photobleaching (FRAP) experiments indicate that IRE1 molecules in the foci remain in equilibrium with\nIRE1 molecules in the surrounding ER network. We determined the structure of IRE1 foci in cells by whole cell correlative light \u2013 electron tomography. Our results show that IRE1 oligomers induce membrane deformations, leading to the protrusion of narrow 30 nm ribosome\u2010free tubes that remain connected to the ER and are twisted into glomeruli of complex topology. The tubes contain two parallel\nfilaments in their lumen, likely representing oligomerized IRE1 ER\u2010lumenal domains. Taken together, our findings define a previously unrecognized subdomain of the ER membrane and shed new light on the structure and organization of active mammalian IRE1 inside the cell.", "date": "2017-12-15", "date_type": "published", "publication": "Molecular Biology of the Cell", "volume": "28", "number": "26", "publisher": "American Society for Cell Biology", "pagerange": "Art. No. P2562", "id_number": "CaltechAUTHORS:20180321-153609538", "issn": "1059-1524", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180321-153609538", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1091/mbc.E17-10-0618", "primary_object": { "basename": "Tran_2017pP2562.pdf", "url": "https://authors.library.caltech.edu/records/bnyd5-6jk12/files/Tran_2017pP2562.pdf" }, "resource_type": "article", "pub_year": "2017", "author_list": "Tran, N. T.; Carter, S. D.; et el." }, { "id": "https://authors.library.caltech.edu/records/k6y68-dw109", "eprint_id": 82569, "eprint_status": "archive", "datestamp": "2023-08-19 06:15:07", "lastmod": "2023-10-17 22:31:43", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Qin-Wei", "name": { "family": "Qin", "given": "Wei" } }, { "id": "Heal-K-R", "name": { "family": "Heal", "given": "Katherine R." } }, { "id": "Ramdasi-R", "name": { "family": "Ramdasi", "given": "Rasika" } }, { "id": "Kobelt-J-N", "name": { "family": "Kobelt", "given": "Julia N." } }, { "id": "Martens-Habbena-W", "name": { "family": "Martens-Habbena", "given": "Willm" } }, { "id": "Bertagnolli-A-D", "name": { "family": "Bertagnolli", "given": "Anthony D." } }, { "id": "Amin-S-A", "name": { "family": "Amin", "given": "Shady A." } }, { "id": "Walker-C-B", "name": { "family": "Walker", "given": "Christopher B." } }, { "id": "Urakawa-Hidetoshi", "name": { "family": "Urakawa", "given": "Hidetoshi" } }, { "id": "K\u00f6nneke-M", "name": { "family": "K\u00f6nneke", "given": "Martin" } }, { "id": "Devol-A-H", "name": { "family": "Devol", "given": "Allan H." } }, { "id": "Moffett-J-W", "name": { "family": "Moffett", "given": "James W." } }, { "id": "Armbrust-E-V", "name": { "family": "Armbrust", "given": "E. Virginia" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Ingalls-A-E", "name": { "family": "Ingalls", "given": "Anitra E." } }, { "id": "Stahl-D-A", "name": { "family": "Stahl", "given": "David A." } } ] }, "title": "Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota", "ispublished": "pub", "full_text_status": "public", "keywords": "Vitamin B12, nitrification, Nitrosopumilales, Nitrosopumilaceae, Nitrosopumilus, Thaumarchaeota", "note": "\u00a9 2017 IUMS. Published by the Microbiology Society. \n\nReceived: 18/10/2016 Accepted: 03/10/2017 Cover date: 16/10/2017. \n\nWe thank B. Schneider and the FHCRC EM staff for performing transmission electron microscopy, and the Captain and crew of the R/V Clifford A. Barnes for their assistance with sample collection. We thank Adam Gee, Emily Chang, Yue Zheng, Jessie Zhou, Dr Robert Morris, and Vega Shah for technical assistance and Andrea Teichgr\u00e4ber and Kelley Meinhardt for helpful discussions. Finally, we thank the editor, Dr Aharon Oren, for particularly helpful comments and suggestions. \n\nThis work was funded by the United States National Science Foundation grants MCB-0604448 (to D. A. S.) and Dimensions of Biodiversity Program OCE-1046017 (to D. A. S., A. E. I., E. V. A., A. H. D., J. W. M.). \n\nThe authors declare that there are no conflicts of interest.\n\nSupplemental Material - 002416_1.pdf
", "abstract": "Four mesophilic, neutrophilic, and aerobic marine ammonia-oxidizing archaea, designated strains SCM1^T, HCA1^T, HCE1^T and PS0^T, were isolated from a tropical marine fish tank, dimly lit deep coastal waters, the lower euphotic zone of coastal waters, and near-surface sediment in the Puget Sound estuary, respectively. Cells are straight or slightly curved small rods, 0.15\u20130.26\u2009\u00b5m in diameter and 0.50\u20131.59\u2009\u00b5m in length. Motility was not observed, although strain PS0^T possesses genes associated with archaeal flagella and chemotaxis, suggesting it may be motile under some conditions. Cell membranes consist of glycerol dibiphytanyl glycerol tetraether (GDGT) lipids, with crenarchaeol as the major component. Strain SCM1^T displays a single surface layer (S-layer) with p6 symmetry, distinct from the p3-S-layer reported for the soil ammonia-oxidizing archaeon Nitrososphaera viennensis EN76^T. Respiratory quinones consist of fully saturated and monounsaturated menaquinones with 6 isoprenoid units in the side chain. Cells obtain energy from ammonia oxidation and use carbon dioxide as carbon source; addition of an \u03b1-keto acid (\u03b1-ketoglutaric acid) was necessary to sustain growth of strains HCA1^T, HCE1^T, and PS0^T. Strain PS0^T uses urea as a source of ammonia for energy production and growth. All strains synthesize vitamin B_1 (thiamine), B_2 (riboflavin), B_6 (pyridoxine), and B_(12) (cobalamin). Optimal growth occurs between 25 and 32\u2009\u00b0C, between pH 6.8 and 7.3, and between 25 and 37\u2009\u2030 salinity. All strains have a low mol% G+C\u2009content of 33.0\u201334.2. Strains are related by 98\u200a% or greater 16S rRNA gene sequence identity, sharing ~85\u200a% 16S rRNA gene sequence identity with Nitrososphaera viennensis EN76^T. All four isolates are well separated by phenotypic and genotypic characteristics and are here assigned to distinct species within the genus Nitrosopumilus gen. nov. Isolates SCM1^T (=ATCC TSD-97^T =NCIMB 15022^T), HCA1^T (=ATCC TSD-96^T), HCE1^T(=ATCC TSD-98^T), and PS0^T (=ATCC TSD-99^T) are type strains of the species Nitrosopumilus maritimus sp. nov., Nitrosopumilus cobalaminigenessp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., respectively. In addition, we propose the family Nitrosopumilaceae fam. nov. and the order Nitrosopumilales ord. nov. within the class Nitrososphaeria.", "date": "2017-12", "date_type": "published", "publication": "International Journal of Systematic and Evolutionary Microbiology", "volume": "67", "number": "12", "publisher": "International Union of Microbiological Societies", "pagerange": "5067-5079", "id_number": "CaltechAUTHORS:20171023-084958349", "issn": "1466-5026", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171023-084958349", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "MCB-0604448" }, { "agency": "NSF", "grant_number": "OCE-1046017" } ] }, "doi": "10.1099/ijsem.0.002416", "primary_object": { "basename": "002416_1.pdf", "url": "https://authors.library.caltech.edu/records/k6y68-dw109/files/002416_1.pdf" }, "resource_type": "article", "pub_year": "2017", "author_list": "Qin, Wei; Heal, Katherine R.; et el." }, { "id": "https://authors.library.caltech.edu/records/02hms-65h71", "eprint_id": 83456, "eprint_status": "archive", "datestamp": "2023-08-19 06:18:31", "lastmod": "2023-10-17 23:08:28", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Oikonomou-C-M", "name": { "family": "Oikonomou", "given": "Catherine M." }, "orcid": "0000-0003-2312-4746" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "The development of cryo-EM and how it has advanced microbiology", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2017 Macmillan Publishers Limited, part of Springer Nature. \n\nPublished online:24 November 2017. \n\nThe authors declare no competing financial interests.", "abstract": "The 2017 Nobel Prize in Chemistry was awarded to Jacques Dubochet, Richard Henderson and Joachim Frank for the development of cryo-electron microscopy, a technique for high-resolution structural determination of biomolecules in solution that has provided unprecedented insight into the biology of microorganisms.", "date": "2017-12", "date_type": "published", "publication": "Nature Microbiology", "volume": "2", "number": "12", "publisher": "Nature Publishing Group", "pagerange": "1577-1579", "id_number": "CaltechAUTHORS:20171127-142132034", "issn": "2058-5276", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171127-142132034", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1038/s41564-017-0073-7", "resource_type": "article", "pub_year": "2017", "author_list": "Oikonomou, Catherine M. and Jensen, Grant J." }, { "id": "https://authors.library.caltech.edu/records/hfef4-hcz55", "eprint_id": 83185, "eprint_status": "archive", "datestamp": "2023-08-21 22:15:40", "lastmod": "2023-10-17 22:58:04", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ortega-Davi-R", "name": { "family": "Ortega", "given": "Davi R." }, "orcid": "0000-0002-8344-2335" }, { "id": "Fleetwood-Aaron-D", "name": { "family": "Fleetwood", "given": "Aaron D." } }, { "id": "Krell-Tino", "name": { "family": "Krell", "given": "Tino" } }, { "id": "Harwood-Caroline-S", "name": { "family": "Harwood", "given": "Caroline S." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Zhulin-Igor-B", "name": { "family": "Zhulin", "given": "Igor B." }, "orcid": "0000-0002-6708-5323" } ] }, "title": "Assigning chemoreceptors to chemosensory pathways in Pseudomonas aeruginosa", "ispublished": "pub", "full_text_status": "public", "keywords": "signal transduction; protein\u2013protein interactions; chemotaxis; computational prediction", "note": "\u00a9 2017 National Academy of Sciences. \n\nEdited by Eugene V. Koonin, National Institutes of Health, Bethesda, MD, and approved October 26, 2017 (received for review May 27, 2017). Published online before print November 13, 2017. \n\nWe thank Jacob Pollack for technical assistance and Ariane Briegel for helpful discussions. This work was supported in part by National Institutes of Health Grants GM072295 (to I.B.Z.) and GM122588 (to G.J.J.). \n\nD.R.O. and A.D.F. contributed equally to this work. \n\nAuthor contributions: D.R.O., A.D.F., and I.B.Z. designed research; D.R.O. and A.D.F. performed research; D.R.O. contributed new reagents/analytic tools; D.R.O., A.D.F., T.K., C.S.H., G.J.J., and I.B.Z. analyzed data; and D.R.O., A.D.F., T.K., C.S.H., G.J.J., and I.B.Z. wrote the paper. \n\nThe authors declare no conflict of interest. \n\nThis article is a PNAS Direct Submission. \n\nThis article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1708842114/-/DCSupplemental. \n\nPublished under the PNAS license.\n\nPublished - PNAS-2017-Ortega-12809-14.pdf
Supplemental Material - pnas.1708842114.sd01.pdf
Supplemental Material - pnas.1708842114.sd02.pdf
Supplemental Material - pnas.1708842114.sd03.pdf
Supplemental Material - pnas.1708842114.sd04.pdf
Supplemental Material - pnas.201708842SI.pdf
", "abstract": "In contrast to Escherichia coli, a model organism for chemotaxis that has 5 chemoreceptors and a single chemosensory pathway, Pseudomonas aeruginosa PAO1 has a much more complex chemosensory network, which consists of 26 chemoreceptors feeding into four chemosensory pathways. While several chemoreceptors were rigorously linked to specific pathways in a series of experimental studies, for most of them this information is not available. Thus, we addressed the problem computationally. Protein\u2013protein interaction network prediction, coexpression data mining, and phylogenetic profiling all produced incomplete and uncertain assignments of chemoreceptors to pathways. However, comparative sequence analysis specifically targeting chemoreceptor regions involved in pathway interactions revealed conserved sequence patterns that enabled us to unambiguously link all 26 chemoreceptors to four pathways. Placing computational evidence in the context of experimental data allowed us to conclude that three chemosensory pathways in P. aeruginosa utilize one chemoreceptor per pathway, whereas the fourth pathway, which is the main system controlling chemotaxis, utilizes the other 23 chemoreceptors. Our results show that while only a very few amino acid positions in receptors, kinases, and adaptors determine their pathway specificity, assigning receptors to pathways computationally is possible. This requires substantial knowledge about interacting partners on a molecular level and focusing comparative sequence analysis on the pathway-specific regions. This general principle should be applicable to resolving many other receptor\u2013pathway interactions.", "date": "2017-11-28", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "114", "number": "48", "publisher": "National Academy of Sciences", "pagerange": "12809-12814", "id_number": "CaltechAUTHORS:20171114-080129120", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171114-080129120", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM072295" }, { "agency": "NIH", "grant_number": "GM122588" } ] }, "doi": "10.1073/pnas.1708842114", "pmcid": "PMC5715753", "primary_object": { "basename": "PNAS-2017-Ortega-12809-14.pdf", "url": "https://authors.library.caltech.edu/records/hfef4-hcz55/files/PNAS-2017-Ortega-12809-14.pdf" }, "related_objects": [ { "basename": "pnas.1708842114.sd01.pdf", "url": "https://authors.library.caltech.edu/records/hfef4-hcz55/files/pnas.1708842114.sd01.pdf" }, { "basename": "pnas.1708842114.sd02.pdf", "url": "https://authors.library.caltech.edu/records/hfef4-hcz55/files/pnas.1708842114.sd02.pdf" }, { "basename": "pnas.1708842114.sd03.pdf", "url": "https://authors.library.caltech.edu/records/hfef4-hcz55/files/pnas.1708842114.sd03.pdf" }, { "basename": "pnas.1708842114.sd04.pdf", "url": "https://authors.library.caltech.edu/records/hfef4-hcz55/files/pnas.1708842114.sd04.pdf" }, { "basename": "pnas.201708842SI.pdf", "url": "https://authors.library.caltech.edu/records/hfef4-hcz55/files/pnas.201708842SI.pdf" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Ortega, Davi R.; Fleetwood, Aaron D.; et el." }, { "id": "https://authors.library.caltech.edu/records/qchpe-k7552", "eprint_id": 80816, "eprint_status": "archive", "datestamp": "2023-08-21 22:04:22", "lastmod": "2023-10-17 18:30:47", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zieli\u0144ska-Aleksandra", "name": { "family": "Zieli\u0144ska", "given": "Aleksandra" } }, { "id": "Billini-Maria", "name": { "family": "Billini", "given": "Maria" } }, { "id": "M\u00f6ll-Andrea", "name": { "family": "M\u00f6ll", "given": "Andrea" } }, { "id": "Kremer-Katharina", "name": { "family": "Kremer", "given": "Katharina" } }, { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Martinez-Adrian-Izquierdo", "name": { "family": "Martinez", "given": "Adrian Izquierdo" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Thanbichler-Martin", "name": { "family": "Thanbichler", "given": "Martin" }, "orcid": "0000-0002-1303-1442" } ] }, "title": "LytM factors affect the recruitment of autolysins to the cell division site in Caulobacter crescentus", "ispublished": "pub", "full_text_status": "public", "keywords": "Peptidoglycan hydrolases; SdpA; SdpB; AmiC; EnvC; NlpD; FtsEX", "note": "\u00a9 2017 John Wiley & Sons Ltd. \n\nIssue online: 23 October 2017; Version of record online: 14 September 2017; Accepted manuscript online: 23 August 2017; Manuscript Accepted: 18 August 2017. \n\nWe thank Stephanie Steede and Julia Rosum for excellent technical assistance, Patrick Viollier for providing plasmids and Erin Goley for sharing data on C. crescentus FtsEX before publication. Moreover, we are grateful to Daniela Kiekebusch and Muriel van Teeseling for critical reading of the manuscript. This work was funded by core support from Philipps-Universit\u00e4t Marburg (to MT), a Max Planck Fellowship from the Max Planck Society (to MT) and funds from the Howard Hughes Medical Institute (to GJJ). AIM acknowledges funding from the International Max Planck Research School for Environmental, Cellular and Molecular Microbiology (IMPRS-Mic). The authors have no conflicts of interest related to this work. \n\nAuthor contributions: MB, AZ, AM and KK performed all genetic and cell biological analyses. AIM contributed to the phenotypic characterization of mutant strains. AB and GJJ conducted the electron cryo-tomography studies. AZ, AM and MT designed the study. AM, MB and MT wrote the manuscript.\n\nSupplemental Material - mmi13775-sup-0001-SuppInfo01.pdf
", "abstract": "Most bacteria possess a peptidoglycan cell wall that determines their morphology and provides mechanical robustness during osmotic challenges. The biosynthesis of this structure is achieved by a large set of synthetic and lytic enzymes with varying substrate specificities. Although the biochemical functions of these proteins are conserved and well-investigated, the precise roles of individual factors and the regulatory mechanisms coordinating their activities in time and space remain incompletely understood. Here, we comprehensively analyze the autolytic machinery of the alphaproteobacterial model organism Caulobacter crescentus, with a specific focus on LytM-like endopeptidases, soluble lytic transglycosylases and amidases. Our data reveal a high degree of redundancy within each protein family but also specialized functions for individual family members under stress conditions. In addition, we identify two lytic transglycosylases and an amidase as new divisome components that are recruited to midcell at distinct stages of the cell cycle. The midcell localization of these proteins is affected by two LytM factors with degenerate catalytic domains, DipM and LdpF, which may serve as regulatory hubs coordinating the activities of multiple autolytic enzymes during cell constriction and fission respectively. These findings set the stage for in-depth studies of the molecular mechanisms that control peptidoglycan remodeling in C. crescentus.", "date": "2017-11", "date_type": "published", "publication": "Molecular Microbiology", "volume": "106", "number": "3", "publisher": "Wiley", "pagerange": "419-438", "id_number": "CaltechAUTHORS:20170825-154246193", "issn": "0950-382X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170825-154246193", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Philipps-Universit\u00e4t Marburg" }, { "agency": "Max Planck Society" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "International Max Planck Research School for Environmental, Cellular and Molecular Microbiology" } ] }, "doi": "10.1111/mmi.13775", "primary_object": { "basename": "mmi13775-sup-0001-SuppInfo01.pdf", "url": "https://authors.library.caltech.edu/records/qchpe-k7552/files/mmi13775-sup-0001-SuppInfo01.pdf" }, "resource_type": "article", "pub_year": "2017", "author_list": "Zieli\u0144ska, Aleksandra; Billini, Maria; et el." }, { "id": "https://authors.library.caltech.edu/records/etmd9-76c07", "eprint_id": 79304, "eprint_status": "archive", "datestamp": "2023-08-21 21:45:15", "lastmod": "2023-10-26 14:47:27", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kaplan-Mohammed", "name": { "family": "Kaplan", "given": "Mohammed" }, "orcid": "0000-0002-0759-0459" }, { "id": "Yoo-Byung-Kuk", "name": { "family": "Yoo", "given": "Byung-Kuk" }, "orcid": "0000-0002-2610-6685" }, { "id": "Tang-Jau", "name": { "family": "Tang", "given": "Jau" }, "orcid": "0000-0003-2078-1513" }, { "id": "Karam-T-E", "name": { "family": "Karam", "given": "Tony E." }, "orcid": "0000-0002-1244-5141" }, { "id": "Liao-Bolin", "name": { "family": "Liao", "given": "Bolin" }, "orcid": "0000-0002-0898-0803" }, { "id": "Majumdar-Devdoot-S", "name": { "family": "Majumdar", "given": "Devdoot" } }, { "id": "Baltimore-D", "name": { "family": "Baltimore", "given": "David" }, "orcid": "0000-0001-8723-8190" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Zewail-A-H", "name": { "family": "Zewail", "given": "Ahmed H." } } ] }, "title": "Photon-induced near-field electron microscopy (PINEM) of eukaryotic cells", "ispublished": "pub", "full_text_status": "public", "keywords": "electron microscopy; electron\u2013photon coupling; eukaryotic cells; femtobiology; PINEM", "note": "\u00a9 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim. \n\nManuscript received: June 15, 2017; Accepted manuscript online: July 23, 2017; Version of record online: August 10, 2017. \n\nWe thank Spencer Baskin and Mohammed Hassan for helpful discussions. This work was supported by the National Science Foundation Grant DMR-0964886 and the Air Force Office of Scientific Research Grant FA9550-11-1-0055 for research conducted in The Gordon and Betty Moore Center for Physical Biology at the California Institute of Technology. \n\nThe authors declare no conflict of interest.\n\nAccepted Version - 6333722ae81a4c71d4abe7c0cc6ac72953025b6e6d80b258cf357af7b8415fa0.pdf
Supplemental Material - anie201706120-sup-0001-SI1.pdf
", "abstract": "Photon-induced near-field electron microscopy (PINEM) is a technique to produce and then image evanescent electromagnetic fields on the surfaces of nanostructures. Most previous applications of PINEM have imaged surface plasmon-polariton waves on conducting nanomaterials. Here, the application of PINEM on whole human cancer cells and membrane vesicles isolated from them is reported. We show that photons induce time-, orientation-, and polarization-dependent evanescent fields on the surfaces of A431 cancer cells and isolated membrane vesicles. Furthermore, the addition of a ligand to the major surface receptor on these cells and vesicles (Epidermal Growth Factor Receptor, EGFR) reduces the intensity of these fields in both preparations. In the absence of plasmon waves in biological samples, we propose these evanescent fields reflect the changes of EGFR kinase domain polarization upon ligand binding.", "date": "2017-09-11", "date_type": "published", "publication": "Angewandte Chemie International Edition", "volume": "56", "number": "38", "publisher": "Wiley", "pagerange": "11498-11501", "id_number": "CaltechAUTHORS:20170724-124156529", "issn": "1433-7851", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170724-124156529", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "DMR-0964886" }, { "agency": "Air Force Office of Scientific Research (AFOSR)", "grant_number": "FA9550-11-1-0055" }, { "agency": "Gordon and Betty Moore Foundation" } ] }, "doi": "10.1002/anie.201706120", "primary_object": { "basename": "6333722ae81a4c71d4abe7c0cc6ac72953025b6e6d80b258cf357af7b8415fa0.pdf", "url": "https://authors.library.caltech.edu/records/etmd9-76c07/files/6333722ae81a4c71d4abe7c0cc6ac72953025b6e6d80b258cf357af7b8415fa0.pdf" }, "related_objects": [ { "basename": "anie201706120-sup-0001-SI1.pdf", "url": "https://authors.library.caltech.edu/records/etmd9-76c07/files/anie201706120-sup-0001-SI1.pdf" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Kaplan, Mohammed; Yoo, Byung-Kuk; et el." }, { "id": "https://authors.library.caltech.edu/records/mjywm-x0q09", "eprint_id": 81518, "eprint_status": "archive", "datestamp": "2023-08-19 05:04:05", "lastmod": "2023-10-23 15:06:30", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Meier-E-L", "name": { "family": "Meier", "given": "Elizabeth L." } }, { "id": "Daitch-A-K", "name": { "family": "Daitch", "given": "Allison K." } }, { "id": "Yao-Qing", "name": { "family": "Yao", "given": "Qing" }, "orcid": "0000-0003-3575-9909" }, { "id": "Bhargava-A", "name": { "family": "Bhargava", "given": "Anant" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Goley-E-D", "name": { "family": "Goley", "given": "Erin D." } } ] }, "title": "FtsEX-mediated regulation of the final stages of cell division reveals morphogenetic plasticity in Caulobacter crescentus", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2017 Meier et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived: April 5, 2017; Accepted: August 25, 2017; Published: September 8, 2017. \n\n\nData Availability Statement: All relevant data are within the paper and its Supporting Information files. \n\nThis work was supported in part by the National Institute of General Medical Sciences through grant numbers R35 GM122588 (GJJ) and R01 GM108640 (EDG). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. \n\nThe authors have declared that no competing interests exist. \n\nWe thank Jasmine Burrell for her work characterizing stalk protein localization in \u0394ftsE; Martin Thanbichler for sharing plasmids, strains and preliminary LdpF data; Yves Brun, Erkin Kuru, and Michael van Nieuwehnze for HADA; Kousik Sundararajan for assistance with TEM; Yves Brun and Ellen Quardokus for assistance with TEM and for sharing the StpX-CFP plasmid; and Zhuo Li for providing the wild-type stalks images in S3 Fig. \n\nAuthor Contributions: \nConceptualization: Elizabeth L. Meier, Erin D. Goley.\nFormal analysis: Elizabeth L. Meier, Allison K. Daitch, Qing Yao, Anant Bhargava, Erin D. Goley.\nFunding acquisition: Grant J. Jensen, Erin D. Goley.\nInvestigation: Elizabeth L. Meier, Allison K. Daitch, Qing Yao, Erin D. Goley.\nMethodology: Elizabeth L. Meier, Allison K. Daitch, Qing Yao, Anant Bhargava.\nSupervision: Grant J. Jensen, Erin D. Goley.\nWriting \u00b1 original draft: Elizabeth L. Meier.\nWriting \u00b1 review & editing: Elizabeth L. Meier, Allison K. Daitch, Qing Yao, Anant Bhargava,\nGrant J. Jensen, Erin D. Goley.\n\nPublished - pgen.1006999.pdf
Accepted Version - journal.pgen.1006999.pdf
Submitted - 124214.full.pdf
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Supplemental Material - journal.pgen.1006999.s003.tif
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Supplemental Material - journal.pgen.1006999.s007.tif
Supplemental Material - journal.pgen.1006999.s008.tif
Supplemental Material - journal.pgen.1006999.s009.docx
Supplemental Material - journal.pgen.1006999.s010.xlsx
", "abstract": "During its life cycle, Caulobacter crescentus undergoes a series of coordinated shape changes, including generation of a polar stalk and reshaping of the cell envelope to produce new daughter cells through the process of cytokinesis. The mechanisms by which these morphogenetic processes are coordinated in time and space remain largely unknown. Here we demonstrate that the conserved division complex FtsEX controls both the early and late stages of cytokinesis in C. crescentus, namely initiation of constriction and final cell separation. \u0394ftsE cells display a striking phenotype: cells are chained, with skinny connections between cell bodies resulting from defects in inner membrane fusion and cell separation. Surprisingly, the thin connections in \u0394ftsE cells share morphological and molecular features with C. crescentus stalks. Our data uncover unanticipated morphogenetic plasticity in C. crescentus, with loss of FtsE causing a stalk-like program to take over at failed division sites.", "date": "2017-09-08", "date_type": "published", "publication": "PLOS Genetics", "volume": "13", "number": "9", "publisher": "Public Library of Science", "pagerange": "Art. No. e1006999", "id_number": "CaltechAUTHORS:20170918-095203888", "issn": "1553-7404", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170918-095203888", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R35 GM122588" }, { "agency": "NIH", "grant_number": "R01 GM108640" } ] }, "doi": "10.1371/journal.pgen.1006999", "pmcid": "PMC5607218", "primary_object": { "basename": "124214.full.pdf", "url": "https://authors.library.caltech.edu/records/mjywm-x0q09/files/124214.full.pdf" }, "related_objects": [ { "basename": "journal.pgen.1006999.pdf", "url": "https://authors.library.caltech.edu/records/mjywm-x0q09/files/journal.pgen.1006999.pdf" }, { "basename": "journal.pgen.1006999.s001.tif", "url": "https://authors.library.caltech.edu/records/mjywm-x0q09/files/journal.pgen.1006999.s001.tif" }, { "basename": "journal.pgen.1006999.s002.tif", "url": "https://authors.library.caltech.edu/records/mjywm-x0q09/files/journal.pgen.1006999.s002.tif" }, { "basename": "journal.pgen.1006999.s010.xlsx", "url": "https://authors.library.caltech.edu/records/mjywm-x0q09/files/journal.pgen.1006999.s010.xlsx" }, { "basename": "pgen.1006999.pdf", "url": "https://authors.library.caltech.edu/records/mjywm-x0q09/files/pgen.1006999.pdf" }, { "basename": "journal.pgen.1006999.s006.tif", "url": "https://authors.library.caltech.edu/records/mjywm-x0q09/files/journal.pgen.1006999.s006.tif" }, { "basename": "journal.pgen.1006999.s003.tif", "url": "https://authors.library.caltech.edu/records/mjywm-x0q09/files/journal.pgen.1006999.s003.tif" }, { "basename": "journal.pgen.1006999.s007.tif", "url": "https://authors.library.caltech.edu/records/mjywm-x0q09/files/journal.pgen.1006999.s007.tif" }, { "basename": "journal.pgen.1006999.s004.tif", "url": "https://authors.library.caltech.edu/records/mjywm-x0q09/files/journal.pgen.1006999.s004.tif" }, { "basename": "journal.pgen.1006999.s005.tif", "url": "https://authors.library.caltech.edu/records/mjywm-x0q09/files/journal.pgen.1006999.s005.tif" }, { "basename": "journal.pgen.1006999.s008.tif", "url": "https://authors.library.caltech.edu/records/mjywm-x0q09/files/journal.pgen.1006999.s008.tif" }, { "basename": "journal.pgen.1006999.s009.docx", "url": "https://authors.library.caltech.edu/records/mjywm-x0q09/files/journal.pgen.1006999.s009.docx" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Meier, Elizabeth L.; Daitch, Allison K.; et el." }, { "id": "https://authors.library.caltech.edu/records/y03jh-kwf60", "eprint_id": 78344, "eprint_status": "archive", "datestamp": "2023-08-21 21:42:44", "lastmod": "2023-10-23 16:05:46", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Oikonomou-C-M", "name": { "family": "Oikonomou", "given": "Catherine M." }, "orcid": "0000-0003-2312-4746" }, { "id": "Chang-Yi-Wei", "name": { "family": "Chang", "given": "Yi-Wei" }, "orcid": "0000-0003-2391-473X" }, { "id": "Kj\u00e6r-Andreas", "name": { "family": "Kj\u00e6r", "given": "Andreas" }, "orcid": "0000-0002-0096-5764" }, { "id": "Huang-Audrey-N", "name": { "family": "Huang", "given": "Audrey N." } }, { "id": "Kim-Ki-Woo", "name": { "family": "Kim", "given": "Ki Woo" }, "orcid": "0000-0002-7010-0336" }, { "id": "Ghosal-Debnath", "name": { "family": "Ghosal", "given": "Debnath" }, "orcid": "0000-0002-2227-0330" }, { "id": "Nguyen-Hong-H", "name": { "family": "Nguyen", "given": "Hong H." } }, { "id": "Kenny-Dorothy", "name": { "family": "Kenny", "given": "Dorothy" }, "orcid": "0000-0002-3631-623X" }, { "id": "Ogorzalek-Loo-Rachel-R", "name": { "family": "Ogorzalek Loo", "given": "Rachel R." }, "orcid": "0000-0002-0580-2833" }, { "id": "Gunsalus-Robert-P", "name": { "family": "Gunsalus", "given": "Robert P." }, "orcid": "0000-0002-1937-8412" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Morphology of the archaellar motor and associated cytoplasmic cone in Thermococcus kodakaraensis", "ispublished": "pub", "full_text_status": "public", "keywords": "archaeal motility; archaella; electron cryotomography; flagella; Thermococcus kodakarensis", "note": "\u00a9 2017 The Authors. \n\nReceived 13 February 2017; Revised 29 June 2017; Accepted 4 July 2017. \n\nThis work was supported by the NIH (grant R01AI127401 to G.J.J.) and the UCLA\u2010DOE Institute (grant DE\u2010FC03\u201002ER26342 to R.P.G.). Author contributions: AB and GJJ conceived the experiments; AB, ANH, KWK, DG, HHN, DK and RROL conducted the experiments; AB, CMO, YWC, AK, ANH, HHN, DK, RROL and RPG performed analysis; CMO and GJJ wrote the manuscript; all authors revised the manuscript. The authors declare that they have no conflict of interest.\n\nSubmitted - 108209.full.pdf
Supplemental Material - inline-supplementary-material-1.pdf
Supplemental Material - inline-supplementary-material-2.zip
Supplemental Material - inline-supplementary-material-3.xlsx
", "abstract": "Archaeal swimming motility is driven by archaella: rotary motors attached to long extracellular filaments. The structure of these motors, and particularly how they are anchored in the absence of a peptidoglycan cell wall, is unknown. Here, we use electron cryotomography to visualize the archaellar basal body in vivo in Thermococcus kodakaraensis KOD1. Compared to the homologous bacterial type IV pilus (T4P), we observe structural similarities as well as several unique features. While the position of the cytoplasmic ATPase appears conserved, it is not braced by linkages that extend upward through the cell envelope as in the T4P, but rather by cytoplasmic components that attach it to a large conical frustum up to 500 nm in diameter at its base. In addition to anchoring the lophotrichous bundle of archaella, the conical frustum associates with chemosensory arrays and ribosome\u2010excluding material and may function as a polar organizing center for the coccoid cells.", "date": "2017-09-01", "date_type": "published", "publication": "EMBO Reports", "volume": "18", "number": "9", "publisher": "European Molecular Biology Organization", "pagerange": "1660-1670", "id_number": "CaltechAUTHORS:20170619-154838039", "issn": "1469-221X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170619-154838039", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01AI127401" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-FC03-02ER26342" } ] }, "doi": "10.15252/embr.201744070", "pmcid": "PMC5579351", "primary_object": { "basename": "108209.full.pdf", "url": "https://authors.library.caltech.edu/records/y03jh-kwf60/files/108209.full.pdf" }, "related_objects": [ { "basename": "inline-supplementary-material-1.pdf", "url": "https://authors.library.caltech.edu/records/y03jh-kwf60/files/inline-supplementary-material-1.pdf" }, { "basename": "inline-supplementary-material-2.zip", "url": "https://authors.library.caltech.edu/records/y03jh-kwf60/files/inline-supplementary-material-2.zip" }, { "basename": "inline-supplementary-material-3.xlsx", "url": "https://authors.library.caltech.edu/records/y03jh-kwf60/files/inline-supplementary-material-3.xlsx" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Briegel, Ariane; Oikonomou, Catherine M.; et el." }, { "id": "https://authors.library.caltech.edu/records/dv6qd-01798", "eprint_id": 78264, "eprint_status": "archive", "datestamp": "2023-08-19 04:49:52", "lastmod": "2023-10-23 15:06:19", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Dobro-M-J", "name": { "family": "Dobro", "given": "Megan J." }, "orcid": "0000-0002-6464-3932" }, { "id": "Oikonomou-C-M", "name": { "family": "Oikonomou", "given": "Catherine M." }, "orcid": "0000-0003-2312-4746" }, { "id": "Piper-Aidan", "name": { "family": "Piper", "given": "Aidan" } }, { "id": "Cohen-John-J", "name": { "family": "Cohen", "given": "John" }, "orcid": "0000-0003-1772-8236" }, { "id": "Guo-Kylie", "name": { "family": "Guo", "given": "Kylie" } }, { "id": "Jensen-Taylor", "name": { "family": "Jensen", "given": "Taylor" }, "orcid": "0000-0002-7503-9079" }, { "id": "Tadayon-J", "name": { "family": "Tadayon", "given": "Jahan" }, "orcid": "0000-0002-2075-6345" }, { "id": "Donermeyer-J", "name": { "family": "Donermeyer", "given": "Joseph" } }, { "id": "Park-Yeram", "name": { "family": "Park", "given": "Yeram" }, "orcid": "0000-0002-6553-5722" }, { "id": "Solis-B-A", "name": { "family": "Solis", "given": "Benjamin A." }, "orcid": "0000-0002-6428-2903" }, { "id": "Kj\u00e6r-Andreas", "name": { "family": "Kj\u00e6r", "given": "Andreas" }, "orcid": "0000-0002-0096-5764" }, { "id": "Jewett-A-I", "name": { "family": "Jewett", "given": "Andrew I." }, "orcid": "0000-0002-6252-9888" }, { "id": "McDowall-A-W", "name": { "family": "McDowall", "given": "Alasdair W." } }, { "id": "Chen-Songye", "name": { "family": "Chen", "given": "Songye" }, "orcid": "0000-0001-5407-5049" }, { "id": "Chang-Yi-Wei", "name": { "family": "Chang", "given": "Yi-Wei" }, "orcid": "0000-0003-2391-473X" }, { "id": "Shi-Jian-CELLBIO", "name": { "family": "Shi", "given": "Jian" }, "orcid": "0000-0003-3810-5302" }, { "id": "Subramanian-Poorna", "name": { "family": "Subramanian", "given": "Poorna" } }, { "id": "Iancu-C-V", "name": { "family": "Iancu", "given": "Cristina V." }, "orcid": "0000-0002-7352-9226" }, { "id": "Li-Zhuo", "name": { "family": "Li", "given": "Zhuo" } }, { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Tocheva-E-I", "name": { "family": "Tocheva", "given": "Elitza I." }, "orcid": "0000-0002-4869-8319" }, { "id": "Pilhofer-M", "name": { "family": "Pilhofer", "given": "Martin" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Uncharacterized bacterial structures revealed by electron cryotomography", "ispublished": "pub", "full_text_status": "public", "keywords": "bacteria, electron cryotomography, cryo-EM, bacterial ultrastructure, uncharacterized structures", "note": "\u00a9 2017 American Society for Microbiology. \n\nReceived 10 March 2017; Accepted 27 May 2017; Accepted manuscript posted online 12 June 2017. \n\nWe thank our collaborators who provided strains for imaging: Andrew Camilli (Streptococcus pneumoniae), Eric Matson (strain JT5), Gladys Alexandre (Azospirillum brasilense mutants), Lotte S\u00f8gaard-Andersen, Simon Ringgaard, and Matthew K. Waldor (Vibrio cholerae wild type and mutants), Michael Marletta (Shewanella putrefaciens), and Gordon Cannon and Sabine Heinhorst (Halothiobacillus neapolitanus and Thiomonas intermedia). We also thank members of the Jensen lab for their helpful discussions. \n\nM.J.D. and G.J.J. conceived the idea for the study; M.J.D., C.M.O., A.P., J.C., K.G., T.J., J.T., J.D., Y.P., A.K., A.I.J., M.P., S.C., E.I.T., Y.-W.C., A.B., J.S., Z.L., P.S., C.V.I., B.A.S., and A.W.M. performed formal analysis and investigation; M.J.D. and C.M.O. wrote and prepared the original article draft; M.J.D., C.M.O., and G.J.J. wrote, reviewed, and edited the final article draft; M.J.D. and G.J.J. acquired funding; G.J.J. provided resources; and M.J.D. and G.J.J. supervised the study. \n\nThis work was supported by the Hampshire College Dr. Lucy fund and the Collaborative Modeling Center, NIH grant R01 AI27401 (to G.J.J.), the Beckman Institute at Caltech, the Gordon and Betty Moore Foundation, the Human Frontier Science Program, the Howard Hughes Medical Institute, and the John Templeton Foundation as part of the Boundaries of Life project. \n\nThe opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the John Templeton Foundation. \n\nWe declare no competing interests.\n\nPublished - J._Bacteriol.-2017-Dobro-.pdf
Supplemental Material - zjb999094502s1.pdf
", "abstract": "Electron cryotomography (ECT) can reveal the native structure and arrangement of macromolecular complexes inside intact cells. This technique has greatly advanced our understanding of the ultrastructure of bacterial cells. We now view bacteria as structurally complex assemblies of macromolecular machines rather than as undifferentiated bags of enzymes. To date, our group has applied ECT to nearly 90 different bacterial species, collecting more than 15,000 cryotomograms. In addition to known structures, we have observed, to our knowledge, several uncharacterized features in these tomograms. Some are completely novel structures; others expand the features or species range of known structure types. Here, we present a survey of these uncharacterized bacterial structures in the hopes of accelerating their identification and study, and furthering our understanding of the structural complexity of bacterial cells.", "date": "2017-09", "date_type": "published", "publication": "Journal of Bacteriology", "volume": "199", "number": "17", "publisher": "American Society for Microbiology", "pagerange": "Art. No. e00100-17", "id_number": "CaltechAUTHORS:20170616-093425610", "issn": "0021-9193", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170616-093425610", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Hampshire College" }, { "agency": "NIH", "grant_number": "R01 AI27401" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Human Frontier Science Program" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "John Templeton Foundation" } ] }, "doi": "10.1128/JB.00100-17", "pmcid": "PMC5553035", "primary_object": { "basename": "J._Bacteriol.-2017-Dobro-.pdf", "url": "https://authors.library.caltech.edu/records/dv6qd-01798/files/J._Bacteriol.-2017-Dobro-.pdf" }, "related_objects": [ { "basename": "zjb999094502s1.pdf", "url": "https://authors.library.caltech.edu/records/dv6qd-01798/files/zjb999094502s1.pdf" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Dobro, Megan J.; Oikonomou, Catherine M.; et el." }, { "id": "https://authors.library.caltech.edu/records/k04rv-xaf49", "eprint_id": 79025, "eprint_status": "archive", "datestamp": "2023-08-21 21:28:28", "lastmod": "2023-10-26 14:32:42", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Jeong-Kwangcheol-C", "name": { "family": "Jeong", "given": "Kwangcheol C." }, "orcid": "0000-0003-4337-0426" }, { "id": "Ghosal-Debnath", "name": { "family": "Ghosal", "given": "Debnath" }, "orcid": "0000-0002-2227-0330" }, { "id": "Chang-Yi-Wei", "name": { "family": "Chang", "given": "Yi-Wei" }, "orcid": "0000-0003-2391-473X" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Vogel-Joseph-P", "name": { "family": "Vogel", "given": "Joseph P." }, "orcid": "0000-0002-8054-5021" } ] }, "title": "Polar delivery of Legionella type IV secretion system substrates is essential for virulence", "ispublished": "pub", "full_text_status": "public", "keywords": "bacterial pathogen; secretion; polar localization; macrophage", "note": "\u00a9 2017 National Academy of Sciences. \n\nEdited by Thomas J. Silhavy, Princeton University, Princeton, NJ, and approved June 1, 2017 (received for review December 30, 2016). Published online before print July 10, 2017. \n\nWe thank Drs. J. Helbig, R. Isberg, Z. Q. Luo, W. Margolin, and A. L. Sonenshein for providing antibodies; Drs. P. Levin, J. Sexton, and Eep Darwin for helpful discussions; Dr. W. Beatty for the transmission electron microscopy analysis; and Dr. H. Shuman for his valuable suggestion to use a bolA deletion. This work was funded by NIH Grants AI48052 (to J.P.V.) and AI127401 (to G.J.J.). \n\nAuthor contributions: J.P.V. designed research; K.C.J., D.G., and J.P.V. performed research; K.C.J., D.G., Y.-W.C., G.J.J., and J.P.V. analyzed data; and J.P.V. wrote the paper. \n\nThe authors declare no conflict of interest. \n\nThis article is a PNAS Direct Submission. \n\nThis article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1621438114/-/DCSupplemental.\n\nPublished - PNAS-2017-Jeong-8077-82.pdf
Supplemental Material - pnas.1621438114.sm01.mp4
Supplemental Material - pnas.1621438114.sm02.mov
Supplemental Material - pnas.1621438114.sm03.mov
", "abstract": "A recurrent emerging theme is the targeting of proteins to subcellular microdomains within bacterial cells, particularly to the poles. In most cases, it has been assumed that this localization is critical to the protein's function. Legionella pneumophila uses a type IVB secretion system (T4BSS) to export a large number of protein substrates into the cytoplasm of host cells. Here we show that the Legionella export apparatus is localized to the bacterial poles, as is consistent with many T4SS substrates being retained on the phagosomal membrane adjacent to the poles of the bacterium. More significantly, we were able to demonstrate that polar secretion of substrates is critically required for Legionella's alteration of the host endocytic pathway, an activity required for this pathogen's virulence.", "date": "2017-07-25", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "114", "number": "30", "publisher": "National Academy of Sciences", "pagerange": "8077-8082", "id_number": "CaltechAUTHORS:20170712-144409863", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170712-144409863", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "AI48052" }, { "agency": "NIH", "grant_number": "AI127401" } ] }, "doi": "10.1073/pnas.1621438114", "pmcid": "PMC5544279", "primary_object": { "basename": "pnas.1621438114.sm01.mp4", "url": "https://authors.library.caltech.edu/records/k04rv-xaf49/files/pnas.1621438114.sm01.mp4" }, "related_objects": [ { "basename": "pnas.1621438114.sm02.mov", "url": "https://authors.library.caltech.edu/records/k04rv-xaf49/files/pnas.1621438114.sm02.mov" }, { "basename": "pnas.1621438114.sm03.mov", "url": "https://authors.library.caltech.edu/records/k04rv-xaf49/files/pnas.1621438114.sm03.mov" }, { "basename": "PNAS-2017-Jeong-8077-82.pdf", "url": "https://authors.library.caltech.edu/records/k04rv-xaf49/files/PNAS-2017-Jeong-8077-82.pdf" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Jeong, Kwangcheol C.; Ghosal, Debnath; et el." }, { "id": "https://authors.library.caltech.edu/records/66ebb-sa119", "eprint_id": 77443, "eprint_status": "archive", "datestamp": "2023-08-21 21:20:02", "lastmod": "2023-10-23 16:06:17", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chang-Yi-Wei", "name": { "family": "Chang", "given": "Yi\u2010Wei" }, "orcid": "0000-0003-2391-473X" }, { "id": "Rettberg-Lee-A", "name": { "family": "Rettberg", "given": "Lee A." } }, { "id": "Ortega-D-R", "name": { "family": "Ortega", "given": "Davi R." }, "orcid": "0000-0002-8344-2335" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "In vivo structures of an intact type VI secretion system revealed by electron cryotomography", "ispublished": "pub", "full_text_status": "public", "keywords": "bacterial molecular weapon; contractile bacteriophage tail; electron cryotomography; sub-tomogram averaging; type VI secretion system", "note": "\u00a9 2017 The Authors. \n\nReceived 13 February 2017; Revised 16 March 2017; Accepted 5 April 2017; Published online 9 May 2017. \n\nData availability: The sub\u2010tomogram averages of the M. xanthus T6SS that support the findings of this study have been deposited in the Electron Microscopy Data Bank with accession codes EMD\u20108600 (membrane\u2010associated region), EMD\u20108601 (extended sheath), EMD\u20108602 (contracted sheath). The coordinates of the extended and contracted sheath models have been deposited in the Protein Data Bank with accession code 5URW and 5URX, respectively. \n\nWe thank Prof. Hong Z. Zhou and Dr. Peng Ge for providing the initial concept of how to place the MyTssBC model in the sub\u2010tomogram average of extended T6SS sheath and Dr. Catherine Oikonomou for discussions and editorial assistance. This work was supported by NIH grant R01 AI127401 to G.J.J. \n\nAuthor contributions: Y\u2010WC and LAR collected, processed, and analyzed the electron cryotomography data. Y\u2010WC built the models. DRO performed the bioinformatics analysis. Y\u2010WC, DRO and GJJ wrote the paper. \n\nThe authors declare that they have no conflict of interest.\n\nSubmitted - 108233.full.pdf
Supplemental Material - inline-supplementary-material-1.pdf
", "abstract": "The type VI secretion system (T6SS) is a versatile molecular weapon used by many bacteria against eukaryotic hosts or prokaryotic competitors. It consists of a cytoplasmic bacteriophage tail\u2010like structure anchored in the bacterial cell envelope via a cytoplasmic baseplate and a periplasmic membrane complex. Rapid contraction of the sheath in the bacteriophage tail\u2010like structure propels an inner tube/spike complex through the target cell envelope to deliver effectors. While structures of purified contracted sheath and purified membrane complex have been solved, because sheaths contract upon cell lysis and purification, no structure is available for the extended sheath. Structural information about the baseplate is also lacking. Here, we use electron cryotomography to directly visualize intact T6SS structures inside Myxococcus xanthus cells. Using sub\u2010tomogram averaging, we resolve the structure of the extended sheath and membrane\u2010associated components including the baseplate. Moreover, we identify novel extracellular bacteriophage tail fiber\u2010like antennae. These results provide new structural insights into how the extended sheath prevents premature disassembly and how this sophisticated machine may recognize targets.", "date": "2017-07", "date_type": "published", "publication": "EMBO Reports", "volume": "18", "number": "7", "publisher": "European Molecular Biology Organization", "pagerange": "1090-1099", "id_number": "CaltechAUTHORS:20170515-095516428", "issn": "1469-221X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170515-095516428", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 AI127401" } ] }, "doi": "10.15252/embr.201744072", "pmcid": "PMC5494534", "primary_object": { "basename": "inline-supplementary-material-1.pdf", "url": "https://authors.library.caltech.edu/records/66ebb-sa119/files/inline-supplementary-material-1.pdf" }, "related_objects": [ { "basename": "108233.full.pdf", "url": "https://authors.library.caltech.edu/records/66ebb-sa119/files/108233.full.pdf" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Chang, Yi\u2010Wei; Rettberg, Lee A.; et el." }, { "id": "https://authors.library.caltech.edu/records/9y1xs-j4r28", "eprint_id": 77194, "eprint_status": "archive", "datestamp": "2023-08-21 21:11:12", "lastmod": "2023-10-25 21:58:06", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Yao-Qing", "name": { "family": "Yao", "given": "Qing" }, "orcid": "0000-0003-3575-9909" }, { "id": "Jewett-A-I", "name": { "family": "Jewett", "given": "Andrew I." }, "orcid": "0000-0002-6252-9888" }, { "id": "Chang-Yi-Wei", "name": { "family": "Chang", "given": "Yi\u2010Wei" }, "orcid": "0000-0003-2391-473X" }, { "id": "Oikonomou-C-M", "name": { "family": "Oikonomou", "given": "Catherine M." }, "orcid": "0000-0003-2312-4746" }, { "id": "Beeby-M-D", "name": { "family": "Beeby", "given": "Morgan" }, "orcid": "0000-0001-6413-9835" }, { "id": "Iancu-C-V", "name": { "family": "Iancu", "given": "Cristina V." }, "orcid": "0000-0002-7352-9226" }, { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Ghosal-Debnath", "name": { "family": "Ghosal", "given": "Debnath" }, "orcid": "0000-0002-2227-0330" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Short FtsZ filaments can drive asymmetric cell envelope constriction at the onset of bacterial cytokinesis", "ispublished": "pub", "full_text_status": "restricted", "keywords": "asymmetric division; bacterial cell division; Caulobacter crescentus; electron cryotomography; FtsZ", "note": "\u00a9 2017 The Authors. \n\nReceived 2 December 2016; Revised 17 March 2017; Accepted 23 March 2017. Published online 24.04.2017. \n\nWe thank Dr. Yves Brun and Mr. Erkin Kuru at Indiana University for providing reagents and technical assistance. We thank Prof. Douglas Weibel at University of Wisconsin\u2010Madison for providing the Proteus mirabilis strain. We thank Dr. Brian Hedlund at the University of Nevada for providing the Belliella baltica\u2010related strain. We are also grateful to all members of the Jensen laboratory for discussion and technical assistance. This work was supported by the Howard Hughes Medical Institute. \n\nAuthor contributions: QY and GJJ conceived and designed the experiments. QY, Y\u2010WC, MB, CVI, AB, and DG performed the experiments. AIJ wrote the software and made measurements. QY, AIJ, CMO, and GJJ analyzed the data. QY, AIJ, Y\u2010WC, CMO, and GJJ wrote the paper. \n\nThe authors declare that they have no conflict of interest.", "abstract": "FtsZ, the bacterial homologue of eukaryotic tubulin, plays a central role in cell division in nearly all bacteria and many archaea. It forms filaments under the cytoplasmic membrane at the division site where, together with other proteins it recruits, it drives peptidoglycan synthesis and constricts the cell. Despite extensive study, the arrangement of FtsZ filaments and their role in division continue to be debated. Here, we apply electron cryotomography to image the native structure of intact dividing cells and show that constriction in a variety of Gram\u2010negative bacterial cells, including Proteus mirabilis and Caulobacter crescentus, initiates asymmetrically, accompanied by asymmetric peptidoglycan incorporation and short FtsZ\u2010like filament formation. These results show that a complete ring of FtsZ is not required for constriction and lead us to propose a model for FtsZ\u2010driven division in which short dynamic FtsZ filaments can drive initial peptidoglycan synthesis and envelope constriction at the onset of cytokinesis, later increasing in length and number to encircle the division plane and complete constriction.", "date": "2017-06-01", "date_type": "published", "publication": "EMBO Journal", "volume": "36", "number": "11", "publisher": "European Molecular Biology Organization", "pagerange": "1577-1589", "id_number": "CaltechAUTHORS:20170504-103226288", "issn": "1460-2075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170504-103226288", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.15252/embj.201696235", "pmcid": "PMC5452018", "resource_type": "article", "pub_year": "2017", "author_list": "Yao, Qing; Jewett, Andrew I.; et el." }, { "id": "https://authors.library.caltech.edu/records/gmxvt-2bw20", "eprint_id": 76800, "eprint_status": "archive", "datestamp": "2023-08-19 03:17:27", "lastmod": "2023-10-25 16:52:32", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Oikonomou-C-M", "name": { "family": "Oikonomou", "given": "Catherine M." }, "orcid": "0000-0003-2312-4746" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Cellular Electron Cryotomography: Toward Structural Biology In Situ", "ispublished": "pub", "full_text_status": "restricted", "keywords": "electron cryotomography, cryo\u2013electron tomography, cryo\u2013electron\nmicroscopy, CLEM, hybrid methods, type VI secretion, type IV pili, cilia, flagella, nuclear pore complex", "note": "\u00a9 2017 Annual Reviews. \n\nReview in Advance first posted online on April 19, 2017. \n\nWe apologize to all of our colleagues whose work could not be cited owing to space constraints. We thank Drs. Daniela Nicastro and Andre Hoelz for insightful comments on the manuscript. ECT research in the Jensen laboratory is supported by the National Institutes of Health (R01 grants GM101425 and AI127401 to G.J.J.), the Howard Hughes Medical Institute, the Beckman Institute at Caltech, Caltech's Center for Environmental Microbial Interactions, gifts to Caltech from the Gordon and Betty Moore Foundation and the Agouron Institute, and the John Templeton Foundation as part of the Boundaries of Life project. The opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the John Templeton Foundation.\n\nDisclosure Statement: The authors are not aware of any affiliations, memberships, funding, or financial holdings that might be perceived as affecting the objectivity of this review.", "abstract": "Electron cryotomography (ECT) provides three-dimensional views of macromolecular complexes inside cells in a native frozen\u2013hydrated state. Over the last two decades, ECT has revealed the ultrastructure of cells in unprecedented detail. It has also allowed us to visualize the structures of macromolecular machines in their native context inside intact cells. In many cases, such machines cannot be purified intact for in vitro study. In other cases, the function of a structure is lost outside the cell, so that the mechanism can be understood only by observation in situ. In this review, we describe the technique and its history and provide examples of its power when applied to cell biology. We also discuss the integration of ECT with other techniques, including lower-resolution fluorescence imaging and higherresolution atomic structure determination, to cover the full scale of cellular processes.", "date": "2017-06", "date_type": "published", "publication": "Annual Review of Biochemistry", "volume": "86", "publisher": "Annual Reviews", "pagerange": "873-896", "id_number": "CaltechAUTHORS:20170421-082204689", "issn": "0066-4154", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170421-082204689", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM101425" }, { "agency": "NIH", "grant_number": "AI127401" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Caltech Center for Environmental Microbial Interactions (CEMI)" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Agouron Institute" }, { "agency": "John Templeton Foundation" } ] }, "collection": "CaltechAUTHORS", "local_group": { "items": [ { "id": "Caltech-Center-for-Environmental-Microbial-Interactions-(CEMI)", "value": "Caltech Center for Environmental Microbial Interactions (CEMI)" } ] }, "doi": "10.1146/annurev-biochem-061516-044741", "resource_type": "article", "pub_year": "2017", "author_list": "Oikonomou, Catherine M. and Jensen, Grant J." }, { "id": "https://authors.library.caltech.edu/records/1fd2n-0wq72", "eprint_id": 76477, "eprint_status": "archive", "datestamp": "2023-08-19 03:17:18", "lastmod": "2023-10-25 16:02:13", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Distelhorst-S-L", "name": { "family": "Distelhorst", "given": "Steven L." } }, { "id": "Jurkovic-D-A", "name": { "family": "Jurkovic", "given": "Dominika A." } }, { "id": "Shi-Jian", "name": { "family": "Shi", "given": "Jian" }, "orcid": "0000-0003-3810-5302" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Balish-M-F", "name": { "family": "Balish", "given": "Mitchell F." } } ] }, "title": "The variable internal structure of the Mycoplasma penetrans attachment organelle revealed by biochemical and microscopic analyses: implications for attachment organelle mechanism and evolution", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2017 American Society for Microbiology. \n\nReceived 1 February 2017; Accepted 27 March 2017; Accepted manuscript posted online 3 April 2017.\n\nThis work was supported by the National Institutes of Health (Public Health Service grant R15 AI073994) to MFB. We thank A. Kiss (Miami University Center for Bioinformatics and Functional Genomics) and K. Pflaum (University of Connecticut) for help with RNA-Seq. We thank R.J. Hickey (Miami University), W. Ambrosius (Wake Forest University), and members of the Balish laboratory for insightful discussions. This work was done in partial fulfillment of SLD's doctoral dissertation requirements.\n\nPublished - J._Bacteriol.-2017-Distelhorst-.pdf
Supplemental Material - zjb999094422sd1.xls
", "abstract": "Although mycoplasmas have small genomes, many of them, including the HIV-associated opportunist Mycoplasma penetrans, construct a polar attachment organelle (AO) that is used for both adherence to host cells and gliding motility. However, the irregular phylogenetic distribution of similar structures within the mycoplasmas, as well as compositional and ultrastructural differences among these AOs, suggests that AOs have arisen several times through convergent evolution. We investigated the ultrastructure and protein composition of the cytoskeleton-like material of the M. penetrans AO with several forms of microscopy and biochemical analysis, to determine whether the M. penetrans AO was constructed at the molecular level on principles similar to those of other mycoplasmas, such as Mycoplasma pneumoniae and Mycoplasma mobile. We found that the M. penetrans AO interior was generally dissimilar from that of other mycoplasmas, in that it exhibited considerable heterogeneity in size and shape, suggesting a gel-like nature. In contrast, several of the 12 potential protein components identified by mass spectrometry of M. penetrans detergent-insoluble proteins shared certain distinctive biochemical characteristics with M. pneumoniae AO proteins, although not with M. mobile proteins. We conclude that convergence between M. penetrans and M. pneumoniae AOs extends to the molecular level, leading to the possibility that the less organized material in both M. pneumoniae and M. penetrans is the substance principally responsible for the organization and function of the AO.", "date": "2017-06", "date_type": "published", "publication": "Journal of Bacteriology", "volume": "199", "number": "12", "publisher": "American Society for Microbiology", "pagerange": "Art. No. e00069-17", "id_number": "CaltechAUTHORS:20170410-125440557", "issn": "0021-9193", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170410-125440557", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R15 AI073994" } ] }, "doi": "10.1128/JB.00069-17", "pmcid": "PMC5446615", "primary_object": { "basename": "J._Bacteriol.-2017-Distelhorst-.pdf", "url": "https://authors.library.caltech.edu/records/1fd2n-0wq72/files/J._Bacteriol.-2017-Distelhorst-.pdf" }, "related_objects": [ { "basename": "zjb999094422sd1.xls", "url": "https://authors.library.caltech.edu/records/1fd2n-0wq72/files/zjb999094422sd1.xls" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Distelhorst, Steven L.; Jurkovic, Dominika A.; et el." }, { "id": "https://authors.library.caltech.edu/records/kn0n2-wv366", "eprint_id": 75060, "eprint_status": "archive", "datestamp": "2023-08-21 20:59:05", "lastmod": "2023-10-23 15:50:54", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ghosal-Debnath", "name": { "family": "Ghosal", "given": "Debnath" }, "orcid": "0000-0002-2227-0330" }, { "id": "Chang-Yi-Wei", "name": { "family": "Chang", "given": "Yi-Wei" }, "orcid": "0000-0003-2391-473X" }, { "id": "Jeong-Kwangcheol-C", "name": { "family": "Jeong", "given": "Kwangcheol C." }, "orcid": "0000-0003-4337-0426" }, { "id": "Vogel-Joseph-P", "name": { "family": "Vogel", "given": "Joseph P." }, "orcid": "0000-0002-8054-5021" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "In situ structure of the Legionella Dot/Icm type IV secretion system by electron cryotomography", "ispublished": "pub", "full_text_status": "public", "keywords": "Dot/Icm; electron cryotomography; Legionella pneumophila; subtomogram averaging; Type IV secretion systems", "note": "\u00a9 2017 The Authors. \n\nReceived 29 October 2016; Revised 15 February 2017; Accepted 21 February 2017; Published online 23 March 2017. \n\nThis work was supported by the NIH (R01AI127401 to G.J.J.). \n\nNational Institute of Allergy and Infectious Diseases (NIAID) R01AI127401. \n\nAccession numbers: Subtomogram averages reported in this study have been deposited in the EMDataBank (EMDB) with accession numbers EMD-8566, EMD-8567, EMD-8568, and EMD-8569. \n\nAuthor contributions: DG and GJJ conceived and designed the study. DG collected and processed ECT data. YWC helped with data processing and analysis. JPV and KCJ constructed and characterized strains. DG, GJJ, and JPV wrote the manuscript. All authors contributed to data analysis and manuscript writing. \n\nThe authors declare that they have no conflict of interest.\n\nSubmitted - 085977.full.pdf
Supplemental Material - 085977-1.pdf
Supplemental Material - 085977-2.avi
Supplemental Material - 085977-3.avi
Supplemental Material - inline-supplementary-material-4.zip
", "abstract": "Type IV secretion systems (T4SSs) are large macromolecular machines that translocate protein and DNA and are involved in the pathogenesis of multiple human diseases. Here, using electron cryotomography (ECT), we report the in situ structure of the Dot/Icm type IVB secretion system (T4BSS) utilized by the human pathogen Legionella pneumophila. This is the first structure of a type IVB secretion system, and also the first structure of any T4SS in situ. While the Dot/Icm system shares almost no sequence similarity with type IVA secretion systems (T4ASSs), its overall structure is seen here to be remarkably similar to previously reported T4ASS structures (those encoded by the R388 plasmid in Escherichia coli and the cag pathogenicity island in Helicobacter pylori). This structural similarity suggests shared aspects of mechanism. However, compared to the negative\u2010stain reconstruction of the purified T4ASS from the R388 plasmid, the L. pneumophila Dot/Icm system is approximately twice as long and wide and exhibits several additional large densities, reflecting type\u2010specific elaborations and potentially better structural preservation in situ.", "date": "2017-05-01", "date_type": "published", "publication": "EMBO Reports", "volume": "18", "number": "5", "publisher": "European Molecular Biology Organization", "pagerange": "726-732", "id_number": "CaltechAUTHORS:20170313-131852950", "issn": "1469-221X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170313-131852950", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01AI127401" } ] }, "doi": "10.15252/embr.201643598", "pmcid": "PMC5412798", "primary_object": { "basename": "085977-3.avi", "url": "https://authors.library.caltech.edu/records/kn0n2-wv366/files/085977-3.avi" }, "related_objects": [ { "basename": "085977.full.pdf", "url": "https://authors.library.caltech.edu/records/kn0n2-wv366/files/085977.full.pdf" }, { "basename": "inline-supplementary-material-4.zip", "url": "https://authors.library.caltech.edu/records/kn0n2-wv366/files/inline-supplementary-material-4.zip" }, { "basename": "085977-1.pdf", "url": "https://authors.library.caltech.edu/records/kn0n2-wv366/files/085977-1.pdf" }, { "basename": "085977-2.avi", "url": "https://authors.library.caltech.edu/records/kn0n2-wv366/files/085977-2.avi" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Ghosal, Debnath; Chang, Yi-Wei; et el." }, { "id": "https://authors.library.caltech.edu/records/f60g2-pwx76", "eprint_id": 75199, "eprint_status": "archive", "datestamp": "2023-08-19 02:50:08", "lastmod": "2023-10-25 14:50:23", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant" }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Progress and Potential of Electron Cryotomography as Illustrated by Its Application to Bacterial Chemoreceptor Arrays", "ispublished": "pub", "full_text_status": "restricted", "keywords": "cryo-EM, imaging, bacteria, chemotaxis, structural biology", "note": "\u00a9 2017 Annual Reviews. \n\nReview in Advance first posted online on February 23, 2017. \n\nThe authors are not aware of any affiliations, memberships, funding, or financial holdings that might be perceived as affecting the objectivity of this review.", "abstract": "Electron cryotomography (ECT) can produce three-dimensional images of biological samples such as intact cells in a near-native, frozen-hydrated state to macromolecular resolution (\u223c4 nm). Because one of its first and most common applications has been to bacterial chemoreceptor arrays, ECT's contributions to this field illustrate well its past, present, and future. Although X-ray crystallography and nuclear magnetic resonance spectroscopy have revealed the structures of nearly all the individual components of chemoreceptor arrays, ECT has revealed the mesoscale information about how the components are arranged within cells. Receptors assemble into a universally conserved 12-nm hexagonal lattice linked by CheA/CheW rings. Membrane-bound arrays are single layered; cytoplasmic arrays are double layered. Images of in vitro reconstitutions have led to a model of how arrays assemble, and images of native arrays in different states have shown that the conformational changes associated with signal transduction are subtle, constraining models of activation and system cooperativity. Phase plates, better detectors, and more stable stages promise even higher resolution and broader application in the near future.", "date": "2017-05", "date_type": "published", "publication": "Annual Review of Biophysics", "volume": "46", "publisher": "Annual Reviews", "pagerange": "1-21", "id_number": "CaltechAUTHORS:20170317-103256482", "issn": "1936-122X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170317-103256482", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1146/annurev-biophys-070816-033555", "resource_type": "article", "pub_year": "2017", "author_list": "Briegel, Ariane and Jensen, Grant" }, { "id": "https://authors.library.caltech.edu/records/ej0bh-6m098", "eprint_id": 76462, "eprint_status": "archive", "datestamp": "2023-08-19 02:34:19", "lastmod": "2023-10-25 16:01:16", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Schulz-F", "name": { "family": "Schulz", "given": "Frederik" } }, { "id": "Yutin-N", "name": { "family": "Yutin", "given": "Natalya" } }, { "id": "Ivanova-N-N", "name": { "family": "Ivanova", "given": "Natalia N." } }, { "id": "Ortega-D-R", "name": { "family": "Ortega", "given": "Davi R." }, "orcid": "0000-0002-8344-2335" }, { "id": "Lee-Tae-Kwon", "name": { "family": "Lee", "given": "Tae Kwon" } }, { "id": "Vierheilig-J", "name": { "family": "Vierheilig", "given": "Julia" } }, { "id": "Daims-H", "name": { "family": "Daims", "given": "Holger" } }, { "id": "Horn-M", "name": { "family": "Horn", "given": "Matthias" } }, { "id": "Wagner-M", "name": { "family": "Wagner", "given": "Michael" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Kyrpides-N-C", "name": { "family": "Kyrpides", "given": "Nikos C." } }, { "id": "Koonin-E-V", "name": { "family": "Koonin", "given": "Eugene V." } }, { "id": "Woykeb-T", "name": { "family": "Woykeb", "given": "Tanja" } } ] }, "title": "Giant viruses with an expanded complement of translation system components", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2017 American Association for the Advancement of Science. \n\n23 November 2016; resubmitted 18 January 2017. Accepted 15 March 2017. \n\nThe work conducted by the U.S. Department of Energy Joint Genome Institute (JGI), a U.S. Department of Energy Office of Science User Facility, is supported under contract no. DE-AC02-05CH11231. N.Y. and E.V.K. were supported by intramural funds of the U.S. Department of Health and Human Services. M.W., H.D., and T.K.L. were supported by the European Research Council via the Advanced Grant project \"NITRICARE 294343\" and the Starting Grant \"EVOCHLAMY\" and by the Austrian Science Fund (FWF) via project P27319-B21. This work was supported in part by the John Templeton Foundation. The opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the John Templeton Foundation. K. Kitzinger, T. Nielsen, H. Na, P. Pjevac, F. Wascher, N. Ahlers, and J. Barrero Canosa are acknowledged for their support in various steps of the project. Klosneuvirus genome assemblies are deposited in GenBank (accession numbers KY684083 to KY684123), and metagenome read data can be accessed on the JGI data portal (http://genomeportal.jgi.doe.gov/) (accession numbers are in tables S1 to S3). Data from phylogenetic and evolutionary analyses are available online (https://bitbucket.org/berkeleylab/klosneuvirus).", "abstract": "The discovery of giant viruses blurred the sharp division between viruses and cellular life. Giant virus genomes encode proteins considered as signatures of cellular organisms, particularly translation system components, prompting hypotheses that these viruses derived from a fourth domain of cellular life. Here we report the discovery of a group of giant viruses (Klosneuviruses) in metagenomic data. Compared with other giant viruses, the Klosneuviruses encode an expanded translation machinery, including aminoacyl transfer RNA synthetases with specificities for all 20 amino acids. Notwithstanding the prevalence of translation system components, comprehensive phylogenomic analysis of these genes indicates that Klosneuviruses did not evolve from a cellular ancestor but rather are derived from a much smaller virus through extensive gain of host genes.", "date": "2017-04-07", "date_type": "published", "publication": "Science", "volume": "356", "number": "6333", "publisher": "American Association for the Advancement of Science", "pagerange": "82-85", "id_number": "CaltechAUTHORS:20170410-065731786", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170410-065731786", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Department of Energy (DOE)", "grant_number": "DE-AC02-05CH11231" }, { "agency": "European Research Council (ERC)", "grant_number": "NITRICARE 294343" }, { "agency": "European Research Council (ERC)", "grant_number": "EVOCHLAMY" }, { "agency": "FWF Der Wissenschaftsfonds", "grant_number": "P27319-B21" }, { "agency": "John Templeton Foundation" }, { "agency": "Department of Health and Human Services" } ] }, "doi": "10.1126/science.aal4657", "resource_type": "article", "pub_year": "2017", "author_list": "Schulz, Frederik; Yutin, Natalya; et el." }, { "id": "https://authors.library.caltech.edu/records/v7c80-zqr03", "eprint_id": 74801, "eprint_status": "archive", "datestamp": "2023-08-22 19:54:11", "lastmod": "2023-10-24 23:18:17", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Racki-Lisa-R", "name": { "family": "Racki", "given": "Lisa R." } }, { "id": "Tocheva-Elitza-I", "name": { "family": "Tocheva", "given": "Elitza I." }, "orcid": "0000-0002-4869-8319" }, { "id": "Dieterle-Michael-G", "name": { "family": "Dieterle", "given": "Michael G." } }, { "id": "Sullivan-Meaghan-C", "name": { "family": "Sullivan", "given": "Meaghan C." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Newman-D-K", "name": { "family": "Newman", "given": "Dianne K." }, "orcid": "0000-0003-1647-1918" } ] }, "title": "Polyphosphate granule biogenesis is temporally and functionally tied to cell cycle exit during starvation in Pseudomonas aeruginosa", "ispublished": "pub", "full_text_status": "public", "keywords": "polyphosphate; nucleoid; cell cycle; starvation; biomineralization", "note": "\u00a9 2017 National Academy of Sciences. \n\nEdited by Christine Jacobs-Wagner, Yale University, West Haven, CT, and approved February 6, 2017 (received for review September 21, 2016). Published online before print March 6, 2017. \n\nWe specially thank Dr. Alasdair McDowall, Howard Hughes Medical Institute, for electron microscopy support. We thank Carol Garland for technical assistance with Energy Dispersive X-ray Spectroscopy (EDS) data collection and analysis using California Institute of Technology (Caltech)'s Applied Physics and Materials Science Department's Transmission Electron Microscopy Facility. We also thank Brittany J Belin and Noah Ollikainen for help with statistical analysis of the granule position modeling and gratefully acknowledge Megan Bergkessel and other D.K.N. laboratory members for constructive comments on the manuscript. The Caltech Electron Microscopy Facility is funded in part by the Gordon and Betty Moore Foundation, the Agouron Institute, and the Beckman Foundation. This work was funded in part by the Howard Hughes Medical Institute, and the National Institutes of Health (5R01HL117328-03). Lisa Racki is a Damon Runyon Fellow supported by the Damon Runyon Cancer Research Foundation (DRG-2126-12). \n\nAuthor contributions: L.R.R., E.I.T., G.J.J., and D.K.N. designed research; L.R.R., E.I.T., and M.C.S. performed research; L.R.R. contributed new reagents/analytic tools; L.R.R., E.I.T., M.G.D., M.C.S., G.J.J., and D.K.N. analyzed data; and L.R.R. and D.K.N. wrote the paper. \n\nThe authors declare no conflict of interest. \n\nThis article is a PNAS Direct Submission. \n\nThis article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1615575114/-/DCSupplemental.\n\nPublished - PNAS-2017-Racki-E2440-9.pdf
Supplemental Material - pnas.1615575114.sapp.pdf
", "abstract": "Polyphosphate (polyP) granule biogenesis is an ancient and ubiquitous starvation response in bacteria. Although the ability to make polyP is important for survival during quiescence and resistance to diverse environmental stresses, granule genesis is poorly understood. Using quantitative microscopy at high spatial and temporal resolution, we show that granule genesis in Pseudomonas aeruginosa is tightly organized under nitrogen starvation. Following nucleation as many microgranules throughout the nucleoid, polyP granules consolidate and become transiently spatially organized during cell cycle exit. Between 1 and 3 h after nitrogen starvation, a minority of cells have divided, yet the total granule number per cell decreases, total granule volume per cell dramatically increases, and individual granules grow to occupy diameters as large as \u223c200 nm. At their peak, mature granules constitute \u223c2% of the total cell volume and are evenly spaced along the long cell axis. Following cell cycle exit, granules initially retain a tight spatial organization, yet their size distribution and spacing relax deeper into starvation. Mutant cells lacking polyP elongate during starvation and contain more than one origin. PolyP promotes cell cycle exit by functioning at a step after DNA replication initiation. Together with the universal starvation alarmone (p)ppGpp, polyP has an additive effect on nucleoid dynamics and organization during starvation. Notably, cell cycle exit is temporally coupled to a net increase in polyP granule biomass, suggesting that net synthesis, rather than consumption of the polymer, is important for the mechanism by which polyP promotes completion of cell cycle exit during starvation.", "date": "2017-03-21", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "114", "number": "12", "publisher": "National Academy of Sciences", "pagerange": "E2440-E2449", "id_number": "CaltechAUTHORS:20170306-140446676", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170306-140446676", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Agouron Institute" }, { "agency": "Arnold and Mabel Beckman Foundation" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "5R01HL117328-03" }, { "agency": "Damon Runyon Cancer Research Foundation", "grant_number": "DRG-2126-12" } ] }, "local_group": { "items": [ { "id": "Division-of-Geological-and-Planetary-Sciences" } ] }, "doi": "10.1073/pnas.1615575114", "pmcid": "PMC5373386", "primary_object": { "basename": "PNAS-2017-Racki-E2440-9.pdf", "url": "https://authors.library.caltech.edu/records/v7c80-zqr03/files/PNAS-2017-Racki-E2440-9.pdf" }, "related_objects": [ { "basename": "pnas.1615575114.sapp.pdf", "url": "https://authors.library.caltech.edu/records/v7c80-zqr03/files/pnas.1615575114.sapp.pdf" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Racki, Lisa R.; Tocheva, Elitza I.; et el." }, { "id": "https://authors.library.caltech.edu/records/2x7xg-8av93", "eprint_id": 73201, "eprint_status": "archive", "datestamp": "2023-08-19 01:43:06", "lastmod": "2023-10-24 15:07:23", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cserti-Em\u00f6ke", "name": { "family": "Cserti", "given": "Em\u00f6ke" } }, { "id": "Rosskopf-Sabine", "name": { "family": "Rosskopf", "given": "Sabine" } }, { "id": "Chang-Yi-Wei", "name": { "family": "Chang", "given": "Yi-Wei" }, "orcid": "0000-0003-2391-473X" }, { "id": "Eisheuer-Sabrina", "name": { "family": "Eisheuer", "given": "Sabrina" } }, { "id": "Selter-Lars", "name": { "family": "Selter", "given": "Lars" } }, { "id": "Shi-Jian", "name": { "family": "Shi", "given": "Jian" }, "orcid": "0000-0003-3810-5302" }, { "id": "Regh-Christina", "name": { "family": "Regh", "given": "Christina" } }, { "id": "Koert-Ulrich", "name": { "family": "Koert", "given": "Ulrich" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Thanbichler-Martin", "name": { "family": "Thanbichler", "given": "Martin" }, "orcid": "0000-0002-1303-1442" } ] }, "title": "Dynamics of the peptidoglycan biosynthetic machinery in the stalked budding bacterium Hyphomonas neptunium", "ispublished": "pub", "full_text_status": "public", "keywords": "Polar growth, stalked bacteria, morphogenesis, Agrobacterium, Caulobacter", "note": "\u00a9 2016 John Wiley & Sons, Inc. \n\nAccepted manuscript online: 20 December 2016; Manuscript Revised: 8 November 2016; Manuscript Received: 31 August 2016. \n\nWe thank Erkin Kuru and Yves Brun for advice on the use and synthesis of HADA, Julia Rosum for excellent technical assistance, and Wolfgang Strobel for support in the initial phases of this work. Moreover, we are grateful to Daniela Kiekebusch, Maria Billini, and Alexandra Jung for critical reading of the manuscript. M.T. acknowledges core support from Philipps-Universit\u00e4t Marburg, funding from the\nGerman Research Foundation (DFG) through Research Training Group (GRK) 1216, and a Max Planck Fellowship from the Max Planck Society. Work in the laboratory of G.J.J. is supported by the Howard Hughes Medical Institute. \n\nAuthors' Contributions: EC, SR, SE, and CR performed the genetic and cell biological analyses. YC, JS, and GJJ conducted the electron cryo-tomography studies. LS and UK carried out the synthesis of HADA. MT designed the study. EC and MT wrote the paper, with input from all other authors. \n\nThe authors have no conflicts of interest related to this work.\n\nAccepted Version - Cserti_et_al-2016-Molecular_Microbiology.pdf
Supplemental Material - mmi13593-sup-0001-SuppMovie.avi
Supplemental Material - mmi13593-sup-0002-SuppMet.pdf
", "abstract": "Most commonly studied bacteria grow symmetrically and divide by binary fission, generating two siblings of equal morphology. An exception to this rule are budding bacteria, in which new offspring emerges de novo from a morphologically invariant mother cell. Although this mode of proliferation is widespread in diverse bacterial lineages, the underlying mechanisms are still incompletely understood. Here, we perform the first molecular-level analysis of growth and morphogenesis in the stalked budding alphaproteobacterium Hyphomonas neptunium. Peptidoglycan labeling shows that, in this species, buds originate from a stalk-like extension of the mother cell whose terminal segment is gradually remodeled into a new cell compartment. As a first step toward identifying the machinery mediating the budding process, we performed comprehensive mutational and localization studies of predicted peptidoglycan biosynthetic proteins in H. neptunium. These analyses identify factors that localize to distinct zones of dispersed and zonal growth, and they suggest a critical role of the MreB-controlled elongasome in cell morphogenesis. Collectively, our work shows that the mechanism of growth in H. neptunium is distinct from that in related, polarly growing members of the order Rhizobiales, setting the stage for in-depth analyses of the molecular principles regulating the fascinating developmental cycle of this species.", "date": "2017-03", "date_type": "published", "publication": "Molecular Microbiology", "volume": "103", "number": "5", "publisher": "Blackwell", "pagerange": "875-895", "id_number": "CaltechAUTHORS:20170104-102831596", "issn": "0950-382X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170104-102831596", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Philipps-Universit\u00e4t Marburg" }, { "agency": "Deutsche Forschungsgemeinschaft (DFG)", "grant_number": "1216" }, { "agency": "Max Planck Society" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "collection": "CaltechAUTHORS", "doi": "10.1111/mmi.13593", "primary_object": { "basename": "Cserti_et_al-2016-Molecular_Microbiology.pdf", "url": "https://authors.library.caltech.edu/records/2x7xg-8av93/files/Cserti_et_al-2016-Molecular_Microbiology.pdf" }, "related_objects": [ { "basename": "mmi13593-sup-0001-SuppMovie.avi", "url": "https://authors.library.caltech.edu/records/2x7xg-8av93/files/mmi13593-sup-0001-SuppMovie.avi" }, { "basename": "mmi13593-sup-0002-SuppMet.pdf", "url": "https://authors.library.caltech.edu/records/2x7xg-8av93/files/mmi13593-sup-0002-SuppMet.pdf" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Cserti, Em\u00f6ke; Rosskopf, Sabine; et el." }, { "id": "https://authors.library.caltech.edu/records/yhxye-6ht23", "eprint_id": 72611, "eprint_status": "archive", "datestamp": "2023-08-19 01:25:51", "lastmod": "2023-10-23 22:46:19", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chang-Yi-Wei", "name": { "family": "Chang", "given": "Yi-Wei" }, "orcid": "0000-0003-2391-473X" }, { "id": "Kj\u00e6r-Andreas", "name": { "family": "Kj\u00e6r", "given": "Andreas" }, "orcid": "0000-0002-0096-5764" }, { "id": "Ortega-Davi-R", "name": { "family": "Ortega", "given": "Davi R." }, "orcid": "0000-0002-8344-2335" }, { "id": "Kovacikova-Gabriela", "name": { "family": "Kovacikova", "given": "Gabriela" } }, { "id": "Sutherland-John-A", "name": { "family": "Sutherland", "given": "John A." } }, { "id": "Rettberg-Lee-A", "name": { "family": "Rettberg", "given": "Lee A." } }, { "id": "Taylor-Ronald-K", "name": { "family": "Taylor", "given": "Ronald K." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Architecture of the Vibrio cholerae toxin-coregulated pilus machine revealed by electron cryotomography", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2017 Macmillan Publishers Limited. \n\nReceived: 16 May 2016; Accepted: 14 December 2016; Published online: 06 February 2017. \n\nThe authors thank C. Oikonomou and C. Shaffer for discussions and editorial assistance. This work was supported by NIH grant R01 AI127401 to G.J.J., the Howard Hughes Medical Institute and the John Templeton Foundation as part of the Boundaries of Life project. The opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the John Templeton Foundation. \n\nData availability: The sub-tomogram averages of TCPMs that support the findings of this study have been deposited in the Electron Microscopy Data Bank under the following accession codes: EMD-8492 (wild-type, non-piliated, aligned on the OM part); EMD-8493 (wild-type, non-piliated, aligned on the IM part); EMD-8494 (wild-type, piliated, aligned on the OM part); EMD-8495 (wild-type, piliated, aligned on the IM part); EMD-8496 (\u0394tcpS, non-piliated, aligned on the OM part); EMD-8497 (\u0394tcpS, non-piliated, aligned on the IM part); EMD-8498 (\u0394tcpB, non-piliated, aligned on the OM part); EMD-8499 (\u0394tcpB, non-piliated, aligned on the IM part); EMD-8500 (\u0394tcpD, non-piliated, aligned on the OM part); EMD-8501 (\u0394tcpD, non-piliated, aligned on the IM part); EMD-8502 (\u0394tcpR, non-piliated, aligned on the OM part); and EMD-8503 (\u0394tcpR, non-piliated, aligned on the IM part). \n\nAuthor Contributions: Y.-W.C. and A.K. collected, processed and analysed the ECT data. D.R.O. performed the bioinformatics analyses. L.A.R. assisted with ECT data processing. G.K., J.A.S. and R.K.T. provided the V. cholerae strains. Y.-W.C., A.K., D.R.O. and G.J.J. wrote the paper. \n\nThe authors declare no competing financial interests.\n\nAccepted Version - nihms836833.pdf
Supplemental Material - nmicrobiol2016269-s1.pdf
Supplemental Material - nmicrobiol2016269-s2.mov
", "abstract": "Type IV pili (T4P) are filamentous appendages found on many Bacteria and Archaea. They are helical fibres of pilin proteins assembled by a multi-component macromolecular machine we call the basal body. Based on pilin features, T4P are classified into type IVa pili (T4aP) and type IVb pili (T4bP). T4aP are more widespread and are involved in cell motility, DNA transfer, host predation and electron transfer. T4bP are less prevalent and are mainly found in enteropathogenic bacteria, where they play key roles in host colonization. Following similar work on T4aP machines, here we use electron cryotomography to reveal the three-dimensional in situ structure of a T4bP machine in its piliated and non-piliated states. The specific machine we analyse is the Vibrio cholerae toxin-coregulated pilus machine (TCPM). Although only about half of the components of the TCPM show sequence homology to components of the previously analysed Myxococcus xanthus T4aP machine (T4aPM), we find that their structures are nevertheless remarkably similar. Based on homologies with components of the M. xanthus T4aPM and additional reconstructions of TCPM mutants in which the non-homologous proteins are individually deleted, we propose locations for all eight TCPM components within the complex. Non-homologous proteins in the T4aPM and TCPM are found to form similar structures, suggesting new hypotheses for their functions and evolutionary histories.", "date": "2017-02-06", "date_type": "published", "publication": "Nature Microbiology", "volume": "2", "number": "2", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 16269", "id_number": "CaltechAUTHORS:20161206-161836906", "issn": "2058-5276", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161206-161836906", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 AI127401" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "John Templeton Foundation" } ] }, "collection": "CaltechAUTHORS", "doi": "10.1038/nmicrobiol.2016.269", "pmcid": "PMC5302817", "primary_object": { "basename": "nmicrobiol2016269-s1.pdf", "url": "https://authors.library.caltech.edu/records/yhxye-6ht23/files/nmicrobiol2016269-s1.pdf" }, "related_objects": [ { "basename": "nmicrobiol2016269-s2.mov", "url": "https://authors.library.caltech.edu/records/yhxye-6ht23/files/nmicrobiol2016269-s2.mov" }, { "basename": "nihms836833.pdf", "url": "https://authors.library.caltech.edu/records/yhxye-6ht23/files/nihms836833.pdf" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Chang, Yi-Wei; Kj\u00e6r, Andreas; et el." }, { "id": "https://authors.library.caltech.edu/records/a71bs-d4n86", "eprint_id": 78709, "eprint_status": "archive", "datestamp": "2023-08-19 01:25:00", "lastmod": "2023-10-26 00:19:03", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Mahinthichaichan-P", "name": { "family": "Mahinthichaichan", "given": "Paween" }, "orcid": "0000-0002-2216-4482" }, { "id": "Morris-D-M", "name": { "family": "Morris", "given": "Dylan" } }, { "id": "Wang-Yi", "name": { "family": "Wang", "given": "Yi" }, "orcid": "0000-0002-4174-8790" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Tajkhorshid-E", "name": { "family": "Tajkhorshid", "given": "Emad" }, "orcid": "0000-0001-8434-1010" } ] }, "title": "Bacterial Carboxysome Shell Proteins are Selectively Permeable to Carbon Fixation Substrates", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2017 Elsevier B.V.\n\nAvailable online 3 February 2017.\n\nMeeting Abstract: 1177PosBoa.", "abstract": "Carboxysome provides an efficient mechanism for cyanobacteria and chemoautotrophs to fix carbon dioxide (CO_2) and organic metabolites into building blocks of biomolecules. It is a polyhedral body that encapsulates ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), an enzyme that carries out the CO_2 fixation and meanwhile competitively reacts with O_2. Its outer surface is coated by the assembly of thousands of small shell proteins. Many of these shell proteins form oligomeric structures with a semi-permeable 2-3\u00c5 radius central pore, suggesting a favorable feature for the binding of anions such as bicarbonate (HCO_3-), the aqueous soluble form of CO_2. The present study examines the translocation HCO_3-, CO_2 and O_2 through the central pores of different isoforms of shell protein complexes from alpha and beta cyanobacteria. We employed umbrella sampling simulations to calculate partitioning free energy profiles of these small molecules and performed detailed electrostatic analysis of the structures. The results demonstrate that carboxysome shell protein oligomers share a unique feature in that their central pores are preferably selective for HCO_3- over hydrophobic CO_2 and O_2 gases. The pores are found to be hydrated and are electropositive, thus favoring HCO_3- and Cl- anions. Hence, as the carboxysome encapsulates carbonic anhydrase enzymes which dehydrates HCO_3- to CO_2, the preferential uptake of HCO_3-(instead of CO_2) into the carboxysomal lumen from the cytoplasm is an intrinsic way to minimize the reaction between O_2 and the RuBisCO and to increase the concentration of CO_2 around the RuBisCO. The results also provide insight into the assembled orientations of the shell proteins, which is necessary for solving a full atomic model of the carboxysome.", "date": "2017-02-03", "date_type": "published", "publication": "Biophysical Journal", "volume": "112", "number": "3", "publisher": "Biophysical Society", "pagerange": "239a", "id_number": "CaltechAUTHORS:20170629-135634085", "issn": "0006-3495", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170629-135634085", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "collection": "CaltechAUTHORS", "doi": "10.1016/j.bpj.2016.11.1309", "resource_type": "article", "pub_year": "2017", "author_list": "Mahinthichaichan, Paween; Morris, Dylan; et el." }, { "id": "https://authors.library.caltech.edu/records/c7wa0-j6j26", "eprint_id": 71196, "eprint_status": "archive", "datestamp": "2023-08-22 19:22:31", "lastmod": "2023-10-23 15:28:33", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Tavormina-P-L", "name": { "family": "Tavormina", "given": "Patricia L." } }, { "id": "Kellermann-M-Y", "name": { "family": "Kellermann", "given": "Matthias Y." } }, { "id": "Antony-C-P", "name": { "family": "Antony", "given": "Chakkiath Paul" } }, { "id": "Tocheva-E-I", "name": { "family": "Tocheva", "given": "Elitza I." }, "orcid": "0000-0002-4869-8319" }, { "id": "Dalleska-N-F", "name": { "family": "Dalleska", "given": "Nathan F." }, "orcid": "0000-0002-2059-1587" }, { "id": "Jensen-A-J", "name": { "family": "Jensen", "given": "Ashley J." } }, { "id": "Valentine-D-L", "name": { "family": "Valentine", "given": "David L." } }, { "id": "Hinrichs-K-U", "name": { "family": "Hinrichs", "given": "Kai-Uwe" }, "orcid": "0000-0002-0739-9291" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Dubilier-N", "name": { "family": "Dubilier", "given": "Nicole" }, "orcid": "0000-0002-9394-825X" }, { "id": "Orphan-V-J", "name": { "family": "Orphan", "given": "Victoria J." }, "orcid": "0000-0002-5374-6178" } ] }, "title": "Starvation and recovery in the deep-sea methanotroph Methyloprofundus sedimenti", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2016 John Wiley & Sons Ltd. \n\nIssue online: \n6 January 2017;\n\nVersion of record online: \n22 November 2016;\n\nAccepted manuscript online: \n14 October 2016;\n\nManuscript Accepted: \n8 October 2016.\n\n\nGC-FID measurements were performed in the Environmental Analysis Center at Caltech. We thank Paul Magyar for assistance with GC-FID, and Songye Chen for assistance segmenting crytomographic files. Special thanks for electron microscopy support from Dr. Alasdair McDowall, Howard Hughes Medical Institute. The Caltech electron microscopy facility is supported in part by the Gordon and Betty Moore Foundation, the Agouron Institute and the Beckman Foundation. Funding for this work was provided by the Gordon and Betty Moore Foundation (GBMF3780, VJO; GBMF3811, ND) and the National Science Foundation (OCE-1046144, DLV; EAR-0950600, MYK).\n\nAccepted Version - Tavormina_et_al-2016-Molecular_Microbiology.pdf
Supplemental Material - mmi13553-sup-0001-SuppMov01.mov
Supplemental Material - mmi13553-sup-0002-SuppMov02.mov
Supplemental Material - mmi13553-sup-0003-SuppInfo.pdf
", "abstract": "In the deep ocean, the conversion of methane into derived carbon and energy drives the establishment of diverse faunal communities. Yet specific biological mechanisms underlying the introduction of methane-derived carbon into the food web remain poorly described, due to a lack of cultured representative deep-sea methanotrophic prokaryotes. Here, the response of the deep-sea aerobic methanotroph Methyloprofundus sedimenti to methane starvation and recovery was characterized. By combining lipid analysis, RNA analysis, and electron cryotomography, it was shown that M. sedimenti undergoes discrete cellular shifts in response to methane starvation, including changes in headgroup-specific fatty acid saturation levels, and reductions in cytoplasmic storage granules. Methane starvation is associated with a significant increase in the abundance of gene transcripts pertinent to methane oxidation. Methane reintroduction to starved cells stimulates a rapid, transient extracellular accumulation of methanol, revealing a way in which methane-derived carbon may be routed to community members. This study provides new understanding of methanotrophic responses to methane starvation and recovery, and lays the initial groundwork to develop Methyloprofundus as a model chemosynthesizing bacterium from the deep sea.", "date": "2017-01", "date_type": "published", "publication": "Molecular Microbiology", "volume": "103", "number": "2", "publisher": "Blackwell", "pagerange": "242-252", "id_number": "CaltechAUTHORS:20161017-155437081", "issn": "0950-382X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161017-155437081", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Agouron Institute" }, { "agency": "Arnold and Mabel Beckman Foundation" }, { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GBMF3780" }, { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GBMF3811" }, { "agency": "NSF", "grant_number": "OCE-1046144" }, { "agency": "NSF", "grant_number": "EAR-0950600" } ] }, "local_group": { "items": [ { "id": "Division-of-Geological-and-Planetary-Sciences" } ] }, "doi": "10.1111/mmi.13553", "primary_object": { "basename": "mmi13553-sup-0003-SuppInfo.pdf", "url": "https://authors.library.caltech.edu/records/c7wa0-j6j26/files/mmi13553-sup-0003-SuppInfo.pdf" }, "related_objects": [ { "basename": "Tavormina_et_al-2016-Molecular_Microbiology.pdf", "url": "https://authors.library.caltech.edu/records/c7wa0-j6j26/files/Tavormina_et_al-2016-Molecular_Microbiology.pdf" }, { "basename": "mmi13553-sup-0001-SuppMov01.mov", "url": "https://authors.library.caltech.edu/records/c7wa0-j6j26/files/mmi13553-sup-0001-SuppMov01.mov" }, { "basename": "mmi13553-sup-0002-SuppMov02.mov", "url": "https://authors.library.caltech.edu/records/c7wa0-j6j26/files/mmi13553-sup-0002-SuppMov02.mov" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Tavormina, Patricia L.; Kellermann, Matthias Y.; et el." }, { "id": "https://authors.library.caltech.edu/records/pc9m1-fze47", "eprint_id": 75600, "eprint_status": "archive", "datestamp": "2023-08-19 00:19:53", "lastmod": "2023-10-25 15:10:15", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Nguyen-Lam-Thanh", "name": { "family": "Nguyen", "given": "L. T." }, "orcid": "0000-0002-0756-0911" }, { "id": "Swulius-Matthew-T", "name": { "family": "Swulius", "given": "M. T." } }, { "id": "Mishra-Mithilesh", "name": { "family": "Mishra", "given": "M." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "G. J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Constriction mechanism of the actomyosin ring", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2016 American Society for Cell Biology.\n\nPublished - Nguyen_2016pP1851.pdf
", "abstract": "Cytokinesis in most eukaryotic cells is orchestrated by a contractile actomyosin ring. While many of the proteins involved are known, the mechanism of constriction remains unclear. Based on the current literature and new 3D molecular details from electron cryotomography, here we developed 3D coarse\u2010grained models of actin filaments, unipolar and bipolar myosins, actin crosslinkers, and membranes and simulated their interactions. Exploring a matrix of possible actomyosin configurations showed \nthat node\u2010based architectures like those presently described for ring assembly result in membrane \npuckers not seen in EM images of real cells. Instead, actin and myosin are more likely uniformly distributed around the ring. In the model that best matches data from fluorescence microscopy, electron cryotomography, and biochemical experiments, ring tension is generated by interactions \nbetween bipolar myosins and actin, and transmitted to the membrane via unipolar myosins.", "date": "2016-12", "date_type": "published", "publication": "Molecular Biology of the Cell", "volume": "27", "publisher": "American Society for Cell Biology", "pagerange": "Art. No. P1851", "id_number": "CaltechAUTHORS:20170331-135448715", "issn": "1059-1524", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170331-135448715", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "collection": "CaltechAUTHORS", "primary_object": { "basename": "Nguyen_2016pP1851.pdf", "url": "https://authors.library.caltech.edu/records/pc9m1-fze47/files/Nguyen_2016pP1851.pdf" }, "resource_type": "article", "pub_year": "2016", "author_list": "Nguyen, L. T.; Swulius, M. T.; et el." }, { "id": "https://authors.library.caltech.edu/records/b3b6r-sk879", "eprint_id": 75593, "eprint_status": "archive", "datestamp": "2023-08-19 00:19:21", "lastmod": "2023-10-25 15:10:00", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Carter-Stephen-D", "name": { "family": "Carter", "given": "S. D." }, "orcid": "0000-0002-4237-4276" }, { "id": "Mageswaran-Shrawan-K", "name": { "family": "Mageswaran", "given": "S. K." } }, { "id": "Farino-Zachary-J", "name": { "family": "Farino", "given": "Z. J." } }, { "id": "Mamede-J-I", "name": { "family": "Mamede", "given": "J. I." } }, { "id": "Hope-Thomas-J", "name": { "family": "Hope", "given": "T. J." } }, { "id": "Frank-J", "name": { "family": "Frank", "given": "J." } }, { "id": "Freyberg-Zachary", "name": { "family": "Freyberg", "given": "Z." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "G. J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Development of cryogenic correlated light electron microscopy methods to study mechanisms of intracellular trafficking and their relationships to the secretory pathway", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2016 American Society for Cell Biology.\n\nPublished - Carter_2016pP30.pdf
", "abstract": "The application of cryogenic electron microscopy (cryo\u2010EM) to the study of cellular ultrastructure provides a resolution several orders of magnitude better than light microscopy. Although this approach is increasingly applied in situ, it suffers from limitations in our ability to target imaging to specific intracellular features including the subcellular localization of specific events of interest. Cryogenic correlated light and electron microscopy (cryo\u2010CLEM) helps to overcome this problem by spatially locating areas of interest inside cells using fluorescence from genetically tagged or stained cellular\nmolecules and allows for the visualization of localized fluorescently\u2010tagged proteins down to the level of individual organelles. Here, we attempted to study the secretory pathway in a specialized mammalian cell line, insulin\u2010secreting INS\u20101E cells, expressing genetically\u2010encoded fluorophores as a model system to develop a cryo\u2010CLEM methodology. We discovered that there are many bright sources of autofluorescence in frozen cells. Based on our initial observations and the current understanding in the\nfield, we hypothesized that autofluorescence from endogenous cellular substrates exhibits a broader spectrum of fluorescence than the fluorescence range of our expressed fluorescent proteins. To test this, we developed a quantitative approach to discriminate between autofluorescence and the fluorescent signal from genetically\u2010encoded fluorophores by measuring fluorescent intensities across different bandwidths. To validate this new methodology, we visualized multiple fluorophore\u2010tagged\norganelle markers in our experimental cell system. We found that DsRed2\u2010cytochrome c oxidase and chromogranin A\u2010GFP proteins were targeted in INS\u20101E cells to mitochondria and secretory granules by cryo\u2010CLEM, consistent with their respective well\u2010established intracellular localizations. Moreover, these fluorescent signals were clearly distinguishable from autofluorescence emanating from endogenous structures including insulin crystals and multilamellar bodies. Overall, our novel cryo\u2010CLEM methods\nopen the door to the study of cellular phenomena and structures with a new degree of specificity.", "date": "2016-12", "date_type": "published", "publication": "Molecular Biology of the Cell", "volume": "27", "publisher": "American Society for Cell Biology", "pagerange": "Art. No. P30", "id_number": "CaltechAUTHORS:20170331-131655781", "issn": "1059-1524", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170331-131655781", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "collection": "CaltechAUTHORS", "primary_object": { "basename": "Carter_2016pP30.pdf", "url": "https://authors.library.caltech.edu/records/b3b6r-sk879/files/Carter_2016pP30.pdf" }, "resource_type": "article", "pub_year": "2016", "author_list": "Carter, S. D.; Mageswaran, S. K.; et el." }, { "id": "https://authors.library.caltech.edu/records/kncjn-2mf52", "eprint_id": 71644, "eprint_status": "archive", "datestamp": "2023-08-22 19:06:56", "lastmod": "2023-10-23 15:58:52", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wang-Haoqing", "name": { "family": "Wang", "given": "Haoqing" }, "orcid": "0000-0003-0277-3018" }, { "id": "Cohen-Alexander-A", "name": { "family": "Cohen", "given": "Alexander A." }, "orcid": "0000-0002-2818-656X" }, { "id": "Galimidi-Rachel-P", "name": { "family": "Galimidi", "given": "Rachel P." } }, { "id": "Gristick-Harry-B", "name": { "family": "Gristick", "given": "Harry B." }, "orcid": "0000-0002-1957-2821" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" } ] }, "title": "Cryo-EM structure of a CD4-bound open HIV-1 envelope trimer reveals structural rearrangements of the gp120 V1V2 loop", "ispublished": "pub", "full_text_status": "public", "keywords": "cryo-EM; HIV-1 Env trimer; CD4; HIV-1 coreceptor; conformational change", "note": "\u00a9 2016 National Academy of Sciences. \n\nContributed by Pamela J. Bjorkman, September 24, 2016 (sent for review September 9, 2016; reviewed by Stephen C. Harrison and Alasdair C. Steven). Published online before print October 31, 2016. \n\nWe thank Zhiheng Yu, Chuan Hong, and Rick Huang (Janelia Farm) for assistance with cryo-EM data collection and motion correction; Hironori Sato for coordinates of the molecular dynamics model of full-length gp120; Sriram Subramaniam for gp120 coordinates from the KNH1144 SOSIP.681\u201317b complex; Alasdair McDowall and Songye Chen for training in cryo-EM techniques and data processing; Anthony West for performing alignment calculations; Jost Vielmetter and the Caltech Protein Expression Center for transfections and protein expression; and members of the P.J.B. and G.J.J. laboratories for helpful discussions and critical reading of the manuscript. This research was supported by the National Institutes of Health Grant 2 P50 GM082545-06 (to P.J.B.), National Institute Of Allergy and Infectious Diseases of the National Institutes of Health Grant HIVRAD P01 AI100148 (to P.J.B.), and the Bill and Melinda Gates Foundation Collaboration for AIDS Vaccine Discovery Grant 1040753 (to P.J.B.). We thank the Gordon and Betty Moore and Beckman Foundations for gifts to Caltech to support electron microscopy. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. \n\nAuthor contributions: H.W. and P.J.B. designed research; H.W. and A.A.C. performed research; H.W., A.A.C., R.P.G., H.B.G., G.J.J., and P.J.B. analyzed data; and H.W., G.J.J., and P.J.B. wrote the paper. \n\nReviewers: S.C.H., Children's Hospital Harvard Medical School and Howard Hughes Medical Institute; and A.C.S., National Institute of Arthritis and Musculoskeletal and Skin Diseases/NIH. \n\nThe authors declare no conflict of interest. \n\nData deposition: Data were deposited into the Protein Data Bank, www.pdb.org (PDB ID code 5THR) and The Electron Microscopy Data Bank, https://www.ebi.ac.uk/pdbe/emdb/ (entry no. EMD-8407). \n\nThis article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1615939113/-/DCSupplemental.\n\nPublished - PNAS-2016-Wang-E7151-8.pdf
Supplemental Material - pnas.1615939113.sapp.pdf
", "abstract": "The HIV-1 envelope (Env) glycoprotein, a trimer of gp120\u2013gp41 heterodimers, relies on conformational flexibility to function in fusing the viral and host membranes. Fusion is achieved after gp120 binds to CD4, the HIV-1 receptor, and a coreceptor, capturing an open conformational state in which the fusion machinery on gp41 gains access to the target cell membrane. In the well-characterized closed Env conformation, the gp120 V1V2 loops interact at the apex of the Env trimer. Less is known about the structure of the open CD4-bound state, in which the V1V2 loops must rearrange and separate to allow access to the coreceptor binding site. We identified two anti\u2013HIV-1 antibodies, the coreceptor mimicking antibody 17b and the gp120\u2013gp41 interface-spanning antibody 8ANC195, that can be added as Fabs to a soluble native-like Env trimer to stabilize it in a CD4-bound conformation. Here, we present an 8.9-\u00c5 cryo-electron microscopy structure of a BG505 Env\u2013sCD4\u201317b\u20138ANC195 complex, which reveals large structural rearrangements in gp120, but small changes in gp41, compared with closed Env structures. The gp120 protomers are rotated and separated in the CD4-bound structure, and the three V1V2 loops are displaced by \u223c40 \u00c5 from their positions at the trimer apex in closed Env to the sides of the trimer in positions adjacent to, and interacting with, the three bound CD4s. These results are relevant to understanding CD4-induced conformational changes leading to coreceptor binding and fusion, and HIV-1 Env conformational dynamics, and describe a target structure relevant to drug design and vaccine efforts.", "date": "2016-11-15", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "113", "number": "46", "publisher": "National Academy of Sciences", "pagerange": "E7151-E7158", "id_number": "CaltechAUTHORS:20161101-072102928", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161101-072102928", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P50 GM082545-06" }, { "agency": "NIH", "grant_number": "P01 AI100148" }, { "agency": "Bill and Melinda Gates Foundation", "grant_number": "1040753" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Arnold and Mabel Beckman Foundation" } ] }, "doi": "10.1073/pnas.1615939113", "pmcid": "PMC5135367", "primary_object": { "basename": "pnas.1615939113.sapp.pdf", "url": "https://authors.library.caltech.edu/records/kncjn-2mf52/files/pnas.1615939113.sapp.pdf" }, "related_objects": [ { "basename": "PNAS-2016-Wang-E7151-8.pdf", "url": "https://authors.library.caltech.edu/records/kncjn-2mf52/files/PNAS-2016-Wang-E7151-8.pdf" } ], "resource_type": "article", "pub_year": "2016", "author_list": "Wang, Haoqing; Cohen, Alexander A.; et el." }, { "id": "https://authors.library.caltech.edu/records/y5wta-5nf96", "eprint_id": 66226, "eprint_status": "archive", "datestamp": "2023-08-20 14:18:13", "lastmod": "2023-10-18 17:17:01", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Skennerton-Connor-T", "name": { "family": "Skennerton", "given": "Connor T." }, "orcid": "0000-0003-1320-4873" }, { "id": "Haroon-Mohamed-F", "name": { "family": "Haroon", "given": "Mohamed F." } }, { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Shi-Jian", "name": { "family": "Shi", "given": "Jian" }, "orcid": "0000-0003-3810-5302" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Tyson-Gene-W", "name": { "family": "Tyson", "given": "Gene W." }, "orcid": "0000-0001-8559-9427" }, { "id": "Orphan-V-J", "name": { "family": "Orphan", "given": "Victoria J." }, "orcid": "0000-0002-5374-6178" } ] }, "title": "Phylogenomic analysis of Candidatus 'Izimaplasma' species: free-living representatives from a Tenericutes clade found in methane seeps", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2016 International Society for Microbial Ecology. \n\nReceived 13 January 2016; Revised 29 February 2016; Accepted 4 March 2016; Advance online publication 8 April 2016. \n\nThis work is funded by the Gordon and Betty Moore Foundation through Grant GBMF3780 and the US Department of Energy, Office of Science, Office of Biological Environmental Research under award numbers DE-SC0003940 and DE-SC0010574 (to VJO). Additional support was provided by Caltech's Center for Environmental Microbial Interactions and the Howard Hughes Medical Institute. We thank D Smith, S Scheller, S Zinder, J Hemp and D Newman for helpful discussions and M Imelfort for bioinformatics assistance. GWT was supported by an ARC Queen Elizabeth II fellowship (ARC-DP1093175). \n\nThe authors declare no conflict of interest.\n\nSupplemental Material - ismej201655x1.doc
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Supplemental Material - ismej201655x9.jpg
", "abstract": "Tenericutes are a unique class of bacteria that lack a cell wall and are typically parasites or commensals of eukaryotic hosts. Environmental 16S rDNA surveys have identified a number of tenericute clades in diverse environments, introducing the possibility that these Tenericutes may represent non-host-associated, free-living microorganisms. Metagenomic sequencing of deep-sea methane seep sediments resulted in the assembly of two genomes from a Tenericutes-affiliated clade currently known as 'NB1-n' (SILVA taxonomy) or 'RF3' (Greengenes taxonomy). Metabolic reconstruction revealed that, like cultured members of the Mollicutes, these 'NB1-n' representatives lack a tricarboxylic acid cycle and instead use anaerobic fermentation of simple sugars for substrate level phosphorylation. Notably, the genomes also contained a number of unique metabolic features including hydrogenases and a simplified electron transport chain containing an RNF complex, cytochrome bd oxidase and complex I. On the basis of the metabolic potential predicted from the annotated genomes, we devised an anaerobic enrichment media that stimulated the growth of these Tenericutes at 10\u2009\u00b0C, resulting in a mixed culture where these organisms represented ~60% of the total cells by targeted fluorescence in situ hybridization (FISH). Visual identification by FISH confirmed these organisms were not directly associated with Eukaryotes and electron cryomicroscopy of cells in the enrichment culture confirmed an ultrastructure consistent with the defining phenotypic property of Tenericutes, with a single membrane and no cell wall. On the basis of their unique gene content, phylogenetic placement and ultrastructure, we propose these organisms represent a novel class within the Tenericutes, and suggest the names Candidatus 'Izimaplasma sp. HR1' and Candidatus 'Izimaplasma sp. HR2' for the two genome representatives.", "date": "2016-11", "date_type": "published", "publication": "ISME Journal", "volume": "10", "number": "11", "publisher": "Nature Publishing Group", "pagerange": "2679-2692", "id_number": "CaltechAUTHORS:20160418-080655842", "issn": "1751-7362", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160418-080655842", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GBMF3780" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-SC0003940" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-SC0010574" }, { "agency": "Caltech" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Australian Research Council", "grant_number": "DP1093175" }, { "agency": "Caltech Center for Environmental Microbial Interactions (CEMI)" } ] }, "local_group": { "items": [ { "id": "Caltech-Center-for-Environmental-Microbial-Interactions-(CEMI)" }, { "id": "Division-of-Geological-and-Planetary-Sciences" } ] }, "doi": "10.1038/ismej.2016.55", "pmcid": "PMC5113845", "primary_object": { "basename": "ismej201655x1.doc", "url": "https://authors.library.caltech.edu/records/y5wta-5nf96/files/ismej201655x1.doc" }, "related_objects": [ { "basename": "ismej201655x4.jpg", "url": "https://authors.library.caltech.edu/records/y5wta-5nf96/files/ismej201655x4.jpg" }, { "basename": "ismej201655x7.jpg", "url": "https://authors.library.caltech.edu/records/y5wta-5nf96/files/ismej201655x7.jpg" }, { "basename": "ismej201655x10.jpg", "url": "https://authors.library.caltech.edu/records/y5wta-5nf96/files/ismej201655x10.jpg" }, { "basename": "ismej201655x11.xls", "url": "https://authors.library.caltech.edu/records/y5wta-5nf96/files/ismej201655x11.xls" }, { "basename": "ismej201655x3.jpg", "url": "https://authors.library.caltech.edu/records/y5wta-5nf96/files/ismej201655x3.jpg" }, { "basename": "ismej201655x5.jpg", "url": "https://authors.library.caltech.edu/records/y5wta-5nf96/files/ismej201655x5.jpg" }, { "basename": "ismej201655x6.jpg", "url": "https://authors.library.caltech.edu/records/y5wta-5nf96/files/ismej201655x6.jpg" }, { "basename": "ismej201655x9.jpg", "url": "https://authors.library.caltech.edu/records/y5wta-5nf96/files/ismej201655x9.jpg" }, { "basename": "ismej201655x8.jpg", "url": "https://authors.library.caltech.edu/records/y5wta-5nf96/files/ismej201655x8.jpg" }, { "basename": "ismej201655x12.xls", "url": "https://authors.library.caltech.edu/records/y5wta-5nf96/files/ismej201655x12.xls" }, { "basename": "ismej201655x13.doc", "url": "https://authors.library.caltech.edu/records/y5wta-5nf96/files/ismej201655x13.doc" }, { "basename": "ismej201655x2.jpg", "url": "https://authors.library.caltech.edu/records/y5wta-5nf96/files/ismej201655x2.jpg" } ], "resource_type": "article", "pub_year": "2016", "author_list": "Skennerton, Connor T.; Haroon, Mohamed F.; et el." }, { "id": "https://authors.library.caltech.edu/records/46fx5-9jm11", "eprint_id": 70053, "eprint_status": "archive", "datestamp": "2023-08-22 18:41:57", "lastmod": "2023-10-20 21:22:26", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Ortega-Davi-R", "name": { "family": "Ortega", "given": "Davi R." }, "orcid": "0000-0002-8344-2335" }, { "id": "Mann-Petra", "name": { "family": "Mann", "given": "Petra" } }, { "id": "Kj\u00e6r-Andreas", "name": { "family": "Kj\u00e6r", "given": "Andreas" }, "orcid": "0000-0002-0096-5764" }, { "id": "Ringgaard-Simon", "name": { "family": "Ringgaard", "given": "Simon" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Chemotaxis cluster 1 proteins form cytoplasmic arrays in Vibrio cholera and are stabilized by a double signaling domain receptor DosM", "ispublished": "pub", "full_text_status": "public", "keywords": "chemotaxis; chemoreceptor arrays; Vibrio cholerae; electron cryotomography; microscopy", "note": "\u00a9 2016 National Academy of Sciences.\n\nEdited by Caroline S. Harwood, University of Washington, Seattle, WA, and approved July 19, 2016 (received for review March 22, 2016). Published online before print August 29, 2016. \n\nWe thank Drs. Zhiheng Yu, Jason de la Cruz, Chuan Hong, and Rick Huang for microscopy support at the Howard Hughes Medical Institute Janelia Research Campus. This work was supported by National Institute of General Medical Sciences Grant GM101425 (to G.J.J.) and by the Max Planck Society (S.R.). \n\nAuthor contributions: A.B., D.R.O., S.R., and G.J.J. designed research; A.B., D.R.O., P.M., and A.K. performed research; A.B., D.R.O., P.M., A.K., and S.R. analyzed data; and A.B., D.R.O., S.R., and G.J.J. wrote the paper. \n\nThe authors declare no conflict of interest. \n\nThis article is a PNAS Direct Submission. \n\nData deposition: The electron cryotomography subtomogram average density map reported in this paper has been deposited in the Electron Microscopy Data Bank, www.emdatabank.org (accession no. EMD-3398).\n\nPublished - PNAS-2016-Briegel-10412-7.pdf
", "abstract": "Nearly all motile bacterial cells use a highly sensitive and adaptable sensory system to detect changes in nutrient concentrations in the environment and guide their movements toward attractants and away from repellents. The best-studied bacterial chemoreceptor arrays are membrane-bound. Many motile bacteria contain one or more additional, sometimes purely cytoplasmic, chemoreceptor systems. Vibrio cholerae contains three chemotaxis clusters (I, II, and III). Here, using electron cryotomography, we explore V. cholerae's cytoplasmic chemoreceptor array and establish that it is formed by proteins from cluster I. We further identify a chemoreceptor with an unusual domain architecture, DosM, which is essential for formation of the cytoplasmic arrays. DosM contains two signaling domains and spans the two-layered cytoplasmic arrays. Finally, we present evidence suggesting that this type of receptor is important for the structural stability of the cytoplasmic array.", "date": "2016-09-13", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "113", "number": "37", "publisher": "National Academy of Sciences", "pagerange": "10412-10417", "id_number": "CaltechAUTHORS:20160831-084712382", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160831-084712382", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM101425" }, { "agency": "Max Planck Society" } ] }, "doi": "10.1073/pnas.1604693113", "pmcid": "PMC5027440", "primary_object": { "basename": "PNAS-2016-Briegel-10412-7.pdf", "url": "https://authors.library.caltech.edu/records/46fx5-9jm11/files/PNAS-2016-Briegel-10412-7.pdf" }, "resource_type": "article", "pub_year": "2016", "author_list": "Briegel, Ariane; Ortega, Davi R.; et el." }, { "id": "https://authors.library.caltech.edu/records/djvkr-da869", "eprint_id": 69339, "eprint_status": "archive", "datestamp": "2023-08-20 13:34:16", "lastmod": "2023-10-23 15:15:19", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Tocheva-E-I", "name": { "family": "Tocheva", "given": "Elitza I." }, "orcid": "0000-0002-4869-8319" }, { "id": "Ortega-D-R", "name": { "family": "Ortega", "given": "Davi R." }, "orcid": "0000-0002-8344-2335" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Author's reply", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2016 Macmillan Publishers Limited. \n\nPublished online 25 July 2016. \n\nThe authors declare no competing interests.", "abstract": "In regard to the comments on our Opinion article (Sporulation, bacterial cell envelopes and the origin of life. Nat. Rev. Microbiol. 14, 535\u2013542 (2016)), by Iain C. Sutcliffe and Lynn G. Dover (Comment on Tocheva et al. \"Sporulation, bacterial cell envelopes and the origin of life\". Nat. Rev. Microbiol. http://dx.doi.org/10.1038/nrmicro.2016.113 (2016)), we wholeheartedly agree that it will be interesting to see how our hypothesis holds up to future discoveries of new and potentially different phyla, and said so ourselves in the 'evolutionary implications' section of our article.", "date": "2016-09", "date_type": "published", "publication": "Nature Reviews Microbiology", "volume": "14", "number": "9", "publisher": "Nature Publishing Group", "pagerange": "600", "id_number": "CaltechAUTHORS:20160801-081533020", "issn": "1740-1526", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160801-081533020", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1038/nrmicro.2016.114", "resource_type": "article", "pub_year": "2016", "author_list": "Tocheva, Elitza I.; Ortega, Davi R.; et el." }, { "id": "https://authors.library.caltech.edu/records/z8z2j-whb03", "eprint_id": 67115, "eprint_status": "archive", "datestamp": "2023-08-20 13:03:29", "lastmod": "2023-10-18 20:33:28", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Tocheva-Elitza-I", "name": { "family": "Tocheva", "given": "Elitza I." }, "orcid": "0000-0002-4869-8319" }, { "id": "Ortega-Davi-R", "name": { "family": "Ortega", "given": "Davi R." }, "orcid": "0000-0002-8344-2335" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Sporulation, bacterial cell envelopes, and the origin of life", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2016 Macmillan Publishers Limited. \n\nPublished online 27 June 2016. \n\nCryotomography in the Jensen laboratory is supported, in part, by the US National Institutes of Health (including grant RO1 GM101425), the Howard Hughes Medical institute (HHMI) and the Beckman Institute at California Institute of Technology (Caltech), Pasadena, USA. Further support for this publication came from the John Templeton Foundation. The opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the John Templeton Foundation. The authors thank C. Cleland, T. Nordheim, L. Brengman, K. Willford and J. Eisen for helpful discussions about the early Earth and possible roots of the tree of life. \n\nThe authors declare no competing interests.\n\nAccepted Version - nihms825452.pdf
Submitted - 041624.full.pdf
", "abstract": "Electron cryotomography (ECT) enables the 3D reconstruction of intact cells in a near-native state. Images produced by ECT have led to the proposal that an ancient sporulation-like event gave rise to the second membrane in diderm bacteria. Tomograms of sporulating monoderm and diderm bacterial cells show how sporulation can lead to the generation of diderm cells. Tomograms of Gram-negative and Gram-positive cell walls and purified sacculi suggest that they are more closely related than previously thought and support the hypothesis that they share a common origin. Mapping the distribution of cell envelope architectures onto a recent phylogenetic tree of life indicates that the diderm cell plan, and therefore the sporulation-like event that gave rise to it, must be very ancient. One explanation for this model is that during the cataclysmic transitions of the early Earth, cellular evolution may have gone through a bottleneck in which only spores survived, which implies that the last bacterial common ancestor was a spore.", "date": "2016-08", "date_type": "published", "publication": "Nature Reviews Microbiology", "volume": "14", "number": "8", "publisher": "Nature Publishing Group", "pagerange": "535-542", "id_number": "CaltechAUTHORS:20160516-095404921", "issn": "1740-1526", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160516-095404921", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "RO1 GM101425" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Caltech Beckman Institute" }, { "agency": "John Templeton Foundation" } ] }, "doi": "10.1038/nrmicro.2016.85", "pmcid": "PMC5327842", "primary_object": { "basename": "041624.full.pdf", "url": "https://authors.library.caltech.edu/records/z8z2j-whb03/files/041624.full.pdf" }, "related_objects": [ { "basename": "nihms825452.pdf", "url": "https://authors.library.caltech.edu/records/z8z2j-whb03/files/nihms825452.pdf" } ], "resource_type": "article", "pub_year": "2016", "author_list": "Tocheva, Elitza I.; Ortega, Davi R.; et el." }, { "id": "https://authors.library.caltech.edu/records/cd1xr-gsa09", "eprint_id": 67885, "eprint_status": "archive", "datestamp": "2023-08-20 12:03:47", "lastmod": "2023-10-19 22:02:35", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Li-Yen-Li", "name": { "family": "Li", "given": "Yen-Li" } }, { "id": "Chandrasekaran-V", "name": { "family": "Chandrasekaran", "given": "Viswanathan" } }, { "id": "Carter-S-D", "name": { "family": "Carter", "given": "Stephen D." }, "orcid": "0000-0002-4237-4276" }, { "id": "Woodward-C-L", "name": { "family": "Woodward", "given": "Cora L." } }, { "id": "Christensen-D-E", "name": { "family": "Christensen", "given": "Devin E." } }, { "id": "Dryden-K-A", "name": { "family": "Dryden", "given": "Kelly A." } }, { "id": "Pornillos-O", "name": { "family": "Pornillos", "given": "Owen" } }, { "id": "Yeager-M", "name": { "family": "Yeager", "given": "Mark" } }, { "id": "Ganser-Pronillos-B-K", "name": { "family": "Ganser-Pornillos", "given": "Barbie K." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Sundquist-W-I", "name": { "family": "Sundquist", "given": "Wesley I." } } ] }, "title": "Primate TRIM5 proteins form hexagonal nets on HIV-1 capsids", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2016, Li et al. This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited. \n\nReceived March 22, 2016. Accepted May 19, 2016. Published June 02, 2016. \n\nDeep-etch electron microscopy was performed by Robyn Roth and John Heuser at the Laboratory of Electron Microscopy Sciences, Department of Cell Biology, Washington University School of Medicine. We are grateful to Ruth Pumroy for contributing TRIM5 proteins used in our co-assembly assays and to members of our laboratories for helpful discussions and critical reading of the manuscript. This work was supported by funds from NIH NIGMS P50 082545 (to MY, BKG-P GJJ and WIS). \n\nCompeting interests:\nWesley I Sundquist, Reviewing editor, eLife. The other authors declare that no competing interests exist.\n\nPublished - e16269-download.pdf
Supplemental Material - elife-16269-supp-v2.zip
", "abstract": "TRIM5 proteins are restriction factors that block retroviral infections by binding viral capsids and preventing reverse transcription. Capsid recognition is mediated by C-terminal domains on TRIM5\u03b1 (SPRY) or TRIMCyp (cyclophilin A), which interact weakly with capsids. Efficient capsid recognition also requires the conserved N-terminal tripartite motifs (TRIM), which mediate oligomerization and create avidity effects. To characterize how TRIM5 proteins recognize viral capsids, we developed methods for isolating native recombinant TRIM5 proteins and purifying stable HIV-1 capsids. Biochemical and EM analyses revealed that TRIM5 proteins assembled into hexagonal nets, both alone and on capsid surfaces. These nets comprised open hexameric rings, with the SPRY domains centered on the edges and the B-box and RING domains at the vertices. Thus, the principles of hexagonal TRIM5 assembly and capsid pattern recognition are conserved across primates, allowing TRIM5 assemblies to maintain the conformational plasticity necessary to recognize divergent and pleomorphic retroviral capsids.", "date": "2016-06-02", "date_type": "published", "publication": "eLife", "volume": "5", "publisher": "eLife Sciences Publications", "pagerange": "Art. No. 16269", "id_number": "CaltechAUTHORS:20160613-141038489", "issn": "2050-084X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160613-141038489", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P50 082545" } ] }, "doi": "10.7554/eLife.16269", "pmcid": "PMC4936896", "primary_object": { "basename": "elife-16269-supp-v2.zip", "url": "https://authors.library.caltech.edu/records/cd1xr-gsa09/files/elife-16269-supp-v2.zip" }, "related_objects": [ { "basename": "e16269-download.pdf", "url": "https://authors.library.caltech.edu/records/cd1xr-gsa09/files/e16269-download.pdf" } ], "resource_type": "article", "pub_year": "2016", "author_list": "Li, Yen-Li; Chandrasekaran, Viswanathan; et el." }, { "id": "https://authors.library.caltech.edu/records/gds2x-21p48", "eprint_id": 67098, "eprint_status": "archive", "datestamp": "2023-08-20 11:39:50", "lastmod": "2023-10-23 15:31:43", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Grime-John-M-A", "name": { "family": "Grime", "given": "John M. A." } }, { "id": "Dama-James-F", "name": { "family": "Dama", "given": "James F." }, "orcid": "0000-0001-5891-679X" }, { "id": "Ganser-Pronillos-Barbie-K", "name": { "family": "Ganser-Pornillos", "given": "Barbie K." }, "orcid": "0000-0001-6453-3891" }, { "id": "Woodward-Cora-L", "name": { "family": "Woodward", "given": "Cora L." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Yeager-Mark-J", "name": { "family": "Yeager", "given": "Mark J." }, "orcid": "0000-0002-3301-640X" }, { "id": "Voth-Gregory-A", "name": { "family": "Voth", "given": "Gregory A." }, "orcid": "0000-0002-3267-6748" } ] }, "title": "Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2016 Macmillan Publishers Limited. This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ \n\nReceived 20 July 2015; Accepted 07 April 2016; Published 13 May 2016. \n\nThis research was supported by National Institutes of Health grants P50 GM082545 (G.A.V. and M.Y.) and R01 GM066087 (M.Y.). The computations in this work are part of the Blue Waters sustained-petascale computing project, which is supported by the National Science Foundation (awards OCI-0725070 and ACI-1238993) and the state of Illinois. Blue Waters is a joint effort of the University of Illinois at Urbana-Champaign and its National Center for Supercomputing Applications. This work is also part of the 'Ultra-Coarse-Grained Simulations of Biomolecular Processes at the Petascale' Petascale Computing Resource Allocation (PRAC) support by the National Science Foundation (award number OCI-1440027). \n\nAuthor contributions: J.M.A.G., J.F.D. and G.A.V. conceived the study, designed the simulations and wrote the manuscript. J.M.A.G. performed the simulations. Additional experimental data were provided by C.L.W. Data analysis was performed by J.M.A.G., J.F.D., B.K.G.-P., G.J.J., M.J.Y. and G.A.V. \n\nThe authors declare no competing financial interests.\n\nPublished - ncomms11568.pdf
Submitted - 040741.full.pdf
Supplemental Material - ncomms11568-s1.pdf
", "abstract": "The maturation of HIV-1 viral particles is essential for viral infectivity. During maturation, many copies of the capsid protein (CA) self-assemble into a capsid shell to enclose the viral RNA. The mechanistic details of the initiation and early stages of capsid assembly remain to be delineated. We present coarse-grained simulations of capsid assembly under various conditions, considering not only capsid lattice self-assembly but also the potential disassembly of capsid upon delivery to the cytoplasm of a target cell. The effects of CA concentration, molecular crowding, and the conformational variability of CA are described, with results indicating that capsid nucleation and growth is a multi-stage process requiring well-defined metastable intermediates. Generation of the mature capsid lattice is sensitive to local conditions, with relatively subtle changes in CA concentration and molecular crowding influencing self-assembly and the ensemble of structural morphologies.", "date": "2016-05-13", "date_type": "published", "publication": "Nature Communications", "volume": "7", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 11568", "id_number": "CaltechAUTHORS:20160516-083514191", "issn": "2041-1723", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160516-083514191", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P50 GM082545" }, { "agency": "NIH", "grant_number": "R01 GM066087" }, { "agency": "NSF", "grant_number": "OCI\u20100725070" }, { "agency": "NSF", "grant_number": "ACI\u20101238993" }, { "agency": "State of Illinois" }, { "agency": "NSF", "grant_number": "OCI\u20101440027" } ] }, "doi": "10.1038/ncomms11568", "pmcid": "PMC4869257", "primary_object": { "basename": "040741.full.pdf", "url": "https://authors.library.caltech.edu/records/gds2x-21p48/files/040741.full.pdf" }, "related_objects": [ { "basename": "ncomms11568-s1.pdf", "url": "https://authors.library.caltech.edu/records/gds2x-21p48/files/ncomms11568-s1.pdf" }, { "basename": "ncomms11568.pdf", "url": "https://authors.library.caltech.edu/records/gds2x-21p48/files/ncomms11568.pdf" } ], "resource_type": "article", "pub_year": "2016", "author_list": "Grime, John M. A.; Dama, James F.; et el." }, { "id": "https://authors.library.caltech.edu/records/wt0ta-be438", "eprint_id": 65102, "eprint_status": "archive", "datestamp": "2023-08-20 11:03:34", "lastmod": "2023-10-23 15:25:15", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Oikonomou-Catherine-M", "name": { "family": "Oikonomou", "given": "Catherine M." }, "orcid": "0000-0003-2312-4746" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "A new view into prokaryotic cell biology from electron cryotomography", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2016 Macmillan Publishers Limited. \n\nPublished online 29 February 2016. \n\nThe authors apologize that they could not discuss all of the work in this burgeoning field. The authors thank members of the Jensen laboratory for helpful comments on the manuscript, and J. Ding and Y.-W. Chang for producing the accompanying movie. The authors also thank L. Sockett (University of Nottingham) for the gift of the Bdellovibrio bacteriovorus strain imaged in figure 1 and shown in the accompanying movie. Microbial electron cryotomography (ECT) in the Jensen laboatory is supported, in part, by the Howard Hughes Medical Institute, the US National Institutes of Health (grants RO1 GM101425 and RO1 GM094800), the Beckman Institute at Caltech, Caltech's Center for Environmental Microbial Interactions, and gifts to Caltech from the Gordon and Betty Moore Foundation and the Agouron Institute. \n\nThe authors declare no competing interest.\n\nIt has recently come to the authors' attention that this Review is the first place in which Figure 1 was published.\nYi-Wei Chang, who collected the data for Figure 1 and helped to revise the text, should have been included as an author.\nTherefore, on the title page, the corrected author list should read Catherine M. Oikonomou, Yi-Wei Chang and Grant J. Jensen.\n\nAccepted Version - nihms882786.pdf
Supplemental Material - nrmicro.2016.7-s1.mov
", "abstract": "Electron cryotomography (ECT) enables intact cells to be visualized in 3D in an essentially native state to 'macromolecular' (~4 nm) resolution, revealing the basic architectures of complete nanomachines and their arrangements in situ. Since its inception, ECT has advanced our understanding of many aspects of prokaryotic cell biology, from morphogenesis to subcellular compartmentalization and from metabolism to complex interspecies interactions. In this Review, we highlight how ECT has provided structural and mechanistic insights into the physiology of bacteria and archaea and discuss prospects for the future.", "date": "2016-04", "date_type": "published", "publication": "Nature Reviews Microbiology", "volume": "14", "number": "4", "publisher": "Nature Publishing Group", "pagerange": "205-220", "id_number": "CaltechAUTHORS:20160307-090319472", "issn": "1740-1526", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160307-090319472", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "RO1 GM101425" }, { "agency": "NIH", "grant_number": "RO1 GM094800" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Agouron Institute" }, { "agency": "Caltech Center for Environmental Microbial Interactions (CEMI)" } ] }, "local_group": { "items": [ { "id": "Caltech-Center-for-Environmental-Microbial-Interactions-(CEMI)" } ] }, "doi": "10.1038/nrmicro.2016.7", "pmcid": "PMC5551487", "primary_object": { "basename": "nihms882786.pdf", "url": "https://authors.library.caltech.edu/records/wt0ta-be438/files/nihms882786.pdf" }, "related_objects": [ { "basename": "nrmicro.2016.7-s1.mov", "url": "https://authors.library.caltech.edu/records/wt0ta-be438/files/nrmicro.2016.7-s1.mov" } ], "resource_type": "article", "pub_year": "2016", "author_list": "Oikonomou, Catherine M. and Jensen, Grant J." }, { "id": "https://authors.library.caltech.edu/records/e8cg0-z2m98", "eprint_id": 65345, "eprint_status": "archive", "datestamp": "2023-08-22 17:38:45", "lastmod": "2023-10-23 20:07:59", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Beeby-Morgan-D", "name": { "family": "Beeby", "given": "Morgan" }, "orcid": "0000-0001-6413-9835" }, { "id": "Ribardo-Deborah-A", "name": { "family": "Ribardo", "given": "Deborah A." } }, { "id": "Brennan-Caitlin-A", "name": { "family": "Brennan", "given": "Caitlin A." }, "orcid": "0000-0002-6074-9502" }, { "id": "Ruby-Edward-G", "name": { "family": "Ruby", "given": "Edward G." }, "orcid": "0000-0002-4112-4830" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Hendrixson-David-R", "name": { "family": "Hendrixson", "given": "David R." }, "orcid": "0000-0001-8496-2466" } ] }, "title": "Diverse high-torque bacterial flagellar motors assemble wider stator rings using a conserved protein scaffold", "ispublished": "pub", "full_text_status": "public", "keywords": "bacterial flagellar motors; electron cryo-tomography; macromolecular evolution; torque; Campylobacter", "note": "\u00a9 2016 National Academy of Sciences. Freely available online through the PNAS open access option. \n\nEdited by Scott J. Hultgren, Washington University School of Medicine, St. Louis, MO, and approved February 8, 2016 (received for review September 24, 2015). Published online before print March 14, 2016. \n\nWe thank Anchi Cheng for advice on programming an additional Leginon node; Kelly Hughes for the generous gift of the Salmonella minicell strain TH16943; Tillmann Pape and Amanda Wilson for technical assistance during electron microscopy data collection; and Bonnie Chaban, Velocity Hughes, Ariane Briegel, Alain Filloux, and Richard Berry for critical reading of the manuscript. This work was supported by Biotechnology and Biological Sciences Research Council Grant BB/L023091/1 (to M.B.), Howard Hughes Medical Institute funding (G.J.J.), and National Institutes of Health Grants 5R01AI065539 and 5R21AI103643 (to D.R.H.). \n\nAuthor contributions: M.B., D.A.R., G.J.J., and D.R.H. designed research; M.B. and D.A.R. performed research; M.B., C.A.B., and E.G.R. contributed new reagents/analytic tools; M.B., G.J.J., and D.R.H. analyzed data; and M.B., G.J.J., and D.R.H. wrote the paper. \n\nThis article is a PNAS Direct Submission. \n\nData deposition: The electron cryo-tomography subtomogram average density maps reported in this paper have been deposited in the Electron Microscopy Data Bank (EMD) (accession nos. Salmonella WT: EMD-3154; Vibrio fischeri WT: EMD-3155; Campylobacter jejuni WT: EMD-3150; V. fischeri motB: EMD-3156; C. jejuni motB: EMD-3157; C. jejuni flgQ: EMD-3158; C. jejuni flgP: EMD-3159; C. jejuni pflA: EMD-3160; C. jejuni pflB: EMD-3161; and V. fischeri flgP: EMD-3162). \n\nThe authors declare no conflict of interest. \n\nThis article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1518952113/-/DCSupplemental.\n\nCorrection for \"Diverse high-torque bacterial flagellar motors assemble wider stator rings using a conserved protein scaffold,\" by Morgan Beeby, Deborah A. Ribardo, Caitlin A. Brennan, Edward G. Ruby, Grant J. Jensen, and David R. Hendrixson, which appeared in issue 13, March 29, 2016, of Proc Natl Acad Sci USA (113:E1917\u2013E1926; first published March 14, 2016; 10.1073/pnas.1518952113).\n\nPublished - PNAS-2016-Beeby-E1917-26.pdf
Supplemental Material - pnas.201518952SI.pdf
Erratum - 1605597113.full.pdf
", "abstract": "Although it is known that diverse bacterial flagellar motors produce different torques, the mechanism underlying torque variation is unknown. To understand this difference better, we combined genetic analyses with electron cryo-tomography subtomogram averaging to determine in situ structures of flagellar motors that produce different torques, from Campylobacter and Vibrio species. For the first time, to our knowledge, our results unambiguously locate the torque-generating stator complexes and show that diverse high-torque motors use variants of an ancestrally related family of structures to scaffold incorporation of additional stator complexes at wider radii from the axial driveshaft than in the model enteric motor. We identify the protein components of these additional scaffold structures and elucidate their sequential assembly, demonstrating that they are required for stator-complex incorporation. These proteins are widespread, suggesting that different bacteria have tailored torques to specific environments by scaffolding alternative stator placement and number. Our results quantitatively account for different motor torques, complete the assignment of the locations of the major flagellar components, and provide crucial constraints for understanding mechanisms of torque generation and the evolution of multiprotein complexes.", "date": "2016-03-29", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "113", "number": "13", "publisher": "National Academy of Sciences", "pagerange": "E1917-E1926", "id_number": "CaltechAUTHORS:20160315-073414510", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160315-073414510", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Biotechnology and Biological Sciences Research Council (BBSRC)", "grant_number": "BB/L023091/1" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "5R01AI065539" }, { "agency": "NIH", "grant_number": "5R21AI103643" } ] }, "doi": "10.1073/pnas.1518952113", "pmcid": "PMC4822576", "primary_object": { "basename": "1605597113.full.pdf", "url": "https://authors.library.caltech.edu/records/e8cg0-z2m98/files/1605597113.full.pdf" }, "related_objects": [ { "basename": "PNAS-2016-Beeby-E1917-26.pdf", "url": "https://authors.library.caltech.edu/records/e8cg0-z2m98/files/PNAS-2016-Beeby-E1917-26.pdf" }, { "basename": "pnas.201518952SI.pdf", "url": "https://authors.library.caltech.edu/records/e8cg0-z2m98/files/pnas.201518952SI.pdf" } ], "resource_type": "article", "pub_year": "2016", "author_list": "Beeby, Morgan; Ribardo, Deborah A.; et el." }, { "id": "https://authors.library.caltech.edu/records/d938q-rte49", "eprint_id": 65350, "eprint_status": "archive", "datestamp": "2023-08-20 10:52:45", "lastmod": "2023-10-23 15:25:01", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chang-Yi-Wei", "name": { "family": "Chang", "given": "Yi-Wei" }, "orcid": "0000-0003-2391-473X" }, { "id": "Rettberg-Lee-A", "name": { "family": "Rettberg", "given": "Lee A." }, "orcid": "0000-0002-5366-1609" }, { "id": "Treuner-Lange-Anke", "name": { "family": "Treuner-Lange", "given": "Anke" }, "orcid": "0000-0001-6435-5642" }, { "id": "Iwasa-Janet", "name": { "family": "Iwasa", "given": "Janet" }, "orcid": "0000-0002-4949-7607" }, { "id": "S\u00f8gaard-Andersen-Lotte", "name": { "family": "S\u00f8gaard-Andersen", "given": "Lotte" }, "orcid": "0000-0002-0674-0013" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Architecture of the type IVa pilus machine", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2016 American Association for the Advancement of Science. \n\nReceived 10 August 2015; accepted 13 January 2016. \n\nWe thank C. Oikonomou and D. Ortega for discussions. Supported by NIH grant R01 GM094800B (G.J.J.), the Howard Hughes Medical Institute, the Max Planck Society, and the Deutsche Forschungsgemeinschaft within the framework of the Collaborative Research Center (SFB) 987 \"Microbial Diversity in Environmental Signal Response.\" The 18 subtomogram averages of T4PMs reported in this study have been deposited in the Electron Microscopy Data Bank with accession numbers EMD-3247 (wild type, piliated); EMD-3248 (wild type, empty); EMD-3249 (\u0394pilP, empty); EMD-3250 (PilP-sfGFP, piliated); EMD-3251 (PilP-sfGFP, empty); EMD-3252 (\u0394tsaP, piliated); EMD-3253 (\u0394tsaP, empty); EMD-3254 (PilO-sfGFP, piliated); EMD-3255 (PilO-sfGFP, empty); EMD-3256 (\u0394pilC, empty); EMD-3257 (\u0394pilA, empty); EMD-3258 (\u0394pilV pilW fimU 1+2+3, empty); EMD-3259 (\u0394pilT, piliated); EMD-3260 (\u0394pilB, empty); EMD-3261 (\u0394pilB \u0394pilT, empty); EMD-3262 (\u0394pilM, empty); EMD-3263 (\u0394pilQ\u03b21-\u03b22, piliated); and EMD-3264 (\u0394pilQ\u03b21-\u03b22, empty). The coordinates of the hypothetical T4PM working models have been deposited in the Protein Data Bank with accession numbers 3JC8 (piliated) and 3JC9 (empty), respectively. Author contributions: Y.-W.C. collected the cryo\u2013electron tomography data, which were analyzed by Y.-W.C. and L.A.R.; Y.-W.C. built the T4PM models and generated the movie describing the modeling process; A.T.-L. and L.S.-A. provided the M. xanthus strains and characterized their motility and T4PM component accumulation and localization; J.I. produced the animation of T4PM dynamics; and Y.-W.C., L.S.-A., and G.J.J. wrote the paper.\n\nAccepted Version - nihms962793.pdf
Supplemental Material - Chang.SM.pdf
Supplemental Material - aad2001s1.mov
Supplemental Material - aad2001s2.mov
Supplemental Material - aad2001s3.mov
", "abstract": "Many bacteria, including important pathogens, move by projecting grappling-hook\u2013like extensions called type IV pili from their cell bodies. After these pili attach to other cells or objects in their environment, the bacteria retract the pili to pull themselves forward. Chang et al. used electron cryotomography of intact cells to image the protein machines that extend and retract the pili, revealing where each protein component resides. Putting the known structures of the individual proteins in place like pieces of a three-dimensional puzzle revealed insights into how the machine works, including evidence that ATP hydrolysis by cytoplasmic motors rotates a membrane-embedded adaptor that slips pilin subunits back and forth from the membrane onto the pilus.", "date": "2016-03-11", "date_type": "published", "publication": "Science", "volume": "351", "number": "6278", "publisher": "American Association for the Advancement of Science", "pagerange": "aad2001", "id_number": "CaltechAUTHORS:20160315-090327567", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160315-090327567", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 GM094800B" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Max Planck Society" }, { "agency": "Deutsche Forschungsgemeinschaft (DFG)" } ] }, "doi": "10.1126/science.aad2001", "pmcid": "PMC5929464", "primary_object": { "basename": "aad2001s2.mov", "url": "https://authors.library.caltech.edu/records/d938q-rte49/files/aad2001s2.mov" }, "related_objects": [ { "basename": "aad2001s3.mov", "url": "https://authors.library.caltech.edu/records/d938q-rte49/files/aad2001s3.mov" }, { "basename": "nihms962793.pdf", "url": "https://authors.library.caltech.edu/records/d938q-rte49/files/nihms962793.pdf" }, { "basename": "Chang.SM.pdf", "url": "https://authors.library.caltech.edu/records/d938q-rte49/files/Chang.SM.pdf" }, { "basename": "aad2001s1.mov", "url": "https://authors.library.caltech.edu/records/d938q-rte49/files/aad2001s1.mov" } ], "resource_type": "article", "pub_year": "2016", "author_list": "Chang, Yi-Wei; Rettberg, Lee A.; et el." }, { "id": "https://authors.library.caltech.edu/records/t9zrn-t3042", "eprint_id": 67691, "eprint_status": "archive", "datestamp": "2023-08-20 10:23:33", "lastmod": "2023-10-18 21:23:59", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chang-Yi-Wei", "name": { "family": "Chang", "given": "Yi-Wei" }, "orcid": "0000-0003-2391-473X" }, { "id": "Rettberg-Lee-A", "name": { "family": "Rettberg", "given": "Lee" } }, { "id": "Treuner-Lange-Anke", "name": { "family": "Treuner-Lange", "given": "Anke" } }, { "id": "Iwasa-Janet", "name": { "family": "Iwasa", "given": "Janet" } }, { "id": "S\u00f8gaard-Andersen-Lotte", "name": { "family": "S\u00f8gaard-Andersen", "given": "Lotte" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant" }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Architecture of the Type IVA Pilus Machine", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2016 Biophysical Society. Published by Elsevier Inc.", "abstract": "Type IV pili are part of a widespread superfamily of bacterial and archaeal cell surface structures important for biofilm formation, motility, host adhesion, predation, DNA uptake, protein secretion and virulence. Type IVa pili are anchored in the cell envelope and undergo cycles of extension, adhesion to surfaces and retraction thereby pulling cells forward. The extension/retraction cycles are powered by the type IVa pilus machine (T4PM), the strongest molecular motor identified. Here, we use electron cryotomography of intact Myxococcus xanthus cells to solve the complete three-dimensional architecture of wild-type T4PM in situ in the piliated and non-piliated states at 3-4 nm resolution. T4PM comprise a multi-layered structure that spans the entire cell envelope including an outer membrane pore, four interconnected ring structures in the periplasm and cytoplasm, a cytoplasmic disc and dome, and a periplasmic stem. Comparison of the two structures reveal that piliation is accompanied by large conformational changes. By systematically imaging mutants lacking defined T4PM proteins or with individual proteins fused to tags, the locations of all ten T4PM core components and minor pilins are mapped to these structural features revealing the overall architecture and component map of T4PM. Using available atomic structures, the component maps were informed by building hypothetical models of both piliated and non-piliated forms, which fit the EM maps well and satisfy all known connectivities and structural constraints. The architecture of the T4PM provides new mechanistic insights into pilus extension and retraction and explains the enigmatic switch from extension to retraction.", "date": "2016-02-16", "date_type": "published", "publication": "Biophysical Journal", "volume": "110", "number": "3", "publisher": "Biophysical Society", "pagerange": "468A-469A", "id_number": "CaltechAUTHORS:20160606-134354848", "issn": "0006-3495", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160606-134354848", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.bpj.2015.11.2509", "resource_type": "article", "pub_year": "2016", "author_list": "Chang, Yi-Wei; Rettberg, Lee; et el." }, { "id": "https://authors.library.caltech.edu/records/ckp97-ke650", "eprint_id": 67690, "eprint_status": "archive", "datestamp": "2023-08-20 10:23:27", "lastmod": "2023-10-18 21:23:55", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Nguyen-Lam-T", "name": { "family": "Nguyen", "given": "Lam T." } }, { "id": "Swulius-M-T", "name": { "family": "Swulius", "given": "Matthew" } }, { "id": "Gumbart-J-C", "name": { "family": "Gumbart", "given": "James C." } }, { "id": "Beeby-M-D", "name": { "family": "Beeby", "given": "Morgan" }, "orcid": "0000-0001-6413-9835" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Coarse-Grained Simulations Reveal Mechanisms of Bacterial Morphogenesis", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2016 Biophysical Society. Published by Elsevier Inc.", "abstract": "How cells maintain their characteristic shapes throughout generations of growth is a fundamental question in bacterial cell biology. In most rod-shaped bacteria, the cell shape is determined by a peptidoglycan (PG) sacculus that surrounds the cell preventing lysis from turgor pressure. Despite decades of experiments, how the activities of PG synthesis enzymes are coordinated at the molecular and cellular levels to preserve the integrity and rod shape of the sacculus remains elusive. To explore different mechanistic models of sacculus growth, we have developed a coarse-grained simulation method that allows us to vary the properties and coordination of PG-remodeling enzymes while mechanical properties of the coarse-grained PG are derived from all-atom MD simulations of isolated PG. (Nguyen et al., PNAS. 112, E3689 (2015)). For the first time to our knowledge, individual enzymes, including transglycosylases, transpeptidases and endopeptidases, are explicitly represented. We have revealed the challenges a cell might face while remodeling its sacculus. For example, lysis can easily occur during bond cleavage because of turgor pressure; aggregation of new PG material can occur if enzymes are not processive; and the regular order and rod shape of the sacculus is easily lost if enzymatic activities are not coordinated. Exploring ways a cell might overcome these challenges, we find that local spatial and temporal coordination of the enzymes alone can be sufficient to maintain rod shape. Our results rationalize several experimental results, for instance explaining why the monofunctional transpeptidase PBP2 is essential and suggesting why different enzymes must exist in a complex that inserts new strands in pairs. Our approach also generates testable biological hypotheses. For instance, we predict a role for a housekeeping glycosidase; while our manuscript was in revision, just such a glycosidase was identified in cells (Cho et al., Cell 159, 1300 (2014)).", "date": "2016-02-16", "date_type": "published", "publication": "Biophysical Journal", "volume": "110", "number": "3", "publisher": "Biophysical Society", "pagerange": "468A", "id_number": "CaltechAUTHORS:20160606-134032836", "issn": "0006-3495", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160606-134032836", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.bpj.2015.11.2505", "resource_type": "article", "pub_year": "2016", "author_list": "Nguyen, Lam T.; Swulius, Matthew; et el." }, { "id": "https://authors.library.caltech.edu/records/k8e92-j8838", "eprint_id": 64641, "eprint_status": "archive", "datestamp": "2023-08-20 10:20:25", "lastmod": "2023-10-17 21:34:17", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cornejo-Elias", "name": { "family": "Cornejo", "given": "Elias" } }, { "id": "Subramanian-Poorna", "name": { "family": "Subramanian", "given": "Poorna" } }, { "id": "Li-Zhuo", "name": { "family": "Li", "given": "Zhuo" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Komeili-Arash", "name": { "family": "Komeili", "given": "Arash" } } ] }, "title": "Dynamic Remodeling of the Magnetosome Membrane Is Triggered by the Initiation of Biomineralization", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2016 Cornejo et al. This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived 2 November 2015. Accepted 20 January 2016. Published 16 February 2016. \n\nEditor Yves V. Brun, Indiana University. \n\nWe thank Doroth\u00e9e Murat for her intellectual contributions and outstanding mentorship during the early stages of this project. \n\nNational Science Foundation (NSF) provided funding to Elias Cornejo under grant number DGE 110640. HHS | NIH | National Institute of General Medical Sciences (NIGMS) provided funding to Elias Cornejo and Arash Komeili under grant number R01GM084122. Howard Hughes Medical Institute (HHMI) provided funding to Poorna Subramanian, Zhuo Li, and Grant J. Jensen. \n\nThe funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.\n\nPublished - mBio-2016-Cornejo-.pdf
Supplemental Material - mbo001162688s1.docx
Supplemental Material - mbo001162688sf1.pdf
Supplemental Material - mbo001162688sf2.pdf
Supplemental Material - mbo001162688sf3.pdf
Supplemental Material - mbo001162688sf4.eps
Supplemental Material - mbo001162688st1.docx
Supplemental Material - mbo001162688st2.docx
Supplemental Material - mbo001162688st3.docx
Supplemental Material - mbo001162688st4.docx
Supplemental Material - mbo001162688st5.docx
", "abstract": "Magnetotactic bacteria produce chains of membrane-bound organelles that direct the biomineralization of magnetic nanoparticles. These magnetosome compartments are a model for studying the biogenesis and subcellular organization of bacterial organelles. Previous studies have suggested that discrete gene products build and assemble magnetosomes in a stepwise fashion. Here, using an inducible system, we show that the stages of magnetosome formation are highly dynamic and interconnected. During de novo formation, magnetosomes first organize into discontinuous chain fragments that are subsequently connected by the bacterial actin-like protein MamK. We also find that magnetosome membranes are not uniform in size and can grow in a biomineralization-dependent manner. In the absence of biomineralization, magnetosome membranes stall at a diameter of ~50 nm. Those that have initiated biomineralization then expand to significantly larger sizes and accommodate mature magnetic particles. We speculate that such a biomineralization-dependent checkpoint for membrane growth establishes the appropriate conditions within the magnetosome to ensure successful nucleation and growth of magnetic particles.\n\nIMPORTANCE Magnetotactic bacteria make magnetic nanoparticles inside membrane-bound organelles called magnetosomes; however, it is unclear how the magnetosome membrane controls the biomineralization that occurs within this bacterial organelle. We placed magnetosome formation under inducible control in Magnetospirillum magneticum AMB-1 and used electron cryo-tomography to capture magnetosomes in their near-native state as they form de novo. An inducible system provided the key evidence that magnetosome membranes grow continuously unless they have not properly initiated biomineralization. Our finding that the size of a bacterial organelle impacts its biochemical function is a fundamental advance that impacts our perception of organelle formation and can inform future attempts aimed at creating designer magnetic particles.", "date": "2016-02-16", "date_type": "published", "publication": "mBio", "volume": "7", "number": "1", "publisher": "American Society for Microbiology", "pagerange": "e01898-15", "id_number": "CaltechAUTHORS:20160222-140321490", "issn": "2150-7511", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160222-140321490", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF Graduate Research Fellowship", "grant_number": "DGE-1106400" }, { "agency": "NIH", "grant_number": "R01GM084122" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1128/mBio.01898-15", "pmcid": "PMC4791847", "primary_object": { "basename": "mbo001162688sf2.pdf", "url": "https://authors.library.caltech.edu/records/k8e92-j8838/files/mbo001162688sf2.pdf" }, "related_objects": [ { "basename": "mbo001162688sf4.eps", "url": "https://authors.library.caltech.edu/records/k8e92-j8838/files/mbo001162688sf4.eps" }, { "basename": "mBio-2016-Cornejo-.pdf", "url": "https://authors.library.caltech.edu/records/k8e92-j8838/files/mBio-2016-Cornejo-.pdf" }, { "basename": "mbo001162688sf1.pdf", "url": "https://authors.library.caltech.edu/records/k8e92-j8838/files/mbo001162688sf1.pdf" }, { "basename": "mbo001162688st1.docx", "url": "https://authors.library.caltech.edu/records/k8e92-j8838/files/mbo001162688st1.docx" }, { "basename": "mbo001162688st2.docx", "url": "https://authors.library.caltech.edu/records/k8e92-j8838/files/mbo001162688st2.docx" }, { "basename": "mbo001162688st3.docx", "url": "https://authors.library.caltech.edu/records/k8e92-j8838/files/mbo001162688st3.docx" }, { "basename": "mbo001162688st4.docx", "url": "https://authors.library.caltech.edu/records/k8e92-j8838/files/mbo001162688st4.docx" }, { "basename": "mbo001162688st5.docx", "url": "https://authors.library.caltech.edu/records/k8e92-j8838/files/mbo001162688st5.docx" }, { "basename": "mbo001162688s1.docx", "url": "https://authors.library.caltech.edu/records/k8e92-j8838/files/mbo001162688s1.docx" }, { "basename": "mbo001162688sf3.pdf", "url": "https://authors.library.caltech.edu/records/k8e92-j8838/files/mbo001162688sf3.pdf" } ], "resource_type": "article", "pub_year": "2016", "author_list": "Cornejo, Elias; Subramanian, Poorna; et el." }, { "id": "https://authors.library.caltech.edu/records/2dr6s-fv091", "eprint_id": 67661, "eprint_status": "archive", "datestamp": "2023-08-20 10:21:15", "lastmod": "2023-10-18 21:21:58", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Subramanian-Poorna", "name": { "family": "Subramanian", "given": "Poorna" } }, { "id": "Pirbadian-Sahand", "name": { "family": "Pirbadian", "given": "Sahand" } }, { "id": "El-Naggar-M-Y", "name": { "family": "El-Naggar", "given": "Mohamed Y." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Electron Cryo-Tomography of Nanowires in Shewanella Oneidensis MR-1", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2016 Biophysical Society. Published by Elsevier Inc.", "abstract": "The dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1 is known to make 'nanowires,' conductive cell appendages used in electron transport. Novel live fluorescence imaging techniques recently clarified that the conductive filaments in S. oneidensis are not pili, as previously thought, but rather extensions of the outer membrane. However, their fine structure and mechanism remained unclear. Here, we report the first high-resolution in vivo images of nanowires in frozen-hydrated cells in a near-native state by electron cryo-tomography (ECT). We first developed a method for in vivo production of nanowires in cells grown on EM grids. Using correlative light microscopy and ECT, we then identified and imaged nanowires at high resolution and in three dimensions. Interestingly, we find that nanowires are composed of outer membrane vesicles (OMVs) strung together to form a chain. The size of the vesicles and the length and thickness of the vesicle chain are highly variable. However, even apparently smooth filaments such as those described previously are in fact, at higher resolution, revealed to be chains of OMVs. This work will help us investigate the electron transport mechanism along Shewanella nanowires. Additionally, this work has implications in understanding how OMVs, ubiquitous in Gram-negative bacteria, can assemble into chains.", "date": "2016-02-16", "date_type": "published", "publication": "Biophysical Journal", "volume": "110", "number": "3", "publisher": "Biophysical Society", "pagerange": "23A", "id_number": "CaltechAUTHORS:20160603-154022255", "issn": "0006-3495", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160603-154022255", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.bpj.2015.11.185", "resource_type": "article", "pub_year": "2016", "author_list": "Subramanian, Poorna; Pirbadian, Sahand; et el." }, { "id": "https://authors.library.caltech.edu/records/9h0kn-vyk50", "eprint_id": 67675, "eprint_status": "archive", "datestamp": "2023-08-20 10:22:30", "lastmod": "2023-10-18 21:22:58", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Pirbadian-Sahand", "name": { "family": "Pirbadian", "given": "Sahand" } }, { "id": "Barchinger-Sarah-E", "name": { "family": "Barchinger", "given": "Sarah E." } }, { "id": "Subramanian-Poorna", "name": { "family": "Subramanian", "given": "Poorna" } }, { "id": "Sambles-Christine-M", "name": { "family": "Sambles", "given": "Christine M." } }, { "id": "Baker-Carol-S", "name": { "family": "Baker", "given": "Carol S." } }, { "id": "Burroughs-Nigel-J", "name": { "family": "Burroughs", "given": "Nigel J." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Golbeck-John-H", "name": { "family": "Golbeck", "given": "John H." } }, { "id": "El-Naggar-M-Y", "name": { "family": "El-Naggar", "given": "Mohamed Y." } } ] }, "title": "Multiheme Cytochromes and the Bacterial Nanowires of Shewanella oneidensis MR-1: Regulation, Structure, and Extracellular Electron Transport Mechanisms", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2016 Biophysical Society. Published by Elsevier Inc.", "abstract": "Dissimilatory metal-reducing bacteria can extract free energy from their environment by performing electron transfer to solid-phase minerals outside the cell. This extracellular electron transport (EET) has important implications in global elemental cycles as well as renewable energy technologies. Among the pathways for EET, bacterial nanowires have received significant attention in the past decade due to their unique ability to mediate long-range electron transport to electron acceptors microns away from the cell surface.\n\nHere we report a comprehensive characterization of the composition, structure, and regulatory network that underlies bacterial nanowires from the metal-reducing bacterium Shewanella oneidensis MR-1. Using fluorescent and atomic force techniques, we find that the Shewanella nanowires are extensions of the outer membrane and periplasm that contain multiple multiheme cytochromes. The localization of decaheme cytochromes MtrC and OmcA supports a multistep redox hopping mechanism, allowing long-range electron transport along a membrane network of heme cofactors that line the nanowires. The electron flux resulting from such a mechanism strongly depends on the cytochrome density and topology. Using correlated electron cryo-tomography and in vivo fluorescent microscopy, we are gaining new insight into the localization patterns of cytochromes along nanowires as well as the morphology and the formation mechanism of these structures. Finally, we report our progress on understanding the underlying regulatory network, by testing targeted mutations and analyzing the transcriptome of Shewanella chemostat cultures as they encounter electron acceptor limitation and form nanowires. The transcriptional response includes an increase in the expression of multiheme cytochromes, heme synthesis enzymes, and cytochrome maturation proteins. Our findings on the regulation, ultrastructure and electron transport mechanism help shape a biophysical understanding of these redox-functionalized membrane and vesicular extensions as a microbial strategy for electron transport and energy distribution.", "date": "2016-02-16", "date_type": "published", "publication": "Biophysical Journal", "volume": "110", "number": "3", "publisher": "Biophysical Society", "pagerange": "314A", "id_number": "CaltechAUTHORS:20160606-082437422", "issn": "0006-3495", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160606-082437422", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.bpj.2015.11.1686", "resource_type": "article", "pub_year": "2016", "author_list": "Pirbadian, Sahand; Barchinger, Sarah E.; et el." }, { "id": "https://authors.library.caltech.edu/records/pmsjg-kzw89", "eprint_id": 67672, "eprint_status": "archive", "datestamp": "2023-08-20 10:22:11", "lastmod": "2023-10-18 21:22:43", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Swulius-M-T", "name": { "family": "Swulius", "given": "Matthew T." } }, { "id": "Nguyen-Lam-Thanh", "name": { "family": "Nguyen", "given": "Lam T." }, "orcid": "0000-0002-0756-0911" }, { "id": "Ladinsky-M-S", "name": { "family": "Ladinsky", "given": "Mark" }, "orcid": "0000-0002-1036-3513" }, { "id": "Mishra-M", "name": { "family": "Mishra", "given": "Mithilesh" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant" }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Using Electron Cryotomography and Coarse-Grained Molecular Dynamics to Study Contractile Mechanisms of Eukaryotic Cell Division Machinery", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2016 Biophysical Society. Published by Elsevier Inc.", "abstract": "Division in eukaryotic cells depends on an actomyosin ring that forms at the midcell and then contracts throughout cytokinesis via interactions between actin filaments and myosin II motor proteins. While the protein players involved are well studied, the ultrastructure of the actomyosin division machinery has been elusive due to its highly dynamic nature, which makes it difficult to preserve without vitrification. Here we use cryo focused ion beam milling and cryosectioning to examine the actomyosin machinery of fission yeast (S. pombe) for the first time in its native state, at different stages of contraction. Due to the machinery's complex and dynamic nature, and because EM images are static, we used structural data from our tomographic reconstructions to inform and guide 3D coarse-grained molecular dynamics simulations of the actomyosin ring contracting. To make our simulations as realistic as possible, for the first time, we have modeled the myosin ATPase cycle step-by-step and a coarse-grained membrane was used to test the ring's ability to constrict the membrane. By simulating all current models (and many variations) of actomyosin architecture and by comparing the results to tomographic data, we propose a working model for the contractile machinery, including how the actin filaments are arranged, how they might be tethered to the membrane and the structure of myosin II in the ring.", "date": "2016-02-16", "date_type": "published", "publication": "Biophysical Journal", "volume": "110", "number": "3", "publisher": "Biophysical Society", "pagerange": "156A", "id_number": "CaltechAUTHORS:20160606-075844512", "issn": "0006-3495", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160606-075844512", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.bpj.2015.11.876", "resource_type": "article", "pub_year": "2016", "author_list": "Swulius, Matthew T.; Nguyen, Lam T.; et el." }, { "id": "https://authors.library.caltech.edu/records/mz66p-5qj98", "eprint_id": 58403, "eprint_status": "archive", "datestamp": "2023-08-22 16:43:45", "lastmod": "2023-10-23 19:18:58", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ding-H-Jane", "name": { "family": "Ding", "given": "H. Jane" } }, { "id": "Oikonomou-Catherine-M", "name": { "family": "Oikonomou", "given": "Catherine M." }, "orcid": "0000-0003-2312-4746" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "The Caltech Tomography Database and Automatic Processing Pipeline", "ispublished": "pub", "full_text_status": "public", "keywords": "Electron tomography; Structural biology database; Image database; Automatic processing; Caltech Tomography Database", "note": "\u00a9 2015 Elsevier B.V. \n\nReceived Date: 20 March 2015; Revised Date: 11 June 2015; Accepted Date: 13 June 2015; Available online 15 June 2015. \n\nWe thank David Mastronarde for assisting with the \"Grab with Note\" plugin and integrating it into the IMOD software. This work was supported in part by NIH grant 2P50GM082545 to GJJ and the Beckman Institute at Caltech. This project/publication was made possible through the support of a grant from the John Templeton Foundation as part of the Boundaries of Life project. The opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the John Templeton Foundation.\n\nAccepted Version - nihms708068.pdf
", "abstract": "Here we describe the Caltech Tomography Database and automatic image processing pipeline, designed to process, store, display, and distribute electron tomographic data including tilt-series, sample information, data collection parameters, 3D reconstructions, correlated light microscope images, snapshots, segmentations, movies, and other associated files. Tilt-series are typically uploaded automatically during collection to a user's \"Inbox\" and processed automatically, but can also be entered and processed in batches via scripts or file-by-file through an internet interface. As with the video website YouTube, each tilt-series is represented on the browsing page with a link to the full record, a thumbnail image and a video icon that delivers a movie of the tomogram in a pop-out window. Annotation tools allow users to add notes and snapshots. The database is fully searchable, and sets of tilt-series can be selected and re-processed, edited, or downloaded to a personal workstation. The results of further processing and snapshots of key results can be recorded in the database, automatically linked to the appropriate tilt-series. While the database is password-protected for local browsing and searching, datasets can be made public and individual files can be shared with collaborators over the Internet. Together these tools facilitate high-throughput tomography work by both individuals and groups.", "date": "2015-11", "date_type": "published", "publication": "Journal of Structural Biology", "volume": "192", "number": "2", "publisher": "Elsevier", "pagerange": "279-286", "id_number": "CaltechAUTHORS:20150622-113741961", "issn": "1047-8477", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150622-113741961", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "2P50GM082545-06" }, { "agency": "Caltech Beckman Institute" }, { "agency": "John Templeton Foundation" } ] }, "doi": "10.1016/j.jsb.2015.06.016", "pmcid": "PMC4633326", "primary_object": { "basename": "nihms708068.pdf", "url": "https://authors.library.caltech.edu/records/mz66p-5qj98/files/nihms708068.pdf" }, "resource_type": "article", "pub_year": "2015", "author_list": "Ding, H. Jane; Oikonomou, Catherine M.; et el." }, { "id": "https://authors.library.caltech.edu/records/sbkxa-wer28", "eprint_id": 60093, "eprint_status": "archive", "datestamp": "2023-08-22 16:14:44", "lastmod": "2023-10-24 14:52:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Woodward-Cora-L", "name": { "family": "Woodward", "given": "Cora L." } }, { "id": "Mendon\u00e7a-Luiza-M", "name": { "family": "Mendon\u00e7a", "given": "Luiza M." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Direct visualization of vaults within intact cells by electron cryo-tomography", "ispublished": "pub", "full_text_status": "public", "keywords": "Vault; Ribonucleoprotein complex; Granules; RNA; Electron cryo-tomography", "note": "\u00a9 2015 Springer Basel.\n\nReceived: 18 December 2014; Revised: 13 March 2015; Accepted: 2 April 2015; Published online: 12 April 2015.\n\nWe thank Zhiheng Yu and M. Jason de la Cruz of the Howard Hughes Medical Institute CryoEM Shared Resource at Janelia Farm for assistance with data collection. This work was supported by NIH Grant 2P50GM082545 (to GJJ).\n\nAccepted Version - nihms680542.pdf
", "abstract": "The vault complex is the largest cellular ribonucleoprotein complex ever characterized and is present across diverse Eukarya. Despite significant information regarding the structure, composition and evolutionary conservation of the vault, little is know about the complex's actual biological function. To determine if intracellular vaults are morphologically similar to previously studied purified and recombinant vaults, we have used electron cryo-tomography to characterize the vault complexes found in the thin edges of primary human cells growing in tissue culture. Our studies confirm that intracellular vaults are similar in overall size and shape to purified and recombinant vaults previously analyzed. Results from subtomogram averaging indicate that densities within the vault lumen are not ordered, but randomly distributed. We also observe that vaults located in the extreme periphery of the cytoplasm predominately associate with granule-like structures and actin. Our ultrastructure studies augment existing biochemical, structural and genetic information on the vault, and provide important intracellular context for the ongoing efforts to understand the biological function of the native cytoplasmic vault.", "date": "2015-09", "date_type": "published", "publication": "Cellular and Molecular Life Sciences", "volume": "72", "number": "17", "publisher": "Springer", "pagerange": "3401-3409", "id_number": "CaltechAUTHORS:20150908-140337636", "issn": "1420-682X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150908-140337636", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "2P50GM082545-06" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1007/s00018-015-1898-y", "pmcid": "PMC4898762", "primary_object": { "basename": "nihms680542.pdf", "url": "https://authors.library.caltech.edu/records/sbkxa-wer28/files/nihms680542.pdf" }, "resource_type": "article", "pub_year": "2015", "author_list": "Woodward, Cora L.; Mendon\u00e7a, Luiza M.; et el." }, { "id": "https://authors.library.caltech.edu/records/cj0jb-ysr89", "eprint_id": 58751, "eprint_status": "archive", "datestamp": "2023-08-22 15:56:11", "lastmod": "2023-10-23 19:41:22", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Nguyen-Lam-Thanh", "name": { "family": "Nguyen", "given": "Lam T." }, "orcid": "0000-0002-0756-0911" }, { "id": "Gumbart-James-C", "name": { "family": "Gumbart", "given": "James C." }, "orcid": "0000-0002-1510-7842" }, { "id": "Beeby-Morgan-D", "name": { "family": "Beeby", "given": "Morgan" }, "orcid": "0000-0001-6413-9835" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Coarse-grained simulations of bacterial cell wall growth reveal that local coordination alone can be sufficient to maintain rod shape", "ispublished": "pub", "full_text_status": "public", "keywords": "coarse-grained modeling; cell wall synthesis; morphogenesis", "note": "\u00a9 2015 National Academy of Sciences. \n\nEdited by Joe Lutkenhaus, University of Kansas Medical Center, Kansas City, KS, and approved June 15, 2015 (received for review March 3, 2015). Published ahead of print June 30, 2015.\n\nThe authors thank Catherine Oikonomou for revising the manuscript for clarity. \n\nAuthor contributions: L.T.N., M.B., and G.J.J. designed research; L.T.N. performed research; L.T.N. and J.C.G. contributed new reagents/analytic tools; L.T.N., J.C.G., M.B., and G.J.J. analyzed data; and L.T.N., J.C.G., M.B., and G.J.J. wrote the paper. \n\nThe authors declare no conflict of interest. \n\nThis article is a PNAS Direct Submission. \n\nThis article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1504281112/-/DCSupplemental.\n\nPublished - PNAS-2015-Nguyen-E3689-98.pdf
Supplemental Material - pnas.1504281112.sapp.pdf
Supplemental Material - pnas.1504281112.sd01.txt
Supplemental Material - pnas.1504281112.sd02.txt
Supplemental Material - pnas.1504281112.sd03.txt
Supplemental Material - pnas.1504281112.sd04.txt
Supplemental Material - pnas.201504281SI.pdf
", "abstract": "Bacteria are surrounded by a peptidoglycan (PG) cell wall that must be remodeled to allow cell growth. While many structural details and properties of PG and the individual enzymes involved are known, how the process is coordinated to maintain cell integrity and rod shape is not understood. We have developed a coarse-grained method to simulate how individual transglycosylases, transpeptidases, and endopeptidases could introduce new material into an existing unilayer PG network. We find that a simple model with no enzyme coordination fails to maintain cell wall integrity and rod shape. We then iteratively analyze failure modes and explore different mechanistic hypotheses about how each problem might be overcome by the macromolecules involved. In contrast to a current theory, which posits that long MreB filaments are needed to coordinate PG insertion sites, we find that local coordination of enzyme activities in individual complexes can be sufficient to maintain cell integrity and rod shape. We also present possible molecular explanations for the existence of monofunctional transpeptidases and glycosidases (glycoside hydrolases), trimeric peptide crosslinks, cell twisting during growth, and synthesis of new strands in pairs.", "date": "2015-07-14", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "112", "number": "28", "publisher": "National Academy of Sciences", "pagerange": "E3689-E3698", "id_number": "CaltechAUTHORS:20150702-111849094", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150702-111849094", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1073/pnas.1504281112", "pmcid": "PMC4507204", "primary_object": { "basename": "pnas.1504281112.sd01.txt", "url": "https://authors.library.caltech.edu/records/cj0jb-ysr89/files/pnas.1504281112.sd01.txt" }, "related_objects": [ { "basename": "pnas.1504281112.sd02.txt", "url": "https://authors.library.caltech.edu/records/cj0jb-ysr89/files/pnas.1504281112.sd02.txt" }, { "basename": "pnas.1504281112.sd03.txt", "url": "https://authors.library.caltech.edu/records/cj0jb-ysr89/files/pnas.1504281112.sd03.txt" }, { "basename": "pnas.1504281112.sd04.txt", "url": "https://authors.library.caltech.edu/records/cj0jb-ysr89/files/pnas.1504281112.sd04.txt" }, { "basename": "pnas.201504281SI.pdf", "url": "https://authors.library.caltech.edu/records/cj0jb-ysr89/files/pnas.201504281SI.pdf" }, { "basename": "PNAS-2015-Nguyen-E3689-98.pdf", "url": "https://authors.library.caltech.edu/records/cj0jb-ysr89/files/PNAS-2015-Nguyen-E3689-98.pdf" }, { "basename": "pnas.1504281112.sapp.pdf", "url": "https://authors.library.caltech.edu/records/cj0jb-ysr89/files/pnas.1504281112.sapp.pdf" } ], "resource_type": "article", "pub_year": "2015", "author_list": "Nguyen, Lam T.; Gumbart, James C.; et el." }, { "id": "https://authors.library.caltech.edu/records/zm7cw-c7p28", "eprint_id": 53919, "eprint_status": "archive", "datestamp": "2023-08-20 06:25:44", "lastmod": "2023-10-19 22:23:23", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Ortega-Davi-R", "name": { "family": "Ortega", "given": "Davi R." }, "orcid": "0000-0002-8344-2335" }, { "id": "Huang-Audrey-N", "name": { "family": "Huang", "given": "Audrey N." } }, { "id": "Oikonomou-Catherine-M", "name": { "family": "Oikonomou", "given": "Catherine M." }, "orcid": "0000-0003-2312-4746" }, { "id": "Gunsalus-Robert-P", "name": { "family": "Gunsalus", "given": "Robert P." }, "orcid": "0000-0002-1937-8412" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Structural conservation of chemotaxis machinery across Archaea and Bacteria", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.\n\nReceived 6 November, 2014; revised 12 December, 2014; accepted\n25 December, 2014.\n\nWe thank Dr. Christine Moissl-Eichinger for sharing Halobacterium salinarum (DSM 3754). We thank Dr. Matthias Koch and Dr. Kristin Wuichet for discussions. This work was funded by the Department of Energy Biosciences Division Award DE-FG02-O8ER64689 and the UCLA-DOE Institute of Genomics and Proteomics Award DE-FC03-02ER6342 to R.P.G., and NIGMS Award GM101425 to G.J.J. This project/publication was made possible through the support of a grant from the John Templeton Foundation as part of the Boundaries of Life project. The opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the John Templeton Foundation.\n\nAccepted Version - nihms-762613.pdf
Supplemental Material - emi412265-sup-0001-si.docx
", "abstract": "Chemotaxis allows cells to sense and respond to their environment. In Bacteria, stimuli are detected by arrays of chemoreceptors that relay the signal to a two-component regulatory system. These arrays take the form of highly stereotyped super-lattices comprising hexagonally packed trimers-of-receptor-dimers networked by rings of histidine kinase and coupling proteins. This structure is conserved across chemotactic Bacteria, and between membrane-bound and cytoplasmic arrays, and gives rise to the highly cooperative, dynamic nature of the signalling system. The chemotaxis system, absent in eukaryotes, is also found in Archaea, where its structural details remain uncharacterized. Here we provide evidence that the chemotaxis machinery was not present in the last archaeal common ancestor, but rather was introduced in one of the waves of lateral gene transfer that occurred after the branching of Eukaryota but before the diversification of Euryarchaeota. Unlike in Bacteria, the chemotaxis system then evolved largely vertically in Archaea, with very few subsequent successful lateral gene transfer events. By electron cryotomography, we find that the structure of both membrane-bound and cytoplasmic chemoreceptor arrays is conserved between Bacteria and Archaea, suggesting the fundamental importance of this signalling architecture across diverse prokaryotic lifestyles.", "date": "2015-06", "date_type": "published", "publication": "Environmental Microbiology Reports", "volume": "7", "number": "3", "publisher": "Wiley-Blackwell", "pagerange": "414-419", "id_number": "CaltechAUTHORS:20150121-081216205", "issn": "1758-2229", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150121-081216205", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02-O8ER64689" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-FC03-02ER6342" }, { "agency": "NIH", "grant_number": "GM101425" }, { "agency": "John Templeton Foundation" }, { "agency": "National Institute of General Medical Sciences" } ] }, "doi": "10.1111/1758-2229.12265", "pmcid": "PMC4782749", "primary_object": { "basename": "emi412265-sup-0001-si.docx", "url": "https://authors.library.caltech.edu/records/zm7cw-c7p28/files/emi412265-sup-0001-si.docx" }, "related_objects": [ { "basename": "nihms-762613.pdf", "url": "https://authors.library.caltech.edu/records/zm7cw-c7p28/files/nihms-762613.pdf" } ], "resource_type": "article", "pub_year": "2015", "author_list": "Briegel, Ariane; Ortega, Davi R.; et el." }, { "id": "https://authors.library.caltech.edu/records/5hfk2-44s45", "eprint_id": 50244, "eprint_status": "archive", "datestamp": "2023-08-20 04:43:07", "lastmod": "2023-10-17 22:52:24", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Jani-C", "name": { "family": "Jani", "given": "Charul" } }, { "id": "Tocheva-E-I", "name": { "family": "Tocheva", "given": "Elitza I." }, "orcid": "0000-0002-4869-8319" }, { "id": "McAuley-S", "name": { "family": "McAuley", "given": "Scott" } }, { "id": "Craney-A", "name": { "family": "Craney", "given": "Arryn" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Nodwell-J", "name": { "family": "Nodwell", "given": "Justin" } } ] }, "title": "Streptomyces: A Screening Tool for Bacterial Cell Division Inhibitors", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2014 Society for Laboratory Automation and Screening.\n\nReceived May 8, 2014, and in revised form Jan 16, 2014. Accepted for\npublication Aug 10, 2014. Published online before print September 25, 2014.\n\nWe thank R. E. Yasbin, University of Missouri\u2013St. Louis, for kindly providing the stain containing dinC-lacZ fusion (dinC18::Tn917Iac metB5 trpC2 xin-1 SP\u03b2\u2013 amyE+, strain ID\u2014YB5018) and Bacillus Genetic Stock Centre (BGSC) for providing liaI-lacZ fusion strain (Em trpC2 liaI::pMUTIN attSPbeta, BGSC ID\u20141A980).\n\nDeclaration of Conflicting Interests:\nThe authors declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.\n\nFunding:\nThe authors disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: This work was supported by funding from the Canadian Institute for Health Research (grant MOP-133636) and NIH (R01 grant GM094800B to GJJ).\n\nAccepted Version - nihms787173.pdf
", "abstract": "Cell division is essential for spore formation but not for viability in the filamentous streptomycetes bacteria. Failure to complete cell division instead blocks spore formation, a phenotype that can be visualized by the absence of gray (in Streptomyces coelicolor) and green (in Streptomyces venezuelae) spore-associated pigmentation. Despite the lack of essentiality, the streptomycetes divisome is similar to that of other prokaryotes. Therefore, the chemical inhibitors of sporulation in model streptomycetes may interfere with the cell division in rod-shaped bacteria as well. To test this, we investigated 196 compounds that inhibit sporulation in S. coelicolor. We show that 19 of these compounds cause filamentous growth in Bacillus subtilis, consistent with impaired cell division. One of the compounds is a DNA-damaging agent and inhibits cell division by activating the SOS response. The remaining 18 act independently of known stress responses and may therefore act on the divisome or on divisome positioning and stability. Three of the compounds (Fil-1, Fil-2, and Fil-3) confer distinct cell division defects on B. subtilis. They also block B. subtilis sporulation, which is mechanistically unrelated to the sporulation pathway of streptomycetes but is also dependent on the divisome. We discuss ways in which these differing phenotypes can be used in screens for cell division inhibitors.", "date": "2015-02", "date_type": "published", "publication": "Journal of Biomolecular Screening", "volume": "20", "number": "2", "publisher": "SAGE Publications", "pagerange": "275-284", "id_number": "CaltechAUTHORS:20141007-152805174", "issn": "1087-0571", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141007-152805174", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Canadian Institute for Health Research", "grant_number": "MOP-133636" }, { "agency": "NIH", "grant_number": "R01 GM094800B" } ] }, "doi": "10.1177/1087057114551334", "pmcid": "PMC4888893", "primary_object": { "basename": "nihms787173.pdf", "url": "https://authors.library.caltech.edu/records/5hfk2-44s45/files/nihms787173.pdf" }, "resource_type": "article", "pub_year": "2015", "author_list": "Jani, Charul; Tocheva, Elitza I.; et el." }, { "id": "https://authors.library.caltech.edu/records/63wsq-q5q79", "eprint_id": 61925, "eprint_status": "archive", "datestamp": "2023-08-20 04:40:00", "lastmod": "2023-10-25 16:04:19", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Nguyen-Lam-T", "name": { "family": "Nguyen", "given": "Lam T." } }, { "id": "Swulius-M-T", "name": { "family": "Swulius", "given": "Matthew T." } }, { "id": "Mishra-M", "name": { "family": "Mishra", "given": "Mithilesh" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Coarse-Grained Simulations Reveal Mechanisms of Fission Yeast Cytokinesis", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2015 Biophysical Society.", "abstract": "Cytokinesis in fission yeast requires the presence of the actomyosin ring that constricts the membrane to divide the cell. Despite lots of effort, the molecular mechanism by which the ring tension is created remains poorly understood. This is largely due to the lack of structural details of of the ring, e.g., how actin filaments (F-actin) are arranged and what myosin conformations exist. As several models exist we decided to develop a computational approach to test whether these models are biophysically reasonable when simulated. Starting with a very simple model in which only actin filaments and bipolar myosin molecules are present we showed that myosin could slide F-actin but contraction did not occur. Addition of actin crosslinkers then helped contract the ring which in turn could pull down a coarse-grained membrane added to the system later. By tuning parameters and properties of the ring's components to match with data from electron cryotomography, we showed that coarse-grained simulations could help reveal the mechanism for the ring constriction.", "date": "2015-01-27", "date_type": "published", "publication": "Biophysical Journal", "volume": "108", "number": "2", "publisher": "Biophysical Society", "pagerange": "298A", "id_number": "CaltechAUTHORS:20151106-080648954", "issn": "0006-3495", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151106-080648954", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.bpj.2014.11.1623", "resource_type": "article", "pub_year": "2015", "author_list": "Nguyen, Lam T.; Swulius, Matthew T.; et el." }, { "id": "https://authors.library.caltech.edu/records/awnhm-g3v57", "eprint_id": 51829, "eprint_status": "archive", "datestamp": "2023-08-20 04:19:29", "lastmod": "2023-10-18 18:00:17", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Woodward-C-L", "name": { "family": "Woodward", "given": "Cora L." } }, { "id": "Cheng-Sarah-N", "name": { "family": "Cheng", "given": "Sarah N." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Electron cryo-tomography studies of maturing HIV-1 particles reveal the assembly pathway of the viral core", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2014 American Society for Microbiology. \n\nReceived 13 October 2014. Accepted 3 November 2014. Accepted manuscript posted online 12 November 2014. \n\nWe thank Ashley Jensen, Audrey Huang, Taylor Jensen, and Luiza Mendon\u00e7a for assistance with data analysis and Megan Dobro for useful discussions. Zhiheng Yu and M. Jason de la Cruz of the Howard Hughes Medical Institute CryoEM Shared Resource at Janelia Farm assisted with data collection. \n\nThis work was supported by NIH grant 2P50GM082545-06 (to G.J.J.).\n\nPublished - 1267.full.pdf
", "abstract": "To better characterize the assembly of the HIV-1 core, we have used electron cryo-tomography (ECT) to image infected cells and the viral particles cryo-preserved next to them. We observed progressive stages of virus assembly and egress including flower-like flat gag lattice assemblies, hemispherical budding profiles and virus buds linked to the plasma membrane via a thin membrane neck. The population of budded viral particles contains immature, maturation intermediate and mature core morphologies. Structural characteristics of the maturation intermediates suggest that the core assembly pathway involves the formation of a CA sheet that associates with the condensed ribonucleoprotein (RNP) complex. Our analysis also reveals a correlation between RNP localization within the viral particle and the formation of conical cores, suggesting that the RNP helps drive conical core assembly. Our findings support an assembly pathway for the HIV-1 core that begins with a small CA sheet that associates with the RNP to form the core base, followed by polymerization of the CA sheet along one side of the conical core towards the tip and then closure around the body of the cone.", "date": "2015-01", "date_type": "published", "publication": "Journal of Virology", "volume": "89", "number": "2", "publisher": "American Society for Microbiology", "pagerange": "1267-1277", "id_number": "CaltechAUTHORS:20141117-100140935", "issn": "0022-538X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141117-100140935", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "2P50GM082545-06" } ] }, "doi": "10.1128/JVI.02997-14", "pmcid": "PMC4300640", "primary_object": { "basename": "1267.full.pdf", "url": "https://authors.library.caltech.edu/records/awnhm-g3v57/files/1267.full.pdf" }, "resource_type": "article", "pub_year": "2015", "author_list": "Woodward, Cora L.; Cheng, Sarah N.; et el." }, { "id": "https://authors.library.caltech.edu/records/8ph3x-sef82", "eprint_id": 47895, "eprint_status": "archive", "datestamp": "2023-08-20 03:03:42", "lastmod": "2023-10-26 21:20:10", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "M\u00fcller-A", "name": { "family": "M\u00fcller", "given": "Axel" } }, { "id": "Beeby-M-D", "name": { "family": "Beeby", "given": "Morgan" }, "orcid": "0000-0001-6413-9835" }, { "id": "McDowall-A-W", "name": { "family": "McDowall", "given": "Alasdair W." } }, { "id": "Chow-Janet", "name": { "family": "Chow", "given": "Janet" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Clemons-W-M-Jr", "name": { "family": "Clemons", "given": "William M., Jr." }, "orcid": "0000-0002-0021-889X" } ] }, "title": "Ultrastructure and complex polar architecture of the human pathogen Campylobacter jejuni", "ispublished": "pub", "full_text_status": "public", "keywords": "Acidocalcisomes, Campylobacterales, chemoreceptors, cryoelectron tomography, cryo-EM, food poisoning, polyphosphate storage granules", "note": "\u00a9 2014 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. \n\nArticle first published online: 25 Jul 2014. Manuscript Accepted: 27 Jun 2014. Manuscript Revised: 17 Jun 2014. Manuscript Received: 18 Mar 2014. \n\nWe thank Sarkis Mazmanian (Caltech) for providing\nfacilities and expertise for microaerophilic growth of\nC. jejuni. We also thank Julien Jorda (Todd Yeates group\nat UCLA) for analyzing the C. jejuni genome for genes\ninvolved in microcompartment genesis. This project was\nfunded by awards from the Searle Scholar program, the\nBurroughs-Wellcome Fund Career Award for the Biological\nSciences (both to W. M. C.), the Howard Hughes\nMedical Institute, the Beckman Center at Caltech, and a\ngift from the Gordon and Betty Moore Foundation.\n\nPublished - mbo3200.pdf
", "abstract": "Campylobacter jejuni is one of the most successful food-borne human pathogens. Here we use electron cryotomography to explore the ultrastructure of C. jejuni cells in logarithmically growing cultures. This provides the first look at this pathogen in a near-native state at macromolecular resolution (~5 nm). We find a surprisingly complex polar architecture that includes ribosome exclusion zones, polyphosphate storage granules, extensive collar-shaped chemoreceptor arrays, and elaborate flagellar motors.", "date": "2014-10", "date_type": "published", "publication": "MicrobiologyOpen", "volume": "3", "number": "5", "publisher": "Wiley Open Access", "pagerange": "702-710", "id_number": "CaltechAUTHORS:20140804-114209444", "issn": "2045-8827", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140804-114209444", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Searle Scholars Program" }, { "agency": "Burroughs-Wellcome Fund" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Gordon and Betty Moore Foundation" } ] }, "doi": "10.1002/mbo3.200", "pmcid": "PMC4234261", "primary_object": { "basename": "mbo3200.pdf", "url": "https://authors.library.caltech.edu/records/8ph3x-sef82/files/mbo3200.pdf" }, "resource_type": "article", "pub_year": "2014", "author_list": "M\u00fcller, Axel; Beeby, Morgan; et el." }, { "id": "https://authors.library.caltech.edu/records/jwnh3-4dz84", "eprint_id": 44615, "eprint_status": "archive", "datestamp": "2023-08-20 01:33:21", "lastmod": "2023-10-26 14:49:21", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chang-Yi-Wei", "name": { "family": "Chang", "given": "Yi-Wei" }, "orcid": "0000-0003-2391-473X" }, { "id": "Chen-Songye", "name": { "family": "Chen", "given": "Songye" }, "orcid": "0000-0001-5407-5049" }, { "id": "Tocheva-E-I", "name": { "family": "Tocheva", "given": "Elitza I." }, "orcid": "0000-0002-4869-8319" }, { "id": "Treuner-Lange-Anke", "name": { "family": "Treuner-Lange", "given": "Anke" } }, { "id": "L\u00f6bach-Stephanie", "name": { "family": "L\u00f6bach", "given": "Stephanie" } }, { "id": "S\u00f8gaard-Andersen-Lotte", "name": { "family": "S\u00f8gaard-Andersen", "given": "Lotte" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Correlated cryogenic photoactivated localization microscopy and cryo-electron tomography", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2014 Macmillan Publishers. \n\nReceived 06 February 2014;Accepted 10 April 2014; Published online 11 May 2014. \n\nWe thank A.W. McDowall, C. Oikonomou, A. Konovalova, L. Cai and T. Zhiyentayev for assistance and discussions. This work was supported in part by US National Institutes of Health grant R01 GM094800B to G.J.J., the Howard Hughes Medical Institute and the Max Planck Society.\n\nContributions: Y.-W.C. and G.J.J. conceived the cryo-PALM idea. Y.-W.C. and S.C. configured the optical system. Y.-W.C., S.C. and E.I.T. tested fluorophores for photoactivatability at low temperatures. Y.-W.C. improved stability of cryo-FLM stage, prepared samples, overcame laser-induced ice crystallization on the sample, acquired and analyzed cryo-PALM data and conducted correlated cryo-PALM-CET. A.T.-L., S.L. and L.S.-A. generated M. xanthus strains and conducted functional analyses. Y.-W.C. and G.J.J. wrote the paper with input from all authors.\n\nCompeting financial interests: Y.-W.C., S.C., E.I.T. and G.J.J. are affiliated with the California Institute of Technology, which has filed a patent application based on this work.\n\nAccepted Version - nihms587569.pdf
Supplemental Material - nmeth.2961-S1.pdf
Supplemental Material - nmeth.2961-sv1.mov
Supplemental Material - nmeth.2961-sv2.mov
", "abstract": "Cryo-electron tomography (CET) produces three-dimensional images of cells in a near-native state at macromolecular resolution, but identifying structures of interest can be challenging. Here we describe a correlated cryo-PALM (photoactivated localization microscopy)-CET method for localizing objects within cryo-tomograms to beyond the diffraction limit of the light microscope. Using cryo-PALM-CET, we identified multiple and new conformations of the dynamic type VI secretion system in the crowded interior of Myxococcus xanthus.", "date": "2014-07", "date_type": "published", "publication": "Nature Methods", "volume": "11", "number": "7", "publisher": "Nature Publishing Group", "pagerange": "737-739", "id_number": "CaltechAUTHORS:20140402-152401360", "issn": "1548-7091", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140402-152401360", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 GM094800B" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Max Planck Society" } ] }, "doi": "10.1038/nmeth.2961", "pmcid": "PMC4081473", "primary_object": { "basename": "nihms587569.pdf", "url": "https://authors.library.caltech.edu/records/jwnh3-4dz84/files/nihms587569.pdf" }, "related_objects": [ { "basename": "nmeth.2961-S1.pdf", "url": "https://authors.library.caltech.edu/records/jwnh3-4dz84/files/nmeth.2961-S1.pdf" }, { "basename": "nmeth.2961-sv1.mov", "url": "https://authors.library.caltech.edu/records/jwnh3-4dz84/files/nmeth.2961-sv1.mov" }, { "basename": "nmeth.2961-sv2.mov", "url": "https://authors.library.caltech.edu/records/jwnh3-4dz84/files/nmeth.2961-sv2.mov" } ], "resource_type": "article", "pub_year": "2014", "author_list": "Chang, Yi-Wei; Chen, Songye; et el." }, { "id": "https://authors.library.caltech.edu/records/30acj-4cq17", "eprint_id": 45785, "eprint_status": "archive", "datestamp": "2023-08-22 12:33:45", "lastmod": "2023-10-26 18:27:31", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Tocheva-E-I", "name": { "family": "Tocheva", "given": "Elitza I." }, "orcid": "0000-0002-4869-8319" }, { "id": "Matson-E-G", "name": { "family": "Matson", "given": "Eric G." } }, { "id": "Cheng-Sarah-N", "name": { "family": "Cheng", "given": "Sarah N." } }, { "id": "Chen-Wesley-G", "name": { "family": "Chen", "given": "Wesley G." } }, { "id": "Leadbetter-J-R", "name": { "family": "Leadbetter", "given": "Jared R." }, "orcid": "0000-0002-7033-0844" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Structure and Expression of Propanediol Utilization Microcompartments in Acetonema longum", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2014 American Society for Microbiology.\n\nReceived 13 January 2014; Accepted 7 February 2014;\nPublished ahead of print 14 February 2014.\n\nThis work was supported by the Howard Hughes Medical Institute and the Department of Energy (grant DE-FG02-07ER64484 to J.R.L.).\n\nPublished - J._Bacteriol.-2014-Tocheva-1651-8.pdf
", "abstract": "Numerous bacteria assemble proteinaceous microcompartments to isolate certain biochemical reactions within the cytoplasm. The assembly, structure, contents, and functions of these microcompartments are active areas of research. Here we show that the Gram-negative sporulating bacterium Acetonema longum synthesizes propanediol utilization (PDU) microcompartments when starved or grown on 1,2-propanediol (1,2-PD) or rhamnose. Electron cryotomography of intact cells revealed that PDU microcompartments are highly irregular in shape and size, similar to purified PDU microcompartments from Salmonella enterica serovar Typhimurium LT2 that were imaged previously. Homology searches identified a 20-gene operon in A. longum that contains most of the structural, enzymatic, and regulatory genes thought to be involved in PDU microcompartment assembly and function. Transcriptional data on PduU and PduC, which are major structural and enzymatic proteins, respectively, as well as imaging, indicate that PDU microcompartment synthesis is induced within 24 h of growth on 1,2-PD and after 48 h of growth on rhamnose.", "date": "2014-05", "date_type": "published", "publication": "Journal of Bacteriology", "volume": "196", "number": "9", "publisher": "American Society for Microbiology", "pagerange": "1651-1658", "id_number": "CaltechAUTHORS:20140516-082115686", "issn": "0021-9193", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140516-082115686", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02-07ER64484" } ] }, "local_group": { "items": [ { "id": "Division-of-Geological-and-Planetary-Sciences" } ] }, "doi": "10.1128/JB.00049-14", "pmcid": "PMC3993321", "primary_object": { "basename": "J._Bacteriol.-2014-Tocheva-1651-8.pdf", "url": "https://authors.library.caltech.edu/records/30acj-4cq17/files/J._Bacteriol.-2014-Tocheva-1651-8.pdf" }, "resource_type": "article", "pub_year": "2014", "author_list": "Tocheva, Elitza I.; Matson, Eric G.; et el." }, { "id": "https://authors.library.caltech.edu/records/r5e2m-mr053", "eprint_id": 45460, "eprint_status": "archive", "datestamp": "2023-08-20 00:03:23", "lastmod": "2023-10-26 18:00:05", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Ladinsky-M-S", "name": { "family": "Ladinsky", "given": "Mark S." }, "orcid": "0000-0002-1036-3513" }, { "id": "Oikonomou-C-M", "name": { "family": "Oikonomou", "given": "Catherine M." }, "orcid": "0000-0003-2312-4746" }, { "id": "Jones-Christopher-W", "name": { "family": "Jones", "given": "Christopher W." } }, { "id": "Harris-Michael-J", "name": { "family": "Harris", "given": "Michael J." } }, { "id": "Fowler-Daniel-J", "name": { "family": "Fowler", "given": "Daniel J." } }, { "id": "Chang-Yi-Wei", "name": { "family": "Chang", "given": "Yi-Wei" }, "orcid": "0000-0003-2391-473X" }, { "id": "Thompson-Lynmarie-K", "name": { "family": "Thompson", "given": "Lynmarie K." } }, { "id": "Armitage-Judith-P", "name": { "family": "Armitage", "given": "Judith P." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Structure of bacterial cytoplasmic chemoreceptor arrays and implications for chemotactic signaling", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2014 Briegel et al. This article is distributed under the\nterms of the Creative Commons Attribution License, which\npermits unrestricted use and redistribution provided that the original author and source are credited.\n\nReceived: 21 December 2013; Accepted: 20 February 2014; Published: 25 March 2014.\n\nThe authors wish to thank Lee Rettberg and Audrey Huang for experimental help, and Dr Matthew Waldor for kindly providing strain MKW1383. Special thanks to Drs Zhiheng Yu and Jason de la Cruz for microscopy support at HHMI Janelia Farms. JPA and CWJ thank BBSRC and Nikon for funding. This\nwork was additionally supported by NIH grant R01-GM085288 to LKT and NIGMS grant GM101425 to GJJ.\n\nPublished - e02151.full.pdf
", "abstract": "Most motile bacteria sense and respond to their environment through a transmembrane chemoreceptor array whose structure and function have been well-studied, but many species also contain an additional cluster of chemoreceptors in their cytoplasm. Although the cytoplasmic cluster is essential for normal chemotaxis in some organisms, its structure and function remain unknown. Here we use electron cryotomography to image the cytoplasmic chemoreceptor\ncluster in Rhodobacter sphaeroides and Vibrio cholerae. We show that just like transmembrane arrays, cytoplasmic clusters contain trimers-of-receptor-dimers organized in 12-nm hexagonal arrays. In contrast to transmembrane arrays, however, cytoplasmic clusters comprise two CheA/\nCheW baseplates sandwiching two opposed receptor arrays. We further show that cytoplasmic fragments of normally transmembrane E. coli chemoreceptors form similar sandwiched structures in the presence of molecular crowding agents. Together these results suggest that the 12-nm\nhexagonal architecture is fundamentally important and that sandwiching and crowding can replace the stabilizing effect of the membrane.", "date": "2014-03-25", "date_type": "published", "publication": "eLife", "volume": "3", "publisher": "eLife Sciences Publications", "pagerange": "Art. No. e02151", "id_number": "CaltechAUTHORS:20140502-092924910", "issn": "2050-084X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140502-092924910", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM101425" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "R01-GM085288" }, { "agency": "Biotechnology and Biological Sciences Research Council (BBSRC)" }, { "agency": "Nikon" }, { "agency": "National Institute of General Medical Sciences" } ] }, "doi": "10.7554/eLife.02151.001", "pmcid": "PMC3964821", "primary_object": { "basename": "e02151.full.pdf", "url": "https://authors.library.caltech.edu/records/r5e2m-mr053/files/e02151.full.pdf" }, "resource_type": "article", "pub_year": "2014", "author_list": "Briegel, Ariane; Ladinsky, Mark S.; et el." }, { "id": "https://authors.library.caltech.edu/records/gtfhn-53976", "eprint_id": 44222, "eprint_status": "archive", "datestamp": "2023-08-20 00:01:53", "lastmod": "2023-10-20 22:57:47", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Wong-Margaret-L", "name": { "family": "Wong", "given": "Margaret L." } }, { "id": "Hodges-Heather-L", "name": { "family": "Hodges", "given": "Heather L." } }, { "id": "Oikonomou-C-M", "name": { "family": "Oikonomou", "given": "Catherine M." }, "orcid": "0000-0003-2312-4746" }, { "id": "Piasta-Kene-N", "name": { "family": "Piasta", "given": "Kene N." } }, { "id": "Harris-Michael-J", "name": { "family": "Harris", "given": "Michael J." } }, { "id": "Fowler-Daniel-J", "name": { "family": "Fowler", "given": "Daniel J." } }, { "id": "Thompson-Lynmarie-K", "name": { "family": "Thompson", "given": "Lynmarie K." } }, { "id": "Falke-J-J", "name": { "family": "Falke", "given": "Joseph J." } }, { "id": "Kiessling-L-L", "name": { "family": "Kiessling", "given": "Laura L." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "New Insights into Bacterial Chemoreceptor Array Structure and\n Assembly from Electron Cryotomography", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2014 American Chemical Society. ACS AuthorChoice - This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes.\n \n\nReceived: January 14, 2014. Revised: February 28, 2014. Publication Date (Web): February 28, 2014. \n\nFunding:\nThis work was supported by National Institutes of Health\nGrant R01-GM085288 to L.K.T., National Institute of General\nMedical Sciences Grant GM101425 to G.J.J., National\nInstitutes of Health Grant R01-GM040731 to J.J.F., National\nInstitutes of Health Grant RO1-GM055984 to L.L.K., and\nNational Institutes of Health CBI training grant T32\nGM008505 to H.L.H.\n\nWe thank Drs. Zhiheng Yu and Jason de la Cruz for microscopy support at Howard Hughes Medical Institute Janelia Farms and\nDr. Dan Toso and Associate Director Ivo Atanasov for support\nusing the University of California TITAN Krios microscope.\nWe thank Drs. Gongpu Zhao and Peijun Zhang for initial\nelectron micrographs of the PEG-mediated complexes of CF,\nCheA, and CheW. We thank Dr. Sandy Parkinson for the gift of\n\u03b1-Tsr and \u03b1-CheA antibodies, strains, and plasmids, as well as\nfor sharing results prior to publication. We thank Dr. John\nHeumann for assistance with PEET software.\n\nPublished - bi5000614.pdf
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Erratum - bi501167j.pdf
", "abstract": "Bacterial chemoreceptors cluster in highly ordered, cooperative, extended arrays with a conserved architecture, but the principles that govern array assembly remain unclear. Here we show images of cellular arrays as well as selected chemoreceptor complexes reconstituted in vitro that reveal new principles of array structure and assembly. First, in every case, receptors clustered in a trimers-of-dimers configuration, suggesting this is a highly favored fundamental building block. Second, these trimers-of-receptor dimers exhibited great versatility in the kinds of contacts they formed with each other and with other components of the signaling pathway, although only one architectural type occurred in native arrays. Third, the membrane, while it likely accelerates the formation of arrays, was neither necessary nor sufficient for lattice formation. Molecular crowding substituted for the stabilizing effect of the membrane and allowed cytoplasmic receptor fragments to form sandwiched lattices that strongly resemble the cytoplasmic chemoreceptor arrays found in some bacterial species. Finally, the effective determinant of array structure seemed to be CheA and CheW, which formed a \"superlattice\" of alternating CheA-filled and CheA-empty rings that linked receptor trimers-of-dimer units into their native hexagonal lattice. While concomitant overexpression of receptors, CheA, and CheW yielded arrays with native spacing, the CheA occupancy was lower and less ordered, suggesting that temporal and spatial coordination of gene expression driven by a single transcription factor may be vital for full order, or that array overgrowth may trigger a disassembly process. The results described here provide new insights into the assembly intermediates and assembly mechanism of this massive macromolecular complex.", "date": "2014-03-18", "date_type": "published", "publication": "Biochemistry", "volume": "53", "number": "10", "publisher": "American Chemical Society", "pagerange": "1575-1585", "id_number": "CaltechAUTHORS:20140310-115046309", "issn": "0006-2960", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140310-115046309", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01-GM085288" }, { "agency": "NIH", "grant_number": "GM101425" }, { "agency": "NIH", "grant_number": "R01-GM040731" }, { "agency": "NIH", "grant_number": "RO1-GM055984" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32 GM008505" } ] }, "doi": "10.1021/bi501167j", "pmcid": "PMC3985956", "primary_object": { "basename": "bi5000614.pdf", "url": "https://authors.library.caltech.edu/records/gtfhn-53976/files/bi5000614.pdf" }, "related_objects": [ { "basename": "bi5000614_si_001.pdf", "url": "https://authors.library.caltech.edu/records/gtfhn-53976/files/bi5000614_si_001.pdf" }, { "basename": "bi5000614_si_002.mov", "url": "https://authors.library.caltech.edu/records/gtfhn-53976/files/bi5000614_si_002.mov" }, { "basename": "bi501167j.pdf", "url": "https://authors.library.caltech.edu/records/gtfhn-53976/files/bi501167j.pdf" } ], "resource_type": "article", "pub_year": "2014", "author_list": "Briegel, Ariane; Wong, Margaret L.; et el." }, { "id": "https://authors.library.caltech.edu/records/3c1y9-y5n57", "eprint_id": 44375, "eprint_status": "archive", "datestamp": "2023-08-19 23:22:32", "lastmod": "2023-10-26 00:26:07", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Pilhofer-M", "name": { "family": "Pilhofer", "given": "Martin" } }, { "id": "Aistleitner-K", "name": { "family": "Aistleitner", "given": "Karin" } }, { "id": "Ladinsky-M-S", "name": { "family": "Ladinsky", "given": "Mark S." }, "orcid": "0000-0002-1036-3513" }, { "id": "K\u00f6nig-L", "name": { "family": "K\u00f6nig", "given": "Lena" } }, { "id": "Horn-M", "name": { "family": "Horn", "given": "Matthias" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Architecture and host interface of environmental chlamydiae revealed by electron cryotomography", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2013 Society for Applied Microbiology and John Wiley & Sons Ltd. Received 8 August, 2013; accepted 26 September, 2013. Article first published online: 8 Nov 2013. This work was funded by the Austrian Science Fund FWF\n(Y277-B03 to MH), the European Research Council (ERC\nStG 'EvoChlamy' to MH), the Caltech Center for Environmental\nMicrobiology Interactions (to GJJ, MP), and a gift from the\nGordon and Betty Moore Foundation to Caltech.\n\nAccepted Version - nihms787614.pdf
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", "abstract": "Chlamydiae comprise important pathogenic and symbiotic bacteria that alternate between morphologically and physiologically different life stages during their developmental cycle. Using electron cryotomography, we characterize the ultrastructure of the developmental stages of three environmental chlamydiae: Parachlamydia acanthamoebae, Protochlamydia amoebophila and Simkania negevensis. We show that chemical fixation and dehydration alter the cell shape of Parachlamydia and that the crescent body is not a developmental stage, but an artefact of conventional electron microscopy. We further reveal type III secretion systems of environmental chlamydiae at macromolecular resolution and find support for a chlamydial needle-tip protein. Imaging bacteria inside their host cells by cryotomography for the first time, we observe marked differences in inclusion morphology and development as well as host organelle recruitment between the three chlamydial organisms, with Simkania inclusions being tightly enveloped by the host endoplasmic reticulum. The study demonstrates the power of electron cryotomography to reveal structural details of bacteria\u2013host interactions that are not accessible using traditional methods.", "date": "2014-02", "date_type": "published", "publication": "Environmental Microbiology", "volume": "16", "number": "2", "publisher": "Blackwell Publishing", "pagerange": "417-429", "id_number": "CaltechAUTHORS:20140318-101020463", "issn": "1462-2912", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140318-101020463", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Austrian Science Fund (FWF)", "grant_number": "Y277-B03" }, { "agency": "European Research Council (ERC StG EvoChlamy)" }, { "agency": "Caltech Center for Environmental Microbial Interactions (CEMI)" }, { "agency": "Gordon and Betty Moore Foundation" } ] }, "local_group": { "items": [ { "id": "Caltech-Center-for-Environmental-Microbial-Interactions-(CEMI)" } ] }, "doi": "10.1111/1462-2920.12299", "pmcid": "PMC4949044", "primary_object": { "basename": "emi12299-sup-0001-fs1-2.pdf", "url": "https://authors.library.caltech.edu/records/3c1y9-y5n57/files/emi12299-sup-0001-fs1-2.pdf" }, "related_objects": [ { "basename": "emi12299-sup-0002-m1.mov", "url": "https://authors.library.caltech.edu/records/3c1y9-y5n57/files/emi12299-sup-0002-m1.mov" }, { "basename": "emi12299-sup-0003-m2.mov", "url": "https://authors.library.caltech.edu/records/3c1y9-y5n57/files/emi12299-sup-0003-m2.mov" }, { "basename": "emi12299-sup-0004-m3.mov", "url": "https://authors.library.caltech.edu/records/3c1y9-y5n57/files/emi12299-sup-0004-m3.mov" }, { "basename": "emi12299-sup-0005-m4.mov", "url": "https://authors.library.caltech.edu/records/3c1y9-y5n57/files/emi12299-sup-0005-m4.mov" }, { "basename": "nihms787614.pdf", "url": "https://authors.library.caltech.edu/records/3c1y9-y5n57/files/nihms787614.pdf" } ], "resource_type": "article", "pub_year": "2014", "author_list": "Pilhofer, Martin; Aistleitner, Karin; et el." }, { "id": "https://authors.library.caltech.edu/records/abmt3-3q727", "eprint_id": 46069, "eprint_status": "archive", "datestamp": "2023-08-19 23:25:19", "lastmod": "2023-10-26 18:39:46", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gumbart-J-C", "name": { "family": "Gumbart", "given": "James C." } }, { "id": "Beeby-M-D", "name": { "family": "Beeby", "given": "Morgan" }, "orcid": "0000-0001-6413-9835" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Roux-B", "name": { "family": "Roux", "given": "Beno\u00eet" } } ] }, "title": "Escherichia coli Peptidoglycan Structure and Mechanics as Predicted by Atomic-Scale Simulations", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2014 Gumbart et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. August 8, 2013; Accepted January 5, 2014; Published February 20, 2014. NIH K22-AI100927 to J.C.G. R01 GM062342 to B.R. HHMI to G.J.J. Gordon and Betty Moore Center for Integrative Study of Cell Regulation at Caltech to G.J.J. Computational resources were provided by the Computation Institute and the Biological Sciences Division of the University of Chicago and Argonne National Laboratory, under grant S10 RR029030-01. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.\n\nPublished - journal.pcbi.1003475.pdf
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Supplemental Material - journal.pcbi.1003475.s012.txt
Supplemental Material - journal.pcbi.1003475.s013.txt
", "abstract": "Bacteria face the challenging requirement to maintain their shape and avoid rupture due to the high internal turgor pressure, but simultaneously permit the import and export of nutrients, chemical signals, and virulence factors. The bacterial cell wall, a mesh-like structure composed of cross-linked strands of peptidoglycan, fulfills both needs by being semi-rigid, yet sufficiently porous to allow diffusion through it. How the mechanical properties of the cell wall are determined by the molecular features and the spatial arrangement of the relatively thin strands in the larger cellular-scale structure is not known. To examine this issue, we have developed and simulated atomic-scale models of Escherichia coli cell walls in a disordered circumferential arrangement. The cell-wall models are found to possess an anisotropic elasticity, as known experimentally, arising from the orthogonal orientation of the glycan strands and of the peptide cross-links. Other features such as thickness, pore size, and disorder are also found to generally agree with experiments, further supporting the disordered circumferential model of peptidoglycan. The validated constructs illustrate how mesoscopic structure and behavior emerge naturally from the underlying atomic-scale properties and, furthermore, demonstrate the ability of all-atom simulations to reproduce a range of macroscopic observables for extended polymer meshes.", "date": "2014-02", "date_type": "published", "publication": "PLOS Computational Biology", "volume": "10", "number": "2", "publisher": "Public Library of Science", "pagerange": "Art. No. e10034", "id_number": "CaltechAUTHORS:20140604-091447469", "issn": "1553-7358", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140604-091447469", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "K22-AI100927" }, { "agency": "NIH", "grant_number": "R01 GM062342" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Argonne National Laboratory", "grant_number": "S10 RR029030-01" } ] }, "doi": "10.1371/journal.pcbi.1003475", "pmcid": "PMC3930494", "primary_object": { "basename": "journal.pcbi.1003475.s010.mpeg", "url": "https://authors.library.caltech.edu/records/abmt3-3q727/files/journal.pcbi.1003475.s010.mpeg" }, "related_objects": [ { "basename": "journal.pcbi.1003475.s012.txt", "url": "https://authors.library.caltech.edu/records/abmt3-3q727/files/journal.pcbi.1003475.s012.txt" }, { "basename": "journal.pcbi.1003475.s013.txt", "url": "https://authors.library.caltech.edu/records/abmt3-3q727/files/journal.pcbi.1003475.s013.txt" }, { "basename": "journal.pcbi.1003475.pdf", "url": "https://authors.library.caltech.edu/records/abmt3-3q727/files/journal.pcbi.1003475.pdf" }, { "basename": "journal.pcbi.1003475.s003.png", "url": "https://authors.library.caltech.edu/records/abmt3-3q727/files/journal.pcbi.1003475.s003.png" }, { "basename": "journal.pcbi.1003475.s009.mpeg", "url": "https://authors.library.caltech.edu/records/abmt3-3q727/files/journal.pcbi.1003475.s009.mpeg" }, { "basename": "journal.pcbi.1003475.s005.png", "url": "https://authors.library.caltech.edu/records/abmt3-3q727/files/journal.pcbi.1003475.s005.png" }, { "basename": "journal.pcbi.1003475.s006.png", "url": "https://authors.library.caltech.edu/records/abmt3-3q727/files/journal.pcbi.1003475.s006.png" }, { "basename": "journal.pcbi.1003475.s007.png", "url": "https://authors.library.caltech.edu/records/abmt3-3q727/files/journal.pcbi.1003475.s007.png" }, { "basename": "journal.pcbi.1003475.s011.pdf", "url": "https://authors.library.caltech.edu/records/abmt3-3q727/files/journal.pcbi.1003475.s011.pdf" }, { "basename": "journal.pcbi.1003475.s008.mpeg", "url": "https://authors.library.caltech.edu/records/abmt3-3q727/files/journal.pcbi.1003475.s008.mpeg" }, { "basename": "journal.pcbi.1003475.s001.png", "url": "https://authors.library.caltech.edu/records/abmt3-3q727/files/journal.pcbi.1003475.s001.png" }, { "basename": "journal.pcbi.1003475.s002.png", "url": "https://authors.library.caltech.edu/records/abmt3-3q727/files/journal.pcbi.1003475.s002.png" }, { "basename": "journal.pcbi.1003475.s004.png", "url": "https://authors.library.caltech.edu/records/abmt3-3q727/files/journal.pcbi.1003475.s004.png" } ], "resource_type": "article", "pub_year": "2014", "author_list": "Gumbart, James C.; Beeby, Morgan; et el." }, { "id": "https://authors.library.caltech.edu/records/pjxb8-32324", "eprint_id": 43345, "eprint_status": "archive", "datestamp": "2023-08-19 23:03:50", "lastmod": "2023-10-25 23:29:04", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Shikuma-Nicholas-J", "name": { "family": "Shikuma", "given": "Nicholas J." }, "orcid": "0000-0001-5518-5020" }, { "id": "Pilhofer-M", "name": { "family": "Pilhofer", "given": "Martin" } }, { "id": "Weiss-G-L", "name": { "family": "Weiss", "given": "Gregor L." } }, { "id": "Hadfield-M-G", "name": { "family": "Hadfield", "given": "Michael G." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Newman-D-K", "name": { "family": "Newman", "given": "Dianne K." }, "orcid": "0000-0003-1647-1918" } ] }, "title": "Marine Tubeworm Metamorphosis Induced by Arrays of Bacterial Phage Tail\u2013Like Structures", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2014 American Association for the Advancement of Science. \nReceived 3 October 2013; accepted 23 December 2013.\nPublished Online January 9 2014.\nWe thank B. Pernet for help with locating and identifying\ntubeworms and for gifting the algal strain used in this work; A. McDowall for\nhelp with electron microscopy; Y. Huang, who created the Str^R-strain (7); A.\nAsahina and S. Wilbur for laboratory assistance; J. Levine for help with timelapse\nmicroscopy; J. Ricci for help with phylogenetic analyses; and members\nof the Newman group for discussions and comments on the manuscript. The\nHoward Hughes Medical Institute, Z. Yu and J. de la Cruz are acknowledged\nfor providing access to the FEI Titan Krios at Janelia Farm and support in data\ncollection. N.J.S. was supported by a Caltech Division of Biology\nPostdoctoral Fellowship. This collaboration was supported by the Caltech\nCenter for Environmental Microbiology Interactions, the Howard Hughes\nMedical Institute (D.K.N. and G.J.J.), Office of Naval Research grants\nN00014-08-1-0413 and N00014-05-1-0579 (M.G.H.), NIH grant\nGM094800B (G.J.J.), and a gift from the Gordon and Betty Moore\nFoundation (Caltech). D.K.N. and G.J.J. are Investigators of the Howard\nHughes Medical Institute. Strains obtained from the American Type Culture\nCollection listed in table S2 (ATCC 33492, ATCC 14393, ATCC 15057).\nDNA sequences encoding for mac, T6SS, and bacteriocin-2 genes are\ndeposited under GenBank accession numbers KF724687, KF724688, and\nKF724689, respectively. Subtomogram averages were deposited in the\nElectron Microscopy Data Bank (accession numbers to be added on proof).\nAuthor contributions: All authors designed research. N.J.S., M.P. and G.L.W.\nperformed research. All authors wrote the paper.\n\nAccepted Version - nihms787618.pdf
", "abstract": "Many benthic marine animal populations are established and maintained by free-swimming larvae that recognize cues from surface-bound bacteria to settle and metamorphose. Larvae of the tubeworm Hydroides elegans, a significant biofouling agent, require contact with surface-bound bacteria to undergo metamorphosis; however, the mechanisms that underpin this microbially mediated developmental transition have been enigmatic. Here, we show that a marine bacterium, Pseudoalteromonas luteoviolacea, produces arrays of phage tail\u2013like structures that trigger metamorphosis of H. elegans. These arrays comprise about 100 contractile structures with outward-facing baseplates, linked by tail fibers and a dynamic hexagonal net. Not only do these arrays suggest a novel form of bacterium-animal interaction, they provide an entry point to understanding how marine biofilms can trigger animal development.", "date": "2014-01-09", "date_type": "published", "publication": "Science", "volume": "343", "number": "6170", "publisher": "American Association for the Advancement of Science", "pagerange": "529-533", "id_number": "CaltechAUTHORS:20140113-134430398", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140113-134430398", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Caltech Division of Biology Postdoctoral Fellowship" }, { "agency": "Caltech Center for Environmental Microbial Interactions (CEMI)" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Office of Naval Research (ONR)", "grant_number": "N00014-08-1-0413" }, { "agency": "Office of Naval Research (ONR)", "grant_number": "N00014-05-1-0579" }, { "agency": "NIH", "grant_number": "GM094800B" }, { "agency": "Gordon and Betty Moore Foundation" } ] }, "local_group": { "items": [ { "id": "Caltech-Center-for-Environmental-Microbial-Interactions-(CEMI)" }, { "id": "Division-of-Geological-and-Planetary-Sciences" } ] }, "doi": "10.1126/science.1246794", "pmcid": "PMC4949041", "primary_object": { "basename": "nihms787618.pdf", "url": "https://authors.library.caltech.edu/records/pjxb8-32324/files/nihms787618.pdf" }, "resource_type": "article", "pub_year": "2014", "author_list": "Shikuma, Nicholas J.; Pilhofer, Martin; et el." }, { "id": "https://authors.library.caltech.edu/records/kf71h-pd414", "eprint_id": 43644, "eprint_status": "archive", "datestamp": "2023-08-22 11:00:19", "lastmod": "2023-10-25 23:44:43", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Pilhofer-M", "name": { "family": "Pilhofer", "given": "Martin" } }, { "id": "Aistleitner-K", "name": { "family": "Aistleitner", "given": "Karin" } }, { "id": "Biboy-J", "name": { "family": "Biboy", "given": "Jacob" } }, { "id": "Gray-J", "name": { "family": "Gray", "given": "Joe" } }, { "id": "Kuru-E", "name": { "family": "Kuru", "given": "Erkin" } }, { "id": "Hall-E", "name": { "family": "Hall", "given": "Edward" } }, { "id": "Brun-Yves-V", "name": { "family": "Brun", "given": "Yves V." } }, { "id": "VanNieuwenhze-M-S", "name": { "family": "VanNieuwenhze", "given": "Michael S." } }, { "id": "Vollmer-W", "name": { "family": "Vollmer", "given": "Waldemar" } }, { "id": "Horn-M", "name": { "family": "Horn", "given": "Matthias" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Discovery of chlamydial peptidoglycan reveals bacteria with murein sacculi but without FtsZ", "ispublished": "pub", "full_text_status": "public", "keywords": "Biological sciences; Biophysics; Cell biology; Microbiology", "note": "\u00a9 2013 Macmillan Publishers Limited. Received 11 September 2013. Accepted 01 November 2013. Published 02 December 2013. Updated online 03 December 2013. This work was funded by the Austrian Science Fund FWF (Y277-B03 to M.H.), the\nEuropean Research Council (ERC StG 'EvoChlamy' to M.H.), NIH grant GM094800B (to G.J.J.), the Caltech Center for Environmental Microbiology Interactions (to G.J.J., M.P.),\na gift from the Gordon and Betty Moore Foundation to Caltech, the BBSRC (BB/I020012/1 to W.V.), NIH grant AI059327 (to M.S.V.) and NIH grant GM051986 (to Y.V.B.). We thank Elitza Tocheva for discussions on the preparation of sacculi.\n\nAuthor contributions:\nM.P. initiated the study. M.P. and K.A. performed all experiments except HPLC/MS\nanalyses of sacculi, which were done by J.B., J.G. and W.V. E.K., E.H., Y.V.B. and M.S.V.\nprovided the FDAA dyes and advice on the FDAA labelling experiments. M.P., K.A.,\nW.V., M.H. and G.J.J. designed the experiments and wrote the manuscript.\n\nAccepted Version - emss-55543.pdf
Supplemental Material - ncomms3856-s1.pdf
", "abstract": "Chlamydiae are important pathogens and symbionts with unique cell biological features. They lack the cell-division protein FtsZ, and the existence of peptidoglycan (PG) in their cell wall has been highly controversial. FtsZ and PG together function in orchestrating cell division and maintaining cell shape in almost all other bacteria. Using electron cryotomography, mass spectrometry and fluorescent labelling dyes, here we show that some environmental chlamydiae have cell wall sacculi consisting of a novel PG type. Treatment with fosfomycin (a PG synthesis inhibitor) leads to lower infection rates and aberrant cell shapes, suggesting that PG synthesis is crucial for the chlamydial life cycle. Our findings demonstrate for the first time the presence of PG in a member of the Chlamydiae. They also present a unique example of a bacterium with a PG sacculus but without FtsZ, challenging the current hypothesis that it is the absence of a cell wall that renders FtsZ non-essential.", "date": "2013-12", "date_type": "published", "publication": "Nature Communications", "volume": "4", "number": "12", "publisher": "Nature Publishing Group", "pagerange": "Art. No. 2856", "id_number": "CaltechAUTHORS:20140204-110344222", "issn": "2041-1723", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140204-110344222", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "FWF Der Wissenschaftsfonds", "grant_number": "Y277-B03" }, { "agency": "European Research Council (ERC)", "grant_number": "EvoChlamy" }, { "agency": "NIH", "grant_number": "GM094800B" }, { "agency": "Caltech Center for Environmental Microbial Interactions (CEMI)" }, { "agency": "Gordon and Betty Moore Foundation", "grant_number": "BB/I020012/1" }, { "agency": "NIH", "grant_number": "AI059327" }, { "agency": "NIH", "grant_number": "GM051986" }, { "agency": "Biotechnology and Biological Sciences Research Council (BBSRC)", "grant_number": "BB/I020012/1" } ] }, "local_group": { "items": [ { "id": "Caltech-Center-for-Environmental-Microbial-Interactions-(CEMI)" } ] }, "doi": "10.1038/ncomms3856", "pmcid": "PMC3847603", "primary_object": { "basename": "ncomms3856-s1.pdf", "url": "https://authors.library.caltech.edu/records/kf71h-pd414/files/ncomms3856-s1.pdf" }, "related_objects": [ { "basename": "emss-55543.pdf", "url": "https://authors.library.caltech.edu/records/kf71h-pd414/files/emss-55543.pdf" } ], "resource_type": "article", "pub_year": "2013", "author_list": "Pilhofer, Martin; Aistleitner, Karin; et el." }, { "id": "https://authors.library.caltech.edu/records/07zyg-ebr11", "eprint_id": 41986, "eprint_status": "archive", "datestamp": "2023-08-19 21:36:38", "lastmod": "2023-10-25 14:59:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gan-Lu", "name": { "family": "Gan", "given": "Lu" }, "orcid": "0000-0002-8685-4896" }, { "id": "Ladinsky-M-S", "name": { "family": "Ladinsky", "given": "Mark S." }, "orcid": "0000-0002-1036-3513" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Chromatin in a marine picoeukaryote is a disordered assemblage of nucleosomes", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2013 The Author(s). This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited.\n\nReceived: 4 February 2013; Revised: 26 May 2013; Accepted: 12 June 2013; Published online: 3 July 2013.\n\nWe thank Drs. J. Huiskonen for advice on Jsubtomo, M. Swulius for discussions on template matching, H. Wong and J. Mozziconacci for sharing their 30-nm fiber model, and Drs. A.\nMcDowall and D. Rhodes for discussions on chromatin. This work was supported by the Howard Hughes Medical Institute and the Gordon and Betty Moore Center for Integrative Study of Cell Regulation. MSL was supported by NIH grant 2 R37 AI041239-06A1 to P. Bj\u00f6rkman. LG was supported by a fellowship from the Damon Runyon Cancer Research Foundation (DRG-1940-07) and startup funds from NUS.\n\nPublished - art_10.1007_s00412-013-0423-z.pdf
Supplemental Material - 412_2013_423_Fig6_ESM.jpg
Supplemental Material - 412_2013_423_Fig7_ESM.jpg
Supplemental Material - 412_2013_423_MOESM1_ESM.tif
Supplemental Material - 412_2013_423_MOESM2_ESM.tif
", "abstract": "Chromatin organization is central to many conserved biological processes, but it is generally unknown how the underlying nucleosomes are arranged in situ. Here, we have used electron cryotomography to study chromatin in the picoplankton Ostreococcus tauri, the smallest known free-living eukaryote. By visualizing the nucleosome densities directly, we find that O. tauri chromosomes do not arrange into discrete, compact bodies or any other higher level of order. In contrast to the textbook 30-nm fiber model, O. tauri chromatin resembles a disordered assemblage of nucleosomes akin to the polymer melt model. This disorganized nucleosome arrangement has important implications for potentially conserved functions in tiny eukaryotes such as the clustering of nonhomologous chromosomes at the kinetochore during mitosis and the independent regulation of closely positioned adjacent genes.", "date": "2013-10", "date_type": "published", "publication": "Chromosoma", "volume": "122", "number": "5", "publisher": "Springer", "pagerange": "377-386", "id_number": "CaltechAUTHORS:20131018-100119675", "issn": "0009-5915", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20131018-100119675", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Gordon and Betty Moore" }, { "agency": "NIH", "grant_number": "2 R37 AI041239-06A1" }, { "agency": "Damon Runyon Cancer Research Foundation", "grant_number": "DRG-1940-07" }, { "agency": "NUS" } ] }, "doi": "10.1007/s00412-013-0423-z", "pmcid": "PMC3777167", "primary_object": { "basename": "art_10.1007_s00412-013-0423-z.pdf", "url": "https://authors.library.caltech.edu/records/07zyg-ebr11/files/art_10.1007_s00412-013-0423-z.pdf" }, "related_objects": [ { "basename": "412_2013_423_Fig6_ESM.jpg", "url": "https://authors.library.caltech.edu/records/07zyg-ebr11/files/412_2013_423_Fig6_ESM.jpg" }, { "basename": "412_2013_423_Fig7_ESM.jpg", "url": "https://authors.library.caltech.edu/records/07zyg-ebr11/files/412_2013_423_Fig7_ESM.jpg" }, { "basename": "412_2013_423_MOESM1_ESM.tif", "url": "https://authors.library.caltech.edu/records/07zyg-ebr11/files/412_2013_423_MOESM1_ESM.tif" }, { "basename": "412_2013_423_MOESM2_ESM.tif", "url": "https://authors.library.caltech.edu/records/07zyg-ebr11/files/412_2013_423_MOESM2_ESM.tif" } ], "resource_type": "article", "pub_year": "2013", "author_list": "Gan, Lu; Ladinsky, Mark S.; et el." }, { "id": "https://authors.library.caltech.edu/records/hdd3w-prt06", "eprint_id": 41193, "eprint_status": "archive", "datestamp": "2023-08-19 21:13:25", "lastmod": "2023-10-24 23:31:22", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Tocheva-E-I", "name": { "family": "Tocheva", "given": "Elitza I." }, "orcid": "0000-0002-4869-8319" }, { "id": "Dekas-A-E", "name": { "family": "Dekas", "given": "Anne E." }, "orcid": "0000-0001-9548-8413" }, { "id": "McGlynn-S-E", "name": { "family": "McGlynn", "given": "Shawn E." }, "orcid": "0000-0002-8199-7011" }, { "id": "Morris-D-M", "name": { "family": "Morris", "given": "Dylan" } }, { "id": "Orphan-V-J", "name": { "family": "Orphan", "given": "Victoria J." }, "orcid": "0000-0002-5374-6178" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Polyphosphate Storage during Sporulation in the Gram-Negative Bacterium Acetonema longum", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2013 American Society for Microbiology.\n\nReceived 16 June 2013 Accepted 20 June 2013;\nPublished ahead of print 28 June 2013.\n\nWe acknowledge the use of electron microscopy facilities at the UCLA\nElectron Imaging Center for NanoMachines at the California NanoSystems\nInstitute (CNSI) and thank Ivo Atanasov and Dan Taso for technical\nassistance with EDX data collection and analysis. We thank Yunbin Guan\nand John Eiler for assistance with the NanoSIMS measurements. We\nthank Adrian Ponce for providing the C. sporogenes spores.\nThe NanoSIMS apparatus is housed within the Caltech Microanalysis\nCenter and is partially funded by the Gordon and Betty Moore Foundation.\nThis work was funded in part by the Howard Hughes Medical Institute,\nthe Caltech Center for Environmental Microbial Interactions, and\ngifts to Caltech from the Gordon and Betty Moore Foundation.\nThis work was partially performed under the auspices of the U.S. Department\nof Energy by Lawrence Livermore National Laboratory under\ncontract DE-AC52-07NA27344.\n\nPublished - J._Bacteriol.-2013-Tocheva-3940-6.pdf
Supplemental Material - zjb999092761so1.pdf
", "abstract": "Using electron cryotomography, we show that the Gram-negative sporulating bacterium Acetonema longum synthesizes high-density storage granules at the leading edges of engulfing membranes. The granules appear in the prespore and increase in size and number as engulfment proceeds. Typically, a cluster of 8 to 12 storage granules closely associates with the inner spore membrane and ultimately accounts for \u223c7% of the total volume in mature spores. Energy-dispersive X-ray spectroscopy (EDX) analyses show that the granules contain high levels of phosphorus, oxygen, and magnesium and therefore are likely composed of polyphosphate (poly-P). Unlike the Gram-positive Bacilli and Clostridia, A. longum spores retain their outer spore membrane upon germination. To explore the possibility that the granules in A. longum may be involved in this unique process, we imaged purified Bacillus cereus, Bacillus thuringiensis, Bacillus subtilis, and Clostridium sporogenes spores. Even though B. cereus and B. thuringiensis contain the ppk and ppx genes, none of the spores from Gram-positive bacteria had granules. We speculate that poly-P in A. longum may provide either the energy or phosphate metabolites needed for outgrowth while retaining an outer membrane.", "date": "2013-09", "date_type": "published", "publication": "Journal of Bacteriology", "volume": "195", "number": "17", "publisher": "American Society for Microbiology", "pagerange": "3940-3946", "id_number": "CaltechAUTHORS:20130909-141442695", "issn": "0021-9193", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130909-141442695", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Caltech Center for Environmental Microbial Interactions (CEMI)" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-AC52-07NA27344" } ] }, "local_group": { "items": [ { "id": "Caltech-Center-for-Environmental-Microbial-Interactions-(CEMI)" }, { "id": "Division-of-Geological-and-Planetary-Sciences" } ] }, "doi": "10.1128/JB.00712-13", "pmcid": "PMC3754598", "primary_object": { "basename": "zjb999092761so1.pdf", "url": "https://authors.library.caltech.edu/records/hdd3w-prt06/files/zjb999092761so1.pdf" }, "related_objects": [ { "basename": "J._Bacteriol.-2013-Tocheva-3940-6.pdf", "url": "https://authors.library.caltech.edu/records/hdd3w-prt06/files/J._Bacteriol.-2013-Tocheva-3940-6.pdf" } ], "resource_type": "article", "pub_year": "2013", "author_list": "Tocheva, Elitza I.; Dekas, Anne E.; et el." }, { "id": "https://authors.library.caltech.edu/records/50qx4-jxt40", "eprint_id": 41445, "eprint_status": "archive", "datestamp": "2023-08-19 21:13:52", "lastmod": "2023-10-24 23:44:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Ames-Peter", "name": { "family": "Ames", "given": "Peter" } }, { "id": "Gumbart-J-C", "name": { "family": "Gumbart", "given": "James C." } }, { "id": "Oikonomou-C-M", "name": { "family": "Oikonomou", "given": "Catherine M." }, "orcid": "0000-0003-2312-4746" }, { "id": "Parkinson-J-S", "name": { "family": "Parkinson", "given": "John S." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "The mobility of two kinase domains in the Escherichia coli chemoreceptor array varies with signalling state", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2013 John Wiley & Sons Ltd. \n\nAccepted 24 June, 2013. Article first published online: 30 Jul. 2013. \n\nThis work was supported in part by NIGMS Grants GM101425 (to G.J.J. and J.C.G.) and GM19559 (to J.S.P.), as well as a gift to Caltech from the Gordon and Betty Moore Foundation. The Protein-DNA Core Facility at the University of Utah receives support from National Cancer Institute Grant CA42014 to the Huntsman Cancer Institute.\n\nPublished - mmi12309.pdf
Accepted Version - nihms-502238.pdf
Supplemental Material - mmi12309-sup-0001-si.pdf
", "abstract": "Motile bacteria sense their physical and chemical environment\nthrough highly cooperative, ordered arrays of\nchemoreceptors. These signalling complexes phosphorylate\na response regulator which in turn governs\nflagellar motor reversals, driving cells towards favourable\nenvironments. The structural changes that translate\nchemoeffector binding into the appropriate kinase\noutput are not known. Here, we apply high-resolution\nelectron cryotomography to visualize mutant chemoreceptor\nsignalling arrays in well-defined kinase activity\nstates. The arrays were well ordered in all signalling\nstates, with no discernible differences in receptor\nconformation at 2\u20133 nm resolution. Differences were\nobserved, however, in a keel-like density that we identify\nhere as CheA kinase domains P1 and P2, the\nphosphorylation site domain and the binding domain\nfor response regulator target proteins. Mutant receptor\narrays with high kinase activities all exhibited small\nkeels and high proteolysis susceptibility, indicative of\nmobile P1 and P2 domains. In contrast, arrays in\nkinase-off signalling states exhibited a range of keel\nsizes. These findings confirm that chemoreceptor\narrays do not undergo large structural changes during\nsignalling, and suggest instead that kinase activity is\nmodulated at least in part by changes in the mobility of\nkey domains.", "date": "2013-09", "date_type": "published", "publication": "Molecular Microbiology", "volume": "89", "number": "5", "publisher": "Wiley", "pagerange": "831-841", "id_number": "CaltechAUTHORS:20130920-104107822", "issn": "0950-382X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130920-104107822", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM101425" }, { "agency": "NIH", "grant_number": "GM19559" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "NIH", "grant_number": "CA42014" } ] }, "doi": "10.1111/mmi.12309", "pmcid": "PMC3763515", "primary_object": { "basename": "mmi12309-sup-0001-si.pdf", "url": "https://authors.library.caltech.edu/records/50qx4-jxt40/files/mmi12309-sup-0001-si.pdf" }, "related_objects": [ { "basename": "mmi12309.pdf", "url": "https://authors.library.caltech.edu/records/50qx4-jxt40/files/mmi12309.pdf" }, { "basename": "nihms-502238.pdf", "url": "https://authors.library.caltech.edu/records/50qx4-jxt40/files/nihms-502238.pdf" } ], "resource_type": "article", "pub_year": "2013", "author_list": "Briegel, Ariane; Ames, Peter; et el." }, { "id": "https://authors.library.caltech.edu/records/m2whj-6nx65", "eprint_id": 41364, "eprint_status": "archive", "datestamp": "2023-08-19 21:01:10", "lastmod": "2023-10-24 23:40:59", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Dobro-Megan-J", "name": { "family": "Dobro", "given": "Megan J." }, "orcid": "0000-0002-6464-3932" }, { "id": "Samson-Rachel-Y", "name": { "family": "Samson", "given": "Rachel Y." } }, { "id": "Yu-Zhiheng", "name": { "family": "Yu", "given": "Zhiheng" } }, { "id": "McCullough-John", "name": { "family": "McCullough", "given": "John" } }, { "id": "Ding-H-Jane", "name": { "family": "Ding", "given": "H. Jane" } }, { "id": "Chong-Parkson-Lee-Gau", "name": { "family": "Chong", "given": "Parkson Lee-Gau" } }, { "id": "Bell-Stephen-D", "name": { "family": "Bell", "given": "Stephen D." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Electron cryotomography of ESCRT assemblies and dividing Sulfolobus cells suggests that spiraling filaments are involved in membrane scission", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2013 Dobro et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution\u2013Noncommercial\u2013Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).\n\nReceived: Nov 6, 2012;\nRevised: May 28, 2013;\nAccepted: May 31, 2013.\nThis article was published online ahead of print in MBoC in Press (http://www\n.molbiolcell.org/cgi/doi/10.1091/mbc.E12-11-0785) on June 12, 2013.\n\nThis work was supported in part by National Institutes of Heath Grant P50 GM082545 to G.J.J., National Science Foundation Grant DMR1105277 to P.L.C., and a gift to Caltech from the Gordon and Betty Moore Foundation. We thank Wesley I. Sundquist for advice and critical reading of the manuscript, Kay Grunewald for use of laboratory equipment, and Morgan Beeby, Jason Porath, and Jean Choi for their help with illustrations.\n\nPublished - Mol._Biol._Cell-2013-Dobro-2319-27.pdf
Supplemental Material - CombinedSupMats.pdf
Supplemental Material - mc-E12-11-0785-s01.mov
Supplemental Material - mc-E12-11-0785-s02.wmv
Supplemental Material - mc-E12-11-0785-s03.mov
Supplemental Material - mc-E12-11-0785-s04.mov
Supplemental Material - mc-E12-11-0785-s05.mov
", "abstract": "The endosomal-sorting complex required for transport (ESCRT) is evolutionarily conserved from Archaea to eukaryotes. The complex drives membrane scission events in a range of processes, including cytokinesis in Metazoa and some Archaea. CdvA is the protein in Archaea that recruits ESCRT-III to the membrane. Using electron cryotomography (ECT), we find that CdvA polymerizes into helical filaments wrapped around liposomes. ESCRT-III proteins are responsible for the cinching of membranes and have been shown to assemble into helical tubes in vitro, but here we show that they also can form nested tubes and nested cones, which reveal surprisingly numerous and versatile contacts. To observe the ESCRT\u2013CdvA complex in a physiological context, we used ECT to image the archaeon Sulfolobus acidocaldarius and observed a distinct protein belt at the leading edge of constriction furrows in dividing cells. The known dimensions of ESCRT-III proteins constrain their possible orientations within each of these structures and point to the involvement of spiraling filaments in membrane scission.", "date": "2013-08-01", "date_type": "published", "publication": "Molecular Biology of the Cell", "volume": "24", "number": "15", "publisher": "American Society for Cell Biology", "pagerange": "2319-2327", "id_number": "CaltechAUTHORS:20130917-104519857", "issn": "1059-1524", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130917-104519857", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P50 GM082545" }, { "agency": "NSF", "grant_number": "DMR1105277" }, { "agency": "Gordon and Betty Moore Foundation" } ] }, "doi": "10.1091/mbc.E12-11-0785", "pmcid": "PMC3727925", "primary_object": { "basename": "CombinedSupMats.pdf", "url": "https://authors.library.caltech.edu/records/m2whj-6nx65/files/CombinedSupMats.pdf" }, "related_objects": [ { "basename": "Mol._Biol._Cell-2013-Dobro-2319-27.pdf", "url": "https://authors.library.caltech.edu/records/m2whj-6nx65/files/Mol._Biol._Cell-2013-Dobro-2319-27.pdf" }, { "basename": "mc-E12-11-0785-s01.mov", "url": "https://authors.library.caltech.edu/records/m2whj-6nx65/files/mc-E12-11-0785-s01.mov" }, { "basename": "mc-E12-11-0785-s02.wmv", "url": "https://authors.library.caltech.edu/records/m2whj-6nx65/files/mc-E12-11-0785-s02.wmv" }, { "basename": "mc-E12-11-0785-s03.mov", "url": "https://authors.library.caltech.edu/records/m2whj-6nx65/files/mc-E12-11-0785-s03.mov" }, { "basename": "mc-E12-11-0785-s04.mov", "url": "https://authors.library.caltech.edu/records/m2whj-6nx65/files/mc-E12-11-0785-s04.mov" }, { "basename": "mc-E12-11-0785-s05.mov", "url": "https://authors.library.caltech.edu/records/m2whj-6nx65/files/mc-E12-11-0785-s05.mov" } ], "resource_type": "article", "pub_year": "2013", "author_list": "Dobro, Megan J.; Samson, Rachel Y.; et el." }, { "id": "https://authors.library.caltech.edu/records/a95kk-7h298", "eprint_id": 40905, "eprint_status": "archive", "datestamp": "2023-08-22 09:44:47", "lastmod": "2023-10-24 22:34:10", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Pilhofer-M", "name": { "family": "Pilhofer", "given": "Martin" } }, { "id": "Mastronarde-D-N", "name": { "family": "Mastronarde", "given": "David N." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards", "ispublished": "pub", "full_text_status": "public", "keywords": "Handedness; Electron tomography; DNA origami", "note": "\u00a9 2013 Elsevier Inc.\n\nReceived 11 October 2012; Received in revised form 17 April 2013; Accepted 19 April 2013; Available online 30 April 2013. \n\nWe thank Tim Liedl and Robert Schreiber for the DNA origami\ngold nanoparticle helices, Mark S. Ladinsky for negative stain sample preparation and cryosectioning, Paul Rothemund for helpful advice and discussions, Lu Gan and Alasdair McDowall for helpful discussions and technical support. We thank Julio Ortiz, Friedrich F\u00f6rster, John Heumann and Martin Beck for helpful communication.\nThis work was supported in part by the Beckman Institute\nat Caltech as well as NIH grants R01 GM094800B and\n2P50GM082545-06 to GJJ and P41GM103431 to A. Hoenger.\n\nAccepted Version - nihms507321.pdf
", "abstract": "The apparent handedness of an EM-tomography reconstruction depends on a number of conventions and can be confused in many ways. As the number of different hardware and software combinations being used for electron tomography continue to climb, and the reconstructions being produced reach higher and higher resolutions, the need to verify the hand of the results has increased. Here we enumerate various steps in a typical tomography experiment that affect handedness and show that DNA origami gold nanoparticle helices can be used as convenient and fail-safe handedness standards.", "date": "2013-07", "date_type": "published", "publication": "Journal of Structural Biology", "volume": "183", "number": "1", "publisher": "Elsevier", "pagerange": "95-98", "id_number": "CaltechAUTHORS:20130822-102116618", "issn": "1047-8477", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130822-102116618", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Caltech Beckman Institute" }, { "agency": "NIH", "grant_number": "R01 GM094800B" }, { "agency": "NIH", "grant_number": "2P50GM082545-06" }, { "agency": "NIH", "grant_number": "P41GM103431" } ] }, "doi": "10.1016/j.jsb.2013.04.008", "pmcid": "PMC3765063", "primary_object": { "basename": "nihms507321.pdf", "url": "https://authors.library.caltech.edu/records/a95kk-7h298/files/nihms507321.pdf" }, "resource_type": "article", "pub_year": "2013", "author_list": "Briegel, Ariane; Pilhofer, Martin; et el." }, { "id": "https://authors.library.caltech.edu/records/2hjxk-sx989", "eprint_id": 39049, "eprint_status": "archive", "datestamp": "2023-08-19 19:42:00", "lastmod": "2023-10-24 15:27:25", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Beeby-M-D", "name": { "family": "Beeby", "given": "Morgan" }, "orcid": "0000-0001-6413-9835" }, { "id": "Gumbart-J-C", "name": { "family": "Gumbart", "given": "James C." } }, { "id": "Roux-B", "name": { "family": "Roux", "given": "Beno\u00eet" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Architecture and assembly of the Gram-positive cell wall", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2013 John Wiley & Sons Ltd.\nAccepted 4 March, 2013.\nArticle first published online: 22 Apr. 2013.\nWe would like to thank Simon Foster for an initial gift of\npurified B. subtilis sacculi and the laboratory of Doug Rees\nfor use of the MPBio FastPrep-24. This work was funded by\nNational Institute of Health Grant R01 GM062342 to B. R., an\nArgonne Director's Postdoctoral Fellowship (J. C. G.), the\nHoward Hughes Medical Institute, and the Gordon and Betty\nMoore Center for Integrative Study of Cell Regulation at\nCaltech. Simulations were carried out with resources provided\nby the Computation Institute and the Biological Sciences\nDivision of the University of Chicago and Argonne\nNational Laboratory, under Grant S10 RR029030-01. We\nwould also like to thank Brigitte Ziervogel for helpful comments\non the manuscript.\n\nAccepted Version - nihms455415.pdf
Supplemental Material - mmi12203-sup-0001-si.zip
", "abstract": "The bacterial cell wall is a mesh polymer of peptidoglycan\n\u2013 linear glycan strands cross-linked by flexible\npeptides \u2013 that determines cell shape and provides\nphysical protection. While the glycan strands in thin\n'Gram-negative' peptidoglycan are known to run circumferentially\naround the cell, the architecture of the\nthicker 'Gram-positive' form remains unclear. Using\nelectron cryotomography, here we show that Bacillus\nsubtilis peptidoglycan is a uniformly dense layer with\na textured surface. We further show it rips circumferentially,\ncurls and thickens at free edges, and extends\nlongitudinally when denatured. Molecular dynamics\nsimulations show that only atomic models based\non the circumferential topology recapitulate the\nobserved curling and thickening, in support of an\n'inside-to-outside' assembly process. We conclude\nthat instead of being perpendicular to the cell surface\nor wrapped in coiled cables (two alternative models),\nthe glycan strands in Gram-positive cell walls run\ncircumferentially around the cell just as they do in\nGram-negative cells. Together with providing insights\ninto the architecture of the ultimate determinant of cell\nshape, this study is important because Gram-positive peptidoglycan is an antibiotic target crucial to the\nviability of several important rod-shaped pathogens\nincluding Bacillus anthracis, Listeria monocytogenes,\nand Clostridium difficile.", "date": "2013-05", "date_type": "published", "publication": "Molecular Microbiology", "volume": "88", "number": "4", "publisher": "Blackwell", "pagerange": "664-672", "id_number": "CaltechAUTHORS:20130624-103414394", "issn": "0950-382X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130624-103414394", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 GM062342" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Argonne National Laboratory", "grant_number": "S10 RR029030-01" } ] }, "doi": "10.1111/mmi.12203", "pmcid": "PMC3663049", "primary_object": { "basename": "mmi12203-sup-0001-si.zip", "url": "https://authors.library.caltech.edu/records/2hjxk-sx989/files/mmi12203-sup-0001-si.zip" }, "related_objects": [ { "basename": "nihms455415.pdf", "url": "https://authors.library.caltech.edu/records/2hjxk-sx989/files/nihms455415.pdf" } ], "resource_type": "article", "pub_year": "2013", "author_list": "Beeby, Morgan; Gumbart, James C.; et el." }, { "id": "https://authors.library.caltech.edu/records/99zwt-etx07", "eprint_id": 39055, "eprint_status": "archive", "datestamp": "2023-08-19 19:42:12", "lastmod": "2023-10-24 16:20:59", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Tocheva-E-I", "name": { "family": "Tocheva", "given": "Elitza I." }, "orcid": "0000-0002-4869-8319" }, { "id": "L\u00f3pez-Garrido-J", "name": { "family": "L\u00f3pez-Garrido", "given": "Javier" } }, { "id": "Hughes-H-V", "name": { "family": "Hughes", "given": "H. Velocity" } }, { "id": "Fredlund-J", "name": { "family": "Fredlund", "given": "Jennifer" } }, { "id": "Kuru-E", "name": { "family": "Kuru", "given": "Erkin" } }, { "id": "VanNieuwenhze-M-S", "name": { "family": "VanNieuwenhze", "given": "Michael S." } }, { "id": "Brun-Yves-V", "name": { "family": "Brun", "given": "Yves V." } }, { "id": "Pogliano-K", "name": { "family": "Pogliano", "given": "Kit" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Peptidoglycan transformations during Bacillus subtilis sporulation", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2013 John Wiley & Sons Ltd. \n\nFirst published online 27 March 2013. \n\nWe thank Poochit Nonejuie for the construction of DponA\nB. subtilis mutant, and Dr Tim Baker and Norm Olsen for\ntraining J.F. in microscopy. This work was supported by the\nHoward Hughes Medical Foundation, gifts to Caltech from the\nGordon and Betty Moore Foundation (to G.J.J.), GM57045 (to\nK.P.), AI059327 (to M.S.V.) and GM051986 (to Y.V.B.).\n\nAccepted Version - nihms544251.pdf
", "abstract": "While vegetative Bacillus subtilis cells and mature\nspores are both surrounded by a thick layer of peptidoglycan\n(PG, a polymer of glycan strands crosslinked\nby peptide bridges), it has remained unclear\nwhether PG surrounds prespores during engulfment.\nTo clarify this issue, we generated a slender DponA\nmutant that enabled high-resolution electron cryotomographic\nimaging. Three-dimensional reconstructions\nof whole cells in near-native states revealed a\nthin PG-like layer extending from the lateral cell wall\naround the prespore throughout engulfment. Cryotomography\nof purified sacculi and fluorescent labelling\nof PG in live cells confirmed that PG surrounds the\nprespore. The presence of PG throughout engulfment\nsuggests new roles for PG in sporulation, including a\nnew model for how PG synthesis might drive engulfment,\nand obviates the need to synthesize a PG layer\nde novo during cortex formation. In addition, it reveals\nthat B. subtilis can synthesize thin, Gram-negativelike\nPG layers as well as its thick, archetypal Grampositive\ncell wall. The continuous transformations\nfrom thick to thin and back to thick during sporulation\nsuggest that both forms of PG have the same basic\narchitecture (circumferential). Endopeptidase activity\nmay be the main switch that governs whether a thin or\na thick PG layer is assembled.", "date": "2013-05", "date_type": "published", "publication": "Molecular Microbiology", "volume": "88", "number": "4", "publisher": "Wiley-Blackwell", "pagerange": "673-686", "id_number": "CaltechAUTHORS:20130624-140301008", "issn": "0950-382X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130624-140301008", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "NIH", "grant_number": "GM57045" }, { "agency": "NIH", "grant_number": "AI059327" }, { "agency": "NIH", "grant_number": "GM051986" } ] }, "doi": "10.1111/mmi.12201/abstract", "pmcid": "PMC3893088", "primary_object": { "basename": "nihms544251.pdf", "url": "https://authors.library.caltech.edu/records/99zwt-etx07/files/nihms544251.pdf" }, "resource_type": "article", "pub_year": "2013", "author_list": "Tocheva, Elitza I.; L\u00f3pez-Garrido, Javier; et el." }, { "id": "https://authors.library.caltech.edu/records/0rk8v-ayp16", "eprint_id": 37695, "eprint_status": "archive", "datestamp": "2023-08-19 14:32:06", "lastmod": "2023-10-23 17:57:38", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Pilhofer-M", "name": { "family": "Pilhofer", "given": "Martin" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "The bacterial cytoskeleton: more than twisted filaments", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2012 Elsevier Ltd. \n\nAvailable online 23rd November 2012. \n\nThanks to Matt Swulius, Ariane Briegel, Morgan Beeby and Elitza Tocheva for helpful discussions and comments on the manuscript. Bacterial cytoskeleton research was supported by the Howard Hughes Medical Institute, NIH grant R01 GM094800B, the Center for Environmental Biology Interactions at Caltech and the Bayerische Forschungsstiftung.\n\nAccepted Version - nihms-422423.pdf
Supplemental Material - mmc1.mov
Supplemental Material - mmc2.mov
", "abstract": "Far from being simple 'bags' of enzymes, bacteria are richly endowed with ultrastructures that challenge and expand standard definitions of the cytoskeleton. Here we review rods, rings, twisted pairs, tubes, sheets, spirals, moving patches, meshes and composites, and suggest defining the term 'bacterial cytoskeleton' as all cytoplasmic protein filaments and their superstructures that move or scaffold (stabilize/position/recruit) other cellular materials. The evolution of each superstructure has been driven by specific functional requirements. As a result, while homologous proteins with different functions have evolved to form surprisingly divergent superstructures, those of unrelated proteins with similar functions have converged.", "date": "2013-02", "date_type": "published", "publication": "Current Opinion in Cell Biology", "volume": "25", "number": "1", "publisher": "Elsevier", "pagerange": "125-133", "id_number": "CaltechAUTHORS:20130401-091857529", "issn": "0955-0674", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130401-091857529", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "R01 GM094800B" }, { "agency": "Caltech Center for Environmental Biology Interactions" }, { "agency": "Bayerische Forschungsstiftung" } ] }, "doi": "10.1016/j.ceb.2012.10.019", "pmcid": "PMC3597445", "primary_object": { "basename": "mmc1.mov", "url": "https://authors.library.caltech.edu/records/0rk8v-ayp16/files/mmc1.mov" }, "related_objects": [ { "basename": "mmc2.mov", "url": "https://authors.library.caltech.edu/records/0rk8v-ayp16/files/mmc2.mov" }, { "basename": "nihms-422423.pdf", "url": "https://authors.library.caltech.edu/records/0rk8v-ayp16/files/nihms-422423.pdf" } ], "resource_type": "article", "pub_year": "2013", "author_list": "Pilhofer, Martin and Jensen, Grant J." }, { "id": "https://authors.library.caltech.edu/records/qnm00-cpp14", "eprint_id": 38121, "eprint_status": "archive", "datestamp": "2023-08-19 14:27:39", "lastmod": "2023-10-23 19:50:15", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gumbart-J-C", "name": { "family": "Gumbart", "given": "James C." } }, { "id": "Beeby-M-D", "name": { "family": "Beeby", "given": "Morgan" }, "orcid": "0000-0001-6413-9835" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Roux-B", "name": { "family": "Roux", "given": "Benoit" } } ] }, "title": "Assembly and Architecture of Gram-Positive and -Negative Cell Walls", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2013 Biophysical Society. Published by Elsevier Inc.\n\nPublished - 1-s2.0-S000634951204790X-main.pdf
", "abstract": "The cell wall, a porous mesh-like structure, provides shape and physical protection for bacteria. At the atomic level, it is composed of peptidoglycan (PG), a polymer of stiff glycan strands cross-linked by short, flexible peptides. However, at the mesoscale, multiple models for the organization of PG have been put forth, distinguished by glycan strands parallel to the cell surface (the so-called \"layered'' model) or perpendicular (the \"scaffold\" model). To test these models, and to resolve the mechanical properties of PG, we have built and simulated at an atomic scale patches of both Gram-positive and negative cell walls in different organizations up to 50 nanometers in size. In the case of Gram-positive PG, molecular dynamics simulations of the layered model are found to elucidate the mechanisms behind a distinct curling effect observed in three-dimensional electron cryo-tomography images of fragmented cell walls. For Gram-negative PG, simulations of patches with different average-glycan-strand lengths reveal an anisotropic elasticity, in good agreement with atomic-force microscopy experiments. Insights from the simulations reveal how mesoscopic and macroscopic properties of a ubiquitous bacterial ultrastructure arise from its atomic-scale interactions and organization.", "date": "2013-01-29", "date_type": "published", "publication": "Biophysical Journal", "volume": "104", "number": "2", "publisher": "Biophysical Society", "pagerange": "642A", "id_number": "CaltechAUTHORS:20130425-135202813", "issn": "0006-3495", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130425-135202813", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.bpj.2012.11.3544", "primary_object": { "basename": "1-s2.0-S000634951204790X-main.pdf", "url": "https://authors.library.caltech.edu/records/qnm00-cpp14/files/1-s2.0-S000634951204790X-main.pdf" }, "resource_type": "article", "pub_year": "2013", "author_list": "Gumbart, James C.; Beeby, Morgan; et el." }, { "id": "https://authors.library.caltech.edu/records/jcbcv-q8q32", "eprint_id": 38131, "eprint_status": "archive", "datestamp": "2023-08-19 14:28:00", "lastmod": "2023-10-23 19:50:52", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Two Case Studies where Electron Cryotomography has Revealed Mechanism: ESCRT and the Type VI Secretion System", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2013 Biophysical Society. Published by Elsevier Inc.", "abstract": "Sometimes all that is really needed to distinguish between competing models is a few really good pictures. Electron cryotomography has increasingly met that need by delivering unprecedented 3-D images of intact cells in a near-native (frozen-hydrated) state to \"macromolecular\" resolution. I will present two case studies. In the first, cryotomograms of dividing Sulfolobus acidocaldarius cells revealed a thin layer of material at the leading edge of ingressing membranes whose structure and development point uniquely to an \"hourglass\" model for how the ESCRT machinery drives membrane scission. In the second, cryotomograms of Vibrio cholerae cells revealed extended cytoplasmic tubes in two different conformational states. Identification of the tubes as Type VI Secretion Systems led immediately to a \"spring-loaded dagger\" model for their ability to deposit toxins into neighboring cells.", "date": "2013-01-29", "date_type": "published", "publication": "Biophysical Journal", "volume": "104", "number": "2", "publisher": "Biophysical Society", "pagerange": "206A-206A", "id_number": "CaltechAUTHORS:20130426-093928748", "issn": "0006-3495", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130426-093928748", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.bpj.2012.11.1166", "resource_type": "article", "pub_year": "2013", "author_list": "Jensen, Grant J." }, { "id": "https://authors.library.caltech.edu/records/36sad-9f481", "eprint_id": 37658, "eprint_status": "archive", "datestamp": "2023-08-22 08:17:50", "lastmod": "2023-10-23 17:54:50", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Yu-Zhiheng", "name": { "family": "Yu", "given": "Zhiheng" } }, { "id": "Dobro-M-J", "name": { "family": "Dobro", "given": "Megan J." }, "orcid": "0000-0002-6464-3932" }, { "id": "Woodward-C-L", "name": { "family": "Woodward", "given": "Cora L." } }, { "id": "Levandovsky-A", "name": { "family": "Levandovsky", "given": "Artem" } }, { "id": "Danielson-C-M", "name": { "family": "Danielson", "given": "Cindy M." } }, { "id": "Sandrin-V", "name": { "family": "Sandrin", "given": "Virginie" } }, { "id": "Shi-Jiong", "name": { "family": "Shi", "given": "Jiong" } }, { "id": "Aiken-C", "name": { "family": "Aiken", "given": "Christopher" } }, { "id": "Zandi-R", "name": { "family": "Zandi", "given": "Roya" } }, { "id": "Hope-T-J", "name": { "family": "Hope", "given": "Thomas J." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Unclosed HIV-1 Capsids Suggest a Curled Sheet Model of Assembly", "ispublished": "pub", "full_text_status": "public", "keywords": "HIV-1; capsid; cryotomography; retroviruses", "note": "\u00a9 2012 Elsevier Ltd. Received 9 October 2012; Accepted 10 October 2012. Available online 16 October 2012. Z.Y. and M.J.D. contributed equally to this work. This work was supported in part by NIH Grants 2P50GM082545-06 (to T.J.H. and G.J.J.), R01 AI076121 (to C.A.), and R01 AI407770 (to T.J.H.); National Science Foundation Grant DMR-06-45668\n(to R.Z.); and gifts to Caltech from the Gordon and\nBetty Moore Foundation and to Northwestern from the James B. Pendleton Charitable Trust. The following was obtained from the NIH AIDS Research and Reference Reagent Program: 183-H12-5C hybridoma from Dr. Bruce Chesebro. We thank\nDr. Ben Chen for providing the HIV Gag-iGFP plasmid, Dr. Joseph Sodroski for cells expressing rhTRIM5\u03b1, Dylan Morris for help with the supplementary movies, Drs. Jordan Schooler and Elizabeth Wright for help with data collection, and Drs. Wesley Sundquist and Edward Campbell for critically reading the manuscript.\n\nAccepted Version - nihms415192.pdf
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", "abstract": "The RNA genome of retroviruses is encased within a protein capsid. To gather insight into the assembly and function of this capsid, we used electron cryotomography to image human immunodeficiency virus (HIV) and equine infectious anemia virus (EIAV) particles. While the majority of viral cores appeared closed, a variety of unclosed structures including rolled sheets, extra flaps, and cores with holes in the tip were also seen. Simulations of nonequilibrium growth of elastic sheets recapitulated each of these aberrations and further predicted the occasional presence of seams, for which tentative evidence was also found within the cryotomograms. To test the integrity of viral capsids in vivo, we observed that ~ 25% of cytoplasmic HIV complexes captured by TRIM5\u03b1 had holes large enough to allow internal green fluorescent protein (GFP) molecules to escape. Together, these findings suggest that HIV assembly at least sometimes involves the union in space of two edges of a curling sheet and results in a substantial number of unclosed forms.", "date": "2013-01-09", "date_type": "published", "publication": "Journal of Molecular Biology", "volume": "425", "number": "1", "publisher": "Elsevier", "pagerange": "112-123", "id_number": "CaltechAUTHORS:20130327-152515876", "issn": "0022-2836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130327-152515876", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "2P50GM082545-06" }, { "agency": "NIH", "grant_number": "R01 AI076121" }, { "agency": "NIH", "grant_number": "R01 AI407770" }, { "agency": "NSF", "grant_number": "DMR-06-45668" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "James B. Pendleton Charitable Trust" } ] }, "doi": "10.1016/j.jmb.2012.10.006", "pmcid": "PMC3597093", "primary_object": { "basename": "mmc5.mov", "url": "https://authors.library.caltech.edu/records/36sad-9f481/files/mmc5.mov" }, "related_objects": [ { "basename": "mmc6.pdf", "url": "https://authors.library.caltech.edu/records/36sad-9f481/files/mmc6.pdf" }, { "basename": "mmc7.pdf", "url": "https://authors.library.caltech.edu/records/36sad-9f481/files/mmc7.pdf" }, { "basename": "nihms415192.pdf", "url": "https://authors.library.caltech.edu/records/36sad-9f481/files/nihms415192.pdf" }, { "basename": "mmc1.mov", "url": "https://authors.library.caltech.edu/records/36sad-9f481/files/mmc1.mov" }, { "basename": "mmc2.mov", "url": "https://authors.library.caltech.edu/records/36sad-9f481/files/mmc2.mov" }, { "basename": "mmc3.mov", "url": "https://authors.library.caltech.edu/records/36sad-9f481/files/mmc3.mov" }, { "basename": "mmc4.mov", "url": "https://authors.library.caltech.edu/records/36sad-9f481/files/mmc4.mov" } ], "resource_type": "article", "pub_year": "2013", "author_list": "Yu, Zhiheng; Dobro, Megan J.; et el." }, { "id": "https://authors.library.caltech.edu/records/c2a0f-yed64", "eprint_id": 36726, "eprint_status": "archive", "datestamp": "2023-08-19 14:08:52", "lastmod": "2023-10-23 15:25:38", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Abrusci-P", "name": { "family": "Abrusci", "given": "Patrizia" } }, { "id": "Vergara-Irigaray-M", "name": { "family": "Vergara-Irigaray", "given": "Marta" } }, { "id": "Johnson-S", "name": { "family": "Johnson", "given": "Steven" }, "orcid": "0000-0001-9487-8583" }, { "id": "Beeby-M-D", "name": { "family": "Beeby", "given": "Morgan D." }, "orcid": "0000-0001-6413-9835" }, { "id": "Hendrixson-D-R", "name": { "family": "Hendrixson", "given": "David R." } }, { "id": "Roversi-P", "name": { "family": "Roversi", "given": "Pietro" } }, { "id": "Friede-M-E", "name": { "family": "Friede", "given": "Miriam E." } }, { "id": "Deane-J-E", "name": { "family": "Deane", "given": "Janet E." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Tang-Christopher-M", "name": { "family": "Tang", "given": "Christopher M." } }, { "id": "Lea-S-M", "name": { "family": "Lea", "given": "Susan M." } } ] }, "title": "Architecture of the major component of the type III secretion system export apparatus", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2012 Nature Publishing Group, a division of Macmillan Publishers Limited. \n\nReceived 30 March; accepted 22 October; published online 9 December 2012.\n\nWe thank N.C. Strynadka for access to InvA coordinates ahead of publication,\nP. Sansonetti (Institute Pasteur, Paris) for providing the polyclonal antibodies to\nIpa proteins, I. Lasa (Universidad P\u00fablica de Navarra, Pamplona) for the pKO3blue plasmid, L. De Colibus, C. King and members of the Lea group for general assistance, the staff of the protein crystallography beamlines at the European Synchrotron Radiation Source, Grenoble (France) and DIAMOND facility, Didcot (UK) for assistance in data collection, and S.K. Mazmanian for use of the microaerobic chamber. P.A. is funded by grant 083599/Z/07/Z and J.E.D. by grant WT083599MA, both from the Wellcome Trust to S.M.L.; S.J. is funded by grant G0900888 from the UK Medical Research Council to S.M.L. and C.M.T.; P.R. is funded by the Oxford Martin School Vaccine Design Institute of which S.M.L. is codirector. M.V.-I. is funded by FP7 Marie Curie EIMID-IAPP-217768 grant. M.B. and G.J.J. were supported by the Howard Hughes Medical Institute.\n\nAuthor Contributions: \nJ.E.D., S.J. and S.M.L. initiated the project, which P.A. later joined; S.M.L. and C.M.T. supervised the project. M.E.F. and J.E.D. designed the MxiAC expression vector and did protein expression and stability trials. P.A. performed the large-scale purification, methylation, crosslinking and SPR of MxiAC and its mutants. S.J. performed the MALS experiments. P.A. designed the 'export apparatus' co-expression vectors and purified the recombinant complex. P.A. crystallized MxiAC and optimized crystals for data collection, and S.M.L. soaked and handled crystals for data collection. P.A., P.R. and S.M.L. contributed to the data collection, structure determination and model building. C.M.T. and M.V.-I. designed and performed the complementation and invasion assays in S. flexneri. D.R.H. created the C. jejuni strains, and M.D.B. and G.J.J. designed and performed cryo-EM tomography. P.A., S.J. and S.M.L. analyzed data and wrote the manuscript.\nAll authors read and approved the manuscript.\n\nAccepted Version - nihms416875.pdf
Supplemental Material - nsmb.2452-S1.pdf
", "abstract": "Type III secretion systems (T3SSs) are bacterial membrane\u2013embedded nanomachines designed to export specifically targeted proteins from the bacterial cytoplasm. Secretion through T3SS is governed by a subset of inner membrane proteins termed the 'export apparatus'. We show that a key member of the Shigella flexneri export apparatus, MxiA, assembles into a ring essential for secretion in vivo. The ring-forming interfaces are well-conserved in both nonflagellar and flagellar homologs, implying that the ring is an evolutionarily conserved feature in these systems. Electron cryo-tomography revealed a T3SS-associated cytoplasmic torus of size and shape corresponding to those of the MxiA ring aligned to the secretion channel located between the secretion pore and the ATPase complex. This defines the molecular architecture of the dominant component of the export apparatus and allows us to propose a model for the molecular mechanisms controlling secretion.", "date": "2013-01", "date_type": "published", "publication": "Nature Structural & Molecular Biology", "volume": "20", "number": "1", "publisher": "Nature Publishing Group", "pagerange": "99-104", "id_number": "CaltechAUTHORS:20130131-161741196", "issn": "1545-9985", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130131-161741196", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Wellcome Trust", "grant_number": "083599/Z/07/Z" }, { "agency": "Wellcome Trust", "grant_number": "WT083599MA" }, { "agency": "Medical Research Council (UK)", "grant_number": "G0900888" }, { "agency": "Oxford Martin School Vaccine Design Institute" }, { "agency": "Marie Curie Fellowship", "grant_number": "EIMID-IAPP-217768" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1038/nsmb.2452", "pmcid": "PMC3537844", "primary_object": { "basename": "nihms416875.pdf", "url": "https://authors.library.caltech.edu/records/c2a0f-yed64/files/nihms416875.pdf" }, "related_objects": [ { "basename": "nsmb.2452-S1.pdf", "url": "https://authors.library.caltech.edu/records/c2a0f-yed64/files/nsmb.2452-S1.pdf" } ], "resource_type": "article", "pub_year": "2013", "author_list": "Abrusci, Patrizia; Vergara-Irigaray, Marta; et el." }, { "id": "https://authors.library.caltech.edu/records/8ebtx-6tg19", "eprint_id": 36171, "eprint_status": "archive", "datestamp": "2023-08-19 13:48:49", "lastmod": "2023-10-20 22:20:02", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Schlimpert-Susan", "name": { "family": "Schlimpert", "given": "Susan" } }, { "id": "Klein-Eric-A", "name": { "family": "Klein", "given": "Eric A." } }, { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Hughes-Velocity", "name": { "family": "Hughes", "given": "Velocity" } }, { "id": "Kahnt-J\u00f6rg", "name": { "family": "Kahnt", "given": "J\u00f6rg" } }, { "id": "Bolte-Kathrin", "name": { "family": "Bolte", "given": "Kathrin" } }, { "id": "Maier-Uwe-G", "name": { "family": "Maier", "given": "Uwe G." } }, { "id": "Brun-Yves-V", "name": { "family": "Brun", "given": "Yves V." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Gitai-Zemer", "name": { "family": "Gitai", "given": "Zemer" }, "orcid": "0000-0002-3280-6178" }, { "id": "Thanbichler-Martin", "name": { "family": "Thanbichler", "given": "Martin" }, "orcid": "0000-0002-1303-1442" } ] }, "title": "General Protein Diffusion Barriers Create Compartments within Bacterial Cells", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2012 Elsevier Inc. \n\nReceived: March 19, 2012. Revised: July 24, 2012. Accepted: October 14, 2012. Published online: November 29, 2012. \n\nWe thank Stephanie Wick for excellent technical assistance; Nikolay Ouzounov for helpful discussions; Juliane K\u00fchn, Patrick Viollier, and Grant Bowman for providing plasmids and strains; and Sarah Cheng for help with image segmentation. This work was supported by funds from the Max Planck Society to M.T., a Young Investigator Grant (RGY0069/2008-C) from the Human Frontier Science Program to Z.G. and M.T., a National Institutes of Health (NIH) Director's New Innovator Award (DP2OD004389) to Z.G., an NRSA postdoctoral fellowship (F32GM906842) from the National Institute of General Medical Sciences to E.A.K., NIH grant GM51986 to Y.V.B, and NIH grant RO1GM094800B to G.J.J.\n\nAccepted Version - nihms428421.pdf
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", "abstract": "In eukaryotes, the differentiation of cellular extensions such as cilia or neuronal axons depends on the partitioning of proteins to distinct plasma membrane domains by specialized diffusion barriers. However, examples of this compartmentalization strategy are still missing for prokaryotes, although complex cellular architectures are also widespread among this group of organisms. This study reveals the existence of a protein-mediated membrane diffusion barrier in the stalked bacterium Caulobacter crescentus. We show that the Caulobacter cell envelope is compartmentalized by macromolecular complexes that prevent the exchange of both membrane and soluble proteins between the polar stalk extension and the cell body. The barrier structures span the cross-sectional area of the stalk and comprise at least four proteins that assemble in a cell-cycle-dependent manner. Their presence is critical for cellular fitness because they minimize the effective cell volume, allowing faster adaptation to environmental changes that require de novo synthesis of envelope proteins.", "date": "2012-12-07", "date_type": "published", "publication": "Cell", "volume": "151", "number": "6", "publisher": "Elsevier", "pagerange": "1270-1282", "id_number": "CaltechAUTHORS:20130104-105656715", "issn": "0092-8674", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130104-105656715", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Max Planck Society" }, { "agency": "Human Frontier Science Program", "grant_number": "RGY0069/2008-C" }, { "agency": "NIH", "grant_number": "DP2OD004389" }, { "agency": "NIH Postdoctoral Fellowship", "grant_number": "F32GM906842" }, { "agency": "NIH", "grant_number": "GM51986" }, { "agency": "NIH", "grant_number": "RO1GM094800B" } ] }, "doi": "10.1016/j.cell.2012.10.046", "pmcid": "PMC3542395", "primary_object": { "basename": "mmc2.mov", "url": "https://authors.library.caltech.edu/records/8ebtx-6tg19/files/mmc2.mov" }, "related_objects": [ { "basename": "mmc3.mp4", "url": "https://authors.library.caltech.edu/records/8ebtx-6tg19/files/mmc3.mp4" }, { "basename": "mmc4.mp4", "url": "https://authors.library.caltech.edu/records/8ebtx-6tg19/files/mmc4.mp4" }, { "basename": "mmc5.mp4", "url": "https://authors.library.caltech.edu/records/8ebtx-6tg19/files/mmc5.mp4" }, { "basename": "mmc6.mov", "url": "https://authors.library.caltech.edu/records/8ebtx-6tg19/files/mmc6.mov" }, { "basename": "mmc7supp.pdf", "url": "https://authors.library.caltech.edu/records/8ebtx-6tg19/files/mmc7supp.pdf" }, { "basename": "nihms428421.pdf", "url": "https://authors.library.caltech.edu/records/8ebtx-6tg19/files/nihms428421.pdf" }, { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/8ebtx-6tg19/files/mmc1.pdf" } ], "resource_type": "article", "pub_year": "2012", "author_list": "Schlimpert, Susan; Klein, Eric A.; et el." }, { "id": "https://authors.library.caltech.edu/records/2vz91-fx697", "eprint_id": 36358, "eprint_status": "archive", "datestamp": "2023-08-19 13:37:53", "lastmod": "2023-10-20 23:04:29", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Patwardhan-Ardan", "name": { "family": "Patwardhan", "given": "Ardan" } }, { "id": "Carazo-Jos\u00e9-Maria", "name": { "family": "Carazo", "given": "Jos\u00e9-Maria" } }, { "id": "Carragher-Bridget", "name": { "family": "Carragher", "given": "Bridget" } }, { "id": "Henderson-Richard", "name": { "family": "Henderson", "given": "Richard" } }, { "id": "Heymann-J-Bernard", "name": { "family": "Heymann", "given": "J. Bernard" } }, { "id": "Hill-Emma", "name": { "family": "Hill", "given": "Emma" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Lagerstedt-Ingvar", "name": { "family": "Lagerstedt", "given": "Ingvar" } }, { "id": "Lawson-Catherine-L", "name": { "family": "Lawson", "given": "Catherine L." } }, { "id": "Ludtke-Steven-J", "name": { "family": "Ludtke", "given": "Steven J." } }, { "id": "Mastronarde-David", "name": { "family": "Mastronarde", "given": "David" } }, { "id": "Moore-William-J", "name": { "family": "Moore", "given": "William J." } }, { "id": "Roseman-Alan", "name": { "family": "Roseman", "given": "Alan" } }, { "id": "Rosenthal-Peter", "name": { "family": "Rosenthal", "given": "Peter" } }, { "id": "Sorzano-Carlos-Oscar-S", "name": { "family": "Sorzano", "given": "Carlos-Oscar S." } }, { "id": "Sanz-Garc\u00eda-Eduardo", "name": { "family": "Sanz-Garc\u00eda", "given": "Eduardo" } }, { "id": "Scheres-Sjors-H-W", "name": { "family": "Scheres", "given": "Sjors H. W." } }, { "id": "Subramaniam-Sriram", "name": { "family": "Subramaniam", "given": "Sriram" } }, { "id": "Westbrook-John", "name": { "family": "Westbrook", "given": "John" } }, { "id": "Winn-Martyn", "name": { "family": "Winn", "given": "Martyn" } }, { "id": "Swedlow-Jason-R", "name": { "family": "Swedlow", "given": "Jason R." } }, { "id": "Kleywegt-Gerard-J", "name": { "family": "Kleywegt", "given": "Gerard J." } } ] }, "title": "Data management challenges in three-dimensional EM", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2012 Nature Publishing Group, a division of Macmillan Publishers Limited. This work is licensed under a Creative Commons Attribution-NonCommercial-Share Alike 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/. \n\nReceived 8 May; accepted 24 September; published\nonline 5 December 2012. \n\nWe thank P. Haslam for help with the manuscript. This workshop and the OMERO-EMDB project are supported by the BBSRC (BB/G022577). The EMDataBank is funded by the US National Institutes of Health National Institute of General Medical Sciences (R01GM079429). The work on the EMDB at the PDBe also profits from funding by European Molecular Biology Laboratory\u2013EBI and the Wellcome Trust (088944).\n\nPublished - nsmb.2426.pdf
Accepted Version - nihms585068.pdf
", "abstract": "This report describes the outcomes of the Data Management Challenges in 3D Electron Microscopy workshop. Key topics discussed include data models, validation and raw-data archiving. The meeting participants agreed that the EMDataBank should take the lead in addressing these issues, and concrete action points were agreed upon that will have a substantial impact on the accessibility of three-dimensional EM data in biology and medicine.", "date": "2012-12", "date_type": "published", "publication": "Nature Structural & Molecular Biology", "volume": "19", "number": "12", "publisher": "Nature Publishing Group", "pagerange": "1203-1207", "id_number": "CaltechAUTHORS:20130114-141533149", "issn": "1545-9985", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130114-141533149", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Biotechnology and Biological Sciences Research Council (BBSRC)", "grant_number": "BB/G022577" }, { "agency": "NIH", "grant_number": "R01GM079429" }, { "agency": "European Molecular Biology Laboratory (EMBL)" }, { "agency": "Wellcome Trust", "grant_number": "088944" } ] }, "doi": "10.1038/nsmb.2426", "pmcid": "PMC4048199", "primary_object": { "basename": "nihms585068.pdf", "url": "https://authors.library.caltech.edu/records/2vz91-fx697/files/nihms585068.pdf" }, "related_objects": [ { "basename": "nsmb.2426.pdf", "url": "https://authors.library.caltech.edu/records/2vz91-fx697/files/nsmb.2426.pdf" } ], "resource_type": "article", "pub_year": "2012", "author_list": "Patwardhan, Ardan; Carazo, Jos\u00e9-Maria; et el." }, { "id": "https://authors.library.caltech.edu/records/f5fwg-4z028", "eprint_id": 36059, "eprint_status": "archive", "datestamp": "2023-08-19 13:36:40", "lastmod": "2023-10-20 22:11:42", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Swulius-M-T", "name": { "family": "Swulius", "given": "Matthew T." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "The Helical MreB Cytoskeleton in Escherichia coli MC1000/pLE7 Is an Artifact of the N-Terminal Yellow Fluorescent Protein Tag", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2012 American Society for Microbiology.\n\nReceived 30 March 2012 Accepted 31 July 2012.\nPublished ahead of print 17 August 2012.\n\nWe thank L. Rothfield for E. coli strains MC1000/pLE7 and MC1000/\npLE6. We also thank Piet De Boer for E. coli strain FB76.\nThis work was supported by NIH grant R01 GM094800B to G.J.J.\n\nPublished - J._Bacteriol.-2012-Swulius-6382-6.pdf
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", "abstract": "Based on fluorescence microscopy, the actin homolog MreB has been thought to form extended helices surrounding the cytoplasm of rod-shaped bacterial cells. The presence of these and other putative helices has come to dominate models of bacterial cell shape regulation, chromosome segregation, polarity, and motility. Here we use electron cryotomography to show that MreB does in fact form extended helices and filaments in Escherichia coli when yellow fluorescent protein (YFP) is fused to its N terminus but native (untagged) MreB expressed to the same levels does not. In contrast, mCherry fused to an internal loop (MreB-RFP^(SW)) does not induce helices. The helices are therefore an artifact of the placement of the fluorescent protein tag. YFP-MreB helices were also clearly distinguishable from the punctate, \"patchy\" localization patterns of MreB-RFP^(SW), even by standard light microscopy. The many interpretations in the literature of such punctate patterns as helices should therefore be reconsidered.", "date": "2012-12", "date_type": "published", "publication": "Journal of Bacteriology", "volume": "194", "number": "23", "publisher": "American Society for Microbiology", "pagerange": "6382-6386", "id_number": "CaltechAUTHORS:20121219-145126195", "issn": "0021-9193", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20121219-145126195", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 GM094800B" } ] }, "doi": "10.1128/JB.00505-12", "pmcid": "PMC3497537", "primary_object": { "basename": "Legends.pdf", "url": "https://authors.library.caltech.edu/records/f5fwg-4z028/files/Legends.pdf" }, "related_objects": [ { "basename": "MovieS1.mov", "url": "https://authors.library.caltech.edu/records/f5fwg-4z028/files/MovieS1.mov" }, { "basename": "MovieS2.mov", "url": "https://authors.library.caltech.edu/records/f5fwg-4z028/files/MovieS2.mov" }, { "basename": "FigS1.pdf", "url": "https://authors.library.caltech.edu/records/f5fwg-4z028/files/FigS1.pdf" }, { "basename": "J._Bacteriol.-2012-Swulius-6382-6.pdf", "url": "https://authors.library.caltech.edu/records/f5fwg-4z028/files/J._Bacteriol.-2012-Swulius-6382-6.pdf" } ], "resource_type": "article", "pub_year": "2012", "author_list": "Swulius, Matthew T. and Jensen, Grant J." }, { "id": "https://authors.library.caltech.edu/records/vddng-s8s29", "eprint_id": 35663, "eprint_status": "archive", "datestamp": "2023-08-22 07:10:04", "lastmod": "2023-10-20 20:08:45", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Yamaichi-Yoshiharu", "name": { "family": "Yamaichi", "given": "Yoshiharu" } }, { "id": "Bruckner-Raphael", "name": { "family": "Bruckner", "given": "Raphael" } }, { "id": "Ringgaard-Simon", "name": { "family": "Ringgaard", "given": "Simon" } }, { "id": "M\u00f6ll-Andrea", "name": { "family": "M\u00f6ll", "given": "Andrea" } }, { "id": "Cameron-D-Ewen", "name": { "family": "Cameron", "given": "D. Ewen" } }, { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Davis-Brigid-M", "name": { "family": "Davis", "given": "Brigid M." } }, { "id": "Waldor-Matthew-K", "name": { "family": "Waldor", "given": "Matthew K." } } ] }, "title": "A multidomain hub anchors the chromosome segregation and chemotactic machinery to the bacterial pole", "ispublished": "pub", "full_text_status": "public", "keywords": "Vibrio cholerae; cell polarity; chemotaxis; chromosome segregation; motility", "note": "\u00a9 2012 by Cold Spring Harbor Laboratory Press. Received June 29, 2012; revised version accepted August 27, 2012. These authors contributed equally to this work. We are grateful to Janet Iwasa for making Figure 6D, Paula\nMontero Llopis for an expert tutorial in Microbe Tracker, and John Mekalanos for providing the mapped transposon library. We also thank Richard Losick, Hubert Lam, and Waldor laboratory members for helpful discussions and comments on the manuscript. S.R. was funded with a post-doctoral fellowship from the Villum Kann Rasmussen Foundation. This work was supported by the NIAID R37 AI-042347 (to M.K.W.), NIGMS R01 GM094800B (to G.J.J), and HHMI (to M.K.W. and G.J.J.).\n\nPublished - Genes_Dev.-2012-Yamaichi-2348-60.pdf
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", "abstract": "The cell poles constitute key subcellular domains that are often critical for motility, chemotaxis, and chromosome segregation in rod-shaped bacteria. However, in nearly all rods, the processes that underlie the formation, recognition, and perpetuation of the polar domains are largely unknown. Here, in Vibrio cholerae, we identified HubP (hub of the pole), a polar transmembrane protein conserved in all vibrios, that anchors three ParA-like ATPases to the cell poles and, through them, controls polar localization of the chromosome origin, the chemotactic machinery, and the flagellum. In the absence of HubP, oriCI is not targeted to the cell poles, chemotaxis is impaired, and a small but increased fraction of cells produces multiple, rather than single, flagella. Distinct cytoplasmic domains within HubP are required for polar targeting of the three ATPases, while a periplasmic portion of HubP is required for its localization. HubP partially relocalizes from the poles to the mid-cell prior to cell division, thereby enabling perpetuation of the polar domain in future daughter cells. Thus, a single polar hub is instrumental for establishing polar identity and organization.", "date": "2012-10-15", "date_type": "published", "publication": "Genes and Development", "volume": "26", "number": "20", "publisher": "Cold Spring Harbor Laboratory Press", "pagerange": "2348-2360", "id_number": "CaltechAUTHORS:20121127-091703726", "issn": "0890-9369", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20121127-091703726", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIAID", "grant_number": "R37 AI-042347" }, { "agency": "NIGMS", "grant_number": "R01 GM094800B" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1101/gad.199869.112", "pmcid": "PMC3475806", "primary_object": { "basename": "MovieS1.mov", "url": "https://authors.library.caltech.edu/records/vddng-s8s29/files/MovieS1.mov" }, "related_objects": [ { "basename": "MovieS2.mov", "url": "https://authors.library.caltech.edu/records/vddng-s8s29/files/MovieS2.mov" }, { "basename": "Supplement_3_4.doc", "url": "https://authors.library.caltech.edu/records/vddng-s8s29/files/Supplement_3_4.doc" }, { "basename": "sup_figs.pdf", "url": "https://authors.library.caltech.edu/records/vddng-s8s29/files/sup_figs.pdf" }, { "basename": "Genes_Dev.-2012-Yamaichi-2348-60.pdf", "url": "https://authors.library.caltech.edu/records/vddng-s8s29/files/Genes_Dev.-2012-Yamaichi-2348-60.pdf" } ], "resource_type": "article", "pub_year": "2012", "author_list": "Yamaichi, Yoshiharu; Bruckner, Raphael; et el." }, { "id": "https://authors.library.caltech.edu/records/w1xah-md257", "eprint_id": 29830, "eprint_status": "archive", "datestamp": "2023-08-19 10:14:05", "lastmod": "2023-10-24 22:29:24", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Basler-M", "name": { "family": "Basler", "given": "M." } }, { "id": "Pilhofer-M", "name": { "family": "Pilhofer", "given": "M." } }, { "id": "Henderson-G-P", "name": { "family": "Henderson", "given": "G. P." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "G. J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Mekalanor-J-J", "name": { "family": "Mekalanos", "given": "J. J." } } ] }, "title": "Type VI secretion requires a dynamic contractile phage tail-like structure", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2012 Macmillan Publishers Limited. Received 03 October 2011. Accepted 09 January 2012. Published online 26 February 2012. We thank T. G. Bernhardt and N. T. Peters for assistance with fluorescence microscopy, discussions and for a gift of plasmids carrying sfGFP and mCherry2 genes. We thank the Nikon Imaging Center at Harvard Medical School for help with fluorescence microscopy, and Research Precision Instruments and Hamamatsu for lending an ORCA-Flash2.8 camera. We thank the Harvard Medical School Electron Microscopy Facility for help with and supervision of transmission\nelectron microscopy. We thank M. K. Waldor for a V. cholerae 2740-80 strain and discussions. We thank D. Ewen Cameron for a knockout construct pWM91-flgG. We thank B. Wen and Z. Li for initial cryotomographic studies. This work was supported by National Institute of Allergy and Infectious Diseases grants AI-018045 and AI-26289 to J.J.M. and National Institute of General Medical Sciences grant GM094800B to G.J.J. Author Contributions: All authors helped design and analyse experiments; M.B., M.P. and G.P.H. performed experiments, and M.B., M.P., G.J.J. and J.J.M. wrote the paper.", "abstract": "Type VI secretion systems are bacterial virulence-associated nanomachines composed of proteins that are evolutionarily related to components of bacteriophage tails. Here we show that protein secretion by the type VI secretion system of Vibrio cholerae requires the action of a dynamic intracellular tubular structure that is structurally and functionally homologous to contractile phage tail sheath. Time-lapse fluorescence light microscopy reveals that sheaths of the type VI secretion system cycle between assembly, quick contraction, disassembly and re-assembly. Whole-cell electron cryotomography further shows that the sheaths appear as long tubular structures in either extended or contracted conformations that are connected to the inner membrane by a distinct basal structure. These data support a model in which the contraction of the type VI secretion system sheath provides the energy needed to translocate proteins out of effector cells and into adjacent target cells.", "date": "2012-03-08", "date_type": "published", "publication": "Nature", "volume": "483", "number": "7388", "publisher": "Nature Publishing Group", "pagerange": "182-187", "id_number": "CaltechAUTHORS:20120326-070420034", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120326-070420034", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Institute of Allergy and Infectious Diseases", "grant_number": "AI 018045" }, { "agency": "National Institute of Allergy and Infectious Diseases", "grant_number": "AI 26289" }, { "agency": "National Institute of General Medical Sciences", "grant_number": "GM094800B" } ] }, "doi": "10.1038/nature10846", "resource_type": "article", "pub_year": "2012", "author_list": "Basler, M.; Pilhofer, M.; et el." }, { "id": "https://authors.library.caltech.edu/records/4nbgg-ned22", "eprint_id": 102629, "eprint_status": "archive", "datestamp": "2023-08-22 05:11:22", "lastmod": "2023-10-20 00:21:33", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Basler-M", "name": { "family": "Basler", "given": "M." } }, { "id": "Pilhofer-M", "name": { "family": "Pilhofer", "given": "M." } }, { "id": "Henderson-G-P", "name": { "family": "Henderson", "given": "G. P." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "G. J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Mekalanor-J-J", "name": { "family": "Mekalanos", "given": "J. J." } } ] }, "title": "Type VI secretion requires a dynamic contractile phage tail-like structure", "ispublished": "pub", "full_text_status": "public", "keywords": "Bacterial evolution; Cryoelectron tomography; Structural biology", "note": "\u00a9 2012 Macmillan Publishers Limited. \n\nReceived 3 October 2011; accepted 9 January 2012. Published online 26 February 2012. \n\nWe thank T. G. Bernhardt and N. T. Peters for assistance with fluorescence microscopy, discussions and for a gift of plasmids carrying sfGFP and mCherry2 genes. We thank the Nikon Imaging Center at Harvard Medical School for help with fluorescence microscopy, and Research Precision Instruments and Hamamatsu for lending an ORCA-Flash2.8 camera. We thank the Harvard Medical School Electron Microscopy Facility for help with and supervision of transmission electron microscopy. We thank M. K. Waldor for a V. cholerae 2740-80 strain and discussions. We thank D. Ewen Cameron for a knockout construct pWM91-flgG. We thank B. Wen and Z. Li for initial cryotomographic studies. This work was supported by National Institute of Allergy and Infectious Diseases grants AI-018045 and AI-26289 to J.J.M. and National Institute of General Medical Sciences grant GM094800B to G.J.J. \n\nM. Basler and M. Pilhofer: These authors contributed equally to this work. \n\nAuthor Contributions: All authors helped design and analyse experiments; M.B., M.P. and G.P.H. performed experiments, and M.B., M.P., G.J.J. and J.J.M. wrote the paper. \n\nThe authors declare no competing financial interests.\n\nAccepted Version - nihms427869.pdf
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Supplemental Material - 41586_2012_BFnature10846_MOESM61_ESM.mov
", "abstract": "Type VI secretion systems are bacterial virulence-associated nanomachines composed of proteins that are evolutionarily related to components of bacteriophage tails. Here we show that protein secretion by the type VI secretion system of Vibrio cholerae requires the action of a dynamic intracellular tubular structure that is structurally and functionally homologous to contractile phage tail sheath. Time-lapse fluorescence light microscopy reveals that sheaths of the type VI secretion system cycle between assembly, quick contraction, disassembly and re-assembly. Whole-cell electron cryotomography further shows that the sheaths appear as long tubular structures in either extended or contracted conformations that are connected to the inner membrane by a distinct basal structure. These data support a model in which the contraction of the type VI secretion system sheath provides the energy needed to translocate proteins out of effector cells and into adjacent target cells.", "date": "2012-03-08", "date_type": "published", "publication": "Nature", "volume": "483", "number": "7388", "publisher": "Nature Publishing Group", "pagerange": "182-186", "id_number": "CaltechAUTHORS:20200417-142717709", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200417-142717709", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "AI-018045" }, { "agency": "NIH", "grant_number": "AI-26289" }, { "agency": "NIH", "grant_number": "GM094800B" } ] }, "doi": "10.1038/nature10846", "pmcid": "PMC3527127", "primary_object": { "basename": "41586_2012_BFnature10846_MOESM47_ESM.ppt", "url": "https://authors.library.caltech.edu/records/4nbgg-ned22/files/41586_2012_BFnature10846_MOESM47_ESM.ppt" }, "related_objects": [ { "basename": "41586_2012_BFnature10846_MOESM56_ESM.mov", "url": "https://authors.library.caltech.edu/records/4nbgg-ned22/files/41586_2012_BFnature10846_MOESM56_ESM.mov" }, { "basename": "41586_2012_BFnature10846_MOESM57_ESM.mov", "url": "https://authors.library.caltech.edu/records/4nbgg-ned22/files/41586_2012_BFnature10846_MOESM57_ESM.mov" }, { "basename": "41586_2012_BFnature10846_MOESM58_ESM.mov", "url": "https://authors.library.caltech.edu/records/4nbgg-ned22/files/41586_2012_BFnature10846_MOESM58_ESM.mov" }, { "basename": "nihms427869.pdf", "url": "https://authors.library.caltech.edu/records/4nbgg-ned22/files/nihms427869.pdf" }, { "basename": "41586_2012_BFnature10846_MOESM46_ESM.ppt", "url": "https://authors.library.caltech.edu/records/4nbgg-ned22/files/41586_2012_BFnature10846_MOESM46_ESM.ppt" }, { "basename": "41586_2012_BFnature10846_MOESM50_ESM.pdf", "url": "https://authors.library.caltech.edu/records/4nbgg-ned22/files/41586_2012_BFnature10846_MOESM50_ESM.pdf" }, { "basename": "41586_2012_BFnature10846_MOESM52_ESM.mov", "url": "https://authors.library.caltech.edu/records/4nbgg-ned22/files/41586_2012_BFnature10846_MOESM52_ESM.mov" }, { "basename": "41586_2012_BFnature10846_MOESM53_ESM.mov", "url": "https://authors.library.caltech.edu/records/4nbgg-ned22/files/41586_2012_BFnature10846_MOESM53_ESM.mov" }, { "basename": "41586_2012_BFnature10846_MOESM59_ESM.mov", "url": "https://authors.library.caltech.edu/records/4nbgg-ned22/files/41586_2012_BFnature10846_MOESM59_ESM.mov" }, { "basename": "41586_2012_BFnature10846_MOESM49_ESM.ppt", "url": "https://authors.library.caltech.edu/records/4nbgg-ned22/files/41586_2012_BFnature10846_MOESM49_ESM.ppt" }, { "basename": "41586_2012_BFnature10846_MOESM54_ESM.mov", "url": "https://authors.library.caltech.edu/records/4nbgg-ned22/files/41586_2012_BFnature10846_MOESM54_ESM.mov" }, { "basename": "41586_2012_BFnature10846_MOESM55_ESM.mov", "url": "https://authors.library.caltech.edu/records/4nbgg-ned22/files/41586_2012_BFnature10846_MOESM55_ESM.mov" }, { "basename": "41586_2012_BFnature10846_MOESM60_ESM.mov", "url": "https://authors.library.caltech.edu/records/4nbgg-ned22/files/41586_2012_BFnature10846_MOESM60_ESM.mov" }, { "basename": "41586_2012_BFnature10846_MOESM61_ESM.mov", "url": "https://authors.library.caltech.edu/records/4nbgg-ned22/files/41586_2012_BFnature10846_MOESM61_ESM.mov" }, { "basename": "41586_2012_BFnature10846_MOESM48_ESM.ppt", "url": "https://authors.library.caltech.edu/records/4nbgg-ned22/files/41586_2012_BFnature10846_MOESM48_ESM.ppt" }, { "basename": "41586_2012_BFnature10846_MOESM51_ESM.mov", "url": "https://authors.library.caltech.edu/records/4nbgg-ned22/files/41586_2012_BFnature10846_MOESM51_ESM.mov" } ], "resource_type": "article", "pub_year": "2012", "author_list": "Basler, M.; Pilhofer, M.; et el." }, { "id": "https://authors.library.caltech.edu/records/aezp1-y9w62", "eprint_id": 29841, "eprint_status": "archive", "datestamp": "2023-08-19 10:12:45", "lastmod": "2023-10-24 22:30:01", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Li-Xiaoxiao", "name": { "family": "Li", "given": "Xiaoxiao" } }, { "id": "Bilwes-A-M", "name": { "family": "Bilwes", "given": "Alexandrine M." } }, { "id": "Hughes-K-T", "name": { "family": "Hughes", "given": "Kelly T." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Crane-B-R", "name": { "family": "Crane", "given": "Brian R." } } ] }, "title": "Bacterial chemoreceptor arrays are hexagonally packed trimers of receptor dimers networked by rings of kinase and coupling proteins", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2012 National Academy of Sciences. Edited by Laura L. Kiessling, University of Wisconsin, Madison, WI, and approved January 13, 2012 (received for review September 23, 2011). Author contributions: A.B., X.L., G.J.J., and B.R.C. designed research; A.B. and X.L.\nperformed research; K.T.H. contributed new reagents/analytic tools; A.B., X.L., A.M.B., and B.R.C. analyzed data; and A.B., X.L., A.M.B., G.J.J., and B.R.C. wrote the paper. The authors declare no conflict of interest. We thank Drs. Morgan Beeby and Songye Chen for collecting\nsome of the tomographic data, Dr. John Heumann for help using the\nPEET software, Dr. Stanley Maloy for suggesting FtsZ overexpression for minicell production, and A. Vu and Dr. F.W. Dahlquist for advice on choosing constructs for crystallization. We also thank the Cornell High Energy Synchrotron Source for access to data collection facilities. This work was supported by the Howard Hughes Medical Institute, by gifts to Caltech from The Gordon and Betty Moore Foundation, and by National Institutes of Health Grant GM066775 (to B.R.C.).\n\nPublished - Briegel2012p17515P_Natl_Acad_Sci_Usa.pdf
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", "abstract": "Chemoreceptor arrays are supramolecular transmembrane machines of unknown structure that allow bacteria to sense their surroundings and respond by chemotaxis. We have combined X-ray crystallography of purified proteins with electron cryotomography of native arrays inside cells to reveal the arrangement of the component transmembrane receptors, histidine kinases (CheA) and CheW coupling proteins. Trimers of receptor dimers lie at the vertices of a hexagonal lattice in a \"two-facing-two\" configuration surrounding a ring of alternating CheA regulatory domains (P5) and CheW couplers. Whereas the CheA kinase domains (P4) project downward below the ring, the CheA dimerization domains (P3) link neighboring rings to form an extended, stable array. This highly interconnected protein architecture underlies the remarkable sensitivity and cooperative nature of transmembrane signaling in bacterial chemotaxis.", "date": "2012-03-06", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "109", "number": "10", "publisher": "National Academy of Sciences", "pagerange": "3766-3771", "id_number": "CaltechAUTHORS:20120326-100949924", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120326-100949924", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "NIH", "grant_number": "GM066775" } ] }, "doi": "10.1073/pnas.1115719109", "pmcid": "PMC3309718", "primary_object": { "basename": "Briegel2012p17515P_Natl_Acad_Sci_Usa.pdf", "url": "https://authors.library.caltech.edu/records/aezp1-y9w62/files/Briegel2012p17515P_Natl_Acad_Sci_Usa.pdf" }, "related_objects": [ { "basename": "SM01.mov", "url": "https://authors.library.caltech.edu/records/aezp1-y9w62/files/SM01.mov" }, { "basename": "pnas.1115719109_SI.pdf", "url": "https://authors.library.caltech.edu/records/aezp1-y9w62/files/pnas.1115719109_SI.pdf" } ], "resource_type": "article", "pub_year": "2012", "author_list": "Briegel, Ariane; Li, Xiaoxiao; et el." }, { "id": "https://authors.library.caltech.edu/records/wkyr3-vra06", "eprint_id": 29755, "eprint_status": "archive", "datestamp": "2023-08-19 10:04:19", "lastmod": "2023-10-24 22:25:21", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Beeby-M-D", "name": { "family": "Beeby", "given": "Morgan" }, "orcid": "0000-0001-6413-9835" }, { "id": "Cho-Mimi", "name": { "family": "Cho", "given": "Mimi" } }, { "id": "Stubbe-J", "name": { "family": "Stubbe", "given": "JoAnne" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Growth and Localization of Polyhydroxybutyrate Granules in Ralstonia eutropha", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2012 American Society for Microbiology. Received 2 September 2011 Accepted 9 December 2011. Published ahead of print 16 December 2011. This work was supported by NIH GM49171 to J. Stubbe and Howard Hughes Medical Institute funding to G. J. Jensen. We thank Wesley Chen for assistance in manual reconstruction of tomograms.\n\nPublished - Beeby2012p17434J_Bacteriol.pdf
Supplemental Material - FigS1-S2.pdf
", "abstract": "The bacterium Ralstonia eutropha forms cytoplasmic granules of polyhydroxybutyrate that are a source of biodegradable thermoplastic. While much is known about the biochemistry of polyhydroxybutyrate production, the cell biology of granule formation and growth remains unclear. Previous studies have suggested that granules form either in the inner membrane, on a central scaffold, or in the cytoplasm. Here we used electron cryotomography to monitor granule genesis and development in 3 dimensions (3-D) in a near-native, \"frozen-hydrated\" state in intact Ralstonia eutropha cells. Neither nascent granules within the cell membrane nor scaffolds were seen. Instead, granules of all sizes resided toward the center of the cytoplasm along the length of the cell and exhibited a discontinuous surface layer more consistent with a partial protein coating than either a lipid mono- or bilayer. Putatively fusing granules were also seen, suggesting that small granules are continually generated and then grow and merge. Together, these observations support a model of biogenesis wherein granules form in the cytoplasm coated not by phospholipid but by protein. Previous thin-section electron microscopy (EM), fluorescence microscopy, and atomic force microscopy (AFM) results to the contrary may reflect both differences in nucleoid condensation and specimen preparation-induced artifacts.", "date": "2012-03", "date_type": "published", "publication": "Journal of Bacteriology", "volume": "194", "number": "5", "publisher": "American Society for Microbiology", "pagerange": "1092-1099", "id_number": "CaltechAUTHORS:20120316-151333425", "issn": "0021-9193", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120316-151333425", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM49171" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1128/JB.06125-11", "pmcid": "PMC3294789", "primary_object": { "basename": "Beeby2012p17434J_Bacteriol.pdf", "url": "https://authors.library.caltech.edu/records/wkyr3-vra06/files/Beeby2012p17434J_Bacteriol.pdf" }, "related_objects": [ { "basename": "FigS1-S2.pdf", "url": "https://authors.library.caltech.edu/records/wkyr3-vra06/files/FigS1-S2.pdf" } ], "resource_type": "article", "pub_year": "2012", "author_list": "Beeby, Morgan; Cho, Mimi; et el." }, { "id": "https://authors.library.caltech.edu/records/r8e1e-vtw77", "eprint_id": 29858, "eprint_status": "archive", "datestamp": "2023-08-19 09:47:28", "lastmod": "2023-10-24 22:30:47", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gan-Lu", "name": { "family": "Gan", "given": "Lu" }, "orcid": "0000-0002-8685-4896" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Electron tomography of cells", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 Cambridge University Press. Published online: 15 November 2011. We thank Morgan Beeby, Ariane Briegel, Mark Ladinsky, Alasdair McDowall and Martin\nPilhofer for comments and Karin Mallard for help with figures and editing. We apologize to\nall our colleagues whose work we could not highlight for space constraints. This work was\nsupported in part by NIH grants GM066521 and GM094800B to G. J. J.\n\nPublished - Gan2012p17514Q_Rev_Biophys.pdf
", "abstract": "The electron microscope has contributed deep insights into biological structure since its invention nearly 80 years ago. Advances in instrumentation and methodology in recent decades have now enabled electron tomography to become the highest resolution three-dimensional (3D) imaging technique available for unique objects such as cells. Cells can be imaged either plastic-embedded or frozen-hydrated. Then the series of projection images are aligned and back-projected to generate a 3D reconstruction or 'tomogram'. Here, we review how electron tomography has begun to reveal the molecular organization of cells and how the existing and upcoming technologies promise even greater insights into structural cell biology.", "date": "2012-02", "date_type": "published", "publication": "Quarterly Reviews of Biophysics", "volume": "45", "number": "1", "publisher": "Cambridge University Press", "pagerange": "27-56", "id_number": "CaltechAUTHORS:20120327-091111234", "issn": "0033-5835", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120327-091111234", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM066521" }, { "agency": "NIH", "grant_number": "GM094800B" } ] }, "doi": "10.1017/S0033583511000102", "primary_object": { "basename": "Gan2012p17514Q_Rev_Biophys.pdf", "url": "https://authors.library.caltech.edu/records/r8e1e-vtw77/files/Gan2012p17514Q_Rev_Biophys.pdf" }, "resource_type": "article", "pub_year": "2012", "author_list": "Gan, Lu and Jensen, Grant J." }, { "id": "https://authors.library.caltech.edu/records/nrms3-9dp34", "eprint_id": 29110, "eprint_status": "archive", "datestamp": "2023-08-19 08:47:44", "lastmod": "2023-10-24 18:22:17", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Pilhofer-M", "name": { "family": "Pilhofer", "given": "Martin" } }, { "id": "Ladinsky-M-S", "name": { "family": "Ladinsky", "given": "Mark S." }, "orcid": "0000-0002-1036-3513" }, { "id": "McDowall-A-W", "name": { "family": "McDowall", "given": "Alasdair W." } }, { "id": "Petroni-G", "name": { "family": "Petroni", "given": "Giulio" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Microtubules in Bacteria: Ancient Tubulins Build a Five-Protofilament Homolog of the Eukaryotic Cytoskeleton", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 Pilhofer et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits\nunrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.\nReceived May 4, 2011; Accepted October 25, 2011; Published December 6, 2011.\nAcademic Editor: Linda Amos, MRC Laboratory of Molecular Biology, United Kingdom.\nFunding: This work was supported in part by NIH grant R01 GM094800B to G.J.J., a gift to Caltech from the Gordon and Betty Moore Foundation, and a stipend\nfrom the Bayerische Forschungsstiftung to M.P. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the\nmanuscript.\n\n\nWe thank K. Downing, D. Stokes, J. Staley, K.- H. Schleifer, W. Ludwig,\nL. Gan, M. Beeby, M. Swulius, and E. Tocheva for discussions; H.\nErickson for anti-BtubA/B antibodies; D. Schlieper and J. Lo\u00a8we for vector\npHIS17; M. Anaya for help with protein purification; C. Eckl for help with\nRT-PCR; S. Cheng for help with segmentations; and M. Beeby for help\nwith Figure 4B.\nAuthor Contributions:\nThe author(s) have made the following declarations about their\ncontributions: Conceived and designed the experiments: MP GJJ.\nPerformed the experiments: MP. Analyzed the data: MP GJJ. Wrote the\npaper: MP GJJ. Performed immuno-EM staining and freeze-substitution:\nMSL. Performed cryo-sectioning: MSL AWM. Performed phylogenetic\nanalyses: MP GP.\n\nPublished - Pilhofer2011p16990Plos_Biol.pdf
Supplemental Material - Figure_S1.pdf
Supplemental Material - Figure_S10.pdf
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Supplemental Material - Figure_S5.pdf
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Supplemental Material - Figure_S8.pdf
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Supplemental Material - Table_S1.pdf
Supplemental Material - Table_S2.pdf
", "abstract": "Microtubules play crucial roles in cytokinesis, transport, and motility, and are therefore superb targets for anti-cancer drugs. All tubulins evolved from a common ancestor they share with the distantly related bacterial cell division protein FtsZ, but while eukaryotic tubulins evolved into highly conserved microtubule-forming heterodimers, bacterial FtsZ presumably continued to function as single homopolymeric protofilaments as it does today. Microtubules have not previously been found in bacteria, and we lack insight into their evolution from the tubulin/FtsZ ancestor. Using electron cryomicroscopy, here we show that the tubulin homologs BtubA and BtubB form microtubules in bacteria and suggest these be referred to as \"bacterial microtubules\" (bMTs). bMTs share important features with their eukaryotic counterparts, such as straight protofilaments and similar protofilament interactions. bMTs are composed of only five protofilaments, however, instead of the 13 typical in eukaryotes. These and other results suggest that rather than being derived from modern eukaryotic tubulin, BtubA and BtubB arose from early tubulin intermediates that formed small microtubules. Since we show that bacterial microtubules can be produced in abundance in vitro without chaperones, they should be useful tools for tubulin research and drug screening.", "date": "2011-12", "date_type": "published", "publication": "PLoS Biology", "volume": "9", "number": "12", "publisher": "Public Library of Science", "pagerange": "Art. No. e1001213", "id_number": "CaltechAUTHORS:20120203-085706225", "issn": "1544-9173", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120203-085706225", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 GM094800B" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Bayerische Forschungsstiftung" } ] }, "doi": "10.1371/journal.pbio.1001213", "pmcid": "PMC3232192", "primary_object": { "basename": "Figure_S6.pdf", "url": "https://authors.library.caltech.edu/records/nrms3-9dp34/files/Figure_S6.pdf" }, "related_objects": [ { "basename": "Figure_S7.pdf", "url": "https://authors.library.caltech.edu/records/nrms3-9dp34/files/Figure_S7.pdf" }, { "basename": "Figure_S1.pdf", "url": "https://authors.library.caltech.edu/records/nrms3-9dp34/files/Figure_S1.pdf" }, { "basename": "Figure_S3.pdf", "url": "https://authors.library.caltech.edu/records/nrms3-9dp34/files/Figure_S3.pdf" }, { "basename": "Figure_S5.pdf", "url": "https://authors.library.caltech.edu/records/nrms3-9dp34/files/Figure_S5.pdf" }, { "basename": "Table_S2.pdf", "url": "https://authors.library.caltech.edu/records/nrms3-9dp34/files/Table_S2.pdf" }, { "basename": "Figure_S2.pdf", "url": "https://authors.library.caltech.edu/records/nrms3-9dp34/files/Figure_S2.pdf" }, { "basename": "Figure_S4.pdf", "url": "https://authors.library.caltech.edu/records/nrms3-9dp34/files/Figure_S4.pdf" }, { "basename": "Figure_S9.pdf", "url": "https://authors.library.caltech.edu/records/nrms3-9dp34/files/Figure_S9.pdf" }, { "basename": "Figure_S10.pdf", "url": "https://authors.library.caltech.edu/records/nrms3-9dp34/files/Figure_S10.pdf" }, { "basename": "Table_S1.pdf", "url": "https://authors.library.caltech.edu/records/nrms3-9dp34/files/Table_S1.pdf" }, { "basename": "Pilhofer2011p16990Plos_Biol.pdf", "url": "https://authors.library.caltech.edu/records/nrms3-9dp34/files/Pilhofer2011p16990Plos_Biol.pdf" }, { "basename": "Figure_S11.pdf", "url": "https://authors.library.caltech.edu/records/nrms3-9dp34/files/Figure_S11.pdf" }, { "basename": "Figure_S8.pdf", "url": "https://authors.library.caltech.edu/records/nrms3-9dp34/files/Figure_S8.pdf" }, { "basename": "Movie_S1.mov", "url": "https://authors.library.caltech.edu/records/nrms3-9dp34/files/Movie_S1.mov" } ], "resource_type": "article", "pub_year": "2011", "author_list": "Pilhofer, Martin; Ladinsky, Mark S.; et el." }, { "id": "https://authors.library.caltech.edu/records/qg2c9-t2680", "eprint_id": 28518, "eprint_status": "archive", "datestamp": "2023-08-19 08:31:29", "lastmod": "2023-10-24 17:57:25", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Beeby-M-D", "name": { "family": "Beeby", "given": "Morgan" }, "orcid": "0000-0001-6413-9835" }, { "id": "Thanbichler-Martin", "name": { "family": "Thanbichler", "given": "Martin" }, "orcid": "0000-0002-1303-1442" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Activated chemoreceptor arrays remain intact and hexagonally packed", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 Blackwell Publishing Ltd. \n\nAccepted 14 September, 2011. Article first published online: 12 Oct 2011. \n\nThis work was supported in part by the Howard Hughes Medical Institute and by gifts to Caltech from the Gordon and Betty Moore Foundation.\n\nAccepted Version - nihms457996.pdf
Supplemental Material - MMI_7854_sm_BriegelFigure1.tif
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Supplemental Material - MMI_7854_sm_Briegelfigure2.tif
Supplemental Material - MMI_7854_sm_movie1WT.mp4
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Supplemental Material - MMI_7854_sm_movie4deltaCHeB.mp4
Supplemental Material - MMI_7854_sm_movie5deltaCheB.mp4
Supplemental Material - MMI_7854_sm_movie6deltaCheR.mp4
", "abstract": "Bacterial chemoreceptors cluster into exquisitively sensitive, tunable, highly ordered, polar arrays. While these arrays serve as paradigms of cell signalling in general, it remains unclear what conformational changes transduce signals from the periplasmic tips, where attractants and repellents bind, to the cytoplasmic signalling domains. Conflicting reports support and contest the hypothesis that activation causes large changes in the packing arrangement of the arrays, up to and including their complete disassembly. Using electron cryotomography, here we show that in Caulobacter crescentus, chemoreceptor arrays in cells grown in different media and immediately after exposure to the attractant galactose all exhibit the same 12 nm hexagonal packing arrangement, array size and other structural parameters. \u0394cheB and \u0394cheR mutants mimicking attractant- or repellent-bound states prior to adaptation also show the same lattice structure. We conclude that signal transduction and amplification must be accomplished through only small, nanoscale conformational changes.", "date": "2011-11", "date_type": "published", "publication": "Molecular Microbiology", "volume": "82", "number": "3", "publisher": "Blackwell", "pagerange": "748-757", "id_number": "CaltechAUTHORS:20111219-115630715", "issn": "0950-382X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111219-115630715", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Gordon and Betty Moore Foundation" } ] }, "doi": "10.1111/j.1365-2958.2011.07854.x", "pmcid": "PMC3641884", "primary_object": { "basename": "MMI_7854_sm_movie2WT.mp4", "url": "https://authors.library.caltech.edu/records/qg2c9-t2680/files/MMI_7854_sm_movie2WT.mp4" }, "related_objects": [ { "basename": "MMI_7854_sm_movie3deltaCheR.mp4", "url": "https://authors.library.caltech.edu/records/qg2c9-t2680/files/MMI_7854_sm_movie3deltaCheR.mp4" }, { "basename": "MMI_7854_sm_movie4deltaCHeB.mp4", "url": "https://authors.library.caltech.edu/records/qg2c9-t2680/files/MMI_7854_sm_movie4deltaCHeB.mp4" }, { "basename": "MMI_7854_sm_movie5deltaCheB.mp4", "url": "https://authors.library.caltech.edu/records/qg2c9-t2680/files/MMI_7854_sm_movie5deltaCheB.mp4" }, { "basename": "nihms457996.pdf", "url": "https://authors.library.caltech.edu/records/qg2c9-t2680/files/nihms457996.pdf" }, { "basename": "MMI_7854_sm_BriegelFigure1.tif", "url": "https://authors.library.caltech.edu/records/qg2c9-t2680/files/MMI_7854_sm_BriegelFigure1.tif" }, { "basename": "MMI_7854_sm_BriegelFigure3.tif", "url": "https://authors.library.caltech.edu/records/qg2c9-t2680/files/MMI_7854_sm_BriegelFigure3.tif" }, { "basename": "MMI_7854_sm_BriegelFigure4.tif", "url": "https://authors.library.caltech.edu/records/qg2c9-t2680/files/MMI_7854_sm_BriegelFigure4.tif" }, { "basename": "MMI_7854_sm_Briegelfigure2.tif", "url": "https://authors.library.caltech.edu/records/qg2c9-t2680/files/MMI_7854_sm_Briegelfigure2.tif" }, { "basename": "MMI_7854_sm_movie1WT.mp4", "url": "https://authors.library.caltech.edu/records/qg2c9-t2680/files/MMI_7854_sm_movie1WT.mp4" }, { "basename": "MMI_7854_sm_movie6deltaCheR.mp4", "url": "https://authors.library.caltech.edu/records/qg2c9-t2680/files/MMI_7854_sm_movie6deltaCheR.mp4" } ], "resource_type": "article", "pub_year": "2011", "author_list": "Briegel, Ariane; Beeby, Morgan; et el." }, { "id": "https://authors.library.caltech.edu/records/09qgf-3mf35", "eprint_id": 28448, "eprint_status": "archive", "datestamp": "2023-08-19 08:14:28", "lastmod": "2023-10-24 17:54:28", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Draper-O", "name": { "family": "Draper", "given": "Olga" } }, { "id": "Byrne-M-E", "name": { "family": "Byrne", "given": "Meghan E." } }, { "id": "Li-Zhuo", "name": { "family": "Li", "given": "Zhuo" } }, { "id": "Keyhani-S", "name": { "family": "Keyhani", "given": "Seperh" } }, { "id": "Cueto-Barrozo-J", "name": { "family": "Cueto Barrozo", "given": "Joyce" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Komeili-A", "name": { "family": "Komeili", "given": "Arash" } } ] }, "title": "MamK, a bacterial actin, forms dynamic filaments in vivo\n that are regulated by the acidic proteins MamJ and LimJ", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2011 Blackwell Publishing Ltd. Accepted 18 August, 2011. Article first published online: 14 Sep 2011. We thank the members of the Komeili laboratory for their valuable research and editorial input. O.D., M.B., and S.K. thank Steve Ruzin and Denise Schichnes at the UC Berkeley Biological Imaging Facility. O.D. and J.C. thank Kent\nMcDonald and Reena Zalpuri at the Robert D. Ogg Electron\nMicroscope Lab. Z.L. thanks Alasdair McDowall and Martin\nPilhofer for help with data collection. The cryotomography\nwork was supported by NIH grant R01 GM094800B to G.J.J.\nA.K. was supported through grants from the Packard Foundation and the National Institutes of Health (R01GM084122).", "abstract": "Bacterial actins, in contrast to their eukaryotic counterparts,\nare highly divergent proteins whose wideranging\nfunctions are thought to correlate with their\nevolutionary diversity. One clade, represented by the\nMamK protein of magnetotactic bacteria, is required\nfor the subcellular organization of magnetosomes,\nmembrane-bound organelles that aid in navigation\nalong the earth's magnetic field. Using a fluorescence\nrecovery after photobleaching assay in Magnetospirillum\nmagneticum AMB-1, we find that, like traditional\nactins, MamK forms dynamic filaments that require\nan intact NTPase motif for their turnover in vivo. We\nalso uncover two proteins, MamJ and LimJ, which\nperform a redundant function to promote the dynamic\nbehaviour of MamK filaments in wild-type cells.\nThe absence of both MamJ and LimJ leads to static\nfilaments, a disrupted magnetosome chain, and\nan anomalous build-up of cytoskeletal filaments\nbetween magnetosomes. Our results suggest that\nMamK filaments, like eukaryotic actins, are intrinsically\nstable and rely on regulators for their dynamic\nbehaviour, a feature that stands in contrast to some\nclasses of bacterial actins characterized to date.", "date": "2011-10", "date_type": "published", "publication": "Molecular Microbiology", "volume": "82", "number": "2", "publisher": "Blackwell Publishing", "pagerange": "342-354", "id_number": "CaltechAUTHORS:20111213-110839663", "issn": "0950-382X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111213-110839663", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 GM094800B" }, { "agency": "Packard Foundation" }, { "agency": "NIH", "grant_number": "R01 GM084122" } ] }, "doi": "10.1111/j.1365-2958.2011.07815.x", "resource_type": "article", "pub_year": "2011", "author_list": "Draper, Olga; Byrne, Meghan E.; et el." }, { "id": "https://authors.library.caltech.edu/records/670cz-xxk21", "eprint_id": 27345, "eprint_status": "archive", "datestamp": "2023-08-19 08:09:34", "lastmod": "2023-10-24 17:05:03", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gan-Lu", "name": { "family": "Gan", "given": "Lu" }, "orcid": "0000-0002-8685-4896" }, { "id": "Ladinsky-M-S", "name": { "family": "Ladinsky", "given": "Mark S." }, "orcid": "0000-0002-1036-3513" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Organization of the Smallest Eukaryotic Spindle", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 Elsevier Ltd. \n\nReceived 4 November 2010; revised 17 June 2011; Accepted 9 August 2011. Published online: September 8, 2011. Available online 8 September 2011.\n\nWe thank G. Henderson, P. Dias, A. McDowall, F.-Y. Bouget, H. Moreau, W. Marshall, J. Azimzadeh, and G. Ou for discussions and the anonymous reviewers for helpful comments. This work was supported in part by National Institutes of Health (NIH) grant P50 GM082545 to G.J.J. and a gift to the California Institute of Technology from the Gordon and Betty Moore Foundation. L.G. is a Damon Runyon Fellow supported by a fellowship from the Damon Runyon Cancer Research Foundation (DRG-1940-07). M.S.L. was supported by NIH grant 2 R37 AI041239-06A1 to P. Bj\u00f6rkman.\n\nAccepted Version - nihms328861.pdf
", "abstract": "In metazoans, plants, and fungi, the spindle checkpoint\ndelays mitosis until each chromosome is attached to one\nor more of its own kinetochore microtubules (kMTs). Some\nunicellular eukaryotes, however, have been reported to\nhave fewer kMTs than chromosomes. If this is the\ncase, it is unclear how the spindle checkpoint could be satisfied. In the vast majority of the previous studies, mitotic cells were chemically fixed at room temperature, but this does not always preserve dynamic and/or small structures like spindle MTs and kinetochores. Indeed, later higher-resolution studies have reversed some earlier claims. Here we show that in Ostreococcus tauri (the smallest eukaryote known), mitosis does involve fewer spindle microtubules than chromosomes. O. tauri cultures were enriched for mitotic cells, high-pressure frozen, and then imaged in 3D both in plastic and in a near-native (\"frozen-hydrated\") state through electron tomography. Mitotic cells have a distinctive intranuclear heterochromatin-free \"spindle tunnel\" with approximately four short and occasionally one long, incomplete (unclosed) microtubule at each end of the spindle tunnel. Because other aspects of O. tauri's spindle checkpoint seem typical, these data suggest that O. tauri's 20 chromosomes are physically linked and segregated as just one or a small number of groups.", "date": "2011-09-27", "date_type": "published", "publication": "Current Biology", "volume": "21", "number": "18", "publisher": "Cell Press", "pagerange": "1578-1583", "id_number": "CaltechAUTHORS:20111021-085847452", "issn": "0960-9822", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111021-085847452", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P50 GM082545" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Damon Runyon Cancer Research Foundation", "grant_number": "DRG-1940-07" }, { "agency": "NIH", "grant_number": "2 R37 AI041239-06A1" } ] }, "doi": "10.1016/j.cub.2011.08.021", "pmcid": "PMC3234289", "primary_object": { "basename": "nihms328861.pdf", "url": "https://authors.library.caltech.edu/records/670cz-xxk21/files/nihms328861.pdf" }, "resource_type": "article", "pub_year": "2011", "author_list": "Gan, Lu; Ladinsky, Mark S.; et el." }, { "id": "https://authors.library.caltech.edu/records/a15cy-5tw22", "eprint_id": 25456, "eprint_status": "archive", "datestamp": "2023-08-22 03:39:17", "lastmod": "2023-10-24 15:53:14", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Tocheva-E-I", "name": { "family": "Tocheva", "given": "Elitza I." }, "orcid": "0000-0002-4869-8319" }, { "id": "Matson-E-G", "name": { "family": "Matson", "given": "Eric G." } }, { "id": "Morris-D-M", "name": { "family": "Morris", "given": "Dylan M." } }, { "id": "Moussavi-F", "name": { "family": "Moussavi", "given": "Farshid" } }, { "id": "Leadbetter-J-R", "name": { "family": "Leadbetter", "given": "Jared R." }, "orcid": "0000-0002-7033-0844" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Peptidoglycan Remodeling and Conversion of an Inner Membrane into an Outer Membrane during Sporulation", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 Elsevier Inc. Received 2 November 2010; revised 25 May 2011; Accepted 9 July 2011. Published: September 1, 2011. Available online 1 September 2011. We thank Alasdair McDowall and Mark Ladinsky for their help with the preparation of mature spores by traditional EM methods and Dr. Martin Pilhofer for helping with the immunofluorescence and western blotting experiments. The GC-MS analysis of LPS was performed at the Complex Carbohydrate Research Center and was supported by DOE grant DE-FG02-09ER20097. We thank Everett Kane for the generation of Movie S2 and Jane H. Ding for helping with the generation of Movie S1 and Movie S2. We thank Ivan Tochev for generating Figure 4B. We thank Dr. Stephen Quake and Richard White at Stanford University for performing the shotgun genome sequencing of A. longum. The authors gratefully acknowledge the IGS annotation engine. This work was supported by a Natural Sciences and Engineering Research Council of Canada Postdoctorate Fellowship (to E.I.T.), the Howard Hughes Medical Foundation, and gifts to Caltech from the Gordon and Betty Moore Foundation, including support for the Caltech Center for Integrative Study of Cell Regulation. E.G.M was supported by the Department of Energy (award DE-FG02-07ER64484 to J.R.L).\n\nAccepted Version - nihms323719.pdf
", "abstract": "Two hallmarks of the Firmicute phylum, which includes the Bacilli and Clostridia classes, are their ability to form endospores and their \"Gram-positive\" single-membraned, thick-cell-wall envelope structure. Acetonema longum is part of a lesser-known family (the Veillonellaceae) of Clostridia that form endospores but that are surprisingly \"Gram negative,\" possessing both an inner and outer membrane and a thin cell wall. Here, we present macromolecular resolution, 3D electron cryotomographic images of vegetative, sporulating, and germinating A. longum cells showing that during the sporulation process, the inner membrane of the mother cell is inverted and transformed to become the outer membrane of the germinating cell. Peptidoglycan persists throughout, leading to a revised, \"continuous\" model of its role in the process. Coupled with genomic analyses, these results point to sporulation as a mechanism by which the bacterial outer membrane may have arisen and A. longum as a potential \"missing link\" between single- and double-membraned bacteria.", "date": "2011-09-02", "date_type": "published", "publication": "Cell", "volume": "146", "number": "5", "publisher": "Elsevier", "pagerange": "799-812", "id_number": "CaltechAUTHORS:20110928-072623751", "issn": "0092-8674", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110928-072623751", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02-09ER20097" }, { "agency": "Natural Sciences and Engineering Research Council of Canada (NSERC)" }, { "agency": "Howard Hughes Medical Foundation" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02-07ER64484" } ] }, "local_group": { "items": [ { "id": "Division-of-Geological-and-Planetary-Sciences" } ] }, "doi": "10.1016/j.cell.2011.07.029", "pmcid": "PMC3176627", "primary_object": { "basename": "nihms323719.pdf", "url": "https://authors.library.caltech.edu/records/a15cy-5tw22/files/nihms323719.pdf" }, "resource_type": "article", "pub_year": "2011", "author_list": "Tocheva, Elitza I.; Matson, Eric G.; et el." }, { "id": "https://authors.library.caltech.edu/records/7whe5-v2e53", "eprint_id": 25249, "eprint_status": "archive", "datestamp": "2023-08-22 03:15:03", "lastmod": "2023-10-24 15:44:06", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chen-Songye", "name": { "family": "Chen", "given": "Songye" }, "orcid": "0000-0001-5407-5049" }, { "id": "Beeby-M-D", "name": { "family": "Beeby", "given": "Morgan" }, "orcid": "0000-0001-6413-9835" }, { "id": "Murphy-G-E", "name": { "family": "Murphy", "given": "Gavin E." } }, { "id": "Leadbetter-J-R", "name": { "family": "Leadbetter", "given": "Jared R." }, "orcid": "0000-0002-7033-0844" }, { "id": "Hendrixson-D-R", "name": { "family": "Hendrixson", "given": "David R." } }, { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Li-Zhuo", "name": { "family": "Li", "given": "Zhuo" } }, { "id": "Shi-Jian-CELLBIO", "name": { "family": "Shi", "given": "Jian" }, "orcid": "0000-0003-3810-5302" }, { "id": "Tocheva-E-I", "name": { "family": "Tocheva", "given": "Elitza I." }, "orcid": "0000-0002-4869-8319" }, { "id": "M\u00fcller-A", "name": { "family": "M\u00fcller", "given": "Axel" } }, { "id": "Dobro-M-J", "name": { "family": "Dobro", "given": "Megan J." }, "orcid": "0000-0002-6464-3932" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Structural diversity of bacterial flagellar motors", "ispublished": "pub", "full_text_status": "public", "keywords": "bacterial flagellar motor; electron cryotomography; motility; phylogenetic profiling; subtomogram average", "note": "\u00a9 2011 European Molecular Biology Organization. \n\nReceived: 20 December 2010; accepted: 17 May 2011; published online: 14 June 2011. \n\nWe thank Drs Jane H Ding and Alasdair McDowall for computational and EM support, respectively; Sarkis K Mazmanian for use of the microaerobic chamber; and Igor Antoshechkin for advice on genome assembly. This work was supported by the Howard Hughes Medical Institute, the Gordon and Betty Moore Foundation Cell Center and the National Science Foundation. Author contributions: GJJ designed the research; SC, MB, GEM, AB, ZL, JS, EIT, AM, JRL and MJD cultured cells and/or collected tomograms; SC averaged subtomograms with help from GEM; JRL and MB coordinated the sequencing and annotation of needed\ngenomes, MB performed bioinformatics, and together with DRH\nidentified export densities, including subtomogram averaging of the comparative wild-type and mutant C. jejuni motors; SC, MB and GJJ analysed the results and wrote the paper.\n\nAccepted Version - nihms457996.pdf
", "abstract": "The bacterial flagellum is one of nature's most amazing\nand well-studied nanomachines. Its cell-wall-anchored\nmotor uses chemical energy to rotate a microns-long\nfilament and propel the bacterium towards nutrients and\naway from toxins. While much is known about flagellar\nmotors from certain model organisms, their diversity\nacross the bacterial kingdom is less well characterized,\nallowing the occasional misrepresentation of the motor as\nan invariant, ideal machine. Here, we present an electron\ncryotomographical survey of flagellar motor architectures\nthroughout the Bacteria. While a conserved structural\ncore was observed in all 11 bacteria imaged, surprisingly\nnovel and divergent structures as well as different symmetries were observed surrounding the core. Correlating the motor structures with the presence and absence of particular motor genes in each organism suggested the locations of five proteins involved in the export apparatus\nincluding FliI, whose position below the C-ring was confirmed by imaging a deletion strain. The combination of\nconserved and specially-adapted structures seen here\nsheds light on how this complex protein nanomachine\nhas evolved to meet the needs of different species.", "date": "2011-07-20", "date_type": "published", "publication": "EMBO Journal", "volume": "30", "number": "14", "publisher": "European Molecular Biology Organization", "pagerange": "2972-2981", "id_number": "CaltechAUTHORS:20110908-081125458", "issn": "0261-4189", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110908-081125458", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "NSF" } ] }, "local_group": { "items": [ { "id": "Division-of-Geological-and-Planetary-Sciences" } ] }, "doi": "10.1038/emboj.2011.186", "pmcid": "PMC3641884", "primary_object": { "basename": "nihms457996.pdf", "url": "https://authors.library.caltech.edu/records/7whe5-v2e53/files/nihms457996.pdf" }, "resource_type": "article", "pub_year": "2011", "author_list": "Chen, Songye; Beeby, Morgan; et el." }, { "id": "https://authors.library.caltech.edu/records/peb4e-7gw53", "eprint_id": 24208, "eprint_status": "archive", "datestamp": "2023-08-22 02:56:26", "lastmod": "2023-10-23 20:23:18", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Guerrero-Ferreira-R-C", "name": { "family": "Guerrero-Ferreira", "given": "Ricardo C." } }, { "id": "Viollier-P-H", "name": { "family": "Viollier", "given": "Patrick H." } }, { "id": "Ely-B", "name": { "family": "Ely", "given": "Bert" } }, { "id": "Poindexter-J-S", "name": { "family": "Poindexter", "given": "Jeanne S." } }, { "id": "Georgieva-M", "name": { "family": "Georgieva", "given": "Maria" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Wright-E-R", "name": { "family": "Wright", "given": "Elizabeth R." } } ] }, "title": "Alternative mechanism for bacteriophage adsorption to the motile bacterium Caulobacter crescentus", "ispublished": "pub", "full_text_status": "public", "keywords": "cryo-electron tomography; alpha-proteobacteria", "note": "\u00a9 2011 National Academy of Sciences. Freely available online through the PNAS open access option. \n\nEdited by Sankar Adhya, National Institutes of Health, National Cancer Institute, Bethesda, MD, and approved April 22, 2011 (received for review August 20, 2010). Published online before print May 25, 2011. \n\nWe thank Dr. Jens M. Holl and Mr. Grant M. Williams\nfor valuable help with manuscript preparation, graphic arts, and helpful discussions; Dr. Ryland Young and Dr. Ian Molineux for advice and mentoring on phage biology; Ms. Jeannette Taylor, Ms. Hong Yi, Dr. Wei Zhang, Dr. Ozan Ugurlu, and Mr. Chris Frethem for assistance during cryo-EM data collection; and Ms. Sabine Pruggnaller for providing the Amira toolbox for 3D segmentation. This work was supported in part by Emory University, Children's Healthcare of Atlanta, and the Georgia Research Alliance (to\nE.R.W.); and Human Frontier Science Program Grant RGP0051 (to P.H.V. and E.R.W.). The work at California Institute of Technology was supported by National Institutes of Health Grant P01 GM066521 (to G.J.J.) and a gift to Caltech from the Gordon and Betty Moore Foundation. Parts of this work\nwere carried out in the Institute of Technology Characterization Facility, University of Minnesota, which receives partial support from National Science Foundation through the Materials Research Science & Engineering Centers (MRSEC) program.\n\nAuthor contributions: R.C.G.-F. and E.R.W. designed research; R.C.G.-F., M.G., and E.R.W.\nperformed research; P.H.V., B.E., J.S.P., and G.J.J. contributed new reagents/analytic tools;\nR.C.G.-F. and E.R.W. analyzed data; R.C.G.-F. and E.R.W. wrote the paper; and P.H.V., B.E.,\nand J.S.P. contributed bacterial strains and phage stocks.\n\nPublished - GuerreroFerreira2011p14282P_Natl_Acad_Sci_Usa.pdf
Supplemental Material - pnas.201012388SI.pdf
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Supplemental Material - sm02.mp4
Supplemental Material - sm03.mp4
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", "abstract": "2D and 3D cryo-electron microscopy, together with adsorption kinetics assays of \u03d5Cb13 and \u03d5CbK phage-infected Caulobacter crescentus, provides insight into the mechanisms of infection. \u03d5Cb13 and \u03d5CbK actively interact with the flagellum and subsequently attach to receptors on the cell pole. We present evidence that the first interaction of the phage with the bacterial flagellum takes place through a filament on the phage head. This contact with the flagellum facilitates concentration of phage particles around the receptor (i.e., the pilus portals) on the bacterial cell surface, thereby increasing the likelihood of infection. Phage head filaments have not been well characterized and their function is described here. Phage head filaments may systematically underlie the initial interactions of phages with their hosts in other systems and possibly represent a widespread mechanism of efficient phage propagation.", "date": "2011-06-14", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "108", "number": "24", "publisher": "National Academy of Sciences", "pagerange": "9963-9968", "id_number": "CaltechAUTHORS:20110624-134716883", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110624-134716883", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Emory University" }, { "agency": "Children's Healthcare of Atlanta" }, { "agency": "Georgia Research Alliance" }, { "agency": "Human Frontier Science Program", "grant_number": "RGP0051" }, { "agency": "NIH", "grant_number": "P01 GM066521" }, { "agency": "Gordon and Betty Moore Foundation" } ] }, "doi": "10.1073/pnas.1012388108", "pmcid": "PMC3116389", "primary_object": { "basename": "pnas.201012388SI.pdf", "url": "https://authors.library.caltech.edu/records/peb4e-7gw53/files/pnas.201012388SI.pdf" }, "related_objects": [ { "basename": "sm01.mp4", "url": "https://authors.library.caltech.edu/records/peb4e-7gw53/files/sm01.mp4" }, { "basename": "sm03.mp4", "url": "https://authors.library.caltech.edu/records/peb4e-7gw53/files/sm03.mp4" }, { "basename": "sm04.mp4", "url": "https://authors.library.caltech.edu/records/peb4e-7gw53/files/sm04.mp4" }, { "basename": "sm05.mp4", "url": "https://authors.library.caltech.edu/records/peb4e-7gw53/files/sm05.mp4" }, { "basename": "GuerreroFerreira2011p14282P_Natl_Acad_Sci_Usa.pdf", "url": "https://authors.library.caltech.edu/records/peb4e-7gw53/files/GuerreroFerreira2011p14282P_Natl_Acad_Sci_Usa.pdf" }, { "basename": "sm02.mp4", "url": "https://authors.library.caltech.edu/records/peb4e-7gw53/files/sm02.mp4" }, { "basename": "sm06.mp4", "url": "https://authors.library.caltech.edu/records/peb4e-7gw53/files/sm06.mp4" }, { "basename": "sm07.mp4", "url": "https://authors.library.caltech.edu/records/peb4e-7gw53/files/sm07.mp4" } ], "resource_type": "article", "pub_year": "2011", "author_list": "Guerrero-Ferreira, Ricardo C.; Viollier, Patrick H.; et el." }, { "id": "https://authors.library.caltech.edu/records/w85wc-nhx36", "eprint_id": 24190, "eprint_status": "archive", "datestamp": "2023-08-19 07:06:26", "lastmod": "2023-10-23 20:22:36", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Shetty-A", "name": { "family": "Shetty", "given": "Ameesha" } }, { "id": "Chen-Shicheng", "name": { "family": "Chen", "given": "Shicheng" } }, { "id": "Tocheva-E-I", "name": { "family": "Tocheva", "given": "Elitza I." }, "orcid": "0000-0002-4869-8319" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Hickey-W-J", "name": { "family": "Hickey", "given": "William J." } } ] }, "title": "Nanopods: A New Bacterial Structure and Mechanism for Deployment of Outer Membrane Vesicles", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2011 Shetty et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits\nunrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.\nReceived December 21, 2010; Accepted May 10, 2011; Published June 7, 2011.\nEditor: Michael Hensel, University of Osnabrueck, Germany.\nFunding: These studies were funded by grants to WJH (NSF MCB0920664) and to GJJ (NIH R01 AI067548); EIT was supported by a Natural Sciences and\nEngineering Research Council of Canada Postdoctorate Fellowship. Sequencing and annotation of the Delftia sp. Cs1-4 genome was done by the U.S. Department\nof Energy Joint Genome Institute, through the Community Sequencing Project (CSP795673 to WJH). The work conducted by the U.S. Department of Energy Joint\nGenome Institute is supported by the Office of Science of the U.S. Department of Energy under contract No. DE-AC02-05CH11231. The funders had no role in\nstudy design, data collection and analysis, decision to publish, or preparation of the manuscript.\n\nThe authors thank the following colleagues for supplying cultures: Jullian\nDavies (Delftia acidovorans SPH1), Eric Roden (Acidovorax delafieldii), David\nStahl (Verminephrobacter eiseniae EF01-2) and Ronald Walcott (Acidovorax\navenae subsp. citrulli AAC00-1).\nAuthor Contributions:\nConceived and designed the experiments: WJH GJJ. Performed the\nexperiments: AS SC EIT. Analyzed the data: WJH EIT GJJ AS.\nContributed reagents/materials/analysis tools: WJH GJJ. Wrote the paper:\nWJH.\n\nPublished - Shetty2011p14283PLoS_ONE.pdf
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", "abstract": "Background:\nBacterial outer membrane vesicles (OMV) are packets of periplasmic material that, via the proteins and other molecules they contain, project metabolic function into the environment. While OMV production is widespread in proteobacteria, they have been extensively studied only in pathogens, which inhabit fully hydrated environments. However, many (arguably most) bacterial habitats, such as soil, are only partially hydrated. In the latter, water is characteristically distributed as films on soil particles that are, on average thinner, than are typical OMV (ca. \u226410 nm water film vs. 20 to >200 nm OMV;).\n\nMethodology/Principal Findings:\nWe have identified a new bacterial surface structure, termed a \"nanopod\", that is a conduit for projecting OMV significant distances (e.g., \u22656 \u00b5m) from the cell. Electron cryotomography was used to determine nanopod three-dimensional structure, which revealed chains of vesicles within an undulating, tubular element. By using immunoelectron microscopy, proteomics, heterologous expression and mutagenesis, the tubes were determined to be an assembly of a surface layer protein (NpdA), and the interior structures identified as OMV. Specific metabolic function(s) for nanopods produced by Delftia sp. Cs1-4 are not yet known. However, a connection with phenanthrene degradation is a possibility since nanopod formation was induced by growth on phenanthrene. Orthologs of NpdA were identified in three other genera of the Comamonadaceae family, and all were experimentally verified to form nanopods.\n\nConclusions/Significance:\nNanopods are new bacterial organelles, and establish a new paradigm in the mechanisms by which bacteria effect long-distance interactions with their environment. Specifically, they create a pathway through which cells can effectively deploy OMV, and the biological activity these transmit, in a diffusion-independent manner. Nanopods would thus allow environmental bacteria to expand their metabolic sphere of influence in a manner previously unknown for these organisms.", "date": "2011-06-07", "date_type": "published", "publication": "PLoS ONE", "volume": "6", "number": "6", "publisher": "Public Library of Science", "pagerange": "Art. No. e20725", "id_number": "CaltechAUTHORS:20110624-091620627", "issn": "1932-6203", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110624-091620627", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "MCB-0920664" }, { "agency": "NIH", "grant_number": "R01 AI067548" }, { "agency": "Natural Sciences and Engineering Research Council of Canada (NSERC)" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-AC02-05CH11231" } ] }, "doi": "10.1371/journal.pone.0020725", "pmcid": "PMC3110197", "primary_object": { "basename": "FigureS1.tif", "url": "https://authors.library.caltech.edu/records/w85wc-nhx36/files/FigureS1.tif" }, "related_objects": [ { "basename": "FigureS2.tif", "url": "https://authors.library.caltech.edu/records/w85wc-nhx36/files/FigureS2.tif" }, { "basename": "FigureS3.tif", "url": "https://authors.library.caltech.edu/records/w85wc-nhx36/files/FigureS3.tif" }, { "basename": "MovieS1.mov", "url": "https://authors.library.caltech.edu/records/w85wc-nhx36/files/MovieS1.mov" }, { "basename": "Shetty2011p14283PLoS_ONE.pdf", "url": "https://authors.library.caltech.edu/records/w85wc-nhx36/files/Shetty2011p14283PLoS_ONE.pdf" } ], "resource_type": "article", "pub_year": "2011", "author_list": "Shetty, Ameesha; Chen, Shicheng; et el." }, { "id": "https://authors.library.caltech.edu/records/017rg-ty753", "eprint_id": 23778, "eprint_status": "archive", "datestamp": "2023-08-22 02:34:36", "lastmod": "2023-10-23 19:56:48", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Swulius-M-T", "name": { "family": "Swulius", "given": "Matthew T." } }, { "id": "Chen-Songye", "name": { "family": "Chen", "given": "Songye" }, "orcid": "0000-0001-5407-5049" }, { "id": "Ding-H-Jane", "name": { "family": "Ding", "given": "H. Jane" } }, { "id": "Li-Zhuo", "name": { "family": "Li", "given": "Zhuo" } }, { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Pilhofer-M", "name": { "family": "Pilhofer", "given": "Martin" } }, { "id": "Tocheva-E-I", "name": { "family": "Tocheva", "given": "Elitza I." }, "orcid": "0000-0002-4869-8319" }, { "id": "Lybarger-S-R", "name": { "family": "Lybarger", "given": "Suzanne R." } }, { "id": "Johnson-T-L", "name": { "family": "Johnson", "given": "Tanya L." } }, { "id": "Sandkvist-M", "name": { "family": "Sandkvist", "given": "Maria" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Long helical filaments are not seen encircling cells in electron cryotomograms of rod-shaped bacteria", "ispublished": "pub", "full_text_status": "public", "keywords": "MreB; Electron cryo-tomography; Helical filament; Rod-shaped; Bacterial shape", "note": "\u00a9 2011 Elsevier Inc.\n\nReceived 4 March 2011; Available online 16 March 2011.\n\nWe thank Drs. Jian Shi and Alasdair McDowall for support of the EM instrumentation. This work was supported by NIH grant R01 GM094800B to G.J.J. and the Gordon and Betty Moore Center for Integrative Study of Cell Regulation. Work done by M.S. was supported by NIH grant RO1 AI049294.\n\nAccepted Version - nihms289169.pdf
Supplemental Material - mmc1.mov
Supplemental Material - mmc2.mov
", "abstract": "How rod-shaped bacteria form and maintain their shape is an important question in bacterial cell biology. Results from fluorescent light microscopy have led many to believe that the actin homolog MreB and a number of other proteins form long helical filaments along the inner membrane of the cell. Here we show using electron cryotomography of six different rod-shaped bacterial species, at macromolecular resolution, that no long (>80 nm) helical filaments exist near or along either surface of the inner membrane. We also use correlated cryo-fluorescent light microscopy (cryo-fLM) and electron cryo-tomography (ECT) to identify cytoplasmic bundles of MreB, showing that MreB filaments are detectable by ECT. In light of these results, the structure and function of MreB must be reconsidered: instead of acting as a large, rigid scaffold that localizes cell-wall synthetic machinery, moving MreB complexes may apply tension to growing peptidoglycan strands to ensure their orderly, linear insertion.", "date": "2011-04-22", "date_type": "published", "publication": "Biochemical and Biophysical Research Communications", "volume": "407", "number": "4", "publisher": "Elsevier", "pagerange": "650-655", "id_number": "CaltechAUTHORS:20110524-100904457", "issn": "0006-291X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110524-100904457", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 GM094800B" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "NIH", "grant_number": "R01 AI049294" } ] }, "doi": "10.1016/j.bbrc.2011.03.062", "pmcid": "PMC3093302", "primary_object": { "basename": "mmc1.mov", "url": "https://authors.library.caltech.edu/records/017rg-ty753/files/mmc1.mov" }, "related_objects": [ { "basename": "mmc2.mov", "url": "https://authors.library.caltech.edu/records/017rg-ty753/files/mmc2.mov" }, { "basename": "nihms289169.pdf", "url": "https://authors.library.caltech.edu/records/017rg-ty753/files/nihms289169.pdf" } ], "resource_type": "article", "pub_year": "2011", "author_list": "Swulius, Matthew T.; Chen, Songye; et el." }, { "id": "https://authors.library.caltech.edu/records/7rsg8-9hh53", "eprint_id": 21750, "eprint_status": "archive", "datestamp": "2023-08-19 04:42:44", "lastmod": "2023-10-21 00:17:41", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Fu-Chi-yu", "name": { "family": "Fu", "given": "Chi-yu" } }, { "id": "Wang-Kang", "name": { "family": "Wang", "given": "Kang" }, "orcid": "0000-0002-9725-3295" }, { "id": "Gan-Lu", "name": { "family": "Gan", "given": "Lu" }, "orcid": "0000-0002-8685-4896" }, { "id": "Lanman-J", "name": { "family": "Lanman", "given": "Jason" } }, { "id": "Khayat-R", "name": { "family": "Khayat", "given": "Reza" } }, { "id": "Young-Mark-J", "name": { "family": "Young", "given": "Mark J." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Doerschuk-P-C", "name": { "family": "Doerschuk", "given": "Peter C." } }, { "id": "Johnson-J-E", "name": { "family": "Johnson", "given": "John E." } } ] }, "title": "In Vivo Assembly of an Archaeal Virus Studied with Whole-Cell Electron Cryotomography", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2010 Elsevier Ltd.\n\nReceived: October 23, 2009; Revised: September 22, 2010; Accepted: October 1, 2010; Published: December 7, 2010. \n\nThis work was supported by the National Institutes of Health (NIH) grant GM54076 to J.E.J., the NIH grant GM082545 to G.J.J. and the National Science Foundation (NSF) grants 0735297 and 0836656 to P.C.D., the NSF grant EF0802200 to M.J.Y., and gifts to Caltech from the Gordon and Betty Moore Foundation.\n\nAccepted Version - nihms250920.pdf
Supplemental Material - Movie_S1.mov
Supplemental Material - mmc1.pdf
", "abstract": "We applied whole-cell electron cryotomography to the archaeon Sulfolobus infected by Sulfolobus turreted icosahedral virus (STIV), which belongs to the PRD1-Adeno lineage of dsDNA viruses. STIV infection induced the formation of pyramid-like protrusions with sharply defined facets on the cell surface. They had a thicker cross-section than the cytoplasmic membrane and did not contain an exterior surface protein layer (S-layer). Intrapyramidal bodies often occupied the volume of the pyramids. Mature virions, procapsids without genome cores, and partially assembled particles were identified, suggesting that the capsid and inner membrane coassemble in the cytoplasm to form a procapsid. A two-class reconstruction using a maximum likelihood algorithm demonstrated that no dramatic capsid transformation occurred upon DNA packaging. Virions tended to form tightly packed clusters or quasicrystalline arrays while procapsids mostly scattered outside or on the edges of the clusters. The study revealed vivid images of STIV assembly, maturation, and particle distribution in cell.", "date": "2010-12-08", "date_type": "published", "publication": "Structure", "volume": "18", "number": "12", "publisher": "Cell Press", "pagerange": "1579-1586", "id_number": "CaltechAUTHORS:20110113-115948690", "issn": "0969-2126", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110113-115948690", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM54076" }, { "agency": "NIH", "grant_number": "GM082545" }, { "agency": "NSF", "grant_number": "0735297" }, { "agency": "NSF", "grant_number": "0836656" }, { "agency": "NSF", "grant_number": "EF0802200" }, { "agency": "Gordon and Betty Moore Foundation" } ] }, "doi": "10.1016/j.str.2010.10.005", "pmcid": "PMC3042139", "primary_object": { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/7rsg8-9hh53/files/mmc1.pdf" }, "related_objects": [ { "basename": "nihms250920.pdf", "url": "https://authors.library.caltech.edu/records/7rsg8-9hh53/files/nihms250920.pdf" }, { "basename": "Movie_S1.mov", "url": "https://authors.library.caltech.edu/records/7rsg8-9hh53/files/Movie_S1.mov" } ], "resource_type": "article", "pub_year": "2010", "author_list": "Fu, Chi-yu; Wang, Kang; et el." }, { "id": "https://authors.library.caltech.edu/records/q1v55-6sf11", "eprint_id": 19706, "eprint_status": "archive", "datestamp": "2023-08-19 03:22:26", "lastmod": "2023-10-20 21:17:05", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ingerson-Mahar-Michael", "name": { "family": "Ingerson-Mahar", "given": "Michael" } }, { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Werner-John-N", "name": { "family": "Werner", "given": "John N." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Gitai-Zemer", "name": { "family": "Gitai", "given": "Zemer" }, "orcid": "0000-0002-3280-6178" } ] }, "title": "The metabolic enzyme CTP synthase forms cytoskeletal filaments", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2010 Macmillan Publishers Limited.\n\nReceived 19 March 2010; accepted 21 June 2010; published online 18 July 2010.\nWe are grateful to B. Bassler, C. Murphy, E. Klein and K. Cowles for critical\nreading of the manuscript. We thank M. Cabeen, C. Jacobs-Wagner, J. Williamson,\nAlison Michaelis and other members of the Gitai lab for reagents and discussions.\nJ.N.W. is supported by a postdoctoral fellowship from the National Institute of\nAllergy and Infectious Diseases (grant 1F32AI073043\u201301A1). A.B. and G.J.J. were\nsupported in part by the National Institutes of Health (NIH) grant R01 AI067548,\nthe Howard Hughes Medical Institute, and a gift to Caltech from the Gordon and\nBetty Moore Foundation. Z.G. is supported by funding from the U.S. Department\nof Energy Office of Science (Biological and Environmental Research; grant\nDE-FG02-05ER64136), NIH grant 1DP2OD004389-01, the Human Frontiers\nScience Program and the Beckman Foundation.\nAuthor Contributions: M.J.I. performed all experiments except for the ECT and fLM-ECT experiments,\nwhich were performed by A.B. J.N.W. performed the initial screen that identified\nCtpS as a linearly localized protein. Experiments were conceived by M.J.I., A.B.,\nG.J.J. and Z.G., and the manuscript was written by M.J.I. and Z.G. with significant\ninput from A.B. and G.J.J.\n\nAccepted Version - nihms215754.pdf
Supplemental Material - ncb2087-s1.pdf
", "abstract": "Filament-forming cytoskeletal proteins are essential for the structure and organization of all cells. Bacterial homologues of the major eukaryotic cytoskeletal families have now been discovered, but studies suggest that yet more remain to be identified. We demonstrate that the metabolic enzyme CTP synthase (CtpS) forms filaments in Caulobacter crescentus. CtpS is bifunctional, as the filaments it forms regulate the curvature of C. crescentus cells independently of its catalytic function. The morphogenic role of CtpS requires its functional interaction with the intermediate filament, crescentin (CreS). Interestingly, the Escherichia coli CtpS homologue also forms filaments both in vivo and in vitro, suggesting that CtpS polymerization may be widely conserved. E. coli CtpS can replace the enzymatic and morphogenic functions of C. crescentus CtpS, indicating that C. crescentus has adapted a conserved filament-forming protein for a secondary role. These results implicate CtpS as a novel bifunctional member of the bacterial cytoskeleton and suggest that localization and polymerization may be important properties of metabolic enzymes.", "date": "2010-08", "date_type": "published", "publication": "Nature Cell Biology", "volume": "12", "number": "8", "publisher": "Nature Publishing Group", "pagerange": "739-746", "id_number": "CaltechAUTHORS:20100830-105222501", "issn": "1465-7392", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100830-105222501", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Postdoctoral Fellowship", "grant_number": "1F32A1073043-01A1" }, { "agency": "NIH", "grant_number": "R01 AI067548" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02-05ER64136" }, { "agency": "NIH", "grant_number": "1DP2OD004389-01" }, { "agency": "Human Frontiers Science Program" }, { "agency": "Arnold and Mabel Beckman Foundation" } ] }, "doi": "10.1038/ncb2087", "pmcid": "PMC3210567", "primary_object": { "basename": "ncb2087-s1.pdf", "url": "https://authors.library.caltech.edu/records/q1v55-6sf11/files/ncb2087-s1.pdf" }, "related_objects": [ { "basename": "nihms215754.pdf", "url": "https://authors.library.caltech.edu/records/q1v55-6sf11/files/nihms215754.pdf" } ], "resource_type": "article", "pub_year": "2010", "author_list": "Ingerson-Mahar, Michael; Briegel, Ariane; et el." }, { "id": "https://authors.library.caltech.edu/records/x6g26-6w386", "eprint_id": 19018, "eprint_status": "archive", "datestamp": "2023-08-19 02:56:37", "lastmod": "2023-10-20 19:17:45", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "M\u00f6ll-Andrea", "name": { "family": "M\u00f6ll", "given": "Andrea" } }, { "id": "Schlimpert-Susan", "name": { "family": "Schlimpert", "given": "Susan" } }, { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Thanbichler-Martin", "name": { "family": "Thanbichler", "given": "Martin" }, "orcid": "0000-0002-1303-1442" } ] }, "title": "DipM, a new factor required for peptidoglycan remodelling during cell division in Caulobacter crescentus", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2010 Blackwell Publishing Ltd. \n\nAccepted 15 May, 2010. Published Online: 24 May 2010. \n\nWe thank Stephanie Wick for excellent technical assistance and Grant R. Bowman, Lucy Shapiro, Yves V. Brun, and Patrick H. Viollier for providing plasmids, strains and antisera. We further thank Sebastian Poggio, Christine Jacobs-Wagner, Erin Goley and Lucy Shapiro for communicating unpublished results. This work was supported by funds from the Max Planck Society, National Institutes of Health (NIH) grant R01 AI067548 to G.J.J., and a gift to Caltech from the Gordon and Betty Moore Foundation.\n\nAccepted Version - nihms-232859.pdf
Supplemental Material - sm001.pdf
", "abstract": "In bacteria, cytokinesis is dependent on lytic enzymes that facilitate remodelling of the cell wall during constriction. In this work, we identify a thus far uncharacterized periplasmic protein, DipM, that is required for cell division and polarity in Caulobacter crescentus. DipM is composed of four peptidoglycan binding (LysM) domains and a C-terminal lysostaphin-like (LytM) peptidase domain. It binds to isolated murein sacculi in vitro, and is recruited to the site of constriction through interaction with the cell division protein FtsN. Mutational analyses showed that the LysM domains are necessary and sufficient for localization of DipM, while its peptidase domain is essential for function. Consistent with a role in cell wall hydrolysis, DipM was found to interact with purified murein sacculi in vitro and to induce cell lysis upon overproduction. Its inactivation causes severe defects in outer membrane invagination, resulting in a significant delay between cytoplasmic compartmentalization and final separation of the daughter cells. Overall, these findings indicate that DipM is a periplasmic component of the C. crescentus divisome that facilitates remodelling of the peptidoglycan layer and, thus, coordinated constriction of the cell envelope during the division process.", "date": "2010-07", "date_type": "published", "publication": "Molecular Microbiology", "volume": "77", "number": "1", "publisher": "Wiley", "pagerange": "90-107", "id_number": "CaltechAUTHORS:20100713-091755026", "issn": "0950-382X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100713-091755026", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Max Planck Society" }, { "agency": "NIH", "grant_number": "R01 AI067548" }, { "agency": "Gordon and Betty Moore Foundation" } ] }, "doi": "10.1111/j.1365-2958.2010.07224.x", "pmcid": "PMC3057925", "primary_object": { "basename": "nihms-232859.pdf", "url": "https://authors.library.caltech.edu/records/x6g26-6w386/files/nihms-232859.pdf" }, "related_objects": [ { "basename": "sm001.pdf", "url": "https://authors.library.caltech.edu/records/x6g26-6w386/files/sm001.pdf" } ], "resource_type": "article", "pub_year": "2010", "author_list": "M\u00f6ll, Andrea; Schlimpert, Susan; et el." }, { "id": "https://authors.library.caltech.edu/records/6jb6c-d4p56", "eprint_id": 24692, "eprint_status": "archive", "datestamp": "2023-08-19 03:03:57", "lastmod": "2023-10-23 23:35:25", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cabeen-M-T", "name": { "family": "Cabeen", "given": "Matthew T." } }, { "id": "Murolo-M-A", "name": { "family": "Murolo", "given": "Michelle A." } }, { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Bui-N-Khai", "name": { "family": "Bui", "given": "N. Khai" } }, { "id": "Vollmer-W", "name": { "family": "Vollmer", "given": "Waldemar" } }, { "id": "Ausmees-N", "name": { "family": "Ausmees", "given": "Nora" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Jacobs-Wagner-C", "name": { "family": "Jacobs-Wagner", "given": "Christine" } } ] }, "title": "Mutations in the Lipopolysaccharide Biosynthesis Pathway Interfere with Crescentin-Mediated Cell Curvature in Caulobacter crescentus", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2010 American Society for Microbiology.\n\nReceived 19 October 2009; Accepted 20 April 2010.\nPublished ahead of print on 30 April 2010.\nWe thank J. Smit for gifts of strains, anti-O-polysaccharide, and\nanti-RsaA antibodies, O. Sliusarenko and T. Emonet for assistance\nwith cell curvature analysis, H. Lam for plasmids, J. Wertz for technical\nhelp, and the members of the Jacobs-Wagner laboratory for critical\nreading of the manuscript.\nThis work was supported by the National Science Foundation GRFP\n(to M.T.C.), the Mustard Seed Foundation (to M.T.C.), a Howard\nHughes Medical Institute predoctoral fellowship (to M.A.M.), NIH\ngrants AI067548 (to G.J.J.) and GM076698 (to C.J.-W.), gifts to\nCaltech from the Gordon and Betty Moore Foundation and Agouron\nInstitute, the Pew Scholars Program in the Biological Sciences, sponsored\nby the Pew Charitable Trust (to C.J.-W.), and the HEALTHF3-2009-223431 DIVINOCELL collaborative project grant from the\nCommission of the European Communities (to W.V.). C.J.-W. and\nG.J.J. are Howard Hughes Medical Institute investigators.\n\nPublished - CABjb10.pdf
Supplemental Material - CABjb10supp.pdf
", "abstract": "Bacterial cell morphogenesis requires coordination among multiple cellular systems, including the bacterial\ncytoskeleton and the cell wall. In the vibrioid bacterium Caulobacter crescentus, the intermediate filament-like\nprotein crescentin forms a cell envelope-associated cytoskeletal structure that controls cell wall growth to\ngenerate cell curvature. We undertook a genetic screen to find other cellular components important for cell\ncurvature. Here we report that deletion of a gene (wbqL) involved in the lipopolysaccharide (LPS) biosynthesis\npathway abolishes cell curvature. Loss of WbqL function leads to the accumulation of an aberrant Opolysaccharide\nspecies and to the release of the S layer in the culture medium. Epistasis and microscopy\nexperiments show that neither S-layer nor O-polysaccharide production is required for curved cell morphology\nper se but that production of the altered O-polysaccharide species abolishes cell curvature by apparently\ninterfering with the ability of the crescentin structure to associate with the cell envelope. Our data suggest that\nperturbations in a cellular pathway that is itself fully dispensable for cell curvature can cause a disruption of\ncell morphogenesis, highlighting the delicate harmony among unrelated cellular systems. Using the wbqL\nmutant, we also show that the normal assembly and growth properties of the crescentin structure are\nindependent of its association with the cell envelope. However, this envelope association is important for\nfacilitating the local disruption of the stable crescentin structure at the division site during cytokinesis.", "date": "2010-07", "date_type": "published", "publication": "Journal of Bacteriology", "volume": "192", "number": "13", "publisher": "American Society for Microbiology", "pagerange": "3368-3378", "id_number": "CaltechAUTHORS:20110804-135325381", "issn": "0021-9193", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110804-135325381", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF" }, { "agency": "Mustard Seed Foundation" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "AI067548" }, { "agency": "NIH", "grant_number": "GM076698" }, { "agency": "Pew Charitable Trust" }, { "agency": "European Commission", "grant_number": "HEALTH-F3-2009-223431" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Agouron Institute" } ] }, "doi": "10.1128/JB.01371-09", "pmcid": "PMC2897673", "primary_object": { "basename": "CABjb10.pdf", "url": "https://authors.library.caltech.edu/records/6jb6c-d4p56/files/CABjb10.pdf" }, "related_objects": [ { "basename": "CABjb10supp.pdf", "url": "https://authors.library.caltech.edu/records/6jb6c-d4p56/files/CABjb10supp.pdf" } ], "resource_type": "article", "pub_year": "2010", "author_list": "Cabeen, Matthew T.; Murolo, Michelle A.; et el." }, { "id": "https://authors.library.caltech.edu/records/t78gy-kcd90", "eprint_id": 19294, "eprint_status": "archive", "datestamp": "2023-08-19 02:40:38", "lastmod": "2023-10-20 20:31:12", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Tocheva-E-I", "name": { "family": "Tocheva", "given": "Elitza I." }, "orcid": "0000-0002-4869-8319" }, { "id": "Li-Zhuo", "name": { "family": "Li", "given": "Zhuo" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Electron Cryotomography", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2010 Cold Spring Harbor Laboratory Press.\n\nPublished - Tocheva2010p10851Csh_Perspect_Biol.pdf
", "abstract": "Electron cryotomography (ECT) is an emerging technology that allows thin samples such as macromolecular complexes and small bacterial cells to be imaged in 3-D in a nearly native state to \"molecular\" (~4 nm) resolution. As such, ECT is beginning to deliver long-awaited insight into the positions and structures of cytoskeletal filaments, cell wall elements, motility machines, chemoreceptor arrays, internal compartments, and other ultrastructures. This article describes the technique and summarizes its contributions to bacterial cell biology. For comparable recent reviews, see (Subramaniam 2005; Jensen and Briegel 2007; Murphy and Jensen 2007; Li and Jensen 2009). For reviews on the history, technical details, and broader application of electron tomography in general, see for example (Subramaniam and Milne 2004; Luci\u0107 et al. 2005; Leis et al. 2008; Midgley and Dunin-Borkowski 2009).", "date": "2010-06", "date_type": "published", "publication": "Cold Spring Harbor Perspectives in Biology", "volume": "2", "number": "6", "publisher": "Cold Spring Harbor Laboratory Press", "pagerange": "Art. No. a003442", "id_number": "CaltechAUTHORS:20100805-110641753", "issn": "1943-0264", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100805-110641753", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1101/cshperspect.a003442", "pmcid": "PMC2869529", "primary_object": { "basename": "Tocheva2010p10851Csh_Perspect_Biol.pdf", "url": "https://authors.library.caltech.edu/records/t78gy-kcd90/files/Tocheva2010p10851Csh_Perspect_Biol.pdf" }, "resource_type": "article", "pub_year": "2010", "author_list": "Tocheva, Elitza I.; Li, Zhuo; et el." }, { "id": "https://authors.library.caltech.edu/records/vp8dj-53p82", "eprint_id": 24694, "eprint_status": "archive", "datestamp": "2023-08-19 02:30:47", "lastmod": "2023-10-23 23:35:29", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chen-Songye", "name": { "family": "Chen", "given": "Songye" }, "orcid": "0000-0001-5407-5049" }, { "id": "McDowall-A-W", "name": { "family": "McDowall", "given": "Alasdair" } }, { "id": "Dobro-M-J", "name": { "family": "Dobro", "given": "Megan J." }, "orcid": "0000-0002-6464-3932" }, { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Ladinsky-M-S", "name": { "family": "Ladinsky", "given": "Mark" }, "orcid": "0000-0002-1036-3513" }, { "id": "Shi-Jian-CELLBIO", "name": { "family": "Shi", "given": "Jian" }, "orcid": "0000-0003-3810-5302" }, { "id": "Tocheva-E-I", "name": { "family": "Tocheva", "given": "Elitza I." }, "orcid": "0000-0002-4869-8319" }, { "id": "Beeby-M-D", "name": { "family": "Beeby", "given": "Morgan" }, "orcid": "0000-0001-6413-9835" }, { "id": "Pilhofer-M", "name": { "family": "Pilhofer", "given": "Martin" } }, { "id": "Ding-H-Jane", "name": { "family": "Ding", "given": "H. Jane" } }, { "id": "Li-Zhuo", "name": { "family": "Li", "given": "Zhuo" } }, { "id": "Gan-Lu", "name": { "family": "Gan", "given": "Lu" }, "orcid": "0000-0002-8685-4896" }, { "id": "Morris-D-M", "name": { "family": "Morris", "given": "Dylan M." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Electron Cryotomography of Bacterial Cells", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2010 Journal of Visualized Experiments.\nThis work was supported in part by National Institutes of Health Grants R01 AI067548, R01 GM081520, R01 GM086200, R01 AI049194, and P01\nGM066521 to GJJ as well as the Howard Hughes Medical Institute, the Beckman Institute at Caltech, and gifts to Caltech from the Gordon and\nBetty Moore Foundation and Agouron Institute. MSL is supported by NIH grant 2R37-A1041239-06A1 to Pamela S. Bj\u00f6rkman. Leica\nMicrosystems Inc. kindly provided video content of cryosection collection. The representative results of Treponema primitia were collected and\nprocessed by Gavin E. Murphy, and published in Molecular Microbiology with the title \"Novel ultrastructures of Treponema primitia and their\nimplications for motility\". (Murphy, G. et al., Mol. Microbiol. 67, 1184-1195, 2008).\n\nPublished - CHEjove10.pdf
Accepted Version - jove-39-1943.pdf
", "abstract": "While much is already known about the basic metabolism of bacterial cells, many fundamental questions are still surprisingly unanswered, including\nfor instance how they generate and maintain specific cell shapes, establish polarity, segregate their genomes, and divide. In order to understand\nthese phenomena, imaging technologies are needed that bridge the resolution gap between fluorescence light microscopy and higher-resolution\nmethods such as X-ray crystallography and NMR spectroscopy.\nElectron cryotomography (ECT) is an emerging technology that does just this, allowing the ultrastructure of cells to be visualized in a near-native\nstate, in three dimensions (3D), with \"macromolecular\" resolution (~4nm). In ECT, cells are imaged in a vitreous, \"frozen-hydrated\" state in a cryo\ntransmission electron microscope (cryoTEM) at low temperature (< -180\u00b0C). For slender cells (up to ~500 nm in thickness), intact cells are\nplunge-frozen within media across EM grids in cryogens such as ethane or ethane/propane mixtures. Thicker cells and biofilms can also be imaged\nin a vitreous state by first \"high-pressure freezing\" and then, \"cryo-sectioning\" them. A series of two-dimensional projection images are then\ncollected through the sample as it is incrementally tilted along one or two axes. A three-dimensional reconstruction, or \"tomogram\" can then be\ncalculated from the images. While ECT requires expensive instrumentation, in recent years, it has been used in a few labs to reveal the structures\nof various external appendages, the structures of different cell envelopes, the positions and structures of cytoskeletal filaments, and the locations\nand architectures of large macromolecular assemblies such as flagellar motors, internal compartments and chemoreceptor arrays.\nIn this video article we illustrate how to image cells with ECT, including the processes of sample preparation, data collection, tomogram\nreconstruction, and interpretation of the results through segmentation and in some cases correlation with light microscopy.", "date": "2010-05-06", "date_type": "published", "publication": "Journal of Visualized Experiments", "number": "39", "publisher": "JoVE", "pagerange": "Art. No. 1943", "id_number": "CaltechAUTHORS:20110804-140527126", "issn": "1940-087X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110804-140527126", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 AI067548" }, { "agency": "NIH", "grant_number": "R01 GM081520" }, { "agency": "NIH", "grant_number": "R01 GM086200" }, { "agency": "NIH", "grant_number": "R01 AI049194" }, { "agency": "NIH", "grant_number": "P01 GM066521" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Agouron Institute" }, { "agency": "NIH", "grant_number": "2R37-A1041239-06A1" } ] }, "doi": "10.3791/1943", "pmcid": "PMC3149996", "primary_object": { "basename": "CHEjove10.pdf", "url": "https://authors.library.caltech.edu/records/vp8dj-53p82/files/CHEjove10.pdf" }, "related_objects": [ { "basename": "jove-39-1943.pdf", "url": "https://authors.library.caltech.edu/records/vp8dj-53p82/files/jove-39-1943.pdf" } ], "resource_type": "article", "pub_year": "2010", "author_list": "Chen, Songye; McDowall, Alasdair; et el." }, { "id": "https://authors.library.caltech.edu/records/pg007-d6719", "eprint_id": 17694, "eprint_status": "archive", "datestamp": "2023-08-21 23:23:16", "lastmod": "2023-10-20 00:09:35", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Iancu-C-V", "name": { "family": "Iancu", "given": "Cristina V." }, "orcid": "0000-0002-7352-9226" }, { "id": "Morris-D-M", "name": { "family": "Morris", "given": "Dylan M." } }, { "id": "Dou-Zhicheng", "name": { "family": "Dou", "given": "Zhicheng" } }, { "id": "Heinhorst-S", "name": { "family": "Heinhorst", "given": "Sabine" } }, { "id": "Cannon-G-C", "name": { "family": "Cannon", "given": "Gordon C." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Organization, Structure, and Assembly of \u03b1-Carboxysomes Determined by Electron Cryotomography of Intact Cells", "ispublished": "pub", "full_text_status": "public", "keywords": "H. neapolitanus; bacterial microcompartment; carboxysome; cryo-EM; electron tomography", "note": "\u00a9 2009 Elsevier Ltd. \n\nReceived 18 June 2009; received in revised form 6 November 2009; accepted 9 November 2009; available online 17 November 2009. \n\nEdited by W. Baumeister. \n\nWe are indebted to Dr. Raj Menon for culturing T. crunogena cells, Dr. Eric Williams for providing purified H. neapolitanus carboxysomes and initial batches of H. neapolitanus cells, Dr. H. Jane Ding for computational help with generation of phosphorus elemental maps, Dr. William F. Tivol for technical assistance in setting up the spectroscopic imaging experiments, and Dr. Elizabeth R. Wright for freezing grids and imaging several T. intermedia cells. This work was supported in part by NIH grants R01 AI067548 and P50 GM082545 to GJJ, DOE grant DE-FG02-04ER63785 to GJJ, NSF grant MCB-0818680 to GCC and SH, the Beckman Institute at Caltech, and gifts to Caltech from the Gordon and Betty Moore Foundation and Agouron Institute.\n\nAccepted Version - nihms-180999.pdf
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Supplemental Material - video1.mov
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Supplemental Material - video4.mov
", "abstract": "Carboxysomes are polyhedral inclusion bodies that play a key role in autotrophic metabolism in many bacteria. Using electron cryotomography, we examined carboxysomes in their native states within intact cells of three chemolithoautotrophic bacteria. We found that carboxysomes generally cluster into distinct groups within the cytoplasm, often in the immediate vicinity of polyphosphate granules, and a regular lattice of density frequently connects granules to nearby carboxysomes. Small granular bodies were also seen within carboxysomes. These observations suggest a functional relationship between carboxysomes and polyphosphate granules. Carboxysomes exhibited greater size, shape, and compositional variability in cells than in purified preparations. Finally, we observed carboxysomes in various stages of assembly, as well as filamentous structures that we attribute to misassembled shell protein. Surprisingly, no more than one partial carboxysome was ever observed per cell. Based on these observations, we propose a model for carboxysome assembly in which the shell and the internal RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) lattice form simultaneously, likely guided by specific interactions between shell proteins and RuBisCOs.", "date": "2010-02-12", "date_type": "published", "publication": "Journal of Molecular Biology", "volume": "396", "number": "1", "publisher": "Elsevier", "pagerange": "105-117", "id_number": "CaltechAUTHORS:20100308-111110207", "issn": "0022-2836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100308-111110207", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 AI067548" }, { "agency": "NIH", "grant_number": "P50 GM082545" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02-04ER63785" }, { "agency": "NSF", "grant_number": "MCB-0818680" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Agouron Institute" } ] }, "doi": "10.1016/j.jmb.2009.11.019", "pmcid": "PMC2853366", "primary_object": { "basename": "applic2.pdf", "url": "https://authors.library.caltech.edu/records/pg007-d6719/files/applic2.pdf" }, "related_objects": [ { "basename": "applic3.pdf", "url": "https://authors.library.caltech.edu/records/pg007-d6719/files/applic3.pdf" }, { "basename": "applic4.pdf", "url": "https://authors.library.caltech.edu/records/pg007-d6719/files/applic4.pdf" }, { "basename": "applic5.pdf", "url": "https://authors.library.caltech.edu/records/pg007-d6719/files/applic5.pdf" }, { "basename": "video1.mov", "url": "https://authors.library.caltech.edu/records/pg007-d6719/files/video1.mov" }, { "basename": "video2.mov", "url": "https://authors.library.caltech.edu/records/pg007-d6719/files/video2.mov" }, { "basename": "video3.mov", "url": "https://authors.library.caltech.edu/records/pg007-d6719/files/video3.mov" }, { "basename": "video4.mov", "url": "https://authors.library.caltech.edu/records/pg007-d6719/files/video4.mov" }, { "basename": "applic1.pdf", "url": "https://authors.library.caltech.edu/records/pg007-d6719/files/applic1.pdf" }, { "basename": "applic6.pdf", "url": "https://authors.library.caltech.edu/records/pg007-d6719/files/applic6.pdf" }, { "basename": "applic7.pdf", "url": "https://authors.library.caltech.edu/records/pg007-d6719/files/applic7.pdf" }, { "basename": "nihms-180999.pdf", "url": "https://authors.library.caltech.edu/records/pg007-d6719/files/nihms-180999.pdf" } ], "resource_type": "article", "pub_year": "2010", "author_list": "Iancu, Cristina V.; Morris, Dylan M.; et el." }, { "id": "https://authors.library.caltech.edu/records/pygmg-5ke46", "eprint_id": 17511, "eprint_status": "archive", "datestamp": "2023-08-21 23:15:53", "lastmod": "2023-10-19 23:57:46", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "K\u00fchn-Juliane", "name": { "family": "K\u00fchn", "given": "Juliane" } }, { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "M\u00f6rschel-Erhard", "name": { "family": "M\u00f6rschel", "given": "Erhard" } }, { "id": "Kahnt-J\u00f6rg", "name": { "family": "Kahnt", "given": "J\u00f6rg" } }, { "id": "Leser-Katja", "name": { "family": "Leser", "given": "Katja" } }, { "id": "Wick-Stephanie", "name": { "family": "Wick", "given": "Stephanie" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Thanbichler-Martin", "name": { "family": "Thanbichler", "given": "Martin" }, "orcid": "0000-0002-1303-1442" } ] }, "title": "Bactofilins, a ubiquitous class of cytoskeletal proteins mediating polar localization of a cell wall synthase in Caulobacter crescentus", "ispublished": "pub", "full_text_status": "restricted", "keywords": "cytoskeleton; Myxococcus xanthus; penicillin-binding protein; peptidoglycan; stalk", "note": "\u00a9 2010 European Molecular Biology Organization. \n\nReceived 8 June 2009; Accepted 26 October 2009. Published online: 3 December 2009. \n\nWe thank Lotte S\u00f8gaard-Andersen for access to the Department of\nEcophysiology mass spectrometry facility and Stefanie Reibmann,\nSusan Schlimpert, and Daniela Kiekebusch for critical reading of the\nmanuscript. This work was supported by funds from the Max\nPlanck Society, a Young Investigator Grant (RGY 69/2008) from\nthe Human Frontier Science Program to MT, and National Institutes\nof Health (NIH) grant R01 AI067548 to GJJ.", "abstract": "The cytoskeleton has a key function in the temporal and spatial organization of both prokaryotic and eukaryotic cells. Here, we report the identification of a new class of polymer-forming proteins, termed bactofilins, that are widely conserved among bacteria. In Caulobacter crescentus, two bactofilin paralogues cooperate to form a sheet-like structure lining the cytoplasmic membrane in proximity of the stalked cell pole. These assemblies mediate polar localization of a peptidoglycan synthase involved in stalk morphogenesis, thus complementing the function of the actin-like cytoskeleton and the cell division machinery in the regulation of cell wall biogenesis. In other bacteria, bactofilins can establish rod-shaped filaments or associate with the cell division apparatus, indicating considerable structural and functional flexibility. Bactofilins polymerize spontaneously in the absence of additional cofactors in vitro, forming stable ribbon- or rod-like filament bundles. Our results suggest that these structures have evolved as an alternative to intermediate filaments, serving as versatile molecular scaffolds in a variety of cellular pathways.", "date": "2010-01-20", "date_type": "published", "publication": "EMBO Journal", "volume": "29", "number": "2", "publisher": "European Molecular Biology Organization", "pagerange": "327-339", "id_number": "CaltechAUTHORS:20100218-083022805", "issn": "0261-4189", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100218-083022805", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Max Planck Society" }, { "agency": "Human Frontier Science Program", "grant_number": "RGY 69/2008" }, { "agency": "NIH", "grant_number": "R01 AI067548" } ] }, "doi": "10.1038/emboj.2009.358", "pmcid": "PMC2824468", "resource_type": "article", "pub_year": "2010", "author_list": "K\u00fchn, Juliane; Briegel, Ariane; et el." }, { "id": "https://authors.library.caltech.edu/records/pzcsm-e6657", "eprint_id": 16387, "eprint_status": "archive", "datestamp": "2023-08-21 22:30:10", "lastmod": "2023-10-19 22:10:39", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Ortega-D-R", "name": { "family": "Ortega", "given": "Davi R." }, "orcid": "0000-0002-8344-2335" }, { "id": "Tocheva-E-I", "name": { "family": "Tocheva", "given": "Elitza I." }, "orcid": "0000-0002-4869-8319" }, { "id": "Wuichet-K", "name": { "family": "Wuichet", "given": "Kristin" } }, { "id": "Li-Zhuo", "name": { "family": "Li", "given": "Zhuo" } }, { "id": "Chen-Songye", "name": { "family": "Chen", "given": "Songye" }, "orcid": "0000-0001-5407-5049" }, { "id": "M\u00fcller-A", "name": { "family": "M\u00fcller", "given": "Axel" } }, { "id": "Iancu-C-V", "name": { "family": "Iancu", "given": "Cristina V." }, "orcid": "0000-0002-7352-9226" }, { "id": "Murphy-G-E", "name": { "family": "Murphy", "given": "Gavin E." } }, { "id": "Dobro-M-J", "name": { "family": "Dobro", "given": "Megan J." }, "orcid": "0000-0002-6464-3932" }, { "id": "Zhulin-I-B", "name": { "family": "Zhulin", "given": "Igor B." }, "orcid": "0000-0002-6708-5323" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Universal architecture of bacterial chemoreceptor arrays", "ispublished": "pub", "full_text_status": "public", "keywords": "bacterial ultrastructure; chemotaxis; electron cryo-tomography", "note": "\u00a9 2009 National Academy of Sciences.\n\nEdited by Laura L. Kiessling, University of Wisconsin, Madison, WI, and approved July 20, 2009 (received for review May 11, 2009).\nAuthor contributions: A.B. and G.J.J. designed research; A.B., D.R.O., E.I.T., K.W., Z.L., S.C., A.M., C.V.I., G.E.M., and M.J.D. performed research; A.B., D.R.O., E.I.T., K.W., and I.B.Z. analyzed data; and A.B., D.R.O., E.I.T., I.B.Z., and G.J.J. wrote the paper. \n\nThe authors wish to thank Eric Matson, Reinhard Rachel, Kevin Bruhn, Gordon Cannon, Alan Barbour, Sarkis Mazmanian, Jeanette Beatty, Maria Sandkvist, Dianne Newman, and John S. Parkinson for bacterial strains; Howard Berg for the penicillin treatment protocol for E. coli; Jane H. Ding for computational support; Juergen Plitzko, Alasdair McDowall and Jian Shi for EM support; and Roger Alexander, Luke Ulrich, and Bhanu Rekapalli for assistance and helpful suggestions. The authors also thank Professor Wolfgang Baumeister (Max Planck Institute for Biochemistry, Martinsried, Germany) for the permission to include the data from T. maritima (which was collected in his laboratory and under his supervision) in this study. \n\nThis work was supported in part by National Institutes of Health Grants R01 AI067548 and P50 GM082545 (to G.J.J.) and R01 GM72285 (to I.B.Z.), as well as the Howard Hughes Medical Institute, the Beckman Institute at Caltech, and gifts to Caltech from the Gordon and Betty Moore Foundation and Agouron Institute.\n\nPublished - Briegel2009p6071P_Natl_Acad_Sci_Usa.pdf
Supplemental Material - 0905181106SI.pdf
Supplemental Material - Appendix_PDF.pdf
", "abstract": "Chemoreceptors are key components of the high-performance signal transduction system that controls bacterial chemotaxis. Chemoreceptors are typically localized in a cluster at the cell pole, where interactions among the receptors in the cluster are thought to contribute to the high sensitivity, wide dynamic range, and precise adaptation of the signaling system. Previous structural and genomic studies have produced conflicting models, however, for the arrangement of the chemoreceptors in the clusters. Using whole-cell electron cryo-tomography, here we show that chemoreceptors of different classes and in many different species representing several major bacterial phyla are all arranged into a highly conserved, 12-nm hexagonal array consistent with the proposed \"trimer of dimers\" organization. The various observed lengths of the receptors confirm current models for the methylation, flexible bundle, signaling, and linker sub-domains in vivo. Our results suggest that the basic mechanism and function of receptor clustering is universal among bacterial species and was thus conserved during evolution.", "date": "2009-10-06", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "106", "number": "40", "publisher": "National Academy of Sciences", "pagerange": "17181-17186", "id_number": "CaltechAUTHORS:20091019-151620276", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20091019-151620276", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 AI067548" }, { "agency": "NIH", "grant_number": "P50 GM082545" }, { "agency": "NIH", "grant_number": "R01 GM72285" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Agouron Institute" } ] }, "doi": "10.1073/pnas.0905181106", "pmcid": "PMC2761316", "primary_object": { "basename": "0905181106SI.pdf", "url": "https://authors.library.caltech.edu/records/pzcsm-e6657/files/0905181106SI.pdf" }, "related_objects": [ { "basename": "Appendix_PDF.pdf", "url": "https://authors.library.caltech.edu/records/pzcsm-e6657/files/Appendix_PDF.pdf" }, { "basename": "Briegel2009p6071P_Natl_Acad_Sci_Usa.pdf", "url": "https://authors.library.caltech.edu/records/pzcsm-e6657/files/Briegel2009p6071P_Natl_Acad_Sci_Usa.pdf" } ], "resource_type": "article", "pub_year": "2009", "author_list": "Briegel, Ariane; Ortega, Davi R.; et el." }, { "id": "https://authors.library.caltech.edu/records/c3bh4-k6593", "eprint_id": 21267, "eprint_status": "archive", "datestamp": "2023-08-21 21:44:33", "lastmod": "2023-10-20 23:53:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Suloway-C", "name": { "family": "Suloway", "given": "Christian" } }, { "id": "Shi-Jian", "name": { "family": "Shi", "given": "Jian" }, "orcid": "0000-0003-3810-5302" }, { "id": "Cheng-Anchi", "name": { "family": "Cheng", "given": "Anchi" } }, { "id": "Pulokas-J", "name": { "family": "Pulokas", "given": "James" } }, { "id": "Carragher-B", "name": { "family": "Carragher", "given": "Bridget" } }, { "id": "Potter-C-S", "name": { "family": "Potter", "given": "Clinton S." } }, { "id": "Zheng-Shawn-Q", "name": { "family": "Zheng", "given": "Shawn Q." } }, { "id": "Agard-D-A", "name": { "family": "Agard", "given": "David A." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Fully automated, sequential tilt-series acquisition with Leginon", "ispublished": "pub", "full_text_status": "public", "keywords": "TEM; Cryo-electron microscopy; Electron microscopy; Automation; Tomography", "note": "\u00a9 2009 Elsevier Inc. \n\nReceived 21 October 2008; revised 27 March 2009; accepted 31 March 2009. Available online 8 April 2009. \n\nWe thank Drs. Bill Tivol, Prabha Dias, Jane Ding, Lu Gan, Ariane\nBriegel, Elizabeth Wright, Zhou Li and Alasdair McDowall for advice\nand testing during the development of MSI Tomography. This\nwork was supported in part by NIH Grants R01 AI067548 and P50 GM082545 and DOE Grant DE-FG02-04ER63785 to GJJ, a\nSearle Scholar Award to GJJ, the Beckman Institute at Caltech,\nand gifts to Caltech from the Gordon and Betty Moore Foundation\nand Agouron Institute. Leginon development at the National Resource\nfor Automated Molecular Microscopy is supported by the\nNational Institutes of Health though the National Center for Research\nResources' P41 program (RR17573 and R01 RR023093).\n\nAccepted Version - nihms-123659.pdf
", "abstract": "Electron tomography has become a uniquely powerful tool for investigating the structures of individual cells, viruses, and macromolecules. Data collection is, however, time consuming and requires expensive instruments. To optimize productivity, we have incorporated one of the existing tilt-series acquisition programs, UCSF Tomo, into the well-developed automatic electron microscopy data collection package Leginon to enable fully automatic, sequential tilt-series acquisition. Here we describe how UCSF Tomo was integrated into Leginon, what users must do to set up a data collection session, how the automatic collection proceeds, how archived data about the process can be accessed and used, and how the software has been tested.", "date": "2009-07", "date_type": "published", "publication": "Journal of Structural Biology", "volume": "167", "number": "1", "publisher": "Elsevier", "pagerange": "11-18", "id_number": "CaltechAUTHORS:20101209-110311836", "issn": "1047-8477", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20101209-110311836", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 AI067548" }, { "agency": "NIH", "grant_number": "P50 GM082545" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02-04ER63785" }, { "agency": "Searle Scholars Program" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Agouron Institute" }, { "agency": "NIH", "grant_number": "RR17573" }, { "agency": "NIH", "grant_number": "R01 RR023093" } ] }, "doi": "10.1016/j.jsb.2009.03.019", "pmcid": "PMC2724967", "primary_object": { "basename": "nihms-123659.pdf", "url": "https://authors.library.caltech.edu/records/c3bh4-k6593/files/nihms-123659.pdf" }, "resource_type": "article", "pub_year": "2009", "author_list": "Suloway, Christian; Shi, Jian; et el." }, { "id": "https://authors.library.caltech.edu/records/2qjes-wbf52", "eprint_id": 15616, "eprint_status": "archive", "datestamp": "2023-08-20 01:50:21", "lastmod": "2023-10-19 14:38:54", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Li-Zhuo", "name": { "family": "Li", "given": "Zhuo" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Electron cryotomography: a new view into microbial ultrastructure", "ispublished": "pub", "full_text_status": "public", "note": "Copyright \u00a9 2009 Elsevier. \n\nAvailable online 6 May 2009. \n\nWe wish to thank Alasdair McDowall, Lu Gan, Morgan Beeby and Ariane Briegel for their help in improving the draft. Ultrastructural research in the Jensen lab is supported by the Howard Hughes Medical Research Institute, NIH grant R01 AI067548 to GJJ, the Beckman Institute at Caltech, and gifts to Caltech from the Gordon and Betty Moore Foundation and Agouron Institute. \n\nSupplementary data associated with this article can be found, in the online version, at doi:10.1016/j.mib.2009.03.007.\n\nAccepted Version - nihms-128649.pdf
Supplemental Material - Limmc1.mov
", "abstract": "Electron cryotomography (ECT) is an emerging technology that allows thin samples such as small bacterial cells to be imaged in 3D in a nearly native state to 'molecular' (not, vert, similar4 nm) resolution. As such, ECT is beginning to deliver long-awaited insight into the positions and structures of cytoskeletal filaments, cell wall elements, motility machines, chemoreceptor arrays, internal compartments, and other ultrastructures. Here we briefly explain ECT, review its recent contributions to microbiology, and conclude with a discussion of future prospects.", "date": "2009-06", "date_type": "published", "publication": "Current Opinion in Microbiology", "volume": "12", "number": "3", "publisher": "Elsevier", "pagerange": "333-340", "id_number": "CaltechAUTHORS:20090904-112844480", "issn": "1369-5274", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090904-112844480", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "NIH", "grant_number": "R01 AI067548" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Agouron Institute" } ] }, "doi": "10.1016/j.mib.2009.03.007", "pmcid": "PMC2747746", "primary_object": { "basename": "Limmc1.mov", "url": "https://authors.library.caltech.edu/records/2qjes-wbf52/files/Limmc1.mov" }, "related_objects": [ { "basename": "nihms-128649.pdf", "url": "https://authors.library.caltech.edu/records/2qjes-wbf52/files/nihms-128649.pdf" } ], "resource_type": "article", "pub_year": "2009", "author_list": "Li, Zhuo and Jensen, Grant J." }, { "id": "https://authors.library.caltech.edu/records/d9qf0-0d390", "eprint_id": 15003, "eprint_status": "archive", "datestamp": "2023-08-21 21:31:30", "lastmod": "2023-10-18 20:26:42", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "He-Yongning", "name": { "family": "He", "given": "Yongning" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" } ] }, "title": "Nanogold as a specific marker for electron cryotomography", "ispublished": "pub", "full_text_status": "public", "keywords": "Nanogold; electron cryotomography; labeling; liposome; FcRn", "note": "\u00a9 2009 Microscopy Society of America. \n\nReceived December 17, 2008; accepted April 3, 2009. \n\nWe thank Noreen Tiangco for preparing Nanogold-Fc, William Tivol for the help with microscopy, and members of the Bjorkman and Jensen laboratories for helpful suggestions. \n\nThis work was supported by a postdoctoral fellowship from the Cancer Research Institute (Y.H.), the National Institutes of Health (2 R37 AI041239-06A1 to P.J.B.), and gifts to Caltech to support electron microscopy from the Gordon and Betty Moore Foundation and the Agouron Institute.\n\nPublished - He2009p4574Microscopy_and_Microanalysis.pdf
Accepted Version - nihms-157152.pdf
", "abstract": "While electron cryotomography (ECT) provides \"molecular\" resolution, three-dimensional images of unique biological specimens, sample crowdedness, and/or resolution limitations can make it difficult to identify specific macromolecular components. Here we used a 1.4 nm Nanogold\u00ae cluster specifically attached to the Fc fragment of IgG to monitor its interaction with the neonatal Fc receptor (FcRn), a membrane-bound receptor that transports IgG across cells in acidic intracellular vesicles. ECT was used to image complexes formed by Nanogold-labeled Fc bound to FcRn attached to the outer surface of synthetic liposomes. In the resulting three-dimensional reconstructions, 1.4 nm Nanogold particles were distributed predominantly along the interfaces where 2:1 FcRn-Fc complexes bridged adjacent lipid bilayers. These results demonstrate that the 1.4 nm Nanogold cluster is visible in tomograms of typically thick samples (250 nm) recorded with defocuses appropriate for large macromolecules and is thus an effective marker.", "date": "2009-06", "date_type": "published", "publication": "Microscopy and Microanalysis", "volume": "15", "number": "3", "publisher": "Cambridge University Press", "pagerange": "183-188", "id_number": "CaltechAUTHORS:20090813-075852803", "issn": "1431-9276", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090813-075852803", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Cancer Research Institute" }, { "agency": "NIH", "grant_number": "2 R37 AI041239-06A1" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Agouron Institute" } ] }, "doi": "10.1017/S1431927609090424", "pmcid": "PMC2785728", "primary_object": { "basename": "He2009p4574Microscopy_and_Microanalysis.pdf", "url": "https://authors.library.caltech.edu/records/d9qf0-0d390/files/He2009p4574Microscopy_and_Microanalysis.pdf" }, "related_objects": [ { "basename": "nihms-157152.pdf", "url": "https://authors.library.caltech.edu/records/d9qf0-0d390/files/nihms-157152.pdf" } ], "resource_type": "article", "pub_year": "2009", "author_list": "He, Yongning; Jensen, Grant J.; et el." }, { "id": "https://authors.library.caltech.edu/records/z8j27-zks66", "eprint_id": 22971, "eprint_status": "archive", "datestamp": "2023-08-20 01:52:11", "lastmod": "2023-10-23 17:46:35", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Garin-J", "name": { "family": "Garin", "given": "J\u00e9r\u00f4me" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Techniques", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2009 Elsevier Ltd.\nAvailable online 22 April 2009.", "abstract": "The past century of microbiological research has produced an impressive\nunderstanding of microbial diversity, relevance, and basic metabolism. As a\ncrowning symbol of this progress, today the complete genome sequences of\nnearly 1000 different bacterial species are available and can be automatically\nannotated (approximately) and mapped onto metabolic networks to show\nwhat pathways are probably accessible to each organism. But even bacterial\ncells are not just 'bags of enzymes', and many aspects of what has been called\n'bacterial cell biology' have now come to the fore. Very broadly speaking,\nwhat we need to know now is how the chromosome/s is/are organized, which\ngenes are transcribed and when, where the gene products go inside the cell,\nand how all the components work together to perform each task, be it\nchemical, structural, or mechanical. Fortunately, many new technologies are\nbeing developed that should reveal these details. In this issue we focus on\nrecent developments in proteomic and structural techniques.", "date": "2009-06", "date_type": "published", "publication": "Current Opinion in Microbiology", "volume": "12", "number": "3", "publisher": "Elsevier", "pagerange": "282-284", "id_number": "CaltechAUTHORS:20110317-143734935", "issn": "1369-5274", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110317-143734935", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.mib.2009.03.003", "resource_type": "article", "pub_year": "2009", "author_list": "Garin, J\u00e9r\u00f4me and Jensen, Grant J." }, { "id": "https://authors.library.caltech.edu/records/vpk4h-ekb11", "eprint_id": 15285, "eprint_status": "archive", "datestamp": "2023-08-20 01:30:47", "lastmod": "2023-10-18 21:36:38", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Garin-J", "name": { "family": "Garin", "given": "J\u00e9r\u00f4me" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Which, when, where, and how?", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2009 Published by Elsevier Ltd.", "abstract": "The past century of microbiological research has produced an impressive understanding of microbial diversity, relevance, and basic metabolism. As a crowning symbol of this progress, today the complete genome sequences of nearly 1000 different bacterial species are available and can be automatically annotated (approximately) and mapped onto metabolic networks to show what pathways are probably accessible to each organism. But even bacterial cells are not just 'bags of enzymes', and many aspects of what has been called 'bacterial cell biology' have now come to the fore. Very broadly speaking, what we need to know now is how the chromosome/s is/are organized, which genes are transcribed and when, where the gene products go inside the cell, and how all the components work together to perform each task, be it chemical, structural, or mechanical. Fortunately, many new technologies are being developed that should reveal these details. In this issue we focus on recent developments in proteomic and structural techniques.", "date": "2009-04-22", "date_type": "published", "publication": "Current Opinion in Microbiology", "volume": "12", "number": "3", "publisher": "Elsevier", "pagerange": "282-284", "id_number": "CaltechAUTHORS:20090824-144411956", "issn": "1369-5274", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090824-144411956", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute" } ] }, "doi": "10.1016/j.mib.2009.03.003", "resource_type": "article", "pub_year": "2009", "author_list": "Garin, J\u00e9r\u00f4me and Jensen, Grant J." }, { "id": "https://authors.library.caltech.edu/records/1k2gg-34393", "eprint_id": 13927, "eprint_status": "archive", "datestamp": "2023-08-20 01:10:28", "lastmod": "2023-10-18 14:34:48", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "He-Yongning", "name": { "family": "He", "given": "Yongning" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" } ] }, "title": "Cryo-electron tomography of homophilic adhesion mediated by the neural cell adhesion molecule L1", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2009 Elsevier Ltd. \n\nReceived 6 November 2008; revised 5 January 2009; accepted 10 January 2009. Published: March 10, 2009. Available online 10 March 2009. \n\nWe thank Jost Vielmetter, Inderjit Nangiana, Chris Foglesong and the Caltech Protein Expression Center for expression of proteins, William Tivol and Prabha Dias for help with microscopy, and members of the Bjorkman and Jensen laboratories for helpful suggestions. Mass spectroscopic analysis and N-terminal sequencing performed by the Protein/Peptide Microanalytical Laboratory was supported by The Beckman Institute at Caltech. This work was supported by a postdoctoral fellowship from the Cancer Research Institute (Y.H.), the Howard Hughes Medical Institute (P.J.B.), and gifts to Caltech to support electron microscopy from the Gordon and Betty Moore Foundation and the Agouron Institute.\n\nAccepted Version - nihms103463.pdf
Supplemental Material - PIIS0969212609000732.mmc1.pdf
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Supplemental Material - PIIS0969212609000732.mmc3.mov
Supplemental Material - PIIS0969212609000732.mmc4.mov
Supplemental Material - PIIS0969212609000732.mmc5.mov
", "abstract": "The neural cell adhesion molecule L1 participates in homophilic interactions important for axon guidance and neuronal development. The structural details of homophilic adhesion mediated by L1 and other immunoglobulin superfamily members containing an N-terminal horseshoe arrangement of four immunoglobulin-like domains are unknown. Here we used cryo-electron tomography to study liposomes to which intact or truncated forms of the L1 ectodomain were attached. Tomographic reconstructions revealed an adhesion interface with a regular and repeating pattern consistent with interactions between paired horseshoes contributed by L1 proteins from neighboring liposomes. The characteristics of the pattern changed when N-linked carbohydrates were altered by removing sialic acids or converting from complex to high mannose or oligomannose glycans, suggesting a regulatory role for carbohydrates in L1-mediated homophilic adhesion. Using the results from tomograms and crystal structures of L1-related molecules, we present a structural model for L1-mediated homophilic adhesion that depends on protein-protein, protein-carbohydrate, and carbohydrate-carbohydrate interactions.", "date": "2009-03-11", "date_type": "published", "publication": "Structure", "volume": "17", "number": "3", "publisher": "Cell Press", "pagerange": "460-471", "id_number": "CaltechAUTHORS:20090410-112112630", "issn": "0969-2126", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090410-112112630", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Cancer Research Institute" }, { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Agouron Institute" } ] }, "doi": "10.1016/j.str.2009.01.009", "pmcid": "PMC2744468", "primary_object": { "basename": "PIIS0969212609000732.mmc1.pdf", "url": "https://authors.library.caltech.edu/records/1k2gg-34393/files/PIIS0969212609000732.mmc1.pdf" }, "related_objects": [ { "basename": "PIIS0969212609000732.mmc2.mov", "url": "https://authors.library.caltech.edu/records/1k2gg-34393/files/PIIS0969212609000732.mmc2.mov" }, { "basename": "PIIS0969212609000732.mmc3.mov", "url": "https://authors.library.caltech.edu/records/1k2gg-34393/files/PIIS0969212609000732.mmc3.mov" }, { "basename": "PIIS0969212609000732.mmc4.mov", "url": "https://authors.library.caltech.edu/records/1k2gg-34393/files/PIIS0969212609000732.mmc4.mov" }, { "basename": "PIIS0969212609000732.mmc5.mov", "url": "https://authors.library.caltech.edu/records/1k2gg-34393/files/PIIS0969212609000732.mmc5.mov" }, { "basename": "nihms103463.pdf", "url": "https://authors.library.caltech.edu/records/1k2gg-34393/files/nihms103463.pdf" } ], "resource_type": "article", "pub_year": "2009", "author_list": "He, Yongning; Jensen, Grant J.; et el." }, { "id": "https://authors.library.caltech.edu/records/0a3f5-kfx50", "eprint_id": 14748, "eprint_status": "archive", "datestamp": "2023-08-20 00:44:18", "lastmod": "2023-10-18 18:46:39", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Cell biology : protein filaments caught in the act", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2009 American Association for the Advancement of Science.", "abstract": "Advances in electron microscopy have allowed bacterial DNA-segregating protein filaments to be visualized.", "date": "2009-01-23", "date_type": "published", "publication": "Science", "volume": "323", "number": "5913", "publisher": "American Association for the Advancement of Science", "pagerange": "472-473", "id_number": "CaltechAUTHORS:20090731-083543833", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090731-083543833", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1126/science.1169829", "resource_type": "article", "pub_year": "2009", "author_list": "Jensen, Grant J." }, { "id": "https://authors.library.caltech.edu/records/6t07x-mqc80", "eprint_id": 12835, "eprint_status": "archive", "datestamp": "2023-08-22 13:47:13", "lastmod": "2023-10-17 20:57:13", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gan-Lu", "name": { "family": "Gan", "given": "Lu" }, "orcid": "0000-0002-8685-4896" }, { "id": "Chen-Songye", "name": { "family": "Chen", "given": "Songye" }, "orcid": "0000-0001-5407-5049" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Molecular organization of Gram-negative peptidoglycan", "ispublished": "pub", "full_text_status": "public", "keywords": "cell wall; Cryo-EM; sacculus; tomography; cell shape", "note": "\u00a9 2008 by the National Academy of Sciences. \n\nEdited by M. J. Osborn, University of Connecticut Health Center, Farmington, CT, and approved October 9, 2008 (received for review August 14, 2008). Published online before print November 24, 2008, doi:10.1073/pnas.0808035105 \n\nWe thank Drs. W. F. Tivol for help with EM; H. Tsuruta and M. Hammel for help at beamlines SSRL 4-2 and ALS 12.3.1, respectively; A. Briegel, D.P. Dias, and Z. Li for sharing data; J. Skerker, K.C. Huang, N. Wingreen, and P. Leong for discussions; and Mr. Everett Kane (SuperSoft Design, New York, NY) for Fig. 1C. This work was supported in part by National Institutes of Health Grants R01 AI067548 and P50 GM082545 to G.J.J., a Searle Scholar Award to G.J.J., the Beckman Institute at Caltech, and gifts to Caltech from the Gordon and Betty Moore Foundation and the Agouron Institute. L.G. is a Damon Runyon Fellow supported by a fellowship from the Damon Runyon Cancer Research Foundation (DRG-1940-07). \n\nAuthor contributions: L.G. and G.J.J. designed research; L.G. and S.C. performed research; L.G., S.C., and G.J.J. analyzed data; and L.G. and G.J.J. wrote the paper. \n\nThe authors declare no conflict of interest. \n\nThis article is a PNAS Direct Submission. \n\nThis article contains supporting information online at www.pnas.org/cgi/content/full/0808035105/DCSupplemental.\n\nPublished - GANpnas08.pdf
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", "abstract": "The stress-bearing component of the bacterial cell wall -\u2014 a multi-gigadalton bag-like molecule called the sacculus -\u2014 is synthesized from peptidoglycan. Whereas the chemical composition and the 3-dimensional structure of the peptidoglycan subunit (in at least one conformation) are known, the architecture of the assembled sacculus is not. Four decades' worth of biochemical and electron microscopy experiments have resulted in two leading 3-D peptidoglycan models: \"Layered\" and \"Scaffold\", in which the glycan strands are parallel and perpendicular to the cell surface, respectively. Here we resolved the basic architecture of purified, frozen-hydrated sacculi through electron cryotomography. In the Gram-negative sacculus, a single layer of glycans lie parallel to the cell surface, roughly perpendicular to the long axis of the cell, encircling the cell in a disorganized hoop-like fashion.", "date": "2008-12-02", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "105", "number": "48", "publisher": "National Academy of Sciences", "pagerange": "18953-18957", "id_number": "CaltechAUTHORS:GANpnas08", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:GANpnas08", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 AI067548" }, { "agency": "NIH", "grant_number": "P50 GM082545" }, { "agency": "Searle Scholars Program" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Agouron Institute" }, { "agency": "Damon Runyon Cancer Research Foundation", "grant_number": "DRG-1940-07" } ] }, "doi": "10.1073/pnas.0808035105", "pmcid": "PMC2596242", "primary_object": { "basename": "GANpnas08.pdf", "url": "https://authors.library.caltech.edu/records/6t07x-mqc80/files/GANpnas08.pdf" }, "related_objects": [ { "basename": "GANpnas08movie1.mov", "url": "https://authors.library.caltech.edu/records/6t07x-mqc80/files/GANpnas08movie1.mov" }, { "basename": "GANpnas08movie2.mov", "url": "https://authors.library.caltech.edu/records/6t07x-mqc80/files/GANpnas08movie2.mov" }, { "basename": "GANpnas08supp.pdf", "url": "https://authors.library.caltech.edu/records/6t07x-mqc80/files/GANpnas08supp.pdf" } ], "resource_type": "article", "pub_year": "2008", "author_list": "Gan, Lu; Chen, Songye; et el." }, { "id": "https://authors.library.caltech.edu/records/gay6n-mhz48", "eprint_id": 12667, "eprint_status": "archive", "datestamp": "2023-08-22 13:28:20", "lastmod": "2023-10-17 20:25:09", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lee-Edwin", "name": { "family": "Lee", "given": "Edwin" } }, { "id": "Fahimian-B-P", "name": { "family": "Fahimian", "given": "Benjamin P." } }, { "id": "Iancu-C-V", "name": { "family": "Iancu", "given": "Cristina V." }, "orcid": "0000-0002-7352-9226" }, { "id": "Suloway-C", "name": { "family": "Suloway", "given": "Christian" } }, { "id": "Murphy-G-E", "name": { "family": "Murphy", "given": "Gavin E." } }, { "id": "Wright-E-R", "name": { "family": "Wright", "given": "Elizabeth R." } }, { "id": "Casta\u00f1o-D\u00edez-D", "name": { "family": "Casta\u00f1o-D\u00edez", "given": "Daniel" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Miao-Jianwei", "name": { "family": "Miao", "given": "Jianwei" } } ] }, "title": "Radiation dose reduction and image enhancement in biological imaging through equally-sloped tomography", "ispublished": "pub", "full_text_status": "public", "keywords": "Equally-sloped tomography; Electron cryomicroscopy; Iterative reconstruction algorithm; Radiation dose reduction; Image enhancement; Computed tomography", "note": "\u00a9 2008 Elsevier. \n\nReceived 5 May 2008; revised 25 July 2008; accepted 31 July 2008. Available online 15 August 2008. \n\nWe thank H. Jiang for the help with the figures. JM thanks O. Levi, W. Chiu and Z.H. Zhou for stimulating discussions. This work was supported in part by the US Department of Energy, Office of Basic Energy Sciences under the contract number DE-FG02-06ER46276, the US National Science Foundation, Division of Materials Research (DMR-0520894), UC Discovery/TomoSoft Technologies, LLC under the Contract Number IT107-10166 and the Alfred P. Sloan foundation. GJJ acknowledges funding from the NIH (R01 AI067548 and P50 GM082545), DOE (Grant DE-FG02-04ER63785), a Searle Scholar Award to GJJ, the Beckman Institute at Caltech, and gifts to Caltech from the Gordon and Betty Moore Foundation and Agouron Institute. \n\nSupplementary data associated with this article can be found, in the online version, at doi:10.1016/j.jsb.2008.07.011.\n\nAccepted Version - nihms-282668.pdf
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", "abstract": "Electron tomography is currently the highest resolution imaging modality available to study the 3D structures of pleomorphic macromolecular assemblies, viruses, organelles and cells. Unfortunately, the resolution is currently limited to 3\u20135 nm by several factors including the dose tolerance of biological specimens and the inaccessibility of certain tilt angles. Here we report the first experimental demonstration of equally-sloped tomography (EST) to alleviate these problems. As a proof of principle, we applied EST to reconstructing frozen-hydrated keyhole limpet hemocyanin molecules from a tilt-series taken with constant slope increments. In comparison with weighted back-projection (WBP), the algebraic reconstruction technique (ART) and the simultaneous algebraic reconstruction technique (SART), EST reconstructions exhibited higher contrast, less peripheral noise, more easily detectable molecular boundaries and reduced missing wedge effects. More importantly, EST reconstructions including only two-thirds the original images appeared to have the same resolution as full WBP reconstructions, suggesting that EST can either reduce the dose required to reach a given resolution or allow higher resolutions to be achieved with a given dose. EST was also applied to reconstructing a frozen-hydrated bacterial cell from a tilt-series taken with constant angular increments. The results confirmed similar benefits when standard tilts are utilized.", "date": "2008-11", "date_type": "published", "publication": "Journal of Structural Biology", "volume": "164", "number": "2", "publisher": "Elsevier", "pagerange": "221-227", "id_number": "CaltechAUTHORS:LEEjsb08", "issn": "1047-8477", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:LEEjsb08", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02-06ER46276" }, { "agency": "NSF", "grant_number": "DMR-0520894" }, { "agency": "UC Discovery/TomoSoft Technologies, LLC", "grant_number": "IT107-10166" }, { "agency": "Alfred P. Sloan Foundation" }, { "agency": "NIH", "grant_number": "R01 AI067548" }, { "agency": "NIH", "grant_number": "P50 GM082545" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02-04ER63785" }, { "agency": "Searle Scholars Program" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Agouron Institute" } ] }, "local_group": { "items": [ { "id": "TAPIR" } ] }, "doi": "10.1016/j.jsb.2008.07.011", "pmcid": "PMC3099251", "primary_object": { "basename": "LEEjsb08movie.gif", "url": "https://authors.library.caltech.edu/records/gay6n-mhz48/files/LEEjsb08movie.gif" }, "related_objects": [ { "basename": "nihms-282668.pdf", "url": "https://authors.library.caltech.edu/records/gay6n-mhz48/files/nihms-282668.pdf" } ], "resource_type": "article", "pub_year": "2008", "author_list": "Lee, Edwin; Fahimian, Benjamin P.; et el." }, { "id": "https://authors.library.caltech.edu/records/wt4as-h5p28", "eprint_id": 13355, "eprint_status": "archive", "datestamp": "2023-08-22 13:12:04", "lastmod": "2023-10-17 23:29:38", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Tivol-W-F", "name": { "family": "Tivol", "given": "William F." } }, { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "An improved cryogen for plunge freezing", "ispublished": "pub", "full_text_status": "public", "keywords": "cryogen; plunge freezing; electron cryomicroscopy; ice embedding; transmission electron microscopy; specimen preparation", "note": "\u00a9 Microscopy Society of America 2008. \n\nReceived December 20, 2007; accepted June 4, 2008. \n\nThis work was supported in part by NIH grants R01 AI067548 and P50 GM082545 to G.J.J., a Searle Scholar Award to G.J.J., the Beckman Institute at Caltech, and gifts to Caltech from the Gordon and Betty Moore Foundation and Agouron Institute.\n\nPublished - TIVmm08.pdf
", "abstract": "The use of an alkane mixture that remains liquid at 77 K to freeze specimens has advantages over the use of a pure alkane that is solid at 77 K. It was found that a mixture of methane and ethane did not give a cooling rate adequate to produce vitreous ice, but a mixture of propane and ethane did result in vitreous ice. Furthermore, the latter mixture produced less damage to specimens mounted on a very thin, fragile holey carbon substrate.", "date": "2008-10", "date_type": "published", "publication": "Microscopy and Microanalysis", "volume": "14", "number": "5", "publisher": "Cambridge University Press", "pagerange": "375-379", "id_number": "CaltechAUTHORS:TIVmm08", "issn": "1431-9276", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:TIVmm08", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 AI067548" }, { "agency": "NIH", "grant_number": "P50 GM082545" }, { "agency": "Searle Scholar Award" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Agouron Institute" } ] }, "doi": "10.1017/S1431927608080781", "pmcid": "PMC3058946", "primary_object": { "basename": "TIVmm08.pdf", "url": "https://authors.library.caltech.edu/records/wt4as-h5p28/files/TIVmm08.pdf" }, "resource_type": "article", "pub_year": "2008", "author_list": "Tivol, William F.; Briegel, Ariane; et el." }, { "id": "https://authors.library.caltech.edu/records/9474y-2h118", "eprint_id": 13276, "eprint_status": "archive", "datestamp": "2023-08-19 23:40:17", "lastmod": "2023-10-17 23:22:41", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "He-Wanzhong", "name": { "family": "He", "given": "Wanzhong" } }, { "id": "Ladinsky-M-S", "name": { "family": "Ladinsky", "given": "Mark S." }, "orcid": "0000-0002-1036-3513" }, { "id": "Huey-Tubman-K-E", "name": { "family": "Huey-Tubman", "given": "Kathryn E." }, "orcid": "0000-0002-4683-8138" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "McIntosh-J-R", "name": { "family": "McIntosh", "given": "J. Richard" } }, { "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "orcid": "0000-0002-2277-3990" } ] }, "title": "FcRn-mediated antibody transport across epithelial cells revealed by electron tomography", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2008 Nature Publishing Group. \n\nWe thank D. Mastronarde for advice about setting up SerialEM on the Caltech microscopes and three-dimensional modelling; C. Kivork for preparing Au-Fc and Au-dextran; B. Tivol for assistance with electron microscopes; M. Murphy for help with schematic figures; M. Morphew for contributions to silver enhancement methods; Y. Nie, A. Feuerabendt, A. Kules, C. Luna, K. McKenzie, R. Sander and L. Zinn-Bjorkman for segmenting tomograms; J. Vielmetter for SPR studies of Au-Fc; and F. Brodsky, F. Maxfield, S. Schmid and D. Tesar for discussions. This work was supported by the National Institutes of Health (2 R37 AI041239-06A1 to P.J.B. and RR000592 to J.R.M.), a Max Planck Research Award (P.J.B.), gifts from the Gordon and Betty Moore Foundation and the Agouron Institute to support electron microscopy at Caltech, and National University of Singapore AcRF start-up funds (R-154-000-339-133 to W.H.). \n\nAuthor Contributions: W.H. and P.J.B. conceived the experiments. Electron microscopy data were collected by W.H. in collaboration with and in the microscopy laboratory established by G.J.J. at Caltech. W.H. configured SerialEM on the Caltech electron microscopes, prepared intestinal samples by chemical fixation or HPF/FSF, conceived and developed the gold enhancement procedures, and collected, processed, interpreted and modelled tomograms. W.H. and K.E.H.T conducted kinetic experiments. Immunolabelling and associated imaging was done by M.S.L. in Boulder with enhanced samples provided by W.H. and K.E.H.T. Initial phases of the project using transfected cells were conducted by P.J.B. in Boulder in collaboration with J.R.M. and the Boulder Laboratory for 3D Microscopy of Cells. All authors discussed and interpreted the results and edited the manuscript.\n\nAccepted Version - nihms-152876.pdf
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", "abstract": "The neonatal Fc receptor (FcRn) transports maternal IgG across epithelial barriers, thereby providing the fetus or newborn with humoral immunity before its immune system is fully functional. In newborn rats, FcRn transfers IgG from milk to blood by apical-to-basolateral transcytosis across intestinal epithelial cells. The pH difference between the apical (pH 6.0\u20136.5) and basolateral (pH 7.4) sides of intestinal epithelial cells facilitates the efficient\nunidirectional transport of IgG, because FcRn binds IgG at\npH 6.0\u20136.5 but not at pH 7 or more. As milk passes through\nthe neonatal intestine, maternal IgG is removed by FcRn-expressing cells in the proximal small intestine (duodenum and jejunum); remaining proteins are absorbed and degraded by FcRn-negative cells in the distal small intestine (ileum). Here we use electron tomography to make jejunal transcytosis visible directly in space and time, developing new labelling and detection methods to map individual nanogold-labelled Fc within transport\nvesicles and simultaneously to characterize these vesicles by immunolabelling. Combining electron tomography with a nonperturbing endocytic label allowed us to conclusively identify receptor-bound ligands, resolve interconnecting vesicles, determine whether a vesicle was microtubule-associated, and accurately trace FcRn-mediated transport of IgG. Our results present a complex picture in which Fc moves through networks of entangled tubular and irregular vesicles, only some of which are microtubule-associated, as it migrates to the basolateral surface. New features\nof transcytosis are elucidated, including transport involving multivesicular body inner vesicles/tubules and exocytosis through clathrin-coated pits. Markers for early, late and recycling endosomes each labelled vesicles in different and overlapping morphological classes, revealing spatial complexity in endo-lysosomal trafficking.", "date": "2008-09-25", "date_type": "published", "publication": "Nature", "volume": "455", "number": "7212", "publisher": "Nature Publishing Group", "pagerange": "542-546", "id_number": "CaltechAUTHORS:HEWnat08", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:HEWnat08", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "2 R37 AI041239-06A1" }, { "agency": "NIH", "grant_number": "RR000592" }, { "agency": "Max Planck Society" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Agouron Institute" }, { "agency": "National University of Singapore", "grant_number": "R-154-000-339-133" } ] }, "doi": "10.1038/nature07255", "pmcid": "PMC2773227", "primary_object": { "basename": "HEWnat08movie4.mov", "url": "https://authors.library.caltech.edu/records/9474y-2h118/files/HEWnat08movie4.mov" }, "related_objects": [ { "basename": "HEWnat08movie6.mov", "url": "https://authors.library.caltech.edu/records/9474y-2h118/files/HEWnat08movie6.mov" }, { "basename": "HEWnat08movie8.mov", "url": "https://authors.library.caltech.edu/records/9474y-2h118/files/HEWnat08movie8.mov" }, { "basename": "HEWnat08supp.pdf", "url": "https://authors.library.caltech.edu/records/9474y-2h118/files/HEWnat08supp.pdf" }, { "basename": "HEWnat08movie2.mov", "url": "https://authors.library.caltech.edu/records/9474y-2h118/files/HEWnat08movie2.mov" }, { "basename": "HEWnat08movie3.mov", "url": "https://authors.library.caltech.edu/records/9474y-2h118/files/HEWnat08movie3.mov" }, { "basename": "HEWnat08movie5.mov", "url": "https://authors.library.caltech.edu/records/9474y-2h118/files/HEWnat08movie5.mov" }, { "basename": "HEWnat08movie7.mov", "url": "https://authors.library.caltech.edu/records/9474y-2h118/files/HEWnat08movie7.mov" }, { "basename": "nihms-152876.pdf", "url": "https://authors.library.caltech.edu/records/9474y-2h118/files/nihms-152876.pdf" }, { "basename": "HEWnat08movie1.mov", "url": "https://authors.library.caltech.edu/records/9474y-2h118/files/HEWnat08movie1.mov" } ], "resource_type": "article", "pub_year": "2008", "author_list": "He, Wanzhong; Ladinsky, Mark S.; et el." }, { "id": "https://authors.library.caltech.edu/records/8cdrf-nby29", "eprint_id": 12246, "eprint_status": "archive", "datestamp": "2023-08-22 13:06:15", "lastmod": "2023-10-17 16:38:12", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ebersbach-G", "name": { "family": "Ebersbach", "given": "Gitte" } }, { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Jacobs-Wagner-C", "name": { "family": "Jacobs-Wagner", "given": "Christine" } } ] }, "title": "A Self-Associating Protein Critical for Chromosome Attachment, Division, and Polar Organization in Caulobacter", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2008 Elsevier. \n\nReceived 26 November 2007; revised 18 April 2008; accepted 11 July 2008. Published: September 18, 2008. Available online 18 September 2008. \n\nWe thank M. Mooseker, E. Dufresne, T. Emonet, and J. Wolenski for valuable discussions; K. Gerdes, J. Gober, A. Newton, N. Ohta, L. Shapiro, M. Thanbichler, and P. Viollier for supplying strains or antibody; P. Angelastro, A. Jackson, H. Lam, and W. Schofield for construction of strains; H. J. Ding and D. Rosenman for computational help; M. Mooseker, Z. Jiang, and G. Charbon for assistance with EM; E. Folta-Stogniew and the Keck Foundation Biotechnology Resource Laboratory at Yale for the biophysical analyses, and the Jacobs-Wagner laboratory and T. Emonet for critical reading of the manuscript. G.E. was supported by postdoctoral fellowships from the Villum Kann Rasmussen Foundation and the Danish Natural Science Research Council. This work was funded in part by National Institutes of Health (GM065835 to C.J.-W. and AI067548 to G.J.J.), gifts to Caltech from the Gordon and Betty Moore Foundation and Agouron Institute (to G.J.J.) and the Pew Scholars Program in the Biological Sciences sponsored by the Pew Charitable trust (to C.J.-W.). C.J.-W. is a Howard Hughes Medical Institute investigator. \n\nSupplemental Data include Supplemental Experimental Procedures, Supplemental References, five figures, and two tables and can be found with this article online at http://www.cell.com/cgi/content/full/134/6/956/DC1/.\n\nAccepted Version - nihms70633.pdf
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", "abstract": "Cell polarization is an integral part of many unrelated bacterial processes. How intrinsic cell polarization is achieved is poorly understood. Here, we provide evidence that Caulobacter crescentus uses a multimeric pole-organizing factor (PopZ) that serves as a hub to concurrently achieve several polarizing functions. During chromosome segregation, polar PopZ captures the ParB\u2022ori complex and thereby anchors sister chromosomes at opposite poles. This step is essential for stabilizing bipolar gradients of a cell division inhibitor and setting up division near midcell. PopZ also affects polar stalk morphogenesis and mediates the polar localization of the morphogenetic and cell cycle signaling proteins CckA and DivJ. Polar accumulation of PopZ, which is central to its polarizing activity, can be achieved independently of division and does not appear to be dictated by the pole curvature. Instead, evidence suggests that localization of PopZ largely relies on PopZ multimerization in chromosome-free regions, consistent with a self-organizing mechanism.", "date": "2008-09-19", "date_type": "published", "publication": "Cell", "volume": "134", "number": "6", "publisher": "Elsevier", "pagerange": "956-968", "id_number": "CaltechAUTHORS:EBEc08", "issn": "0092-8674", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:EBEc08", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Villum Kann Rasmussen Foundation" }, { "agency": "Danish Natural Science Research Council" }, { "agency": "NIH", "grant_number": "GM065835" }, { "agency": "NIH", "grant_number": "AI067548" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Agouron Institute" }, { "agency": "Pew Charitable Trust" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1016/j.cell.2008.07.016", "pmcid": "PMC2614312", "primary_object": { "basename": "EBEc08movie2.mov", "url": "https://authors.library.caltech.edu/records/8cdrf-nby29/files/EBEc08movie2.mov" }, "related_objects": [ { "basename": "EBEc08movie3.mov", "url": "https://authors.library.caltech.edu/records/8cdrf-nby29/files/EBEc08movie3.mov" }, { "basename": "EBEc08movie6.mov", "url": "https://authors.library.caltech.edu/records/8cdrf-nby29/files/EBEc08movie6.mov" }, { "basename": "EBEc08movie7.mov", "url": "https://authors.library.caltech.edu/records/8cdrf-nby29/files/EBEc08movie7.mov" }, { "basename": "EBEc08movie1.mov", "url": "https://authors.library.caltech.edu/records/8cdrf-nby29/files/EBEc08movie1.mov" }, { "basename": "EBEc08movie10.mov", "url": "https://authors.library.caltech.edu/records/8cdrf-nby29/files/EBEc08movie10.mov" }, { "basename": "EBEc08movie4.mov", "url": "https://authors.library.caltech.edu/records/8cdrf-nby29/files/EBEc08movie4.mov" }, { "basename": "EBEc08movie5.mov", "url": "https://authors.library.caltech.edu/records/8cdrf-nby29/files/EBEc08movie5.mov" }, { "basename": "EBEc08movie8.mov", "url": "https://authors.library.caltech.edu/records/8cdrf-nby29/files/EBEc08movie8.mov" }, { "basename": "EBEc08movie9.mov", "url": "https://authors.library.caltech.edu/records/8cdrf-nby29/files/EBEc08movie9.mov" }, { "basename": "EBEc08supp.pdf", "url": "https://authors.library.caltech.edu/records/8cdrf-nby29/files/EBEc08supp.pdf" }, { "basename": "nihms70633.pdf", "url": "https://authors.library.caltech.edu/records/8cdrf-nby29/files/nihms70633.pdf" } ], "resource_type": "article", "pub_year": "2008", "author_list": "Ebersbach, Gitte; Briegel, Ariane; et el." }, { "id": "https://authors.library.caltech.edu/records/m8s4e-vfw43", "eprint_id": 24671, "eprint_status": "archive", "datestamp": "2023-08-19 23:00:42", "lastmod": "2023-10-23 23:34:36", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Ding-H-Jane", "name": { "family": "Ding", "given": "H. Jane" } }, { "id": "Li-Zhuo", "name": { "family": "Li", "given": "Zhuo" } }, { "id": "Werner-John-N", "name": { "family": "Werner", "given": "John" } }, { "id": "Gitai-Zemer", "name": { "family": "Gitai", "given": "Zemer" }, "orcid": "0000-0002-3280-6178" }, { "id": "Dias-D-P", "name": { "family": "Dias", "given": "D. Prabha" } }, { "id": "Jensen-Rasmus-B", "name": { "family": "Jensen", "given": "Rasmus B." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Location and architecture of the Caulobacter crescentus chemoreceptor array", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2008 The Authors. Journal compilation \u00a9 2008 Blackwell Publishing Ltd. \n\nAccepted 13 March, 2008. Article first published online: 28 Jun. 2008. \n\nWe thank Brian Crane for helpful discussions. This work was supported in part by NIH grants R01 AI067548 and P50 G082545, and DOE grant DE-FG02-04ER63785 to G.J.J., the Beckman Institute at Caltech, and gifts to Caltech from the Agouron Institute and the Gordon and Betty Moore Foundation. Zemer Gitai and John Werner were supported by Grant No. DE-FG02-05ER64136 from the Office of Science (BER), US Department of Energy. Rasmus B. Jensen thanks the 'The Danish Natural Science Research Council' for funding.\n\nAccepted Version - nihms281759.pdf
Supplemental Material - BRImm08Movie_S1.doc
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", "abstract": "A new method for recording both fluorescence and cryo-EM images of small bacterial cells was developed and used to identify chemoreceptor arrays in cryotomograms of intact Caulobacter crescentus cells. We show that in wild-type cells preserved in a near-native state, the chemoreceptors are hexagonally packed with a lattice spacing of 12 nm, just a few tens of nanometers away from the flagellar motor that they control. The arrays were always found on the convex side of the cell, further demonstrating that Caulobacter cells maintain dorsal/ventral as well as anterior/posterior asymmetry. Placing the known crystal structure of a trimer of receptor dimers at each vertex of the lattice accounts well for the density and agrees with other constraints. Based on this model for the arrangement of receptors, there are between one and two thousand receptors per array.", "date": "2008-07", "date_type": "published", "publication": "Molecular Microbiology", "volume": "69", "number": "1", "publisher": "Blackwell", "pagerange": "30-41", "id_number": "CaltechAUTHORS:20110803-163826561", "issn": "0950-382X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110803-163826561", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 AI067548" }, { "agency": "NIH", "grant_number": "P50 G082545" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02-04ER63785" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Agouron Institute" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02-05ER64136" }, { "agency": "Danish Natural Science Research Council" } ] }, "doi": "10.1111/j.1365-2958.2008.06219.x", "pmcid": "PMC3090075", "primary_object": { "basename": "nihms281759.pdf", "url": "https://authors.library.caltech.edu/records/m8s4e-vfw43/files/nihms281759.pdf" }, "related_objects": [ { "basename": "BRImm08Movie_S1.doc", "url": "https://authors.library.caltech.edu/records/m8s4e-vfw43/files/BRImm08Movie_S1.doc" }, { "basename": "BRImm08Movie_S1.mov", "url": "https://authors.library.caltech.edu/records/m8s4e-vfw43/files/BRImm08Movie_S1.mov" } ], "resource_type": "article", "pub_year": "2008", "author_list": "Briegel, Ariane; Ding, H. Jane; et el." }, { "id": "https://authors.library.caltech.edu/records/6dmy7-qgn44", "eprint_id": 14205, "eprint_status": "archive", "datestamp": "2023-08-22 12:23:42", "lastmod": "2023-10-18 16:20:22", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Morris-D-M", "name": { "family": "Morris", "given": "Dylan M." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Toward a biomechanical understanding of whole bacterial cells", "ispublished": "pub", "full_text_status": "restricted", "keywords": "bacterial cell biology; biomechanics; cell modeling; cellular microscopies; prokaryotic ultrastructure", "note": "\u00a9 2009 Annual Reviews.\nFirst published online as a Review in Advance on March 20, 2008.\nThe authors thank their many colleagues and collaborators who influenced the content of\nthis manuscript through both specific critiques and general discussions. We regret that our\nbroad scope has prevented mention or even referencing of so many important and relevant studies. This work was supported in part by NIH grant R01 AI067548, DOE grant DE-FG02-\n04ER63785, and a Searle Scholar Award to G. J. J.", "abstract": "Following decades of research in genetics and biochemistry, the basic metabolism of bacteria is now well understood. In addition to core metabolism, however, bacterial cells also perform a number of mechanical tasks such as maintaining a characteristic shape, moving within their environment, segregating their genome, and dividing. Major advances in imaging technologies including fluorescence light microscopy (fLM) and electron cryotomography (ECT) have provided new insight into the bacterial ultrastructures that accomplish these tasks. It is now clear, for instance, that bacteria are highly organized, possessing cytoskeletons, specifically arranged genomes, internal compartments, and carefully positioned macromolecular machines. These structures and their functions are reviewed here in the form of a progress report toward a complete biomechanical understanding of a generalized bacterial cell. The goal of eventually integrating genetic, biochemical, imaging, and biophysical data into spatially explicit, mechanically predictive models of whole cells is highlighted.", "date": "2008-07", "date_type": "published", "publication": "Annual Review of Biochemistry", "volume": "77", "publisher": "Annual Reviews", "pagerange": "583-613", "id_number": "CaltechAUTHORS:20090512-112554576", "issn": "0066-4154", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090512-112554576", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 AI067548" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02-04ER63785" }, { "agency": "Searle Scholars Program" } ] }, "doi": "10.1146/annurev.biochem.77.061206.173846", "resource_type": "article", "pub_year": "2008", "author_list": "Morris, Dylan M. and Jensen, Grant J." }, { "id": "https://authors.library.caltech.edu/records/7nwx7-8ag44", "eprint_id": 24670, "eprint_status": "archive", "datestamp": "2023-08-22 11:23:19", "lastmod": "2023-10-23 23:34:32", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Yu-Zhiheng", "name": { "family": "Yu", "given": "Zhiheng" } }, { "id": "Gonciarz-M-D", "name": { "family": "Gonciarz", "given": "Malgorzata D." } }, { "id": "Sundquist-W-I", "name": { "family": "Sundquist", "given": "Wesley I." } }, { "id": "Hill-C-P", "name": { "family": "Hill", "given": "Christopher P." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Cryo-EM Structure of Dodecameric Vps4p and Its 2:1 Complex with Vta1p", "ispublished": "pub", "full_text_status": "public", "keywords": "Vps4; Vta1; AAA ATPase; HIV budding; Cryo-EM", "note": "Copyright \u00a9 2008 Elsevier Ltd. \n\nReceived 10 August 2007; revised 1 January 2008; accepted 4 January 2008. Available online 12 January 2008. \n\nEdited by W. Baumeister. \n\nThis work was supported in part by the National Institutes of Health through grant P50 GM082545 (awarded to W.I.S., C.P.H., and G.J.J.), the Beckman Institute at Caltech, and gifts to Caltech from the Ralph M. Parsons Foundation, the Agouron Institute, and the Gordon and Betty Moore Foundation. We thank E. Kubalek for sharing her cryo-EM structure of p97. \n\nSupplementary data associated with this article can be found, in the online version, at doi:10.1016/j.jmb.2008.01.009\n\nAccepted Version - nihms42854.pdf
Supplemental Material - YUZjmb08supp.pdf
", "abstract": "The type I AAA (ATPase associated with a variety of cellular activities) ATPase Vps4 and its co-factor Vta1p/LIP5 function in membrane remodeling events that accompany cytokinesis, multivesicular body biogenesis, and retrovirus budding, apparently by driving disassembly and recycling of membrane-associated ESCRT (endosomal sorting complex required for transport)-III complexes. Here, we present electron cryomicroscopy reconstructions of dodecameric yeast Vps4p complexes with and without their microtubule interacting and transport (MIT) N-terminal domains and Vta1p co-factors. The ATPase domains of Vps4p form a bowl-like structure composed of stacked hexameric rings. The two rings adopt dramatically different conformations, with the \"upper\" ring forming an open assembly that defines the sides of the bowl and the lower ring forming a closed assembly that forms the bottom of the bowl. The N-terminal MIT domains of the upper ring localize on the symmetry axis above the cavity of the bowl, and the binding of six extended Vta1p monomers causes additional density to appear both above and below the bowl. The structures suggest models in which Vps4p MIT and Vta1p domains engage ESCRT-III substrates above the bowl and help transfer them into the bowl to be pumped through the center of the dodecameric assembly.", "date": "2008-03-21", "date_type": "published", "publication": "Journal of Molecular Biology", "volume": "377", "number": "2", "publisher": "Elsevier", "pagerange": "364-377", "id_number": "CaltechAUTHORS:20110803-162803480", "issn": "0022-2836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110803-162803480", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P50 GM082545" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "Agouron Institute" }, { "agency": "Gordon and Betty Moore Foundation" } ] }, "doi": "10.1016/j.jmb.2008.01.009", "pmcid": "PMC2279015", "primary_object": { "basename": "YUZjmb08supp.pdf", "url": "https://authors.library.caltech.edu/records/7nwx7-8ag44/files/YUZjmb08supp.pdf" }, "related_objects": [ { "basename": "nihms42854.pdf", "url": "https://authors.library.caltech.edu/records/7nwx7-8ag44/files/nihms42854.pdf" } ], "resource_type": "article", "pub_year": "2008", "author_list": "Yu, Zhiheng; Gonciarz, Malgorzata D.; et el." }, { "id": "https://authors.library.caltech.edu/records/8krq9-1px22", "eprint_id": 13361, "eprint_status": "archive", "datestamp": "2023-08-22 11:13:34", "lastmod": "2023-10-17 23:50:09", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Murphy-G-E", "name": { "family": "Murphy", "given": "Gavin E." } }, { "id": "Matson-E-G", "name": { "family": "Matson", "given": "Eric G." } }, { "id": "Leadbetter-J-R", "name": { "family": "Leadbetter", "given": "Jared R." }, "orcid": "0000-0002-7033-0844" }, { "id": "Berg-H-C", "name": { "family": "Berg", "given": "Howard C." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Novel ultrastructures of Treponema primitia and their implications for motility", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2008 The Authors. Journal compilation \u00a9 2008 Blackwell Publishing. \n\nAccepted 8 January, 2008. Published Online: 1 February 2008. \n\nWe thank H. Jane Ding for creating an Amira module for analysis, Dylan Morris for Fig. 11C and Everett Kane for creating the animation. This work was supported in part by NIH Grants P01 G66521 and R01 AI067548 to G.J.J., DOE Grant DE-FG02-04ER63785 to G.J.J., a Searle Scholar Award to G.J.J., NSF Grants DEB-0321753 and EF-0523267 to J.R.L., NIH Grant AI016478 to H.C.B., NIH Graduate Fellowship F31 EB 004179 to G.E.M., and gifts to Caltech from the Ralph M. Parsons Foundation, the Agouron Institute, and the Gordon and Betty Moore Foundation.\n\nAccepted Version - nihms281761.pdf
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", "abstract": "Members of the bacterial phylum Spirochaetes are generally helical cells propelled by periplasmic flagella. The spirochete Treponema primitia is interesting because of its mutualistic role in the termite gut, where it is believed to cooperate with protozoa that break down cellulose and produce H2 as a by-product. Here we report the ultrastructure of T. primitia as obtained by electron cryotomography of intact, frozen-hydrated cells. Several previously unrecognized external structures were revealed, including bowl-like objects decorating the outer membrane, arcades of hook-shaped proteins winding along the exterior and tufts of fibrils extending from the cell tips. Inside the periplasm, cone-like structures were found at each pole. Instead of the single peptidoglycan layer typical of other Gram-negative bacteria, two distinct periplasmic layers were observed. These layers formed a central open space that contained two flagella situated adjacent to each other. In some areas, the inner membrane formed flattened invaginations that protruded into the cytoplasm. High-speed light microscopic images of swimming T. primitia cells showed that cell bodies remained rigid and moved in a helical rather than planar motion. Together, these findings support the 'rolling cylinder' model for T. primitia motility that posits rotation of the protoplasmic cylinder within the outer sheath.", "date": "2008-03", "date_type": "published", "publication": "Molecular Microbiology", "volume": "67", "number": "6", "publisher": "Blackwell", "pagerange": "1184-1195", "id_number": "CaltechAUTHORS:MURmm08", "issn": "0950-382X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:MURmm08", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P01 G66521" }, { "agency": "NIH", "grant_number": "R01 AI067548" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02-04ER63785" }, { "agency": "Searle Scholars Program" }, { "agency": "NSF", "grant_number": "DEB-0321753" }, { "agency": "NSF", "grant_number": "EF-0523267" }, { "agency": "NIH", "grant_number": "AI016478" }, { "agency": "NIH", "grant_number": "F31 EB 004179" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "Agouron Institute" }, { "agency": "Gordon and Betty Moore Foundation" } ] }, "local_group": { "items": [ { "id": "Division-of-Geological-and-Planetary-Sciences" } ] }, "doi": "10.1111/j.1365-2958.2008.06120.x", "pmcid": "PMC3082362", "primary_object": { "basename": "sm003.mov", "url": "https://authors.library.caltech.edu/records/8krq9-1px22/files/sm003.mov" }, "related_objects": [ { "basename": "sm005.mov", "url": "https://authors.library.caltech.edu/records/8krq9-1px22/files/sm005.mov" }, { "basename": "sm008.pdf", "url": "https://authors.library.caltech.edu/records/8krq9-1px22/files/sm008.pdf" }, { "basename": "sm010.mov", "url": "https://authors.library.caltech.edu/records/8krq9-1px22/files/sm010.mov" }, { "basename": "sm001.pdf", "url": "https://authors.library.caltech.edu/records/8krq9-1px22/files/sm001.pdf" }, { "basename": "sm007.mov", "url": "https://authors.library.caltech.edu/records/8krq9-1px22/files/sm007.mov" }, { "basename": "sm009.mov", "url": "https://authors.library.caltech.edu/records/8krq9-1px22/files/sm009.mov" }, { "basename": "sm011.mov", "url": "https://authors.library.caltech.edu/records/8krq9-1px22/files/sm011.mov" }, { "basename": "nihms281761.pdf", "url": "https://authors.library.caltech.edu/records/8krq9-1px22/files/nihms281761.pdf" }, { "basename": "sm013.mov", "url": "https://authors.library.caltech.edu/records/8krq9-1px22/files/sm013.mov" }, { "basename": "sm002.mov", "url": "https://authors.library.caltech.edu/records/8krq9-1px22/files/sm002.mov" }, { "basename": "sm004.mov", "url": "https://authors.library.caltech.edu/records/8krq9-1px22/files/sm004.mov" }, { "basename": "sm006.mov", "url": "https://authors.library.caltech.edu/records/8krq9-1px22/files/sm006.mov" }, { "basename": "sm012.mov", "url": "https://authors.library.caltech.edu/records/8krq9-1px22/files/sm012.mov" }, { "basename": "sm014.mov", "url": "https://authors.library.caltech.edu/records/8krq9-1px22/files/sm014.mov" } ], "resource_type": "article", "pub_year": "2008", "author_list": "Murphy, Gavin E.; Matson, Eric G.; et el." }, { "id": "https://authors.library.caltech.edu/records/rs4rv-x5c71", "eprint_id": 24667, "eprint_status": "archive", "datestamp": "2023-08-19 21:28:23", "lastmod": "2023-10-23 23:34:21", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Li-Zhuo", "name": { "family": "Li", "given": "Zhuo" } }, { "id": "Trimble-M-J", "name": { "family": "Trimble", "given": "Michael J." } }, { "id": "Brun-Yves-V", "name": { "family": "Brun", "given": "Yves V." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "The structure of FtsZ filaments in vivo suggests a force-generating role in cell division", "ispublished": "pub", "full_text_status": "public", "keywords": "bacterial cytoskeleton, cell division, cryoelectron microscopy, FtsZ, tomography", "note": "\u00a9 2007 European Molecular Biology Organization. \n\nReceived: 25 May 2007; accepted: 26 September 2007; published online: 18 October 2007. \n\nWe thank H Jane Ding and David J Rosenman for computational help. This work was supported in part by NIH grant R01 AI067548 to GJJ, R01 GM51986 to YVB, DOE grant DE-FG02-04ER63785 to GJJ, a Searle Scholar Award to GJJ, the Beckman Institute at Caltech, and gifts to Caltech from the Gordon and Betty Moore Foundation and Agouron Institute.\n\nSupplemental Material - 7601895s1.pdf
Supplemental Material - LIZemboj07.mov
", "abstract": "In prokaryotes, FtsZ (the filamentous temperature sensitive protein Z) is a nearly ubiquitous GTPase that localizes in a ring at the leading edge of constricting plasma membranes during cell division. Here we report electron cryotomographic reconstructions of dividing Caulobacter crescentus cells wherein individual arc-like filaments were resolved just underneath the inner membrane at constriction sites. The filaments' position, orientation, time of appearance, and resistance to A22 all suggested that they were FtsZ. Predictable changes in the number, length, and distribution of filaments in cells where the expression levels and stability of FtsZ were altered supported that conclusion. In contrast to the thick, closed-ring-like structure suggested by fluorescence light microscopy, throughout the constriction process the Z-ring was seen here to consist of just a few short (~100 nm) filaments spaced erratically near the division site. Additional densities connecting filaments to the cell wall, occasional straight segments, and abrupt kinks were also seen. An 'iterative pinching' model is proposed wherein FtsZ itself generates the force that constricts the membrane in a GTP-hydrolysis-driven cycle of polymerization, membrane attachment, conformational change, depolymerization, and nucleotide exchange.", "date": "2007-11-14", "date_type": "published", "publication": "EMBO Journal", "volume": "26", "number": "22", "publisher": "European Molecular Biology Organization", "pagerange": "4694-4708", "id_number": "CaltechAUTHORS:20110803-153142337", "issn": "0261-4189", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110803-153142337", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 AI067548" }, { "agency": "NIH", "grant_number": "R01 GM51986" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02-04ER63785" }, { "agency": "Searle Scholar Award" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Agouron Institute" } ] }, "doi": "10.1038/sj.emboj.7601895", "pmcid": "PMC2080809", "primary_object": { "basename": "7601895s1.pdf", "url": "https://authors.library.caltech.edu/records/rs4rv-x5c71/files/7601895s1.pdf" }, "related_objects": [ { "basename": "LIZemboj07.mov", "url": "https://authors.library.caltech.edu/records/rs4rv-x5c71/files/LIZemboj07.mov" } ], "resource_type": "article", "pub_year": "2007", "author_list": "Li, Zhuo; Trimble, Michael J.; et el." }, { "id": "https://authors.library.caltech.edu/records/xznpz-zee63", "eprint_id": 24669, "eprint_status": "archive", "datestamp": "2023-08-19 21:02:19", "lastmod": "2023-10-23 23:34:27", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Murphy-G-E", "name": { "family": "Murphy", "given": "Gavin E." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Electron Cryotomography", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2007 BioTechniques. \n\nWe would like to thank Wolfgang Baumeister for allowing us to re-use Figure 1; Giovanni Cardone and Alasdair Steven for Figure 2E; and Ping Zhu, Ken Taylor and Kenneth Roux for Figure 2, F\u2013H. This work was supported in part by NIH grants no. P01 GM66521 and R01 AI067548 to G.J.J., DOE grant no. DE-FG02-04ER63785 to G.J.J., a Searle Scholar Award to G.J.J., NIH graduate fellowship F31 EB 004179 to G.E.M., and gifts to Caltech from the Ralph M. Parsons Foundation, the Agouron Institute, and the Gordon and Betty Moore Foundation.", "abstract": "Electron cryotomography is an emerging technique that allows the structures of unique biological objects such as individual macromolecules, viruses, and even small whole cells to be reconstructed in their near-native states in three dimensions (3-D) to an approximate 5-nm resolution. The required instrumentation, sample preparation and limitations, data collection, typical results, and future prospects are summarized briefly.", "date": "2007-10", "date_type": "published", "publication": "BioTechniques", "volume": "43", "number": "4", "publisher": "Informa Healthcare", "pagerange": "413-420", "id_number": "CaltechAUTHORS:20110803-161436056", "issn": "0736-6205", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110803-161436056", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "PO1 GM66521" }, { "agency": "NIH", "grant_number": "R01 AI067548" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02-04ER63785" }, { "agency": "Searle Scholar Award" }, { "agency": "NIH", "grant_number": "F31 EB 004179" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "Agouron Institute" }, { "agency": "Gordon and Betty Moore Foundation" } ] }, "resource_type": "article", "pub_year": "2007", "author_list": "Murphy, Gavin E. and Jensen, Grant J." }, { "id": "https://authors.library.caltech.edu/records/0kw7a-03v79", "eprint_id": 24666, "eprint_status": "archive", "datestamp": "2023-08-22 10:04:06", "lastmod": "2023-10-23 23:34:15", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Iancu-C-V", "name": { "family": "Iancu", "given": "Cristina V." }, "orcid": "0000-0002-7352-9226" }, { "id": "Ding-H-Jane", "name": { "family": "Ding", "given": "H. Jane" } }, { "id": "Morris-D-M", "name": { "family": "Morris", "given": "Dylan M." } }, { "id": "Dias-D-P", "name": { "family": "Dias", "given": "D. Prabha" } }, { "id": "Gonzales-A-D", "name": { "family": "Gonzales", "given": "Arlene D." } }, { "id": "Martino-A", "name": { "family": "Martino", "given": "Anthony" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "The Structure of Isolated Synechococcus Strain WH8102 Carboxysomes as Revealed by Electron Cryotomography", "ispublished": "pub", "full_text_status": "public", "keywords": "carboxysomes; electron cryotomography; bacterial ultrastructure; Calvin cycle", "note": "\u00a9 2007 Elsevier Ltd. \n\nReceived 3 February 2007; revised 25 May 2007; accepted 25 June 2007. Available online 29 June 2007. \n\nEdited by W. Baumeister. \n\nThis work was supported by NIH grants P01 GM66521 and R01 AI067548 (to G.J.J.), DOE grant DE-FG02-04ER63785 (to G.J.J.), a Searle Scholar Award (to G.J.J.), and gifts to Caltech from the Ralph M. Parsons Foundation, the Agouron Institute, and the Gordon and Betty Moore Foundation. We thank Dr Wolfgang Baumeister's group at the Max Planck Institute for Biochemistry for the most current version of the MolMatch template matching software and Dr Hong Zhuo for discussion of heterogeneity in the sizes of icosahedral viruses, and Dr. Todd Yeates for pointing out an error in our original calculation of T numbers. \n\nSupplementary data associated with this article\ncan be found, in the online version, at doi:10.1016/j.jmb.2007.06.059\n\nAccepted Version - nihms30376.pdf
Supplemental Material - IANjmb07video1.mov
Supplemental Material - IANjmb07video2.mov
", "abstract": "Carboxysomes are organelle-like polyhedral bodies found in cyanobacteria and many chemoautotrophic bacteria that are thought to facilitate carbon fixation. Carboxysomes are bounded by a proteinaceous outer shell and filled with ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO), the first enzyme in the CO_2 fixation pathway, but exactly how they enhance carbon fixation is unclear. Here we report the three-dimensional structure of purified carboxysomes from Synechococcus species strain WH8102 as revealed by electron cryotomography. We found that while the sizes of individual carboxysomes in this organism varied from 114 nm to 137 nm, surprisingly, all were approximately icosahedral. There were on average ~250 RuBisCOs per carboxysome, organized into three to four concentric layers. Some models of carboxysome function depend on specific contacts between individual RuBisCOs and the shell, but no evidence of such contacts was found: no systematic patterns of connecting densities or RuBisCO positions against the shell's presumed hexagonal lattice could be discerned, and simulations showed that packing forces alone could account for the layered organization of RuBisCOs.", "date": "2007-09-21", "date_type": "published", "publication": "Journal of Molecular Biology", "volume": "372", "number": "3", "publisher": "Elsevier", "pagerange": "764-773", "id_number": "CaltechAUTHORS:20110803-151551421", "issn": "0022-2836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110803-151551421", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "PO1 GM665211" }, { "agency": "NIH", "grant_number": "R01 AI067548" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02-04ER63785" }, { "agency": "Searle Scholars Program" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "Agouron Institute" }, { "agency": "Gordon and Betty Moore Foundation" } ] }, "doi": "10.1016/j.jmb.2007.06.059", "pmcid": "PMC2453779", "primary_object": { "basename": "IANjmb07video1.mov", "url": "https://authors.library.caltech.edu/records/0kw7a-03v79/files/IANjmb07video1.mov" }, "related_objects": [ { "basename": "IANjmb07video2.mov", "url": "https://authors.library.caltech.edu/records/0kw7a-03v79/files/IANjmb07video2.mov" }, { "basename": "nihms30376.pdf", "url": "https://authors.library.caltech.edu/records/0kw7a-03v79/files/nihms30376.pdf" } ], "resource_type": "article", "pub_year": "2007", "author_list": "Iancu, Cristina V.; Ding, H. Jane; et el." }, { "id": "https://authors.library.caltech.edu/records/4zhh5-cww77", "eprint_id": 9469, "eprint_status": "archive", "datestamp": "2023-08-22 09:45:30", "lastmod": "2023-10-16 22:18:39", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Henderson-G-P", "name": { "family": "Henderson", "given": "Gregory P." } }, { "id": "Gan-Lu", "name": { "family": "Gan", "given": "Lu" }, "orcid": "0000-0002-8685-4896" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "3-D Ultrastructure of O. tauri: Electron Cryotomography of an Entire Eukaryotic Cell", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2007 Henderson et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. \n\nReceived: May 21, 2007; Accepted: July 16, 2007; Published: August 15, 2007. \n\nWe thank Herv\u00e9 Moreau (Observatoire Oc\u00e9anologique, Laboratoire Arago) and Brian Palenik (Scripps Institution of Oceanography) for helping us obtain and work with O. tauri cultures and for reading the manuscript, Kent L. McDonald (U.C. Berkeley) for help high-pressure freezing, Wolfgang Baumeister's group (Max Planck Institute for Biochemistry) for the most current version of the MolMatch software, Andrea Manuell for discussions on the chloroplast, Christian Suloway (Caltech) for assistance with Leginon and Jane Ding (Caltech) for help running the cross-correlation search on the supercomputer. \n\nAuthor Contributions: Conceived and designed the experiments: GJ GH LG. Performed the experiments: GH LG. Analyzed the data: GH LG. Contributed reagents/materials/analysis tools: GJ. Wrote the paper: GJ GH LG. \n\nFunding: This work was supported in part by NIH grants R01 AI067548 and PO1 GM66521 and DOE grant DE-FG02-04ER63785 to GJJ, a Searle Scholar Award to GJJ, the Beckman Institute at Caltech, and gifts to Caltech from the Gordon and Betty Moore Foundation and Agouron Institute. Lu Gan was supported by a fellowship from the Damon Runyon Cancer Research Foundation (DRG-1940-07). These sponsors/funders had no role in the design and conduct of the study, in the collection, analysis, and interpretation of the data, and in the preparation, review, or approval of the manuscript. \n\nCompeting interests: The authors have declared that no competing interests exist.\n\nPublished - HENplosone07.pdf
", "abstract": "The hallmark of eukaryotic cells is their segregation of key biological functions into discrete, membrane-bound organelles. Creating accurate models of their ultrastructural complexity has been difficult in part because of the limited resolution of light microscopy and the artifact-prone nature of conventional electron microscopy. Here we explored the potential of the emerging technology electron cryotomography to produce three-dimensional images of an entire eukaryotic cell in a near-native state. Ostreococcus tauri was chosen as the specimen because as a unicellular picoplankton with just one copy of each organelle, it is the smallest known eukaryote and was therefore likely to yield the highest resolution images. Whole cells were imaged at various stages of the cell cycle, yielding 3-D reconstructions of complete chloroplasts, mitochondria, endoplasmic reticula, Golgi bodies, peroxisomes, microtubules, and putative ribosome distributions in-situ. Surprisingly, the nucleus was seen to open long before mitosis, and while one microtubule (or two in some predivisional cells) was consistently present, no mitotic spindle was ever observed, prompting speculation that a single microtubule might be sufficient to segregate multiple chromosomes.", "date": "2007-08-15", "date_type": "published", "publication": "PLoS ONE", "volume": "2", "number": "8", "publisher": "Public Library of Science", "pagerange": "Art. No. e749", "id_number": "CaltechAUTHORS:HENplosone07", "issn": "1932-6203", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:HENplosone07", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1371/journal.pone.0000749", "pmcid": "PMC1939878", "primary_object": { "basename": "HENplosone07.pdf", "url": "https://authors.library.caltech.edu/records/4zhh5-cww77/files/HENplosone07.pdf" }, "resource_type": "article", "pub_year": "2007", "author_list": "Henderson, Gregory P.; Gan, Lu; et el." }, { "id": "https://authors.library.caltech.edu/records/0qvff-k2k46", "eprint_id": 24664, "eprint_status": "archive", "datestamp": "2023-08-19 20:03:10", "lastmod": "2023-10-23 23:33:46", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wright-E-R", "name": { "family": "Wright", "given": "Elizabeth R." } }, { "id": "Schooler-J-B", "name": { "family": "Schooler", "given": "Jordan B." } }, { "id": "Ding-H-Jane", "name": { "family": "Ding", "given": "H. Jane" } }, { "id": "Kieffer-C", "name": { "family": "Kieffer", "given": "Collin" }, "orcid": "0000-0001-9051-3819" }, { "id": "Fillmore-C", "name": { "family": "Fillmore", "given": "Christopher" } }, { "id": "Sundquist-W-I", "name": { "family": "Sundquist", "given": "Wesley I." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Electron cryotomography of immature HIV-1 virions reveals the structure of the CA and SP1 Gag shells", "ispublished": "pub", "full_text_status": "public", "keywords": "electron cryotomography, Gag, human immunodeficiency virus type 1 (HIV-1), spacer peptide 1 (SP1)", "note": "\u00a9 2007 European Molecular Biology Organization. \n\nReceived: 3 January 2007; accepted: 5 March 2007; published online: 29 March 2007. \n\nThis work was supported in part by NIH Grant PO1 GM66521 (to WIS and GJJ), NIH Grant A145405 (to WIS), NIH Grant F32 GM075543 (to ERW), the Beckman Institute at Caltech, and gifts to Caltech from the Ralph M Parsons Foundation, the Agouron Institute, and the Gordon and Betty Moore Foundation. \n\nSupplementary data are available at The EMBO Journal Online (http://www.embojournal.org).\n\nSupplemental Material - WRIemboj07.mov
", "abstract": "The major structural elements of retroviruses are contained in a single polyprotein, Gag, which in human immunodeficiency virus type 1 (HIV-1) comprises the MA, CA, spacer peptide 1 (SP1), NC, SP2, and p6 polypeptides. In the immature HIV-1 virion, the domains of Gag are arranged radially with the N-terminal MA domain at the membrane and C-terminal NC-SP2-p6 region nearest to the center. Here, we report the three-dimensional structures of individual immature HIV-1 virions, as obtained by electron cryotomography. The concentric shells of the Gag polyprotein are clearly visible, and radial projections of the different Gag layers reveal patches of hexagonal order within the CA and SP1 shells. Averaging well-ordered unit cells leads to a model in which each CA hexamer is stabilized by a bundle of six SP1 helices. This model suggests why the SP1 spacer is essential for assembly of the Gag lattice and how cleavage between SP1 and CA acts as a structural switch controlling maturation.", "date": "2007-04-18", "date_type": "published", "publication": "EMBO Journal", "volume": "26", "number": "8", "publisher": "European Molecular Biology Organization", "pagerange": "2218-2226", "id_number": "CaltechAUTHORS:20110803-142323319", "issn": "0261-4189", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110803-142323319", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "PO1 GM66521" }, { "agency": "NIH", "grant_number": "A145405" }, { "agency": "NIH Postdoctoral Fellowship", "grant_number": "F32 GM075543" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "Agouron Institute" }, { "agency": "Gordon and Betty Moore Foundation" } ] }, "doi": "10.1038/sj.emboj.7601664", "pmcid": "PMC1852790", "primary_object": { "basename": "WRIemboj07.mov", "url": "https://authors.library.caltech.edu/records/0qvff-k2k46/files/WRIemboj07.mov" }, "resource_type": "article", "pub_year": "2007", "author_list": "Wright, Elizabeth R.; Schooler, Jordan B.; et el." }, { "id": "https://authors.library.caltech.edu/records/q9taf-4jq53", "eprint_id": 24665, "eprint_status": "archive", "datestamp": "2023-08-19 19:55:55", "lastmod": "2023-10-23 23:33:50", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" } ] }, "title": "How electron cryotomography is opening a new window onto prokaryotic ultrastructure", "ispublished": "pub", "full_text_status": "restricted", "note": "Copyright \u00a9 2006 Elsevier. \n\nAvailable online 29th March 2007. \n\nWe wish to thank Gavin Murphy for Figure 4 and D Prabha Dias for critiquing the manuscript. This work was supported in part by National Institutes of Health grants P01 GM66521 and R01 AI067548 to GJJ, Department of the Environment grant DE-FG02-04ER63785 to GJJ, a Searle Scholar Award to GJJ, the Gosney fellowship to AB, and gifts to Caltech from the Ralph M Parsons Foundation, the Agouron Institute, and the Gordon and Betty Moore Foundation. \n\nThis review comes from a themed issue on Macromolecular assemblages; Edited by Eva Nogales and Wesley I Sundquist.", "abstract": "Electron cryotomography is an emerging technology that enables thin samples, including small intact prokaryotic cells, to be imaged in three dimensions in a near-native 'frozen-hydrated' state to a resolution sufficient to recognize very large macromolecular complexes in situ. Following years of visionary technology development by a few key pioneers, several laboratories are now using the technique to produce biological results of major significance in the field of prokaryotic ultrastructure. Recent discoveries have included the surprising generality and complexity of the cytoskeleton, the connectivity of key membrane compartments, the location and architecture of large macromolecular machines such as the ribosome and flagellar motors, and the structure of some extraordinary external appendages. Through further technology development, identification of the most revealing model systems and sustained effort, electron cryotomography is poised to help resolve many fundamentally important questions about prokaryotic ultrastructure.", "date": "2007-04", "date_type": "published", "publication": "Current Opinion in Structural Biology", "volume": "17", "number": "2", "publisher": "Elsevier", "pagerange": "260-267", "id_number": "CaltechAUTHORS:20110803-144316990", "issn": "0959-440X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110803-144316990", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "PO1 GM66521" }, { "agency": "NIH", "grant_number": "R01 AI067548" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02-04ER63785" }, { "agency": "Searle Scholars Program" }, { "agency": "Gosney Postdoctoral Fellowship" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "Agouron Institute" }, { "agency": "Gordon and Betty Moore Foundation" } ] }, "doi": "10.1016/j.sbi.2007.03.002", "resource_type": "article", "pub_year": "2007", "author_list": "Jensen, Grant J. and Briegel, Ariane" }, { "id": "https://authors.library.caltech.edu/records/g58t4-5mn44", "eprint_id": 24663, "eprint_status": "archive", "datestamp": "2023-08-19 19:35:59", "lastmod": "2023-10-23 23:33:42", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Burns-D-G", "name": { "family": "Burns", "given": "David G." } }, { "id": "Janssen-P-H", "name": { "family": "Janssen", "given": "Peter H." } }, { "id": "Itoh-Takashi", "name": { "family": "Itoh", "given": "Takashi" } }, { "id": "Kamekura-Masahiro", "name": { "family": "Kamekura", "given": "Masahiro" } }, { "id": "Li-Zhuo", "name": { "family": "Li", "given": "Zhuo" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Rodr\u00edguez-Valera-F", "name": { "family": "Rodr\u00edguez-Valera", "given": "Francisco" } }, { "id": "Bolhuis-H", "name": { "family": "Bolhuis", "given": "Henk" } }, { "id": "Dyall-Smith-M-L", "name": { "family": "Dyall-Smith", "given": "Mike L." } } ] }, "title": "Haloquadratum walsbyi gen. nov., sp. nov., the square haloarchaeon of Walsby, isolated from saltern crystallizers in Australia and Spain", "ispublished": "pub", "full_text_status": "restricted", "note": "Copyright \u00a9 2007 International Union of Microbiological Societies. \n\nThe authors thank Professor Dr Hans G. Tr\u00fcper for his advice\nregarding nomenclature. We thank Dr Jane Ding for her help in writing\na module of measuring the distance between membrane layers. D. G. B.\nwas supported by an Australian Post-graduate Award. M. L. D.-S. was\nsupported by a University of Melbourne MRGS award in 2005 and by\nthe Department of Microbiology and Immunology. G. J. was supported\nby NIH grant R01 AI067548. H. B. was supported by a grant from the\nNetherlands Organization of Science NWO/ALW/NPP-851.20.023. \n\nThe GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of isolates C23^T and HBSQ001 are respectively AY676200 and AM180088.", "abstract": "Strains C23^T and HBSQ001 were isolated from solar salterns and are novel square-shaped, aerobic, extremely halophilic members of the domain Archaea and family Halobacteriaceae. Cells stained Gram-negative and grew optimally in media containing 18\u200a% salts at around neutral pH. Mg^(2+) is not required. The DNA G+C content of both isolates was 46.9\u2005mol% and DNA\u2013DNA cross-hybridization showed a relatedness of 80\u200a%. Their 16S rRNA gene sequences showed only 2\u2005nucleotide differences (99.9\u200a% identity) and phylogenetic tree reconstructions with other recognized members of the Halobacteriaceae indicated that they formed a distinct clade, with the closest relative being Halogeometricum borinquense PR 3^T (91.2\u200a% sequence identity). The major polar glycolipid of both isolates was the sulfated diglycosyl diether lipid S-DGD-1. Electron cryomicrosopy of whole cells revealed similar internal structures, such as gas vesicles and polyhydroxyalkanoate granules, but the cell wall of isolate HBSQ001 displayed a more complex S-layer compared with that of isolate C23^T. The phenotypic characterization and phylogenetic data support the placement of isolates C23^T and HBSQ001 in a novel species in a new genus within the Halobacteriaceae, for which we propose the name Haloquadratum walsbyi gen. nov., sp. nov. The type strain of Haloquadratum walsbyi is C23^T (=JCM 12705^T=DSM 16854^T).", "date": "2007-02", "date_type": "published", "publication": "International Journal of Systematic and Evolutionary Microbiology", "volume": "57", "number": "2", "publisher": "International Union of Microbiological Societies", "pagerange": "387-392", "id_number": "CaltechAUTHORS:20110803-134318931", "issn": "1466-5026", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110803-134318931", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Australian Post-graduate Award" }, { "agency": "University of Melbourne" }, { "agency": "NIH", "grant_number": "R01 AI067548" }, { "agency": "Netherlands Organization of Science", "grant_number": "NWO/ALW/NPP-851.20.023" } ] }, "doi": "10.1099/ijs.0.64690-0", "resource_type": "article", "pub_year": "2007", "author_list": "Burns, David G.; Janssen, Peter H.; et el." }, { "id": "https://authors.library.caltech.edu/records/2sb47-sh915", "eprint_id": 12817, "eprint_status": "archive", "datestamp": "2023-08-19 19:25:38", "lastmod": "2023-10-17 20:56:31", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "A nanoengine for gliding motility", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2006 The Author. Journal compilation \u00a9 2006 Blackwell Publishing Ltd. \n\nAccepted 30 October, 2006. Published Online: 9 November 2006. \n\nThe author thanks Dylan Morris, Gregory Henderson, Duncan Krause and Tony Pugsley for comments on the draft and Everett Kane for creating the figure. G.J. acknowledges funding by the NIH, DOE and the Searle Foundation.", "abstract": "The terminal organelle present in some mycoplasma species is a very large, complex, flexible structure involved in cell adherence, motility and cell division. In this issue of Molecular Microbiology, Hasselbring and Krause report on a mutant in which the terminal organelle is only weakly connected to the rest of the cell. 'Run-away' terminal organelles first stretch the cells, then break away and continue moving independently for more than half an hour. This remarkable observation proves that the 'nanoengine' driving motility is indeed associated with the terminal organelle, and opens up new opportunities for dissecting and understanding its mechanism.", "date": "2007-01", "date_type": "published", "publication": "Molecular Microbiology", "volume": "63", "number": "1", "publisher": "Blackwell Publishing", "pagerange": "4-6", "id_number": "CaltechAUTHORS:JENmm07", "issn": "0950-382X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:JENmm07", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Institutes of Health" }, { "agency": "Department of Energy" }, { "agency": "Searle Scholars Program" } ] }, "doi": "10.1111/j.1365-2958.2006.05508.x", "resource_type": "article", "pub_year": "2007", "author_list": "Jensen, Grant J." }, { "id": "https://authors.library.caltech.edu/records/4e0z3-q5n96", "eprint_id": 24662, "eprint_status": "archive", "datestamp": "2023-08-19 18:58:39", "lastmod": "2023-10-23 23:33:37", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Iancu-C-V", "name": { "family": "Iancu", "given": "Cristina V." }, "orcid": "0000-0002-7352-9226" }, { "id": "Tivol-W-F", "name": { "family": "Tivol", "given": "William F." } }, { "id": "Schooler-J-B", "name": { "family": "Schooler", "given": "Jordan B." } }, { "id": "Dias-D-P", "name": { "family": "Dias", "given": "D. Prabha" } }, { "id": "Henderson-G-P", "name": { "family": "Henderson", "given": "Gregory P." } }, { "id": "Murphy-G-E", "name": { "family": "Murphy", "given": "Gavin E." } }, { "id": "Wright-E-R", "name": { "family": "Wright", "given": "Elizabeth R." } }, { "id": "Li-Zhuo", "name": { "family": "Li", "given": "Zhuo" } }, { "id": "Yu-Zhiheng", "name": { "family": "Yu", "given": "Zhiheng" } }, { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Gan-Lu", "name": { "family": "Gan", "given": "Lu" }, "orcid": "0000-0002-8685-4896" }, { "id": "He-Yongning", "name": { "family": "He", "given": "Yongning" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Electron cryotomography sample preparation using the Vitrobot", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2006 Nature Publishing Group. \n\nPublished online: 18 January 2007. \n\nThe authors declare no competing financial interests.\n\nSupplemental Material - IANnp06fig1.jpg
", "abstract": "Electron cryotomography is the highest-resolution structural technique currently available that can be applied to unique objects such as flexible large protein complexes, irregular viruses, organelles and small cells. Specimens are preserved in a near-native, 'frozen-hydrated' state by vitrification. The thickness of the vitreous ice must be optimized for each specimen, and gold fiducials are typically added to facilitate image alignment. Here, we describe in detail our protocols for electron cryotomography sample preparation including (i) introduction of fiducial markers into the sample and (ii) sample vitrification. Because we almost exclusively use an automated, climate-controlled plunge-freezing device (the FEI Vitrobot) to vitrify our samples, we discuss its operation and parameters in detail. A session in which eight grids are prepared takes 1.5\u20132 h.", "date": "2006-12", "date_type": "published", "publication": "Nature Protocols", "volume": "1", "number": "6", "publisher": "Nature Publishing Group", "pagerange": "2813-2819", "id_number": "CaltechAUTHORS:20110803-133119203", "issn": "1754-2189", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110803-133119203", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1038/nprot.2006.432", "primary_object": { "basename": "IANnp06fig1.jpg", "url": "https://authors.library.caltech.edu/records/4e0z3-q5n96/files/IANnp06fig1.jpg" }, "related_objects": [ { "basename": "medium.png", "url": "https://authors.library.caltech.edu/records/4e0z3-q5n96/files/medium.png" }, { "basename": "small.png", "url": "https://authors.library.caltech.edu/records/4e0z3-q5n96/files/small.png" } ], "resource_type": "article", "pub_year": "2006", "author_list": "Iancu, Cristina V.; Tivol, William F.; et el." }, { "id": "https://authors.library.caltech.edu/records/pk4c0-ftz37", "eprint_id": 22359, "eprint_status": "archive", "datestamp": "2023-08-19 18:40:08", "lastmod": "2023-10-23 15:53:24", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Briegel-Ariane", "name": { "family": "Briegel", "given": "Ariane" }, "orcid": "0000-0003-3733-3725" }, { "id": "Prabha-Dias-D", "name": { "family": "Prabha-Dias", "given": "D." } }, { "id": "Li-Zhuo", "name": { "family": "Li", "given": "Zhuo" } }, { "id": "Jensen-R-B", "name": { "family": "Jensen", "given": "Rasmus B." } }, { "id": "Frangakis-A-S", "name": { "family": "Frangakis", "given": "Achilleas S." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Multiple large filament bundles observed in Caulobacter crescentus by electron cryotomography", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2006 The Authors. Journal compilation \u00a9 2006 Blackwell Publishing Ltd. \n\nAccepted 27 July, 2006. Article first published online: 29 Aug. 2006. \n\nThe authors thank Christine Jacobs-Wagner for the crescentin knockout strains and discussions and L. Shapiro and Z. Gitai for discussions. This work was supported in part by NIH Grants P01 G66521 and R01 AI067548 to G.J.J., DOE Grant\nDE-FG02\u201304ER63785 to G.J.J., a Searle Scholar Award to\nG.J.J., a grant from the Danish Natural Sciences Research\nCouncil to R.B.J., and gifts to Caltech from the Ralph M.\nParsons Foundation, the Agouron Institute, and the Gordon\nand Betty Moore Foundation.\n\nSupplemental Material - MMI5355MovieS1.mp4
Supplemental Material - MMI5355MovieS2.mp4
Supplemental Material - MMI5355MovieS3.mp4
", "abstract": "While the absence of any cytoskeleton was once recognized as a distinguishing feature of prokaryotes, it is now clear that a number of different bacterial proteins do form filaments in vivo. Despite the critical roles these proteins play in cell shape, genome segregation and cell division, molecular mechanisms have remained obscure in part for lack of electron microscopy-resolution images where these filaments can be seen acting within their cellular context. Here, electron cryotomography was used to image the widely studied model prokaryote Caulobacter crescentus in an intact, near-native state, producing three-dimensional reconstructions of these cells with unprecedented clarity and fidelity. We observed many instances of large filament bundles in various locations throughout the cell and at different stages of the cell cycle. The bundles appear to fall into four major classes based on shape and location, referred to here as 'inner curvature', 'cytoplasmic', 'polar' and 'ring-like'. In an attempt to identify at least some of the filaments, we imaged cells where crescentin and MreB filaments would not be present. The inner curvature and cytoplasmic bundles persisted, which together with their localization patterns, suggest that they are composed of as-yet unidentified cytoskeletal proteins. Thus bacterial filaments are frequently found as bundles, and their variety and abundance is greater than previously suspected.", "date": "2006-10", "date_type": "published", "publication": "Molecular Microbiology", "volume": "62", "number": "1", "publisher": "Blackwell", "pagerange": "5-14", "id_number": "CaltechAUTHORS:20110217-125744917", "issn": "0950-382X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110217-125744917", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P01 G66521" }, { "agency": "NIH", "grant_number": "R01 AI067548" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02\u201304ER63785" }, { "agency": "Danish Natural Sciences Research Council" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "Agouron Institute" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Searle Scholars Program" } ] }, "doi": "10.1111/j.1365-2958.2006.05355.x", "primary_object": { "basename": "MMI5355MovieS1.mp4", "url": "https://authors.library.caltech.edu/records/pk4c0-ftz37/files/MMI5355MovieS1.mp4" }, "related_objects": [ { "basename": "MMI5355MovieS2.mp4", "url": "https://authors.library.caltech.edu/records/pk4c0-ftz37/files/MMI5355MovieS2.mp4" }, { "basename": "MMI5355MovieS3.mp4", "url": "https://authors.library.caltech.edu/records/pk4c0-ftz37/files/MMI5355MovieS3.mp4" } ], "resource_type": "article", "pub_year": "2006", "author_list": "Briegel, Ariane; Prabha-Dias, D.; et el." }, { "id": "https://authors.library.caltech.edu/records/1rdb9-atj62", "eprint_id": 24661, "eprint_status": "archive", "datestamp": "2023-08-22 06:24:18", "lastmod": "2023-10-23 23:33:33", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Murphy-G-E", "name": { "family": "Murphy", "given": "Gavin E." } }, { "id": "Leadbetter-J-R", "name": { "family": "Leadbetter", "given": "Jared R." }, "orcid": "0000-0002-7033-0844" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "In situ structure of the complete Treponema primitia flagellar motor", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2006 Nature Publishing Group. \n\nReceived 7 April 2006; Accepted 21 June 2006; Published online 2 August 2006. \n\nWe thank E. Matson for growing the T. primitia cultures. This work was supported, in part, by NIH grants to G.J.J., a DOE grant to G.J.J., a Searle Scholar Award to G.J.J., an NSF grant to J.R.L., an NIH graduate fellowship to G.E.M., and gifts to Caltech from the Ralph M. Parsons Foundation, the Agouron Institute, and the Gordon and Betty Moore Foundation. \n\nAuthor Contributions: G.E.M. collected and analysed the data, and drafted the text and figures; J.R.L. provided cells and discourse; and G.J.J. guided the research and manuscript editing throughout. \n\nAuthor Information: The averaged and symmetrized structure has been deposited in the EM Data Bank (http://www.ebi.ac.uk/msd/index.html) with the accession code EMD-1235. \n\nCompeting interests statement: The authors declare no competing financial interests. \n\nSupplementary information accompanies this paper.\n\nSupplemental Material - MURn06s1.pdf
Supplemental Material - MURn06s2.mov
", "abstract": "The bacterial flagellar motor is an amazing nanomachine: built from approximately 25 different proteins, it uses an electrochemical ion gradient to drive rotation at speeds of up to 300\u2009Hz (refs 1, 2). The flagellar motor consists of a fixed, membrane-embedded, torque-generating stator and a typically bidirectional, spinning rotor that changes direction in response to chemotactic signals. Most structural analyses so far have targeted the purified rotor (refs 3, 4), and hence little is known about the stator and its interactions. Here we show, using electron cryotomography of whole cells, the in situ structure of the complete flagellar motor from the spirochaete Treponema primitia at 7\u2009nm resolution. Twenty individual motor particles were computationally extracted from the reconstructions, aligned and then averaged. The stator assembly, revealed for the first time, possessed 16-fold symmetry and was connected directly to the rotor, C ring and a novel P-ring-like structure. The unusually large size of the motor suggested mechanisms for increasing torque and supported models wherein critical interactions occur atop the C ring, where our data suggest that both the carboxy-terminal and middle domains of FliG are found.", "date": "2006-08-31", "date_type": "published", "publication": "Nature", "volume": "442", "number": "7106", "publisher": "Nature Publishing Group", "pagerange": "1062-1064", "id_number": "CaltechAUTHORS:20110803-131941991", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110803-131941991", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH" }, { "agency": "Department of Energy (DOE)" }, { "agency": "Searle Scholars Program" }, { "agency": "NSF" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "Agouron Institute" }, { "agency": "Gordon and Betty Moore Foundation" } ] }, "local_group": { "items": [ { "id": "Division-of-Geological-and-Planetary-Sciences" } ] }, "doi": "10.1038/nature05015", "primary_object": { "basename": "MURn06s2.mov", "url": "https://authors.library.caltech.edu/records/1rdb9-atj62/files/MURn06s2.mov" }, "related_objects": [ { "basename": "MURn06s1.pdf", "url": "https://authors.library.caltech.edu/records/1rdb9-atj62/files/MURn06s1.pdf" } ], "resource_type": "article", "pub_year": "2006", "author_list": "Murphy, Gavin E.; Leadbetter, Jared R.; et el." }, { "id": "https://authors.library.caltech.edu/records/kbs9p-q7v19", "eprint_id": 3529, "eprint_status": "archive", "datestamp": "2023-08-22 05:25:15", "lastmod": "2023-10-16 15:58:13", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Henderson-G-P", "name": { "family": "Henderson", "given": "Gregory P." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Three-dimensional structure of Mycoplasma pneumoniae's attachment organelle and a model for its role in gliding motility", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2006 The Authors. \n\nAccepted 7 February, 2006. \n\nThis work was supported in part by NIH Grant P01 G66521 to G.J.J., DOE Grant DE-FG02-04ER63785 to G.J.J., a Searle Scholar Award to G.J.J., and gifts to Caltech from the Ralph M. Parsons Foundation, the Agouron Institute, and the Gordon and Betty Moore Foundation. We thank Duncan C. Krause of the University of Georgia for providing M. pneumoniae M129, for repeated discussions, for sharing unpublished data, and for his reading of the manuscript.\n\nPublished - HENmm06.pdf
", "abstract": "While most motile bacteria propel themselves with flagella, other mechanisms have been described including retraction of surface-attached pili, secretion of polysaccharides, or movement of motors along surface protein tracks. These have been referred to collectively as forms of 'gliding' motility. Despite being simultaneously one of the smallest and simplest of all known cells, Mycoplasma pneumoniae builds a surprisingly large and complex cell extension known as the attachment organelle that enables it to glide. Here, three-dimensional images of the attachment organelle were produced with unprecedented clarity and authenticity using state-of-the-art electron cryotomography. The attachment organelle was seen to contain a multisubunit, jointed, dynamic motor much larger than a flagellar basal body and comparable in complexity. A new model for its function is proposed wherein inchworm-like conformational changes of its electron-dense core are leveraged against a cytoplasmic anchor and transmitted to the surface through layered adhesion proteins.", "date": "2006-04", "date_type": "published", "publication": "Molecular Microbiology", "volume": "60", "number": "2", "publisher": "Blackwell", "pagerange": "376-385", "id_number": "CaltechAUTHORS:HENmm06", "issn": "0950-382X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:HENmm06", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P01 G66521" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02-04ER63785" }, { "agency": "Searle Scholars Program" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "Agouron Institute" }, { "agency": "Gordon and Betty Moore Foundation" } ] }, "doi": "10.1111/j.1365-2958.2006.05113.x", "primary_object": { "basename": "HENmm06.pdf", "url": "https://authors.library.caltech.edu/records/kbs9p-q7v19/files/HENmm06.pdf" }, "resource_type": "article", "pub_year": "2006", "author_list": "Henderson, Gregory P. and Jensen, Grant J." }, { "id": "https://authors.library.caltech.edu/records/ghc9b-0bx50", "eprint_id": 24645, "eprint_status": "archive", "datestamp": "2023-08-19 17:27:03", "lastmod": "2023-10-23 23:32:26", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ackerson-C-J", "name": { "family": "Ackerson", "given": "Christopher J." } }, { "id": "Jadzinsky-P-D", "name": { "family": "Jadzinsky", "given": "Pablo D." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Kronberg-R-D", "name": { "family": "Kornberg", "given": "Roger D." } } ] }, "title": "Rigid, Specific, and Discrete Gold Nanoparticle/Antibody Conjugates", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2006 American Chemical Society. \n\nReceived August 28, 2005. Publication Date (Web): February 2, 2006. \n\nWe thank Christopher Chidsey for many helpful discussions. pGC-NC10 was a kind gift from Olan Dolezal. C.J.A. received support from NIH training grant T32 GM0829. This research was supported by NIH grants AI21144 and NIH GM63025.\n\nSupplemental Material - ja0555668si20050815_124012.jpg
", "abstract": "A general method of rigid, specific labeling of proteins with gold clusters has been devised. The method relies on the conjugation of a glutathione monolayer-protected gold cluster (MPC) with a single chain Fv antibody fragment (scFv), mutated to present an exposed cysteine residue. Efficient formation of a gold\u2212thiolate bond between the MPC and scFv depends on activation of the gold cluster by chemical oxidation. Once formed, the MPC\u2212scFv conjugate is treated with a reductant to quench cluster reactivity. The procedure has been performed with an MPC with an average Au71 core and an scFv directed against a tetrameric protein, the influenza neuraminidase. A complex of the MPC\u2212scFv conjugate with the neuraminidase was isolated, and the presence of four gold clusters was verified by cryoelectron microscopy.", "date": "2006-03-01", "date_type": "published", "publication": "Journal of the American Chemical Society", "volume": "128", "number": "8", "publisher": "American Chemical Society", "pagerange": "2635-2640", "id_number": "CaltechAUTHORS:20110803-092706578", "issn": "0002-7863", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110803-092706578", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32 GM0829" }, { "agency": "NIH", "grant_number": "AI21144" }, { "agency": "NIH", "grant_number": "GM63025" } ] }, "doi": "10.1021/ja0555668", "primary_object": { "basename": "ja0555668si20050815_124012.jpg", "url": "https://authors.library.caltech.edu/records/ghc9b-0bx50/files/ja0555668si20050815_124012.jpg" }, "resource_type": "article", "pub_year": "2006", "author_list": "Ackerson, Christopher J.; Jadzinsky, Pablo D.; et el." }, { "id": "https://authors.library.caltech.edu/records/jddnq-1s307", "eprint_id": 24659, "eprint_status": "archive", "datestamp": "2023-08-22 05:16:08", "lastmod": "2023-10-23 23:33:26", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Iancu-C-V", "name": { "family": "Iancu", "given": "Cristina V." }, "orcid": "0000-0002-7352-9226" }, { "id": "Wright-E-R", "name": { "family": "Wright", "given": "Elizabeth R." } }, { "id": "Heymann-J-B", "name": { "family": "Heymann", "given": "J. Bernard" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "A comparison of liquid nitrogen and liquid helium as cryogens for electron cryotomography", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Electron cryomicroscopy; Tomography; Helium cooling; Radiation damage; CryoEM", "note": "\u00a9 2006 Elsevier Inc. \n\nReceived 29 June 2005; received in revised form 16 November 2005; accepted 7 December 2005. Available online 4 January 2006. \n\nWe thank Y. He for providing liposomes; T. Wagenknecht and J. Berkowitz for pyruvate dehydrogenase; J. Benjamin, P. Leong, and J. Ding for help with data collection and image processing; and W. Tivol for reading the manuscript. This work was supported in part by NIH Grant PO1 GM66521 to G.J.J., DOE Grant DE-FG02-04ER63785 to G.J.J., a Searle Scholar Award to G.J.J., the Beckman Institute at Caltech, and gifts to Caltech from the Ralph M. Parsons Foundation, the Agouron Institute, and the Gordon and Betty Moore Foundation.", "abstract": "The principal resolution limitation in electron cryomicroscopy of frozen-hydrated biological samples is radiation damage. It has long been hoped that cooling such samples to just a few kelvins with liquid helium would slow this damage and allow statistically better-defined images to be recorded. A new \"G2 Polara\" microscope from FEI Company was used to image various biological samples cooled by either liquid nitrogen or liquid helium to ~82 or ~12 K, respectively, and the results were compared with particular interest in the doses (10\u2013200 e^\u2212/\u00c5^2) and resolutions (3\u20138 nm) typical for electron cryotomography. Simple dose series revealed a gradual loss of contrast at ~12 K through the first several tens of e^\u2212/\u00c5^2, after which small bubbles appeared. Single particle reconstructions from each image in a dose series showed no difference in the preservation of medium-resolution (3\u20135 nm) structural detail at the two temperatures. Tomographic reconstructions produced with total doses between 10 and 350 e^\u2212/\u00c5^2 showed better results at ~82K than ~12 K for every dose tested. Thus disappointingly, cooling with liquid helium is actually disadvantageous for cryotomography.", "date": "2006-03", "date_type": "published", "publication": "Journal of Structural Biology", "volume": "153", "number": "3", "publisher": "Elsevier", "pagerange": "231-240", "id_number": "CaltechAUTHORS:20110803-124019191", "issn": "1047-8477", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110803-124019191", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "PO1 GM66521" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02-04ER63785" }, { "agency": "Searle Scholars Program" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "Agouron Institute" }, { "agency": "Gordon and Betty Moore Foundation" } ] }, "doi": "10.1016/j.jsb.2005.12.004", "resource_type": "article", "pub_year": "2006", "author_list": "Iancu, Cristina V.; Wright, Elizabeth R.; et el." }, { "id": "https://authors.library.caltech.edu/records/vy9kr-gxp84", "eprint_id": 24660, "eprint_status": "archive", "datestamp": "2023-08-22 05:16:16", "lastmod": "2023-10-23 23:33:28", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wright-E-R", "name": { "family": "Wright", "given": "Elizabeth R." } }, { "id": "Iancu-C-V", "name": { "family": "Iancu", "given": "Cristina V." }, "orcid": "0000-0002-7352-9226" }, { "id": "Tivol-W-F", "name": { "family": "Tivol", "given": "William F." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Observations on the behavior of vitreous ice at ~82 and ~12K", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Liquid helium; Radiation damage; Vitreous ice; Amorphous ice; Cryoelectron microscopy", "note": "\u00a9 2005 Elsevier Inc. \n\nReceived 29 June 2005; received in revised form 16 November 2005; accepted 7 December 2005. Available online 5 January 2006. \n\nWe thank H. Jane Ding for help preparing figures. This work was supported in part by NIH Grant PO1 GM66521 to G.J.J., DOE Grant DE-FG02-04ER63785 to G.J.J., a Searle Scholar Award to G.J.J., the Beckman Institute at Caltech, and gifts to Caltech from the Ralph M. Parsons Foundation, the Agouron Institute, and the Gordon and Betty Moore Foundation.", "abstract": "In an attempt to determine why cooling with liquid helium actually proved disadvantageous in our electron cryotomography experiments, further tests were performed to explore the differences in vitreous ice at ~82 and ~12 K. Electron diffraction patterns showed clearly that the vitreous ice of interest in biological electron cryomicroscopy (i.e., plunge-frozen, buffered protein solutions) does indeed collapse into a higher density phase when irradiated with as few as 2\u20133 e^\u2212/\u00c5^2 at ~12 K. The high density phase spontaneously expanded back to a state resembling the original, low density phase over a period of hours at ~82 K. Movements of gold fiducials and changes in the lengths of tunnels drilled through the ice confirmed these phase changes, and also revealed gross changes in the concavity of the ice layer spanning circular holes in the carbon support. Brief warmup\u2013cooldown cycles from ~12 to ~82 K and back, as would be required by the flip-flop cryorotation stage, did not induce a global phase change, but did allow certain local strains to relax. Several observations including the rates of tunnel collapse and the production of beam footprints suggested that the high density phase flows more readily in response to irradiation. Finally, the patterns of bubbling were different at the two temperatures. It is concluded that the collapse of vitreous ice at ~12 K around macromolecules is too rapid to account alone for the problematic loss of contrast seen, which must instead be due to secondary effects such as changes in the mobility of radiolytic fragments and water.", "date": "2006-03", "date_type": "published", "publication": "Journal of Structural Biology", "volume": "153", "number": "3", "publisher": "Elsevier", "pagerange": "241-252", "id_number": "CaltechAUTHORS:20110803-130902686", "issn": "1047-8477", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110803-130902686", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "PO1 GM66521" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02-04ER63785" }, { "agency": "Searle Scholars Program" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "Agouron Institute" }, { "agency": "Gordon and Betty Moore Foundation" } ] }, "doi": "10.1016/j.jsb.2005.12.003", "resource_type": "article", "pub_year": "2006", "author_list": "Wright, Elizabeth R.; Iancu, Cristina V.; et el." }, { "id": "https://authors.library.caltech.edu/records/td9tx-4hj39", "eprint_id": 24658, "eprint_status": "archive", "datestamp": "2023-08-22 04:59:07", "lastmod": "2023-10-23 23:33:22", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Komeili-A", "name": { "family": "Komeili", "given": "Arash" } }, { "id": "Li-Zhou", "name": { "family": "Li", "given": "Zhou" } }, { "id": "Newman-D-K", "name": { "family": "Newman", "given": "Dianne K." }, "orcid": "0000-0003-1647-1918" }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Magnetosomes Are Cell Membrane Invaginations Organized by the Actin-Like Protein MamK", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2005 American Association for the Advancement of Science. \n\nReceived for publication 5 October 2005. Accepted for publication 12 December 2005. Published online 22 December 2005. \n\nWe thank W. Tivol and G. Henderson for technical assistance, D. Morris for help with image processing, and K. Ryan for critical reading of the manuscript. This work was supported in part by NIH grant PO1 GM66521 to G.J.J., DOE grant DE-FG02-04ER63785 to G.J.J., a Searle Scholar Award to G.J.J., and gifts to Caltech from the Ralph M. Parsons Foundation, the Agouron Institute, and the Gordon and Betty Moore Foundation. D.K.N. was supported by grants from the Packard and Luce Foundations. A.K. was a Senior Research Fellow of the Beckman Institute and was supported by the Arnold and Mabel Beckman Foundation. \n\nSupporting Online Material: http://www.sciencemag.org/cgi/content/full/1123231/DC1\n\nMaterials and Methods\nReferences\nMovies S1 to S4\n\nSupplemental Material - KOMs06s1.mov
Supplemental Material - KOMs06s2.mov
Supplemental Material - KOMs06s3.mov
Supplemental Material - KOMs06s4.mov
Supplemental Material - KOMs06supp.pdf
", "abstract": "Magnetosomes are membranous bacterial organelles sharing many features of eukaryotic organelles. Using electron cryotomography, we found that magnetosomes are invaginations of the cell membrane flanked by a network of cytoskeletal filaments. The filaments appeared to be composed of MamK, a homolog of the bacterial actin-like protein MreB, which formed filaments in vivo. In a mamK deletion strain, the magnetosome-associated cytoskeleton was absent and individual magnetosomes were no longer organized into chains. Thus, it seems that prokaryotes can use cytoskeletal filaments to position organelles within the cell.", "date": "2006-01-13", "date_type": "published", "publication": "Science", "volume": "311", "number": "5758", "publisher": "American Association for the Advancement of Science", "pagerange": "242-245", "id_number": "CaltechAUTHORS:20110803-122522248", "issn": "0036-8075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110803-122522248", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "PO1 GM66521" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02-04ER63785" }, { "agency": "Searle Scholars Program" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "Agouron Institute" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "David and Lucile Packard Foundation" }, { "agency": "Henry Luce Foundation" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Arnold and Mabel Beckman Foundation" } ] }, "local_group": { "items": [ { "id": "Division-of-Geological-and-Planetary-Sciences" } ] }, "doi": "10.1126/science.1123231", "primary_object": { "basename": "KOMs06s1.mov", "url": "https://authors.library.caltech.edu/records/td9tx-4hj39/files/KOMs06s1.mov" }, "related_objects": [ { "basename": "KOMs06s2.mov", "url": "https://authors.library.caltech.edu/records/td9tx-4hj39/files/KOMs06s2.mov" }, { "basename": "KOMs06s3.mov", "url": "https://authors.library.caltech.edu/records/td9tx-4hj39/files/KOMs06s3.mov" }, { "basename": "KOMs06s4.mov", "url": "https://authors.library.caltech.edu/records/td9tx-4hj39/files/KOMs06s4.mov" }, { "basename": "KOMs06supp.pdf", "url": "https://authors.library.caltech.edu/records/td9tx-4hj39/files/KOMs06supp.pdf" } ], "resource_type": "article", "pub_year": "2006", "author_list": "Komeili, Arash; Li, Zhou; et el." }, { "id": "https://authors.library.caltech.edu/records/q1rem-y3d35", "eprint_id": 24653, "eprint_status": "archive", "datestamp": "2023-08-19 16:43:03", "lastmod": "2023-10-23 23:33:02", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Murphy-G-E", "name": { "family": "Murphy", "given": "Gavin E." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Electron Cryotomography of the E. coli Pyruvate and 2-Oxoglutarate Dehydrogenase Complexes", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2005 Elsevier. \n\nReceived 27 May 2005; revised 27 July 2005; accepted 1 August 2005. Published: December 13, 2005. Available online 13 December 2005. \n\nWe thank T. Wagenknecht and J. Berkowitz for the protein samples and A. Rawlinson for help preparing the figures. This work was supported in part by National Institutes of Health Grant PO1 GM66521 to G.J.J., Department of Energy grant DE-FG02-04ER63785 to G.J.J., the Beckman Institute at Caltech, and gifts to Caltech from the Ralph M. Parsons Foundation, the Agouron Institute, and the Gordon and Betty Moore Foundation. \n\nAccession Numbers: One extracted PDHC particle and one OGDHC particle were submitted to the EM Data Bank with the accession codes EMD-1151 and EMD-1152, respectively.", "abstract": "The E. coli pyruvate and 2-oxoglutarate dehydrogenases are two closely related, large complexes that exemplify a growing number of multiprotein \"machines\" whose domains have been studied extensively and modeled in atomic detail, but whose quaternary structures have remained unclear for lack of an effective imaging technology. Here, electron cryotomography was used to show that the E1 and E3 subunits of these complexes are flexibly tethered ~11 nm away from the E2 core. This result demonstrates unambiguously that electron cryotomography can reveal the relative positions of features as small as 80 kDa in individual complexes, elucidating quaternary structure and conformational flexibility.", "date": "2005-12", "date_type": "published", "publication": "Structure", "volume": "13", "number": "12", "publisher": "Cell Press", "pagerange": "1765-1773", "id_number": "CaltechAUTHORS:20110803-110300203", "issn": "0969-2126", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110803-110300203", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "PO1 GM66521" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02-04ER63785" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "Agouron Institute" }, { "agency": "Gordon and Betty Moore Foundation" } ] }, "doi": "10.1016/j.str.2005.08.016", "resource_type": "article", "pub_year": "2005", "author_list": "Murphy, Gavin E. and Jensen, Grant J." }, { "id": "https://authors.library.caltech.edu/records/7agdf-0zf94", "eprint_id": 24652, "eprint_status": "archive", "datestamp": "2023-08-22 04:06:59", "lastmod": "2023-10-23 23:32:55", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Iancu-C-V", "name": { "family": "Iancu", "given": "Cristina V." }, "orcid": "0000-0002-7352-9226" }, { "id": "Wright-E-R", "name": { "family": "Wright", "given": "Elizabeth R." } }, { "id": "Benjamin-J", "name": { "family": "Benjamin", "given": "Jordan" } }, { "id": "Tivol-W-F", "name": { "family": "Tivol", "given": "William F." } }, { "id": "Dias-D-P", "name": { "family": "Dias", "given": "D. Prabha" } }, { "id": "Murphy-G-E", "name": { "family": "Murphy", "given": "Gavin E." } }, { "id": "Morrison-R-C", "name": { "family": "Morrison", "given": "Robert C." } }, { "id": "Heymann-J-B", "name": { "family": "Heymann", "given": "J. Bernard" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "A \"flip\u2013flop\" rotation stage for routine dual-axis electron cryotomography", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Tomography; Electron microscopy; cryoEM; Dual-axis; Cryoholder; Missing wedge", "note": "\u00a9 2005 Elsevier Inc. \n\nReceived 3 March 2005; revised 6 June 2005; accepted 6 July 2005. Available online 11 August 2005. \n\nWe thank D. Mastronarde for assistance with IMOD, H.J. Ding and B. Wen for image processing, A. Martino for providing purified carboxysomes, W. Sundquist for purified HIV-1 virus-like particles, and S. Tivol for reading the manuscript. This work was supported in part by NIH Grant PO1 GM66521 to G.J.J., DOE Grant DE-FG02-04ER63785 to G.J.J., the Beckman Institute at Caltech, and gifts to Caltech from the Ralph M. Parsons Foundation, the Agouron Institute, and the Gordon and Betty Moore Foundation.", "abstract": "Electron cryotomography can be used to solve the three-dimensional structures of individual large macromolecules, assemblies, and even small intact cells to medium (~4\u20138 nm) resolution in a near-native state, but restrictions in the range of accessible views are a major limitation. Here we report on the design, characterization, and demonstration of a new \"flip\u2013flop\" rotation stage that allows facile and routine collection of two orthogonal tilt-series of cryosamples. Single- and dual-axis tomograms of a variety of samples are compared to illustrate qualitatively the improvement produced by inclusion of the second tilt-series. Exact quantitative expressions are derived for the volume of the remaining \"missing pyramid\" in reciprocal space. When orthogonal tilt-series are recorded to \u00b165\u00b0 in each direction, as this new cryostage permits, only 11% of reciprocal space is left unmeasured. The tomograms suggest that further improvement could be realized, however, through better software to align and merge dual-axis tilt-series of cryosamples.", "date": "2005-09", "date_type": "published", "publication": "Journal of Structural Biology", "volume": "151", "number": "3", "publisher": "Elsevier", "pagerange": "288-297", "id_number": "CaltechAUTHORS:20110803-105303474", "issn": "1047-8477", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110803-105303474", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "PO1 GM66521" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02-04ER63785" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "Agouron Institute" }, { "agency": "Gordon and Betty Moore Foundation" } ] }, "doi": "10.1016/j.jsb.2005.07.004", "resource_type": "article", "pub_year": "2005", "author_list": "Iancu, Cristina V.; Wright, Elizabeth R.; et el." }, { "id": "https://authors.library.caltech.edu/records/8bk32-w3049", "eprint_id": 42365, "eprint_status": "archive", "datestamp": "2023-08-19 16:08:42", "lastmod": "2023-10-25 15:52:37", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Iancu-C-V", "name": { "family": "Iancu", "given": "Cristina V." }, "orcid": "0000-0002-7352-9226" }, { "id": "Murphy-G-E", "name": { "family": "Murphy", "given": "Gavin E." } }, { "id": "Wright-E-R", "name": { "family": "Wright", "given": "Elizabeth R." } }, { "id": "Benjamin-J", "name": { "family": "Benjamin", "given": "Jordan" } }, { "id": "Tivol-W-F", "name": { "family": "Tivol", "given": "William F." } }, { "id": "Dias-D-P", "name": { "family": "Dias", "given": "D. Prabha" } }, { "id": "Heymann-J-B", "name": { "family": "Heymann", "given": "J. Bernard" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant" }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Recent advances in electron cryotomography and their application to imaging purified protein complexes, isolated organelles, and small cells", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2005 Microscopy Society of America. \n\nPublished online: 01 August 2005. \n\nExtended abstract of a paper presented at Microscopy and Microanalysis 2005 in Honolulu, Hawaii, USA, July 31-August 4, 2005.\n\nPublished - Iancu_2005p1052.pdf
", "abstract": "A new 300kV, FEG, helium-cooled, energy-filtered \"G2 Polara\" electron cryoTEM was recently installed at Caltech. Using this instrument, we have now extensively tested the potential advantages of liquid helium cooling and the inclusion of two orthogonal tilt-series in the context of electron cryotomography. These results and the application of the technology to several specific biological problems are reported.", "date": "2005-08", "date_type": "published", "publication": "Microscopy and Microanalysis", "volume": "11", "number": "S2", "publisher": "Cambridge University Press", "pagerange": "1052-1053", "id_number": "CaltechAUTHORS:20131112-082151375", "issn": "1431-9276", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20131112-082151375", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1017/S1431927605509255", "primary_object": { "basename": "Iancu_2005p1052.pdf", "url": "https://authors.library.caltech.edu/records/8bk32-w3049/files/Iancu_2005p1052.pdf" }, "resource_type": "article", "pub_year": "2005", "author_list": "Iancu, Cristina V.; Murphy, Gavin E.; et el." }, { "id": "https://authors.library.caltech.edu/records/2k0ew-bvf71", "eprint_id": 24648, "eprint_status": "archive", "datestamp": "2023-08-19 15:34:12", "lastmod": "2023-10-23 23:32:43", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Leong-Peter-A", "name": { "family": "Leong", "given": "Peter A." } }, { "id": "Heymann-J-B", "name": { "family": "Heymann", "given": "J. Bernard" } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Peach: A Simple Perl-Based System for Distributed Computation and Its Application to Cryo-EM Data Processing", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2005 Elsevier. \n\nReceived 30 November 2004; revised 12 January 2005; accepted 14 January 2005. Published: April 11, 2005. Available online 13 April 2005. \n\nWe thank C. Iancu for her willingness to test and use Peach during development stages; P. Ober for the early development of ideas for distributed processing; and W. Tivol, S. Tivol, and D. Morris for reviewing the manuscript. This work was supported in part by NIH Grant PO1 GM66521 to G.J.J., DOE grant DE-FG02-04ER63785 to G.J.J., the Beckman Institute at Caltech, and gifts from the Ralph M. Parsons Foundation, the Agouron Institute, and the Gordon and Betty Moore Foundation to Caltech.", "abstract": "A simple distributed processing system named \"Peach\" was developed to meet the rising computational demands of modern structural biology (and other) laboratories without additional expense by using existing hardware resources more efficiently. A central server distributes jobs to idle workstations in such a way that each computer is used maximally, but without disturbing intermittent interactive users. As compared to other distributed systems, Peach is simple, easy to install, easy to administer, easy to use, scalable, and robust. While it was designed to queue and distribute large numbers of small tasks to participating computers, it can also be used to send single jobs automatically to the fastest currently available computer and/or survey the activity of an entire laboratory's computers. Tests of robustness and scalability are reported, as are three specific electron cryomicroscopy applications where Peach enabled projects that would not otherwise have been feasible without an expensive, dedicated cluster.", "date": "2005-04", "date_type": "published", "publication": "Structure", "volume": "13", "number": "4", "publisher": "Cell Press", "pagerange": "505-511", "id_number": "CaltechAUTHORS:20110803-103531523", "issn": "0969-2126", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110803-103531523", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "PO1 GM66521" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-FG02-04ER63785" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "Agouron Institute" }, { "agency": "Gordon and Betty Moore Foundation" } ] }, "doi": "10.1016/j.str.2005.01.015", "resource_type": "article", "pub_year": "2005", "author_list": "Leong, Peter A.; Heymann, J. Bernard; et el." }, { "id": "https://authors.library.caltech.edu/records/gh9nz-evq20", "eprint_id": 24647, "eprint_status": "archive", "datestamp": "2023-08-22 03:13:05", "lastmod": "2023-10-23 23:32:38", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Benjamin-J", "name": { "family": "Benjamin", "given": "Jordan" } }, { "id": "Ganser-Pronillos-B-K", "name": { "family": "Ganser-Pornillos", "given": "Barbie K." } }, { "id": "Tivol-W-F", "name": { "family": "Tivol", "given": "William F." } }, { "id": "Sundquist-W-I", "name": { "family": "Sundquist", "given": "Wesley I." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Three-dimensional Structure of HIV-1 Virus-like Particles by Electron Cryotomography", "ispublished": "pub", "full_text_status": "public", "keywords": "HIV; virus structure; tomography; electron cryomicroscopy; capsid", "note": "\u00a9 2004 Elsevier Ltd. \n\nReceived 24 September 2004; revised 18 November 2004; accepted 23 November 2004. Available online 8 December 2004. \n\nEdited by M. F. Summers. \n\nThis work was supported by NIH grant PO1 GM66521 to W.I.S. and G.J.J., as well as gifts from the Ralph M. Parsons Foundation, the Agouron Institute, and the Gordon and Betty Moore Foundation to the California Institute of Technology. We are grateful to Uta von Schwedler and Kirsten Stray for assistance with VLP preparations, and we thank Simon Wain\u2013Hobsen for suggesting that we estimate the concentrations of enzymes in the viral core.\n\nAccepted Version - nihms-1032670.pdf
", "abstract": "While the structures of nearly every HIV-1 protein are known in atomic detail from X-ray crystallography and NMR spectroscopy, many questions remain about how the individual proteins are arranged in the mature infectious viral particle. Here, we report the three-dimensional structures of individual HIV-1 virus-like particles (VLPs) as obtained by electron cryotomography. These reconstructions revealed that while the structures and positions of the conical cores within each VLP were unique, they exhibited several surprisingly consistent features, including similarities in the size and shape of the wide end of the capsid (the \"base\"), uniform positioning of the base and other regions of the capsid 11 nm away from the envelope/MA layer, a cone angle that typically varied from 24\u00b0 to 18\u00b0 around the long axis of the cone, and an internal density (presumably part of the NC/RNA complex) cupped within the base. Multiple and nested capsids were observed. These results support the fullerene cone model for the viral capsid, indicate that viral maturation involves a free re-organization of the capsid shell rather than a continuous condensation, imply that capsid assembly is both concentration-driven and template-driven, suggest that specific interactions exist between the capsid and the adjacent envelope/MA and NC/RNA layers, and show that a particular capsid shape is favored strongly in-vivo.", "date": "2005-02-18", "date_type": "published", "publication": "Journal of Molecular Biology", "volume": "346", "number": "2", "publisher": "Elsevier", "pagerange": "577-588", "id_number": "CaltechAUTHORS:20110803-095002336", "issn": "0022-2836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110803-095002336", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "PO1 GM66521" }, { "agency": "Ralph M. Parsons Foundation" }, { "agency": "Gordon and Betty Moore Foundation" } ] }, "doi": "10.1016/j.jmb.2004.11.064", "pmcid": "PMC6608732", "primary_object": { "basename": "nihms-1032670.pdf", "url": "https://authors.library.caltech.edu/records/gh9nz-evq20/files/nihms-1032670.pdf" }, "resource_type": "article", "pub_year": "2005", "author_list": "Benjamin, Jordan; Ganser-Pornillos, Barbie K.; et el." }, { "id": "https://authors.library.caltech.edu/records/qk6hm-67664", "eprint_id": 91765, "eprint_status": "archive", "datestamp": "2023-08-21 21:59:35", "lastmod": "2023-10-19 23:43:35", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" } ] }, "title": "Alignment Error Envelopes for Single Particle Analysis", "ispublished": "pub", "full_text_status": "restricted", "keywords": "alignment; electron microscopy; envelope functions; image processing; resolution; single particle analysis", "note": "\u00a9 2001 Academic Press. \n\nReceived 14 November 2000, Revised 8 January 2001. \n\nThe author thanks Kenneth Downing for extensive discussions and comments on the manuscript, as well as Robert Glaeser, David DeRosier, Nigel Unwin, and Roger Kornberg for critically reading the text. The author was supported by the Cancer Research Fund of the Damon Runyon\u2013Walter Winchell Foundation Fellowship, DRG-#1591, and by Medical Scientist Training Program Grant GM07365 provided by the National Institutes of Health.", "abstract": "To determine the structure of a biological particle to high resolution by electron microscopy, image averaging is required to combine information from different views and to increase the signal-to-noise ratio. Starting from the number of noiseless views necessary to resolve features of a given size, four general factors are considered that increase the number of images actually needed: (1) the physics of electron scattering introduces shot noise, (2) thermal motion and particle inhomogeneity cause the scattered electrons to describe a mixture of structures, (3) the microscope system fails to usefully record all the information carried by the scattered electrons, and (4) image misalignment leads to information loss through incoherent averaging. The compound effect of factors 2\u20134 is approximated by the product of envelope functions. The problem of incoherent image averaging is developed in detail through derivation of five envelope functions that account for small errors in 11 \"alignment\" parameters describing particle location, orientation, defocus, magnification, and beam tilt. The analysis provides target error tolerances for single particle analysis to near-atomic (3.5 \u00c5) resolution, and this prospect is shown to depend critically on image quality, defocus determination, and microscope alignment.", "date": "2001-02", "date_type": "published", "publication": "Journal of Structural Biology", "volume": "133", "number": "2-3", "publisher": "Elsevier", "pagerange": "143-155", "id_number": "CaltechAUTHORS:20181213-110052609", "issn": "1047-8477", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181213-110052609", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Damon Runyon-Walter Winchell Cancer Fund", "grant_number": "DRG-1591" }, { "agency": "NIH", "grant_number": "GM07365" } ] }, "doi": "10.1006/jsbi.2001.4334", "resource_type": "article", "pub_year": "2001", "author_list": "Jensen, Grant J." }, { "id": "https://authors.library.caltech.edu/records/y3b17-vqk10", "eprint_id": 91764, "eprint_status": "archive", "datestamp": "2023-08-21 21:20:43", "lastmod": "2023-10-19 23:43:28", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Kronberg-R-D", "name": { "family": "Kornberg", "given": "Roger D." } } ] }, "title": "Defocus-gradient corrected back-projection", "ispublished": "pub", "full_text_status": "restricted", "keywords": "Data processing; Image processing; Three-dimensional reconstruction", "note": "\u00a9 2000 Elsevier. \n\nReceived 2 September 1999, Revised 20 December 1999, Available online 15 June 2000. \n\nG.J.J. was supported by a Medical Scientist Training Program grant (GM07365) provided by the National Institute of General Medical Science at the National Institutes of Health. This research was supported by National Institutes of Health Grant AI21144 to R.D.K.", "abstract": "Three-dimensional reconstructions of icosahedral viruses from cryoelectron microscope images have reached resolutions where the microscope depth of field is a significant resolution-limiting factor. An analytical treatment presented here shows how the depth of field limitation can be understood as an envelope function which gradually attenuates the signal, starting well before the numerical depth of field is actually reached. A simple modification to the well-known back-projection reconstruction algorithm is described, called the defocus-gradient corrected back-projection, which computationally corrects for the contrast transfer function along a defocus gradient. Computer simulations demonstrate how the algorithm effectively eliminates the depth of field limitation.", "date": "2000-07", "date_type": "published", "publication": "Ultramicroscopy", "volume": "84", "number": "1-2", "publisher": "Elsevier", "pagerange": "57-64", "id_number": "CaltechAUTHORS:20181213-110052503", "issn": "0304-3991", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181213-110052503", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM07365" }, { "agency": "NIH", "grant_number": "AI21144" } ] }, "doi": "10.1016/s0304-3991(00)00005-x", "resource_type": "article", "pub_year": "2000", "author_list": "Jensen, Grant J. and Kornberg, Roger D." }, { "id": "https://authors.library.caltech.edu/records/6783k-s0r90", "eprint_id": 91762, "eprint_status": "archive", "datestamp": "2023-08-19 04:43:15", "lastmod": "2023-10-19 23:43:23", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Poglitsch-C-L", "name": { "family": "Poglitsch", "given": "Claudia L." } }, { "id": "Meredith-G-D", "name": { "family": "Meredith", "given": "Gavin D." } }, { "id": "Gnatt-A-L", "name": { "family": "Gnatt", "given": "Averell L." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Chang-Wei-hau", "name": { "family": "Chang", "given": "Wei-hau" } }, { "id": "Fu-Jianhua", "name": { "family": "Fu", "given": "Jianhua" } }, { "id": "Kronberg-R-D", "name": { "family": "Kornberg", "given": "Roger D." } } ] }, "title": "Electron Crystal Structure of an RNA Polymerase II Transcription Elongation Complex", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1999 Cell Press. \n\nReceived 7 July 1999, Revised 10 August 1999. \n\nWe thank Lynne Mercer for advice on electron microscopy, Yang Li for polymerase used in a portion of the work, and members of our research group for helpful advice and discussions, especially Kerstin Leuther, David Bushnell, and Francisco Asturias. C. L. P. was a Damon Runyon-Walter Winchell Postdoctoral Fellow (DRG-1209) and a Katherine McCormick Scholar. G. D. M. was a National Science Foundation Fellow and a National Institutes of Health (NIH) Molecular Biophysics Training Program grant (2T32GM082494) trainee. A. G. was sponsored by the USAMRMC, DOD, Breast Cancer Initiative, DAMD17-97-7099. G. J. J. was supported by a Medical Scientist Training Program grant (GM07365) provided by the National Institute of General Medical Sciences at the NIH. This research was supported by NIH grant AI21144 to R. D. K.", "abstract": "The structure of an actively transcribing complex, containing yeast RNA polymerase II with associated template DNA and product RNA, was determined by electron crystallography. Nucleic acid, in all likelihood the \"transcription bubble\" at the active center of the enzyme, occupies a previously noted 25 \u00c5 channel in the protein structure. Details are indicative of a roughly 90\u00b0 bend of the DNA between upstream and downstream regions. The DNA apparently lies entirely on one face of the polymerase, rather than passing through a hole to the opposite side, as previously suggested.", "date": "1999-09-17", "date_type": "published", "publication": "Cell", "volume": "98", "number": "6", "publisher": "Elsevier", "pagerange": "791-798", "id_number": "CaltechAUTHORS:20181213-110052278", "issn": "0092-8674", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181213-110052278", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Damon Runyon-Walter Winchell Cancer Fund", "grant_number": "DRG-1209" }, { "agency": "Stanford University" }, { "agency": "NSF Graduate Research Fellowship" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "2T32GM082494" }, { "agency": "Army Medical Research and Materiel Command", "grant_number": "DAMD17-97-7099" }, { "agency": "NIH", "grant_number": "GM07365" }, { "agency": "NIH", "grant_number": "AI21144" } ] }, "doi": "10.1016/s0092-8674(00)81513-5", "resource_type": "article", "pub_year": "1999", "author_list": "Poglitsch, Claudia L.; Meredith, Gavin D.; et el." }, { "id": "https://authors.library.caltech.edu/records/mjax8-q4e32", "eprint_id": 91766, "eprint_status": "archive", "datestamp": "2023-08-19 04:43:23", "lastmod": "2023-10-19 23:43:38", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Fu-Jianhua", "name": { "family": "Fu", "given": "Jianhua" } }, { "id": "Gnatt-A-L", "name": { "family": "Gnatt", "given": "Averell L." } }, { "id": "Bushnell-D-A", "name": { "family": "Bushnell", "given": "David A." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Thompson-N-E", "name": { "family": "Thompson", "given": "Nancy E." } }, { "id": "Burgess-R-R", "name": { "family": "Burgess", "given": "Richard R." } }, { "id": "David-P-R", "name": { "family": "David", "given": "Peter R." } }, { "id": "Kronberg-R-D", "name": { "family": "Kornberg", "given": "Roger D." } } ] }, "title": "Yeast RNA Polymerase II at 5 \u00c5 Resolution", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 1999 Cell Press. Under an Elsevier user license.\n\nReceived 7 July 1999, Revised 10 August 1999. \n\n\nWe thank Michael Pope (George Washington University) for tungsten clusters; Henry Bellemy of SSRL for advice on anomalous scattering experiments; Gunter Schneider (Karolinska Institute, Sweden) for the Ta_6Br_(14) complex; Robert Huber (Max-Planck-Institute, Germany) for various heavy atom compounds; Ken Ng, Anand Kolatkar, and Joseph Wedekind for assistance with X-ray facilities; Mincheng Zhang for help with protein purification; and Katherine Nolan for help in the preparation of monoclonal antibody. J. F. acknowledges fellowship support from the Universitywide AIDS Research Program, University of California (#F96-ST-015) and American Cancer Society (#PF-99-112-01-GMC). The contribution of A. L. G. was sponsored by USAMRC Breast Cancer Initiative, DAMD17-97-1-7099 and does not necessarily reflect the position or policy of the government. Work done at SSRL is supported by the NIH (National Center for Research Resources, Biomedical Technology Program) and by the Department of Energy. This research was supported by NIH grant GM49985 to R. D. K.", "abstract": "Appropriate treatment of X-ray diffraction from an unoriented 18-heavy atom cluster derivative of a yeast RNA polymerase II crystal gave significant phase information to 5 \u00c5 resolution. The validity of the phases was shown by close similarity of a 6 \u00c5 electron density map to a 16 \u00c5 molecular envelope of the polymerase from electron crystallography. Comparison of the 6 \u00c5 X-ray map with results of electron crystallography of a paused transcription elongation complex suggests functional roles for two mobile protein domains: the tip of a flexible arm forms a downstream DNA clamp; and a hinged domain may serve as an RNA clamp, enclosing the transcript from about 8\u201318 residues upstream of the 3\u2032-end in a tunnel.", "date": "1999-09-17", "date_type": "published", "publication": "Cell", "volume": "98", "number": "6", "publisher": "Elsevier", "pagerange": "799-810", "id_number": "CaltechAUTHORS:20181213-132118627", "issn": "0092-8674", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181213-132118627", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "University of California", "grant_number": "F96-ST-015" }, { "agency": "American Cancer Society", "grant_number": "PF-99-112-01-GMC" }, { "agency": "Army Medical Research and Materiel Command", "grant_number": "DAMD17-97-1-7099" }, { "agency": "NIH", "grant_number": "GM49985" }, { "agency": "Department of Energy (DOE)" } ] }, "doi": "10.1016/s0092-8674(00)81514-7", "resource_type": "article", "pub_year": "1999", "author_list": "Fu, Jianhua; Gnatt, Averell L.; et el." }, { "id": "https://authors.library.caltech.edu/records/2qb7b-80229", "eprint_id": 91761, "eprint_status": "archive", "datestamp": "2023-08-19 03:13:06", "lastmod": "2023-10-19 23:43:20", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Kronberg-R-D", "name": { "family": "Kornberg", "given": "Roger D." } } ] }, "title": "Single-particle selection and alignment with heavy atom cluster-antibody conjugates", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1998, The National Academy of Sciences. \n\nContributed by Roger D. Kornberg, May 26, 1998. \n\nWe thank Sarah Harris, Dan Millward, Dave Bushnell, Patrice Koehl, Max Vasquez, Jay Tso, and Naoya Tsurushita for helpful discussions. We thank Aaron Klug, Michael Levitt, James Hainfeld, Seth Darst, Ken Downing, and Arun Malhotra for comments on the manuscript. G.J.J. was supported by a Medical Scientist Training Program grant (GM07365) provided by the National Institute of General Medical Sciences at the National Institutes of Health. This research was supported by National Institutes of Health Grant AI21144 to R.D.K. \n\nThe publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked ''advertisement'' in accordance with 18 U.S.C. \u00a71734 solely to indicate this fact.\n\nPublished - 9262.full.pdf
", "abstract": "A method is proposed for selecting and aligning images of single biological particles to obtain high-resolution structural information by cryoelectron microscopy. The particles will be labeled with multiple heavy atom clusters to permit the precise determination of particle locations and relative orientations even when imaged close to focus with a low electron dose, conditions optimal for recording high-resolution detail. Heavy atom clusters should also allow selection of images free from many kinds of defects, including specimen movement and particle inhomogeneity. Heavy atom clusters may be introduced in a general way by the construction of \"adaptor\" molecules based on single-chain Fv antibody fragments, consisting of a constant framework region engineered for optimal cluster binding and a variable antigen binding region selected for a specific target. The success of the method depends on the mobility of the heavy atom cluster on the particle, on the precision to which clusters can be located in an image, and on the sufficiency of cluster projections alone to orient and select particles for averaging. The necessary computational algorithms were developed and implemented in simulations that address the feasibility of the method.", "date": "1998-08-04", "date_type": "published", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "volume": "95", "number": "16", "publisher": "National Academy of Sciences", "pagerange": "9262-9267", "id_number": "CaltechAUTHORS:20181213-110052175", "issn": "0027-8424", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181213-110052175", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM07365" }, { "agency": "NIH", "grant_number": "AI21144" } ] }, "collection": "CaltechAUTHORS", "doi": "10.1073/pnas.95.16.9262", "pmcid": "PMC21326", "primary_object": { "basename": "9262.full.pdf", "url": "https://authors.library.caltech.edu/records/2qb7b-80229/files/9262.full.pdf" }, "resource_type": "article", "pub_year": "1998", "author_list": "Jensen, Grant J. and Kornberg, Roger D." }, { "id": "https://authors.library.caltech.edu/records/85k5v-dn622", "eprint_id": 91760, "eprint_status": "archive", "datestamp": "2023-08-19 02:45:15", "lastmod": "2023-10-19 23:43:17", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Meredith-G", "name": { "family": "Meredith", "given": "Gavin" } }, { "id": "Bushnell-D-A", "name": { "family": "Bushnell", "given": "David A." } }, { "id": "Kronberg-R-D", "name": { "family": "Kornberg", "given": "Roger D." } } ] }, "title": "Structure of wild-type yeast RNA polymerase II and location of Rpb4 and Rpb7", "ispublished": "pub", "full_text_status": "restricted", "keywords": "electron crystallography / Rpb4 / Rpb7 / transcription", "note": "\u00a9 1998 EMBO. \n\nReceived September 1, 1997; revised and accepted February 6, 1998. \n\nWe thank Steve Orlicky and Al Edwards for providing purified recombinant Rpb4 and Rpb7 complex, and Seth Darst for helpful advice. G.J.J. was supported by a Medical Scientist Training Program grant (GM07365) provided by the National Institute of General Medical Sciences at the NIH. This research was funded by NIH grant AI21144 to R.D.K.", "abstract": "The three\u2010dimensional structure of wild\u2010type yeast RNA polymerase II has been determined at a nominal resolution of 24 \u00c5. A difference map between this structure and that of the polymerase lacking subunits Rpb4 and Rpb7 showed these two subunits forming part of the floor of the DNA\u2010binding (active center) cleft, and revealed a slight inward movement of the protein domain surrounding the cleft. Surface plasmon resonance measurements showed that Rpb4 and Rpb7 stabilize a minimal pre\u2010initiation complex containing promoter DNA, TATA box\u2010binding protein (TBP), transcription factor TFIIB and the polymerase. These findings suggest that Rpb4 and Rpb7 play a role in coupling the entry of DNA into the active center cleft to closure of the cleft. Such a role can explain why these subunits are necessary for promoter\u2010specific transcription in vitro and for a normal stress response in vivo.", "date": "1998-04-15", "date_type": "published", "publication": "EMBO Journal", "volume": "17", "number": "8", "publisher": "European Molecular Biology Organization", "pagerange": "2353-2358", "id_number": "CaltechAUTHORS:20181213-110052088", "issn": "1460-2075", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181213-110052088", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "GM07365" }, { "agency": "NIH", "grant_number": "AI21144" } ] }, "doi": "10.1093/emboj/17.8.2353", "pmcid": "PMC1170578", "resource_type": "article", "pub_year": "1998", "author_list": "Jensen, Grant J.; Meredith, Gavin; et el." }, { "id": "https://authors.library.caltech.edu/records/1hymy-7jf85", "eprint_id": 91757, "eprint_status": "archive", "datestamp": "2023-08-20 04:44:12", "lastmod": "2023-10-19 23:43:00", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Yoshida-Tatsuro", "name": { "family": "Yoshida", "given": "Tatsuro" } }, { "id": "Willardson-B-M", "name": { "family": "Willardson", "given": "Barry M." } }, { "id": "Wilkins-J-F", "name": { "family": "Wilkins", "given": "Jon F." } }, { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864" }, { "id": "Thornton-B-D", "name": { "family": "Thornton", "given": "Brian D." } }, { "id": "Bitensky-M-W", "name": { "family": "Bitensky", "given": "Mark W." } } ] }, "title": "The phosphorylation state of phosducin determines its ability to block transducin subunit interactions and inhibit transducin binding to activated rhodopsin", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 1994 American Society for Biochemistry and Molecular Biology. \n\n(Received for publication, May 31, 1994, and in revised form, July 15, 1994) \n\nThis work was supported by National Institutes of Health Grant EY 06816. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked \"advertisement\" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.\n\nPublished - J._Biol._Chem.-1994-Yoshida-24050-7.pdf
", "abstract": "Heterotrimeric GTP-binding proteins (G-proteins) serve many different signal transduction pathways. Phosducin, a 28-kDa phosphoprotein, is expressed in a variety of mammalian cell types and blocks activation of several classes of G-proteins. Phosphorylation of phosducin by cyclic AMP-dependent protein kinase prevents phosducin-mediated inhibition of G-protein GTPase activity (Bauer, P. H., M\u00fcller, S., Puzicha, M., Pippig, S., Obermaier, B., Helmreich, E. J. M., and Lohse, M. J. (1992) Nature 358, 73-76). In retinal rods, phosducin inhibits transducin (G_t) activation by binding its \u03b2 gamma subunits. While rod phosducin is phosphorylated in the dark and dephosphorylated after illumination (Lee, R.-H., Brown, B. M., and Lolley, R. N. (1984) Biochemistry 23, 1972-1977), the significance of these reactions is still unclear. The data presented here permit a more precise characterization of phosducin function and the consequences of its phosphorylation. Dephosphophosducin blocked binding of the G_t\u03b1^1 subunit to activated rhodopsin in the presence of stoichiometric amounts of G_t\u03b2\u03b3, whereas phosphophosducin did not. Surprisingly, the binding affinity of phosphophosducin for G_t\u03b2\u03b3 was not significantly reduced compared with the binding affinity of dephosphophosducin. However, the association of phosducin with G_t\u03b2\u03b3 in a size exclusion column matrix was dependent on the phosphorylation state of phosducin. Moreover, the ability of phosducin to compete with G_t\u03b1 for binding to G_t\u03b2\u03b3 was also dependent on the phosphorylation state of phosducin. No interaction was found between phosducin and G_t\u03b1. These data indicate that phosducin decreases rod responsiveness by binding to the \u03b2\u03b3 subunits of G_t and preventing their interaction with G_t\u03b1, thereby inhibiting G_t\u03b1 activation by the activated receptor. Moreover, phosphorylation of phosducin blocks its ability to compete with G_t\u03b1 for binding to G_t\u03b2\u03b3.", "date": "1994-09-30", "date_type": "published", "publication": "Journal of Biological Chemistry", "volume": "269", "number": "39", "publisher": "American Society for Biochemistry and Molecular Biology", "pagerange": "24050-24057", "id_number": "CaltechAUTHORS:20181213-105800611", "issn": "0021-9258", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181213-105800611", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "EY 06816" } ] }, "primary_object": { "basename": "J._Biol._Chem.-1994-Yoshida-24050-7.pdf", "url": "https://authors.library.caltech.edu/records/1hymy-7jf85/files/J._Biol._Chem.-1994-Yoshida-24050-7.pdf" }, "resource_type": "article", "pub_year": "1994", "author_list": "Yoshida, Tatsuro; Willardson, Barry M.; et el." } ]