[ { "id": "https://authors.library.caltech.edu/records/4k9d0-2a571", "eprint_id": 120173, "eprint_status": "archive", "datestamp": "2023-08-20 08:48:38", "lastmod": "2023-12-13 17:07:24", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Murali-Ranjani", "name": { "family": "Murali", "given": "Ranjani" }, "orcid": "0000-0003-4073-9910" }, { "id": "Yu-Hang-Hank", "name": { "family": "Yu", "given": "Hang" }, "orcid": "0000-0002-7600-1582" }, { "id": "Speth-Daan-R", "name": { "family": "Speth", "given": "Daan R." }, "orcid": "0000-0002-2361-5935" }, { "id": "Wu-Fabai", "name": { "family": "Wu", "given": "Fabai" }, "orcid": "0000-0001-5812-5621" }, { "id": "Metcalfe-Kyle-S", "name": { "family": "Metcalfe", "given": "Kyle S." }, "orcid": "0000-0002-2963-765X" }, { "id": "Cr\u00e9mi\u00e8re-Antoine", "name": { "family": "Cr\u00e9mi\u00e8re", "given": "Antoine" }, "orcid": "0000-0001-7382-2097" }, { "id": "Laso-P\u00e9rez-Rafael", "name": { "family": "Laso-P\u00e9rez", "given": "Rafael" }, "orcid": "0000-0002-6912-7865" }, { "id": "Malmstrom-Rex-R", "name": { "family": "Malmstrom", "given": "Rex R." }, "orcid": "0000-0002-4758-7369" }, { "id": "Goudeau-Danielle", "name": { "family": "Goudeau", "given": "Danielle" }, "orcid": "0000-0002-3785-032X" }, { "id": "Woyke-Tanja", "name": { "family": "Woyke", "given": "Tanja" }, "orcid": "0000-0002-9485-5637" }, { "id": "Hatzenpichler-Roland", "name": { "family": "Hatzenpichler", "given": "Roland" }, "orcid": "0000-0002-5489-3444" }, { "id": "Chadwick-Grayson-L", "name": { "family": "Chadwick", "given": "Grayson L." }, "orcid": "0000-0003-0700-9350" }, { "id": "Orphan-V-J", "name": { "family": "Orphan", "given": "Victoria J." }, "orcid": "0000-0002-5374-6178" } ] }, "title": "Physiological adaptation of sulfate reducing bacteria in syntrophic partnership with anaerobic methanotrophic archaea", "ispublished": "unpub", "full_text_status": "public", "note": "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. \n\nWe thank the DOE and the Moore Foundation for funding this research (Principle Investigator: Dr. Victoria J. Orphan). We acknowledge the Dalio Foundation and Woods Hole Oceanographic Institute for supporting the NA091 research cruise to South Pescadero Basin on E/V Nautilus operated by the Ocean Exploration Trust in October-November 2017. The work (Award doi: 10.46936/fics.proj.2017.49956/60006219) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231. We would also like to thank Magdalena Mayr for her thoughtful comments on this manuscript and Fernanda Jimenez-Otero for sharing her thoughts and expertise in the field of extracellular electron transfer. We are also grateful to Alon Philosof, Aditi Narayan, Kriti Sharma and James Hemp for many productive discussions on broad scientific questions in microbial ecology and evolution, metabolism and scientific writing that lent itself to the framing of this manuscript. \n\nThe authors have declared no competing interest.\n\n
Submitted - 2022.11.23.517749v1.full.pdf
Supplemental Material - media-1.pdf
Supplemental Material - media-2.zip
Supplemental Material - media-3.xlsx
Supplemental Material - media-4.xlsx
", "abstract": "Sulfate-coupled anaerobic oxidation of methane (AOM) is performed by multicellular consortia of anaerobic methanotrophic archaea (ANME) in obligate syntrophic partnership with sulfate-reducing bacteria (SRB). Diverse ANME and SRB clades co-associate but the physiological basis for their adaptation and diversification is not well understood. In this work, we explore the metabolic adaptation of four syntrophic SRB clades (HotSeep-1, Seep-SRB2, Seep-SRB1a and Seep-SRB1g) from a phylogenomics perspective, tracing the evolution of conserved proteins in the syntrophic SRB clades, and comparing the genomes of syntrophic SRB to their nearest evolutionary neighbors in the phylum Desulfobacterota. We note several examples of gain, loss or biochemical adaptation of proteins within pathways involved in extracellular electron transfer, electron transport chain, nutrient sharing, biofilm formation and cell adhesion. We demonstrate that the metabolic adaptations in each of these syntrophic clades are unique, suggesting that they have independently evolved, converging to a syntrophic partnership with ANME. Within the clades we also investigated the specialization of different syntrophic SRB species to partnerships with different ANME clades, using metagenomic sequences obtained from ANME and SRB partners in individual consortia after fluorescent-sorting of cell aggregates from anaerobic sediments. In one instance of metabolic adaptation to different partnerships, we show that Seep-SRB1a partners of ANME-2c appear to lack nutritional auxotrophies, while the related Seep-SRB1a partners of a different methanotrophic archaeal lineage, ANME-2a, are missing the cobalamin synthesis pathway, suggesting that the Seep-SRB1a partners of ANME-2a may have a nutritional dependence on its partner. Together, our paired genomic analysis of AOM consortia highlights the specific adaptation and diversification of syntrophic SRB clades linked to their associated ANME lineages.", "date": "2023-03-17", "date_type": "published", "id_number": "CaltechAUTHORS:20230316-182819000.64", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230316-182819000.64", "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": "Gordon and Betty Moore Foundation" }, { "agency": "Dalio Foundation" }, { "agency": "Woods Hole Oceanographic Institution" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2022.11.23.517749", "primary_object": { "basename": "media-4.xlsx", "url": "https://authors.library.caltech.edu/records/4k9d0-2a571/files/media-4.xlsx" }, "related_objects": [ { "basename": "2022.11.23.517749v1.full.pdf", "url": "https://authors.library.caltech.edu/records/4k9d0-2a571/files/2022.11.23.517749v1.full.pdf" }, { "basename": "media-1.pdf", "url": "https://authors.library.caltech.edu/records/4k9d0-2a571/files/media-1.pdf" }, { "basename": "media-2.zip", "url": "https://authors.library.caltech.edu/records/4k9d0-2a571/files/media-2.zip" }, { "basename": "media-3.xlsx", "url": "https://authors.library.caltech.edu/records/4k9d0-2a571/files/media-3.xlsx" } ], "resource_type": "monograph", "pub_year": "2023", "author_list": "Murali, Ranjani; Yu, Hang; et el." }, { "id": "https://authors.library.caltech.edu/records/bzbxb-4t885", "eprint_id": 116176, "eprint_status": "archive", "datestamp": "2023-08-20 08:09:42", "lastmod": "2023-12-22 23:36:21", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Laso-P\u00e9rez-Rafael", "name": { "family": "Laso-P\u00e9rez", "given": "Rafael" }, "orcid": "0000-0002-6912-7865" }, { "id": "Wu-Fabai", "name": { "family": "Wu", "given": "Fabai" }, "orcid": "0000-0001-5812-5621" }, { "id": "Cr\u00e9mi\u00e8re-Antoine", "name": { "family": "Cr\u00e9mi\u00e8re", "given": "Antoine" }, "orcid": "0000-0001-7382-2097" }, { "id": "Speth-Daan-R", "name": { "family": "Speth", "given": "Daan R." }, "orcid": "0000-0002-2361-5935" }, { "id": "Magyar-John-S", "name": { "family": "Magyar", "given": "John S." }, "orcid": "0000-0002-3586-8286" }, { "id": "Krupovic-Mart", "name": { "family": "Krupovic", "given": "Mart" }, "orcid": "0000-0001-5486-0098" }, { "id": "Orphan-V-J", "name": { "family": "Orphan", "given": "Victoria J." }, "orcid": "0000-0002-5374-6178" } ] }, "title": "Evolutionary Diversification of Methanotrophic Ca. Methanophagales (ANME-1) and Their Expansive Virome", "ispublished": "unpub", "full_text_status": "public", "note": "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. \n\nWe are indebted to the crews from R/V Falkor (cruise FK181031) and E/V Nautilus (cruise NA091) and the pilots of ROVs SuBastian and Hercules. Sample collection permits for FK181031 (25/07/2018) were granted by la Direcci\u00f3n General de Ordenamiento Pesquero y Acu\u00edcola, Comisi\u00f3n Nacional de Acuacultura y Pesca (CONAPESCA: Permiso de Pesca de Fomento No. PPFE/DGOPA-200/18) and la Direcci\u00f3n General de Geograf\u00eda y Medio Ambiente, Instituto Nacional de Estad\u00edstica y Geograf\u00eda (INEGI: Autorizaci\u00f3n EG0122018), with the associated Diplomatic Note number 18-2083 (CTC/07345/18) from la Secretar\u00eda de Relaciones Exteriores - Agencia Mexicana de Cooperaci\u00f3n Internacional para el Desarrollo / Direcci\u00f3n General de Cooperaci\u00f3n T\u00e9cnica y Cient\u00edfica. Sample collection permit for cruise NA091 (18/04/2017) was obtained by the Ocean Exploration Trust under permit number EG0072017. This research used samples provided by the Ocean Exploration Trust's Nautilus Exploration Program, cruise NA091. E/V Nautlius operated by the Ocean Exploration Trust, with cruise NA091 supported by the Dalio Foundation and Woods Hole Oceanographic Institute, and R/V Falkor operated by the Schmidt Ocean Institute. Funding for this work was provided by grants from the National Science Foundation Center For Dark Energy Biosphere Investigations (C-DEBI) and the NOMIS foundation (V.J.O.). VJO contribution was supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under Award Number DE-SC0020373. This work was also supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Initiative/Strategy through the Cluster of Excellence \"The Ocean Floor-Earth's Uncharted Interface\" (EXC-2077-390741603 R.L.-P. and V.J.O). M.K. was supported by l'Agence Nationale de la Recherche grant ANR-20-CE20-0009-02. F.W. was supported by the Dutch Research Council Rubicon Award 019.162LW.037, the Human Frontiers Science Program Long-term fellowship LT000468/2017, and a ZJU-HIC Independent PI Startup Grant. \n\nAuthor contributions. R. L.-P., F.W., A.C., and V.J.O. conceived and designed the study. D.R.S, V.J.O. and J.S.M. retrieved the original samples. A.C. and F.W. carried out rock incubations and FISH microscopy. R.L.-P., F.W. and A.C. performed DNA extraction. R.L.-P. and F.W. performed metagenomic assembly and analysis. F.W. performed CRISPR-based mobilome discovery. M.K. and F.W. performed analyses of viruses. R.L.-P., F.W., M.K. and V.J.O wrote the manuscript with contributions from all coauthors. We declare no competing financial interests. \n\nData availability. All MAGs and sequence data can be found in the figshare link https://figshare.com/projects/Laso-Perez_and_Wu_-_ANME-1_project/140453 (except some large libraries), and will be deposited onto NCBI database prior to peer-reviewed publication. \n\nThis report was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor any agency thereof, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof.\n\nSubmitted - 2022.07.04.498658v4.full.pdf
Supplemental Material - media-1.pdf
Supplemental Material - media-2.xlsx
", "abstract": "'Candidatus Methanophagales' (ANME-1) is a major order-level clade of archaea responsible for methane removal in deep-sea sediments through anaerobic oxidation of methane. Yet the extent of their diversity and factors which drive their dynamics and evolution remain poorly understood. Here, by sampling hydrothermal rocks and sediments, we expand their phylogenetic diversity and characterize a new deep-branching, thermophilic ANME-1 family, 'Candidatus Methanoxibalbaceae' (ANME-1c). They are phylogenetically closest to the short-chain-alkane oxidizers 'Candidatus Syntrophoarchaeales' and 'Candidatus Alkanophagales', and encode ancestral features including a methyl coenzyme M reductase chaperone McrD and a hydrogenase complex. Global phylogeny and near-complete genomes clarified that the debated hydrogen metabolism within ANME-1 is an ancient trait that was vertically inherited but differentially lost during lineage diversification. Our expanded genomic and metagenomic sampling allowed the discovery of viruses constituting 3 new orders and 16 new families that so far are exclusive to ANME-1 hosts. These viruses represent 4 major archaeal virus assemblages, characterized by tailless icosahedral, head-tailed, rod-shaped, and spindle-shaped virions, but display unique structural and replicative signatures. Exemplified by the analyses of thymidylate synthases that unveiled a virus-mediated ancestral process of host gene displacement, this expansive ANME-1 virome carries a large gene repertoire that can influence their hosts across different timescales. Our study thus puts forth an emerging evolutionary continuum between anaerobic methane and short-chain-alkane oxidizers and opens doors for exploring the impacts of viruses on the dynamics and evolution of the anaerobic methane-driven ecosystems.", "date": "2022-08-12", "date_type": "published", "id_number": "CaltechAUTHORS:20220808-886882000", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220808-886882000", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Ocean Exploration Trust" }, { "agency": "Dalio Foundation" }, { "agency": "Woods Hole Oceanographic Institution" }, { "agency": "NSF" }, { "agency": "NOMIS Foundation" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-SC0020373" }, { "agency": "Deutsche Forschungsgemeinschaft (DFG)", "grant_number": "EXC-2077-390741603" }, { "agency": "Agence Nationale de la Recherche (ANR)", "grant_number": "ANR-20-CE20-0009-02" }, { "agency": "Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)", "grant_number": "019.162LW.037" }, { "agency": "Human Frontier Science Program", "grant_number": "LT000468" }, { "agency": "Zhejiang University" } ] }, "local_group": { "items": [ { "id": "Division-of-Geological-and-Planetary-Sciences" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2022.07.04.498658", "primary_object": { "basename": "media-2.xlsx", "url": "https://authors.library.caltech.edu/records/bzbxb-4t885/files/media-2.xlsx" }, "related_objects": [ { "basename": "2022.07.04.498658v4.full.pdf", "url": "https://authors.library.caltech.edu/records/bzbxb-4t885/files/2022.07.04.498658v4.full.pdf" }, { "basename": "media-1.pdf", "url": "https://authors.library.caltech.edu/records/bzbxb-4t885/files/media-1.pdf" } ], "resource_type": "monograph", "pub_year": "2022", "author_list": "Laso-P\u00e9rez, Rafael; Wu, Fabai; et el." }, { "id": "https://authors.library.caltech.edu/records/ddbgb-8jb47", "eprint_id": 110149, "eprint_status": "archive", "datestamp": "2023-08-22 10:47:40", "lastmod": "2023-12-22 23:35:33", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Speth-Daan-R", "name": { "family": "Speth", "given": "Daan R." }, "orcid": "0000-0002-2361-5935" }, { "id": "Yu-Feiqiao-B", "name": { "family": "Yu", "given": "Feiqiao B." }, "orcid": "0000-0003-3416-3046" }, { "id": "Connon-Stephanie-A", "name": { "family": "Connon", "given": "Stephanie A." } }, { "id": "Lim-Sujung", "name": { "family": "Lim", "given": "Sujung" }, "orcid": "0000-0001-6040-729X" }, { "id": "Magyar-John-S", "name": { "family": "Magyar", "given": "John S." }, "orcid": "0000-0002-3586-8286" }, { "id": "Pe\u00f1a-Manet-E", "name": { "family": "Pe\u00f1a", "given": "Manet E." }, "orcid": "0000-0002-5835-0455" }, { "id": "Quake-Stephen-R", "name": { "family": "Quake", "given": "Stephen R." }, "orcid": "0000-0002-1613-0809" }, { "id": "Orphan-V-J", "name": { "family": "Orphan", "given": "Victoria J." }, "orcid": "0000-0002-5374-6178" } ] }, "title": "Microbial community of recently discovered Auka vent field sheds light on vent biogeography and evolutionary history of thermophily", "ispublished": "unpub", "full_text_status": "public", "note": "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. \n\nThis version posted August 2, 2021. \n\nWe thank the pilots, crew, and participants on the cruises to the southern Gulf of California: R/V Western Flyer operated by the Monterey Bay Aquarium Research Institute (MBARI), E/V Nautlius operated by the Ocean Exploration Trust, with cruise NA091 supported by the Dalio Foundation and Woods Hole Oceanographic Institute, and R/V Falkor operated by the Schmidt Ocean Institute. We appreciate the support and opportunity to sail with chief scientists Scott Wankel and Anna Michel on NA091. We also thank David W. Caress and Jennifer B. Paduan (MBARI) for providing the high resolution version of the bathymetric map in Figure 1, David Sauer for recalculating the optimal growth temperature prediction model to be appropriate for metagenomics, and Haley Sapers for providing a framework for the 16S rRNA gene amplicon processing. This research used samples provided by the Ocean Exploration Trust's Nautilus Exploration Program, cruise NA091. \n\nThis work was supported by the Center for Dark Energy Biosphere investigations (C-DEBI), Canadian Institute for Advanced Science (CIFAR), the US Department of Energy, Office of Science, Office of Biological and Environmental Research under award number DE-SC0016469 to Victoria J. Orphan. Daan R. Speth was supported by the Netherlands Organisation for Scientific Research, Rubicon award 019.153LW.039. Feiqiao B. Yu and Stephen R. Quake were supported by the John Templeton Foundation grant 51250 and the Chan Zuckerberg Biohub. Victoria J. Orphan is a CIFAR fellow in the Earth 4D program. \n\nSample collection permits were granted by la Direcci\u00f3n General de Ordenamiento Pesquero y Acu\u00edcola, Comisi\u00f3n Nacional de Acuacultura y Pesca (CONAPESCA: Permiso de Pesca de Fomento No. PPFE/DGOPA-200/18) and l a Direcci\u00f3n G eneral de G eograf\u00eda y Medio A mbiente, Instituto Nacional de Estad\u00edstica y Geograf\u00eda (INEGI: Autorizaci\u00f3n EG0122018), with t he associated Diplomatic Note number 18-2083 (CTC/07345/18) f rom l a Secretar\u00eda d e R elaciones Exteriores - Agencia Mexicana de Cooperaci\u00f3n I nternacional para el Desarrollo / Direcci\u00f3n General de Cooperaci\u00f3n T\u00e9cnica y Cient\u00edfica. Sample collection permit for cruise NA091 was obtained by the Ocean Exploration T rust under permit number EG0072017. \n\nData availability: Raw metagenome reads, assembled metagenome bins, and 16S rRNA gene amplicon sequencing data are available in GenBank under BioProject accession number PRJNA713414. \n\nThe authors have declared no competing interest.\n\nSubmitted - 2021.08.02.454472v1.full.pdf
Supplemental Material - media-1.pdf
Supplemental Material - media-2.xlsx
Supplemental Material - media-3.xlsx
Supplemental Material - media-4.csv
Supplemental Material - media-5.gz
Supplemental Material - media-6.xlsx
Supplemental Material - media-7.tsv
Supplemental Material - media-8.gz
", "abstract": "Hydrothermal vents have been key to our understanding of the limits of life, and the metabolic and phylogenetic diversity of thermophilic organisms. Here we used environmental metagenomics combined with analysis of physico-chemical data and 16S rRNA amplicons to characterize the diversity, temperature optima, and biogeographic distribution of sediment-hosted microorganisms at the recently discovered Auka vents in the Gulf of California, the deepest known hydrothermal vent field in the Pacific Ocean. We recovered 325 metagenome assembled genomes (MAGs) representing 54 phyla, over 1/3 of the currently known phylum diversity, showing the microbial community in Auka hydrothermal sediments is highly diverse. Large scale 16S rRNA amplicon screening of 227 sediment samples across the vent field indicates that the MAGs are largely representative of the microbial community. Metabolic reconstruction of a vent-specific, deeply branching clade within the Desulfobacterota (Tharpobacteria) suggests these organisms metabolize sulfur using novel octaheme cytochrome-c proteins related to hydroxylamine oxidoreductase. Community-wide comparison of the average nucleotide identity of the Auka MAGs with MAGs from the Guaymas Basin vent field, found 400 km to the Northwest, revealed a remarkable 20% species-level overlap between vent sites, suggestive of long-distance species transfer and sediment colonization. An adapted version of a recently developed model for predicting optimal growth temperature to the Auka and Guaymas MAGs indicates several of these uncultured microorganisms could grow at temperatures exceeding the currently known upper limit of life. Extending this analysis to reference data shows that thermophily is a trait that has evolved frequently among Bacteria and Archaea. Combined, our results show that Auka vent field offers new perspectives on our understanding of hydrothermal vent microbiology.", "date": "2021-08-04", "date_type": "published", "id_number": "CaltechAUTHORS:20210804-220359405", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210804-220359405", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Center for Dark Energy Biosphere investigations (C-DEBI)" }, { "agency": "Canadian Institute for Advanced Research (CIFAR)" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-SC0016469" }, { "agency": "Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)", "grant_number": "019.153LW.039" }, { "agency": "John Templeton Foundation", "grant_number": "51250" }, { "agency": "Chan Zuckerberg Initiative" } ] }, "local_group": { "items": [ { "id": "Division-of-Geological-and-Planetary-Sciences" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2021.08.02.454472", "primary_object": { "basename": "media-5.gz", "url": "https://authors.library.caltech.edu/records/ddbgb-8jb47/files/media-5.gz" }, "related_objects": [ { "basename": "media-6.xlsx", "url": "https://authors.library.caltech.edu/records/ddbgb-8jb47/files/media-6.xlsx" }, { "basename": "media-7.tsv", "url": "https://authors.library.caltech.edu/records/ddbgb-8jb47/files/media-7.tsv" }, { "basename": "2021.08.02.454472v1.full.pdf", "url": "https://authors.library.caltech.edu/records/ddbgb-8jb47/files/2021.08.02.454472v1.full.pdf" }, { "basename": "media-2.xlsx", "url": "https://authors.library.caltech.edu/records/ddbgb-8jb47/files/media-2.xlsx" }, { "basename": "media-4.csv", "url": "https://authors.library.caltech.edu/records/ddbgb-8jb47/files/media-4.csv" }, { "basename": "media-8.gz", "url": "https://authors.library.caltech.edu/records/ddbgb-8jb47/files/media-8.gz" }, { "basename": "media-1.pdf", "url": "https://authors.library.caltech.edu/records/ddbgb-8jb47/files/media-1.pdf" }, { "basename": "media-3.xlsx", "url": "https://authors.library.caltech.edu/records/ddbgb-8jb47/files/media-3.xlsx" } ], "resource_type": "monograph", "pub_year": "2021", "author_list": "Speth, Daan R.; Yu, Feiqiao B.; et el." }, { "id": "https://authors.library.caltech.edu/records/cyt72-4zt71", "eprint_id": 99083, "eprint_status": "archive", "datestamp": "2023-08-22 02:39:56", "lastmod": "2023-10-18 17:50:46", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Speth-D-R", "name": { "family": "Speth", "given": "Daan R." }, "orcid": "0000-0002-2361-5935" }, { "id": "Orphan-V-J", "name": { "family": "Orphan", "given": "Victoria J." }, "orcid": "0000-0002-5374-6178" } ] }, "title": "ASM-Clust: classifying functionally diverse protein families using alignment score matrices", "ispublished": "unpub", "full_text_status": "public", "note": "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. \n\nbioRxiv preprint first posted online Oct. 3, 2019. \n\nThis work was supported by the US Department of Energy, Office of Science, Office of Biological and Environmental Research under award number DE-SC0016469 to Victoria J. Orphan. Daan R. Speth was supported by the Netherlands Organisation for Scientific Research, Rubicon award 019.153LW.039.\n\nSubmitted - 792739.full.pdf
Supplemental Material - media-1.pdf
", "abstract": "Rapid advances in sequencing technology have resulted in the availability of genomes from organisms across the tree of life. Accurately interpreting the function of proteins in these genomes is a major challenge, as annotation transfer based on homology frequently results in misannotation and error propagation. This challenge is especially pressing for organisms whose genomes are directly obtained from environmental samples, as interpretation of their physiology and ecology is often based solely on the genome sequence. For complex protein (super)families containing a large number of sequences, classification can be used to determine whether annotation transfer is appropriate, or whether experimental evidence for function is lacking. Here we present a novel computational approach for de novo classification of large protein (super)families, based on clustering an alignment score matrix obtained by aligning all sequences in the family to a small subset of the data. We evaluate our approach on the enolase family in the Structure Function Linkage Database.", "date": "2019-10-04", "date_type": "published", "id_number": "CaltechAUTHORS:20191004-102107177", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20191004-102107177", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Department of Energy (DOE)", "grant_number": "DE-SC0016469" }, { "agency": "Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)", "grant_number": "019.153LW.039" } ] }, "local_group": { "items": [ { "id": "Division-of-Geological-and-Planetary-Sciences" } ] }, "doi": "10.1101/792739", "primary_object": { "basename": "792739.full.pdf", "url": "https://authors.library.caltech.edu/records/cyt72-4zt71/files/792739.full.pdf" }, "related_objects": [ { "basename": "media-1.pdf", "url": "https://authors.library.caltech.edu/records/cyt72-4zt71/files/media-1.pdf" } ], "resource_type": "monograph", "pub_year": "2019", "author_list": "Speth, Daan R. and Orphan, Victoria J." }, { "id": "https://authors.library.caltech.edu/records/h37x3-kbc45", "eprint_id": 94306, "eprint_status": "archive", "datestamp": "2023-08-22 01:13:11", "lastmod": "2023-10-20 17:51:49", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Murali-R", "name": { "family": "Murali", "given": "Ranjani" } }, { "id": "Hemp-J", "name": { "family": "Hemp", "given": "James" }, "orcid": "0000-0001-7193-0553" }, { "id": "Orphan-V-J", "name": { "family": "Orphan", "given": "Victoria" }, "orcid": "0000-0002-5374-6178" }, { "id": "Bisk-Y", "name": { "family": "Bisk", "given": "Yonatan" } } ] }, "title": "FIND: Identifying Functionally and Structurally Important Features in Protein Sequences with Deep Neural Networks", "ispublished": "unpub", "full_text_status": "public", "note": "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. \n\nThis work was funding by DARPA's CwC program through ARO (W911NF-15-1-0543), the Moore Foundation(Award to VJO: GBMF3780), the Department of Energy (Award to VJO: DE-SC0016469) and the Center for Dark Biosphere Investigations (NSF Award to VJO: OCE-0939564). We are grateful to Daan Speth for reading the manuscript at multiple stages of completion and for his useful comments throughout the process. We would also like to thank Dr. Robert Gennis for reading the manuscript and offering helpful comments, Grayson Chadwick for useful discussion on bioinformatics strategies and Haley Sapers for her instructive critique of the figures.\n\nSubmitted - 592808.full.pdf
", "abstract": "The ability to correctly predict the functional role of proteins from their amino acid sequences would significantly advance biological studies at the molecular level by improving our ability to understand the biochemical capability of biological organisms from their genomic sequence. Existing methods that are geared towards protein function prediction or annotation mostly use alignment-based approaches and probabilistic models such as Hidden-Markov Models. In this work we introduce a deep learning architecture (Function Identification with Neural Descriptions or FIND) which performs protein annotation from primary sequence. The accuracy of our methods matches state of the art techniques, such as protein classifiers based on Hidden Markov Models. Further, our approach allows for model introspection via a neural attention mechanism, which weights parts of the amino acid sequence proportionally to their relevance for functional assignment. In this way, the attention weights automatically uncover structurally and functionally relevant features of the classified protein and find novel functional motifs in previously uncharacterized proteins. While this model is applicable to any database of proteins, we chose to apply this model to superfamilies of homologous proteins, with the aim of extracting features inherent to divergent protein families within a larger superfamily. This provided insight into the functional diversification of an enzyme superfamily and its adaptation to different physiological contexts. We tested our approach on three families (nitrogenases, cytochrome bd-type oxygen reductases and heme-copper oxygen reductases) and present a detailed analysis of the sequence characteristics identified in previously characterized proteins in the heme-copper oxygen reductase (HCO) superfamily. These are correlated with their catalytic relevance and evolutionary history. FIND was then applied to discover features in previously uncharacterized members of the HCO superfamily, providing insight into their unique sequence features. This modeling approach demonstrates the power of neural networks to recognize patterns in large datasets and can be utilized to discover biochemically and structurally important features in proteins from their amino acid sequences.", "date": "2019-04-01", "date_type": "published", "id_number": "CaltechAUTHORS:20190401-084306692", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190401-084306692", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Department of Energy (DOE)" }, { "agency": "Army Research Office (ARO)", "grant_number": "W911NF-15-1-0543" }, { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GBMF3780" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-SC0016469" }, { "agency": "NSF", "grant_number": "OCE-0939564" } ] }, "local_group": { "items": [ { "id": "Division-of-Geological-and-Planetary-Sciences" } ] }, "doi": "10.1101/592808", "primary_object": { "basename": "592808.full.pdf", "url": "https://authors.library.caltech.edu/records/h37x3-kbc45/files/592808.full.pdf" }, "resource_type": "monograph", "pub_year": "2019", "author_list": "Murali, Ranjani; Hemp, James; et el." }, { "id": "https://authors.library.caltech.edu/records/3gcg3-khn91", "eprint_id": 86060, "eprint_status": "archive", "datestamp": "2023-08-19 07:11:55", "lastmod": "2023-10-18 19:13:51", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Yung-Y-L", "name": { "family": "Yung", "given": "Yuk L." }, "orcid": "0000-0002-4263-2562" }, { "id": "Chen-Pin", "name": { "family": "Chen", "given": "Pin" } }, { "id": "Nealson-K-H", "name": { "family": "Nealson", "given": "Kenneth" }, "orcid": "0000-0001-5189-3732" }, { "id": "Atreya-S-K", "name": { "family": "Atreya", "given": "Sushil" }, "orcid": "0000-0002-1972-1815" }, { "id": "Beckett-P", "name": { "family": "Beckett", "given": "Patrick" } }, { "id": "Blank-J-G", "name": { "family": "Blank", "given": "Jennifer" } }, { "id": "Ehlmann-B-L", "name": { "family": "Ehlmann", "given": "Bethany" }, "orcid": "0000-0002-2745-3240" }, { "id": "Eiler-J-M", "name": { "family": "Eiler", "given": "John" } }, { "id": "Etiope-G", "name": { "family": "Etiope", "given": "Giuseppe" } }, { "id": "Ferry-J-G", "name": { "family": "Ferry", "given": "James G." } }, { "id": "Forget-F", "name": { "family": "Forget", "given": "Francois" } }, { "id": "Gao-Peter", "name": { "family": "Gao", "given": "Peter" }, "orcid": "0000-0002-8518-9601" }, { "id": "Hu-Renyu", "name": { "family": "Hu", "given": "Renyu" }, "orcid": "0000-0003-2215-8485" }, { "id": "Kleinb\u00f6hl-A", "name": { "family": "Kleinb\u00f6hl", "given": "Armin" } }, { "id": "Klusman-R", "name": { "family": "Klusman", "given": "Ronald" } }, { "id": "Lef\u00e8vre-F", "name": { "family": "Lef\u00e8vre", "given": "Franck" } }, { "id": "Miller-C-E", "name": { "family": "Miller", "given": "Charles" }, "orcid": "0000-0002-9380-4838" }, { "id": "Mischna-M-A", "name": { "family": "Mischna", "given": "Michael" }, "orcid": "0000-0002-8022-5319" }, { "id": "Mumma-M-J", "name": { "family": "Mumma", "given": "Michael" } }, { "id": "Newman-S", "name": { "family": "Newman", "given": "Sally" }, "orcid": "0000-0003-0710-995X" }, { "id": "Oehler-D-Z", "name": { "family": "Oehler", "given": "Dorothy" } }, { "id": "Okumura-M", "name": { "family": "Okumura", "given": "Mitchio" }, "orcid": "0000-0001-6874-1137" }, { "id": "Oremland-R-S", "name": { "family": "Oremland", "given": "Ronald" } }, { "id": "Orphan-V-J", "name": { "family": "Orphan", "given": "Victoria" }, "orcid": "0000-0002-5374-6178" }, { "id": "Popa-R", "name": { "family": "Popa", "given": "Radu" } }, { "id": "Russell-M-J", "name": { "family": "Russell", "given": "Michael" } }, { "id": "Shen-Linhan", "name": { "family": "Shen", "given": "Linhan" }, "orcid": "0000-0003-3871-655X" }, { "id": "Sherwood-Lollar-B", "name": { "family": "Sherwood Lollar", "given": "Barbara" } }, { "id": "Stamenkovi\u0107-V", "name": { "family": "Stamenkovi\u0107", "given": "Vlada" }, "orcid": "0000-0003-2416-3683" }, { "id": "Staehle-R-L", "name": { "family": "Staehle", "given": "Robert" } }, { "id": "Stolper-D-A", "name": { "family": "Stolper", "given": "Daniel" }, "orcid": "0000-0003-3299-3177" }, { "id": "Templeton-A", "name": { "family": "Templeton", "given": "Alexis" } }, { "id": "Vandaele-A-C", "name": { "family": "Vandaele", "given": "Ann C." } }, { "id": "Viscardy-S", "name": { "family": "Viscardy", "given": "S\u00e9bastien" } }, { "id": "Webster-C-R", "name": { "family": "Webster", "given": "Chris" } }, { "id": "Wennberg-P-O", "name": { "family": "Wennberg", "given": "Paul O." }, "orcid": "0000-0002-6126-3854" }, { "id": "Wong-Michael-L", "name": { "family": "Wong", "given": "Michael" } }, { "id": "Worden-J-R", "name": { "family": "Worden", "given": "John" }, "orcid": "0000-0003-0257-9549" } ] }, "title": "Methane on Mars and Habitability: Challenges and Responses", "ispublished": "unpub", "full_text_status": "public", "note": "Study Report prepared for the Keck Institute for Space Studies (KISS).\n\nWe dedicate this report to JPL scientist Mark Allen, whose spirit of generosity inspired many of the conversations and much of the work that brought us together. We thank the Director of the Keck Institute for Space Studies, Tom Prince, the Executive Director, Michele Judd, and the fantastic KISS staff for hosting our workshop and providing a wonderful environment for these discussions.\n\nAccepted Version - Methane_final_report.pdf
", "abstract": "Recent measurements of methane (CH_4) by the Mars Science Laboratory (MSL) now confront us with robust data that demand interpretation. Thus far, the MSL data have revealed a baseline level of CH_4 (\u223c0.4 parts per billion by volume [ppbv]), with seasonal variations, as well as greatly enhanced spikes of CH_4 with peak abundances of \u223c7\u2009ppbv. What do these CH_4 revelations with drastically different abundances and temporal signatures represent in terms of interior geochemical processes, or is martian CH_4 a biosignature? Discerning how CH_4 generation occurs on Mars may shed light on the potential habitability of Mars. There is no evidence of life on the surface of Mars today, but microbes might reside beneath the surface. In this case, the carbon flux represented by CH_4 would serve as a link between a putative subterranean biosphere on Mars and what we can measure above the surface. Alternatively, CH_4 records modern geochemical activity. Here we ask the fundamental question: how active is Mars, geochemically and/or biologically? In this article, we examine geological, geochemical, and biogeochemical processes related to our overarching question. The martian atmosphere and surface are an overwhelmingly oxidizing environment, and life requires pairing of electron donors and electron acceptors, that is, redox gradients, as an essential source of energy. Therefore, a fundamental and critical question regarding the possibility of life on Mars is, \"Where can we find redox gradients as energy sources for life on Mars?\" Hence, regardless of the pathway that generates CH_4 on Mars, the presence of CH_4, a reduced species in an oxidant-rich environment, suggests the possibility of redox gradients supporting life and habitability on Mars. Recent missions such as ExoMars Trace Gas Orbiter may provide mapping of the global distribution of CH_4. To discriminate between abiotic and biotic sources of CH_4 on Mars, future studies should use a series of diagnostic geochemical analyses, preferably performed below the ground or at the ground/atmosphere interface, including measurements of CH_4 isotopes, methane/ethane ratios, H_2 gas concentration, and species such as acetic acid. Advances in the fields of Mars exploration and instrumentation will be driven, augmented, and supported by an improved understanding of atmospheric chemistry and dynamics, deep subsurface biogeochemistry, astrobiology, planetary geology, and geophysics. Future Mars exploration programs will have to expand the integration of complementary areas of expertise to generate synergistic and innovative ideas to realize breakthroughs in advancing our understanding of the potential of life and habitable conditions having existed on Mars. In this spirit, we conducted a set of interdisciplinary workshops. From this series has emerged a vision of technological, theoretical, and methodological innovations to explore the martian subsurface and to enhance spatial tracking of key volatiles, such as CH_4.", "date": "2018-01", "date_type": "published", "publisher": "Astrobiology", "id_number": "CaltechAUTHORS:20180426-110252898", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180426-110252898", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "local_group": { "items": [ { "id": "Keck-Institute-for-Space-Studies" }, { "id": "Astronomy-Department" }, { "id": "Division-of-Geological-and-Planetary-Sciences" } ] }, "doi": "10.7907/Z990220K", "primary_object": { "basename": "Methane_final_report.pdf", "url": "https://authors.library.caltech.edu/records/3gcg3-khn91/files/Methane_final_report.pdf" }, "resource_type": "monograph", "pub_year": "2018", "author_list": "Yung, Yuk L.; Chen, Pin; et el." } ]