Across diverse contexts, bacteria experience loss of electron acceptors due to fluctuating environmental conditions, leading to growth-arrest and reductive stress. Yet, microbial metabolism has been primarily studied with cells growing under nutrient-replete conditions. To study how cells preserve metabolic flux under reductively stressed growth-arrest, we explored how the opportunistic pathogen Pseudomonas aeruginosa remodels its metabolism under such conditions. During anaerobic survival on glucose, P. aeruginosa utilizes the upper Embden-Meyerhoff-Parnas pathway and pentose-phosphate pathway to generate metabolite precursors for a previously undescribed phosphoketolase (herein termed xfp) used to produce acetyl-P and indirectly ATP via subsequent acetate formation. This re-routing bypasses P. aeruginosa's canonical glucose-catabolizing Entner-Doudoroff pathway (EDP), allowing for metabolic flux without exacerbating reductive stress. Moreover, anaerobic survival on diverse carbon sources triggers purine degradation and metabolite accumulation, requiring xfp to maintain metabolic balance and viability. Thus, our data suggest that phosphoketolases may play an additional role in ribonucleotide balance. This study expands our understanding of P. aeruginosa's anaerobic survival strategies and serves as a reminder that large gaps remain in our understanding of growth arrest physiology even in well-studied model organisms, highlighting the potential for basic discovery in the realm of non-growth metabolism.
", "doi": "10.1111/mmi.70059", "pmcid": "PMC13033310", "issn": "0950-382X", "publisher": "Wiley", "publication": "Molecular Microbiology", "publication_date": "2026-05-03", "series_number": "5", "volume": "125", "issue": "5", "pages": "361-374" }, { "id": "authors:fpyjb-qw793", "collection": "authors", "collection_id": "fpyjb-qw793", "cite_using_url": "https://authors.library.caltech.edu/records/fpyjb-qw793", "type": "article", "title": "Extracellular matrix chemistry tunes bacterial biofilm metabolism and optimizes fitness", "author": [ { "family_name": "Li", "given_name": "Jinyang", "orcid": "0000-0003-3190-4021", "clpid": "Li-Jinyang" }, { "family_name": "Squyres", "given_name": "Georgia R.", "orcid": "0000-0002-8717-2897", "clpid": "Squyres-Georgia-R" }, { "family_name": "Duong", "given_name": "Kathy" }, { "family_name": "Reichhardt", "given_name": "Courtney", "orcid": "0000-0002-1022-5110" }, { "family_name": "Parsek", "given_name": "Matthew R.", "orcid": "0000-0003-2932-7966" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Chemically complex extracellular matrices define cellular microenvironments and shape cell behavior across all domains of life. But how has evolution optimized these materials to ensure the success of multicellular communities? Inspired by the well-established composition\u2013properties\u2013function relationships in engineered materials, we hypothesized that analogous relationships exist in extracellular matrices, where the composition and interactions among various matrix components govern material properties and cellular physiology. Here, we examine\n Pseudomonas aeruginosa\n biofilms\u2014representative of ubiquitous multicellular microbial assemblies in nature and disease. We show that electrostatic interactions between the cationic polysaccharide Pel and extracellular DNA (eDNA) compete with eDNA binding to pyocyanin (PYO), a diffusible redox-active metabolite that supports anaerobic metabolism via extracellular electron transfer (EET). From a materials perspective, biofilm-mimetic hydrogels and natural biofilms revealed that altering Pel's charge via pH adjustment or chemical acetylation, or tuning the Pel:eDNA ratio, directly and predictably modulates PYO retention and EET efficiency. Biologically, a lower Pel:eDNA ratio enhances biofilm metabolism under oxygen limitation, whereas a higher ratio promotes survival under antibiotic stress. Notably, these perturbations (pH, Pel structure, and abundance) can be achieved directly or indirectly through biological activities. Together, these findings highlight how biologically regulated matrix chemistry encodes tunable material properties that, in turn, affect cellular responses that confer biofilm fitness advantages. They further suggest cells might actively fine-tune the surrounding matrix chemistry to maximize survival across diverse environments. More broadly, our work establishes a materials-based framework for a mechanistic understanding of the biological functions of extracellular matrix components in multicellular communities.", "doi": "10.1073/pnas.2528666123", "pmcid": "PMC13055754", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences", "publication_date": "2026-04-14", "series_number": "15", "volume": "123", "issue": "15", "pages": "e2528666123" }, { "id": "authors:zy2xp-md064", "collection": "authors", "collection_id": "zy2xp-md064", "cite_using_url": "https://authors.library.caltech.edu/records/zy2xp-md064", "type": "article", "title": "mGem: Facilitated fermentation\u2014an underappreciated mode of energy conservation", "author": [ { "family_name": "Ciemniecki", "given_name": "John A.", "orcid": "0000-0003-2789-6700" }, { "family_name": "Glasser", "given_name": "Nathaniel R.", "orcid": "0000-0002-2833-5166", "clpid": "Glasser-Nathaniel-Robert" }, { "family_name": "Gralnick", "given_name": "Jeffrey A.", "orcid": "0000-0001-9250-7770" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Here, we introduce a new name into the bacterial energy conservation lexicon: facilitated fermentation. This name is necessary because the more familiar terms \"respiration\" and \"fermentation\" do not adequately describe how electron balancing is coupled to energy conservation for organisms that engage in this metabolism. Facilitated fermentation is when ATP is predominantly made via a substrate-level pathway that is redox-coupled to a terminal electron acceptor reduced outside of the cell. The coupling is often facilitated by an extracellular electron shuttle or outer membrane protein that shuttles electrons from the electron transport chain to the extracellular acceptor. Naming facilitated fermentation is timely because it has recently been demonstrated to support both growth and non-growth states in bacteria that are important in nature and disease. We hope that the introduction of this term will inspire future research to evaluate the extent of facilitated fermentation's prevalence and impact in the microbial world and beyond.
", "doi": "10.1128/mbio.02494-25", "pmcid": "PMC13059778", "issn": "2150-7511", "publisher": "American Society for Microbiology", "publication": "mBio", "publication_date": "2026-04-08", "series_number": "4", "volume": "17", "issue": "4", "pages": "e02494-25" }, { "id": "authors:qf8bs-eqr98", "collection": "authors", "collection_id": "qf8bs-eqr98", "cite_using_url": "https://authors.library.caltech.edu/records/qf8bs-eqr98", "type": "article", "title": "Drought drives elevated antibiotic resistance across soils", "author": [ { "family_name": "Shan", "given_name": "Xiaoyu", "orcid": "0000-0001-9631-3244", "clpid": "Shan-Xiaoyu" }, { "family_name": "Cao", "given_name": "Karen", "orcid": "0009-0006-8636-5941", "clpid": "Cao-Karen" }, { "family_name": "Jeckel", "given_name": "Hannah", "orcid": "0000-0002-7080-4907", "clpid": "Jeckel-Hannah" }, { "family_name": "Alcalde", "given_name": "Reinaldo E.", "orcid": "0000-0002-3430-5393", "clpid": "Alcalde-Reinaldo-E" }, { "family_name": "Trindade", "given_name": "In\u00eas B.", "orcid": "0000-0002-6746-8455", "clpid": "Trindade-In\u00eas-B" }, { "family_name": "Kwiecinski", "given_name": "Jarek V.", "orcid": "0000-0003-1485-9302", "clpid": "Kwiecinski-Jarek-V" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Antibiotic resistance is a growing threat to human health and is often attributed to excessive clinical usage that selects for resistance. Although many antibiotics are derived from soil microorganisms, how environmental changes to soil ecosystems might promote resistance is poorly understood. Here we establish drought as a driving force of antibiotic resistance in the soil, with potentially far-reaching public health consequences. Across various geographic regions and soil types, we consistently observe metagenomic signatures of enrichment for antibiotic producers under drought conditions. Experimentally, we demonstrate that drought-induced lowering of water content concentrates natural antibiotics, thereby intensifying selection against sensitive strains and favouring antibiotic-resistant bacteria. Using clinical surveillance data from 116 countries, we show that the average frequency of hospital antibiotic resistance is strongly correlated with the local aridity index, even after controlling for regional income differences. Together, our findings reveal an underrecognized link between climate factors and antibiotic resistance.
\nMachine learning has enabled powerful biological discoveries using models trained on large datasets. However, for many important biological questions, such as identifying enzymes that transform understudied substrates, sparsity of training data is often a major bottleneck. Here, using phenazine natural products as a case study, we show that integrating genome-informed data augmentation with contrastive learning in protein language space enables identification of phenazine-interacting proteins starting from only 14 known phenazine modifying sequences. Applying this framework led to the discovery of PTC (Phenazine-Thiol Conjugase), the first enzyme known to catalyze phenazine thioconjugation, a phenazine modification reaction long observed but previously presumed to occur only through non-enzymatic chemistry. In silico simulation and experimental measurements demonstrate that PTC binds to both phenazine and glutathione as substrates. Recombinant expression and biochemical characterization reveal that PTC promotes glutathione-dependent modification of phenazines, yielding distinct reaction outcomes that depend on substrate identity. Although thiol-conjugated phenazine products exhibit reduced toxicity to bacterial cells, deletion of the gene encoding PTC does not confer a strong fitness disadvantage, illustrating how direct learning of sequences can uncover relevant enzymes that might evade phenotype-based genetic screens. Together, these results demonstrate that coupling comparative genomics with protein machine learning can convert “small data” typically outside the scope of machine learning into actionable predictive power, thereby facilitating enzyme discovery.
\nSignificance Machine learning excels when large, well-labeled datasets are available, yet many biologically important problems lack sufficient experimental data to support such approaches to discovery. This limitation is particularly acute for identifying enzymes acting on rare or understudied substrates. Here, we show that genomic organization can be leveraged as an additional source of biological information to address data sparsity. Starting with only 14 enzymes experimentally shown to modify phenazines, we developed a model identifying phenazine-interacting enzymes by integrating genome-informed data augmentation with protein machine learning. Guided by the model, we discovered the first enzyme known to catalyze thioconjugation modifications of phenazines, demonstrating a simple yet powerful strategy for extracting predictive insight from sparse biological knowledge.
\nMicrobial metabolism is impressively flexible, enabling growth even when available nutrients differ greatly from biomass in redox state. Escherichia coli, for example, rearranges its physiology to grow on reduced and oxidized carbon sources through several forms of fermentation and respiration. To understand the limits on and evolutionary consequences of this metabolic flexibility, we developed a coarse-grained mathematical framework coupling redox chemistry with principles of cellular resource allocation. Our models inherit key qualities from both of their antecedents: i) describing diverse metabolic chemistries and ii) enforcing the simultaneous balancing of atom (e.g., carbon), electron, and energy (adenosine triphosphate) flows, as in redox models, while iii) treating biomass as both the product and catalyst of the growth process, as in resource allocation models. Assembling integrated models of respiration, fermentation, and photosynthesis clarified key microbiological phenomena, including demonstrating that autotrophs grow more slowly than heterotrophs because of constraints imposed by the intracellular production of reduced carbon. Our model further predicted that heterotrophic growth is improved by matching the redox state of biomass to the nutrient environment. Through analysis of ≈60,000 genomes and diverse proteomic datasets, we found evidence that proteins indeed accumulate amino acid substitutions promoting redox matching. We therefore propose an unexpected mode of genome evolution where substitutions neutral or even deleterious to the individual biochemical or structural functions of proteins can nonetheless be selected due to a redox-chemical benefit to the population.
", "doi": "10.1073/pnas.2404048121", "pmcid": "PMC11725909", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences", "publication_date": "2025-01-07", "series_number": "1", "volume": "122", "issue": "1", "pages": "e2404048121" }, { "id": "authors:dn87m-jkm82", "collection": "authors", "collection_id": "dn87m-jkm82", "cite_using_url": "https://authors.library.caltech.edu/records/dn87m-jkm82", "type": "article", "title": "Soil microbiome interventions for carbon sequestration and climate mitigation", "author": [ { "family_name": "Beattie", "given_name": "Gwyn A.", "orcid": "0000-0002-0531-6843" }, { "family_name": "Edlund", "given_name": "Anna", "orcid": "0000-0002-3394-4804" }, { "family_name": "Esiobu", "given_name": "Nwadiuto", "orcid": "0000-0003-2164-0026" }, { "family_name": "Gilbert", "given_name": "Jack", "orcid": "0000-0001-7920-7001" }, { "family_name": "Nicolaisen", "given_name": "Mette Haubjerg", "orcid": "0000-0002-0983-2466" }, { "family_name": "Jansson", "given_name": "Janet K.", "orcid": "0000-0002-5487-4315" }, { "family_name": "Jensen", "given_name": "Paul", "orcid": "0000-0003-2349-1888" }, { "family_name": "Keiluweit", "given_name": "Marco", "orcid": "0000-0002-7061-8346" }, { "family_name": "Lennon", "given_name": "Jay T.", "orcid": "0000-0003-3126-6111" }, { "family_name": "Martiny", "given_name": "Jennifer", "orcid": "0000-0002-2415-1247" }, { "family_name": "Minnis", "given_name": "Vanessa R." }, { "family_name": "Newman", "given_name": "Dianne", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Peixoto", "given_name": "Raquel", "orcid": "0000-0002-9536-3132" }, { "family_name": "Schadt", "given_name": "Christopher", "orcid": "0000-0001-8759-2448" }, { "family_name": "van der Meer", "given_name": "Jan Roelof", "orcid": "0000-0003-1485-3082" } ], "editor": [ { "family_name": "Hernandez", "given_name": "Marcela" } ], "abstract": "Mitigating climate change in soil ecosystems involves complex plant and microbial processes regulating carbon pools and flows. Here, we advocate for the use of soil microbiome interventions to help increase soil carbon stocks and curb greenhouse gas emissions from managed soils. Direct interventions include the introduction of microbial strains, consortia, phage, and soil transplants, whereas indirect interventions include managing soil conditions or additives to modulate community composition or its activities. Approaches to increase soil carbon stocks using microbially catalyzed processes include increasing carbon inputs from plants, promoting soil organic matter (SOM) formation, and reducing SOM turnover and production of diverse greenhouse gases. Marginal or degraded soils may provide the greatest opportunities for enhancing global soil carbon stocks. Among the many knowledge gaps in this field, crucial gaps include the processes influencing the transformation of plant-derived soil carbon inputs into SOM and the identity of the microbes and microbial activities impacting this transformation. As a critical step forward, we encourage broadening the current widespread screening of potentially beneficial soil microorganisms to encompass functions relevant to stimulating soil carbon stocks. Moreover, in developing these interventions, we must consider the potential ecological ramifications and uncertainties, such as incurred by the widespread introduction of homogenous inoculants and consortia, and the need for site-specificity given the extreme variation among soil habitats. Incentivization and implementation at large spatial scales could effectively harness increases in soil carbon stocks, helping to mitigate the impacts of climate change.
", "doi": "10.1128/msystems.01129-24", "pmcid": "PMC11748500", "issn": "2379-5077", "publisher": "American Society for Microbiology", "publication": "mSystems", "publication_date": "2025-01", "series_number": "1", "volume": "10", "issue": "1", "pages": "e01129-24" }, { "id": "authors:9try3-cyw51", "collection": "authors", "collection_id": "9try3-cyw51", "cite_using_url": "https://authors.library.caltech.edu/records/9try3-cyw51", "type": "article", "title": "Biofilms as more than the sum of their parts: lessons from developmental biology", "author": [ { "family_name": "Squyres", "given_name": "Georgia R", "clpid": "Squyres-Georgia-R" }, { "family_name": "Newman", "given_name": "Dianne", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "The proton-motive force (PMF), consisting of a pH gradient and a membrane potential (ΔΨ) underpins many processes essential to bacterial growth and/or survival. Yet bacteria often enter a bioenergetically diminished state characterized by a low PMF. Consequently, they have increased tolerance for diverse stressors, including clinical antibiotics. Despite the ubiquity of low metabolic rates in the environment, the extent to which bacteria have agency over entry into such a low-bioenergetic state has received relatively little attention. Here, we tested the hypothesis that production of redox-active metabolites (RAMs) could drive such a physiological transition. Pseudomonas aeruginosa is an opportunistic pathogen that produces phenazines, model RAMs that are highly toxic in the presence of molecular oxygen (O2). Under oxic conditions, the phenazines pyocyanin and phenazine-1-carboximide, as well as toxoflavin—a RAM produced by Burkholderia species—suppress the ΔΨ in distinct ways across distributions of single cells, reduce the efficiency of proton pumping, and lower cellular adenosine-triphosphate (ATP) levels. In planktonic culture, the degree and rate by which each RAM lowers the ΔΨ correlates with the protection it confers against antibiotics that strongly impact cellular energy flux. This bioenergetic suppression requires the RAM’s presence and corresponds to its cellular reduction rate and abiotic oxidation rate by O2; it can be reversed by increasing the ΔΨ with nigericin. RAMs similarly impact the bioenergetic state of cells in (hyp)oxic biofilm aggregates. Collectively, these findings demonstrate that bacteria can suppress their bioenergetic state by the production of endogenous toxins in a manner that bolsters stress resilience.
", "doi": "10.1073/pnas.2406555121", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences", "publication_date": "2024-11-12", "series_number": "46", "volume": "121", "issue": "46", "pages": "e2406555121" }, { "id": "authors:2b7eq-e6f31", "collection": "authors", "collection_id": "2b7eq-e6f31", "cite_using_url": "https://authors.library.caltech.edu/records/2b7eq-e6f31", "type": "article", "title": "Annotation-free prediction of microbial dioxygen utilization", "author": [ { "family_name": "Flamholz", "given_name": "Avi I.", "orcid": "0000-0002-9278-5479", "clpid": "Flamholz-Avi-I" }, { "family_name": "Goldford", "given_name": "Joshua E.", "orcid": "0000-0001-7315-8018", "clpid": "Goldford-Joshua-E" }, { "family_name": "Richter", "given_name": "Philippa A.", "clpid": "Richter-Philippa-A" }, { "family_name": "Larsson", "given_name": "Elin M.", "orcid": "0000-0003-1341-5937" }, { "family_name": "Jinich", "given_name": "Adrian", "orcid": "0000-0001-8616-9250" }, { "family_name": "Fischer", "given_name": "Woodward W.", "orcid": "0000-0002-8836-3054", "clpid": "Fischer-W-W" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Aerobes require dioxygen (O2) to grow; anaerobes do not. However, nearly all microbes—aerobes, anaerobes, and facultative organisms alike—express enzymes whose substrates include O2, if only for detoxification. This presents a challenge when trying to assess which organisms are aerobic from genomic data alone. This challenge can be overcome by noting that O2 utilization has wide-ranging effects on microbes: aerobes typically have larger genomes encoding distinctive O2-utilizing enzymes, for example. These effects permit high-quality prediction of O2 utilization from annotated genome sequences, with several models displaying ≈80% accuracy on a ternary classification task for which blind guessing is only 33% accurate. Since genome annotation is compute-intensive and relies on many assumptions, we asked if annotation-free methods also perform well. We discovered that simple and efficient models based entirely on genomic sequence content—e.g., triplets of amino acids—perform as well as intensive annotation-based classifiers, enabling rapid processing of genomes. We further show that amino acid trimers are useful because they encode information about protein composition and phylogeny. To showcase the utility of rapid prediction, we estimated the prevalence of aerobes and anaerobes in diverse natural environments cataloged in the Earth Microbiome Project. Focusing on a well-studied O2 gradient in the Black Sea, we found quantitative correspondence between local chemistry (O2:sulfide concentration ratio) and the composition of microbial communities. We, therefore, suggest that statistical methods like ours might be used to estimate, or “sense,” pivotal features of the chemical environment using DNA sequencing data.
", "doi": "10.1128/msystems.00763-24", "pmcid": "PMC11494890", "issn": "2379-5077", "publisher": "American Society for Microbiology", "publication": "mSystems", "publication_date": "2024-10", "series_number": "10", "volume": "9", "issue": "10", "pages": "e00763-24" }, { "id": "authors:xb3nm-mp669", "collection": "authors", "collection_id": "xb3nm-mp669", "cite_using_url": "https://authors.library.caltech.edu/records/xb3nm-mp669", "type": "article", "title": "Investigating 3D microbial community dynamics of the rhizosphere using quantitative phase and fluorescence microscopy", "author": [ { "family_name": "Zhang", "given_name": "Oumeng", "orcid": "0000-0001-7318-2130", "clpid": "Zhang-Oumeng" }, { "family_name": "Alcalde", "given_name": "Reinaldo E.", "orcid": "0000-0002-3430-5393", "clpid": "Alcalde-Reinalde-E" }, { "family_name": "Zhou", "given_name": "Haowen", "orcid": "0000-0003-0955-4010", "clpid": "Zhou-Haowen" }, { "family_name": "Yin", "given_name": "Siyuan", "clpid": "Yin-Siyuan" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Yang", "given_name": "Changhuei", "orcid": "0000-0001-8791-0354", "clpid": "Yang-Changhuei" } ], "abstract": "Microbial interactions in the rhizosphere contribute to soil health, making understanding these interactions crucial for sustainable agriculture and ecosystem management. Yet it is difficult to understand what we cannot see; among the limitations in rhizosphere imaging are challenges associated with rapidly and noninvasively imaging microbial cells over field depths relevant to plant roots. Here, we present a bimodal imaging technique called complex-field and fluorescence microscopy using the aperture scanning technique (CFAST) that addresses these limitations. CFAST integrates quantitative phase imaging using synthetic aperture imaging based on Kramers–Kronig relations, along with three-dimensional (3D) fluorescence imaging using an engineered point spread function. We showcase CFAST’s practicality and versatility in two ways. First, by harnessing its depth of field of more than 100 μm, we significantly reduce the number of captures required for 3D imaging of plant roots and bacteria in the rhizoplane. This minimizes potential photobleaching and phototoxicity issues. Second, by leveraging CFAST’s phase sensitivity and fluorescence specificity, we track microbial growth, competition, and gene expression at early stages of colony biofilm development. Specifically, we resolve bacterial growth dynamics of mixed populations without the need for genetically labeling environmental isolates. Moreover, we find that gene expression related to phosphorus sensing and antibiotic production varies spatiotemporally within microbial populations that are surface attached and appears distinct from their expression in planktonic cultures. Together, CFAST’s attributes overcome commercial imaging platform limitations and enable insights to be gained into microbial behavioral dynamics in experimental systems of relevance to the rhizosphere.
", "doi": "10.1073/pnas.2403122121", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences", "publication_date": "2024-08-13", "series_number": "33", "volume": "121", "issue": "33", "pages": "e2403122121" }, { "id": "authors:etr6e-vc915", "collection": "authors", "collection_id": "etr6e-vc915", "cite_using_url": "https://authors.library.caltech.edu/records/etr6e-vc915", "type": "article", "title": "Widespread detoxifying NO reductases impart a distinct isotopic fingerprint on N\u2082O under anoxia", "author": [ { "family_name": "Wang", "given_name": "Ren\u00e9e Z.", "orcid": "0000-0003-3994-3244", "clpid": "Wang-Ren\u00e9e-Z" }, { "family_name": "Lonergan", "given_name": "Zachery R.", "orcid": "0000-0001-7694-2166", "clpid": "Lonergan-Zachery-R" }, { "family_name": "Wilbert", "given_name": "Steven A.", "orcid": "0009-0008-4409-8974", "clpid": "Wilbert-Steven-A" }, { "family_name": "Eiler", "given_name": "John M.", "orcid": "0000-0001-5768-7593", "clpid": "Eiler-J-M" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Pseudomonas aeruginosa (PA) is an opportunistic pathogen frequently isolated from cutaneous chronic wounds. How PA, in the presence of oxidative stress (OS), colonizes chronic wounds and forms a biofilm is still unknown. The purpose of this study is to investigate the changes in gene expression seen when PA is challenged with the high levels of OS present in chronic wounds. We used a biofilm-forming PA strain isolated from the chronic wounds of our murine model (RPA) and performed a qPCR to obtain gene expression patterns as RPA developed a biofilm in vitro in the presence of high levels of OS, and then compared the findings in vivo, in our mouse model of chronic wounds. We found that the planktonic bacteria under OS conditions overexpressed quorum sensing genes that are important for the bacteria to communicate with each other, antioxidant stress genes important to reduce OS in the microenvironment for survival, biofilm formation genes and virulence genes. Additionally, we performed RNAseq in vivo and identified the activation of novel genes/pathways of the Type VI Secretion System (T6SS) involved in RPA pathogenicity. In conclusion, RPA appears to survive the high OS microenvironment in chronic wounds and colonizes these wounds by turning on virulence, biofilm-forming and survival genes. These findings reveal pathways that may be promising targets for new therapies aimed at disrupting PA-containing biofilms immediately after debridement to facilitate the treatment of chronic human wounds.
\nThe capacity for bacterial extracellular electron transfer via secreted metabolites is widespread in natural, clinical, and industrial environments. Recently, we discovered the biological oxidation of phenazine-1-carboxylic acid (PCA), the first example of biological regeneration of a naturally produced extracellular electron shuttle. However, it remained unclear how PCA oxidation was catalyzed. Here, we report the mechanism, which we uncovered by genetically perturbing the branched electron transport chain (ETC) of the soil isolate Citrobacter portucalensis MBL. Biological PCA oxidation is coupled to anaerobic respiration with nitrate, fumarate, dimethyl sulfoxide, or trimethylamine-N-oxide as terminal electron acceptors. Genetically inactivating the catalytic subunits for all redundant complexes for a given terminal electron acceptor abolishes PCA oxidation. In the absence of quinones, PCA can still donate electrons to certain terminal reductases, albeit much less efficiently. In C. portucalensis MBL, PCA oxidation is largely driven by flux through the ETC, which suggests a generalizable mechanism that may be employed by any anaerobically respiring bacterium with an accessible cytoplasmic membrane. This model is supported by analogous genetic experiments during nitrate respiration by Pseudomonas aeruginosa.
", "doi": "10.1371/journal.pgen.1011064", "issn": "1553-7390", "publisher": "Public Library of Science", "publication": "PLOS Genetics", "publication_date": "2024-05", "pages": "1011064" }, { "id": "authors:sedrt-1d729", "collection": "authors", "collection_id": "sedrt-1d729", "cite_using_url": "https://authors.library.caltech.edu/records/sedrt-1d729", "type": "article", "title": "Polyphosphate affects cytoplasmic and chromosomal dynamics in nitrogen-starved Pseudomonas aeruginosa", "author": [ { "family_name": "Magkiriadou", "given_name": "Sofia", "orcid": "0000-0001-7660-5012", "clpid": "Magkiriadou-Sofia" }, { "family_name": "Stepp", "given_name": "Willi L.", "orcid": "0000-0001-9818-0377", "clpid": "Stepp-Willi-L" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Manley", "given_name": "Suliana", "orcid": "0000-0002-4755-4778" }, { "family_name": "Racki", "given_name": "Lisa R.", "orcid": "0000-0003-2209-7301", "clpid": "Racki-Lisa-R" } ], "abstract": "Objective: Pseudomonas aeruginosa is an opportunistic pathogen that can establish chronic infections and form biofilm in wounds. Because the wound environment is largely devoid of oxygen, P. aeruginosa may rely on anaerobic metabolism, such as nitrate respiration, to survive in wounds. While nitrate reductase (Nar) typically reduces nitrate to nitrite, it can also reduce chlorate to chlorite, which is a toxic oxidizing agent. Therefore, chlorate can act as a prodrug to specifically eradicate hypoxic/anoxic, nitrate-respiring P. aeruginosa populations, which are often tolerant to conventional antibiotic treatments.
\nApproach: Using a diabetic mouse model for chronic wounds, we tested the role that anaerobic nitrate respiration plays in supporting chronic P. aeruginosa infections.
\nResults: P. aeruginosa forms biofilm deep within the wound where the environment is anoxic. Daily treatment of P. aeruginosa-infected wounds with chlorate supported wound healing. Chlorate treatment was as effective as a treatment with ciprofloxacin (a conventional antibiotic that targets both oxic and hypoxic/anoxic P. aeruginosa populations). Chlorate-treated wounds showed markers of good-quality wound healing, including well-formed granulation tissue, reepithelialization and microvessel development. Loss- and gain-of-function experiments showed that P. aeruginosa requires nitrate respiration to establish a chronic wound infection and form biofilms.
\nInnovation: We show that the small molecule chlorate, kills the opportunistic pathogen, P. aeruginosa, by targeting a form of anaerobic metabolism called nitrate respiration.
\nConclusion: Chlorate holds promise as a treatment to combat diverse bacterial infections where oxygen is limiting and/or where pathogens grow as biofilms because many other pathogens possess Nar and survive using anaerobic metabolism.
", "doi": "10.1089/wound.2023.0036", "issn": "2162-1918", "publisher": "Mary Ann Liebert", "publication": "Advances in Wound Care", "publication_date": "2024-02", "series_number": "2", "volume": "13", "issue": "2", "pages": "53-69" }, { "id": "authors:wcnwq-0mw52", "collection": "authors", "collection_id": "wcnwq-0mw52", "cite_using_url": "https://authors.library.caltech.edu/records/wcnwq-0mw52", "type": "article", "title": "Engineering the Soil Bacterium Pseudomonas synxantha 2\u201379 into a Ratiometric Bioreporter for Phosphorus Limitation", "author": [ { "family_name": "Larsson", "given_name": "Elin M.", "orcid": "0000-0003-1341-5937", "clpid": "Larsson-Elin-M" }, { "family_name": "Murray", "given_name": "Richard M.", "orcid": "0000-0002-5785-7481", "clpid": "Murray-R-M" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Microbial bioreporters hold promise for addressing challenges in medical and environmental applications. However, the difficulty in ensuring their stable persistence and function within the target environment remains a challenge. One strategy is to integrate information about the host strain and target environment into the design-build-test cycle of the bioreporter itself. Here, we present a case study for such an environmentally motivated design process by engineering the wheat commensal bacterium Pseudomonas synxantha 2–79 into a ratiometric bioreporter for phosphorus limitation. Comparative analysis showed that an exogenous P-responsive promoter outperformed its native counterparts. This reporter can selectively sense and report phosphorus limitation at plant-relevant concentrations of 25–100 μM without cross-activation from carbon or nitrogen limitation or high cell densities. Its performance is robust over a field-relevant pH range (5.8–8), and it responds only to inorganic phosphorus, even in the presence of common soil organic P. Finally, we used fluorescein-calibrated flow cytometry to assess whether the reporter’s performance in shaken liquid culture predicts its performance in soil, finding that although the reporter is still functional at the bulk level, its variability in performance increases when grown in a soil slurry as compared to planktonic culture, with a fraction of the population not expressing the reporter proteins. Together, our environmentally aware design process provides an example of how laboratory bioengineering efforts can generate microbes with a greater promise to function reliably in their applied contexts.
\nNitrous oxide (N2O), a potent greenhouse gas, can be generated by compositionally complex microbial populations in diverse contexts. Accurately tracking the dominant biological sources of N2O has the potential to improve our understanding of N2O fluxes from soils as well as inform the diagnosis of human infections. Isotopic “Site Preference” (SP) values have been used towards this end, as bacterial and fungal nitric oxide reductases produce N2O with different isotopic fingerprints. Here we show that flavohemoglobin, a hitherto biogeochemically neglected yet widely distributed detoxifying bacterial NO reductase, imparts a distinct SP value onto N2O under anoxic conditions that correlates with typical environmental N2O SP measurements. We suggest a new framework to guide the attribution of N2O biological sources in nature and disease.
\n", "doi": "10.1101/2023.10.13.562248", "pmcid": "PMC10592819", "publication_date": "2023-10-14" }, { "id": "authors:pqhb4-a1z59", "collection": "authors", "collection_id": "pqhb4-a1z59", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230615-473807000.4", "type": "article", "title": "A phenazine-inspired framework for identifying biological functions of microbial redox-active metabolites", "author": [ { "family_name": "Thalhammer", "given_name": "Korbinian O.", "orcid": "0000-0001-6882-8611", "clpid": "Thalhammer-Korbinian-O" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "While the list of small molecules known to be secreted by environmental microbes continues to grow, our understanding of their in situ biological functions remains minimal. The time has come to develop a framework to parse the meaning of these \"secondary metabolites,\" which are ecologically ubiquitous and have direct applications in medicine and biotechnology. Here, we focus on a particular subset of molecules, redox active metabolites (RAMs), and review the well-studied phenazines as archetypes of this class. We argue that efforts to characterize the chemical, physical and biological makeup of the microenvironments, wherein these molecules are produced, coupled with measurements of the molecules' basic chemical properties, will enable significant progress in understanding the precise roles of novel RAMs.", "doi": "10.1016/j.cbpa.2023.102320", "issn": "1367-5931", "publisher": "Elsevier", "publication": "Current Opinion in Chemical Biology", "publication_date": "2023-08", "volume": "75", "pages": "Art. No. 102320" }, { "id": "authors:361jr-kmt64", "collection": "authors", "collection_id": "361jr-kmt64", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230615-473786000.3", "type": "article", "title": "Pyocyanin-dependent electrochemical inhibition of Pseudomonas aeruginosa biofilms is synergistic with antibiotic treatment", "author": [ { "family_name": "Jim\u00e9nez Otero", "given_name": "Fernanda", "clpid": "Jim\u00e9nez-Otero-Fernanda" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Tender", "given_name": "Leonard M.", "clpid": "Tender-Leonard-M" } ], "abstract": "Pseudomonas aeruginosa biofilms are common in chronic wound infections and recalcitrant to treatment. Survival of cells within oxygen-limited regions in these biofilms is enabled by extracellular electron transfer (EET), whereby small redox active molecules act as electron shuttles to access distal oxidants. Here, we report that electrochemically controlling the redox state of these electron shuttles, specifically pyocyanin (PYO), can impact cell survival within anaerobic P. aeruginosa biofilms and can act synergistically with antibiotic treatment. Prior results demonstrated that under anoxic conditions, an electrode poised at sufficiently oxidizing potential (+100 mV vs Ag/AgCl) promotes EET within P. aeruginosa biofilms by re-oxidizing PYO for reuse by the cells. Here, when a reducing potential (\u2212400 mV vs Ag/AgCl) was used to disrupt PYO redox cycling by maintaining PYO in the reduced state, we observed a 100-fold decrease in colony forming units within these biofilms compared with those exposed to electrodes poised at +100 mV vs Ag/AgCl. Phenazine-deficient \u0394phz* biofilms were unaffected by the potential applied to the electrode but were re-sensitized by adding PYO. The effect at \u2212400 mV was exacerbated when biofilms were treated with sub-MICs of a range of antibiotics. Most notably, addition of the aminoglycoside gentamicin in a reductive environment almost completely eradicated wild-type biofilms but had no effect on the survival of \u0394phz* biofilms in the absence of phenazines. These data suggest that antibiotic treatment combined with the electrochemical disruption of PYO redox cycling, either through the toxicity of accumulated reduced PYO or the disruption of EET, or both, can lead to extensive killing.", "doi": "10.1128/mbio.00702-23", "pmcid": "PMC10470778", "issn": "2150-7511", "publisher": "American Society for Microbiology", "publication": "mBio", "publication_date": "2023-07", "series_number": "4", "volume": "14", "issue": "4", "pages": "e0070223" }, { "id": "authors:1zqpp-rha08", "collection": "authors", "collection_id": "1zqpp-rha08", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230328-708572000.63", "type": "article", "title": "NADH dehydrogenases are the predominant phenazine reductases in the electron transport chain of Pseudomonas aeruginosa", "author": [ { "family_name": "Ciemniecki", "given_name": "John A.", "orcid": "0000-0003-2789-6700", "clpid": "Ciemniecki-John-A" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Phenazines are redox-active secondary metabolites produced by diverse bacteria including the opportunistic pathogen Pseudomonas aeruginosa. Extracellular electron transfer via phenazines enhances anaerobic survival by serving as an electron sink for glucose catabolism. However, the specific phenazine reductase(s) used to support this catabolism are unknown. Because electron transport chain components have been previously implicated in phenazine reduction, we sought to determine which of them possess phenazine reductase activity. We show that phenazine-1-carboxamide (PCN) and pyocyanin (PYO) are reduced at the highest rate by cells and are localized to the cell envelope while reduced. Using a coupled genetic and biochemical approach, we show that phenazine reductase activity in membrane fractions is attributable to the three NADH dehydrogenases present in P. aeruginosa and that their order of phenazine reductase activity is Nqr\u2009>\u2009Nuo\u2009>\u2009Ndh. In mutants possessing only one functional NADH dehydrogenase, whole cell reduction rates of PCN, but not PYO, recapitulate the pattern of biochemical results, implying that PYO reduction is predominantly occurring in the cytosol. Lastly, we show that ubiquinone rapidly and non-enzymatically oxidizes reduced phenazines, demonstrating that phenazines have the capability to serve in a redox loop between the NADH and ubiquinone pools, a finding that carries bioenergetic implications.", "doi": "10.1111/mmi.15049", "pmcid": "PMC11129870", "issn": "0950-382X", "publisher": "Wiley", "publication": "Molecular Microbiology", "publication_date": "2023-05", "series_number": "5", "volume": "119", "issue": "5", "pages": "560-573" }, { "id": "authors:r5t9w-ed325", "collection": "authors", "collection_id": "r5t9w-ed325", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230602-251523000.6", "type": "article", "title": "The chemical ecology of coumarins and phenazines affects iron acquisition by pseudomonads", "author": [ { "family_name": "McRose", "given_name": "Darcy\u00a0L.", "orcid": "0000-0001-9637-7176", "clpid": "McRose-Darcy-L" }, { "family_name": "Liang", "given_name": "Jinyang", "clpid": "Liang-Jinyang" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Secondary metabolites are important facilitators of plant\u2013microbe interactions in the rhizosphere, contributing to communication, competition, and nutrient acquisition. However, at first glance, the rhizosphere seems full of metabolites with overlapping functions, and we have a limited understanding of basic principles governing metabolite use. Increasing access to the essential nutrient iron is one important, but seemingly redundant role performed by both plant and microbial Redox-Active Metabolites (RAMs). We used coumarins, RAMs made by the model plant Arabidopsis thaliana, and phenazines, RAMs made by soil-dwelling pseudomonads, to ask whether plant and microbial RAMs might each have distinct functions under different environmental conditions. We show that variations in oxygen and pH lead to predictable differences in the capacity of coumarins vs phenazines to increase the growth of iron-limited pseudomonads and that these effects depend on whether pseudomonads are grown on glucose, succinate, or pyruvate: carbon sources commonly found in root exudates. Our results are explained by the chemical reactivities of these metabolites and the redox state of phenazines as altered by microbial metabolism. This work shows that variations in the chemical microenvironment can profoundly affect secondary metabolite function and suggests plants may tune the utility of microbial secondary metabolites by altering the carbon released in root exudates. Together, these findings suggest that RAM diversity may be less overwhelming when viewed through a chemical ecological lens: Distinct molecules can be expected to be more or less important to certain ecosystem functions, such as iron acquisition, depending on the local chemical microenvironments in which they reside.", "doi": "10.1073/pnas.2217951120", "pmcid": "PMC10083548", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2023-04-04", "series_number": "14", "volume": "120", "issue": "14", "pages": "Art. No. e2217951120" }, { "id": "authors:q3p8t-5rb66", "collection": "authors", "collection_id": "q3p8t-5rb66", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20221117-155838300.12", "type": "article", "title": "Optical O\u2082 Sensors Also Respond to Redox Active Molecules Commonly Secreted by Bacteria", "author": [ { "family_name": "Flamholz", "given_name": "Avi I.", "clpid": "Flamholz-Avi-I" }, { "family_name": "Saccomano", "given_name": "Samuel", "clpid": "Saccomano-Sameul-C" }, { "family_name": "Cash", "given_name": "Kevin", "clpid": "Cash-Kevin" }, { "family_name": "Newman", "given_name": "Dianne", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "From a metabolic perspective, molecular oxygen (O\u2082) is arguably the most significant constituent of Earth's atmosphere. Nearly every facet of microbial physiology is sensitive to the presence and concentration of O\u2082, which is the most favorable terminal electron acceptor used by organisms and also a dangerously reactive oxidant. As O\u2082 has such sweeping implications for physiology, researchers have developed diverse approaches to measure O\u2082 concentrations in natural and laboratory settings. Recent improvements to phosphorescent O\u2082 sensors piqued our interest due to the promise of optical measurement of spatiotemporal O\u2082 dynamics. However, we found that our preferred bacterial model, Pseudomonas aeruginosa PA14, secretes more than one molecule that quenches such sensors, complicating O\u2082 measurements in PA14 cultures and biofilms. Assaying supernatants from cultures of 9 bacterial species demonstrated that this phenotype is common: all supernatants quenched a soluble O\u2082 probe substantially. Phosphorescent O\u2082 probes are often embedded in solid support for protection, but an embedded probe called O\u2082NS was quenched by most supernatants as well. Measurements using pure compounds indicated that quenching is due to interactions with redox-active small molecules, including phenazines and flavins. Uncharged and weakly polar molecules like pyocyanin were especially potent quenchers of O\u2082NS. These findings underscore that optical O\u2082 measurements made in the presence of bacteria should be carefully controlled to ensure that O\u2082, and not bacterial secretions, is measured, and motivate the design of custom O\u2082 probes for specific organisms to circumvent sensitivity to redox-active metabolites.", "doi": "10.1128/mbio.02076-22", "pmcid": "PMC9765510", "issn": "2150-7511", "publisher": "American Society for Microbiology", "publication": "mBio", "publication_date": "2022-12-20", "series_number": "6", "volume": "13", "issue": "6", "pages": "Art. No. e0207622" }, { "id": "authors:hkr7w-yes43", "collection": "authors", "collection_id": "hkr7w-yes43", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230203-893210800.2", "type": "article", "title": "The contrasting roles of nitric oxide drive microbial community organization as a function of oxygen presence", "author": [ { "family_name": "Wilbert", "given_name": "Steven A.", "orcid": "0009-0008-4409-8974", "clpid": "Wilbert-Steven-A" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Microbial assemblages are omnipresent in the biosphere, forming communities on the surfaces of roots and rocks and within living tissues. These communities can exhibit strikingly beautiful compositional structures, with certain members reproducibly occupying particular spatiotemporal microniches. Despite this reproducibility, we lack the ability to explain these spatial patterns. We hypothesize that certain spatial patterns in microbial communities may be explained by the exchange of redox-active metabolites whose biological function is sensitive to microenvironmental gradients. To test this, we developed a simple community consisting of synthetic Pseudomonas aeruginosa strains with a partitioned denitrification pathway: a strict consumer and strict producer of nitric oxide (NO), a key pathway intermediate. Because NO can be both toxic or beneficial depending on the amount of oxygen present, this system provided an opportunity to investigate whether dynamic oxygen gradients can tune metabolic cross-feeding and fitness outcomes in a predictable fashion. Using a combination of genetic analysis, controlled growth environments, and imaging, we show that oxygen availability dictates whether NO cross-feeding is deleterious or mutually beneficial and that this organizing principle maps to the microscale. More generally, this work underscores the importance of considering the double-edged and microenvironmentally tuned roles redox-active metabolites can play in shaping microbial communities.", "doi": "10.1016/j.cub.2022.10.008", "pmcid": "PMC9772256", "issn": "0960-9822", "publisher": "Cell Press", "publication": "Current Biology", "publication_date": "2022-12-19", "series_number": "24", "volume": "32", "issue": "24", "pages": "5221-5234.e4" }, { "id": "authors:55c4m-41492", "collection": "authors", "collection_id": "55c4m-41492", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220808-223822000", "type": "article", "title": "Mechanisms of chlorate toxicity and resistance in Pseudomonas aeruginosa", "author": [ { "family_name": "Spero", "given_name": "Melanie A.", "orcid": "0000-0003-3291-2138", "clpid": "Spero-Melanie-A" }, { "family_name": "Jones", "given_name": "Jeff", "orcid": "0000-0002-7142-2222", "clpid": "Jones-Jeffrey-J" }, { "family_name": "Lomenick", "given_name": "Brett", "orcid": "0000-0002-5023-9998", "clpid": "Lomenick-Brett" }, { "family_name": "Chou", "given_name": "Tsui-Fen", "orcid": "0000-0003-2410-2186", "clpid": "Chou-Tsui-Fen" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Pseudomonas aeruginosa is an opportunistic bacterial pathogen that often encounters hypoxic/anoxic environments within the host, which increases its tolerance to many conventional antibiotics. Towards identifying novel treatments, we explored the therapeutic potential of chlorate, a pro-drug that kills hypoxic/anoxic, antibiotic-tolerant P. aeruginosa populations. While chlorate itself is relatively nontoxic, it is enzymatically reduced to the toxic oxidizing agent, chlorite, by hypoxically-induced nitrate reductase. To better assess chlorate's therapeutic potential, we investigated mechanisms of chlorate toxicity and resistance in P. aeruginosa. We used transposon mutagenesis to identify genes that alter P. aeruginosa fitness during chlorate treatment, finding that methionine sulfoxide reductases (Msr), which repair oxidized methionine residues, support survival during chlorate stress. Chlorate treatment leads to proteome-wide methionine oxidation, which is exacerbated in a \u2206msrA\u2206msrB strain. In response to chlorate, P. aeruginosa upregulates proteins involved in a wide range of functions, including metabolism, DNA replication/repair, protein repair, transcription, and translation, and these newly synthesized proteins are particularly vulnerable to methionine oxidation. The addition of exogenous methionine partially rescues P. aeruginosa survival during chlorate treatment, suggesting that widespread methionine oxidation contributes to death. Finally, we found that mutations that decrease nitrate reductase activity are a common mechanism of chlorate resistance.", "doi": "10.1111/mmi.14972", "pmcid": "PMC9589919", "issn": "0950-382X", "publisher": "Wiley", "publication": "Molecular Microbiology", "publication_date": "2022-10", "series_number": "4", "volume": "118", "issue": "4", "pages": "321-335" }, { "id": "authors:skw34-qy914", "collection": "authors", "collection_id": "skw34-qy914", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230322-367168000.14", "type": "monograph", "title": "Electrochemical disruption of extracellular electron transfer inhibits Pseudomonas aeruginosa cell survival within biofilms and is synergistic with antibiotic treatment", "author": [ { "family_name": "Jim\u00e9nez Otero", "given_name": "Fernanda", "orcid": "0000-0003-1583-6495", "clpid": "Jim\u00e9nez-Otero-Fernanda" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Tender", "given_name": "Leonard M.", "orcid": "0000-0001-8784-991X", "clpid": "Tender-Leonard-M" } ], "abstract": "Survival of cells within oxygen-limited regions in Pseudomonas aeruginosa biofilms is enabled by using small redox active molecules as electron shuttles to access distal oxidants. This respiratory versatility makes P. aeruginosa biofilms common in chronic wound infections and recalcitrant to treatment. Here, we show that electrochemically controlling the redox state of these electron shuttles, specifically pyocyanin, can impact cell survival within anaerobic P. aeruginosa biofilms and can act synergistically with antibiotic treatment. We inhibited pyocyanin redox cycling under anoxic conditions by blocking its ability to be re-oxidized and thus serve as an electron shuttle via poising an electrode at a reductive potential that cannot regenerate oxidized pyocyanin (i.e. \u2212400mV vs Ag/AgCl). This resulted in a decrease in CFUs within the biofilm of 100x compared to samples exposed to an electrode poised at an oxidizing potential that permits pyocyanin re-oxidation (i.e. +100mV vs Ag/AgCl). Phenazine-deficient \u0394phz* biofilms were not affected by the redox potential of the electrode, but were re-sensitized by adding pyocyanin. The effect of EET disruption was exacerbated when biofilms were treated with sub-MICs of a range of antibiotics. Most notably, 4 \u03bcg/ml of the aminoglycoside gentamicin in a reductive environment almost completely eradicated wild type biofilms but had no effect on the survival of \u0394phz* biofilms, suggesting reduced phenazines are toxic, and combined with antibiotic treatment can lead to extensive killing.ImportanceBiofilms provide a protective environment but they also present challenges to the cells living within them, such as overcoming diffusion limitation of nutrients and oxygen. Pseudomonas aeruginosa overcomes oxygen limitation by secreting soluble redox active molecules as electron shuttles to access distal oxygen. Here, we show that electrochemically blocking the redox cycling of one of these electron shuttles, pyocyanin, decreases cell survival within biofilms and acts synergistically with gentamicin to kill cells. Our results highlight the importance of the role that the redox cycling of electron shuttles fulfills within P. aeruginosa biofilms.", "doi": "10.1101/2022.09.15.508205", "publication_date": "2022-09-19" }, { "id": "authors:eaa21-b8008", "collection": "authors", "collection_id": "eaa21-b8008", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220810-751722000", "type": "monograph", "title": "Optical O\u2082 sensors also respond to redox active molecules commonly secreted by bacteria", "author": [ { "family_name": "Flamholz", "given_name": "Avi I.", "orcid": "0000-0002-9278-5479", "clpid": "Flamholz-Avi-I" }, { "family_name": "Saccomano", "given_name": "Samuel", "orcid": "0000-0001-9105-2663", "clpid": "Saccomano-Sameul-C" }, { "family_name": "Cash", "given_name": "Kevin", "orcid": "0000-0002-8059-0922", "clpid": "Cash-Kevin-J" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "From a metabolic perspective, molecular oxygen (O\u2082) is arguably the most significant constituent of Earth's atmosphere. Nearly every facet of microbial physiology is sensitive to the presence and concentration of O\u2082, which is the most favorable terminal electron acceptor used by biology and also a dangerously reactive oxidant. As O\u2082 has such sweeping implications for physiology, researchers have developed diverse approaches to measure O\u2082 concentrations in natural and laboratory settings. Recent improvements to phosphorescent O\u2082 sensors piqued our interest due to the promise of optical measurement of spatiotemporal O\u2082 dynamics. However, we found that our preferred bacterial model, Pseudomonas aeruginosa PA14, secretes more than one molecule that quenches such sensors, complicating O\u2082 measurements in PA14 cultures and biofilms. Assaying supernatants from cultures of 9 bacterial species demonstrated that this phenotype is common: all supernatants quenched a soluble O\u2082 probe substantially. Phosphorescent O\u2082 probes are often embedded in solid support for protection, but an embedded probe called O\u2082 NS was quenched by most supernatants as well. Measurements using pure compounds indicated that quenching is due to interactions with redox-active small molecules including phenazines and flavins. Uncharged and weakly-polar molecules like pyocyanin were especially potent quenchers of O\u2082 NS. These findings underscore that optical O\u2082 measurements made in the presence of bacteria should be carefully controlled to ensure that O2, and not bacterial secretions, is measured, and motivate the design of custom O\u2082 probes for specific organisms to circumvent sensitivity to redox-active metabolites.", "doi": "10.1101/2022.08.08.503264", "publication_date": "2022-08-10" }, { "id": "authors:hddm6-jdn37", "collection": "authors", "collection_id": "hddm6-jdn37", "cite_using_url": "https://authors.library.caltech.edu/records/hddm6-jdn37", "type": "article", "title": "Search for Resonances Decaying to Three W Bosons in Proton-Proton Collisions at \u221as=13TeV", "author": [ { "family_name": "Tumasyan", "given_name": "A." }, { "family_name": "Adam", "given_name": "W." }, { "family_name": "Andrejkovic", "given_name": "J.\u2009W." }, { "family_name": "Bergauer", "given_name": "T." }, { "family_name": "Chatterjee", "given_name": "S.", "orcid": "0000-0003-2660-0349" }, { "family_name": "Dragicevic", "given_name": "M.", "orcid": "0000-0003-1967-6783" }, { "family_name": "Del Valle", "given_name": "A. Escalante", "orcid": "0000-0002-9702-6359" }, { "family_name": "Fr\u00fchwirth", "given_name": "R." }, { "family_name": "Jeitler", "given_name": "M." }, { "family_name": "Krammer", "given_name": "N." }, { "family_name": "Lechner", "given_name": "L.", "orcid": "0000-0002-3065-1141" }, { "family_name": "Liko", "given_name": "D." }, { "family_name": "Mikulec", "given_name": "I." }, { "family_name": "Paulitsch", "given_name": "P.", "orcid": "0000-0001-8236-7532" }, { "family_name": "Pitters", "given_name": "F.\u2009M." }, { "family_name": "Schieck", "given_name": "J.", "orcid": "0000-0002-1058-8093" }, { "family_name": "Sch\u00f6fbeck", "given_name": "R." }, { "family_name": "Spanring", "given_name": "M." }, { "family_name": "Templ", "given_name": "S." }, { "family_name": "Waltenberger", "given_name": "W.", "orcid": "0000-0002-6215-7228" }, { "family_name": "Wulz", "given_name": "C.-E." }, { "family_name": "Chekhovsky", "given_name": "V." }, { "family_name": "Litomin", "given_name": "A." }, { "family_name": "Makarenko", "given_name": "V." }, { "family_name": "Darwish", "given_name": "M.\u2009R." }, { "family_name": "De Wolf", "given_name": "E.\u2009A." }, { "family_name": "Janssen", "given_name": "T.", "orcid": "0000-0002-3998-4081" }, { "family_name": "Kello", "given_name": "T." }, { "family_name": "Lelek", "given_name": "A." }, { "family_name": "Sfar", "given_name": "H. 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"family_name": "Tuo", "given_name": "S." }, { "family_name": "Velkovska", "given_name": "J." }, { "family_name": "Arenton", "given_name": "M.\u2009W." }, { "family_name": "Cox", "given_name": "B." }, { "family_name": "Cummings", "given_name": "G." }, { "family_name": "Hakala", "given_name": "J." }, { "family_name": "Hirosky", "given_name": "R." }, { "family_name": "Joyce", "given_name": "M." }, { "family_name": "Ledovskoy", "given_name": "A." }, { "family_name": "Li", "given_name": "A." }, { "family_name": "Neu", "given_name": "C." }, { "family_name": "Tannenwald", "given_name": "B." }, { "family_name": "White", "given_name": "S." }, { "family_name": "Wolfe", "given_name": "E." }, { "family_name": "Poudyal", "given_name": "N.", "orcid": "0000-0003-4278-3464" }, { "family_name": "Black", "given_name": "K." }, { "family_name": "Bose", "given_name": "T." }, { "family_name": "Buchanan", "given_name": "J.", "orcid": "0000-0001-8207-5556" }, { "family_name": "Caillol", "given_name": "C." }, { "family_name": "Dasu", "given_name": "S." }, { "family_name": "De Bruyn", "given_name": "I." }, { "family_name": "Everaerts", "given_name": "P.", "orcid": "0000-0003-3848-324X" }, { "family_name": "Fienga", "given_name": "F.", "orcid": "0000-0001-5978-4952" }, { "family_name": "Galloni", "given_name": "C." }, { "family_name": "He", "given_name": "H." }, { "family_name": "Herndon", "given_name": "M.", "orcid": "0000-0003-3043-1090" }, { "family_name": "Herv\u00e9", "given_name": "A." }, { "family_name": "Hussain", "given_name": "U." }, { "family_name": "Lanaro", "given_name": "A." }, { "family_name": "Loeliger", "given_name": "A." }, { "family_name": "Loveless", "given_name": "R." }, { "family_name": "Sreekala", "given_name": "J. Madhusudanan" }, { "family_name": "Mallampalli", "given_name": "A." }, { "family_name": "Mohammadi", "given_name": "A." }, { "family_name": "Pinna", "given_name": "D.", "orcid": "0000-0002-0947-1357" }, { "family_name": "Savin", "given_name": "A." }, { "family_name": "Shang", "given_name": "V." }, { "family_name": "Sharma", "given_name": "V." }, { "family_name": "Smith", "given_name": "W.\u2009H.", "orcid": "0000-0003-3195-0909" }, { "family_name": "Teague", "given_name": "D." }, { "family_name": "Trembath-Reichert", "given_name": "S." }, { "family_name": "Vetens", "given_name": "W.", "orcid": "0000-0003-1058-1163" }, { "literal": "CMS Collaboration" } ], "abstract": "A search for resonances decaying into a \ud835\udc4a boson and a radion, where the radion decays into two \ud835\udc4a bosons, is presented. The data analyzed correspond to an integrated luminosity of 138 fb−1 recorded in proton-proton collisions with the CMS detector at √\ud835\udc60=13 TeV. One isolated charged lepton is required, together with missing transverse momentum and one or two massive large-radius jets, containing the decay products of either two or one \ud835\udc4a bosons, respectively. No excess over the background estimation is observed. The results are combined with those from a complementary channel with an all-hadronic final state, described in an accompanying paper. Limits are set on parameters of an extended warped extra-dimensional model. These searches are the first of their kind at the LHC.
", "doi": "10.1103/physrevlett.129.021802", "issn": "0031-9007", "publisher": "American Physical Society", "publication": "Physical Review Letters", "publication_date": "2022-07-08", "series_number": "2", "volume": "129", "issue": "2", "pages": "021802" }, { "id": "authors:myk7s-dkk86", "collection": "authors", "collection_id": "myk7s-dkk86", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210902-193802546", "type": "article", "title": "Hopanoids Confer Robustness to Physicochemical Variability in the Niche of the Plant Symbiont Bradyrhizobium diazoefficiens", "author": [ { "family_name": "Tookmanian", "given_name": "Elise", "orcid": "0000-0003-3114-2354", "clpid": "Tookmanian-Elise-M" }, { "family_name": "Junghans", "given_name": "Lisa", "clpid": "Junghans-Lisa" }, { "family_name": "Kulkarni", "given_name": "Gargi", "clpid": "Kulkarni-Gargi" }, { "family_name": "Ledermann", "given_name": "Raphael", "orcid": "0000-0003-4612-1708", "clpid": "Ledermann-Raphael" }, { "family_name": "Saenz", "given_name": "James", "orcid": "0000-0001-8901-4377", "clpid": "Saenz-James-Peter" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Rhizobia are a group of bacteria that increase soil nitrogen content through symbiosis with legume plants. The soil and symbiotic host are potentially stressful environments, and the soil will likely become even more stressful as the climate changes. Many rhizobia within the Bradyrhizobium clade, like Bradyrhizobium diazoefficiens, possess the genetic capacity to synthesize hopanoids, steroid-like lipids similar in structure and function to cholesterol. Hopanoids are known to protect against stresses relevant to the niche of B. diazoefficiens. Paradoxically, mutants unable to synthesize the extended class of hopanoids participate in symbioses with success similar to that of the wild type, despite being delayed in root nodule initiation. Here, we show that in B. diazoefficiens, the growth defects of extended-hopanoid-deficient mutants can be at least partially compensated for by the physicochemical environment, specifically, by optimal osmotic and divalent cation concentrations. Through biophysical measurements of lipid packing and membrane permeability, we show that extended hopanoids confer robustness to environmental variability. These results help explain the discrepancy between previous in-culture and in planta results and indicate that hopanoids may provide a greater fitness advantage to rhizobia in the variable soil environment than the more controlled environments within root nodules. To improve the legume-rhizobium symbiosis through either bioengineering or strain selection, it will be important to consider the full life cycle of rhizobia, from soil to symbiosis.", "doi": "10.1128/jb.00442-21", "pmcid": "PMC9295548", "issn": "0021-9193", "publisher": "American Society for Microbiology", "publication": "Journal of Bacteriology", "publication_date": "2022-07", "series_number": "7", "volume": "204", "issue": "7", "pages": "jb.00442-21" }, { "id": "authors:kqse5-2v453", "collection": "authors", "collection_id": "kqse5-2v453", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211203-174950532", "type": "article", "title": "Phenazines and toxoflavin act as interspecies modulators of resilience to diverse antibiotics", "author": [ { "family_name": "Meirelles", "given_name": "Lucas A.", "orcid": "0000-0003-3194-7136", "clpid": "Meirelles-Lucas-A" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Bacterial opportunistic pathogens make diverse secondary metabolites both in the natural environment and when causing infections, yet how these molecules mediate microbial interactions and their consequences for antibiotic treatment are still poorly understood. Here, we explore the role of three redox-active secondary metabolites, pyocyanin, phenazine-1-carboxylic acid, and toxoflavin, as interspecies modulators of antibiotic resilience. We find that these molecules dramatically change susceptibility levels of diverse bacteria to clinical antibiotics. Pyocyanin and phenazine-1-carboxylic acid are made by Pseudomonas aeruginosa, while toxoflavin is made by Burkholderia gladioli, organisms that infect cystic fibrosis and other immunocompromised patients. All molecules alter the susceptibility profile of pathogenic species within the \"Burkholderia cepacia complex\" to different antibiotics, either antagonizing or potentiating their effects, depending on the drug's class. Defense responses regulated by the redox-sensitive transcription factor SoxR potentiate the antagonistic effects these metabolites have against fluoroquinolones, and the presence of genes encoding SoxR and the efflux systems it regulates can be used to predict how these metabolites will affect antibiotic susceptibility of different bacteria. Finally, we demonstrate that inclusion of secondary metabolites in standard protocols used to assess antibiotic resistance can dramatically alter the results, motivating the development of new tests for more accurate clinical assessment.", "doi": "10.1111/mmi.14915", "pmcid": "PMC10249331", "issn": "0950-382X", "publisher": "Wiley", "publication": "Molecular Microbiology", "publication_date": "2022-06", "series_number": "6", "volume": "117", "issue": "6", "pages": "1384-1404" }, { "id": "authors:2rf5c-fpt24", "collection": "authors", "collection_id": "2rf5c-fpt24", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220315-626233000", "type": "article", "title": "Visualization of mRNA Expression in Pseudomonas aeruginosa Aggregates Reveals Spatial Patterns of Fermentative and Denitrifying Metabolism", "author": [ { "family_name": "Livingston", "given_name": "Jadzia", "clpid": "Livingston-Jadzia" }, { "family_name": "Spero", "given_name": "Melanie A.", "orcid": "0000-0003-3291-2138", "clpid": "Spero-Melanie-A" }, { "family_name": "Lonergan", "given_name": "Zachery R.", "clpid": "Lonergan-Zachary-R" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Gaining insight into the behavior of bacteria at the single-cell level is important given that heterogeneous microenvironments strongly influence microbial physiology. The hybridization chain reaction (HCR) is a technique that provides in situ molecular signal amplification, enabling simultaneous mapping of multiple target RNAs at small spatial scales. To refine this method for biofilm applications, we designed and validated new probes to visualize the expression of key catabolic genes in Pseudomonas aeruginosa aggregates. In addition to using existing probes for the dissimilatory nitrate reductase (narG), we developed probes for a terminal oxidase (ccoN1), nitrite reductase (nirS), nitrous oxide reductase (nosZ), and acetate kinase (ackA). These probes can be used to determine gene expression levels across heterogeneous populations such as biofilms. Using these probes, we quantified gene expression across oxygen gradients in aggregate populations grown using the agar block biofilm assay (ABBA). We observed distinct patterns of catabolic gene expression, with upregulation occurring in particular ABBA regions both within individual aggregates and over the aggregate population. Aerobic respiration (ccoN1) showed peak expression under oxic conditions, whereas fermentation (ackA) showed peak expression in the anoxic cores of high metabolic activity aggregates near the air-agar interface. Denitrification genes narG, nirS, and nosZ showed peak expression in hypoxic and anoxic regions, although nirS expression remained at peak levels deeper into anoxic environments than other denitrification genes. These results reveal that the microenvironment correlates with catabolic gene expression in aggregates, and they demonstrate the utility of HCR in unveiling cellular activities at the microscale level in heterogeneous populations.", "doi": "10.1128/aem.00439-22", "issn": "0099-2240", "publisher": "American Society for Microbiology", "publication": "Applied and Environmental Microbiology", "publication_date": "2022-06", "series_number": "11", "volume": "88", "issue": "11", "pages": "Art. No. aem.00439-22" }, { "id": "authors:szapg-0zc26", "collection": "authors", "collection_id": "szapg-0zc26", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220318-882662036", "type": "article", "title": "Microbial communities: The metabolic rate is the trait", "author": [ { "family_name": "Flamholz", "given_name": "Avi I.", "orcid": "0000-0002-9278-5479", "clpid": "Flamholz-Avi-I" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Making sense of the metabolism of microbial communities is a daunting task. Using denitrification as a model metabolism, a new paper shows that the rate of denitrification can often be predicted from genome contents, and dynamical models can be composed to predict denitrification rates of communities of two to five species.", "doi": "10.1016/j.cub.2022.02.002", "issn": "0960-9822", "publisher": "Cell Press", "publication": "Current Biology", "publication_date": "2022-03-14", "series_number": "5", "volume": "32", "issue": "5", "pages": "R215-R218" }, { "id": "authors:rd7t7-rx934", "collection": "authors", "collection_id": "rd7t7-rx934", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210917-143518027", "type": "article", "title": "From the soil to the clinic: the impact of microbial secondary metabolites on antibiotic tolerance and resistance", "author": [ { "family_name": "Perry", "given_name": "Elena K.", "orcid": "0000-0002-7151-1479", "clpid": "Perry-Elena-K" }, { "family_name": "Meirelles", "given_name": "Lucas A.", "orcid": "0000-0003-3194-7136", "clpid": "Meirelles-Lucas-A" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Secondary metabolites profoundly affect microbial physiology, metabolism and stress responses. Increasing evidence suggests that these molecules can modulate microbial susceptibility to commonly used antibiotics; however, secondary metabolites are typically excluded from standard antimicrobial susceptibility assays. This may in part account for why infections by diverse opportunistic bacteria that produce secondary metabolites often exhibit discrepancies between clinical antimicrobial susceptibility testing results and clinical treatment outcomes. In this Review, we explore which types of secondary metabolite alter antimicrobial susceptibility, as well as how and why this phenomenon occurs. We discuss examples of molecules that opportunistic and enteric pathogens either generate themselves or are exposed to from their neighbours, and the nuanced impacts these molecules can have on tolerance and resistance to certain antibiotics.", "doi": "10.1038/s41579-021-00620-w", "pmcid": "PMC8857043", "issn": "1740-1526", "publisher": "Nature Publishing Group", "publication": "Nature Reviews Microbiology", "publication_date": "2022-03", "series_number": "3", "volume": "20", "issue": "3", "pages": "129-142" }, { "id": "authors:v9k41-6mf70", "collection": "authors", "collection_id": "v9k41-6mf70", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211129-175740276", "type": "article", "title": "Prevalence and Correlates of Phenazine Resistance in Culturable Bacteria from a Dryland Wheat Field", "author": [ { "family_name": "Perry", "given_name": "Elena K.", "orcid": "0000-0002-7151-1479", "clpid": "Perry-Elena-K" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Phenazines are a class of bacterially produced redox-active natural antibiotics that have demonstrated potential as a sustainable alternative to traditional pesticides for the biocontrol of fungal crop diseases. However, the prevalence of bacterial resistance to agriculturally relevant phenazines is poorly understood, limiting both the understanding of how these molecules might shape rhizosphere bacterial communities and the ability to perform a risk assessment for off-target effects. Here, we describe profiles of susceptibility to the antifungal agent phenazine-1-carboxylic acid (PCA) across more than 100 bacterial strains isolated from a wheat field where PCA producers are indigenous and abundant. We found that Gram-positive bacteria are typically more sensitive to PCA than Gram-negative bacteria, and there was significant variability in susceptibility both within and across phyla. Phenazine-resistant strains were more likely to be isolated from the wheat rhizosphere, where PCA producers were also more abundant, compared to bulk soil. Furthermore, PCA toxicity was pH-dependent for most susceptible strains and broadly correlated with PCA reduction rates, suggesting that uptake and redox-cycling were important determinants of phenazine toxicity. Our results shed light on which classes of bacteria are most likely to be susceptible to phenazine toxicity in acidic or neutral soils. In addition, the taxonomic and phenotypic diversity of our strain collection represents a valuable resource for future studies on the role of natural antibiotics in shaping wheat rhizosphere communities.", "doi": "10.1128/aem.02320-21", "pmcid": "PMC8939311", "issn": "0099-2240", "publisher": "American Society for Microbiology", "publication": "Applied and Environmental Microbiology", "publication_date": "2022-03", "series_number": "6", "volume": "88", "issue": "6", "pages": "Art. No. e02320-21" }, { "id": "authors:8rxt3-fyb77", "collection": "authors", "collection_id": "8rxt3-fyb77", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211208-560304000", "type": "article", "title": "Soil bacteria protect fungi from phenazines by acting as toxin sponges", "author": [ { "family_name": "Dahlstrom", "given_name": "Kurt M.", "orcid": "0000-0001-6590-6020", "clpid": "Dahlstrom-Kurt-M" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Many environmentally and clinically important fungi are sensitive to toxic, bacterially produced, redox-active molecules called phenazines. Despite being vulnerable to phenazine assault, fungi inhabit microbial communities that contain phenazine producers. Because many fungi cannot withstand phenazine challenge but some bacterial species can, we hypothesized that bacterial partners may protect fungi in phenazine-replete environments. From a single soil sample, we were able to co-isolate several such physically associated pairings. We discovered the novel species Paraburkholderia edwinii and demonstrated it can protect a co-isolated Aspergillus species from phenazine-1-carboxylic acid (PCA) by sequestering it, acting as a toxin sponge; in turn, it also gains protection. When challenged with PCA, P. edwinii changes its morphology, forming aggregates within the growing fungal colony. Further, the fungal partner triggers P. edwinii to sequester PCA and maintains conditions that limit PCA toxicity by promoting an anoxic and highly reducing environment. A mutagenic screen of P. edwinii revealed this protective program depends on the stress-inducible transcriptional repressor HrcA. We show that one relevant stressor in response to PCA challenge is fungal acidification and that acid stress causes P. edwinii to behave as though the fungus were present. Finally, we reveal this phenomenon as widespread among Paraburkholderia with moderate specificity among bacterial and fungal partners, including plant and human pathogens. Our discovery suggests a common mechanism by which fungi can gain access to phenazine-replete environments and provides a tractable model system for its study. These results have implications for how microbial communities in the rhizosphere as well as in plant and human infection sites negotiate community membership via a chemical dialectic.", "doi": "10.1016/j.cub.2021.11.002", "issn": "0960-9822", "publisher": "Cell Press", "publication": "Current Biology", "publication_date": "2022-01-24", "series_number": "2", "volume": "32", "issue": "2", "pages": "275-288" }, { "id": "authors:tjwxh-wyn19", "collection": "authors", "collection_id": "tjwxh-wyn19", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220104-461622500", "type": "monograph", "title": "Polyphosphate affects cytoplasmic and chromosomal dynamics in nitrogen-starved Pseudomonas aeruginosa", "author": [ { "family_name": "Magkiriadou", "given_name": "S.", "orcid": "0000-0001-7660-5012", "clpid": "Magkiriadou-Sofia" }, { "family_name": "Habel", "given_name": "A.", "clpid": "Habel-A" }, { "family_name": "Stepp", "given_name": "W. L.", "orcid": "0000-0001-9818-0377", "clpid": "Stepp-Willi-L" }, { "family_name": "Newman", "given_name": "D. K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Manley", "given_name": "S.", "orcid": "0000-0002-4755-4778", "clpid": "Manley-Suliana" }, { "family_name": "Racki", "given_name": "L. R.", "clpid": "Racki-L-R" } ], "abstract": "Polyphosphate (polyP) synthesis is a ubiquitous stress and starvation response in bacteria. In diverse species, mutants unable to make polyP have a wide variety of physiological defects, but the mechanisms by which this simple polyanion exerts its effects remain unclear. One possibility is that polyP's many functions stem from global effects on the biophysical properties of the cell. We characterize the effect of polyphosphate on cytoplasmic mobility under nitrogen-starvation conditions in the opportunistic pathogen Pseudomonas aeruginosa. Using fluorescence microscopy and particle tracking, we characterize the motion of chromosomal loci and free tracer particles in the cytoplasm. In the absence of polyP and upon starvation, we observe an increase in mobility both for chromosomal loci and for tracer particles. Tracer particles reveal that polyP also modulates the partitioning between a 'more mobile' and a 'less mobile' population: small particles in cells unable to make polyP are more likely to be 'mobile' and explore more of the cytoplasm, particularly during starvation. We speculate that this larger freedom of motion may be a consequence of nucleoid decompaction, which we also observe in starved cells deficient in polyP. Our observations suggest that polyP limits cytoplasmic mobility and accessibility during nitrogen starvation, which may help to explain the pleiotropic phenotypes observed in the absence of polyP.", "doi": "10.1101/2021.12.23.473106", "publication_date": "2021-12-24" }, { "id": "authors:t2agr-dms53", "collection": "authors", "collection_id": "t2agr-dms53", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211210-238484000", "type": "monograph", "title": "The contrasting roles of nitric oxide drive microbial community organization as a function of oxygen presence", "author": [ { "family_name": "Wilbert", "given_name": "Steven A.", "clpid": "Wilbert-Steven-A" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Microbial assemblages are omnipresent in the biosphere, forming communities on the surfaces of roots, rocks, and within living tissues. These communities can exhibit strikingly beautiful compositional structures, with certain members reproducibly occupying particular spatiotemporal microniches. Yet often, we lack the ability to explain the spatial patterns we see within them. To test the hypothesis that certain spatial patterns in microbial communities may be explained by the exchange of redox-active metabolites whose biological function is sensitive to environmental gradients, here we developed a simple community consisting of synthetic Pseudomonas aeruginosa strains with a partitioned denitrification pathway: a strict consumer and strict producer of nitric oxide (NO), a key pathway intermediate. Because NO can be both toxic or beneficial depending on the amount of oxygen present, this system provided an opportunity to investigate whether dynamic oxygen gradients can tune metabolic cross-feeding in a predictable fashion. Using a combination of genetic analysis, different growth environments and imaging, we show that oxygen availability controls whether NO cross-feeding is commensal or mutually beneficial, and that this organizing principle maps to the microscale. More generally, this work underscores the importance of considering the double-edged roles redox-active metabolites can play in shaping microbial communities.", "doi": "10.1101/2021.12.09.472001", "publication_date": "2021-12-10" }, { "id": "authors:x70j9-kd757", "collection": "authors", "collection_id": "x70j9-kd757", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211116-212551206", "type": "article", "title": "Model Systems to Study the Chronic, Polymicrobial Infections in Cystic Fibrosis: Current Approaches and Exploring Future Directions", "author": [ { "family_name": "O'Toole", "given_name": "George A.", "orcid": "0000-0002-2861-4392", "clpid": "O'Toole-George-A" }, { "family_name": "Crabb\u00e9", "given_name": "Aur\u00e9lie", "orcid": "0000-0003-3084-4418" }, { "family_name": "K\u00fcmmerli", "given_name": "Rolf", "orcid": "0000-0003-4084-6679" }, { "family_name": "LiPuma", "given_name": "John J.", "orcid": "0000-0003-4033-7794" }, { "family_name": "Bomberger", "given_name": "Jennifer M.", "orcid": "0000-0003-4767-6238" }, { "family_name": "Davies", "given_name": "Jane C." }, { "family_name": "Limoli", "given_name": "Dominique", "orcid": "0000-0002-4130-337X" }, { "family_name": "Phelan", "given_name": "Vanessa V.", "orcid": "0000-0001-7156-9294" }, { "family_name": "Bliska", "given_name": "James B.", "orcid": "0000-0002-6047-8837" }, { "family_name": "DePas", "given_name": "William H.", "orcid": "0000-0001-8532-2567" }, { "family_name": "Dietrich", "given_name": "Lars E.", "orcid": "0000-0003-2049-1137" }, { "family_name": "Hampton", "given_name": "Thomas H.", "orcid": "0000-0003-0543-402X" }, { "family_name": "Hunter", "given_name": "Ryan", "orcid": "0000-0003-3841-1676" }, { "family_name": "Khursigara", "given_name": "Cezar M.", "orcid": "0000-0001-9263-7604" }, { "family_name": "Price-Whelan", "given_name": "Alexa", "orcid": "0000-0003-0872-7098" }, { "family_name": "Ashare", "given_name": "Alix" }, { "family_name": "Cramer", "given_name": "Robert A.", "orcid": "0000-0001-5503-5006" }, { "family_name": "Goldberg", "given_name": "Joanna B.", "orcid": "0000-0002-5285-5188" }, { "family_name": "Harrison", "given_name": "Freya" }, { "family_name": "Hogan", "given_name": "Deborah A.", "orcid": "0000-0002-6366-2971" }, { "family_name": "Henson", "given_name": "Michael A." }, { "family_name": "Madden", "given_name": "Dean R.", "orcid": "0000-0002-1810-6984" }, { "family_name": "Mayers", "given_name": "Jared R.", "orcid": "0000-0002-8607-1787" }, { "family_name": "Nadell", "given_name": "Carey", "orcid": "0000-0003-1751-4895" }, { "family_name": "Newman", "given_name": "Dianne", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Prince", "given_name": "Alice", "orcid": "0000-0002-7399-9295" }, { "family_name": "Rivett", "given_name": "Damian W.", "orcid": "0000-0002-1852-6137" }, { "family_name": "Schwartzman", "given_name": "Joseph D." }, { "family_name": "Schultz", "given_name": "Daniel" }, { "family_name": "Sheppard", "given_name": "Donald C.", "orcid": "0000-0001-8877-880X" }, { "family_name": "Smyth", "given_name": "Alan R.", "orcid": "0000-0001-5494-5438" }, { "family_name": "Spero", "given_name": "Melanie A.", "orcid": "0000-0003-3291-2138" }, { "family_name": "Stanton", "given_name": "Bruce A.", "orcid": "0000-0002-1661-407X" }, { "family_name": "Turner", "given_name": "Paul E." }, { "family_name": "van der Gast", "given_name": "Chris", "orcid": "0000-0003-1101-4048" }, { "family_name": "Whelan", "given_name": "Fiona J.", "orcid": "0000-0001-9165-4859" }, { "family_name": "Whitaker", "given_name": "Rachel", "orcid": "0000-0003-2263-5798" }, { "family_name": "Whiteson", "given_name": "Katrine", "orcid": "0000-0002-5423-6014" } ], "abstract": "A recent workshop titled \"Developing Models to Study Polymicrobial Infections,\" sponsored by the Dartmouth Cystic Fibrosis Center (DartCF), explored the development of new models to study the polymicrobial infections associated with the airways of persons with cystic fibrosis (CF). The workshop gathered 35+ investigators over two virtual sessions. Here, we present the findings of this workshop, summarize some of the challenges involved with developing such models, and suggest three frameworks to tackle this complex problem. The frameworks proposed here, we believe, could be generally useful in developing new model systems for other infectious diseases. Developing and validating new approaches to study the complex polymicrobial communities in the CF airway could open windows to new therapeutics to treat these recalcitrant infections, as well as uncovering organizing principles applicable to chronic polymicrobial infections more generally.", "doi": "10.1128/mbio.01763-21", "pmcid": "PMC8546538", "issn": "2150-7511", "publisher": "American Society for Microbiology", "publication": "mBio", "publication_date": "2021-09", "series_number": "5", "volume": "12", "issue": "5", "pages": "Art. No. mBio.01763-21" }, { "id": "authors:ejqar-fpe07", "collection": "authors", "collection_id": "ejqar-fpe07", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210226-074209469", "type": "article", "title": "Spatial transcriptomics of planktonic and sessile bacterial populations at single-cell resolution", "author": [ { "family_name": "Dar", "given_name": "Daniel", "orcid": "0000-0002-6650-5488", "clpid": "Dar-Daniel" }, { "family_name": "Dar", "given_name": "Nina", "clpid": "Dar-Nina" }, { "family_name": "Cai", "given_name": "Long", "orcid": "0000-0002-7154-5361", "clpid": "Cai-Long" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Within any community of organisms, gene expression is heterogeneous, which can manifest in genetically identical individuals having a different phenotype. One has to look at individuals in context and analyze patterns in both space and time to see the full picture. Aiming to fill a gap in current methods, Dar et al. developed a transcriptome-imaging method named parallel sequential fluorescence in situ hybridization (par-seqFISH). They applied this technique to the opportunistic pathogen Pseudomonas aeruginosa, focusing on biofilms where growth conditions can change at microscopic scale. Development of these communities, as revealed by mRNA composition, were followed in space and time. The results revealed a heterogeneous phenotypic landscape, with oxygen availability shaping the metabolism at a spatial scale of microns within a single contiguous biofilm segment. This tool should be applicable to complex microbial communities in the environment and the human microbiome.", "doi": "10.1126/science.abi4882", "pmcid": "PMC8454218", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2021-08-13", "series_number": "6556", "volume": "373", "issue": "6556", "pages": "Art. No. eabi4882" }, { "id": "authors:p2tdc-5gy21", "collection": "authors", "collection_id": "p2tdc-5gy21", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210714-151655967", "type": "article", "title": "Evidence of a Streamlined Extracellular Electron Transfer Pathway from Biofilm Structure, Metabolic Stratification, and Long-Range Electron Transfer Parameters", "author": [ { "family_name": "Jim\u00e9nez Otero", "given_name": "Fernanda", "orcid": "0000-0003-1583-6495", "clpid": "Jim\u00e9nez-Otero-Fernanda" }, { "family_name": "Chadwick", "given_name": "Grayson L.", "orcid": "0000-0003-0700-9350", "clpid": "Chadwick-Grayson-L" }, { "family_name": "Yates", "given_name": "Matthew D.", "orcid": "0000-0003-4373-3864", "clpid": "Yates-Matthew-D" }, { "family_name": "Mickol", "given_name": "Rebecca L.", "orcid": "0000-0002-4493-7263", "clpid": "Mickol-Rebecca-L" }, { "family_name": "Saunders", "given_name": "Scott H.", "orcid": "0000-0003-4224-9106", "clpid": "Saunders-Scott-H" }, { "family_name": "Glaven", "given_name": "Sarah M.", "orcid": "0000-0003-0857-3391", "clpid": "Glaven-Sarah-M" }, { "family_name": "Gralnick", "given_name": "Jeffrey A.", "orcid": "0000-0001-9250-7770", "clpid": "Gralnick-Jeffrey-A" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Tender", "given_name": "Leonard M.", "orcid": "0000-0001-8784-991X", "clpid": "Tender-Leonard-M" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Bond", "given_name": "Daniel R.", "orcid": "0000-0001-8083-7107", "clpid": "Bond-Daniel-R" } ], "abstract": "A strain of Geobacter sulfurreducens, an organism capable of respiring solid extracellular substrates, lacking four of five outer membrane cytochrome complexes (extABCD\u207a strain) grows faster and produces greater current density than the wild type grown under identical conditions. To understand cellular and biofilm modifications in the extABCD\u207a strain responsible for this increased performance, biofilms grown using electrodes as terminal electron acceptors were sectioned and imaged using electron microscopy to determine changes in thickness and cell density, while parallel biofilms incubated in the presence of nitrogen and carbon isotopes were analyzed using NanoSIMS (nanoscale secondary ion mass spectrometry) to quantify and localize anabolic activity. Long-distance electron transfer parameters were measured for wild-type and extABCD\u207a biofilms spanning 5-\u03bcm gaps. Our results reveal that extABCD\u207a biofilms achieved higher current densities through the additive effects of denser cell packing close to the electrode (based on electron microscopy), combined with higher metabolic rates per cell compared to the wild type (based on increased rates of \u00b9\u2075N incorporation). We also observed an increased rate of electron transfer through extABCD\u207a versus wild-type biofilms, suggesting that denser biofilms resulting from the deletion of unnecessary multiheme cytochromes streamline electron transfer to electrodes. The combination of imaging, physiological, and electrochemical data confirms that engineered electrogenic bacteria are capable of producing more current per cell and, in combination with higher biofilm density and electron diffusion rates, can produce a higher final current density than the wild type.", "doi": "10.1128/aem.00706-21", "pmcid": "PMC8357294", "issn": "0099-2240", "publisher": "American Society for Microbiology", "publication": "Applied and Environmental Microbiology", "publication_date": "2021-08", "series_number": "17", "volume": "87", "issue": "17", "pages": "Art. No. AEM.00706-21" }, { "id": "authors:jhb0x-3mf33", "collection": "authors", "collection_id": "jhb0x-3mf33", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210607-115053770", "type": "article", "title": "Nitrate Reduction Stimulates and Is Stimulated by Phenazine-1-Carboxylic Acid Oxidation by Citrobacter portucalensis MBL", "author": [ { "family_name": "Tsypin", "given_name": "Lev M.", "orcid": "0000-0002-0642-8468", "clpid": "Tsypin-Lev-M" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Phenazines are secreted metabolites that microbes use in diverse ways, from quorum sensing to antimicrobial warfare to energy conservation. Phenazines are able to contribute to these activities due to their redox activity. The physiological consequences of cellular phenazine reduction have been extensively studied, but the counterpart phenazine oxidation has been largely overlooked. Phenazine-1-carboxylic acid (PCA) is common in the environment and readily reduced by its producers. Here, we describe its anaerobic oxidation by Citrobacter portucalensis strain MBL, which was isolated from topsoil in Falmouth, MA, and which does not produce phenazines itself. This activity depends on the availability of a suitable terminal electron acceptor, specifically nitrate. When C. portucalensis MBL is provided reduced PCA and nitrate, it oxidizes the PCA at a rate that is environmentally relevant. We compared this terminal electron acceptor-dependent PCA-oxidizing activity of C. portucalensis MBL to that of several other gammaproteobacteria with various capacities to respire nitrate. We found that PCA oxidation by these strains in a nitrate-dependent manner is decoupled from growth and strain dependent. We infer that bacterial PCA oxidation is widespread and genetically determined. Notably, oxidizing PCA enhances the rate of nitrate reduction to nitrite by C. portucalensis MBL beyond the stoichiometric exchange of electrons from PCA to nitrate, which we attribute to C. portucalensis MBL's ability to also reduce oxidized PCA, thereby catalyzing a complete PCA redox cycle. This bidirectionality highlights the versatility of PCA as a biological redox agent.", "doi": "10.1128/mBio.02265-21", "issn": "2150-7511", "publisher": "American Society for Microbiology", "publication": "mBio", "publication_date": "2021-07", "series_number": "4", "volume": "12", "issue": "4", "pages": "Art. No. e02265-21" }, { "id": "authors:rbfcc-qj980", "collection": "authors", "collection_id": "rbfcc-qj980", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210518-093548632", "type": "article", "title": "The role of hopanoids in fortifying rhizobia against a changing climate", "author": [ { "family_name": "Tookmanian", "given_name": "Elise M.", "clpid": "Tookmanian-Elise-M" }, { "family_name": "Belin", "given_name": "Brittany J.", "clpid": "Belin-Brittany-J" }, { "family_name": "Saenz", "given_name": "James P.", "clpid": "Saenz-James-P" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Bacteria are a globally sustainable source of fixed nitrogen, which is essential for life and crucial for modern agriculture. Many nitrogen-fixing bacteria are agriculturally important, including bacteria known as rhizobia that participate in growth-promoting symbioses with legume plants throughout the world. To be effective symbionts, rhizobia must overcome multiple environmental challenges: from surviving in the soil, to transitioning to the plant environment, to maintaining high metabolic activity within root nodules. Climate change threatens to exacerbate these challenges, especially through fluctuations in soil water potential. Understanding how rhizobia cope with environmental stress is crucial for maintaining agricultural yields in the coming century. The bacterial outer membrane is the first line of defence against physical and chemical environmental stresses, and lipids play a crucial role in determining the robustness of the outer membrane. In particular, structural remodelling of lipid A and sterol-analogues known as hopanoids are instrumental in stress acclimation. Here, we discuss how the unique outer membrane lipid composition of rhizobia may underpin their resilience in the face of increasing osmotic stress expected due to climate change, illustrating the importance of studying microbial membranes and highlighting potential avenues towards more sustainable soil additives.", "doi": "10.1111/1462-2920.15594", "issn": "1462-2912", "publisher": "Wiley", "publication": "Environmental Microbiology", "publication_date": "2021-06", "series_number": "6", "volume": "23", "issue": "6", "pages": "2906-2918" }, { "id": "authors:0dwhc-w7b94", "collection": "authors", "collection_id": "0dwhc-w7b94", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210603-082221478", "type": "article", "title": "Chlorate And Antibiotic Treatment Dismantle Pseudomonas Aeruginosa Biofilm And Lead To Healing Of Chronic Wounds", "author": [ { "family_name": "Kim", "given_name": "Jane H.", "clpid": "Kim-Jane-H" }, { "family_name": "Spero", "given_name": "Melanie", "clpid": "Spero-Melanie" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Martins-Green", "given_name": "Manuela", "clpid": "Martins-Green-Manuela" } ], "abstract": "Background: Pseudomonas aeruginosa (PA) is an opportunistic pathogen commonly found in human chronic wound. When within biofilm, PA is tolerant or resistant to conventional antibiotic therapy by using metabolites/enzymes that significantly increase pathogenicity during chronic infections. To survive in hypoxic wound microenvironments and the interior of biofilm, PA uses nitrate reductase (nar), an enzyme that facilitates anaerobic respiration after oxygen is depleted from the microenvironment. In addition to reducing nitrates, nar can reduce internalized chlorate to hypochlorite. This reaction not only converts a non-toxic chemical into a toxic one, but also provides a targeted mechanism that kills anaerobically respiring bacteria which are difficult to eradicate with antibiotics. We hypothesize that treating PA-infected chronic wounds with chlorate and the antibiotic ciprofloxacin, will remove aerobic and anaerobic respiring bacterial populations, respectively, to facilitate wound healing. To test the efficacy of ciprofloxacin +chlorate treatment, we used a murine chronic wound model infected by with a nar activity-containing PA strain isolated from these mice chronic wounds. Briefly, wounds are treated with inhibitors of antioxidant enzymes at wounding to induce high oxidative stress and 24hr after injury, PA is inoculated into the wounds resulting in development of chronic wounds that contain strong biofilm and do not heal. We found that wounds treated daily with low doses of ciprofloxacin+chlorate increased survival of the mice with biofilm-containing chronic wounds compared to chlorate or ciprofloxacin alone. Treatment with ciprofloxacin+chlorate greatly reduced PA bioburden. The biofilm is dismantled, and the wounds go on to heal and close within 40 days. Wound swab samples taken 20 days after treatment began, show very few viable bacteria after treatment with ciprofloxacin+chlorate compared to ciprofloxacin or chlorate alone. Using MiPACT, a method to detect fluorescently label bacteria in wounds tissues, that have healed, show that PA infection is resolved and cleared from the tissue. These results indicate that in chronic wounds, chlorate kills PA in anaerobic areas of the wound, dismantling the biofilm and making the bacteria in aerobic regions planktonic and susceptible to ciprofloxacin. In conclusion, because our chronic wound model mimics biofilm-containing human chronic wounds, our results point to proof-of-concept studies in humans using chlorate and antibiotic to improve healing.", "doi": "10.1111/wrr.12921", "issn": "1067-1927", "publisher": "Wiley", "publication": "Wound Repair and Regeneration", "publication_date": "2021-05", "series_number": "3", "volume": "29", "issue": "3", "pages": "A44-A45" }, { "id": "authors:hbm1w-gfy69", "collection": "authors", "collection_id": "hbm1w-gfy69", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210419-152102811", "type": "monograph", "title": "Paraburkholderia edwinii protects Aspergillus sp. from phenazines by acting as a toxin sponge", "author": [ { "family_name": "Dahlstrom", "given_name": "Kurt M.", "orcid": "0000-0001-6590-6020", "clpid": "Dahlstrom-Kurt-M" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Many environmentally and clinically important fungi are sensitive to toxic, bacterially-produced, redox-active molecules called phenazines. Despite being vulnerable to phenazine-assault, fungi inhabit microbial communities that contain phenazine producers. Because many fungi cannot withstand phenazine challenge, but some bacterial species can, we hypothesized that bacterial partners may protect fungi in phenazine-replete environments. In the first soil sample we collected, we co-isolated several such physically associated pairings. We discovered the novel species Paraburkholderia edwinii and demonstrated it can protect a co-isolated Aspergillus species from phenazine-1-carboxylic acid (PCA) by sequestering it, acting as a toxin sponge; in turn, it also gains protection. When challenged with PCA, P. edwinii changes its morphology, forming aggregates within the growing fungal colony. Further, the fungal partner triggers P. edwinii to sequester PCA and maintains conditions that limit PCA toxicity by promoting an anoxic and highly reducing environment. A mutagenic screen revealed this program depends on the stress-inducible transcriptional repressor HrcA. We show that one relevant stressor in response to PCA challenge is fungal acidification and that acid stress causes P. edwinii to behave as though the fungus were present. Finally, we reveal this phenomenon as widespread among Paraburkholderia with moderate specificity among bacterial and fungal partners, including plant and human pathogens. Our discovery suggests a common mechanism by which fungi can gain access to phenazine-replete environments, and provides a tractable model system for its study. These results have implications for how rhizosphere microbial communities as well as plant and human infection sites are policed for fungal membership.", "doi": "10.1101/2021.03.28.437412", "publication_date": "2021-03-29" }, { "id": "authors:96tt4-myh33", "collection": "authors", "collection_id": "96tt4-myh33", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210316-072135929", "type": "article", "title": "Computationally designed pyocyanin demethylase acts synergistically with tobramycin to kill recalcitrant Pseudomonas aeruginosa biofilms", "author": [ { "family_name": "VanDrisse", "given_name": "Chelsey M.", "orcid": "0000-0001-9139-0443", "clpid": "VanDrisse-Chelsey-M" }, { "family_name": "Lipsh-Sokolik", "given_name": "Rosalie", "orcid": "0000-0002-5548-7309", "clpid": "Lipsh-Sokolik-Rosalie" }, { "family_name": "Khersonsky", "given_name": "Olga", "orcid": "0000-0001-8065-2241", "clpid": "Khersonsky-Olga" }, { "family_name": "Fleishman", "given_name": "Sarel J.", "orcid": "0000-0003-3177-7560", "clpid": "Fleishman-Sarel-J" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Pseudomonas aeruginosa is an opportunistic human pathogen that develops difficult-to-treat biofilms in immunocompromised individuals, cystic fibrosis patients, and in chronic wounds. P. aeruginosa has an arsenal of physiological attributes that enable it to evade standard antibiotic treatments, particularly in the context of biofilms where it grows slowly and becomes tolerant to many drugs. One of its survival strategies involves the production of the redox-active phenazine, pyocyanin, which promotes biofilm development. We previously identified an enzyme, PodA, that demethylated pyocyanin and disrupted P. aeruginosa biofilm development in vitro. Here, we asked if this protein could be used as a potential therapeutic for P. aeruginosa infections together with tobramycin, an antibiotic typically used in the clinic. A major roadblock to answering this question was the poor yield and stability of wild-type PodA purified from standard Escherichia coli overexpression systems. We hypothesized that the insufficient yields were due to poor packing within PodA's obligatory homotrimeric interfaces. We therefore applied the protein design algorithm, AffiLib, to optimize the symmetric core of this interface, resulting in a design that incorporated five mutations leading to a 20-fold increase in protein yield from heterologous expression and purification and a substantial increase in stability to environmental conditions. The addition of the designed PodA with tobramycin led to increased killing of P. aeruginosa cultures under oxic and hypoxic conditions in both the planktonic and biofilm states. This study highlights the potential for targeting extracellular metabolites to assist the control of P. aeruginosa biofilms that tolerate conventional antibiotic treatment.", "doi": "10.1073/pnas.2022012118", "pmcid": "PMC8000102", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2021-03-23", "series_number": "12", "volume": "118", "issue": "12", "pages": "Art. No. e2022012118" }, { "id": "authors:m6002-4r618", "collection": "authors", "collection_id": "m6002-4r618", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210503-104005111", "type": "article", "title": "How are methodological developments enabling insights into cell behavior in cellular communities?", "author": [ { "family_name": "Piddini", "given_name": "Eugenia", "clpid": "Piddini-Eugenia" }, { "family_name": "Shalek", "given_name": "Alex K.", "clpid": "Shalek-Alex-K" }, { "family_name": "Habib", "given_name": "Naomi", "clpid": "Habib-Naomi" }, { "family_name": "Tape", "given_name": "Christopher", "clpid": "Tape-Christopher" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Pittet", "given_name": "Mika\u00ebl", "clpid": "Pittet-Mika\u00ebl" }, { "family_name": "Pringle", "given_name": "Anne", "clpid": "Pringle-Anne" } ], "abstract": "[no abstract]", "doi": "10.1016/j.cels.2021.02.005", "issn": "2405-4712", "publisher": "Cell Press", "publication": "Cell Systems", "publication_date": "2021-03-17", "series_number": "3", "volume": "12", "issue": "3", "pages": "207-209" }, { "id": "authors:x777t-a5843", "collection": "authors", "collection_id": "x777t-a5843", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200421-132753787", "type": "article", "title": "Bacterial defenses against a natural antibiotic promote collateral resilience to clinical antibiotics", "author": [ { "family_name": "Meirelles", "given_name": "Lucas A.", "orcid": "0000-0003-3194-7136", "clpid": "Meirelles-Lucas-A" }, { "family_name": "Perry", "given_name": "Elena K.", "orcid": "0000-0002-7151-1479", "clpid": "Perry-Elena-K" }, { "family_name": "Bergkessel", "given_name": "Megan", "orcid": "0000-0002-4530-1224", "clpid": "Bergkessel-Megan" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Bacterial opportunistic human pathogens frequently exhibit intrinsic antibiotic tolerance and resistance, resulting in infections that can be nearly impossible to eradicate. We asked whether this recalcitrance could be driven by these organisms' evolutionary history as environmental microbes that engage in chemical warfare. Using Pseudomonas aeruginosa as a model, we demonstrate that the self-produced antibiotic pyocyanin (PYO) activates defenses that confer collateral tolerance specifically to structurally similar synthetic clinical antibiotics. Non-PYO-producing opportunistic pathogens, such as members of the Burkholderia cepacia complex, likewise display elevated antibiotic tolerance when cocultured with PYO-producing strains. Furthermore, by widening the population bottleneck that occurs during antibiotic selection and promoting the establishment of a more diverse range of mutant lineages, PYO increases apparent rates of mutation to antibiotic resistance to a degree that can rival clinically relevant hypermutator strains. Together, these results reveal an overlooked mechanism by which opportunistic pathogens that produce natural toxins can dramatically modulate the efficacy of clinical antibiotics and the evolution of antibiotic resistance, both for themselves and other members of clinically relevant polymicrobial communities.", "doi": "10.1371/journal.pbio.3001093", "issn": "1544-9173", "publisher": "Public Library of Science", "publication": "PLoS Biology", "publication_date": "2021-03-10", "series_number": "3", "volume": "19", "issue": "3", "pages": "Art. No. e3001093" }, { "id": "authors:33s7q-peq69", "collection": "authors", "collection_id": "33s7q-peq69", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210304-154532731", "type": "article", "title": "Redox-active antibiotics enhance phosphorus bioavailability", "author": [ { "family_name": "McRose", "given_name": "Darcy L.", "orcid": "0000-0001-9637-7176", "clpid": "McRose-Darcy-L" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Microbial production of antibiotics is common, but our understanding of their roles in the environment is limited. In this study, we explore long-standing observations that microbes increase the production of redox-active antibiotics under phosphorus limitation. The availability of phosphorus, a nutrient required by all life on Earth and essential for agriculture, can be controlled by adsorption to and release from iron minerals by means of redox cycling. Using phenazine antibiotic production by pseudomonads as a case study, we show that phenazines are regulated by phosphorus, solubilize phosphorus through reductive dissolution of iron oxides in the lab and field, and increase phosphorus-limited microbial growth. Phenazines are just one of many examples of phosphorus-regulated antibiotics. Our work suggests a widespread but previously unappreciated role for redox-active antibiotics in phosphorus acquisition and cycling.", "doi": "10.1126/science.abd1515", "pmcid": "PMC8051141", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2021-03-05", "series_number": "6533", "volume": "371", "issue": "6533", "pages": "1033-1037" }, { "id": "authors:jstqa-tst54", "collection": "authors", "collection_id": "jstqa-tst54", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211029-213538184", "type": "patent", "title": "Phenazine degrading agents and related compositions, methods and systems for interfering with viability of bacteria", "author": [ { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Costa", "given_name": "Kyle C.", "clpid": "Costa-K-C" } ], "abstract": "Provided herein are phenazine degrading agents, methods and systems for interfering with viability of bacteria and related antimicrobial and compositions.", "publisher": "U.S. Patent Office", "publication_date": "2021-02-04" }, { "id": "authors:4fhd5-k6q10", "collection": "authors", "collection_id": "4fhd5-k6q10", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210114-164619982", "type": "article", "title": "Draft Genome Sequence of the Free-Living, Iridescent Bacterium Tenacibaculum mesophilum Strain ECR", "author": [ { "family_name": "Mickol", "given_name": "Rebecca L.", "orcid": "0000-0002-4493-7263", "clpid": "Mickol-Rebecca-L" }, { "family_name": "Louyakis", "given_name": "Artemis S.", "clpid": "Louyakis-Artemis-S" }, { "family_name": "Kee", "given_name": "H. Lynn", "orcid": "0000-0001-7683-187X", "clpid": "Kee-H-Lynn" }, { "family_name": "Johnson", "given_name": "Lisa K.", "clpid": "Johnson-Lisa-K" }, { "family_name": "Dawson", "given_name": "Scott C.", "orcid": "0000-0002-0843-1759", "clpid": "Dawson-Scott-C" }, { "family_name": "Hargreaves", "given_name": "Katherine R.", "clpid": "Hargreaves-Katherine-R" }, { "family_name": "Chadwick", "given_name": "Grayson L.", "orcid": "0000-0003-0700-9350", "clpid": "Chadwick-Grayson-L" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Leadbetter", "given_name": "Jared R.", "orcid": "0000-0002-7033-0844", "clpid": "Leadbetter-J-R" }, { "family_name": "Brown", "given_name": "C. Titus", "orcid": "0000-0001-6001-2677", "clpid": "Brown-C-T" } ], "abstract": "Here, we report the genome sequence of Tenacibaculum mesophilum strain ECR, which was isolated from the river/ocean interface at Trunk River in Falmouth, Massachusetts. The isolation and sequencing were performed as part of the 2016 and 2018 Microbial Diversity courses at the Marine Biological Laboratory in Woods Hole, Massachusetts.", "doi": "10.1128/mra.01302-20", "issn": "2576-098X", "publisher": "American Society for Microbiology", "publication": "Microbiology Resource Announcements", "publication_date": "2021-01", "series_number": "1", "volume": "10", "issue": "1", "pages": "Art. No. e01302-20" }, { "id": "authors:47nw6-c7553", "collection": "authors", "collection_id": "47nw6-c7553", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201124-104632686", "type": "monograph", "title": "Bidirectional redox cycling of phenazine-1-carboxylic acid by Citrobacter portucalensis MBL drives increased nitrate reduction", "author": [ { "family_name": "Tsypin", "given_name": "Lev M.", "orcid": "0000-0002-0642-8468", "clpid": "Tsypin-Lev-M" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Phenazines are secreted metabolites that microbes use in diverse ways, from quorum sensing to antimicrobial warfare to energy conservation. Phenazines are able to contribute to these activities due to their redox activity. The physiological consequences of cellular phenazine reduction have been extensively studied, but the counterpart phenazine oxidation has been largely overlooked. Phenazine-1-carboxylic acid (PCA) is common in the environment and readily reduced by its producers. Here, we describe its anaerobic oxidation by Citrobacter portucalensis strain MBL, which was isolated from topsoil in Falmouth, MA, and which does not produce phenazines itself. This activity depends on the availability of a suitable terminal electron acceptor, specifically nitrate or fumarate. When C. portucalensis MBL is provided reduced PCA and either nitrate or fumarate, it continuously oxidizes the PCA. We compared this terminal electron acceptor-dependent PCA-oxidizing activity of C. portucalensis MBL to that of several other \u03b3-proteobacteria with varying capacities to respire nitrate and/or fumarate. We found that PCA oxidation by these strains in a fumarate-or nitrate-dependent manner is decoupled from growth and correlated with their possession of the fumarate or periplasmic nitrate reductases, respectively. We infer that bacterial PCA oxidation is widespread and genetically determined. Notably, reduced PCA enhances the rate of nitrate reduction to nitrite by C. portucalensis MBL beyond the stoichiometric prediction, which we attribute to C. portucalensis MBL's ability to also reduce oxidized PCA, thereby catalyzing a complete PCA redox cycle. This bidirectionality highlights the versatility of PCA as a biological redox agent.", "doi": "10.1101/2020.11.23.395335", "publication_date": "2020-11-24" }, { "id": "authors:gzzr8-65753", "collection": "authors", "collection_id": "gzzr8-65753", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201006-131015350", "type": "article", "title": "Keystone metabolites of crop rhizosphere microbiomes", "author": [ { "family_name": "Dahlstrom", "given_name": "Kurt M.", "orcid": "0000-0001-6590-6020", "clpid": "Dahlstrom-Kurt-M" }, { "family_name": "McRose", "given_name": "Darcy L.", "orcid": "0000-0001-9637-7176", "clpid": "McRose-Darcy-L" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "The role of microbes in sustaining agricultural plant growth has great potential consequences for human prosperity. Yet we have an incomplete understanding of the basic function of rhizosphere microbial communities and how they may change under future stresses, let alone how these processes might be harnessed to sustain or improve crop yields. A reductionist approach may aid the generation and testing of hypotheses that can ultimately be translated to agricultural practices. With this in mind, we ask whether some rhizosphere microbial communities might be governed by 'keystone metabolites', envisioned here as microbially produced molecules that, through antibiotic and/or growth-promoting properties, may play an outsized role in shaping the development of the community spatiotemporally. To illustrate this point, we use the example of redox-active metabolites, and in particular phenazines, which are produced by many bacteria found in agricultural soils and have well-understood catalytic properties. Phenazines can act as potent antibiotics against a variety of cell types, yet they also can promote the acquisition of essential inorganic nutrients. In this essay, we suggest the ways these metabolites might affect microbial communities and ultimately agricultural productivity in two specific scenarios: firstly, in the biocontrol of beneficial and pathogenic fungi in increasingly arid crop soils and, secondly, through promotion of phosphorus bioavailability and sustainable fertilizer use. We conclude with specific proposals for future research.", "doi": "10.1016/j.cub.2020.08.005", "pmcid": "PMC8059773", "issn": "0960-9822", "publisher": "Cell Press", "publication": "Current Biology", "publication_date": "2020-10-05", "series_number": "19", "volume": "30", "issue": "19", "pages": "R1131-R1137" }, { "id": "authors:4be0p-bxj61", "collection": "authors", "collection_id": "4be0p-bxj61", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200609-075446759", "type": "article", "title": "Global landscape of phenazine biosynthesis and biodegradation reveals species-specific colonization patterns in agricultural soils and crop microbiomes", "author": [ { "family_name": "Dar", "given_name": "Daniel", "orcid": "0000-0002-6650-5488", "clpid": "Dar-Daniel" }, { "family_name": "Thomashow", "given_name": "Linda S.", "orcid": "0000-0002-0809-3606", "clpid": "Thomashow-L-S" }, { "family_name": "Weller", "given_name": "David M.", "orcid": "0000-0001-8533-7136", "clpid": "Weller-D-M" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Phenazines are natural bacterial antibiotics that can protect crops from disease. However, for most crops it is unknown which producers and specific phenazines are ecologically relevant, and whether phenazine biodegradation can counter their effects. To better understand their ecology, we developed and environmentally-validated a quantitative metagenomic approach to mine for phenazine biosynthesis and biodegradation genes, applying it to >800 soil and plant-associated shotgun-metagenomes. We discover novel producer-crop associations and demonstrate that phenazine biosynthesis is prevalent across habitats and preferentially enriched in rhizospheres, whereas biodegrading bacteria are rare. We validate an association between maize and Dyella japonica, a putative producer abundant in crop microbiomes. D. japonica upregulates phenazine biosynthesis during phosphate limitation and robustly colonizes maize seedling roots. This work provides a global picture of phenazines in natural environments and highlights plant-microbe associations of agricultural potential. Our metagenomic approach may be extended to other metabolites and functional traits in diverse ecosystems.", "doi": "10.7554/eLife.59726", "issn": "2050-084X", "publisher": "eLife Sciences Publications", "publication": "eLife", "publication_date": "2020-09-15", "series_number": "9", "volume": "2020", "issue": "9", "pages": "Art. No. e59726" }, { "id": "authors:qtd0v-e8n18", "collection": "authors", "collection_id": "qtd0v-e8n18", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20191213-144717393", "type": "article", "title": "Extracellular DNA Promotes Efficient Extracellular Electron Transfer by Pyocyanin in Pseudomonas aeruginosa Biofilms", "author": [ { "family_name": "Saunders", "given_name": "Scott H.", "orcid": "0000-0003-4224-9106", "clpid": "Saunders-Scott-H" }, { "family_name": "Tse", "given_name": "Edmund C. M.", "orcid": "0000-0002-9313-1290", "clpid": "Tse-Edmund-Chun-Ming" }, { "family_name": "Yates", "given_name": "Matthew D.", "orcid": "0000-0003-4373-3864", "clpid": "Yates-Matthew-D" }, { "family_name": "Jim\u00e9nez Otero", "given_name": "Fernanda", "orcid": "0000-0003-1583-6495", "clpid": "Jim\u00e9nez-Otero-F" }, { "family_name": "Trammell", "given_name": "Scott A.", "orcid": "0000-0002-7996-590X", "clpid": "Trammell-Scott-A" }, { "family_name": "Stemp", "given_name": "Eric D. A.", "orcid": "0000-0003-2098-4214", "clpid": "Stemp-Eric-D-A" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Tender", "given_name": "Leonard M.", "orcid": "0000-0001-8784-991X", "clpid": "Tender-Leonard-M" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Redox cycling of extracellular electron shuttles can enable the metabolic activity of subpopulations within multicellular bacterial biofilms that lack direct access to electron acceptors or donors. How these shuttles catalyze extracellular electron transfer (EET) within biofilms without being lost to the environment has been a long-standing question. Here, we show that phenazines mediate efficient EET through interactions with extracellular DNA (eDNA) in Pseudomonas aeruginosa biofilms. Retention of pyocyanin (PYO) and phenazine carboxamide in the biofilm matrix is facilitated by eDNA binding. In vitro, different phenazines can exchange electrons in the presence or absence of DNA and can participate directly in redox reactions through DNA. In vivo, biofilm eDNA can also support rapid electron transfer between redox active intercalators. Together, these results establish that PYO:eDNA interactions support an efficient redox cycle with rapid EET that is faster than the rate of PYO loss from the biofilm.", "doi": "10.1016/j.cell.2020.07.006", "pmcid": "PMC7457544", "issn": "0092-8674", "publisher": "Cell Press", "publication": "Cell", "publication_date": "2020-08-20", "series_number": "4", "volume": "182", "issue": "4", "pages": "919-932" }, { "id": "authors:2x0nw-vwd56", "collection": "authors", "collection_id": "2x0nw-vwd56", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200806-153947593", "type": "article", "title": "Draft Genome Sequence of the Redox-Active Enteric Bacterium Citrobacter portucalensis Strain MBL", "author": [ { "family_name": "Tsypin", "given_name": "Lev M.", "orcid": "0000-0002-0642-8468", "clpid": "Tsypin-Lev-M" }, { "family_name": "Saunders", "given_name": "Scott H.", "orcid": "0000-0003-4224-9106", "clpid": "Saunders-Scott-H" }, { "family_name": "Bar-On", "given_name": "Yinon", "orcid": "0000-0001-8477-609X", "clpid": "Bar-On-Yinon-M" }, { "family_name": "Leadbetter", "given_name": "Jared R.", "orcid": "0000-0002-7033-0844", "clpid": "Leadbetter-J-R" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "We grew a soil enrichment culture to identify organisms that anaerobically oxidize phenazine-1-carboxylic acid. A strain of Citrobacter portucalensis was isolated from this enrichment and sequenced by both Illumina and PacBio technologies. It has a genome with a length of 5.3\u2009Mb, a G+C content of 51.8%, and at least one plasmid.", "doi": "10.1128/mra.00695-20", "pmcid": "PMC7409854", "issn": "2576-098X", "publisher": "American Society for Microbiology", "publication": "Microbiology Resource Announcements", "publication_date": "2020-08-06", "series_number": "32", "volume": "9", "issue": "32", "pages": "Art. No. e00695-20" }, { "id": "authors:tqkj2-etr46", "collection": "authors", "collection_id": "tqkj2-etr46", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200219-111358713", "type": "article", "title": "The potential for redox-active metabolites (RAMs) to enhance or unlock anaerobic survival metabolisms in aerobes", "author": [ { "family_name": "Ciemniecki", "given_name": "John A.", "orcid": "0000-0003-2789-6700", "clpid": "Ciemniecki-John-A" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Classifying microorganisms as \"obligate\" aerobes has colloquially implied death without air, leading to the erroneous assumption that, without oxygen, they are unable to survive. However, over the past few decades, more than a few obligate aerobes have been found to possess anaerobic energy conservation strategies that sustain metabolic activity in the absence of growth or at very low growth rates. Similarly, studies emphasizing the aerobic prowess of certain facultative aerobes have sometimes led to underrecognition of their anaerobic capabilities. Yet an inescapable consequence of the affinity both obligate and facultative aerobes have for oxygen is that the metabolism of these organisms may drive this substrate to scarcity, making anoxic survival an essential skill. To illustrate this, we highlight the importance of anaerobic survival strategies for Pseudomonas aeruginosa and Streptomyces coelicolor, representative facultative and obligate aerobes, respectively. Included among these strategies, we describe a role for redox-active secondary metabolites (RAMs), such as phenazines made by P. aeruginosa, in enhancing substrate-level phosphorylation. Importantly, RAMs are made by diverse bacteria, often during stationary phase in the absence of oxygen, and can sustain anoxic survival. We present a hypothesis for how RAMs may enhance or even unlock energy conservation pathways that facilitate the anaerobic survival of both RAM producers and nonproducers.", "doi": "10.1128/jb.00797-19", "pmcid": "PMC7221258", "issn": "0021-9193", "publisher": "American Society for Microbiology", "publication": "Journal of Bacteriology", "publication_date": "2020-06", "series_number": "11", "volume": "202", "issue": "11", "pages": "Art. No. e00797-19" }, { "id": "authors:yk5ha-kz013", "collection": "authors", "collection_id": "yk5ha-kz013", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200504-083728290", "type": "article", "title": "Upregulation of virulence genes promotes Vibrio cholerae biofilm hyperinfectivity", "author": [ { "family_name": "Gallego-Hernandez", "given_name": "A. L.", "orcid": "0000-0001-7818-2244", "clpid": "Gallego-Hernandez-A-L" }, { "family_name": "DePas", "given_name": "W. H.", "clpid": "DePas-W-H" }, { "family_name": "Park", "given_name": "J. H.", "clpid": "Park-J-H" }, { "family_name": "Teschler", "given_name": "J. K.", "clpid": "Teschler-J-K" }, { "family_name": "Hartmann", "given_name": "R.", "clpid": "Hartmann-R" }, { "family_name": "Jeckel", "given_name": "H.", "clpid": "Jeckel-H" }, { "family_name": "Drescher", "given_name": "K.", "orcid": "0000-0002-7340-2444", "clpid": "Drescher-K" }, { "family_name": "Beyhan", "given_name": "S.", "clpid": "Beyhan-S" }, { "family_name": "Newman", "given_name": "D. K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Yildiz", "given_name": "F. H.", "clpid": "Yildiz-F-H" } ], "abstract": "Vibrio cholerae remains a major global health threat, disproportionately impacting parts of the world without adequate infrastructure and sanitation resources. In aquatic environments, V. cholerae exists both as planktonic cells and as biofilms, which are held together by an extracellular matrix. V. cholerae biofilms have been shown to be hyperinfective, but the mechanism of hyperinfectivity is unclear. Here we show that biofilm-grown cells, irrespective of the surfaces on which they are formed, are able to markedly outcompete planktonic-grown cells in the infant mouse. Using an imaging technique designed to render intestinal tissue optically transparent and preserve the spatial integrity of infected intestines, we reveal and compare three-dimensional V. cholerae colonization patterns of planktonic-grown and biofilm-grown cells. Quantitative image analyses show that V. cholerae colonizes mainly the medial portion of the small intestine and that both the abundance and localization patterns of biofilm-grown cells differ from that of planktonic-grown cells. In vitro biofilm-grown cells activate expression of the virulence cascade, including the toxin coregulated pilus (TCP), and are able to acquire the cholera toxin-carrying CTX\u0424 phage. Overall, virulence factor gene expression is also higher in vivo when infected with biofilm-grown cells, and modulation of their regulation is sufficient to cause the biofilm hyperinfectivity phenotype. Together, these results indicate that the altered biogeography of biofilm-grown cells and their enhanced production of virulence factors in the intestine underpin the biofilm hyperinfectivity phenotype.", "doi": "10.1073/pnas.1916571117", "pmcid": "PMC7245069", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2020-05-19", "series_number": "20", "volume": "117", "issue": "20", "pages": "11010-11017" }, { "id": "authors:dwnae-f1c66", "collection": "authors", "collection_id": "dwnae-f1c66", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200206-163326208", "type": "article", "title": "Heat-shock proteases promote survival of Pseudomonas aeruginosa during growth arrest", "author": [ { "family_name": "Basta", "given_name": "David W.", "orcid": "0000-0003-4176-6566", "clpid": "Basta-David-Wagdi" }, { "family_name": "Angeles-Albores", "given_name": "David", "orcid": "0000-0001-5497-8264", "clpid": "Angeles-Albores-D" }, { "family_name": "Spero", "given_name": "Melanie A.", "orcid": "0000-0003-3291-2138", "clpid": "Spero-M-A" }, { "family_name": "Ciemniecki", "given_name": "John A.", "clpid": "Ciemniecki-John-A" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "When nutrients in their environment are exhausted, bacterial cells become arrested for growth. During these periods, a primary challenge is maintaining cellular integrity with a reduced capacity for renewal or repair. Here, we show that the heat-shock protease FtsH is generally required for growth arrest survival of Pseudomonas aeruginosa, and that this requirement is independent of a role in regulating lipopolysaccharide synthesis, as has been suggested for Escherichia coli. We find that ftsH interacts with diverse genes during growth and overlaps functionally with the other heat-shock protease-encoding genes hslVU, lon, and clpXP to promote survival during growth arrest. Systematic deletion of the heat-shock protease-encoding genes reveals that the proteases function hierarchically during growth arrest, with FtsH and ClpXP having primary, nonredundant roles, and HslVU and Lon deploying a secondary response to aging stress. This hierarchy is partially conserved during growth at high temperature and alkaline pH, suggesting that heat, pH, and growth arrest effectively impose a similar type of proteostatic stress at the cellular level. In support of this inference, heat and growth arrest act synergistically to kill cells, and protein aggregation appears to occur more rapidly in protease mutants during growth arrest and correlates with the onset of cell death. Our findings suggest that protein aggregation is a major driver of aging and cell death during growth arrest, and that coordinated activity of the heat-shock response is required to ensure ongoing protein quality control in the absence of growth.", "doi": "10.1073/pnas.1912082117", "pmcid": "PMC7049150", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2020-02-25", "series_number": "8", "volume": "117", "issue": "8", "pages": "4358-4367" }, { "id": "authors:54pxq-ycw55", "collection": "authors", "collection_id": "54pxq-ycw55", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181128-093526010", "type": "article", "title": "Refinement of metabolite detection in cystic fibrosis sputum reveals heme correlates with lung function decline", "author": [ { "family_name": "Glasser", "given_name": "Nathaniel R.", "orcid": "0000-0002-2833-5166", "clpid": "Glasser-Nathaniel-R" }, { "family_name": "Hunter", "given_name": "Ryan C.", "orcid": "0000-0003-3841-1676", "clpid": "Hunter-Ryan-C" }, { "family_name": "Liou", "given_name": "Theodore G.", "orcid": "0000-0003-0121-4847", "clpid": "Liou-Theodore-G" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "literal": "Mountain West CF Consortium Investigators" } ], "abstract": "The bacterial growth environment within cystic fibrosis (CF) sputum is complex, dynamic, and shaped by both host and microbial processes. Characterization of the chemical parameters within sputum that stimulate the in vivo growth of airway pathogens (e.g. Pseudomonas aeruginosa) and their associated virulence factors may lead to improved CF treatment strategies. Motivated by conflicting reports of the prevalence and abundance of P. aeruginosa-derived metabolites known as phenazines within CF airway secretions, we sought to quantify these metabolites in sputum using quadrupole time-of-flight mass spectrometry. In contrast to our previous work, all phenazines tested (pyocyanin (PYO), phenazine-1-carboxylic acid (PCA), phenazine-1-carboxamide, and 1-hydroxyphenazine) were below detection limits of the instrument (0.1 \u03bcM). Instead, we identified a late-eluting compound that shared retention time and absorbance characteristics with PCA, yet generated mass spectra and a fragmentation pattern consistent with ferriprotoporphyrin IX, otherwise known as heme B. These data suggested that UV-vis chromatographic peaks previously attributed to PCA and PYO in sputum were mis-assigned. Indeed, retrospective analysis of raw data from our prior study found that the heme B peak closely matched the peaks assigned to PCA, indicating that the previous study likely uncovered a positive correlation between pulmonary function (percent predicted forced expiratory volume in 1 second, or ppFEV1) and heme B, not PCA or any other phenazine. To independently test this observation, we performed a new tandem mass-spectrometry analysis of 71 additional samples provided by the Mountain West CF Consortium Sputum Biomarker study and revealed a positive correlation (\u03c1 = \u22120.47, p<0.001) between sputum heme concentrations and ppFEV1. Given that hemoptysis is strongly associated with airway inflammation, pulmonary exacerbations and impaired lung function, these new data suggest that heme B may be a useful biomarker of CF pathophysiology.", "doi": "10.1371/journal.pone.0226578", "pmcid": "PMC6919587", "issn": "1932-6203", "publisher": "Public Library of Science", "publication": "PLoS ONE", "publication_date": "2019-12-18", "series_number": "12", "volume": "14", "issue": "12", "pages": "Art. No. e0226578" }, { "id": "authors:vkxqj-dxx04", "collection": "authors", "collection_id": "vkxqj-dxx04", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190510-105529016", "type": "article", "title": "Quantitative Visualization of Gene Expression in Mucoid and Nonmucoid Pseudomonas aeruginosa Aggregates Reveals Localized Peak Expression of Alginate in the Hypoxic Zone", "author": [ { "family_name": "Jorth", "given_name": "Peter", "orcid": "0000-0002-0981-740X", "clpid": "Jorth-Peter" }, { "family_name": "Spero", "given_name": "Melanie A.", "orcid": "0000-0003-3291-2138", "clpid": "Spero-Melanie-A" }, { "family_name": "Livingston", "given_name": "J.", "clpid": "Livingston-Jade" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "It is well appreciated that oxygen- and other nutrient-limiting gradients characterize microenvironments within chronic infections that foster bacterial tolerance to treatment and the immune response. However, determining how bacteria respond to these microenvironments has been limited by a lack of tools to study bacterial functions at the relevant spatial scales in situ. Here, we report the application of the hybridization chain reaction (HCR) v3.0 to provide analog mRNA relative quantitation of Pseudomonas aeruginosa single cells as a step toward this end. To assess the potential for this method to be applied to bacterial populations, we visualized the expression of genes needed for the production of alginate (algD) and the dissimilatory nitrate reductase (narG) at single-cell resolution within laboratory-grown aggregates. After validating new HCR probes, we quantified algD and narG expression across microenvironmental gradients within both single aggregates and aggregate populations using the agar block biofilm assay (ABBA). For mucoid and nonmucoid ABBA populations, narG was expressed in hypoxic and anoxic regions, while alginate expression was restricted to the hypoxic zone (\u223c40 to 200\u2009\u03bcM O2). Within individual aggregates, surface-adjacent cells expressed alginate genes at higher levels than interior cells, revealing that alginate expression is not constitutive in mucoid P. aeruginosa but instead varies with oxygen availability. These results establish HCR v3.0 as a versatile and robust tool to resolve subtle differences in gene expression at spatial scales relevant to microbial assemblages. This advance has the potential to enable quantitative studies of microbial gene expression in diverse contexts, including pathogen activities during infections. IMPORTANCE: A goal for microbial ecophysiological research is to reveal microbial activities in natural environments, including sediments, soils, or infected human tissues. Here, we report the application of the hybridization chain reaction (HCR) v3.0 to quantitatively measure microbial gene expression in situ at single-cell resolution in bacterial aggregates. Using quantitative image analysis of thousands of Pseudomonas aeruginosa cells, we validated new P. aeruginosa HCR probes. Within in vitro P. aeruginosa aggregates, we found that bacteria just below the aggregate surface are the primary cells expressing genes that protect the population against antibiotics and the immune system. This observation suggests that therapies targeting bacteria growing with small amounts of oxygen may be most effective against these hard-to-treat infections. More generally, this proof-of-concept study demonstrates that HCR v3.0 has the potential to identify microbial activities in situ at small spatial scales in diverse contexts.", "doi": "10.1128/mbio.02622-19", "pmcid": "PMC6918079", "issn": "2150-7511", "publisher": "American Society for Microbiology", "publication": "mBio", "publication_date": "2019-12", "series_number": "6", "volume": "10", "issue": "6", "pages": "Art. No. e02622-19" }, { "id": "authors:92exk-3wf88", "collection": "authors", "collection_id": "92exk-3wf88", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190926-131636762", "type": "article", "title": "Chlorate's Potential as a Pro-Drug for Killing Antibiotic-Tolerant Pathogens in the Cystic Fibrosis Lung", "author": [ { "family_name": "Spero", "given_name": "M. A.", "orcid": "0000-0003-3291-2138", "clpid": "Spero-M-A" }, { "family_name": "Silveira", "given_name": "C. B.", "clpid": "Silveira-C-B" }, { "family_name": "Rohwer", "given_name": "F.", "clpid": "Rohwer-F" }, { "family_name": "Newman", "given_name": "D. K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Chronic lung infections are a major contributor to morbidity and\nmortality in cystic fibrosis (CF) patients. Perhaps the most notorious CF pathogen is Pseudomonas aeruginosa, which establishes decades-long lung infections despite aggressive antibiotic treatment. In part, drugs fail to clear P. aeruginosa lung infections because some pathogen populations exhibit antibiotic tolerance, a metabolic state that reduces a cell's susceptibility to drugs. Antibiotic tolerance is associated with low metabolic activity, and P. aeruginosa growth is limited by oxygen availability in the largely hypoxic/anoxic CF sputum.", "doi": "10.1002/ppul.22495", "issn": "8755-6863", "publisher": "Wiley", "publication": "Pediatric Pulmonology", "publication_date": "2019-10", "series_number": "S2", "volume": "54", "issue": "S2", "pages": "S281" }, { "id": "authors:csjzt-mxt49", "collection": "authors", "collection_id": "csjzt-mxt49", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181218-110603835", "type": "article", "title": "Extended hopanoid loss reduces bacterial motility and surface attachment, and leads to heterogeneity in root nodule growth kinetics in a Bradyrhizobium-Aeschynomene symbiosis", "author": [ { "family_name": "Belin", "given_name": "Brittany J.", "clpid": "Belin-B-J" }, { "family_name": "Tookmanian", "given_name": "Elise T.", "clpid": "Tookmanian-E-T" }, { "family_name": "de Anda", "given_name": "Jaime", "orcid": "0000-0003-2129-0775", "clpid": "de-Anda-J" }, { "family_name": "Wong", "given_name": "Gerard C. L.", "orcid": "0000-0003-0893-6383", "clpid": "Wong-Gerard-C-L" }, { "family_name": "Newman", "given_name": "Dianne", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Hopanoids are steroid-like bacterial lipids that enhance membrane rigidity and promote bacterial growth under diverse stresses. Roughly 10% of bacteria contain genes involved in hopanoid biosynthesis, and these genes are particularly conserved in plant-associated organisms. We previously found that the extended class of hopanoids (C35) in the nitrogen-fixing soil bacterium Bradyrhizobium diazoefficiens promotes its root nodule symbiosis with the tropical legume Aeschynomene afraspera. By quantitatively modeling root nodule development, we identify independent consequences of extended hopanoid loss in the initiation of root nodule formation and in the rate of root nodule maturation. In vitro studies demonstrate that extended hopanoids support B. diazoefficiens motility and surface attachment, which may correlate with stable root colonization in planta. Confocal microscopy of maturing root nodules reveals that root nodules infected with extended hopanoid-deficient B. diazoefficiens contain unusually low densities of bacterial symbionts, indicating that extended hopanoids are necessary for persistent, high levels of host infection.", "doi": "10.1094/MPMI-04-19-0111-R", "issn": "0894-0282", "publisher": "American Phytopathological Society", "publication": "Molecular Plant-Microbe Interactions", "publication_date": "2019-10", "series_number": "10", "volume": "32", "issue": "10", "pages": "1415-1428" }, { "id": "authors:y17wj-dja60", "collection": "authors", "collection_id": "y17wj-dja60", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190926-103130771", "type": "article", "title": "Nontuberculous Mycobacterial Aggregation is Regulated by C:N Balance", "author": [ { "family_name": "DePas", "given_name": "W.", "clpid": "DePas-W" }, { "family_name": "Bergkessel", "given_name": "M.", "orcid": "0000-0002-4530-1224", "clpid": "Bergkessel-M" }, { "family_name": "Newman", "given_name": "D. K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "The current treatment regimen for nontuberculous mycobacteria (NTM) involves long courses of antibiotic cocktails that demonstrate limited efficacy and cause frequent and serious side effects. Mycobacterium abscessus, in particular, is difficult to treat, motivating studies to identify new therapeutic targets. Experiments using zebrafish and human cell culture lines have demonstrated that M. abscessus is more virulent when aggregated into cord-like biofilms, at least in part because of the decreased ability of phagocytes to efficiently engulf and kill corded M. abscessus cells.", "doi": "10.1002/ppul.22495", "issn": "8755-6863", "publisher": "Wiley", "publication": "Pediatric Pulmonology", "publication_date": "2019-10", "series_number": "S2", "volume": "54", "issue": "S2", "pages": "S310" }, { "id": "authors:73zas-98f87", "collection": "authors", "collection_id": "73zas-98f87", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190923-092135402", "type": "article", "title": "A contractile injection system stimulates tubeworm metamorphosis by translocating a proteinaceous effector", "author": [ { "family_name": "Ericson", "given_name": "Charles F.", "orcid": "0000-0002-2854-0696", "clpid": "Ericson-C-F" }, { "family_name": "Eisenstein", "given_name": "Fabian", "clpid": "Eisenstein-F" }, { "family_name": "Medeiros", "given_name": "Jo\u00e3o M.", "orcid": "0000-0001-9075-548X", "clpid": "Medeiros-J-M" }, { "family_name": "Malter", "given_name": "Kyle E.", "orcid": "0000-0002-3056-8751", "clpid": "Malter-K-E" }, { "family_name": "Cavalcanti", "given_name": "Giselle S.", "clpid": "Cavalcanti-G-S" }, { "family_name": "Zeller", "given_name": "Robert W.", "clpid": "Zeller-R-W" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Pilhofer", "given_name": "Martin", "clpid": "Pilhofer-M" }, { "family_name": "Shikuma", "given_name": "Nicholas J.", "orcid": "0000-0001-5518-5020", "clpid": "Shikuma-Nicholas-J" } ], "abstract": "The swimming larvae of many marine animals identify a location on the sea floor to undergo metamorphosis based on the presence of specific bacteria. Although this microbe\u2013animal interaction is critical for the life cycles of diverse marine animals, what types of biochemical cues from bacteria that induce metamorphosis has been a mystery. Metamorphosis of larvae of the tubeworm Hydroides elegans is induced by arrays of phage tail-like contractile injection systems, which are released by the bacterium Pseudoalteromonas luteoviolacea. Here we identify the novel effector protein Mif1. By cryo-electron tomography imaging and functional assays, we observe Mif1 as cargo inside the tube lumen of the contractile injection system and show that the mif1 gene is required for inducing metamorphosis. Purified Mif1 is sufficient for triggering metamorphosis when electroporated into tubeworm larvae. Our results indicate that the delivery of protein effectors by contractile injection systems may orchestrate microbe\u2013animal interactions in diverse contexts.", "doi": "10.7554/elife.46845", "pmcid": "PMC6748791", "issn": "2050-084X", "publisher": "eLife Sciences Publications", "publication": "eLife", "publication_date": "2019-09-17", "volume": "8", "pages": "Art. No. e46845" }, { "id": "authors:zrv1e-7qx96", "collection": "authors", "collection_id": "zrv1e-7qx96", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181029-102517113", "type": "article", "title": "The dormancy-specific regulator, SutA, is intrinsically disordered and modulates transcription initiation in Pseudomonas aeruginosa", "author": [ { "family_name": "Bergkessel", "given_name": "Megan", "orcid": "0000-0002-4530-1224", "clpid": "Bergkessel-M" }, { "family_name": "Babin", "given_name": "Brett M.", "orcid": "0000-0002-4133-6665", "clpid": "Babin-B-M" }, { "family_name": "VanderVelde", "given_name": "David", "orcid": "0000-0002-2907-0366", "clpid": "VanderVelde-D-G" }, { "family_name": "Sweredoski", "given_name": "Michael J.", "orcid": "0000-0003-0878-3831", "clpid": "Sweredoski-M-J" }, { "family_name": "Moradian", "given_name": "Annie", "orcid": "0000-0002-0407-2031", "clpid": "Moradian-A" }, { "family_name": "Eggleston-Rangel", "given_name": "Roxana", "clpid": "Eggleston-Rangel-R" }, { "family_name": "Hess", "given_name": "Sonja", "orcid": "0000-0002-5904-9816", "clpid": "Hess-S" }, { "family_name": "Tirrell", "given_name": "David", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" }, { "family_name": "Artsimovitch", "given_name": "Irina", "clpid": "Artsimovitch-I" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Though most bacteria in nature are nutritionally limited and grow slowly, our understanding of core processes like transcription comes largely from studies in model organisms doubling rapidly. We previously identified a small protein of unknown function, SutA, in a screen of proteins synthesized in Pseudomonas aeruginosa during dormancy. SutA binds RNA polymerase (RNAP), causing widespread changes in gene expression, including upregulation of the ribosomal RNA genes. Here, using biochemical and structural methods, we examine how SutA interacts with RNAP and the functional consequences of these interactions. We show that SutA comprises a central \u03b1\u2010helix with unstructured N\u2010 and C\u2010terminal tails, and binds to the \u03b21 domain of RNAP. It activates transcription from the rrn promoter by both the housekeeping sigma factor holoenzyme (E\u03c3^(70)) and the stress sigma factor holoenzyme (E\u03c3^S) in vitro, but has a greater impact on E\u03c3^S. In both cases, SutA appears to affect intermediates in the open complex formation and its N\u2010terminal tail is required for activation. The small magnitudes of in vitro effects are consistent with a role in maintaining activity required for homeostasis during dormancy. Our results add SutA to a growing list of transcription regulators that use their intrinsically disordered regions to remodel transcription complexes.", "doi": "10.1111/mmi.14337", "pmcid": "PMC6736744", "issn": "0950-382X", "publisher": "Wiley", "publication": "Molecular Microbiology", "publication_date": "2019-09", "series_number": "3", "volume": "112", "issue": "3", "pages": "992-1009" }, { "id": "authors:1syan-5pn73", "collection": "authors", "collection_id": "1syan-5pn73", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190509-154449662", "type": "article", "title": "Aggregation of nontuberculous mycobacteria is regulated by carbon:nitrogen balance", "author": [ { "family_name": "DePas", "given_name": "William H.", "orcid": "0000-0001-8532-2567", "clpid": "DePas-William-H" }, { "family_name": "Bergkessel", "given_name": "Megan", "orcid": "0000-0002-4530-1224", "clpid": "Bergkessel-Megan" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Nontuberculous mycobacteria (NTM) are emerging opportunistic pathogens that colonize household water systems and cause chronic lung infections in susceptible patients. The ability of NTM to form surface-attached biofilms in the nonhost environment and corded aggregates in vivo is important to their ability to persist in both contexts. Underlying the development of these multicellular structures is the capacity of mycobacterial cells to adhere to one another. Unlike most other bacteria, NTM spontaneously and constitutively aggregate in vitro, hindering our ability to understand the transition between planktonic and aggregated cells. While culturing a model NTM, Mycobacterium smegmatis, in rich medium, we fortuitously discovered that planktonic cells accumulate after \u223c3\u2009days of growth. By providing selective pressure for bacteria that disperse earlier, we isolated a strain with two mutations in the oligopeptide permease operon (opp). A mutant lacking the opp operon (\u0394opp) disperses earlier than wild type (WT) due to a defect in nutrient uptake. Experiments with WT M. smegmatis revealed that growth as aggregates is favored when carbon is replete, but under conditions of low available carbon relative to available nitrogen, M. smegmatis grows as planktonic cells. By adjusting carbon and nitrogen sources in defined medium, we tuned the cellular C/N ratio such that M. smegmatis grows either as aggregates or as planktonic cells. C/N-mediated aggregation regulation is widespread among NTM with the possible exception of rough-colony Mycobacterium abscessus isolates. Altogether, we show that NTM aggregation is a controlled process that is governed by the relative availability of carbon and nitrogen for metabolism.", "doi": "10.1128/mBio.01715-19", "pmcid": "PMC6692514", "issn": "2150-7511", "publisher": "American Society for Microbiology", "publication": "mBio", "publication_date": "2019-07", "series_number": "4", "volume": "10", "issue": "4", "pages": "Art. No. e01715-19" }, { "id": "authors:yv62w-n4g70", "collection": "authors", "collection_id": "yv62w-n4g70", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190419-100142089", "type": "article", "title": "The transcription factors ActR and SoxR differentially affect the phenazine tolerance of Agrobacterium tumefaciens", "author": [ { "family_name": "Perry", "given_name": "Elena K.", "orcid": "0000-0002-7151-1479", "clpid": "Perry-Elena-K" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Bacteria in soils encounter redox\u2010active compounds, such as phenazines, that can generate oxidative stress, but the mechanisms by which different species tolerate these compounds are not fully understood. Here, we identify two transcription factors, ActR and SoxR, that play contrasting yet complementary roles in the tolerance of the soil bacterium Agrobacterium tumefaciens to phenazines. We show that ActR promotes phenazine tolerance by proactively driving expression of a more energy\u2010efficient terminal oxidase at the expense of a less efficient alternative, which may affect the rate at which phenazines abstract electrons from the electron transport chain (ETC) and thereby generate reactive oxygen species. SoxR, on the other hand, responds to phenazines by inducing expression of several efflux pumps and redox\u2010related genes, including one of three copies of superoxide dismutase and five novel members of its regulon that could not be computationally predicted. Notably, loss of ActR is far more detrimental than loss of SoxR at low concentrations of phenazines, and also increases dependence on the otherwise functionally redundant SoxR\u2010regulated superoxide dismutase. Our results thus raise the intriguing possibility that the composition of an organism's ETC may be the driving factor in determining sensitivity or tolerance to redox\u2010active compounds.", "doi": "10.1111/mmi.14263", "pmcid": "PMC6615960", "issn": "0950-382X", "publisher": "Blackwell Publishing", "publication": "Molecular Microbiology", "publication_date": "2019-07", "series_number": "1", "volume": "112", "issue": "1", "pages": "199-218" }, { "id": "authors:tpa9m-tf409", "collection": "authors", "collection_id": "tpa9m-tf409", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190131-104830799", "type": "article", "title": "Draft Genome Sequence of the Iridescent Marine Bacterium Tenacibaculum discolor Strain IMLK18", "author": [ { "family_name": "Kee", "given_name": "H. Lynn", "orcid": "0000-0001-7683-187X", "clpid": "Kee-H-Lynn" }, { "family_name": "Mikheyeva", "given_name": "Irina V.", "orcid": "0000-0001-7584-9947", "clpid": "Mikheyeva-Bridges-Irina-V" }, { "family_name": "Mickol", "given_name": "Rebecca L.", "orcid": "0000-0002-4493-7263", "clpid": "Mickol-Rebecca-L" }, { "family_name": "Dawson", "given_name": "Scott C.", "orcid": "0000-0002-0843-1759", "clpid": "Dawson-Scott-C" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Leadbetter", "given_name": "Jared R.", "orcid": "0000-0002-7033-0844", "clpid": "Leadbetter-J-R" } ], "abstract": "We report here the draft genome sequence of a strain of Tenacibaculum discolor (Bacteroidetes) that was isolated from the river-ocean interface at Trunk River in Falmouth, Massachusetts. The isolation and genomic sequencing were performed during the 2016 and 2018 Microbial Diversity summer programs at the Marine Biological Laboratory in Woods Hole, Massachusetts.", "doi": "10.1128/mra.01683-18", "pmcid": "PMC6357648", "issn": "2576-098X", "publisher": "American Society for Microbiology", "publication": "Microbiology Resource Announcements", "publication_date": "2019-01", "series_number": "5", "volume": "8", "issue": "5", "pages": "Art. No. e01683-18" }, { "id": "authors:cce66-3kd70", "collection": "authors", "collection_id": "cce66-3kd70", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181003-105017642", "type": "article", "title": "Towards measuring growth rates of pathogens during infections by D_2O-labeling lipidomics", "author": [ { "family_name": "Neubauer", "given_name": "Cajetan", "orcid": "0000-0002-5348-5609", "clpid": "Neubauer-C" }, { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Booth", "given_name": "Ian R.", "clpid": "Booth-I-R" }, { "family_name": "Bowen", "given_name": "Benjamin P.", "orcid": "0000-0003-1368-3958", "clpid": "Bowen-B-P" }, { "family_name": "Kopf", "given_name": "Sebastian H.", "orcid": "0000-0002-2044-0201", "clpid": "Kopf-S-H" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Dalleska", "given_name": "Nathan F.", "orcid": "0000-0002-2059-1587", "clpid": "Dalleska-N-F" } ], "abstract": "Rationale: Microbial growth rate is an important physiological parameter that is challenging to measure in situ, partly because microbes grow slowly in many environments. Recently, it has been demonstrated that generation times of S. aureus in cystic fibrosis (CF) infections can be determined by D_2O\u2010labeling of actively synthesized fatty acids. To improve species specificity and allow growth rate monitoring for a greater range of pathogens during the treatment of infections, it is desirable to accurately quantify trace incorporation of deuterium into phospholipids. \n\nMethods: Lipid extracts of D_2O\u2010treated E. coli cultures were measured on liquid chromatography/electrospray ionization mass spectrometry (LC/ESI\u2010MS) instruments equipped with time\u2010of\u2010flight (TOF) and orbitrap mass analyzers, and used for comparison with the analysis of fatty acids by isotope\u2010ratio gas chromatography (GC)/MS. We then developed an approach to enable tracking of lipid labeling, by following the transition from stationary into exponential growth in pure cultures. Lastly, we applied D_2O\u2010labeling lipidomics to clinical samples from CF patients with chronic lung infections. \n\nResults: Lipidomics facilitates deuterium quantification in lipids at levels that are useful for many labeling applications (>0.03 at% D). In the E. coli cultures, labeling dynamics of phospholipids depend largely on their acyl chains and between phospholipids we notice differences that are not obvious from absolute concentrations alone. For example, cyclopropyl\u2010containing lipids reflect the regulation of cyclopropane fatty acid synthase, which is predominantly expressed at the beginning of stationary phase. The deuterium incorporation into a lipid that is specific for S. aureus in CF sputum indicates an average generation time of the pathogen on the order of one cell doubling per day. \n\nConclusions: This study demonstrates how trace level measurement of stable isotopes in intact lipids can be used to quantify lipid metabolism in pure cultures and provides guidelines that enable growth rate measurements in microbiome samples after incubation with a low percentage of D_2O.", "doi": "10.1002/rcm.8288", "issn": "0951-4198", "publisher": "Wiley", "publication": "Rapid Communications in Mass Spectrometry", "publication_date": "2018-12-30", "series_number": "24", "volume": "32", "issue": "24", "pages": "2129-2140" }, { "id": "authors:cn4e9-pbm07", "collection": "authors", "collection_id": "cn4e9-pbm07", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181004-081517527", "type": "article", "title": "Refining the Application of Microbial Lipids as Tracers of Staphylococcus aureus Growth Rates in Cystic Fibrosis Sputum", "author": [ { "family_name": "Neubauer", "given_name": "Cajetan", "orcid": "0000-0002-5348-5609", "clpid": "Neubauer-Cajetan" }, { "family_name": "Kasi", "given_name": "Ajay S.", "orcid": "0000-0003-0435-2807", "clpid": "Kasi-Ajay-S" }, { "family_name": "Grahl", "given_name": "Nora", "clpid": "Grahl-Nora" }, { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Kopf", "given_name": "Sebastian H.", "orcid": "0000-0002-2044-0201", "clpid": "Kopf-Sebastian-H" }, { "family_name": "Kato", "given_name": "Roberta M.", "clpid": "Kato-Roberta-M" }, { "family_name": "Hogan", "given_name": "Deborah A.", "orcid": "0000-0002-6366-2971", "clpid": "Hogan-Deborah-A" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Chronic lung infections in cystic fibrosis (CF) could be treated more effectively if the effects of antimicrobials on pathogens in situ were known. Here, we compared changes in the microbial community composition and pathogen growth rates in longitudinal studies of seven pediatric CF patients undergoing intravenous antibiotic administration during pulmonary exacerbations. The microbial community composition was determined by counting rRNA with NanoString DNA analysis, and growth rates were obtained by incubating CF sputum with heavy water and tracing incorporation of deuterium into two branched-chain (\"anteiso\") fatty acids (a-C_(15:0) and a-C_(17:0)) using gas chromatography-mass spectrometry (GC/MS). Prior to this study, both lipids were thought to be specific for Staphylococcaceae; hence, their isotopic enrichment was interpreted as a growth proxy for Staphylococcus aureus. Our experiments revealed, however, that Prevotella is also a relevant microbial producer of a-C_(17:0) fatty acid in some CF patients; thus, deuterium incorporation into these lipids is better interpreted as a more general pathogen growth rate proxy. Even accounting for a small nonmicrobial background source detected in some patient samples, a-C_(15:0) fatty acid still appears to be a relatively robust proxy for CF pathogens, revealing a median generation time of \u223c1.5 days, similar to prior observations. Contrary to our expectation, pathogen growth rates remained relatively stable throughout exacerbation treatment. We suggest two straightforward \"best practices\" for application of stable-isotope probing to CF sputum metabolites: (i) parallel determination of microbial community composition in CF sputum using culture-independent tools and (ii) assessing background levels of the diagnostic metabolite.", "doi": "10.1128/jb.00365-18", "pmcid": "PMC6256016", "issn": "0021-9193", "publisher": "American Society for Microbiology", "publication": "Journal of Bacteriology", "publication_date": "2018-12", "series_number": "24", "volume": "200", "issue": "24", "pages": "Art. No. e00365-18" }, { "id": "authors:qpr1y-4gd45", "collection": "authors", "collection_id": "qpr1y-4gd45", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180924-131756393", "type": "article", "title": "Both toxic and beneficial effects of pyocyanin contribute to the lifecycle of Pseudomonas aeruginosa", "author": [ { "family_name": "Meirelles", "given_name": "Lucas A.", "orcid": "0000-0003-3194-7136", "clpid": "Meirelles-Lucas-A" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Pseudomonas aeruginosa, an opportunistic pathogen, produces redox\u2010active pigments called phenazines. Pyocyanin (PYO, the blue phenazine) plays an important role during biofilm development. Paradoxically, PYO auto\u2010poisoning can stimulate cell death and release of extracellular DNA (eDNA), yet PYO can also promote survival within biofilms when cells are oxidant\u2010limited. Here, we identify the environmental and physiological conditions in planktonic culture that promote PYO\u2010mediated cell death. We demonstrate that PYO auto\u2010poisoning is enhanced when cells are starved for carbon. In the presence of PYO, cells activate a set of genes involved in energy\u2010dependent defenses, including: (i) the oxidative stress response, (ii) RND efflux systems and (iii) iron\u2010sulfur cluster biogenesis factors. P. aeruginosa can avoid PYO poisoning when reduced carbon is available, but blockage of adenosine triphosphate (ATP) synthesis either through carbon limitation or direct inhibition of the F_0F_1\u2010ATP synthase triggers death and eDNA release. Finally, even though PYO is toxic to the majority of the population when cells are nutrient limited, a subset of cells is intrinsically PYO resistant. The effect of PYO on the producer population thus appears to be dynamic, playing dramatically different yet predictable roles throughout distinct stages of growth, helping rationalize its multifaceted contributions to biofilm development.", "doi": "10.1111/mmi.14132", "pmcid": "PMC6281804", "issn": "0950-382X", "publisher": "Wiley", "publication": "Molecular Microbiology", "publication_date": "2018-12", "series_number": "6", "volume": "110", "issue": "6", "pages": "995-1010" }, { "id": "authors:4hdan-90d22", "collection": "authors", "collection_id": "4hdan-90d22", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181114-140802025", "type": "article", "title": "Extracellular Electron Transfer Transcends Microbe-Mineral Interactions", "author": [ { "family_name": "Saunders", "given_name": "Scott H.", "orcid": "0000-0003-4224-9106", "clpid": "Saunders-Scott-H" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Extracellular electron transfer (EET) allows microbes to drive their metabolism through interactions with minerals or electrodes. In recent work, Light et al. (2018) discover a specialized EET pathway in Listeria monocytogenes with homologs in pathogens and gut commensals, suggesting that EET plays important roles in diverse environments.", "doi": "10.1016/j.chom.2018.10.018", "issn": "1931-3128", "publisher": "Cell Press", "publication": "Cell Host & Microbe", "publication_date": "2018-11-14", "series_number": "5", "volume": "24", "issue": "5", "pages": "611-613" }, { "id": "authors:tr7cb-1tr53", "collection": "authors", "collection_id": "tr7cb-1tr53", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180816-125733829", "type": "article", "title": "Scanning the isotopic structure of molecules by tandem mass spectrometry", "author": [ { "family_name": "Neubauer", "given_name": "Cajetan", "orcid": "0000-0002-5348-5609", "clpid": "Neubauer-C" }, { "family_name": "Sweredoski", "given_name": "Michael J.", "orcid": "0000-0003-0878-3831", "clpid": "Sweredoski-M-J" }, { "family_name": "Moradian", "given_name": "Annie", "orcid": "0000-0002-0407-2031", "clpid": "Moradian-A" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Robins", "given_name": "Richard J.", "clpid": "Robins-R-J" }, { "family_name": "Eiler", "given_name": "John M.", "orcid": "0000-0001-5768-7593", "clpid": "Eiler-J-M" } ], "abstract": "Biomolecules generally exist as mixtures of diverse isotopologues that differ in the number and sites of rare-isotope substitutions. The exact proportion of isotopologues of a biomolecule may depend on the molecular, cellular, organismal and environmental factors involved in its biosynthesis, localization and consumption. Molecular isotopic structure can thus be a valuable tool to elucidate biochemical mechanisms and for the reconstruction of physiological, ecological and climatic processes. However, little information about this record is accessible by conventional methods of stable isotope chemistry. Here, we report an easy to implement mass spectrometric method that quantifies intramolecular isotope distributions and is specifically designed for use on samples containing low, natural abundances of the rare isotopes. Its essential feature is the use of a narrow initial mass selection window to isolate ions that are heavier due to the presence of one or more isotopic substitutions. This pre-selection greatly increases the relative proportions of the various rare-isotope substituted isotopologues. The selected ions are then fragmented, and within seconds to minutes the isotopic pattern of the fragment peaks reveals information about the intramolecular distribution of isotopes. This approach requires ~0.1 to 10 nanomole of analyte, which is about five orders of magnitude less than NMR. We demonstrate the ability to measure the site-specific isotope ratios of metabolites by resolving the ^(13)C content in the amino acid methionine among multiple non-equivalent carbon sites. This technique enables rapid origin assignments for a wide range of organic molecules and can be used for new applications of molecular isotopic structure in medicine and environmental sciences.", "doi": "10.1016/j.ijms.2018.08.001", "issn": "1387-3806", "publisher": "Elsevier", "publication": "International Journal of Mass Spectrometry", "publication_date": "2018-11", "volume": "434", "pages": "276-286" }, { "id": "authors:n1phb-9ae10", "collection": "authors", "collection_id": "n1phb-9ae10", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181004-090829440", "type": "article", "title": "Chlorate Specifically Targets Oxidant-Starved, Antibiotic-Tolerant Populations of Pseudomonas aeruginosa Biofilms", "author": [ { "family_name": "Spero", "given_name": "Melanie A.", "orcid": "0000-0003-3291-2138", "clpid": "Spero-M-A" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Nitrate respiration is a widespread mode of anaerobic energy generation used by many bacterial pathogens, and the respiratory nitrate reductase, Nar, has long been known to reduce chlorate to the toxic oxidizing agent chlorite. Here, we demonstrate the antibacterial activity of chlorate against Pseudomonas aeruginosa, a representative pathogen that can inhabit hypoxic or anoxic host microenvironments during infection. Aerobically grown P. aeruginosa cells are tobramycin sensitive but chlorate tolerant. In the absence of oxygen or an alternative electron acceptor, cells are tobramycin tolerant but chlorate sensitive via Nar-dependent reduction. The fact that chlorite, the product of chlorate reduction, is not detected in culture supernatants suggests that it may react rapidly and be retained intracellularly. Tobramycin and chlorate target distinct populations within metabolically stratified aggregate biofilms; tobramycin kills cells on the oxic periphery, whereas chlorate kills hypoxic and anoxic cells in the interior. In a matrix populated by multiple aggregates, tobramycin-mediated death of surface aggregates enables deeper oxygen penetration into the matrix, benefiting select aggregate populations by increasing survival and removing chlorate sensitivity. Finally, lasR mutants, which commonly arise in P. aeruginosa infections and are known to withstand conventional antibiotic treatment, are hypersensitive to chlorate. A lasR mutant shows a propensity to respire nitrate and reduce chlorate more rapidly than the wild type does, consistent with its heightened chlorate sensitivity. These findings illustrate chlorate's potential to selectively target oxidant-starved pathogens, including physiological states and genotypes of P. aeruginosa that represent antibiotic-tolerant populations during infections.", "doi": "10.1128/mbio.01400-18", "pmcid": "PMC6156191", "issn": "2150-7511", "publisher": "American Society for Microbiology", "publication": "mBio", "publication_date": "2018-09-25", "series_number": "5", "volume": "9", "issue": "5", "pages": "Art. No. e01400-18" }, { "id": "authors:tvf44-tvw68", "collection": "authors", "collection_id": "tvf44-tvw68", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180927-114224832", "type": "monograph", "title": "Extended hopanoid lipids promote bacterial motility, surface attachment, and root nodule development in the Bradyrhizobium diazoefficiens-Aeschynomene afraspera symbiosis", "author": [ { "family_name": "Belin", "given_name": "Brittany J.", "clpid": "Belin-B-J" }, { "family_name": "Tookmanian", "given_name": "Elise T.", "clpid": "Tookmanian-E-T" }, { "family_name": "de Anda", "given_name": "Jaime", "orcid": "0000-0003-2129-0775", "clpid": "de-Anda-J" }, { "family_name": "Wong", "given_name": "Gerard", "orcid": "0000-0003-0893-6383", "clpid": "Wong-Gerard-C-L" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Hopanoids are steroid-like bacterial lipids that enhance membrane rigidity and promote bacterial growth under diverse stresses. Roughly 10% of bacteria contain genes involved in hopanoid biosynthesis, and these genes are particularly conserved in plant-associated organisms. We previously found that the extended class of hopanoids (C35) in the nitrogen-fixing soil bacterium Bradyrhizobium diazoefficiens promotes its root nodule symbiosis with the tropical legume Aeschynomene afraspera. By quantitatively modeling root nodule development, we identify independent roles for hopanoids in the initiation of root nodule formation and in determining the rate of root nodule maturation. In vitro studies demonstrate that extended hopanoids support B. diazoefficiens motility and surface attachment, which may correlate with stable root colonization in planta. Confocal microscopy of maturing root nodules reveals that root nodules infected with extended hopanoid-deficient B. diazoefficiens contain unusually low densities of bacterial symbionts, indicating that extended hopanoids are necessary for persistent, high levels of host infection. This work identifies extended hopanoids as regulators of the efficiency of Bradyrhizobia nitrogen-fixing symbioses, agriculturally and economically significant associations with growing importance in a changing climate.", "doi": "10.1101/423301", "publication_date": "2018-09-21" }, { "id": "authors:24k4c-8z842", "collection": "authors", "collection_id": "24k4c-8z842", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180813-133514351", "type": "article", "title": "Structural and mechanistic analysis of the arsenate respiratory reductase provides insight into environmental arsenic transformations", "author": [ { "family_name": "Glasser", "given_name": "Nathaniel R.", "orcid": "0000-0002-2833-5166", "clpid": "Glasser-Nathaniel-R" }, { "family_name": "Oyala", "given_name": "Paul H.", "orcid": "0000-0002-8761-4667", "clpid": "Oyala-Paul-H" }, { "family_name": "Osborne", "given_name": "Thomas H.", "clpid": "Osborne-Thomas-H" }, { "family_name": "Santini", "given_name": "Joanne M.", "clpid": "Santini-Joanne-M" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Arsenate respiration by bacteria was discovered over two decades ago and is catalyzed by diverse organisms using the well-conserved Arr enzyme complex. Until now, the mechanisms underpinning this metabolism have been relatively opaque. Here, we report the structure of an Arr complex (solved by X-ray crystallography to 1.6-\u00c5 resolution), which was enabled by an improved Arr expression method in the genetically tractable arsenate respirer Shewanella sp. ANA-3. We also obtained structures bound with the substrate arsenate (1.8 \u00c5), the product arsenite (1.8 \u00c5), and the natural inhibitor phosphate (1.7 \u00c5). The structures reveal a conserved active-site motif that distinguishes Arr [(R/K)GRY] from the closely related arsenite respiratory oxidase (Arx) complex (XGRGWG). Arr activity assays using methyl viologen as the electron donor and arsenate as the electron acceptor display two-site ping-pong kinetics. A Mo(V) species was detected with EPR spectroscopy, which is typical for proteins with a pyranopterin guanine dinucleotide cofactor. Arr is an extraordinarily fast enzyme that approaches the diffusion limit (K_m = 44.6 \u00b1 1.6 \u03bcM, k_(cat) = 9,810 \u00b1 220 seconds^(\u22121)), and phosphate is a competitive inhibitor of arsenate reduction (K_i = 325 \u00b1 12 \u03bcM). These observations, combined with knowledge of typical sedimentary arsenate and phosphate concentrations and known rates of arsenate desorption from minerals in the presence of phosphate, suggest that (i) arsenate desorption limits microbiologically induced arsenate reductive mobilization and (ii) phosphate enhances arsenic mobility by stimulating arsenate desorption rather than by inhibiting it at the enzymatic level.", "doi": "10.1073/pnas.1807984115", "pmcid": "PMC6140538", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2018-09-11", "series_number": "37", "volume": "115", "issue": "37", "pages": "E8614-E8623" }, { "id": "authors:jfkd7-ytb30", "collection": "authors", "collection_id": "jfkd7-ytb30", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180910-091617013", "type": "article", "title": "A personal tribute to Terry Beveridge", "author": [ { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "I met Terry Beveridge in the fall of 1994, when my Ph.D. advisor, Francois Morel, sent me to visit Terry's lab at the University of Guelph, Ontario, for a week. Francois had met Terry at a meeting in France a few years prior, and they had hit it off discussing science over some good wine (or perhaps it was scotch?). Only a year into my Ph.D. studies, I was excited by the opportunity to visit Guelph, yet without the perspective to fully appreciate what an act of generosity this was on both their parts. Now, over two decades later, I realize just how special it was \u2014 my primary mentor was enabling me to pursue a research project that was tangential to his own research interests, and my soon-to-be microbiology mentor was opening his lab to a young stranger from another country.", "doi": "10.1139/cjm-2017-0515", "issn": "0008-4166", "publisher": "National Research Council Canada", "publication": "Canadian Journal of Microbiology", "publication_date": "2018-09", "series_number": "9", "volume": "64", "issue": "9", "pages": "ix-xi" }, { "id": "authors:zv0wd-cw222", "collection": "authors", "collection_id": "zv0wd-cw222", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181009-123252928", "type": "article", "title": "In situ gene expression analysis of mucoid P. aeruginosa biofilms suggests that alginate expression is restricted to microaerobic regions of the biofilm", "author": [ { "family_name": "Jorth", "given_name": "P.", "orcid": "0000-0002-0981-740X", "clpid": "Jorth-P" }, { "family_name": "Spero", "given_name": "M. A.", "orcid": "0000-0003-3291-2138", "clpid": "Spero-M-A" }, { "family_name": "Newman", "given_name": "D. K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Mucoid Pseudomonas aeruginosa evolve during chronic cystic fibrosis (CF) infections and make robust biofilms that protect against antibiotics and the immune response. Previous measurements suggested that alginate gene\nexpression is induced in response to low oxygen, however, these measurements were made in bulk liquid cultures. Because P. aeruginosa is thought to grow as biofilms in vivo and biofilms are known to exhibit large oxygen\ngradients, we wondered whether alginate production within biofilms might be localized to particular regions. We used confocal microscopy to determine where alginate transcripts are expressed within biofilm populations grown using the agar block biofilm assay (ABBA), which permits\nrapid study of biofilms; the ABBA assay establishes oxygen gradients over the entire aggregate population and within individual aggregates.", "doi": "10.1002/ppul.24152", "issn": "8755-6863", "publisher": "Wiley", "publication": "Pediatric Pulmonology", "publication_date": "2018-09", "series_number": "S2", "volume": "53", "issue": "S2", "pages": "Art. No. 462" }, { "id": "authors:jw0hg-a5937", "collection": "authors", "collection_id": "jw0hg-a5937", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180723-080501925", "type": "article", "title": "Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry", "author": [ { "family_name": "Zhalnina", "given_name": "Kateryna", "clpid": "Zhalnina-K" }, { "family_name": "Zengler", "given_name": "Karsten", "clpid": "Zengler-K" }, { "family_name": "Newman", "given_name": "Dianne", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Northen", "given_name": "Trent R.", "clpid": "Northen-T-R" } ], "abstract": "The chemistry underpinning microbial interactions provides an integrative framework for linking the activities of individual microbes, microbial communities, plants, and their environments. Currently, we know very little about the functions of genes and metabolites within these communities because genome annotations and functions are derived from the minority of microbes that have been propagated in the laboratory. Yet the diversity, complexity, inaccessibility, and irreproducibility of native microbial consortia limit our ability to interpret chemical signaling and map metabolic networks. In this perspective, we contend that standardized laboratory ecosystems are needed to dissect the chemistry of soil microbiomes. We argue that dissemination and application of standardized laboratory ecosystems will be transformative for the field, much like how model organisms have played critical roles in advancing biochemistry and molecular and cellular biology. Community consensus on fabricated ecosystems (\"EcoFABs\") along with protocols and data standards will integrate efforts and enable rapid improvements in our understanding of the biochemical ecology of microbial communities.", "doi": "10.1128/mBio.01175-18", "pmcid": "PMC6050955", "issn": "2150-7511", "publisher": "American Society for Microbiology", "publication": "mBio", "publication_date": "2018-07-17", "series_number": "4", "volume": "9", "issue": "4", "pages": "Art. No. e01175-18" }, { "id": "authors:bd2e2-sg052", "collection": "authors", "collection_id": "bd2e2-sg052", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180306-084603442", "type": "article", "title": "PhdA catalyzes the first step of phenazine-1-carboxylic acid degradation in Mycobacterium fortuitum", "author": [ { "family_name": "Costa", "given_name": "Kyle C.", "clpid": "Costa-K-C" }, { "family_name": "Moskatel", "given_name": "Leon S.", "clpid": "Moskatel-L-S" }, { "family_name": "Meirelles", "given_name": "Lucas A.", "clpid": "Meirelles-L-A" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Phenazines are a class of bacterially produced redox-active metabolites that are found in natural, industrial, and clinical environments. In Pseudomonas spp., phenazine-1-carboxylic acid (PCA)\u2014the precursor of all phenazine metabolites\u2014facilitates nutrient acquisition, biofilm formation, and competition with other organisms. While the removal of phenazines negatively impacts these activities, little is known about the genes or enzymes responsible for phenazine degradation by other organisms. Here, we report that the first step of PCA degradation by Mycobacterium fortuitum is catalyzed by a phenazine-degrading decarboxylase (PhdA). PhdA is related to members of the UbiD protein family that rely on a prenylated flavin mononucleotide cofactor for activity. The gene for PhdB, the enzyme responsible for cofactor synthesis, is present in a putative operon with the gene encoding PhdA in a region of the M. fortuitum genome that is essential for PCA degradation. PhdA and PhdB are present in all known PCA-degrading organisms from the Actinobacteria. M. fortuitum can also catabolize other Pseudomonas-derived phenazines such as phenazine-1-carboxamide, 1-hydroxyphenazine, and pyocyanin. On the basis of our previous work and the current characterization of PhdA, we propose that degradation converges on a common intermediate: dihydroxyphenazine. An understanding of the genes responsible for degradation will enable targeted studies of phenazine degraders in diverse environments.", "doi": "10.1128/JB.00763-17", "pmcid": "PMC5915785", "issn": "0021-9193", "publisher": "American Society for Microbiology", "publication": "Journal of Bacteriology", "publication_date": "2018-05", "series_number": "10", "volume": "200", "issue": "10", "pages": "Art. No. e00763-17" }, { "id": "authors:pdchx-w6n59", "collection": "authors", "collection_id": "pdchx-w6n59", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181206-104542777", "type": "article", "title": "Intracellular Persistence of Pseudomonas Aeruginosa in Airway Epithelial Cells and in Cystic Fibrosis Lung", "author": [ { "family_name": "Faure", "given_name": "E.", "clpid": "Faure-E" }, { "family_name": "Jorth", "given_name": "P.", "orcid": "0000-0002-0981-740X", "clpid": "Jorth-P" }, { "family_name": "Berube", "given_name": "J.", "clpid": "Berube-J" }, { "family_name": "Brochiero", "given_name": "E.", "clpid": "Brochiero-E" }, { "family_name": "Newman", "given_name": "D.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Rousseau", "given_name": "S.", "clpid": "Rousseau-S" }, { "family_name": "Nguyen", "given_name": "D.", "clpid": "Nguyen-D" } ], "abstract": "Rationale: Cystic Fibrosis (CF) lung disease is characterized by chronic Pseudomonas aeruginosa infections in airways. Why P. aeruginosa persists despite antimicrobial and activation of immune responses remains incompletely understood. To date, the prevailing view suggests that impaired muco-cilliary clearance and biofilm lifestyle are the primary mechanisms contributing to the persistence in CF lung. Although P. aeruginosa is an extracellular pathogen, previous in vitro studies have reported that it is internalized in epithelial cells. This led us to hypothesize that P. aeruginosa is internalized and persists in lung epithelial cells, contributing to\nP. aeruginosa's evasion of extracellular antibacterials and host defenses. Methods: We have developed an in vitro model of long-term intracellular persistence of P. aeruginosa in human airway epithelial cells, using several cell lines (Beas-2B, CBFE and CFBE\u0394F508), and have tested different P. aeruginosa strains (PAO1, CHA, isogenic mutants). Epithelial cells, grown as immersed monolayers, or polarized at the air-liquid interface, and incubated with P. aeruginosa at MOl 1 during 4 hours. For the following 5 days, epithelial cells are treated with tobramycin to\nmaintain the extracellular culture milieu sterile. Intracellular bacterial burden was measured at\ndifferent time points by plate counting of CFU. We assessed cell death by LOH assay. Confocal microscopy was used to localize and count intracellular P. aeruginosa. Finally, we use MiPACT, (Microbial identification after Passive CLARITY Technique), a technique that allows direct visualization of P. aeruginosa, using targeted antibody or RNA probe, in cleared lungs from CF patient, creating a three-dimensional biogeographical map of the lung tissue and the infecting\npathogens. Results: We showed that P. aeruginosa persists and replicates in B2B and CFBE cells over 5 days without causing significant host cell cytotoxicity. Approximately 15% of initial bacterial inoculum is internalized, and the intracellular bacterial burden increases 2-fold over 5\ndays. Moreover, bacterial persistence is increased ~2-fold in CFBE\u0394F508 cells compared to CFBE. Non-flagellated mutant was showed increased persistence. Additionally, we showed that P. aeruginosa co-localizes with LAMP-1. Using MiPACT, we showed a positive intracellular staining of P. aeruginosa in airway epithelial cells from CF lung explants. Conclusion: Our in vitro model suggests that P. aeruginosa is readily internalized and persists more in CF airway epithelial cell. The possibility that P. aeruginosa may have an intracellular niche within the CF lung highlights a potentially new mechanism of bacterial persistence in CF lung disease. \n\nThis abstract is funded by: None", "issn": "1073-449X", "publisher": "American Thoracic Society", "publication": "American Journal of Respiratory and Critical Care Medicine", "publication_date": "2018-05", "volume": "197", "pages": "Art. No. A6262" }, { "id": "authors:g2pzb-zpw71", "collection": "authors", "collection_id": "g2pzb-zpw71", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180221-160552040", "type": "article", "title": "Hopanoid lipids: from membranes to plant\u2013bacteria interactions", "author": [ { "family_name": "Belin", "given_name": "Brittany J.", "clpid": "Belin-B-J" }, { "family_name": "Busset", "given_name": "Nicolas", "clpid": "Busset-N" }, { "family_name": "Giraud", "given_name": "Eric", "clpid": "Giraud-E" }, { "family_name": "Molinaro", "given_name": "Antonio", "clpid": "Molinaro-A" }, { "family_name": "Silipo", "given_name": "Alba", "clpid": "Silipo-A" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Lipid research represents a frontier for microbiology, as showcased by hopanoid lipids. Hopanoids, which resemble sterols and are found in the membranes of diverse bacteria, have left an extensive molecular fossil record. They were first discovered by petroleum geologists. Today, hopanoid-producing bacteria remain abundant in various ecosystems, such as the rhizosphere. Recently, great progress has been made in our understanding of hopanoid biosynthesis, facilitated in part by technical advances in lipid identification and quantification. A variety of genetically tractable, hopanoid-producing bacteria have been cultured, and tools to manipulate hopanoid biosynthesis and detect hopanoids are improving. However, we still have much to learn regarding how hopanoid production is regulated, how hopanoids act biophysically and biochemically, and how their production affects bacterial interactions with other organisms, such as plants. The study of hopanoids thus offers rich opportunities for discovery.", "doi": "10.1038/nrmicro.2017.173", "pmcid": "PMC6087623", "issn": "1740-1526", "publisher": "Nature Publishing Group", "publication": "Nature Reviews Microbiology", "publication_date": "2018-05", "series_number": "5", "volume": "16", "issue": "5", "pages": "304-315" }, { "id": "authors:jga11-5d250", "collection": "authors", "collection_id": "jga11-5d250", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180510-091834521", "type": "article", "title": "Probing Phenazine Electron Transfer and Retention in Pseudomonas Aeruginosa Biofilms", "author": [ { "family_name": "Saunders", "given_name": "Scott H.", "orcid": "0000-0003-4224-9106", "clpid": "Saunders-Scott-H" }, { "family_name": "Yates", "given_name": "Matthew D.", "orcid": "0000-0003-4373-3864", "clpid": "Yates-Matthew-D" }, { "family_name": "Tse", "given_name": "Edmund C. M.", "clpid": "Tse-Edmund-C-M" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Tender", "given_name": "Leonard M.", "orcid": "0000-0001-8784-991X", "clpid": "Tender-Leonard-M" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "The opportunistic pathogen Pseudomonas aeruginosa forms metabolically stratified biofilms. Redox-active phenazine metabolites shuttle metabolic electrons from the oxygen depleted biofilm interior to the oxygen saturated exterior, facilitating anoxic survival. We are testing the hypothesis that phenazine retention and/or charge transfer through the biofilm matrix are mediated by extracellular DNA (eDNA), which is the most abundant polymer in the P. aeruginosa matrix and is known to provide structural integrity to the biofilm. Specifically, we are growing biofilms on electrode arrays and performing in vitro studies of phenazine interactions with DNA. Biofilm experiments show that conductivity through the matrix is mediated by sequential electron transfer between phenazine molecules. Transferring electrode grown biofilms to fresh liquid medium demonstrates that some phenazines are retained tightly in the biofilm matrix, while others rapidly diffuse away. The retention of different phenazines corresponds to their affinity for DNA in vitro, consistent with the idea that some phenazines might bind the eDNA in the biofilm. We are testing whether phenazines bound to DNA can also mediate charge transfer. Collectively, these experiments are helping us better understand how P. aeruginosa utilizes its self-produced extracellular electron shuttles to survive biofilm oxidant limitation, and are opening up new perspectives on the role(s) that eDNA may play in the biofilm matrix.", "doi": "10.1016/j.bpj.2017.11.198", "issn": "0006-3495", "publisher": "Biophysical Society", "publication": "Biophysical Journal", "publication_date": "2018-02-02", "series_number": "3", "volume": "114", "issue": "3", "pages": "28a" }, { "id": "authors:72t40-dkx78", "collection": "authors", "collection_id": "72t40-dkx78", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171205-204626357", "type": "article", "title": "Identification of Fitness Determinants during Energy-Limited Growth Arrest in Pseudomonas aeruginosa", "author": [ { "family_name": "Basta", "given_name": "David W.", "orcid": "0000-0003-4176-6566", "clpid": "Basta-David-Wagdi" }, { "family_name": "Bergkessel", "given_name": "Megan", "orcid": "0000-0002-4530-1224", "clpid": "Bergkessel-M" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "contributor": [ { "family_name": "Whiteley", "given_name": "Marvin", "clpid": "Whiteley-M" } ], "abstract": "Microbial growth arrest can be triggered by diverse factors, one of which is energy limitation due to scarcity of electron donors or acceptors. Genes that govern fitness during energy-limited growth arrest and the extent to which they overlap between different types of energy limitation are poorly defined. In this study, we exploited the fact that Pseudomonas aeruginosa can remain viable over several weeks when limited for organic carbon (pyruvate) as an electron donor or oxygen as an electron acceptor. ATP values were reduced under both types of limitation, yet more severely in the absence of oxygen. Using transposon-insertion sequencing (Tn-seq), we identified fitness determinants in these two energy-limited states. Multiple genes encoding general functions like transcriptional regulation and energy generation were required for fitness during carbon or oxygen limitation, yet many specific genes, and thus specific activities, differed in their relevance between these states. For instance, the global regulator RpoS was required during both types of energy limitation, while other global regulators such as DksA and LasR were required only during carbon or oxygen limitation, respectively. Similarly, certain ribosomal and tRNA modifications were specifically required during oxygen limitation. We validated fitness defects during energy limitation using independently generated mutants of genes detected in our screen. Mutants in distinct functional categories exhibited different fitness dynamics: regulatory genes generally manifested a phenotype early, whereas genes involved in cell wall metabolism were required later. Together, these results provide a new window into how P. aeruginosa survives growth arrest.", "doi": "10.1128/mBio.01170-17", "pmcid": "PMC5705914", "issn": "2150-7511", "publisher": "American Society for Microbiology", "publication": "mBio", "publication_date": "2017-11", "series_number": "6", "volume": "8", "issue": "6", "pages": "Art. No. e01170" }, { "id": "authors:h8vez-t1538", "collection": "authors", "collection_id": "h8vez-t1538", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171030-071731344", "type": "article", "title": "Selective Proteomic Analysis of Antibiotic-Tolerant Cellular Subpopulations in Pseudomonas aeruginosa Biofilms", "author": [ { "family_name": "Babin", "given_name": "Brett M.", "orcid": "0000-0002-4133-6665", "clpid": "Babin-B-M" }, { "family_name": "Atangcho", "given_name": "Lydia", "clpid": "Atangcho-L" }, { "family_name": "van Eldijk", "given_name": "Mark B.", "clpid": "van-Eldijk-M-B" }, { "family_name": "Sweredoski", "given_name": "Michael J.", "orcid": "0000-0003-0878-3831", "clpid": "Sweredoski-M-J" }, { "family_name": "Moradian", "given_name": "Annie", "orcid": "0000-0002-0407-2031", "clpid": "Moradian-A" }, { "family_name": "Hess", "given_name": "Sonja", "orcid": "0000-0002-5904-9816", "clpid": "Hess-S" }, { "family_name": "Tolker-Nielsen", "given_name": "Tim", "clpid": "Tolker-Nielsen-T" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" } ], "abstract": "Biofilm infections exhibit high tolerance against antibiotic treatment. The study of biofilms is complicated by phenotypic heterogeneity; biofilm subpopulations differ in their metabolic activities and their responses to antibiotics. Here, we describe the use of the bio-orthogonal noncanonical amino acid tagging (BONCAT) method to enable selective proteomic analysis of a Pseudomonas aeruginosa biofilm subpopulation. Through controlled expression of a mutant methionyl-tRNA synthetase, we targeted BONCAT labeling to cells in the regions of biofilm microcolonies that showed increased tolerance to antibiotics. We enriched and identified proteins synthesized by cells in these regions. Compared to the entire biofilm proteome, the labeled subpopulation was characterized by a lower abundance of ribosomal proteins and was enriched in proteins of unknown function. We performed a pulse-labeling experiment to determine the dynamic proteomic response of the tolerant subpopulation to supra-MIC treatment with the fluoroquinolone antibiotic ciprofloxacin. The adaptive response included the upregulation of proteins required for sensing and repairing DNA damage and substantial changes in the expression of enzymes involved in central carbon metabolism. We differentiated the immediate proteomic response, characterized by an increase in flagellar motility, from the long-term adaptive strategy, which included the upregulation of purine synthesis. This targeted, selective analysis of a bacterial subpopulation demonstrates how the study of proteome dynamics can enhance our understanding of biofilm heterogeneity and antibiotic tolerance.IMPORTANCE Bacterial growth is frequently characterized by behavioral heterogeneity at the single-cell level. Heterogeneity is especially evident in the physiology of biofilms, in which distinct cellular subpopulations can respond differently to stresses, including subpopulations of pathogenic biofilms that are more tolerant to antibiotics. Global proteomic analysis affords insights into cellular physiology but cannot identify proteins expressed in a particular subpopulation of interest. Here, we report a chemical biology method to selectively label, enrich, and identify proteins expressed by cells within distinct regions of biofilm microcolonies. We used this approach to study changes in protein synthesis by the subpopulation of antibiotic-tolerant cells throughout a course of treatment. We found substantial differences between the initial response and the long-term adaptive strategy that biofilm cells use to cope with antibiotic stress. The method we describe is readily applicable to investigations of bacterial heterogeneity in diverse contexts.", "doi": "10.1128/mBio.01593-17", "pmcid": "PMC5654934", "issn": "2150-7511", "publisher": "American Society for Microbiology", "publication": "mBio", "publication_date": "2017-10-24", "series_number": "5", "volume": "8", "issue": "5", "pages": "Art. No. e01593-17" }, { "id": "authors:41wsf-mr159", "collection": "authors", "collection_id": "41wsf-mr159", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171012-103413414", "type": "conference_item", "title": "Aggregation of Nontuberculous Mycobacteria in Vitro and in Situ", "author": [ { "family_name": "DePas", "given_name": "W.", "clpid": "DePas-W" }, { "family_name": "Bergkessel", "given_name": "M.", "orcid": "0000-0002-4530-1224", "clpid": "Bergkessel-M" }, { "family_name": "Newman", "given_name": "D. K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "The incidence of nontuberculous mycobacterial (NTM) infections in cystic fibrosis (CF) patients is increasing, with some CF clinics in the US reporting NTM prevalence upwards of 25%. In addition, the current treatment\nregimen for NTM involves long courses of antibiotic cocktails that demonstrate limited efficacy and cause frequent and serious side effects.\nMycobacterium abscessus, in particular, is difficult to treat and correlates with a more rapid decline in lung function compared to Mycobacterium avium complex. Studies with zebrafish and human cell cultures have demonstrated that M. abscessus is more virulent when aggregated into cord-like biofilms, in part because of the decreased ability of phagocytes to efficiently engulf and kill corded M. abscessus compared to diffuse M. abscessus cells. Translating these findings into useful clinical strategies\nfor treating NTM infections will be greatly aided by 1.) A thorough understanding of the environmental conditions and genetic networks that control NTM aggregation, and 2.) Information about the in vivo aggregation state of NTM during infection. To address item 1, we developed an in\nvitro aggregation assay in which NTM such as M. abscessus and the model strain Mycobacterium smegmatis aggregate and disperse regularly in liquid culture. We found that M. smegmatis aggregation was dependent on carbon source type and availability. In particular, glycerol catabolism induces\naggregation while pyruvate or amino acid catabolism leads to growth as dispersed cells. In contrast, oxygen availability does not induce changes in aggregation state. Currently, we are performing experiments in order to elucidate the genetic regulators that trigger aggregation in response to glycerol catabolism.", "doi": "10.1002/ppul.23840", "publisher": "Wiley", "publication_date": "2017-09" }, { "id": "authors:xd2v1-pe260", "collection": "authors", "collection_id": "xd2v1-pe260", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171012-103857991", "type": "conference_item", "title": "Clarifying the Intracellular and Extracellular Lifestyles of CF Microbes in Three Dimensions", "author": [ { "family_name": "Jorth", "given_name": "P.", "orcid": "0000-0002-0981-740X", "clpid": "Jorth-P" }, { "family_name": "Newman", "given_name": "D. K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Imaging of sputum smears and thin sections have suggested that P. aeruginosa persists as extracellular bacterial aggregates, or biofilms, during chronic CF infections. However, emerging evidence indicates that host cells may also provide a protective reservoir for P. aeruginosa\nduring infection. While phagocytes that flood the CF airways normally kill infecting bacteria, CFTR-deficient murine macrophages fail to kill P. aeruginosa,\nraising the possibility that CF macrophages could house viable bacteria. Epithelial cells may also provide an intracellular home for P. aeruginosa, since P. aeruginosa can invade epithelial cells in tissue culture systems. Together, these results have led to our hypothesis that the intracellular environment is a protective reservoir for P. aeruginosa during chronic CF infections. We are using a state-of-the-art imaging technique termed MiPACT to study\nhow bacteria are spatially organized and functioning in CF sputum in relation to host cells. MiPACT was previously developed for the characterization of growth rates and spatial organization of microbes in millimeter thick\nthree-dimensional CF sputum specimens. A major advantage to MiPACT is that the sputum specimens are embedded in a hydrogel and passively cleared with a detergent, which renders the sputum optically transparent and maintains the original biogeography of the specimens. This represents\na substantial advance over traditional techniques like smears and thin sections, which were essentially limited to analyses in two dimensions. In this study, we have further advanced MiPACT in two ways to study how P. aeruginosa interacts with host cells. First, we can now detect bacterial gene expression in situ with fluorescent nucleic acid probes, which will allow us to determine whether specific genes are expressed when bacteria associate\nwith host cells. Second, we have combined MiPACT with immunofluorescence to label bacteria and host cell proteins with fluorescent antibodies. In these preliminary studies, we have developed probes to detect P. aeruginosa\nalginate gene expression in vitro and successfully used immunofluorescence to label neutrophils, macrophages, and P. aeruginosa in CF sputum in situ. The immunofluorescence revealed that P. aeruginosa can be detected as extracellular and intracellular aggregates in sputum. Ongoing work is being performed to determine which host cells are housing intracellular P. aeruginosa and whether intracellular bacteria are viable or in the process\nof being killed. These new methods will shed important light on how P. aeruginosa persists in the CF airways.", "doi": "10.1002/ppul.23840", "publisher": "Wiley", "publication_date": "2017-09" }, { "id": "authors:942tg-2a578", "collection": "authors", "collection_id": "942tg-2a578", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171012-102706675", "type": "article", "title": "SutA is a Global Transcriptional Regulator Operating during Slow Growth in Pseudomonas Aeruginosa", "author": [ { "family_name": "Bergkessel", "given_name": "M.", "orcid": "0000-0002-4530-1224", "clpid": "Bergkessel-M" }, { "family_name": "Newman", "given_name": "D. K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Babin", "given_name": "B.", "orcid": "0000-0002-4133-6665", "clpid": "Babin-B-M" }, { "family_name": "Tirrell", "given_name": "D. A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" } ], "abstract": "Chronic Pseudomonas aeruginosa infections, a major cause of morbidity and mortality for CF patients, are highly resistant to antibiotic treatment, and many lines of evidence suggest that this is due in part to slow-growing\nstates imposed by the lung environment. In previously published work (Babin BM, et al. Proc Natl Acad Sci 2016;113(5):E597-605), we identified a novel RNA polymerase-binding protein that is post-transcriptionally upregulated under such slow-growth conditions. We named this small,\nacidic protein SutA, and showed using RNA-Seq and ChIP-Seq that it associates with RNA polymerase (RNAP) at many genomic regions, and tends to positively affect transcript levels for genes with which it associates. The genes that are affected include ribosomal RNA and protein genes, and other genes with roles in metabolism and stress survival. Furthermore, we showed that deletion of the sutA gene confers a disadvantage on cells subjected to fluctuations between growth-arrested and growth-promoting states. Thus,\nSutA may contribute to survival of Pseudomonas aeruginosa in environments like the CF lung, where oxygen and nutrient availability are likely to be heterogeneous in time and space.", "doi": "10.1002/ppul.23840", "issn": "8755-6863", "publisher": "Wiley", "publication": "Pediatric Pulmonology", "publication_date": "2017-09", "series_number": "S47", "volume": "52", "issue": "S47", "pages": "S366-S367" }, { "id": "authors:mpg16-qvr61", "collection": "authors", "collection_id": "mpg16-qvr61", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170724-072743727", "type": "article", "title": "The Colorful World of Extracellular Electron Shuttles", "author": [ { "family_name": "Glasser", "given_name": "Nathaniel R.", "orcid": "0000-0002-2833-5166", "clpid": "Glasser-Nathaniel-R" }, { "family_name": "Saunders", "given_name": "Scott H.", "orcid": "0000-0003-4224-9106", "clpid": "Saunders-Scott-H" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Descriptions of the changeable, striking colors associated with secreted natural products date back well over a century. These molecules can serve as extracellular electron shuttles (EESs) that permit microbes to access substrates at a distance. In this review, we argue that the colorful world of EESs has been too long neglected. Rather than simply serving as a diagnostic attribute of a particular microbial strain, redox-active natural products likely play fundamental, underappreciated roles in the biology of their producers, particularly those that inhabit biofilms. Here, we describe the chemical diversity and potential distribution of EES producers and users, discuss the costs associated with their biosynthesis, and critically evaluate strategies for their economical usage. We hope this review will inspire efforts to identify and explore the importance of EES cycling by a wide range of microorganisms so that their contributions to shaping microbial communities can be better assessed and exploited.", "doi": "10.1146/annurev-micro-090816-093913", "pmcid": "PMC5679407", "issn": "0066-4227", "publisher": "Annual Reviews", "publication": "Annual Review of Microbiology", "publication_date": "2017-07-24", "volume": "71", "pages": "731-751" }, { "id": "authors:0wsvd-v9b84", "collection": "authors", "collection_id": "0wsvd-v9b84", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170615-092601345", "type": "article", "title": "Bacterial Growth Rate In Cystic Fibrosis Pulmonary Exacerbation", "author": [ { "family_name": "Kasi", "given_name": "Ajay S.", "clpid": "Kasi-A-S" }, { "family_name": "Neubauer", "given_name": "Cajetan", "orcid": "0000-0002-5348-5609", "clpid": "Neubauer-C" }, { "family_name": "Kato", "given_name": "Robeta M.", "clpid": "Kato-R-M" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "There is significant microbial diversity in the spectrum produced by cystic fibrosis (CF) patients. Bacterial load in sputum has been reported to be a poor predictor of pulmonary exacerbations (PE). Our previous cross sectional study that Stapnyiococcus aureus (SA) generation times in vivo are far slower and more heterogeneous in CF patients than the growth rates that characterize SA grown in the laboratory. SA generation time was found to be slowest in acutely ill patients during PE and significantly higher in patients who were well. During treatment of a PE, there was an initial decrease in sputum SA grown rate followed by a return to baseline growth rate over the course of a hospital stay. Bacterial growth rate heterogeneity could contribute to inconsistent recovery time from a CF PE. In this study, we performed a longitudinal analysis of SA growth rate during the treatment of PE.", "issn": "1073-449X", "publisher": "American Thoracic Society", "publication": "American Journal of Respiratory and Critical Care Medicine", "publication_date": "2017-05", "volume": "195", "pages": "Art. No. A4856" }, { "id": "authors:e85mx-1ta62", "collection": "authors", "collection_id": "e85mx-1ta62", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170213-091715272", "type": "article", "title": "The pyruvate and \u03b1-ketoglutarate dehydrogenase complexes of Pseudomonas aeruginosa catalyze pyocyanin and phenazine-1-carboxylic acid reduction via the subunit dihydrolipoamide dehydrogenase", "author": [ { "family_name": "Glasser", "given_name": "Nathaniel R.", "orcid": "0000-0002-2833-5166", "clpid": "Glasser-Nathaniel-R" }, { "family_name": "Wang", "given_name": "Benjamin X.", "clpid": "Wang-Benjamin-X" }, { "family_name": "Hoy", "given_name": "Julie A.", "clpid": "Hoy-Julie-A" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Phenazines are a class of redox-active molecules produced by diverse bacteria and archaea. Many of the biological functions of phenazines, such as mediating signaling, iron acquisition, and redox homeostasis, derive from their redox activity. Although prior studies have focused on extracellular phenazine oxidation by oxygen and iron, here we report a search for reductants and catalysts of intracellular phenazine reduction in Pseudomonas aeruginosa. Enzymatic assays in cell-free lysate, together with crude fractionation and chemical inhibition, indicate that P. aeruginosa contains multiple enzymes that catalyze the reduction of the endogenous phenazines pyocyanin and phenazine-1-carboxylic acid in both cytosolic and membrane fractions. We used chemical inhibitors to target general enzyme classes and found that an inhibitor of flavoproteins and heme-containing proteins, diphenyleneiodonium, effectively inhibited phenazine reduction in vitro, suggesting that most phenazine reduction derives from these enzymes. Using natively purified proteins, we demonstrate that the pyruvate and \u03b1-ketoglutarate dehydrogenase complexes directly catalyze phenazine reduction with pyruvate or \u03b1-ketoglutarate as electron donors. Both complexes transfer electrons to phenazines through the common subunit dihydrolipoamide dehydrogenase, a flavoprotein encoded by the gene lpdG. Although we were unable to co-crystallize LpdG with an endogenous phenazine, we report its X-ray crystal structure in the apo-form (refined to 1.35 \u00c5), bound to NAD+ (1.45 \u00c5), and bound to NADH (1.79 \u00c5). In contrast to the notion that phenazines support intracellular redox homeostasis by oxidizing NADH, our work suggests that phenazines may substitute for NAD+ in LpdG and other enzymes, achieving the same end by a different mechanism.", "doi": "10.1074/jbc.M116.772848", "pmcid": "PMC5392700", "issn": "0021-9258", "publisher": "American Society for Biochemistry and Molecular Biology", "publication": "Journal of Biological Chemistry", "publication_date": "2017-03-31", "series_number": "13", "volume": "292", "issue": "13", "pages": "5593-5607" }, { "id": "authors:v7c80-zqr03", "collection": "authors", "collection_id": "v7c80-zqr03", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170306-140446676", "type": "article", "title": "Polyphosphate granule biogenesis is temporally and functionally tied to cell cycle exit during starvation in Pseudomonas aeruginosa", "author": [ { "family_name": "Racki", "given_name": "Lisa R.", "clpid": "Racki-Lisa-R" }, { "family_name": "Tocheva", "given_name": "Elitza I.", "orcid": "0000-0002-4869-8319", "clpid": "Tocheva-Elitza-I" }, { "family_name": "Dieterle", "given_name": "Michael G.", "clpid": "Dieterle-Michael-G" }, { "family_name": "Sullivan", "given_name": "Meaghan C.", "clpid": "Sullivan-Meaghan-C" }, { "family_name": "Jensen", "given_name": "Grant J.", "orcid": "0000-0003-1556-4864", "clpid": "Jensen-G-J" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "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.", "doi": "10.1073/pnas.1615575114", "pmcid": "PMC5373386", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2017-03-21", "series_number": "12", "volume": "114", "issue": "12", "pages": "E2440-E2449" }, { "id": "authors:zm1t8-asw51", "collection": "authors", "collection_id": "zm1t8-asw51", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161208-131717229", "type": "article", "title": "Pyocyanin degradation by a tautomerizing demethylase inhibits Pseudomonas aeruginosa biofilms", "author": [ { "family_name": "Costa", "given_name": "Kyle C.", "clpid": "Costa-Kyle-C" }, { "family_name": "Glasser", "given_name": "Nathaniel R.", "orcid": "0000-0002-2833-5166", "clpid": "Glasser-Nathaniel-R" }, { "family_name": "Conway", "given_name": "Stuart J.", "clpid": "Conway-Stuart-J" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "The opportunistic pathogen Pseudomonas aeruginosa produces colorful redox-active metabolites called phenazines, which underpin biofilm development, virulence, and clinical outcomes. Although phenazines exist in many forms, the best studied is pyocyanin. Here, we describe pyocyanin demethylase (PodA), a hitherto uncharacterized protein that oxidizes the pyocyanin methyl group to formaldehyde and reduces the pyrazine ring via an unusual tautomerizing demethylation reaction. Treatment with PodA disrupts P. aeruginosa biofilm formation similarly to DNase, suggesting interference with the pyocyanin-dependent release of extracellular DNA into the matrix. PodA-dependent pyocyanin demethylation also restricts established biofilm aggregate populations experiencing anoxic conditions. Together, these results show that modulating extracellular redox-active metabolites can influence the fitness of a biofilm-forming microorganism.", "doi": "10.1126/science.aag3180", "pmcid": "PMC5303695", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2017-01-13", "series_number": "6321", "volume": "355", "issue": "6321", "pages": "170-173" }, { "id": "authors:phx5h-dq970", "collection": "authors", "collection_id": "phx5h-dq970", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160822-074307063", "type": "article", "title": "Hopanoids play a role in stress tolerance and nutrient storage in the cyanobacterium Nostoc punctiforme", "author": [ { "family_name": "Ricci", "given_name": "J. N.", "clpid": "Ricci-J-N" }, { "family_name": "Morton", "given_name": "R.", "clpid": "Morton-R" }, { "family_name": "Kulkarni", "given_name": "G.", "clpid": "Kulkarni-G" }, { "family_name": "Summers", "given_name": "M. L.", "clpid": "Summers-M-L" }, { "family_name": "Newman", "given_name": "D. K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Hopanes are abundant in ancient sedimentary rocks at discrete intervals in Earth history, yet interpreting their significance in the geologic record is complicated by our incomplete knowledge of what their progenitors, hopanoids, do in modern cells. To date, few studies have addressed the breadth of diversity of physiological functions of these lipids and whether those functions are conserved across the hopanoid-producing bacterial phyla. Here, we generated mutants in the filamentous cyanobacterium, Nostoc punctiforme, that are unable to make all hopanoids (shc) or 2-methylhopanoids (hpnP). While the absence of hopanoids impedes growth of vegetative cells at high temperature, the shc mutant grows faster at low temperature. This finding is consistent with hopanoids acting as membrane rigidifiers, a function shared by other hopanoid-producing phyla. Apart from impacting fitness under temperature stress, hopanoids are dispensable for vegetative cells under other stress conditions. However, hopanoids are required for stress tolerance in akinetes, a resting survival cell type. While 2-methylated hopanoids do not appear to contribute to any stress phenotype, total hopanoids and to a lesser extent 2-methylhopanoids were found to promote the formation of cyanophycin granules in akinetes. Finally, although hopanoids support symbiotic interactions between Alphaproteobacteria and plants, they do not appear to facilitate symbiosis between N. punctiforme and the hornwort Anthoceros punctatus. Collectively, these findings support interpreting hopanes as general environmental stress biomarkers. If hopanoid-mediated enhancement of nitrogen-rich storage products turns out to be a conserved phenomenon in other organisms, a better understanding of this relationship may help us parse the enrichment of 2-methylhopanes in the rock record during episodes of disrupted nutrient cycling.", "doi": "10.1111/gbi.12204", "issn": "1472-4677", "publisher": "Blackwell Publishing", "publication": "Geobiology", "publication_date": "2017-01", "series_number": "1", "volume": "15", "issue": "1", "pages": "173-183" }, { "id": "authors:8vcpd-ea950", "collection": "authors", "collection_id": "8vcpd-ea950", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170310-155640184", "type": "article", "title": "Primary functions for \"secondary\" metabolites in microbial communities", "author": [ { "family_name": "Newman", "given_name": "D. K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "[no abstract]", "doi": "10.1091/mbc.E16-10-0736", "issn": "1059-1524", "publisher": "American Society for Cell Biology", "publication": "Molecular Biology of the Cell", "publication_date": "2016-12", "series_number": "25", "volume": "27", "issue": "25", "pages": "S13" }, { "id": "authors:z27p8-phb40", "collection": "authors", "collection_id": "z27p8-phb40", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161011-070233463", "type": "article", "title": "Mapping a multiplexed zoo of mRNA expression", "author": [ { "family_name": "Choi", "given_name": "Harry M. T.", "orcid": "0000-0002-1530-0773", "clpid": "Choi-Harry-M-T" }, { "family_name": "Calvert", "given_name": "Colby R.", "clpid": "Calvert-Colby-R" }, { "family_name": "Husain", "given_name": "Naeem", "orcid": "0000-0003-4962-7237", "clpid": "Husain-Naeem" }, { "family_name": "Barsi", "given_name": "Julius C.", "orcid": "0000-0002-5161-6708", "clpid": "Barsi-Julius-C" }, { "family_name": "Deverman", "given_name": "Benjamin E.", "orcid": "0000-0002-6223-9303", "clpid": "Deverman-Benjamin-E" }, { "family_name": "Hunter", "given_name": "Ryan C.", "orcid": "0000-0003-3841-1676", "clpid": "Hunter-Ryan-C" }, { "family_name": "Kato", "given_name": "Mihoko", "orcid": "0000-0003-3827-8879", "clpid": "Kato-Mihoko" }, { "family_name": "Lee", "given_name": "S. Melanie", "clpid": "Lee-S-Melanie" }, { "family_name": "Abelin", "given_name": "Anna C. T.", "clpid": "Abelin-Anna-C-T" }, { "family_name": "Rosenthal", "given_name": "Adam Z.", "orcid": "0000-0002-6936-3665", "clpid": "Rosenthal-Adam-Z" }, { "family_name": "Akbari", "given_name": "Omar S.", "orcid": "0000-0002-6853-9884", "clpid": "Akbari-Omar-S" }, { "family_name": "Li", "given_name": "Yuwei", "orcid": "0000-0001-7753-4869", "clpid": "Li-Yuwei" }, { "family_name": "Hay", "given_name": "Bruce A.", "orcid": "0000-0002-5486-0482", "clpid": "Hay-B-A" }, { "family_name": "Sternberg", "given_name": "Paul W.", "orcid": "0000-0002-7699-0173", "clpid": "Sternberg-P-W" }, { "family_name": "Patterson", "given_name": "Paul H.", "clpid": "Patterson-P-H" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Mazmanian", "given_name": "Sarkis K.", "orcid": "0000-0003-2713-1513", "clpid": "Mazmanian-S-K" }, { "family_name": "Prober", "given_name": "David A.", "orcid": "0000-0002-7371-4675", "clpid": "Prober-D-A" }, { "family_name": "Leadbetter", "given_name": "Jared R.", "orcid": "0000-0002-7033-0844", "clpid": "Leadbetter-J-R" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Readhead", "given_name": "Carol", "clpid": "Readhead-Carol" }, { "family_name": "Bronner", "given_name": "Marianne E.", "orcid": "0000-0003-4274-1862", "clpid": "Bronner-M-E" }, { "family_name": "Wold", "given_name": "Barbara", "orcid": "0000-0003-3235-8130", "clpid": "Wold-B-J" }, { "family_name": "Fraser", "given_name": "Scott E.", "orcid": "0000-0002-5377-0223", "clpid": "Fraser-S-E" }, { "family_name": "Pierce", "given_name": "Niles A.", "orcid": "0000-0003-2367-4406", "clpid": "Pierce-N-A" } ], "abstract": "In situ hybridization methods are used across the biological sciences to map mRNA expression within intact specimens. Multiplexed experiments, in which multiple target mRNAs are mapped in a single sample, are essential for studying regulatory interactions, but remain cumbersome in most model organisms. Programmable in situ amplifiers based on the mechanism of hybridization chain reaction (HCR) overcome this longstanding challenge by operating independently within a sample, enabling multiplexed experiments to be performed with an experimental timeline independent of the number of target mRNAs. To assist biologists working across a broad spectrum of organisms, we demonstrate multiplexed in situ HCR in diverse imaging settings: bacteria, whole-mount nematode larvae, whole-mount fruit fly embryos, whole-mount sea urchin embryos, whole-mount zebrafish larvae, whole-mount chicken embryos, whole-mount mouse embryos and formalin-fixed paraffin-embedded human tissue sections. In addition to straightforward multiplexing, in situ HCR enables deep sample penetration, high contrast and subcellular resolution, providing an incisive tool for the study of interlaced and overlapping expression patterns, with implications for research communities across the biological sciences.", "doi": "10.1242/dev.140137", "pmcid": "PMC5087610", "issn": "0950-1991", "publisher": "Company of Biologists", "publication": "Development", "publication_date": "2016-10-01", "series_number": "19", "volume": "143", "issue": "19", "pages": "3632-3637" }, { "id": "authors:295ch-51360", "collection": "authors", "collection_id": "295ch-51360", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161111-085149507", "type": "article", "title": "Pathogen Growth Rates in CF Sputum are Slow and Heterogeneous: Implications for Research and Treatment Strategies", "author": [ { "family_name": "Newman", "given_name": "Dianne", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Conventionally, microorganisms are grown in the\nlaboratory under conditions where doubling times are\nless than an hour. While it is well appreciated that\nmicrobes experience nutrient limitation in nature, we\nknow very little about how quickly they are growing or\nwhat limits them in any particular environment. This is\nparticularly true in chronic infections, yet our ignorance\nof these environments (and the ensuing physiological\nresponse of pathogens) is one of the main reasons current\nantibiotic treatments are not fully effective. In collaboration with clinicians at Children's Hospital Los Angeles and geochemists and bioengineers at Caltech, we have\nbeen developing and applying new methods to better\ncharacterize the chemical and biological states that occur\nin CF sputum. Such information is necessary to design\nrelevant laboratory experiments to elucidate pathogen\nsurvival strategies in vivo. I will discuss the implications\nour findings for treating CF infections.", "doi": "10.1002/ppul.23575", "issn": "8755-6863", "publisher": "Wiley", "publication": "Pediatric Pulmonology", "publication_date": "2016-10", "series_number": "S45", "volume": "51", "issue": "S45", "pages": "162" }, { "id": "authors:e2n6h-2v807", "collection": "authors", "collection_id": "e2n6h-2v807", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160927-144217261", "type": "article", "title": "Exposing the Three-Dimensional Biogeography and Metabolic States of Pathogens in Cystic Fibrosis Sputum via Hydrogel Embedding, Clearing, and rRNA Labeling", "author": [ { "family_name": "DePas", "given_name": "William H.", "clpid": "DePas-W-H" }, { "family_name": "Starwalt-Lee", "given_name": "Ruth", "clpid": "Starwalt-Lee-R" }, { "family_name": "Van Sambeek", "given_name": "Lindsey", "orcid": "0000-0002-7206-7410", "clpid": "Van-Sambeek-L" }, { "family_name": "Ravindra Kumar", "given_name": "Sripriya", "orcid": "0000-0001-6033-7631", "clpid": "Ravindra-Kumar-S" }, { "family_name": "Gradinaru", "given_name": "Viviana", "orcid": "0000-0001-5868-348X", "clpid": "Gradinaru-V" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Physiological resistance to antibiotics confounds the treatment of many chronic bacterial infections, motivating researchers to identify novel therapeutic approaches. To do this effectively, an understanding of how microbes survive in vivo is needed. Though much can be inferred from bulk approaches to characterizing complex environments, essential information can be lost if spatial organization is not preserved. Here, we introduce a tissue-clearing technique, termed MiPACT, designed to retain and visualize bacteria with associated proteins and nucleic acids in situ on various spatial scales. By coupling MiPACT with hybridization chain reaction (HCR) to detect rRNA in sputum samples from cystic fibrosis (CF) patients, we demonstrate its ability to survey thousands of bacteria (or bacterial aggregates) over millimeter scales and quantify aggregation of individual species in polymicrobial communities. By analyzing aggregation patterns of four prominent CF pathogens, Staphylococcus aureus, Pseudomonas aeruginosa, Streptococcus sp., and Achromobacter xylosoxidans, we demonstrate a spectrum of aggregation states: from mostly single cells (A. xylosoxidans), to medium-sized clusters (S. aureus), to a mixture of single cells and large aggregates (P. aeruginosa and Streptococcus sp.). Furthermore, MiPACT-HCR revealed an intimate interaction between Streptococcus sp. and specific host cells. Lastly, by comparing standard rRNA fluorescence in situ hybridization signals to those from HCR, we found that different populations of S. aureus and A. xylosoxidans grow slowly overall yet exhibit growth rate heterogeneity over hundreds of microns. These results demonstrate the utility of MiPACT-HCR to directly capture the spatial organization and metabolic activity of bacteria in complex systems, such as human sputum.", "doi": "10.1128/mBio.00796-16", "pmcid": "PMC5040109", "issn": "2150-7511", "publisher": "American Society for Microbiology", "publication": "mBio", "publication_date": "2016-09-27", "series_number": "5", "volume": "7", "issue": "5", "pages": "e00796-16" }, { "id": "authors:p9jhj-7sj29", "collection": "authors", "collection_id": "p9jhj-7sj29", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160823-074209373", "type": "article", "title": "Stepwise metamorphosis of the tubeworm Hydroides elegans is mediated by a bacterial inducer and MAPK signaling", "author": [ { "family_name": "Shikuma", "given_name": "Nicholas J.", "orcid": "0000-0001-5518-5020", "clpid": "Shikuma-Nicholas-J" }, { "family_name": "Antoshechkin", "given_name": "Igor", "orcid": "0000-0002-9934-3040", "clpid": "Antoshechkin-Igor-A" }, { "family_name": "Medeiros", "given_name": "Jo\u00e3o M.", "orcid": "0000-0001-9075-548X", "clpid": "Medeiros-Jo\u00e3o-M" }, { "family_name": "Pilhofer", "given_name": "Martin", "clpid": "Pilhofer-Martin" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Diverse animal taxa metamorphose between larval and juvenile phases in response to bacteria. Although bacteria-induced metamorphosis is widespread among metazoans, little is known about the molecular changes that occur in the animal upon stimulation by bacteria. Larvae of the tubeworm Hydroides elegans metamorphose in response to surface-bound Pseudoalteromonas luteoviolacea bacteria, producing ordered arrays of phage tail-like metamorphosis-associated contractile structures (MACs). Sequencing the Hydroides genome and transcripts during five developmental stages revealed that MACs induce the regulation of groups of genes important for tissue remodeling, innate immunity, and mitogen-activated protein kinase (MAPK) signaling. Using two MAC mutations that block P. luteoviolacea from inducing settlement or metamorphosis and three MAPK inhibitors, we established a sequence of bacteria-induced metamorphic events: MACs induce larval settlement; then, particular properties of MACs encoded by a specific locus in P. luteoviolacea initiate cilia loss and activate metamorphosis-associated transcription; finally, signaling through p38 and c-Jun N-terminal kinase (JNK) MAPK pathways alters gene expression and leads to morphological changes upon initiation of metamorphosis. Our results reveal that the intricate interaction between Hydroides and P. luteoviolacea can be dissected using genomic, genetic, and pharmacological tools. Hydroides' dependency on bacteria for metamorphosis highlights the importance of external stimuli to orchestrate animal development. The conservation of Hydroides genome content with distantly related deuterostomes (urchins, sea squirts, and humans) suggests that mechanisms of bacteria-induced metamorphosis in Hydroides may have conserved features in diverse animals. As a major biofouling agent, insight into the triggers of Hydroides metamorphosis might lead to practical strategies for fouling control.", "doi": "10.1073/pnas.1603142113", "pmcid": "PMC5018781", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2016-09-06", "series_number": "36", "volume": "113", "issue": "36", "pages": "10097-10102" }, { "id": "authors:s8zwh-djv17", "collection": "authors", "collection_id": "s8zwh-djv17", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160812-091235598", "type": "article", "title": "The physiology of growth arrest: uniting molecular and environmental microbiology", "author": [ { "family_name": "Bergkessel", "given_name": "Megan", "orcid": "0000-0002-4530-1224", "clpid": "Bergkessel-M" }, { "family_name": "Basta", "given_name": "David W.", "orcid": "0000-0003-4176-6566", "clpid": "Basta-David-Wagdi" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Most bacteria spend the majority of their time in prolonged states of very low metabolic activity and little or no growth, in which electron donors, electron acceptors and/or nutrients are limited, but cells are poised to undergo rapid division cycles when resources become available. These non-growing states are far less studied than other growth states, which leaves many questions regarding basic bacterial physiology unanswered. In this Review, we discuss findings from a small but diverse set of systems that have been used to investigate how growth-arrested bacteria adjust metabolism, regulate transcription and translation, and maintain their chromosomes. We highlight major questions that remain to be addressed, and suggest that progress in answering them will be aided by recent methodological advances and by dialectic between environmental and molecular microbiology perspectives.", "doi": "10.1038/nrmicro.2016.107", "pmcid": "PMC10069271", "issn": "1740-1526", "publisher": "Nature Publishing Group", "publication": "Nature Reviews Microbiology", "publication_date": "2016-09", "series_number": "9", "volume": "14", "issue": "9", "pages": "549-562" }, { "id": "authors:c0ef1-7w226", "collection": "authors", "collection_id": "c0ef1-7w226", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160531-084725317", "type": "article", "title": "Cellular and Molecular Biological Approaches to Interpreting Ancient Biomarkers", "author": [ { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Neubauer", "given_name": "Cajetan", "orcid": "0000-0002-5348-5609", "clpid": "Neubauer-C" }, { "family_name": "Ricci", "given_name": "Jessica N.", "clpid": "Ricci-J-N" }, { "family_name": "Wu", "given_name": "Chia-Hung", "clpid": "Wu-Chia-Hung" }, { "family_name": "Pearson", "given_name": "Ann", "orcid": "0000-0003-2785-8405", "clpid": "Pearson-A" } ], "abstract": "Our ability to read the molecular fossil record has advanced significantly in the past decade. Improvements in biomarker sampling and quantification methods, expansion of molecular sequence databases, and the application of genetic and cellular biological tools to problems in biomarker research have enabled much of this progress. By way of example, we review how attempts to understand the biological function of 2-methylhopanoids in modern bacteria have changed our interpretation of what their molecular fossils tell us about the early history of life. They were once thought to be biomarkers of cyanobacteria and hence the evolution of oxygenic photosynthesis, but we now believe that 2-methylhopanoid biosynthetic capacity originated in the Alphaproteobacteria, that 2-methylhopanoids are regulated in response to stress, and that hopanoid 2-methylation enhances membrane rigidity. We present a new interpretation of 2-methylhopanes that bridges the gap between studies of the functions of 2-methylhopanoids and their patterns of occurrence in the rock record.", "doi": "10.1146/annurev-earth-050212-123958", "issn": "0084-6597", "publisher": "Annual Reviews", "publication": "Annual Review of Earth and Planetary Sciences", "publication_date": "2016-06", "volume": "44", "pages": "493-522" }, { "id": "authors:gs2e9-bhm64", "collection": "authors", "collection_id": "gs2e9-bhm64", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160120-081453238", "type": "article", "title": "SutA is a bacterial transcription factor expressed during slow growth in Pseudomonas aeruginosa", "author": [ { "family_name": "Babin", "given_name": "Brett M.", "orcid": "0000-0002-4133-6665", "clpid": "Babin-Brett-M" }, { "family_name": "Bergkessel", "given_name": "Megan", "orcid": "0000-0002-4530-1224", "clpid": "Bergkessel-Megan" }, { "family_name": "Sweredoski", "given_name": "Michael J.", "orcid": "0000-0003-0878-3831", "clpid": "Sweredoski-Michael-J" }, { "family_name": "Moradian", "given_name": "Annie", "orcid": "0000-0002-0407-2031", "clpid": "Moradian-Annie" }, { "family_name": "Hess", "given_name": "Sonja", "orcid": "0000-0002-5904-9816", "clpid": "Hess-Sonja" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" } ], "abstract": "Microbial quiescence and slow growth are ubiquitous physiological states, but their study is complicated by low levels of metabolic activity. To address this issue, we used a time-selective proteome-labeling method [bioorthogonal noncanonical amino acid tagging (BONCAT)] to identify proteins synthesized preferentially, but at extremely low rates, under anaerobic survival conditions by the opportunistic pathogen Pseudomonas aeruginosa. One of these proteins is a transcriptional regulator that has no homology to any characterized protein domains and is posttranscriptionally up-regulated during survival and slow growth. This small, acidic protein associates with RNA polymerase, and chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing suggests that the protein associates with genomic DNA through this interaction. ChIP signal is found both in promoter regions and throughout the coding sequences of many genes and is particularly enriched at ribosomal protein genes and in the promoter regions of rRNA genes. Deletion of the gene encoding this protein affects expression of these and many other genes and impacts biofilm formation, secondary metabolite production, and fitness in fluctuating conditions. On the basis of these observations, we have designated the protein SutA (survival under transitions A).", "doi": "10.1073/pnas.1514412113", "pmcid": "PMC4747698", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2016-02-02", "series_number": "5", "volume": "113", "issue": "5", "pages": "E597-E605" }, { "id": "authors:f77p5-wfy55", "collection": "authors", "collection_id": "f77p5-wfy55", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160104-065151473", "type": "article", "title": "Trace incorporation of heavy water reveals slow and heterogeneous pathogen growth rates in cystic fibrosis sputum", "author": [ { "family_name": "Kopf", "given_name": "Sebastian H.", "orcid": "0000-0002-2044-0201", "clpid": "Kopf-Sebastian-H" }, { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Cowley", "given_name": "Elise S.", "clpid": "Cowley-Elise-S" }, { "family_name": "Reyes", "given_name": "Carmen", "clpid": "Reyes-Carmen" }, { "family_name": "Van Sambeek", "given_name": "Lindsey", "orcid": "0000-0002-7206-7410", "clpid": "Van-Sambeek-Lindsey" }, { "family_name": "Hu", "given_name": "Yang", "clpid": "Hu-Yang" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Kato", "given_name": "Roberta M.", "clpid": "Kato-Roberta-M" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Effective treatment for chronic infections is undermined by a significant gap in understanding of the physiological state of pathogens at the site of infection. Chronic pulmonary infections are responsible for the morbidity and mortality of millions of immunocompromised individuals worldwide, yet drugs that are successful in laboratory culture are far less effective against pathogen populations persisting in vivo. Laboratory models, upon which preclinical development of new drugs is based, can only replicate host conditions when we understand the metabolic state of the pathogens and the degree of heterogeneity within the population. In this study, we measured the anabolic activity of the pathogen Staphylococcus aureus directly in the sputum of pediatric patients with cystic fibrosis (CF), by combining the high sensitivity of isotope ratio mass spectrometry with a heavy water labeling approach to capture the full range of in situ growth rates. Our results reveal S. aureus generation times with a median of 2.1 d, with extensive growth rate heterogeneity at the single-cell level. These growth rates are far below the detection limit of previous estimates of CF pathogen growth rates, and the rates are slowest in acutely sick patients undergoing pulmonary exacerbations; nevertheless, they are accessible to experimental replication within laboratory models. Treatment regimens that include specific antibiotics (vancomycin, piperacillin/tazobactam, tobramycin) further appear to correlate with slow growth of S. aureus on average, but follow-up longitudinal studies must be performed to determine whether this effect holds for individual patients.", "doi": "10.1073/pnas.1512057112", "pmcid": "PMC4720290", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2016-01-12", "series_number": "2", "volume": "113", "issue": "2", "pages": "E110-E116" }, { "id": "authors:e6etk-g5t77", "collection": "authors", "collection_id": "e6etk-g5t77", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160106-065143620", "type": "article", "title": "Predicting the impact of promoter variability on regulatory outputs", "author": [ { "family_name": "Kreamer", "given_name": "Naomi N.", "clpid": "Kreamer-Naomi-N-K" }, { "family_name": "Phillips", "given_name": "Rob", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Boedicker", "given_name": "James Q.", "orcid": "0000-0003-4107-3719", "clpid": "Boedicker-J-Q" } ], "abstract": "The increased availability of whole genome sequences calls for quantitative models of global gene expression, yet predicting gene expression patterns directly from genome sequence remains a challenge. We examine the contributions of an individual regulator, the ferrous iron-responsive regulatory element, BqsR, on global patterns of gene expression in Pseudomonas aeruginosa. The position weight matrix (PWM) derived for BqsR uncovered hundreds of likely binding sites throughout the genome. Only a subset of these potential binding sites had a regulatory consequence, suggesting that BqsR/DNA interactions were not captured within the PWM or that the broader regulatory context at each promoter played a greater role in setting promoter outputs. The architecture of the BqsR operator was systematically varied to understand how binding site parameters influence expression. We found that BqsR operator affinity was predicted by the PWM well. At many promoters the surrounding regulatory context, including overlapping operators of BqsR or the presence of RhlR binding sites, were influential in setting promoter outputs. These results indicate more comprehensive models that include local regulatory contexts are needed to develop a predictive understanding of global regulatory outputs.", "doi": "10.1038/srep18238", "pmcid": "PMC4682146", "issn": "2045-2322", "publisher": "Nature Publishing Group", "publication": "Scientific Reports", "publication_date": "2015-12-17", "volume": "5", "pages": "Art. No. 18238" }, { "id": "authors:faef9-m7t84", "collection": "authors", "collection_id": "faef9-m7t84", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151102-105401926", "type": "article", "title": "Enzymatic Degradation of Phenazines Can Generate Energy and Protect Sensitive Organisms from Toxicity", "author": [ { "family_name": "Costa", "given_name": "Kyle C.", "clpid": "Costa-K-C" }, { "family_name": "Bergkessel", "given_name": "Megan", "orcid": "0000-0002-4530-1224", "clpid": "Bergkessel-M" }, { "family_name": "Saunders", "given_name": "Scott", "clpid": "Saunders-S-H" }, { "family_name": "Korlach", "given_name": "Jonas", "clpid": "Korlach-J" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Diverse bacteria, including several Pseudomonas species, produce a class of redox-active metabolites called phenazines that impact different cell types in nature and disease. Phenazines can affect microbial communities in both positive and negative ways, where their presence is correlated with decreased species richness and diversity. However, little is known about how the concentration of phenazines is modulated in situ and what this may mean for the fitness of members of the community. Through culturing of phenazine-degrading mycobacteria, genome sequencing, comparative genomics, and molecular analysis, we identified several conserved genes that are important for the degradation of three Pseudomonas-derived phenazines: phenazine-1-carboxylic acid (PCA), phenazine-1-carboxamide (PCN), and pyocyanin (PYO). PCA can be used as the sole carbon source for growth by these organisms. Deletion of several genes in Mycobacterium fortuitum abolishes the degradation phenotype, and expression of two genes in a heterologous host confers the ability to degrade PCN and PYO. In cocultures with phenazine producers, phenazine degraders alter the abundance of different phenazine types. Not only does degradation support mycobacterial catabolism, but also it provides protection to bacteria that would otherwise be inhibited by the toxicity of PYO. Collectively, these results serve as a reminder that microbial metabolites can be actively modified and degraded and that these turnover processes must be considered when the fate and impact of such compounds in any environment are being assessed.", "doi": "10.1128/mBio.01520-15", "pmcid": "PMC4626857", "issn": "2150-7511", "publisher": "American Society for Microbiology", "publication": "mBio", "publication_date": "2015-11", "series_number": "6", "volume": "6", "issue": "6", "pages": "Art. No. e01520-15" }, { "id": "authors:y31w0-ax642", "collection": "authors", "collection_id": "y31w0-ax642", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160111-090546456", "type": "article", "title": "Complete Genome Sequence of Curtobacterium sp. Strain MR_MD2014, Isolated from Topsoil in Woods Hole, Massachusetts", "author": [ { "family_name": "Mariita", "given_name": "Richard M.", "orcid": "0000-0003-4430-464X", "clpid": "Mariita-Richard-M" }, { "family_name": "Bhatnagar", "given_name": "Srijak", "orcid": "0000-0003-0240-2655", "clpid": "Bhatnagar-Srijak" }, { "family_name": "Hanselmann", "given_name": "Kurt", "clpid": "Hanselmann-K" }, { "family_name": "Hossain", "given_name": "Mohammad J.", "orcid": "0000-0003-3848-9035", "clpid": "Hossain-Mohammad-J" }, { "family_name": "Korlach", "given_name": "Jonas", "clpid": "Korlach-Jonas" }, { "family_name": "Boitano", "given_name": "Matthew", "clpid": "Boitano-Matthew" }, { "family_name": "Roberts", "given_name": "Richard J.", "orcid": "0000-0002-4348-0169", "clpid": "Roberts-Richard-J" }, { "family_name": "Liles", "given_name": "Mark R.", "orcid": "0000-0002-9313-8150", "clpid": "Liles-Mark-R" }, { "family_name": "Moss", "given_name": "Anthony G.", "orcid": "0000-0001-7303-4285", "clpid": "Moss-Anthony-G" }, { "family_name": "Leadbetter", "given_name": "Jared R.", "orcid": "0000-0002-7033-0844", "clpid": "Leadbetter-J-R" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Dawson", "given_name": "Scott C.", "orcid": "0000-0002-0843-1759", "clpid": "Dawson-Scott-C" } ], "abstract": "Here, we present the 3,443,800-bp complete genome sequence of Curtobacterium sp. strain MR_MD2014 (phylum Actinobacteria). This strain was isolated from soil in Woods Hole, MA, as part of the 2014 Microbial Diversity Summer Program at the Marine Biological Laboratory in Woods Hole, MA.", "doi": "10.1128/genomeA.01504-15", "pmcid": "PMC4698388", "issn": "2169-8287", "publisher": "American Society for Microbiology", "publication": "Genome Announcements", "publication_date": "2015-11", "series_number": "6", "volume": "3", "issue": "6", "pages": "Art. No. e01504-15" }, { "id": "authors:k35x0-3ch90", "collection": "authors", "collection_id": "k35x0-3ch90", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160111-095010392", "type": "article", "title": "Complete Genome Sequence of Streptomyces sp. Strain CCM_MD2014, Isolated from Topsoil in Woods Hole, Massachusetts", "author": [ { "family_name": "Mariita", "given_name": "Richard M.", "orcid": "0000-0003-4430-464X", "clpid": "Mariita-Richard-M" }, { "family_name": "Bhatnagar", "given_name": "Srijak", "orcid": "0000-0003-0240-2655", "clpid": "Bhatnagar-Srijak" }, { "family_name": "Hanselmann", "given_name": "Kurt", "clpid": "Hanselmann-Kurt" }, { "family_name": "Hossain", "given_name": "Mohammad J.", "orcid": "0000-0003-3848-9035", "clpid": "Hossain-Mohammad-J" }, { "family_name": "Korlach", "given_name": "Jonas", "clpid": "Korlach-Jonas" }, { "family_name": "Boitano", "given_name": "Matthew", "clpid": "Boitano-Matthew" }, { "family_name": "Roberts", "given_name": "Richard J.", "orcid": "0000-0002-4348-0169", "clpid": "Roberts-Richard-J" }, { "family_name": "Liles", "given_name": "Mark R.", "orcid": "0000-0002-9313-8150", "clpid": "Liles-Mark-R" }, { "family_name": "Moss", "given_name": "Anthony G.", "orcid": "0000-0001-7303-4285", "clpid": "Moss-Anthony-G" }, { "family_name": "Leadbetter", "given_name": "Jared R.", "orcid": "0000-0002-7033-0844", "clpid": "Leadbetter-J-R" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Dawson", "given_name": "Scott C.", "orcid": "0000-0002-0843-1759", "clpid": "Dawson-Scott-C" } ], "abstract": "Here, we present the complete genome sequence of Streptomyces sp. strain CCM_MD2014 (phylum Actinobacteria), isolated from surface soil in Woods Hole, MA. Its single linear chromosome of 8,274,043 bp in length has a 72.13% G+C content and contains 6,948 coding sequences.", "doi": "10.1128/genomeA.01506-15", "pmcid": "PMC4698389", "issn": "2169-8287", "publisher": "American Society for Microbiology", "publication": "Genome Announcements", "publication_date": "2015-11", "series_number": "6", "volume": "3", "issue": "6", "pages": "Art. No. e01506-15" }, { "id": "authors:wb2te-9pf13", "collection": "authors", "collection_id": "wb2te-9pf13", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151008-142740942", "type": "article", "title": "Specific hopanoid classes differentially affect free-living and symbiotic states of Bradyrhizobium diazoefficiens", "author": [ { "family_name": "Kulkarni", "given_name": "Gargi", "clpid": "Kulkarni-G" }, { "family_name": "Busset", "given_name": "Nicolas", "clpid": "Busset-N" }, { "family_name": "Molinaro", "given_name": "Antonio", "clpid": "Molinaro-A" }, { "family_name": "Gargani", "given_name": "Daniel", "clpid": "Gargani-D" }, { "family_name": "Chaintreuil", "given_name": "Clemence", "clpid": "Chaintreuil-C" }, { "family_name": "Silipo", "given_name": "Alba", "clpid": "Silipo-A" }, { "family_name": "Giraud", "given_name": "Eric", "clpid": "Giraud-E" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "A better understanding of how bacteria resist stresses encountered during the progression of plant-microbe symbioses will advance our ability to stimulate plant growth. Here, we show that the symbiotic system comprising the nitrogen-fixing bacterium Bradyrhizobium diazoefficiens and the legume Aeschynomene afraspera requires hopanoid production for optimal fitness. While methylated (2Me) hopanoids contribute to growth under plant-cell-like microaerobic and acidic conditions in the free-living state, they are dispensable during symbiosis. In contrast, synthesis of extended (C35) hopanoids is required for growth microaerobically and under various stress conditions (high temperature, low pH, high osmolarity, bile salts, oxidative stress, and antimicrobial peptides) in the free-living state and also during symbiosis. These defects might be due to a less rigid membrane resulting from the absence of free or lipidA-bound C35 hopanoids or the accumulation of the C30 hopanoid diploptene. Our results also show that C35 hopanoids are necessary for symbiosis only with the host Aeschynomene afraspera but not with soybean. This difference is likely related to the presence of cysteine-rich antimicrobial peptides in Aeschynomene nodules that induce drastic modification in bacterial morphology and physiology. The study of hopanoid mutants in plant symbionts thus provides an opportunity to gain insight into host-microbe interactions during later stages of symbiotic progression, as well as the microenvironmental conditions for which hopanoids provide a fitness advantage.", "doi": "10.1128/mBio.01251-15", "pmcid": "PMC4620461", "issn": "2150-7511", "publisher": "American Society for Microbiology", "publication": "mBio", "publication_date": "2015-10-20", "series_number": "5", "volume": "6", "issue": "5", "pages": "e01251-15" }, { "id": "authors:5hcmg-zsr04", "collection": "authors", "collection_id": "5hcmg-zsr04", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170518-163637436", "type": "book_section", "title": "Molecular Methods in Geomicrobiology", "book_title": "Ehrlich's Geomicrobiology, Sixth Edition", "author": [ { "family_name": "Coleman", "given_name": "Maureen L.", "clpid": "Coleman-M-L" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "contributor": [ { "family_name": "Ehrlich", "given_name": "Henry Lutz", "clpid": "Ehrlich-H-L" }, { "family_name": "Newman", "given_name": "Dianne K.", "clpid": "Newman-D-K" }, { "family_name": "Kappler", "given_name": "Andreas", "clpid": "Kappler-A" } ], "abstract": "In addition to the techniques described in Chapter 8, molecular tools have become increasingly important in the study of the presence, activity, and mechanisms of catalysis by geomicrobial organisms. Today, various molecules (deoxyribonucleic acid [DNA], ribonucleic acid [RNA], protein, and lipids) are used to detect specific geomicrobial agents in situ and make inferences about their metabolic activity. DNA sequencing has become routine, expanding our appreciation of the genetic potential of uncultivated organisms and complex natural communities from the environment. Isotope labeling approaches allow us to measure metabolic activity more directly and to specifically link organisms with geochemical fluxes. Finally, the application of molecular genetic, cell biological, and biochemical techniques to study the genes and gene products that catalyze geochemically significant reactions is unraveling the mechanisms underlying these processes. Together, these molecular approaches provide a window into the interactions between microorganisms and their geochemical environment and enable predictions about how these geomicrobial processes may be altered in response to environmental perturbations.", "doi": "10.1201/b19121-10", "isbn": "9781466592407", "publisher": "CRC Press", "place_of_publication": "Boca Raton, FL", "publication_date": "2015-10", "pages": "187-207" }, { "id": "authors:5hr5k-xzg86", "collection": "authors", "collection_id": "5hr5k-xzg86", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150504-103056372", "type": "article", "title": "Lipid remodeling in Rhodopseudomonas palustris TIE-1 upon loss of hopanoids and hopanoid methylation", "author": [ { "family_name": "Neubauer", "given_name": "C.", "orcid": "0000-0002-5348-5609", "clpid": "Neubauer-C" }, { "family_name": "Dalleska", "given_name": "N. F.", "orcid": "0000-0002-2059-1587", "clpid": "Dalleska-N-F" }, { "family_name": "Cowley", "given_name": "E. S.", "clpid": "Cowley-E-S" }, { "family_name": "Shikuma", "given_name": "N. J.", "orcid": "0000-0001-5518-5020", "clpid": "Shikuma-Nicholas-J" }, { "family_name": "Wu", "given_name": "C.-H.", "clpid": "Wu-C-H" }, { "family_name": "Sessions", "given_name": "A. L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Newman", "given_name": "D. K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "The sedimentary record of molecular fossils (biomarkers) can potentially provide important insights into the composition of ancient organisms; however, it only captures a small portion of their original lipid content. To interpret what remains, it is important to consider the potential for functional overlap between different lipids in living cells, and how the presence of one type might impact the abundance of another. Hopanoids are a diverse class of steroid analogs made by bacteria and found in soils, sediments, and sedimentary rocks. Here, we examine the trade-off between hopanoid production and that of other membrane lipids. We compare lipidomes of the metabolically versatile \u03b1-proteobacterium Rhodopseudomonas palustris TIE-1 and two hopanoid mutants, detecting native hopanoids simultaneously with other types of polar lipids by electrospray ionization mass spectrometry. In all strains, the phospholipids contain high levels of unsaturated fatty acids (often >80 %). The degree to which unsaturated fatty acids are modified to cyclopropyl fatty acids varies by phospholipid class. Deletion of the capacity for hopanoid production is accompanied by substantive changes to the lipidome, including a several-fold rise of cardiolipins. Deletion of the ability to make methylated hopanoids has a more subtle effect; however, under photoautotrophic growth conditions, tetrahymanols are upregulated twofold. Together, these results illustrate that the 'lipid fingerprint' produced by a micro-organism can vary depending on the growth condition or loss of single genes, reminding us that the absence of a biomarker does not necessarily imply the absence of a particular source organism.", "doi": "10.1111/gbi.12143", "issn": "1472-4677", "publisher": "Wiley-Blackwell", "publication": "Geobiology", "publication_date": "2015-09", "series_number": "5", "volume": "13", "issue": "5", "pages": "443-453" }, { "id": "authors:j45gj-5th78", "collection": "authors", "collection_id": "j45gj-5th78", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151002-111813971", "type": "article", "title": "Pediatric Cystic Fibrosis Sputum Can Be Chemically Dynamic, Anoxic, and Extremely Reduced Due to Hydrogen Sulfide Formation", "author": [ { "family_name": "Cowley", "given_name": "Elise S.", "clpid": "Cowley-E-S" }, { "family_name": "Kopf", "given_name": "Sebastian H.", "orcid": "0000-0002-2044-0201", "clpid": "Kopf-S-H" }, { "family_name": "LaRiviere", "given_name": "Alejandro", "clpid": "LaRiviere-A" }, { "family_name": "Ziebis", "given_name": "Wiebke", "clpid": "Ziebis-W" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Severe and persistent bacterial lung infections characterize cystic fibrosis (CF). While several studies have documented the microbial diversity within CF lung mucus, we know much less about the inorganic chemistry that constrains microbial metabolic processes and their distribution. We hypothesized that sputum is chemically heterogeneous both within and between patients. To test this, we measured microprofiles of oxygen and sulfide concentrations as well as pH and oxidation-reduction potentials in 48 sputum samples from 22 pediatric patients with CF. Inorganic ions were measured in 20 samples from 12 patients. In all cases, oxygen was depleted within the first few millimeters below the sputum-air interface. Apart from this steep oxycline, anoxia dominated the sputum environment. Different sputum samples exhibited a broad range of redox conditions, with either oxidizing (16 mV to 355 mV) or reducing (\u2212300 to \u2212107 mV) potentials. The majority of reduced samples contained hydrogen sulfide and had a low pH (2.9 to 6.5). Sulfide concentrations increased at a rate of 0.30 \u00b5M H_2S/min. Nitrous oxide was detected in only one sample that also contained sulfide. Microenvironmental variability was observed both within a single patient over time and between patients. Modeling oxygen dynamics within CF mucus plugs indicates that anoxic zones vary as a function of bacterial load and mucus thickness and can occupy a significant portion of the mucus volume. Thus, aerobic respiration accounts only partially for pathogen survival in CF sputum, motivating research to identify mechanisms of survival under conditions that span fluctuating redox states, including sulfidic environments.", "doi": "10.1128/mBio.00767-15", "pmcid": "PMC4551978", "issn": "2150-7511", "publisher": "American Society for Microbiology", "publication": "mBio", "publication_date": "2015-07-28", "series_number": "4", "volume": "6", "issue": "4", "pages": "Art. No. e00767" }, { "id": "authors:hbf0r-9tt28", "collection": "authors", "collection_id": "hbf0r-9tt28", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150421-104932645", "type": "article", "title": "Quantitative hopanoid analysis enables robust pattern detection and comparison between laboratories", "author": [ { "family_name": "Wu", "given_name": "C.-H.", "clpid": "Wu-Chia-Hung" }, { "family_name": "Kong", "given_name": "L.", "clpid": "Kong-L" }, { "family_name": "Bialecka-Fornal", "given_name": "M.", "clpid": "Bialecka-Fornal-M" }, { "family_name": "Park", "given_name": "S.", "clpid": "Park-S" }, { "family_name": "Thompson", "given_name": "A. L.", "clpid": "Thompson-A-L" }, { "family_name": "Kulkarni", "given_name": "G.", "clpid": "Kulkarni-G" }, { "family_name": "Conway", "given_name": "S. J.", "clpid": "Conway-S-J" }, { "family_name": "Newman", "given_name": "D. K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Hopanoids are steroid-like lipids from the isoprenoid family that are produced primarily by bacteria. Hopanes, molecular fossils of hopanoids, offer the potential to provide insight into environmental transitions on the early Earth, if their sources and biological functions can be constrained. Semiquantitative methods for mass spectrometric analysis of hopanoids from cultures and environmental samples have been developed in the last two decades. However, the structural diversity of hopanoids, and possible variability in their ionization efficiencies on different instruments, have thus far precluded robust quantification and hindered comparison of results between laboratories. These ionization inconsistencies give rise to the need to calibrate individual instruments with purified hopanoids to reliably quantify hopanoids. Here, we present new approaches to obtain both purified and synthetic quantification standards. We optimized 2-methylhopanoid production in Rhodopseudomonas palustris TIE-1 and purified 2Me-diplopterol, 2Me-bacteriohopanetetrol (2Me-BHT), and their unmethylated species (diplopterol and BHT). We found that 2-methylation decreases the signal intensity of diplopterol between 2 and 34% depending on the instrument used to detect it, but decreases the BHT signal less than 5%. In addition, 2Me-diplopterol produces 10\u00d7 higher ion counts than equivalent quantities of 2Me-BHT. Similar deviations were also observed using a flame ionization detector for signal quantification in GC. In LC-MS, however, 2Me-BHT produces 11\u00d7 higher ion counts than 2Me-diplopterol but only 1.2\u00d7 higher ion counts than the sterol standard pregnane acetate. To further improve quantification, we synthesized tetradeuterated (D_4) diplopterol, a precursor for a variety of hopanoids. LC-MS analysis on a mixture of (D4)-diplopterol and phospholipids showed that under the influence of co-eluted phospholipids, the D_4-diplopterol internal standard quantifies diplopterol more accurately than external diplopterol standards. These new quantitative approaches permit meaningful comparisons between studies, allowing more accurate hopanoid pattern detection in both laboratory and environmental samples.", "doi": "10.1111/gbi.12132", "pmcid": "PMC4676935", "issn": "1472-4677", "publisher": "Wiley", "publication": "Geobiology", "publication_date": "2015-07", "series_number": "4", "volume": "13", "issue": "4", "pages": "391-407" }, { "id": "authors:7v4s2-d5h36", "collection": "authors", "collection_id": "7v4s2-d5h36", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150220-131055817", "type": "article", "title": "Heavy water and \u00b9\u2075N labeling with NanoSIMS analysis reveals growth-rate dependent metabolic heterogeneity in chemostats", "author": [ { "family_name": "Kopf", "given_name": "Sebastian H.", "orcid": "0000-0002-2044-0201", "clpid": "Kopf-S-H" }, { "family_name": "McGlynn", "given_name": "Shawn E.", "orcid": "0000-0002-8199-7011", "clpid": "McGlynn-S-E" }, { "family_name": "Green-Saxena", "given_name": "Abigail", "orcid": "0000-0002-8502-6589", "clpid": "Saxena-A-G" }, { "family_name": "Guan", "given_name": "Yunbin", "orcid": "0000-0002-7636-3735", "clpid": "Guan-Yunbin" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "To measure single cell microbial activity and substrate utilization patterns in environmental systems, we employ a new technique using stable isotope labeling of microbial populations with heavy water (a passive tracer) and \u00b9\u2075N ammonium in combination with multi-isotope imaging mass spectrometry. We demonstrate simultaneous NanoSIMS analysis of hydrogen, carbon and nitrogen at high spatial and mass resolution, and report calibration data linking single cell isotopic compositions to the corresponding bulk isotopic equivalents for Pseudomonas aeruginosa and Staphylococcus aureus. Our results show that heavy water is capable of quantifying in situ single cell microbial activities ranging from generational time scales of minutes to years, with only light isotopic incorporation (~0.1 atom % \u00b2H). Applying this approach to study the rates of fatty acid biosynthesis by single cells of S. aureus growing at different rates in chemostat culture (~6 hours, 1 day and 2 week generation times), we observe the greatest anabolic activity diversity in the slowest growing populations. By using heavy water to constrain cellular growth activity, we can further infer the relative contributions of ammonium vs. amino acid assimilation to the cellular nitrogen pool. The approach described here can be applied to disentangle individual cell activities even in nutritionally complex environments.", "doi": "10.1111/1462-2920.12752", "pmcid": "PMC4587896", "issn": "1462-2912", "publisher": "Wiley", "publication": "Environmental Microbiology", "publication_date": "2015-07", "series_number": "7", "volume": "17", "issue": "7", "pages": "2542-2556" }, { "id": "authors:b0wb6-1w815", "collection": "authors", "collection_id": "b0wb6-1w815", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160701-094042706", "type": "article", "title": "Sputum Iron Levels During Cystic Fibrosis Pulmonary Exacerbation: A Longitudinal Study", "author": [ { "family_name": "McCallin", "given_name": "Kyle", "clpid": "McCallin-K" }, { "family_name": "Cowley", "given_name": "Elise", "clpid": "Cowley-E" }, { "family_name": "Reyes", "given_name": "Maria C.", "clpid": "Reyes-M-C" }, { "family_name": "Van Sambeek", "given_name": "Lindsay", "orcid": "0000-0002-7206-7410", "clpid": "Van-Sambeek-L" }, { "family_name": "Hunter", "given_name": "Ryan C.", "orcid": "0000-0003-3841-1676", "clpid": "Hunter-Ryan-C" }, { "family_name": "Asfour", "given_name": "Fadi", "clpid": "Asfour-F" }, { "family_name": "Newman", "given_name": "Dianne", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Kato", "given_name": "Roberta M.", "clpid": "Kato-R-M" } ], "abstract": "The airways of patients with cystic fibrosis are frequently colonized with bacteria, particularly Pseudomonas aeruginosa. Repeated pulmonary exacerbations contribute to decline in lung function. Iron is an important cofactor in bacterial growth and biofilm production in Pseudomonas aeruginosa. We demonstrated sputum ferrous iron and Pseudomonas bacterial burden are associated with worse lung function as measured by FEV_1 in cross-sectional studies. Ferrous iron constitutes a greater amount of total iron measured as lung function worsens. We hypothesized that sputum iron will decrease as lung function improves over the course of pulmonary exacerbation.", "issn": "1073-449X", "publisher": "American Thoracic Society", "publication": "American Journal of Respiratory and Critical Care Medicine", "publication_date": "2015-05-06", "volume": "191", "pages": "Art. No. A3343" }, { "id": "authors:1mjc6-z2428", "collection": "authors", "collection_id": "1mjc6-z2428", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150202-095339879", "type": "article", "title": "Phylogenetic analysis of HpnP reveals the origin of 2-methylhopanoid production in Alphaproteobacteria", "author": [ { "family_name": "Ricci", "given_name": "J. N.", "clpid": "Ricci-J-N" }, { "family_name": "Michel", "given_name": "A. J.", "orcid": "0000-0002-0273-4097", "clpid": "Michel-Alice-J" }, { "family_name": "Newman", "given_name": "D. K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Hopanoids are bacterial steroid-like lipids that can be preserved in the rock record on billion-year timescales. 2-Methylhopanoids are of particular interest to geobiologists because methylation is one of the few chemical modifications that remain after diagenesis and catagenesis. 2-Methylhopanes, the molecular fossils of 2-methylhopanoids, are episodically enriched in the rock record, but we do not have a robust interpretation for their abundance patterns. Here, we exploit the evolutionary record found in molecular sequences from extant organisms to reconstruct the biosynthetic history of 2-methylhopanoids using the C-2 hopanoid methylase, HpnP. Based on HpnP phylogenetic analysis, we find that 2-methylhopanoids originated in a subset of the Alphaproteobacteria. This conclusion is statistically robust and reproducible in multiple trials varying the outgroup, trimming stringency, and ingroup dataset used to infer the evolution of this protein family. The capacity for 2-methylhopanoid production was likely horizontally transferred from the Alphaproteobacteria into the Cyanobacteria after the Cyanobacteria's major divergences. Together, these results suggest that the ancestral function of 2-methylhopanoids was not related to oxygenic photosynthesis but instead to a trait already present in the Alphaproteobacteria. Moreover, given that early 2-methylhopane deposits could have been made solely by Alphaproteobacteria before the acquisition of hpnP by Cyanobacteria, and that the Alphaproteobacteria are thought to be ancestrally aerobic, we infer that 2-methylhopanoids likely arose after the oxygenation of the atmosphere. This finding is consistent with the geologic record\u2014the oldest syngenetic 2-methylhopanes occur after the rise of oxygen, in middle Proterozoic strata of the Barney Creek Formation.", "doi": "10.1111/gbi.12129", "issn": "1472-4677", "publisher": "Wiley-Blackwell", "publication": "Geobiology", "publication_date": "2015-05", "series_number": "3", "volume": "13", "issue": "3", "pages": "267-277" }, { "id": "authors:g95hp-mxv71", "collection": "authors", "collection_id": "g95hp-mxv71", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150706-082030436", "type": "article", "title": "A Conversation with James J. Morgan", "author": [ { "family_name": "Morgan", "given_name": "James J.", "clpid": "Morgan-J-J" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "In conversation with professor Dianne Newman, Caltech geobiologist, James \"Jim\" J. Morgan recalls his early days in Ireland and New York City, education in parochial and public schools, and introduction to science in Cardinal Hayes High School, Bronx. In 1950, Jim entered Manhattan College, where he elected study of civil engineering, in particular water quality. Donald O'Connor motivated Jim's future study of O_2 in rivers at Michigan, where in his MS work he learned to model O_2 dynamics of rivers. As an engineering instructor at Illinois, Jim worked on rivers polluted by synthetic detergents. He chose to focus on chemical studies, seeing it as crucial for the environment. Jim enrolled for PhD studies with Werner Stumm at Harvard, who mentored his research in chemistry of particle coagulation and oxidation processes of Mn(II) and (IV). In succeeding decades, until retirement in 2000, Jim's teaching and research centered on aquatic chemistry; major themes comprised rates of abiotic manganese oxidation on particle surfaces and flocculation of natural water particles, and chemical speciation proved the key.", "doi": "10.1146/annurev-earth-060614-105439", "issn": "0084-6597", "publisher": "Annual Reviews", "publication": "Annual Review of Earth and Planetary Sciences", "publication_date": "2015-05", "volume": "43", "pages": "1-27" }, { "id": "authors:awtb7-x6q21", "collection": "authors", "collection_id": "awtb7-x6q21", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150604-131000659", "type": "article", "title": "Sputum Glucose and Glycemic Control in Cystic Fibrosis-Related Diabetes: A Cross-Sectional Study", "author": [ { "family_name": "Van Sambeek", "given_name": "Lindsey", "orcid": "0000-0002-7206-7410", "clpid": "Van-Sambeek-L" }, { "family_name": "Cowley", "given_name": "Elise S.", "clpid": "Cowley-E-S" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Kato", "given_name": "Roberta", "clpid": "Kato-R-M" } ], "abstract": "Cystic fibrosis-related diabetes affects up to half of cystic fibrosis patients and is associated with increased mortality and more frequent pulmonary exacerbations. However, it is unclear to what degree good glycemic control might mitigate these risks and clinical outcomes have not previously been studied in relation to glucose from the lower airways, the site of infection and CF disease progression. We initially hypothesized that diabetic cystic fibrosis patients with glycosylated hemoglobin (HbA_(1c)) > 6.5% have worse pulmonary function, longer and more frequent exacerbations and also higher sputum glucose levels than patients with HbA_(1c) \u2264 6.5% or cystic fibrosis patients without diabetes. To test this, we analyzed spontaneously expectorated sputum samples from 88 cystic fibrosis patients. The median sputum glucose concentration was 0.70 mM (mean, 4.75 mM; range, 0-64.6 mM). Sputum glucose was not correlated with age, sex, body mass index, diabetes diagnosis, glycemic control, exacerbation frequency or length, or pulmonary function. Surprisingly, sputum glucose was highest in subjects with normal glucose tolerance, suggesting the dynamics of glycemic control, sputum glucose and pulmonary infections are more complex than previously thought. Two-year mean HbA_(1c) was positively correlated with the length of exacerbation admission (p < 0.01), and negatively correlated with measures of pulmonary function (p < 0.01). While total number of hospitalizations for exacerbations were not significantly different, subjects with an HbA_(1c) > 6.5% were hospitalized on average 6 days longer than those with HbA_(1c) \u2264 6.5% (p < 0.01). Current clinical care guidelines for cystic fibrosis-related diabetes target HbA_(1c) \u2264 7% to limit long-term microvascular damage, but more stringent glycemic control (HbA_(1c) \u2264 6.5%) may further reduce the short-term pulmonary complications.", "doi": "10.1371/journal.pone.0119938", "pmcid": "PMC4372582", "issn": "1932-6203", "publisher": "Public Library of Science", "publication": "PLoS ONE", "publication_date": "2015-03-24", "series_number": "3", "volume": "10", "issue": "3", "pages": "Art. No. e0119938" }, { "id": "authors:vxfq2-rrv68", "collection": "authors", "collection_id": "vxfq2-rrv68", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150619-085839244", "type": "article", "title": "The Ferrous Iron-Responsive BqsRS Two-Component System Activates Genes That Promote Cationic Stress Tolerance", "author": [ { "family_name": "Kreamer", "given_name": "Naomi N.", "clpid": "Kreamer-N-N-K" }, { "family_name": "Costa", "given_name": "Flavia", "clpid": "Costa-F" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "The physiological resistance of pathogens to antimicrobial treatment is a severe problem in the context of chronic infections. For example, the mucus-filled lungs of cystic fibrosis (CF) patients are readily colonized by diverse antibiotic-resistant microorganisms, including Pseudomonas aeruginosa. Previously, we showed that bioavailable ferrous iron [Fe(II)] is present in CF sputum at all stages of infection and constitutes a significant portion of the iron pool at advanced stages of lung function decline [R. C. Hunter et al., mBio 4(4):e00557-13, 2013]. P. aeruginosa, a dominant CF pathogen, senses Fe(II) using a two-component signal transduction system, BqsRS, which is transcriptionally active in CF sputum [R. C. Hunter et al., mBio 4(4):e00557-13, 2013; N. N. Kreamer, J. C. Wilks, J. J. Marlow, M. L. Coleman, and D. K. Newman, J Bacteriol 194:1195\u20131204, 2012]. Here, we show that an RExxE motif in BqsS is required for BqsRS activation. Once Fe(II) is sensed, BqsR binds a tandem repeat DNA sequence, activating transcription. The BqsR regulon\u2014defined through iterative bioinformatic predictions and experimental validation\u2014includes several genes whose products are known to drive antibiotic resistance to aminoglycosides and polymyxins. Among them are genes encoding predicted determinants of polyamine transport and biosynthesis. Compared to the wild type, bqsS and bqsR deletion mutants are sensitive to high levels of Fe(II), produce less spermidine in high Fe(II), and are more sensitive to tobramycin and polymyxin B but not arsenate, chromate, or cefsulodin. BqsRS thus mediates a physiological response to Fe(II) that guards the cell against positively charged molecules but not negatively charged stressors. These results suggest Fe(II) is an important environmental signal that, via BqsRS, bolsters tolerance of a variety of cationic stressors, including clinically important antimicrobial agents.", "doi": "10.1128/mBio.02549-14", "pmcid": "PMC4358008", "issn": "2150-7511", "publisher": "American Society for Microbiology", "publication": "mBio", "publication_date": "2015-03", "series_number": "2", "volume": "6", "issue": "2", "pages": "Art. No. e02549-14" }, { "id": "authors:mdy2m-e4c44", "collection": "authors", "collection_id": "mdy2m-e4c44", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150303-083043246", "type": "article", "title": "Methylation at the C-2 position of hopanoids increases rigidity in native bacterial membranes", "author": [ { "family_name": "Wu", "given_name": "Chia-Hung", "clpid": "Wu-Chia-Hung" }, { "family_name": "Bialecka-Fornal", "given_name": "Maja", "clpid": "Bialecka-Fornal-M" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Sedimentary rocks host a vast reservoir of organic carbon, such as 2-methylhopane biomarkers, whose evolutionary significance we poorly understand. Our ability to interpret this molecular fossil record is constrained by ignorance of the function of their molecular antecedents. To gain insight into the meaning of 2-methylhopanes, we quantified the dominant (des)methylated hopanoid species in the membranes of the model hopanoid-producing bacterium Rhodopseudomonas palustris TIE-1. Fluorescence polarization studies of small unilamellar vesicles revealed that hopanoid 2-methylation specifically renders native bacterial membranes more rigid at concentrations that are relevant in vivo. That hopanoids differentially modify native membrane rigidity as a function of their methylation state indicates that methylation itself promotes fitness under stress. Moreover, knowing the in vivo (2Me)-hopanoid concentration range in different cell membranes, and appreciating that (2Me)-hopanoids' biophysical effects are tuned by the lipid environment, permits the design of more relevant in vitro experiments to study their physiological functions.", "doi": "10.7554/eLife.05663", "pmcid": "PMC4337730", "issn": "2050-084X", "publisher": "eLife Sciences Publications", "publication": "eLife", "publication_date": "2015-01-19", "volume": "4", "pages": "Art. No. e05663" }, { "id": "authors:edrvt-vx355", "collection": "authors", "collection_id": "edrvt-vx355", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150504-143203439", "type": "conference_item", "title": "Characterization, Comparative Genomics and Genome Mining for Antibiotics and Secondary Metabolite of two Actinomycetales isolates", "author": [ { "family_name": "Mariita", "given_name": "R. M.", "clpid": "Mariita-R-M" }, { "family_name": "Bhatnagar", "given_name": "S.", "clpid": "Bhatnagar-S" }, { "family_name": "Hanselmann", "given_name": "K.", "clpid": "Hanselmann-K" }, { "family_name": "Hossain", "given_name": "M.", "orcid": "0000-0003-3848-9035", "clpid": "Hossain-Mohammad-J" }, { "family_name": "Liles", "given_name": "M.", "clpid": "Liles-M" }, { "family_name": "Moss", "given_name": "A. G.", "clpid": "Moss-A-G" }, { "family_name": "Leadbetter", "given_name": "J. R.", "orcid": "0000-0002-7033-0844", "clpid": "Leadbetter-J-R" }, { "family_name": "Newman", "given_name": "D. K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "contributor": [ { "family_name": "Lippincott-Schwartz", "given_name": "Jennifer", "clpid": "Lippincott-Schwartz-J" }, { "family_name": "Marshall", "given_name": "Wallace", "clpid": "Marshall-W" }, { "family_name": "Marks", "given_name": "Michael", "clpid": "Marks-M" } ], "abstract": "Actinomycetes are ubiquitous Gram (+) bacteria commonly found to have high G+C content and best\nknown for their metabolic by-products and novel enzymes [1]. Isolates CCMMD2014 & MRMD2014\nwere co-cultured from soil impacted by a rusty fire hydrant in Woods Hole, MA. The Streptomyces sp.\nand Curtobacterium sp. isolates were identified by marker genes for 16S rRNA, rpoB, xylose isomerase,\ntryptophan synthase beta chain and Cytochrome P450 monooxygenase. Both isolates showed lactic acid\nfermentation and urease activity. The co-isolates were separated by selective culturing with antibiotics.\nIn addition, whole genome sequencing revealed distinct inherent metabolic pathways in each culture\nthat allowed for mutually exclusive selective culture conditions. Assembly was done using HGAP3 with\nCelera8 assembler using SMRT portal [2,3]. Annotation was done using the RAST server [4], with 7540\nand 3969 CDS for Streptomyces sp. and Curtobacterium sp. respectively being revealed by AMIGene and\nBASys [5,6]. Subsequently, antiSMASH [7], was used to predict 52 and 26 secondary metabolite\nbiosynthetic clusters that included genes for lantipeptides, terpenes, siderophores, polyketide synthases\ntype I and II, bacteriocin and nonribosomal peptide synthase genes for Streptomyces sp. and\nCurtobacterium sp. respectively. The isolates have genes of potentially beneficial traits that could help\nstudy, among others, the role of fimbrial adhesins and iron in biofilm formation and investigation on\nnatural products.", "publisher": "Caltech Library", "publication_date": "2014-12" }, { "id": "authors:2jtqs-thr57", "collection": "authors", "collection_id": "2jtqs-thr57", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141208-104816963", "type": "article", "title": "Covalently linked hopanoid-lipid A improves outer-membrane resistance of a Bradyrhizobium symbiont of legumes", "author": [ { "family_name": "Silipo", "given_name": "Alba", "clpid": "Silipo-A" }, { "family_name": "Vitiello", "given_name": "Giuseppe", "clpid": "Vitiello-G" }, { "family_name": "Gully", "given_name": "Djamel", "clpid": "Gully-D" }, { "family_name": "Sturiale", "given_name": "Luisa", "clpid": "Sturiale-L" }, { "family_name": "Chaintreuil", "given_name": "Cl\u00e9mence", "clpid": "Chaintreuil-" }, { "family_name": "Fardoux", "given_name": "Joel", "clpid": "Fardoux-J" }, { "family_name": "Gargani", "given_name": "Daniel", "clpid": "Gargani-D" }, { "family_name": "Lee", "given_name": "Hae-In", "clpid": "Lee-Hae-In" }, { "family_name": "Kulkarni", "given_name": "Gargi", "clpid": "Kulkarni-Gargi" }, { "family_name": "Busset", "given_name": "Nicolas", "clpid": "Busset-N" }, { "family_name": "Marchetti", "given_name": "Roberta", "clpid": "Marchetti-R" }, { "family_name": "Palmigiano", "given_name": "Angelo", "clpid": "Palmigiano-A" }, { "family_name": "Moll", "given_name": "Herman", "clpid": "Moll-H" }, { "family_name": "Engel", "given_name": "Regina", "clpid": "Engel-R" }, { "family_name": "Lanzetta", "given_name": "Rosa", "clpid": "Lanzetta-R" }, { "family_name": "Paduano", "given_name": "Luigi", "clpid": "Paduano-L" }, { "family_name": "Parrilli", "given_name": "Michelangelo", "clpid": "Parrilli-M" }, { "family_name": "Chang", "given_name": "Woo-Suk", "clpid": "Chang-Woo-Suk" }, { "family_name": "Holst", "given_name": "Otto", "clpid": "Holst-O" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Garozzo", "given_name": "Domenico", "clpid": "Garozzo-D" }, { "family_name": "D'Errico", "given_name": "Eric", "clpid": "D'Errico-E" }, { "family_name": "Giraud", "given_name": "Eric", "clpid": "Giraud-E" }, { "family_name": "Molinaro", "given_name": "Antonio", "clpid": "Molinaro-A" } ], "abstract": "Lipopolysaccharides (LPSs) are major components of the outer membrane of Gram-negative bacteria and are essential for their growth and survival. They act as a structural barrier and play an important role in the interaction with eukaryotic hosts. Here we demonstrate that a photosynthetic Bradyrhizobium strain, symbiont of Aeschynomene legumes, synthesizes a unique LPS bearing a hopanoid covalently attached to lipid A. Biophysical analyses of reconstituted liposomes indicate that this hopanoid-lipid A structure reinforces the stability and rigidity of the outer membrane. In addition, the bacterium produces other hopanoid molecules not linked to LPS. A hopanoid-deficient strain, lacking a squalene hopene cyclase, displays increased sensitivity to stressful conditions and reduced ability to survive intracellularly in the host plant. This unusual combination of hopanoid and LPS molecules may represent an adaptation to optimize bacterial survival in both free-living and symbiotic states.", "doi": "10.1038/ncomms6106", "issn": "2041-1723", "publisher": "Nature Publishing Group", "publication": "Nature Communications", "publication_date": "2014-10-30", "series_number": "10", "volume": "5", "issue": "10", "pages": "Art. No. 5106" }, { "id": "authors:wv630-86921", "collection": "authors", "collection_id": "wv630-86921", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141020-141511951", "type": "article", "title": "Anaerobic Bacteria Grow within Candida albicans Biofilms and Induce Biofilm Formation in Suspension Cultures", "author": [ { "family_name": "Fox", "given_name": "Emily P.", "clpid": "Fox-E-P" }, { "family_name": "Cowley", "given_name": "Elise S.", "clpid": "Cowley-E-S" }, { "family_name": "Nobile", "given_name": "Clarissa J.", "clpid": "Nobile-C-J" }, { "family_name": "Hartooni", "given_name": "Nairi", "clpid": "Hartooni-N" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Johnson", "given_name": "Alexander D.", "clpid": "Johnson-A-D" } ], "abstract": "The human microbiome contains diverse microorganisms, which share and compete for the same environmental niches. A major microbial growth form in the human body is the biofilm state, where tightly packed bacterial, archaeal, and fungal cells must cooperate and/or compete for resources in order to survive. We examined mixed biofilms composed of the major fungal species of the gut microbiome, Candida albicans, and each of five prevalent bacterial gastrointestinal inhabitants: Bacteroides fragilis, Clostridium perfringens, Escherichia coli, Klebsiella pneumoniae, and Enterococcus faecalis. We observed that biofilms formed by C. albicans provide a hypoxic microenvironment that supports the growth of two anaerobic bacteria, even when cultured in ambient oxic conditions that are normally toxic to the bacteria. We also found that coculture with bacteria in biofilms induces massive gene expression changes in C. albicans, including upregulation of WOR1, which encodes a transcription regulator that controls a phenotypic switch in C. albicans, from the \"white\" cell type to the \"opaque\" cell type. Finally, we observed that in suspension cultures, C. perfringens induces aggregation of C. albicans into \"mini-biofilms,\" which allow C. perfringens cells to survive in a normally toxic environment. This work indicates that bacteria and C. albicans interactions modulate the local chemistry of their environment in multiple ways to create niches favorable to their growth and survival.", "doi": "10.1016/j.cub.2014.08.057", "pmcid": "PMC4252622", "issn": "0960-9822", "publisher": "Cell Press", "publication": "Current Biology", "publication_date": "2014-10-20", "series_number": "20", "volume": "24", "issue": "20", "pages": "2411-2416" }, { "id": "authors:eyjp7-2mr20", "collection": "authors", "collection_id": "eyjp7-2mr20", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141007-095444557", "type": "article", "title": "Fosmidomycin Decreases Membrane Hopanoids and Potentiates the Effects of Colistin on Burkholderia multivorans Clinical Isolates", "author": [ { "family_name": "Malott", "given_name": "Rebecca J.", "clpid": "Malott-R-J" }, { "family_name": "Wu", "given_name": "Chia-Hung", "clpid": "Wu-Chia-Hung" }, { "family_name": "Lee", "given_name": "Tracy D.", "clpid": "Lee-Tracy-D" }, { "family_name": "Hird", "given_name": "Trevor J.", "clpid": "Hird-T-J" }, { "family_name": "Dalleska", "given_name": "Nathan F.", "orcid": "0000-0002-2059-1587", "clpid": "Dalleska-N-F" }, { "family_name": "Zlosnik", "given_name": "James E. A.", "clpid": "Zlosnik-J-E-A" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Speert", "given_name": "David P.", "clpid": "Speert-D-P" } ], "abstract": "Burkholderia cepacia complex (Bcc) pulmonary infections in people living with cystic fibrosis (CF) are difficult to treat because of the extreme intrinsic resistance of most isolates to a broad range of antimicrobials. Fosmidomycin is an antibacterial and antiparasitic agent that disrupts the isoprenoid biosynthesis pathway, a precursor to hopanoid biosynthesis. Hopanoids are involved in membrane stability and contribute to polymyxin resistance in Bcc bacteria. Checkerboard MIC assays determined that although isolates of the Bcc species B. multivorans were highly resistant to treatment with fosmidomycin or colistin (polymyxin E), antimicrobial synergy was observed in certain isolates when the antimicrobials were used in combination. Treatment with fosmidomycin decreased the MIC of colistin for isolates as much as 64-fold to as low as 8 \u03bcg/ml, a concentration achievable with colistin inhalation therapy. A liquid chromatography-tandem mass spectrometry technique was developed for the accurate quantitative determination of underivatized hopanoids in total lipid extracts, and bacteriohopanetetrol cyclitol ether (BHT-CE) was found to be the dominant hopanoid made by B. multivorans. The amount of BHT-CE made was significantly reduced upon fosmidomycin treatment of the bacteria. Uptake assays with 1-N-phenylnaphthylamine were used to determine that dual treatment with fosmidomycin and colistin increases membrane permeability, while binding assays with boron-dipyrromethene-conjugated polymyxin B illustrated that the addition of fosmidomycin had no impact on polymyxin binding. This work indicates that pharmacological suppression of membrane hopanoids with fosmidomycin treatment can increase the susceptibility of certain clinical B. multivorans isolates to colistin, an agent currently in use to treat pulmonary infections in CF patients.", "doi": "10.1128/AAC.02705-14", "pmcid": "PMC4135860", "issn": "0066-4804", "publisher": "American Society for Microbiology", "publication": "Antimicrobial Agents and Chemotherapy", "publication_date": "2014-09", "series_number": "9", "volume": "58", "issue": "9", "pages": "5211-5219" }, { "id": "authors:m0f29-kqv05", "collection": "authors", "collection_id": "m0f29-kqv05", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170518-165224584", "type": "book_section", "title": "Extraction and Measurement of NAD(P)+ and NAD(P)H", "book_title": "Pseudomonas Methods and Protocols", "author": [ { "family_name": "Kern", "given_name": "Suzanne E.", "clpid": "Kern-S-E" }, { "family_name": "Price-Whelan", "given_name": "Alexa", "orcid": "0000-0003-0872-7098", "clpid": "Price-Whelan-A" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "contributor": [ { "family_name": "Filloux", "given_name": "Alain", "clpid": "Filloux-A" }, { "family_name": "Ramos", "given_name": "Juan-Luis", "clpid": "Ramos-J-L" } ], "abstract": "Nicotinamide adenine dinucleotides are critical redox-active substrates for countless catabolic and anabolic reactions. Ratios of NAD+ to NADH and NADP+ to NADPH are therefore considered key indicators of the overall intracellular redox potential and metabolic state. These ratios can be measured in bulk conditions using a highly sensitive enzyme cycling-based colorimetric assay (detection limit at or below 0.05 \u03bcM or 1 pmol) following a simple extraction procedure involving solutions of acid and base. Special considerations are necessary to avoid measurement artifacts caused by the presence of endogenous redox-active metabolites, such as phenazines made by diverse Pseudomonas species (see Chapter 25).", "doi": "10.1007/978-1-4939-0473-0_26", "isbn": "9781493904723", "publisher": "Humana Press", "place_of_publication": "New York, NY", "publication_date": "2014-06-04", "pages": "311-323" }, { "id": "authors:m8t2v-y5n21", "collection": "authors", "collection_id": "m8t2v-y5n21", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140401-104038513", "type": "article", "title": "Phenazine redox cycling enhances anaerobic survival in Pseudomonas aeruginosa by facilitating generation of ATP and a proton-motive force", "author": [ { "family_name": "Glasser", "given_name": "Nathaniel R.", "orcid": "0000-0002-2833-5166", "clpid": "Glasser-Nathaniel-R" }, { "family_name": "Kern", "given_name": "Suzanne E.", "clpid": "Kern-Suzanne-E" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "While many studies have explored the growth of Pseudomonas aeruginosa, comparatively few have focused on its survival. Previously, we reported that endogenous phenazines support the anaerobic survival of P.\u2009aeruginosa, yet the physiological mechanism underpinning survival was unknown. Here, we demonstrate that phenazine redox cycling enables P.\u2009aeruginosa to oxidize glucose and pyruvate into acetate, which promotes survival by coupling acetate and ATP synthesis through the activity of acetate kinase. By measuring intracellular NAD(H) and ATP concentrations, we show that survival is correlated with ATP synthesis, which is tightly coupled to redox homeostasis during pyruvate fermentation but not during arginine fermentation. We also show that ATP hydrolysis is required to generate a proton-motive force using the ATP synthase complex during fermentation. Together, our results suggest that phenazines enable maintenance of the proton-motive force by promoting redox homeostasis and ATP synthesis. This work demonstrates the more general principle that extracellular redox-active molecules, such as phenazines, can broaden the metabolic versatility of microorganisms by facilitating energy generation.", "doi": "10.1111/mmi.12566", "pmcid": "PMC4046897", "issn": "0950-382X", "publisher": "Wiley", "publication": "Molecular Microbiology", "publication_date": "2014-04", "series_number": "2", "volume": "92", "issue": "2", "pages": "399-412" }, { "id": "authors:6c0bf-d7z50", "collection": "authors", "collection_id": "6c0bf-d7z50", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170522-090349682", "type": "book_section", "title": "Measurement of Phenazines in Bacterial Cultures", "book_title": "Pseudomonas Methods and Protocols", "author": [ { "family_name": "Kern", "given_name": "Suzanne E.", "clpid": "Kern-S-E" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "contributor": [ { "family_name": "Filloux", "given_name": "Alain", "clpid": "Filloux-A" }, { "family_name": "Ramos", "given_name": "Juan-Luis", "clpid": "Ramos-J-L" } ], "abstract": "Certain pseudomonads are capable of producing phenazines\u2014pigmented, reversibly redox-active metabolites that induce a variety of physiological effects on the producing organism as well as others in their vicinity. Environmental conditions and the specific physiological state of cells can dramatically affect the absolute amounts and relative proportions of the various phenazines produced. The method detailed here\u2014high-performance liquid chromatography coupled to detection by UV\u2013Vis absorption\u2014can be used to separate and quantify the amount of phenazines in a Pseudomonas culture. Simple spectrophotometric measurements of filtered culture supernatants can be used to quantify certain oxidized phenazines, such as pyocyanin, in cultures. For cases where the conditions under study are not planktonic cultures (e.g., soil or biofilms) extracting the phenazines may be a necessary first step.", "doi": "10.1007/978-1-4939-0473-0_25", "isbn": "9781493904723", "publisher": "Springer", "place_of_publication": "New York", "publication_date": "2014-03-29", "pages": "303-310" }, { "id": "authors:4j2za-44r54", "collection": "authors", "collection_id": "4j2za-44r54", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140407-105009295", "type": "article", "title": "Diverse capacity for 2-methylhopanoid production correlates with a specific ecological niche", "author": [ { "family_name": "Ricci", "given_name": "Jessica N.", "clpid": "Ricci-J-N" }, { "family_name": "Coleman", "given_name": "Maureen L.", "clpid": "Coleman-M-L" }, { "family_name": "Welander", "given_name": "Paul V.", "clpid": "Welander-P-V" }, { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Summons", "given_name": "Roger E.", "orcid": "0000-0002-7144-8537", "clpid": "Summons-R-E" }, { "family_name": "Spear", "given_name": "John R.", "orcid": "0000-0002-4664-7438", "clpid": "Spear-J-R" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Molecular fossils of 2-methylhopanoids are prominent biomarkers in modern and ancient sediments that have been used as proxies for cyanobacteria and their main metabolism, oxygenic photosynthesis. However, substantial culture and genomic-based evidence now indicates that organisms other than cyanobacteria can make 2-methylhopanoids. Because few data directly address which organisms produce 2-methylhopanoids in the environment, we used metagenomic and clone library methods to determine the environmental diversity of hpnP, the gene encoding the C-2 hopanoid methylase. Here we show that hpnP copies from alphaproteobacteria and as yet uncultured organisms are found in diverse modern environments, including some modern habitats representative of those preserved in the rock record. In contrast, cyanobacterial hpnP genes are rarer and tend to be localized to specific habitats. To move beyond understanding the taxonomic distribution of environmental 2-methylhopanoid producers, we asked whether hpnP presence might track with particular variables. We found hpnP to be significantly correlated with organisms, metabolisms and environments known to support plant\u2013microbe interactions (P-value<10^\u22126); in addition, we observed diverse hpnP types in closely packed microbial communities from other environments, including stromatolites, hot springs and hypersaline microbial mats. The common features of these niches indicate that 2-methylhopanoids are enriched in sessile microbial communities inhabiting environments low in oxygen and fixed nitrogen with high osmolarity. Our results support the earlier conclusion that 2-methylhopanoids are not reliable biomarkers for cyanobacteria or any other taxonomic group, and raise the new hypothesis that, instead, they are indicators of a specific environmental niche.", "doi": "10.1038/ismej.2013.191", "pmcid": "PMC3930323", "issn": "1751-7362", "publisher": "Nature Publishing Group", "publication": "ISME Journal", "publication_date": "2014-03", "series_number": "3", "volume": "8", "issue": "3", "pages": "675-684" }, { "id": "authors:fanyv-68q02", "collection": "authors", "collection_id": "fanyv-68q02", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140407-131828981", "type": "article", "title": "Nonredundant Roles for Cytochrome c_2 and Two High-Potential Iron-Sulfur Proteins in the Photoferrotroph Rhodopseudomonas palustris TIE-1", "author": [ { "family_name": "Bird", "given_name": "Lina J.", "orcid": "0000-0003-4127-4756", "clpid": "Bird-L-J" }, { "family_name": "Saralva", "given_name": "Ivo H.", "clpid": "Saralva-I-H" }, { "family_name": "Park", "given_name": "Shannon", "clpid": "Park-Shannon" }, { "family_name": "Cal\u00e7ada", "given_name": "Eduardo O.", "clpid": "Cal\u00e7ada-E-O" }, { "family_name": "Salgueiro", "given_name": "Carlos A.", "clpid": "Salgueiro-C-A" }, { "family_name": "Nitschke", "given_name": "Wolfang", "clpid": "Nitschke-W" }, { "family_name": "Louro", "given_name": "Ricardo O.", "clpid": "Louro-R-O" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "The purple bacterium Rhodopseudomonas palustris TIE-1 expresses multiple small high-potential redox proteins during photoautotrophic growth, including two high-potential iron-sulfur proteins (HiPIPs) (PioC and Rpal_4085) and a cytochrome c_2. We evaluated the role of these proteins in TIE-1 through genetic, physiological, and biochemical analyses. Deleting the gene encoding cytochrome c_2 resulted in a loss of photosynthetic ability by TIE-1, indicating that this protein cannot be replaced by either HiPIP in cyclic electron flow. PioC was previously implicated in photoferrotrophy, an unusual form of photosynthesis in which reducing power is provided through ferrous iron oxidation. Using cyclic voltammetry (CV), electron paramagnetic resonance (EPR) spectroscopy, and flash-induced spectrometry, we show that PioC has a midpoint potential of 450 mV, contains all the typical features of a HiPIP, and can reduce the reaction centers of membrane suspensions in a light-dependent manner at a much lower rate than cytochrome c_2. These data support the hypothesis that PioC linearly transfers electrons from iron, while cytochrome c_2 is required for cyclic electron flow. Rpal_4085, despite having spectroscopic characteristics and a reduction potential similar to those of PioC, is unable to reduce the reaction center. Rpal_4085 is upregulated by the divalent metals Fe(II), Ni(II), and Co(II), suggesting that it might play a role in sensing or oxidizing metals in the periplasm. Taken together, our results suggest that these three small electron transfer proteins perform different functions in the cell.", "doi": "10.1128/JB.00843-13", "pmcid": "PMC3911180", "issn": "0021-9193", "publisher": "American Society for Microbiology", "publication": "Journal of Bacteriology", "publication_date": "2014-02", "series_number": "4", "volume": "196", "issue": "4", "pages": "850-858" }, { "id": "authors:pjxb8-32324", "collection": "authors", "collection_id": "pjxb8-32324", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140113-134430398", "type": "article", "title": "Marine Tubeworm Metamorphosis Induced by Arrays of Bacterial Phage Tail\u2013Like Structures", "author": [ { "family_name": "Shikuma", "given_name": "Nicholas J.", "orcid": "0000-0001-5518-5020", "clpid": "Shikuma-Nicholas-J" }, { "family_name": "Pilhofer", "given_name": "Martin", "clpid": "Pilhofer-M" }, { "family_name": "Weiss", "given_name": "Gregor L.", "clpid": "Weiss-G-L" }, { "family_name": "Hadfield", "given_name": "Michael G.", "clpid": "Hadfield-M-G" }, { "family_name": "Jensen", "given_name": "Grant J.", "orcid": "0000-0003-1556-4864", "clpid": "Jensen-G-J" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "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.", "doi": "10.1126/science.1246794", "pmcid": "PMC4949041", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2014-01-09", "series_number": "6170", "volume": "343", "issue": "6170", "pages": "529-533" }, { "id": "authors:7hnw0-46t70", "collection": "authors", "collection_id": "7hnw0-46t70", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140206-114311185", "type": "article", "title": "Probing the Subcellular Localization of Hopanoid Lipids in Bacteria Using NanoSIMS", "author": [ { "family_name": "Doughty", "given_name": "David M.", "clpid": "Doughty-D-M" }, { "family_name": "Dieterle", "given_name": "Michael", "clpid": "Dieterle-M" }, { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Fischer", "given_name": "Woodward W.", "orcid": "0000-0002-8836-3054", "clpid": "Fischer-W-W" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "The organization of lipids within biological membranes is poorly understood. Some studies have suggested lipids group\ninto microdomains within cells, but the evidence remains controversial due to non-native imaging techniques. A recently developed NanoSIMS technique indicated that sphingolipids group into microdomains within membranes of human fibroblast cells. We extended this NanoSIMS approach to study the localization of hopanoid lipids in bacterial cells by developing a stable isotope labeling method to directly detect subcellular localization of specific lipids in bacteria with ca. 60 nm resolution. Because of the relatively small size of bacterial cells and the relative abundance of hopanoid lipids in membranes, we employed a primary ^2H-label to maximize our limit of detection. This approach permitted the analysis of multiple stable isotope labels within the same sample, enabling visualization of subcellular lipid microdomains within different cell types using a secondary label to mark the growing end of the cell. Using this technique, we demonstrate subcellular localization of hopanoid lipids within alpha-proteobacterial and cyanobacterial cells. Further, we provide evidence of hopanoid lipid domains in between cells of the filamentous cyanobacterium Nostoc punctiforme. More broadly, our method provides a means to image lipid microdomains in a wide range of cell types and test hypotheses for their functions in membranes.", "doi": "10.1371/journal.pone.0084455", "pmcid": "PMC3883690", "issn": "1932-6203", "publisher": "Public Library of Science", "publication": "PLoS ONE", "publication_date": "2014-01", "series_number": "1", "volume": "9", "issue": "1", "pages": "Art. No. e84455" }, { "id": "authors:vth3k-1d892", "collection": "authors", "collection_id": "vth3k-1d892", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180516-113554814", "type": "book_section", "title": "The Yin and Yang of Phenazine Physiology", "book_title": "Microbial Phenazines: Biosynthesis, Agriculture and Health", "author": [ { "family_name": "Grahl", "given_name": "Nora", "clpid": "Grahl-N" }, { "family_name": "Kern", "given_name": "Suzanne E.", "clpid": "Kern-S-E" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Hogan", "given_name": "Deborah A.", "orcid": "0000-0002-6366-2971", "clpid": "Hogan-D-A" } ], "contributor": [ { "family_name": "Chincholkar", "given_name": "Sudhir", "clpid": "Chincholkar-S" }, { "family_name": "Thomashow", "given_name": "Linda", "clpid": "Thomashow-L" } ], "abstract": "Microorganisms are seldom solitary. They are surrounded by both clonal cells and other members of the local microbial community, and they often exist in, on, or in close proximity to multi-cellular host organisms like plants and humans. Whether in vivo during infection or in situ in the nutrient rich rhizosphere, microorganisms affect each other and the host. Phenazines, a class of secondary metabolites secreted by diverse bacteria, are best known for their antibiotic properties and have been shown to affect a broad spectrum of organisms ranging from bacteria over fungi, plants, nematodes, parasites, and humans. However, phenazines are also involved in numerous aspects of bacterial physiology like survival, iron acquisition, signaling, and biofilm formation in ways that have the potential to increase the fitness of both the phenazine-producing strain and non-producers alike. The overarching theme of this chapter is that phenazines can be beneficial or detrimental to organisms, depending on the milieu and one's perspective. In this chapter, we will highlight specific examples to discuss the yin and yang of phenazine physiology.", "doi": "10.1007/978-3-642-40573-0_3", "isbn": "9783642405730", "publisher": "Springer", "place_of_publication": "Berlin", "publication_date": "2013-12-06", "pages": "43-69" }, { "id": "authors:4pnw6-x7v16", "collection": "authors", "collection_id": "4pnw6-x7v16", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140220-100231898", "type": "article", "title": "Bacterial Argonaute Samples the Transcriptome to Identify Foreign DNA", "author": [ { "family_name": "Olovnikov", "given_name": "Ivan", "clpid": "Olovnikov-I" }, { "family_name": "Chan", "given_name": "Ken", "clpid": "Chan-Ken" }, { "family_name": "Sachidanandam", "given_name": "Ravi", "clpid": "Sachidanandam-R" }, { "family_name": "Newman", "given_name": "Diane K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Aravin", "given_name": "Alexei A.", "orcid": "0000-0002-6956-8257", "clpid": "Aravin-A-A" } ], "abstract": "Eukaryotic Argonautes bind small RNAs and use them as guides to find complementary RNA targets and induce gene silencing. Though homologs of eukaryotic Argonautes are present in many bacteria and archaea, their small RNA partners and functions are unknown. We found that the Argonaute of Rhodobacter sphaeroides (RsAgo) associates with 15\u201319 nt RNAs that correspond to the majority of transcripts. RsAgo also binds single-stranded 22\u201324 nt DNA molecules that are complementary to the small RNAs and enriched in sequences derived from exogenous plasmids as well as genome-encoded foreign nucleic acids such as transposons and phage genes. Expression of RsAgo in the heterologous E. coli system leads to formation of plasmid-derived small RNA and DNA and plasmid degradation. In a R. sphaeroides mutant lacking RsAgo, expression of plasmid-encoded genes is elevated. Our results indicate that RNAi-related processes found in eukaryotes are also conserved in bacteria and target foreign nucleic acids.", "doi": "10.1016/j.molcel.2013.08.014", "pmcid": "PMC3809076", "issn": "1097-2765", "publisher": "Elsevier", "publication": "Molecular Cell", "publication_date": "2013-09-12", "series_number": "5", "volume": "51", "issue": "5", "pages": "594-605" }, { "id": "authors:rthm6-bs408", "collection": "authors", "collection_id": "rthm6-bs408", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170524-074650388", "type": "article", "title": "Ferrous Iron Is a Significant Component of Bioavailable Iron in Cystic Fibrosis Airways", "author": [ { "family_name": "Hunter", "given_name": "Ryan C.", "orcid": "0000-0003-3841-1676", "clpid": "Hunter-Ryan-C" }, { "family_name": "Asfour", "given_name": "Fadi", "clpid": "Asfour-F" }, { "family_name": "Dingemans", "given_name": "Jozef", "clpid": "Dingemans-J" }, { "family_name": "Osuna", "given_name": "Brenda L.", "clpid": "Osuna-B-L" }, { "family_name": "Samad", "given_name": "Tahoura", "clpid": "Samad-T" }, { "family_name": "Malfroot", "given_name": "Anne", "clpid": "Malfroot-A" }, { "family_name": "Cornelis", "given_name": "Pierre", "clpid": "Cornelis-P" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Chronic, biofilm-like infections by the opportunistic pathogen Pseudomonas aeruginosa are a major cause of mortality in cystic fibrosis (CF) patients. While much is known about P. aeruginosa from laboratory studies, far less is understood about what it experiences in vivo. Iron is an important environmental parameter thought to play a central role in the development and maintenance of P. aeruginosa infections, for both anabolic and signaling purposes. Previous studies have focused on ferric iron [Fe(III)] as a target for antimicrobial therapies; however, here we show that ferrous iron [Fe(II)] is abundant in the CF lung (~39 \u00b5M on average for severely sick patients) and significantly correlates with disease severity (\u03c1 = \u22120.56, P = 0.004), whereas ferric iron does not (\u03c1 = \u22120.28, P = 0.179). Expression of the P. aeruginosa genes bqsRS, whose transcription is upregulated in response to Fe(II), was high in the majority of patients tested, suggesting that increased Fe(II) is bioavailable to the infectious bacterial population. Because limiting Fe(III) acquisition inhibits biofilm formation by P. aeruginosa in various oxic in vitro systems, we also tested whether interfering with Fe(II) acquisition would improve biofilm control under anoxic conditions; concurrent sequestration of both iron oxidation states resulted in a 58% reduction in biofilm accumulation and 28% increase in biofilm dissolution, a significant improvement over Fe(III) chelation treatment alone. This study demonstrates that the chemistry of infected host environments coevolves with the microbial community as infections progress, which should be considered in the design of effective treatment strategies at different stages of disease.\n\nIMPORTANCE: Iron is an important environmental parameter that helps pathogens thrive in sites of infection, including those of cystic fibrosis (CF) patients. Ferric iron chelation therapy has been proposed as a novel therapeutic strategy for CF lung infections, yet until now, the iron oxidation state has not been measured in the host. In studying mucus from the infected lungs of multiple CF patients from Europe and the United States, we found that ferric and ferrous iron change in concentration and relative proportion as infections progress; over time, ferrous iron comes to dominate the iron pool. This information is relevant to the design of novel CF therapeutics and, more broadly, to developing accurate models of chronic CF infections.", "doi": "10.1128/mBio.00557-13", "pmcid": "PMC3753050", "issn": "2150-7511", "publisher": "American Society for Microbiology", "publication": "mBio", "publication_date": "2013-08-20", "series_number": "4", "volume": "4", "issue": "4", "pages": "Art. No. e00557-13" }, { "id": "authors:pn356-4df63", "collection": "authors", "collection_id": "pn356-4df63", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130627-100549056", "type": "article", "title": "The General Stress Response Factor EcfG Regulates Expression of the C-2 Hopanoid Methylase HpnP in Rhodopseudomonas palustris TIE-1", "author": [ { "family_name": "Kulkarni", "given_name": "Gargi", "clpid": "Kulkarni-Gargi" }, { "family_name": "Wu", "given_name": "Chia-Hung", "clpid": "Wu-Chia-Hung" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Lipid molecules preserved in sedimentary rocks facilitate the reconstruction of events that have shaped the evolution of the Earth's biosphere. A key limitation for the interpretation of many of these molecular fossils is that their biological roles are still poorly understood. Here, we use Rhodopseudomonas palustris TIE-1 to identify factors that induce biosynthesis of 2-methyl hopanoids (2-MeBHPs), progenitors of 2-methyl hopanes, one of the most abundant biomarkers in the rock record. This is the first dissection of the regulation of hpnP, the gene encoding the C-2 hopanoid methylase, at the molecular level. We demonstrate that EcfG, the general stress response factor of alphaproteobacteria, regulates expression of hpnP under a variety of challenges, including high temperature, pH stress, and presence of nonionic osmolytes. Although higher hpnP transcription levels did not always result in higher amounts of total methylated hopanoids, the fraction of a particular kind of hopanoid, 2-methyl bacteriohopanetetrol, was consistently higher in the presence of most stressors in the wild type, but not in the \u0394ecfG mutant, supporting a beneficial role for 2-MeBHPs in stress tolerance. The \u0394hpnP mutant, however, did not exhibit a growth defect under the stress conditions tested except in acidic medium. This indicates that the inability to make 2-MeBHPs under most of these conditions can readily be compensated. Although stress is necessary to regulate 2-MeBHP production, the specific conditions under which 2-MeBHP biosynthesis is essential remain to be determined.", "doi": "10.1128/JB.00186-13", "pmcid": "PMC3676068", "issn": "0021-9193", "publisher": "American Society for Microbiology", "publication": "Journal of Bacteriology", "publication_date": "2013-06", "series_number": "11", "volume": "195", "issue": "11", "pages": "2490-2498" }, { "id": "authors:vjgq9-gdr22", "collection": "authors", "collection_id": "vjgq9-gdr22", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130709-082907927", "type": "article", "title": "Iron and Copper Act Synergistically To Delay Anaerobic Growth of Bacteria", "author": [ { "family_name": "Bird", "given_name": "Lina J.", "orcid": "0000-0003-4127-4756", "clpid": "Bird-L-J" }, { "family_name": "Coleman", "given_name": "Maureen L.", "clpid": "Coleman-M-L" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Transition metals are known to cause toxic effects through their interaction with oxygen, but toxicity under anoxic conditions is poorly understood. Here we investigated the effects of iron (Fe) and copper (Cu) on the anaerobic growth and gene expression of the purple phototrophic bacterium Rhodopseudomonas palustris TIE-1. We found that Fe(II) and Cu(II) act synergistically to delay anaerobic growth at environmentally relevant metal concentrations. Cu(I) and Cu(II) had similar effects both alone and in the presence of ascorbate, a Cu(II) reductant, indicating that reduction of Cu(II) to Cu(I) by Fe(II) is not sufficient to explain the growth inhibition. Addition of Cu(II) increased the toxicity of Co(II) and Ni(II); in contrast, Ni(II) toxicity was diminished in the presence of Fe(II). The synergistic anaerobic toxicity of Fe(II) and Cu(II) was also observed for Escherichia coli MG1655, Shewanella oneidensis MR-1, and Rhodobacter capsulatus SB1003. Gene expression analyses for R. palustris identified three regulatory genes that respond to Cu(II) and not to Fe(II): homologs of cueR and cusR, two known proteobacterial copper homeostasis regulators, and csoR, a copper regulator recently identified in Mycobacterium tuberculosis. Two P-type ATPase efflux pumps, along with an F_oF_1 ATP synthase, were also upregulated by Cu(II) but not by Fe(II). An Escherichia coli mutant deficient in copA, cus, and cueO showed a smaller synergistic effect, indicating that iron might interfere with one or more of the copper homeostasis systems. Our results suggest that interactive effects of transition metals on microbial physiology may be widespread under anoxic conditions, although the molecular mechanisms remain to be more fully elucidated.", "doi": "10.1128/AEM.03944-12", "pmcid": "PMC3675935", "issn": "0099-2240", "publisher": "American Society for Microbiology", "publication": "Applied and Environmental Microbiology", "publication_date": "2013-06", "series_number": "12", "volume": "79", "issue": "12", "pages": "3619-3627" }, { "id": "authors:643s4-m3k76", "collection": "authors", "collection_id": "643s4-m3k76", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130506-103435647", "type": "article", "title": "Bacterial Community Morphogenesis Is Intimately Linked to the Intracellular Redox State", "author": [ { "family_name": "Dietrich", "given_name": "Lars E. P.", "clpid": "Dietrich-L-E-P" }, { "family_name": "Okegbe", "given_name": "Chinweike", "clpid": "Okegbe-C" }, { "family_name": "Price-Whelan", "given_name": "Alexa", "orcid": "0000-0003-0872-7098", "clpid": "Price-Whelan-A" }, { "family_name": "Sakhtah", "given_name": "Hassan", "clpid": "Sakhtah-H" }, { "family_name": "Hunter", "given_name": "Ryan C.", "orcid": "0000-0003-3841-1676", "clpid": "Hunter-Ryan-C" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Many microbial species form multicellular structures comprising elaborate wrinkles and concentric rings, yet the rules governing their architecture are poorly understood. The opportunistic pathogen Pseudomonas aeruginosa produces phenazines, small molecules that act as alternate electron acceptors to oxygen and nitrate to oxidize the intracellular redox state and that influence biofilm morphogenesis. Here, we show that the depth occupied by cells within colony biofilms correlates well with electron acceptor availability. Perturbations in the environmental provision, endogenous production, and utilization of electron acceptors affect colony development in a manner consistent with redox control. Intracellular NADH levels peak before the induction of colony wrinkling. These results suggest that redox imbalance is a major factor driving the morphogenesis of P. aeruginosa biofilms and that wrinkling itself is an adaptation that maximizes oxygen accessibility and thereby supports metabolic homeostasis. This type of redox-driven morphological change is reminiscent of developmental processes that occur in metazoans.", "doi": "10.1128/JB.02273-12", "pmcid": "PMC3624522", "issn": "0021-9193", "publisher": "American Society for Microbiology", "publication": "Journal of Bacteriology", "publication_date": "2013-04", "series_number": "7", "volume": "195", "issue": "7", "pages": "1371-1380" }, { "id": "authors:ntptt-gr985", "collection": "authors", "collection_id": "ntptt-gr985", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130429-093249361", "type": "article", "title": "Ligand-Enhanced Abiotic Iron Oxidation and the Effects of Chemical versus Biological Iron Cycling in Anoxic Environments", "author": [ { "family_name": "Kopf", "given_name": "Sebastian H.", "orcid": "0000-0002-2044-0201", "clpid": "Kopf-S-H" }, { "family_name": "Henny", "given_name": "Cynthia", "clpid": "Henny-C" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "This study introduces a newly isolated, genetically tractable bacterium (Pseudogulbenkiania sp. strain MAI-1) and explores the extent to which its nitrate-dependent iron-oxidation activity is directly biologically catalyzed. Specifically, we focused on the role of iron chelating ligands in promoting chemical oxidation of Fe(II) by nitrite under anoxic conditions. Strong organic ligands such as nitrilotriacetate and citrate can substantially enhance chemical oxidation of Fe(II) by nitrite at circumneutral pH. We show that strain MAI-1 exhibits unambiguous biological Fe(II) oxidation despite a significant contribution (~30\u201335%) from ligand-enhanced chemical oxidation. Our work with the model denitrifying strain Paracoccus denitrificans further shows that ligand-enhanced chemical oxidation of Fe(II) by microbially produced nitrite can be an important general side effect of biological denitrification. Our assessment of reaction rates derived from literature reports of anaerobic Fe(II) oxidation, both chemical and biological, highlights the potential competition and likely co-occurrence of chemical Fe(II) oxidation (mediated by microbial production of nitrite) and truly biological Fe(II) oxidation.", "doi": "10.1021/es3049459", "pmcid": "PMC3604861", "issn": "0013-936X", "publisher": "American Chemical Society", "publication": "Environmental Science and Technology", "publication_date": "2013-03-19", "series_number": "6", "volume": "47", "issue": "6", "pages": "2602-2611" }, { "id": "authors:zfsjt-6m593", "collection": "authors", "collection_id": "zfsjt-6m593", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130503-154036933", "type": "article", "title": "Identification and quantification of polyfunctionalized hopanoids by high temperature gas chromatography\u2013mass spectrometry", "author": [ { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Zhang", "given_name": "Lichun", "clpid": "Zhang-Lichun" }, { "family_name": "Welander", "given_name": "Paula V.", "clpid": "Welander-P-V" }, { "family_name": "Doughty", "given_name": "David", "clpid": "Doughty-D-M" }, { "family_name": "Summons", "given_name": "Roger E.", "orcid": "0000-0002-7144-8537", "clpid": "Summons-R-E" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Hopanoids are triterpenoids produced mainly by bacteria, are ubiquitous in the environment, and have many important applications as biological markers. A wide variety of related hopanoid structures exists, many of which are polyfunctionalized. These modifications render the hopanoids too involatile for conventional gas chromatography (GC) separation, so require either laborious oxidative cleavage of the functional groups or specialized high temperature (HT) columns. Here we describe the systematic evaluation and optimization of a HT\u2013GC method for the analysis of polyfunctionalized hopanoids and their methylated homologs. Total lipid extracts are derivatized with acetic anhydride and no further treatment or workup is required. We show that acid or base hydrolysis to remove di- and triacylglycerides leads to degradation of several BHP structures. DB-XLB type columns can elute hopanoids up to bacteriohopanetetrol at 350 \u00b0C, with baseline separation of all 2-methyl/desmethyl homologs. DB-5HT type columns can additionally elute bacteriohopaneaminotriol and bacteriohopaneaminotetrol, but do not fully separate 2-methyl/desmethyl homologs. The method gave 2- to 7-fold higher recovery of hopanoids than oxidative cleavage and can provide accurate quantification of all analytes including 2-methyl hopanoids. By comparing data from mass spectra with those from a flame ionization detector, we show that the mass spectromet (MS) response factors for different hopanoids using either total ion counts or m/z 191 vary substantially. Similarly, 2-methyl ratios estimated from selected-ion data are lower than those from FID by 10\u201330% for most hopanoids, but higher by ca. 10% for bacteriohopanetetrol. Mass spectra for a broad suite of hopanoids, including 2-methyl homologs, from Rhodopseudomonas palustris are presented, together with the tentative assignment of several new hopanoid degradation products.", "doi": "10.1016/j.orggeochem.2012.12.009", "pmcid": "PMC3780965", "issn": "0146-6380", "publisher": "Elsevier", "publication": "Organic Geochemistry", "publication_date": "2013-03", "volume": "56", "pages": "120-130" }, { "id": "authors:a6ycd-hy686", "collection": "authors", "collection_id": "a6ycd-hy686", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20121018-154043571", "type": "article", "title": "Crystallization and preliminary crystallographic studies of FoxE from Rhodobacter ferrooxidans SW2, an FeII oxidoreductase involved in photoferrotrophy", "author": [ { "family_name": "Pereira", "given_name": "L.", "clpid": "Pereira-L" }, { "family_name": "Saraiva", "given_name": "I. H.", "clpid": "Saraiva-I-H" }, { "family_name": "Coelho", "given_name": "R.", "clpid": "Coelho-R" }, { "family_name": "Newman", "given_name": "D. K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Louro", "given_name": "R. O.", "clpid": "Louro-R-O" }, { "family_name": "Fraz\u00e3o", "given_name": "C.", "clpid": "Fraz\u00e3o-C" } ], "abstract": "FoxE is a protein encoded by the foxEYZ operon of Rhodobacter ferrooxidans SW2 that is involved in Fe^II-based anoxygenic photosynthesis (`photoferrotrophy'). It is thought to reside in the periplasm, where it stimulates light-dependent Fe^II oxidation. It contains 259 residues, including two haem c-binding motifs. As no three-dimensional model is available and there is no structure with a similar sequence, crystals of FoxE were produced. They diffracted to 2.44 \u00c5 resolution using synchrotron radiation at the Fe edge. The phase problem was solved by SAD using SHELXC/D/E and the experimental maps confirmed the presence of two haems per molecule.", "doi": "10.1107/S174430911203271X", "pmcid": "PMC3433209", "issn": "1744-3091", "publisher": "International Union of Crystallography", "publication": "Acta Crystallographica. Section F, Structural Biology and Crystallization Communications", "publication_date": "2012-09", "series_number": "9", "volume": "68", "issue": "9", "pages": "1106-1108" }, { "id": "authors:k5x4g-nv634", "collection": "authors", "collection_id": "k5x4g-nv634", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120827-113105549", "type": "article", "title": "Functional Characterization of the FoxE Iron Oxidoreductase from the Photoferrotroph Rhodobacter ferrooxidans SW2", "author": [ { "family_name": "Saraiva", "given_name": "Ivo H.", "clpid": "Saraiva-I-H" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Louro", "given_name": "Ricardo O.", "clpid": "Louro-R-O" } ], "abstract": "Photoferrotrophy is presumed to be an ancient type of photosynthetic metabolism in which bacteria use the reducing power of ferrous iron to drive carbon fixation. In this work the putative iron oxidoreductase of the photoferrotroph Rhodobacter ferrooxidans SW2 was cloned, purified, and characterized for the first time. This protein, FoxE, was characterized using spectroscopic,\nthermodynamic, and kinetic techniques. It is a c-type\ncytochrome that forms a trimer or tetramer in solution; the two hemes of each monomer are hexacoordinated by histidine and methionine. The hemes have positive reduction potentials that allow downhill electron transfer from many geochemically relevant ferrous iron forms to the photosynthetic reaction center. The reduction potentials of the hemes are different and are cross-assigned to fast and slow kinetic phases of ferrous iron oxidation in vitro. Lower reactivity was observed at high pH and may contribute to prevent ferric iron precipitation inside or at the surface of the cell. These results help fill in the molecular details of a metabolic process that likely contributed to the deposition of precambrian banded iron formations, globally important sedimentary rocks that are found on every continent today.", "doi": "10.1074/jbc.M112.360636", "pmcid": "PMC3408196", "issn": "0021-9258", "publisher": "American Society for Biochemistry and Molecular Biology", "publication": "Journal of Biological Chemistry", "publication_date": "2012-07-20", "series_number": "30", "volume": "287", "issue": "30", "pages": "25541-25548" }, { "id": "authors:ac6p0-vgs73", "collection": "authors", "collection_id": "ac6p0-vgs73", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120507-075239308", "type": "article", "title": "Photomixotrophic growth of Rhodobacter capsulatus SB1003 on ferrous iron", "author": [ { "family_name": "Kopf", "given_name": "S. H.", "orcid": "0000-0002-2044-0201", "clpid": "Kopf-S-H" }, { "family_name": "Newman", "given_name": "D. K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "This study investigates the role iron oxidation plays in the purple non-sulfur bacterium Rhodobacter capsulatus SB1003. This organism is unable to grow photoautotrophically on unchelated ferrous iron [Fe(II)] despite its ability to oxidize chelated Fe(II). This apparent paradox was partly resolved by the discovery that SB1003 can grow photoheterotrophically on the photochemical breakdown products of certain ferric iron\u2013ligand complexes, yet whether it could concomitantly benefit from the oxidation of Fe(II) to fix CO_2 was unknown. Here, we examine carbon fixation by stable isotope labeling of the inorganic carbon pool in cultures growing phototrophically on acetate with and without Fe(II). We show that R. capsulatus SB1003, an organism formally thought incapable of phototrophic growth on Fe(II), can actually harness the reducing power of this substrate and grow photomixotrophically, deriving carbon both from organic sources and from fixation of inorganic carbon. This suggests the possibility of a wider occurrence of photoferrotrophy than previously assumed.", "doi": "10.1111/j.1472-4669.2011.00313.x", "pmcid": "PMC4587904", "issn": "1472-4677", "publisher": "Blackwell Publishing", "publication": "Geobiology", "publication_date": "2012-05", "series_number": "3", "volume": "10", "issue": "3", "pages": "216-222" }, { "id": "authors:nv60r-x8h44", "collection": "authors", "collection_id": "nv60r-x8h44", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120302-134849665", "type": "article", "title": "Identification and characterization of Rhodopseudomonas palustris TIE-1 hopanoid biosynthesis mutants", "author": [ { "family_name": "Welander", "given_name": "P. V.", "clpid": "Welander-P-V" }, { "family_name": "Doughty", "given_name": "D. M.", "clpid": "Doughty-D-M" }, { "family_name": "Wu", "given_name": "C.-H.", "clpid": "Wu-Chia-Hung" }, { "family_name": "Mehay", "given_name": "S.", "clpid": "Mehay-S" }, { "family_name": "Summons", "given_name": "R. E.", "orcid": "0000-0002-7144-8537", "clpid": "Summons-R-E" }, { "family_name": "Newman", "given_name": "D. K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Hopanes preserved in both modern and ancient sediments are recognized as the molecular fossils of bacteriohopanepolyols, pentacyclic hopanoid lipids. Based on the phylogenetic distribution of hopanoid production by extant bacteria, hopanes have been used as indicators of specific bacterial groups and/or their metabolisms. However, our ability to interpret them ultimately depends on understanding the physiological roles of hopanoids in modern bacteria. Toward this end, we set out to identify genes required for hopanoid biosynthesis in the anoxygenic phototroph Rhodopseudomonas palustris TIE-1 to enable selective control of hopanoid production. We attempted to delete 17 genes within a putative hopanoid biosynthetic gene cluster to determine their role, if any, in hopanoid biosynthesis. Two genes, hpnH and hpnG, are required to produce both bacteriohopanetetrol and aminobacteriohopanetriol, whereas a third gene, hpnO, is required only for aminobacteriohopanetriol production. None of the genes in this cluster are required to exclusively synthesize bacteriohopanetetrol, indicating that at least one other hopanoid biosynthesis gene is located elsewhere on the chromosome. Physiological studies with the different deletion mutants demonstrated that unmethylated and C_30 hopanoids are sufficient to maintain cytoplasmic but not outer membrane integrity. These results imply that hopanoid modifications, including methylation of the A-ring and the addition of a polar head group, may have biologic functions beyond playing a role in membrane permeability.", "doi": "10.1111/j.1472-4669.2011.00314.x", "pmcid": "PMC3553210", "issn": "1472-4677", "publisher": "Blackwell Publishing", "publication": "Geobiology", "publication_date": "2012-03", "series_number": "2", "volume": "10", "issue": "2", "pages": "163-177" }, { "id": "authors:ftpg0-0v412", "collection": "authors", "collection_id": "ftpg0-0v412", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120323-082322420", "type": "article", "title": "BqsR/BqsS Constitute a Two-Component System That Senses Extracellular Fe(II) in Pseudomonas aeruginosa", "author": [ { "family_name": "Kreamer", "given_name": "Naomi N. K.", "clpid": "Kreamer-N-N-K" }, { "family_name": "Wilks", "given_name": "Jessica C.", "clpid": "Wilks-J-C" }, { "family_name": "Marlow", "given_name": "Jeffrey J.", "clpid": "Marlow-J-J" }, { "family_name": "Coleman", "given_name": "Maureen L.", "clpid": "Coleman-M-L" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Pseudomonas aeruginosa is a ubiquitous Gram-negative bacterium best known as the predominant opportunistic pathogen infecting the lungs of cystic fibrosis patients. In this context, it is thought to form biofilms, within which locally reducing and acidic conditions can develop that favor the stability of ferrous iron [Fe(II)]. Because iron is a signal that stimulates biofilm formation, we performed a microarray study to determine whether P. aeruginosa strain PA14 exhibits a specific transcriptional response to extracellular Fe(II). Among the genes that were most upregulated in response to Fe(II) were those encoding the two-component system BqsR/BqsS, previously identified for its role in P. aeruginosa strain PAO1 biofilm decay (13); here, we demonstrate its role in extracellular Fe(II) sensing. bqsS and bqsR form an operon together with two small upstream genes, bqsP and bqsQ, and one downstream gene, bqsT. BqsR/BqsS sense extracellular Fe(II) at physiologically relevant concentrations (>10 \u03bcM) and elicit a specific transcriptional response, including its autoregulation. The sensor distinguishes between Fe(II), Fe(III), and other dipositive cations [Ca(II), Cu(II), Mg(II), Mn(II), Zn(II)] under aerobic or anaerobic conditions. The gene that is most upregulated by BqsR/BqsS, as measured by quantitative reverse transcription-PCR (qRT-PCR), is PA14_04180, which is predicted to encode a periplasmic oligonucleotide/oligosaccharide-binding domain (OB-fold) protein. Coincident with phenazine production during batch culture growth, Fe(II) becomes the majority of the total iron pool and bqsS is upregulated. The existence of a two-component system that senses Fe(II) indicates that extracellular Fe(II) is an important environmental signal for P. aeruginosa.", "doi": "10.1128/JB.05634-11", "pmcid": "PMC3294787", "issn": "0021-9193", "publisher": "American Society for Microbiology", "publication": "Journal of Bacteriology", "publication_date": "2012-03", "series_number": "5", "volume": "194", "issue": "5", "pages": "1195-1204" }, { "id": "authors:n7g2e-cr643", "collection": "authors", "collection_id": "n7g2e-cr643", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20121106-134254144", "type": "book_section", "title": "Molecular biology's contributions to geobiology", "book_title": "Fundamentals of Geobiology", "author": [ { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Reysenbach", "given_name": "Anna-Louise", "clpid": "Reysenbach-A-L" } ], "contributor": [ { "family_name": "Knoll", "given_name": "Andrew H.", "clpid": "Knoll-A-H" }, { "family_name": "Canfield", "given_name": "Donald E.", "clpid": "Canfield-D-E" }, { "family_name": "Konhauser", "given_name": "Kurt O.", "clpid": "Konhauser-K-O" } ], "abstract": "On August 7, 1996, US President Bill Clinton held a press conference to announce the possibility that the Allan Hills 84001 meteorite might provide insight into ancient life on Mars. With soaring rhetoric, he declared: 'Today, rock 84001 speaks to us across all those billions of years and millions of miles. It speaks of the possibility of life. If this discovery is confirmed, it will surely be one of the most stunning insights into our universe that science has ever uncovered. Its implications are as far-reaching and awe-inspiring as can be imagined. Even as it promises answers to some of our oldest questions, it poses still others even more fundamental.' Shortly thereafter, NASA expanded its support for astro-and geobiological research, which marked the beginning of a renaissance in geobiology. Seemingly overnight, geobiology was transformed from a somewhat arcane discipline to a glamorous field that promised to reveal the secrets of life. While today, most geobiologists would agree that the evidence for past life in AH84001 is inconclusive at best, and find the hype surrounding its discovery to be comical, nonetheless, the excitement it engendered has had a long-lasting and positive impact on our science. The enduring consequence of Clinton's press conference was that it called attention to the fact that life has been leaving signatures in its environment (be it earthly or extraterrestrial) for billions of years. In the years following the meteorite's discovery, it has become clear that to understand life's traces and-more importantly---effects on its environment, it is necessary to understand how life leaves its imprint and whether this can be distinguished from similar imprints left by abiotic processes. This is a central challenge in geobiology.", "isbn": "9781118280812", "publisher": "Wiley-Blackwell", "place_of_publication": "Hoboken, NJ", "publication_date": "2012", "pages": "228-249" }, { "id": "authors:vkdjt-py709", "collection": "authors", "collection_id": "vkdjt-py709", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130410-131113193", "type": "book_section", "title": "In Pursuit of Billion-Year-Old Rosetta Stones", "book_title": "Microbes and Evolution: The World That Darwin Never Saw", "author": [ { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "contributor": [ { "family_name": "Kolter", "given_name": "Roberto", "clpid": "Kolter-R" }, { "family_name": "Maloy", "given_name": "Stanley R.", "clpid": "Maloy-S-R" } ], "abstract": "If I have learned anything about evolution, it is that the path life takes moves in mysterious ways. If someone had told me 20 years ago that I would wind up a professor of geobiology, I would have laughed. It certainly wasn't something I aspired to in college, where, as a German studies major, I didn't take a single biology class and took only one geology class. I didn't even know that\ngeobiology existed as a discipline at the time!", "doi": "10.1128/9781555818470.ch29", "isbn": "978-1-55581-540-0", "publisher": "ASM Press", "place_of_publication": "Washington, DC", "publication_date": "2012", "pages": "209-215" }, { "id": "authors:prr8s-y3373", "collection": "authors", "collection_id": "prr8s-y3373", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111128-101611198", "type": "article", "title": "The RND-family transporter, HpnN, is required for hopanoid localization to the outer membrane of Rhodopseudomonas palustris TIE-1", "author": [ { "family_name": "Doughty", "given_name": "David M.", "clpid": "Doughty-D-M" }, { "family_name": "Coleman", "given_name": "Maureen L.", "clpid": "Coleman-M-L" }, { "family_name": "Hunter", "given_name": "Ryan C.", "orcid": "0000-0003-3841-1676", "clpid": "Hunter-Ryan-C" }, { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Summons", "given_name": "Roger E.", "orcid": "0000-0002-7144-8537", "clpid": "Summons-R-E" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Rhodopseudomonas palustris TIE-1 is a Gram-negative bacterium that produces structurally diverse hopanoid lipids that are similar to eukaryotic steroids. Its genome encodes several homologues to proteins involved in eukaryotic steroid trafficking. In this study, we explored the possibility that two of these proteins are involved\nin intracellular hopanoid transport. R. palustris has a sophisticated membrane system comprising outer, cytoplasmic, and inner cytoplasmic membranes. It also divides asymmetrically, producing a mother and swarmer cell. We deleted genes encoding two putative hopanoid transporters that belong to the resistance\u2013nodulation\u2013\ncell division superfamily. Phenotypic analyses revealed that\none of these putative transporters (HpnN) is essential for the movement of hopanoids from the cytoplasmic to the outer membrane, whereas the other (Rpal_4267) plays a minor role. C30 hopanoids, such as diploptene, are evenly distributed between mother and swarmer cells, whereas hpnN is required for the C35 hopanoid, bacteriohopanetetrol, to remain localized to the mother cell type. Mutant cells lacking HpnN grow like the WT at 30 \u00b0C but slower at 38 \u00b0C. Following cell division at 38 \u00b0C, the \u0394hpnN cells remain\nconnected by their cell wall, forming long filaments. This phenotype may be attributed to hopanoid mislocalization because a double mutant deficient in both hopanoid biosynthesis and transport does not form filaments. However, the lack of hopanoids severely compromises cell growth at higher temperatures more generally. Because hopanoid mutants only manifest a strong phenotype under\ncertain conditions, R. palustris is an attractive model organism in which to study their transport and function.", "doi": "10.1073/pnas.1104209108", "pmcid": "PMC3215060", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2011-11-08", "series_number": "45", "volume": "108", "issue": "45", "pages": "E1045-E1051" }, { "id": "authors:zbg4g-9gw73", "collection": "authors", "collection_id": "zbg4g-9gw73", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111005-113650941", "type": "article", "title": "Quantifying the Dynamics of Bacterial Secondary Metabolites by Spectral Multiphoton Microscopy", "author": [ { "family_name": "Sullivan", "given_name": "Nora L.", "clpid": "Sullivan-N-L" }, { "family_name": "Tzeranis", "given_name": "Dimitrios S.", "clpid": "Tzeranis-D-S" }, { "family_name": "Wang", "given_name": "Yun", "clpid": "Wang-Yun" }, { "family_name": "So", "given_name": "Peter T. C.", "clpid": "So-Peter-T-C" }, { "family_name": "Newman", "given_name": "Dianne", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Phenazines, a group of fluorescent small molecules produced by the bacterium Pseudomonas aeruginosa, play a role in maintaining cellular redox homeostasis. Phenazines have been challenging to study in vivo due to their redox activity, presence both intra- and extracellularly, and their diverse chemical properties. Here, we describe a noninvasive in vivo optical technique to monitor phenazine concentrations within bacterial cells using time-lapsed spectral multiphoton fluorescence microscopy. This technique enables simultaneous monitoring of multiple weakly fluorescent molecules (phenazines, siderophores, NAD(P)H) expressed by bacteria in culture. This work provides the first in vivo measurements of reduced phenazine concentration as well as the first description of the temporal dynamics of the phenazine-NAD(P)H redox system in Pseudomonas aeruginosa, illuminating an unanticipated role for 1-hydroxyphenazine. Similar approaches could be used to study the abundance and redox dynamics of a wide range of small molecules within bacteria, both as single cells and in communities.", "doi": "10.1021/cb200094w", "pmcid": "PMC3212935", "issn": "1554-8929", "publisher": "American Chemical Society", "publication": "ACS Chemical Biology", "publication_date": "2011-09", "series_number": "9", "volume": "6", "issue": "9", "pages": "893-899" }, { "id": "authors:38d0z-mxv96", "collection": "authors", "collection_id": "38d0z-mxv96", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130403-162415003", "type": "article", "title": "Microaerobic steroid biosynthesis and the molecular fossil record of Archean life", "author": [ { "family_name": "Waldbauer", "given_name": "Jacob R.", "clpid": "Waldbauer-J-R" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Summons", "given_name": "Roger E.", "orcid": "0000-0002-7144-8537", "clpid": "Summons-R-E" } ], "abstract": "The power of molecular oxygen to drive many crucial biogeochemical processes, from cellular respiration to rock weathering, makes reconstructing the history of its production and accumulation a first-order question for understanding Earth's evolution. Among the various geochemical proxies for the presence of O_2 in the environment, molecular fossils offer a unique record of O_2 where it was first produced and consumed by biology: in sunlit aquatic habitats. As steroid biosynthesis requires molecular oxygen, fossil steranes have been used to draw inferences about aerobiosis in the early Precambrian. However, better quantitative constraints on the O_2 requirement of this biochemistry would clarify the implications of these molecular fossils for environmental conditions at the time of their production. Here we demonstrate that steroid biosynthesis is a microaerobic process, enabled by dissolved O_2 concentrations in the nanomolar range. We present evidence that microaerobic marine environments (where steroid biosynthesis was possible) could have been widespread and persistent for long periods of time prior to the earliest geologic and isotopic evidence for atmospheric O_2. In the late Archean, molecular oxygen likely cycled as a biogenic trace gas, much as compounds such as dimethylsulfide do today.", "doi": "10.1073/pnas.1104160108", "pmcid": "PMC3158215", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2011-08-16", "series_number": "33", "volume": "108", "issue": "33", "pages": "13409-13414" }, { "id": "authors:rfys4-n9r57", "collection": "authors", "collection_id": "rfys4-n9r57", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110822-094630738", "type": "article", "title": "Caenorhabditis elegans NPR-1\u2013mediated behaviors are suppressed in the presence of mucoid bacteria", "author": [ { "family_name": "Reddy", "given_name": "Kirthi C.", "clpid": "Reddy-K-C" }, { "family_name": "Hunter", "given_name": "Ryan C.", "orcid": "0000-0003-3841-1676", "clpid": "Hunter-Ryan-C" }, { "family_name": "Bhatla", "given_name": "Nikhil", "clpid": "Bhatla-N" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Kim", "given_name": "Dennis H.", "clpid": "Kim-Dennis-H" } ], "abstract": "Caenorhabditis elegans exhibits a diverse range of behaviors in response to bacteria. The presence of bacterial food influences C. elegans aerotaxis, aggregation, locomotion, and pathogen avoidance behaviors through the activity of the NPR-1 neuropeptide receptor. Here, we show that mucoid strains of bacteria that produce an exopolysaccharide matrix do not induce NPR-1\u2013dependent behaviors. In the presence of mucoid strains of bacteria, the C. elegans laboratory wild-type (WT) strain N2 exhibits behaviors characteristic of wild isolates and mutants with reduced NPR-1 activity. Specifically, N2 exhibits lawn bordering and roaming behavior on mucoid nonpathogenic bacteria and loss of pathogen avoidance on mucoid Pseudomonas aeruginosa. Alginate biosynthesis by laboratory and clinical isolates of mucoid P. aeruginosa is necessary and sufficient to attenuate NPR-1\u2013mediated behavior and it suppresses C. elegans pathogen avoidance behavior. Our data suggest that the specific interaction with nonmucoid bacteria induces NPR-1\u2013dependent behaviors of C. elegans. These observations provide an example of how exopolysaccharide matrix biosynthesis by a community of bacteria may inhibit specific host responses to microbes.", "doi": "10.1073/pnas.1108265108", "pmcid": "PMC3150904", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2011-08-02", "series_number": "31", "volume": "108", "issue": "31", "pages": "12887-12892" }, { "id": "authors:rvqn7-97n42", "collection": "authors", "collection_id": "rvqn7-97n42", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130403-141504385", "type": "article", "title": "Phenazine-1-Carboxylic Acid Promotes Bacterial Biofilm Development via Ferrous Iron Acquisition", "author": [ { "family_name": "Wang", "given_name": "Yun", "clpid": "Wang-Yun" }, { "family_name": "Wilks", "given_name": "Jessica C.", "clpid": "Wilks-J-C" }, { "family_name": "Danhorn", "given_name": "Thomas", "clpid": "Danhorn-T" }, { "family_name": "Ramos", "given_name": "Itzel", "clpid": "Ramos-I" }, { "family_name": "Croal", "given_name": "Laura R.", "clpid": "Croal-L-R" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "The opportunistic pathogen Pseudomonas aeruginosa forms biofilms, which render it more resistant to antimicrobial agents. Levels of iron in excess of what is required for planktonic growth have been shown to promote biofilm formation, and therapies that interfere with ferric iron [Fe(III)] uptake combined with antibiotics may help treat P. aeruginosa infections. However, use of these therapies presumes that iron is in the Fe(III) state in the context of infection. Here we report the ability of phenazine-1-carboxylic acid (PCA), a common phenazine made by all phenazine-producing pseudomonads, to help P. aeruginosa alleviate Fe(III) limitation by reducing Fe(III) to ferrous iron [Fe(II)]. In the presence of PCA, a P. aeruginosa mutant lacking the ability to produce the siderophores pyoverdine and pyochelin can still develop into a biofilm. As has been previously reported (P. K. Singh, M. R. Parsek, E. P. Greenberg, and M. J. Welsh, Nature 417:552-555, 2002), biofilm formation by the wild type is blocked by subinhibitory concentrations of the Fe(III)-binding innate-immunity protein conalbumin, but here we show that this blockage can be rescued by PCA. FeoB, an Fe(II) uptake protein, is required for PCA to enable this rescue. Unlike PCA, the phenazine pyocyanin (PYO) can facilitate biofilm formation via an iron-independent pathway. While siderophore-mediated Fe(III) uptake is undoubtedly important at early stages of infection, these results suggest that at later stages of infection, PCA present in infected tissues may shift the redox equilibrium between Fe(III) and Fe(II), thereby making iron more bioavailable.", "doi": "10.1128/JB.00396-11", "pmcid": "PMC3133341", "issn": "0021-9193", "publisher": "American Society for Microbiology", "publication": "Journal of Bacteriology", "publication_date": "2011-07", "series_number": "14", "volume": "193", "issue": "14", "pages": "3606-3617" }, { "id": "authors:45pdt-xsr75", "collection": "authors", "collection_id": "45pdt-xsr75", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110805-100811696", "type": "article", "title": "Bioenergetic challenges of microbial iron metabolisms", "author": [ { "family_name": "Bird", "given_name": "Lina J.", "orcid": "0000-0003-4127-4756", "clpid": "Bird-L-J" }, { "family_name": "Bonnefoy", "given_name": "Violaine", "clpid": "Bonnefoy-V" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Before cyanobacteria invented oxygenic photosynthesis and O_2 and H_2O began to cycle between respiration and photosynthesis, redox cycles between other elements were used to sustain microbial metabolism on a global scale. Today these cycles continue to occur in more specialized niches. In this review we focus on the bioenergetic aspects of one of these cycles \u2013 the iron cycle \u2013 because iron presents unique and fascinating challenges for cells that use it for energy. Although iron is an important nutrient for nearly all life forms, we restrict our discussion to energy-yielding pathways that use ferrous iron [Fe(II)] as an electron donor or ferric iron [Fe(III)] as an electron acceptor. We briefly review general concepts in bioenergetics, focusing on what is known about the mechanisms of electron transfer in Fe(II)-oxidizing and Fe(III)-reducing bacteria, and highlight aspects of their bioenergetic pathways that are poorly understood.", "doi": "10.1016/j.tim.2011.05.001", "issn": "0966-842X", "publisher": "Elsevier", "publication": "Trends in Microbiology", "publication_date": "2011-07", "series_number": "7", "volume": "19", "issue": "7", "pages": "330-340" }, { "id": "authors:db2va-gec91", "collection": "authors", "collection_id": "db2va-gec91", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110307-110335931", "type": "article", "title": "Where reductionism meets complexity: a call for growth in the study of non-growth", "author": [ { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Coleman", "given_name": "Maureen L.", "clpid": "Coleman-M-L" } ], "abstract": "With the advent of metagenomics, we have unprecedented\naccess to the genetic blueprint of the microbial\nworld. Yet as metagenomic databases keep growing, our\nability to interpret the information contained within\nthem has not kept up. This conundrum arises from the\nfact that we cannot assign functions to the vast majority\nof their genes. As Jo Handelsman pointed out in a\nCrystal Ball piece two years ago, 'the glory of the last 50\nyears of microbiology is founded, in large part, on\ngenetic analysis' (Handelsman, 2009). Amen. Yet as\nenticing as the prospect of environmental genetics or\n'metagenetics' seems, how can we hope to interpret the\nunchartered world of environmental metagenomes when\nafter more than a half-century of rigorous genetic and\nbiochemical analyses, the functions of roughly a quarter\nof the genes in Escherichia coli \u2013 arguably the most\nwell-studied organism on the planet \u2013 are still unknown\n(Karp et al., 2007)? Where have we gone wrong?\nPerhaps it is time to re-examine our assumptions about\nhow to assign gene functions in light of lessons from the\nfield.", "doi": "10.1111/j.1758-2229.2010.00236.x", "issn": "1758-2229", "publisher": "Wiley-Blackwell", "publication": "Environmental Microbiology Reports", "publication_date": "2011-02", "series_number": "1", "volume": "3", "issue": "1", "pages": "14-15" }, { "id": "authors:8bgh7-gpr97", "collection": "authors", "collection_id": "8bgh7-gpr97", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110308-123056256", "type": "article", "title": "Regulation of the phototrophic iron oxidation (pio) genes in Rhodopseudomonas palustris TIE-1 is mediated by the global regulator, FixK", "author": [ { "family_name": "Bose", "given_name": "Arpita", "clpid": "Bose-A" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "The pioABC operon is required for phototrophic iron oxidative (photoferrotrophic) growth by the \u03b1-proteobacterium Rhodopseudomonas palustris TIE-1. Expression analysis of this operon showed that it was transcribed and translated during anaerobic growth, upregulation being observed only under photoferrotrophic conditions. Very low levels of transcription were observed during aerobic growth, suggesting expression was induced by anoxia. The presence of two canonical FixK boxes upstream of\nthe identified pioABC transcription start site implicated\nFixK as a likely regulator. To test this possibility,\na \u0394fixK mutant of R. palustris TIE-1 was assessed for pioABC expression. pioABC expression decreased dramatically in \u0394fixK versus WT during photoferrotrophic growth, implying that FixK positively regulates its expression; coincidently, the onset of iron oxidation was prolonged in this mutant. In contrast, pioABC expression increased in \u0394fixK under all non-photoferrotrophic conditions tested, suggesting the presence of additional levels of regulation.\nPurified FixK directly bound only the proximal FixK\nbox in gel mobility-shift assays. Mutant expression\nanalysis revealed that FixK regulates anaerobic phototrophic\nexpression of other target genes with FixK binding sites in their promoters. This study shows that FixK regulates key iron metabolism genes in an \u03b1-proteobacterium, pointing to a departure from the canonical Fur/Irr mode of regulation.", "doi": "10.1111/j.1365-2958.2010.07430.x", "issn": "0950-382X", "publisher": "Wiley-Blackwell", "publication": "Molecular Microbiology", "publication_date": "2011-01", "series_number": "1", "volume": "79", "issue": "1", "pages": "63-75" }, { "id": "authors:mnn0f-zaw48", "collection": "authors", "collection_id": "mnn0f-zaw48", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130403-084205757", "type": "book_section", "title": "From Geocycles to Genomes and Back", "book_title": "Microbial metal and metalloid metabolism: advances and applications", "author": [ { "family_name": "Bose", "given_name": "Arpita", "clpid": "Bose-A" }, { "family_name": "Kopf", "given_name": "Sebastian", "orcid": "0000-0002-2044-0201", "clpid": "Kopf-S-H" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "contributor": [ { "family_name": "Stolz", "given_name": "John F.", "clpid": "Stolz-J-F" }, { "family_name": "Oremland", "given_name": "Ronald S.", "clpid": "Oremland-R-S" } ], "abstract": "A holy grail for environmental microbiologists\nis being able to predict the effects of any given\nmicrobial community on a particular environment.\nIn an era of increasingly dramatic\nchanges in global climate, this goal is becoming\nevermore important. It is now well accepted\nthat microorganisms have had and continue\nto have a profound influence on shaping the\nchemistry of the Earth. It would thus be both\nintellectually satisfying and practically useful if\nwe could enumerate the microbial players in a\nspecific locale, and, knowing their metabolic\npotential and how they regulate their various\nmetabolisms, make predictions about how\ntheir presence would shape the geochemistry\nof that locale as it evolves in time.", "isbn": "9781613444030", "publisher": "ASM Press", "place_of_publication": "Washington, D.C.", "publication_date": "2011", "pages": "13-38" }, { "id": "authors:z4td4-dy242", "collection": "authors", "collection_id": "z4td4-dy242", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20101103-111826151", "type": "article", "title": "A Putative ABC Transporter, HatABCDE, Is among Molecular Determinants of Pyomelanin Production in Pseudomonas aeruginosa", "author": [ { "family_name": "Hunter", "given_name": "Ryan C.", "orcid": "0000-0003-3841-1676", "clpid": "Hunter-Ryan-C" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Pyomelanin overproduction is a common phenotype among Pseudomonas aeruginosa isolates recovered from cystic fibrosis and urinary tract infections. Its prevalence suggests that it contributes to the persistence of the producing microbial community, yet little is known about the mechanisms of its production. Using transposon mutagenesis, we identified factors that contribute to melanogenesis in a clinical isolate of P. aeruginosa. In addition to two enzymes already known to be involved in its biosynthesis (homogentisate dioxygenase and hydroxyphenylpyruvate dioxygenase), we identified 26 genes that encode regulatory, metabolic, transport, and hypothetical proteins that contribute to the production of homogentisic acid (HGA), the monomeric precursor of pyomelanin. One of these, PA14_57880, was independently identified four times and is predicted to encode the ATP-binding cassette of an ABC transporter homologous to proteins in Pseudomonas putida responsible for the extrusion of organic solvents from the cytosol. Quantification of HGA production by P. aeruginosa PA14 strains missing the predicted subcomponents of this transporter confirmed its role in HGA production: mutants unable to produce the ATP-binding cassette (PA14_57880) or the permease (PA14_57870) produced substantially less extracellular HGA after growth for 20 h than the parental strain. In these mutants, concurrent accumulation of intracellular HGA was observed. In addition, quantitative real-time PCR revealed that intracellular accumulation of HGA elicits upregulation of these transport genes. Based on their involvement in homogentisic acid transport, we rename the genes of this operon hatABCDE.", "doi": "10.1128/JB.01021-10", "pmcid": "PMC2976449", "issn": "0021-9193", "publisher": "American Society for Microbiology", "publication": "Journal of Bacteriology", "publication_date": "2010-11", "series_number": "22", "volume": "192", "issue": "22", "pages": "5962-5971" }, { "id": "authors:hrydq-cwf32", "collection": "authors", "collection_id": "hrydq-cwf32", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100528-114059025", "type": "article", "title": "Evidence for equilibrium iron isotope fractionation by nitrate-reducing iron(II)-oxidizing bacteria", "author": [ { "family_name": "Kappler", "given_name": "A.", "clpid": "Kappler-A" }, { "family_name": "Johnson", "given_name": "C. M.", "clpid": "Johnson-C-M" }, { "family_name": "Crosby", "given_name": "H. A.", "clpid": "Crosby-H-A" }, { "family_name": "Beard", "given_name": "B. L.", "clpid": "Beard-B-L" }, { "family_name": "Newman", "given_name": "D. K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Iron isotope fractionations produced during chemical and biological Fe(II) oxidation are sensitive to the proportions and nature of dissolved and solid-phase Fe species present, as well as the extent of isotopic exchange between precipitates and aqueous Fe. Iron isotopes therefore potentially constrain the mechanisms and pathways of Fe redox transformations in modern and ancient environments. In the present study, we followed in batch experiments Fe isotope fractionations between Fe(II)_(aq) and Fe(III) oxide/hydroxide precipitates produced by the Fe(III) mineral encrusting, nitrate-reducing, Fe(II)-oxidizing Acidovorax sp. strain BoFeN1. Isotopic fractionation in ^(56)Fe/^(54)Fe approached that expected for equilibrium conditions, assuming an equilibrium \u0394^(56)Fe_(Fe(OH)3\u2013Fe(II)aq) fractionation factor of +3.0\u2030. Previous studies have shown that Fe(II) oxidation by this Acidovorax strain occurs in the periplasm, and we propose that Fe isotope equilibrium is maintained through redox cycling via coupled electron and atom exchange between Fe(II)_(aq) and Fe(III) precipitates in the contained environment of the periplasm. In addition to the apparent equilibrium isotopic fractionation, these experiments also record the kinetic effects of initial rapid oxidation, and possible phase transformations of the Fe(III) precipitates. Attainment of Fe isotope equilibrium between Fe(III) oxide/hydroxide precipitates and Fe(II)_(aq) by neutrophilic, Fe(II)-oxidizing bacteria or through abiologic Fe(II)_(aq) oxidation is generally not expected or observed, because the poor solubility of their metabolic product, i.e. Fe(III), usually leads to rapid precipitation of Fe(III) minerals, and hence expression of a kinetic fractionation upon precipitation; in the absence of redox cycling between Fe(II)_(aq) and precipitate, kinetic isotope fractionations are likely to be retained. These results highlight the distinct Fe isotope fractionations that are produced by different pathways of biological and abiological Fe(II) oxidation.", "doi": "10.1016/j.gca.2010.02.017", "pmcid": "PMC2873596", "issn": "0016-7037", "publisher": "Elsevier", "publication": "Geochimica et Cosmochimica Acta", "publication_date": "2010-05-15", "series_number": "10", "volume": "74", "issue": "10", "pages": "2826-2842" }, { "id": "authors:n0ee3-8ax91", "collection": "authors", "collection_id": "n0ee3-8ax91", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100601-111422016", "type": "article", "title": "Identification of a methylase required for 2-methylhopanoid production and implications for the interpretation of sedimentary hopanes", "author": [ { "family_name": "Welander", "given_name": "Paula V.", "clpid": "Welander-P-V" }, { "family_name": "Coleman", "given_name": "Maureen L.", "clpid": "Coleman-M-L" }, { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Summons", "given_name": "Roger E.", "orcid": "0000-0002-7144-8537", "clpid": "Summons-R-E" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "The rise of atmospheric oxygen has driven environmental change and biological evolution throughout much of Earth's history and was enabled by the evolution of oxygenic photosynthesis in the cyanobacteria. Dating this metabolic innovation using inorganic proxies from sedimentary rocks has been difficult and one important approach has been to study the distributions of fossil lipids, such as steranes and 2-methylhopanes, as biomarkers for this process. 2-methylhopanes arise from degradation of 2-methylbacteriohopanepolyols (2-MeBHPs), lipids thought to be synthesized primarily by cyanobacteria. The discovery that 2-MeBHPs are produced by an anoxygenic phototroph, however, challenged both their taxonomic link with cyanobacteria and their functional link with oxygenic photosynthesis. Here, we identify a radical SAM methylase encoded by the hpnP gene that is required for methylation at the C-2 position in hopanoids. This gene is found in several, but not all, cyanobacteria and also in \u03b1 -proteobacteria and acidobacteria. Thus, one cannot extrapolate from the presence of 2-methylhopanes alone, in modern environments or ancient sedimentary rocks, to a particular taxonomic group or metabolism. To understand the origin of this gene, we reconstructed the evolutionary history of HpnP. HpnP proteins from cyanobacteria, Methylobacterium species, and other \u03b1-proteobacteria form distinct phylogenetic clusters, but the branching order of these clades could not be confidently resolved. Hence,it is unclear whether HpnP, and 2-methylhopanoids, originated first in the cyanobacteria. In summary, existing evidence does not support the use of 2-methylhopanes as biomarkers for oxygenic photosynthesis.", "doi": "10.1073/pnas.0912949107", "pmcid": "PMC2889317", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2010-05-11", "series_number": "19", "volume": "107", "issue": "19", "pages": "8537-8542" }, { "id": "authors:ye8kk-rh540", "collection": "authors", "collection_id": "ye8kk-rh540", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130312-080720662", "type": "article", "title": "Phenazines affect biofilm formation by Pseudomonas aeruginosa in similar ways at various scales", "author": [ { "family_name": "Ramos", "given_name": "Itzel", "clpid": "Ramos-I" }, { "family_name": "Dietrich", "given_name": "Lars E. P.", "clpid": "Dietrich-L-E-P" }, { "family_name": "Price-Whelan", "given_name": "Alexa", "orcid": "0000-0003-0872-7098", "clpid": "Price-Whelan-A" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Some pseudomonads produce phenazines, a group of small, redox-active compounds with diverse physiological functions. In this study, we compared the phenotypes of Pseudomonas aeruginosa strain PA14 and a mutant unable to synthesize phenazines in flow cell and colony biofilms quantitatively. Although phenazine production does not impact the ability of PA14 to attach to surfaces, as has been shown for Pseudomonas chlororaphis Maddula et al., 2006 and Maddula et al., 2008, it influences swarming motility and the surface-to-volume ratio of mature biofilms. These results indicate that phenazines affect biofilm development across a large range of scales, but in unique ways for different Pseudomonas species.", "doi": "10.1016/j.resmic.2010.01.003", "pmcid": "PMC2886020", "issn": "0923-2508", "publisher": "Elsevier", "publication": "Research in Microbiology", "publication_date": "2010-04", "series_number": "3", "volume": "161", "issue": "3", "pages": "187-191" }, { "id": "authors:a45eq-zwd93", "collection": "authors", "collection_id": "a45eq-zwd93", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130311-151426036", "type": "article", "title": "Feasting on Minerals", "author": [ { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Far up in the Chilean Andes, in remote arid regions seemingly inhospitable to life, intrepid microorganisms thrive on a diet of rocks and air. Unfazed by long periods of desiccation or high ultraviolet energy flux, they grow in baths of sulfuric acid replete with toxic metals. The microbes fix carbon dioxide into biomass by exploiting the energy to be gained by \"eating\" (oxidizing) minerals that contain reduced forms of iron and sulfur, such as chalcopyrite (CuFeS_2). Through their metabolism, these microbes mobilize precious metals from ore deposits into solution, making them powerful catalysts for biomining (see the first figure) (1). Recent research has begun to elucidate how they achieve this remarkable feat.", "doi": "10.1126/science.1184229", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2010-02-12", "series_number": "5967", "volume": "327", "issue": "5967", "pages": "793-794" }, { "id": "authors:b4f1a-np498", "collection": "authors", "collection_id": "b4f1a-np498", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130405-104044575", "type": "article", "title": "Endogenous Phenazine Antibiotics Promote Anaerobic Survival of Pseudomonas aeruginosa via Extracellular Electron Transfer", "author": [ { "family_name": "Wang", "given_name": "Yun", "clpid": "Wang-Yun" }, { "family_name": "Kern", "given_name": "Suzanne E.", "clpid": "Kern-S-E" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Antibiotics are increasingly recognized as having other, important physiological functions for the cells that produce them. An example of this is the effect that phenazines have on signaling and community development for Pseudomonas aeruginosa (L. E. Dietrich, T. K. Teal, A. Price-Whelan, and D. K. Newman, Science 321:1203-1206, 2008). Here we show that phenazine-facilitated electron transfer to poised-potential electrodes promotes anaerobic survival but not growth of Pseudomonas aeruginosa PA14 under conditions of oxidant limitation. Other electron shuttles that are reduced but not made by PA14 do not facilitate survival, suggesting that the survival effect is specific to endogenous phenazines.", "doi": "10.1128/JB.01188-09", "pmcid": "PMC2798253", "issn": "0021-9193", "publisher": "American Society for Microbiology", "publication": "Journal of Bacteriology", "publication_date": "2010-01", "series_number": "1", "volume": "192", "issue": "1", "pages": "365-369" }, { "id": "authors:f29wq-7rr05", "collection": "authors", "collection_id": "f29wq-7rr05", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130417-105815720", "type": "article", "title": "2-Methylhopanoids are maximally produced in akinetes of Nostoc punctiforme: geobiological implications", "author": [ { "family_name": "Doughty", "given_name": "D. M.", "clpid": "Doughty-D-M" }, { "family_name": "Hunter", "given_name": "R. C.", "orcid": "0000-0003-3841-1676", "clpid": "Hunter-Ryan-C" }, { "family_name": "Summons", "given_name": "R. E.", "orcid": "0000-0002-7144-8537", "clpid": "Summons-R-E" }, { "family_name": "Newman", "given_name": "D. K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "2-Methylhopanes, molecular fossils of 2-methylbacteriohopanepolyol (2-MeBHP) lipids, have been proposed as biomarkers for cyanobacteria, and by extension, oxygenic photosynthesis. However, the robustness of this interpretation is unclear, as 2-methylhopanoids occur in organisms besides cyanobacteria and their physiological functions are unknown. As a first step toward understanding the role of 2-MeBHP in cyanobacteria, we examined the expression and intercellular localization of hopanoids in the three cell types of Nostoc punctiforme: vegetative cells, akinetes, and heterocysts. Cultures in which N. punctiforme had differentiated into akinetes contained approximately 10-fold higher concentrations of 2-methylhopanoids than did cultures that contained only vegetative cells. In contrast, 2-methylhopanoids were only present at very low concentrations in heterocysts. Hopanoid production initially increased threefold in cells starved of nitrogen but returned to levels consistent with vegetative cells within 2 weeks. Vegetative and akinete cell types were separated into cytoplasmic, thylakoid, and outer membrane fractions; the increase in hopanoid expression observed in akinetes was due to a 34-fold enrichment of hopanoid content in their outer membrane relative to vegetative cells. Akinetes formed in response either to low light or phosphorus limitation, exhibited the same 2-methylhopanoid localization and concentration, demonstrating that 2-methylhopanoids are associated with the akinete cell type per se. Because akinetes are resting cells that are not photosynthetically active, 2-methylhopanoids cannot be functionally linked to oxygenic photosynthesis in N. punctiforme.", "doi": "10.1111/j.1472-4669.2009.00217.x", "pmcid": "PMC2860729", "issn": "1472-4677", "publisher": "Blackwell Publishing", "publication": "Geobiology", "publication_date": "2009-12", "series_number": "5", "volume": "7", "issue": "5", "pages": "524-532" }, { "id": "authors:bxfrj-pjy16", "collection": "authors", "collection_id": "bxfrj-pjy16", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130430-132656400", "type": "article", "title": "Rhodobacter capsulatus Catalyzes Light-Dependent Fe(II) Oxidation under Anaerobic Conditions as a Potential Detoxification Mechanism", "author": [ { "family_name": "Poulain", "given_name": "Alexandre J.", "clpid": "Poulain-A-J" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Diverse bacteria are known to oxidize millimolar concentrations of ferrous iron [Fe(II)] under anaerobic conditions, both phototrophically and chemotrophically. Yet whether they can do this under conditions that are relevant to natural systems is understood less well. In this study, we tested how light, Fe(II) speciation, pH, and salinity affected the rate of Fe(II) oxidation by Rhodobacter capsulatus SB1003. Although R. capsulatus cannot grow photoautotrophically on Fe(II), it oxidizes Fe(II) at rates comparable to those of bacteria that do grow photoautotrophically on Fe(II) as soon as it is exposed to light, provided it has a functional photosystem. Chelation of Fe(II) by diverse organic ligands promotes Fe(II) oxidation, and as the pH increases, so does the oxidation rate, except in the presence of nitrilotriacetate; nonchelated forms of Fe(II) are also more rapidly oxidized at higher pH. Salt concentrations typical of marine environments inhibit Fe(II) oxidation. When growing photoheterotrophically on humic substances, R. capsulatus is highly sensitive to low concentrations of Fe(II); it is inhibited in the presence of concentrations as low as 5 \u03bcM. The product of Fe(II) oxidation, ferric iron, does not hamper growth under these conditions. When other parameters, such as pH or the presence of chelators, are adjusted to promote Fe(II) oxidation, the growth inhibition effect of Fe(II) is alleviated. Together, these results suggest that Fe(II) is toxic to R. capsulatus growing under strictly anaerobic conditions and that Fe(II) oxidation alleviates this toxicity.", "doi": "10.1128/AEM.00054-09", "pmcid": "PMC2772431", "issn": "0099-2240", "publisher": "American Society for Microbiology", "publication": "Applied and Environmental Microbiology", "publication_date": "2009-11-01", "series_number": "21", "volume": "75", "issue": "21", "pages": "6639-6646" }, { "id": "authors:tv52g-bzj52", "collection": "authors", "collection_id": "tv52g-bzj52", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20091002-105243373", "type": "article", "title": "Hopanoids Play a Role in Membrane Integrity and pH Homeostasis in Rhodopseudomonas palustris TIE-1", "author": [ { "family_name": "Welander", "given_name": "Paula V.", "clpid": "Welander-P-V" }, { "family_name": "Hunter", "given_name": "Ryan C.", "orcid": "0000-0003-3841-1676", "clpid": "Hunter-Ryan-C" }, { "family_name": "Zhang", "given_name": "Lichun", "clpid": "Zhang-Lichun" }, { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Summons", "given_name": "Roger E.", "orcid": "0000-0002-7144-8537", "clpid": "Summons-R-E" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Sedimentary hopanes are pentacyclic triterpenoids that serve as biomarker proxies for bacteria and certain bacterial metabolisms, such as oxygenic photosynthesis and aerobic methanotrophy. Their parent molecules, the bacteriohopanepolyols (BHPs), have been hypothesized to be the bacterial equivalent of sterols. However, the actual function of BHPs in bacterial cells is poorly understood. Here, we report the physiological study of a mutant in Rhodopseudomonas palustris TIE-1 that is unable to produce any hopanoids. The deletion of the gene encoding the squalene-hopene cyclase protein (Shc), which cyclizes squalene to the basic hopene structure, resulted in a strain that no longer produced any polycyclic triterpenoids. This strain was able to grow chemoheterotrophically, photoheterotrophically, and photoautotrophically, demonstrating that hopanoids are not required for growth under normal conditions. A severe growth defect, as well as significant morphological damage, was observed when cells were grown under acidic and alkaline conditions. Although minimal changes in shc transcript expression were observed under certain conditions of pH shock, the total amount of hopanoid production was unaffected; however, the abundance of methylated hopanoids significantly increased. This suggests that hopanoids may play an indirect role in pH homeostasis, with certain hopanoid derivatives being of particular importance.", "doi": "10.1128/JB.00460-09", "pmcid": "PMC2747905", "issn": "0021-9193", "publisher": "American Society for Microbiology", "publication": "Journal of Bacteriology", "publication_date": "2009-10", "series_number": "19", "volume": "191", "issue": "19", "pages": "6145-6156" }, { "id": "authors:w7cbm-08h76", "collection": "authors", "collection_id": "w7cbm-08h76", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090923-143133443", "type": "article", "title": "Redox signaling between DNA repair proteins for efficient lesion detection", "author": [ { "family_name": "Boal", "given_name": "Amie K.", "orcid": "0000-0002-1234-8472", "clpid": "Boal-A-K" }, { "family_name": "Genereux", "given_name": "Joseph C.", "orcid": "0000-0002-5093-7710", "clpid": "Genereux-J-C" }, { "family_name": "Sontz", "given_name": "Pamela A.", "clpid": "Sontz-P-A" }, { "family_name": "Gralnick", "given_name": "Jeffrey A.", "orcid": "0000-0001-9250-7770", "clpid": "Gralnick-J-A" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Base excision repair (BER) enzymes maintain the integrity of the genome, and in humans, BER mutations are associated with cancer. Given the remarkable sensitivity of DNA-mediated charge transport (CT) to mismatched and damaged base pairs, we have proposed that DNA repair glycosylases (EndoIII and MutY) containing a redox-active [4Fe4S] cluster could use DNA CT in signaling one another to search cooperatively for damage in the genome. Here, we examine this model, where we estimate that electron transfers over a few hundred base pairs are sufficient for rapid interrogation of the full genome. Using atomic force microscopy, we found a redistribution of repair proteins onto DNA strands containing a single base mismatch, consistent with our model for CT scanning. We also demonstrated in Escherichia coli a cooperativity between EndoIII and MutY that is predicted by the CT scanning model. This relationship does not require the enzymatic activity of the glycosylase. Y82A EndoIII, a mutation that renders the protein deficient in DNA-mediated CT, however, inhibits cooperativity between MutY and EndoIII. These results illustrate how repair proteins might efficiently locate DNA lesions and point to a biological role for DNA-mediated CT within the cell.", "doi": "10.1073/pnas.0908059106", "pmcid": "PMC2741234", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2009-09-08", "series_number": "36", "volume": "106", "issue": "36", "pages": "15237-15242" }, { "id": "authors:2gcg4-reg90", "collection": "authors", "collection_id": "2gcg4-reg90", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090817-144818780", "type": "article", "title": "The Continuing Puzzle of the Great Oxidation Event", "author": [ { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Doughty", "given_name": "David M.", "clpid": "Doughty-D-M" }, { "family_name": "Welander", "given_name": "Paula V.", "clpid": "Welander-P-V" }, { "family_name": "Summons", "given_name": "Roger E.", "orcid": "0000-0002-7144-8537", "clpid": "Summons-R-E" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "The rise of atmospheric O_2 was a milestone in the history of life. Although O_2 itself is not a climate-active gas, its appearance would have removed a methane greenhouse present on the early Earth and potentially led to dramatic cooling. Moreover, by fundamentally altering the biogeochemical cycles of C, N, S and Fe, its rise first in the atmosphere and later in the oceans would also have had important indirect effects on Earth's climate. Here, we summarize major lines of evidence from the geological literature that pertain to when and how O_2 first appeared in significant amounts in the atmosphere. On the early Earth, atmospheric O_2 would initially have been very low, probably <10^(\u22125) of the present atmospheric level. Around 2.45 billion years ago, atmospheric O_2 rose suddenly in what is now termed the Great Oxidation Event. While the rise of oxygen has been the subject of considerable attention by Earth scientists, several important aspects of this problem remain unresolved. Our goal in this review is to provide a short summary of the current state of the field, and make the case that future progress towards solving the riddle of oxygen will benefit greatly from the involvement of molecular biologists.", "doi": "10.1016/j.cub.2009.05.054", "issn": "0960-9822", "publisher": "Cell Press", "publication": "Current Biology", "publication_date": "2009-07-28", "series_number": "14", "volume": "19", "issue": "14", "pages": "R567-R574" }, { "id": "authors:9cm46-45003", "collection": "authors", "collection_id": "9cm46-45003", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130312-090049618", "type": "article", "title": "From Iron Oxides to Infections", "author": [ { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Cellular electron transfer under diverse anaerobic conditions is a primary topic of research conducted by the Newman group. In this Viewpoint, a summary is given of how a geobiological approach has been used to investigate these processes.", "doi": "10.1002/cssc.200900038", "issn": "1864-5631", "publisher": "Wiley", "publication": "ChemSusChem", "publication_date": "2009-05-25", "series_number": "5", "volume": "2", "issue": "5", "pages": "380-382" }, { "id": "authors:9vee6-yej59", "collection": "authors", "collection_id": "9vee6-yej59", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130312-101350418", "type": "article", "title": "Phototrophic Fe(II) oxidation in an atmosphere of H_2: implications for Archean banded iron formations", "author": [ { "family_name": "Croal", "given_name": "L. R.", "clpid": "Croal-L-R" }, { "family_name": "Jiao", "given_name": "Y.", "orcid": "0000-0002-1189-1676", "clpid": "Jiao-Yuling" }, { "family_name": "Kappler", "given_name": "A.", "clpid": "Kappler-A" }, { "family_name": "Newman", "given_name": "D. K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "The effect of hydrogen on the rate of phototrophic Fe(II) oxidation by two species of purple bacteria was measured at two different bicarbonate concentrations. Hydrogen slowed Fe(II) oxidation to varying degrees depending on the bicarbonate concentration, but even the slowest rate of Fe(II) oxidation remained on the same order of magnitude as that estimated to have been necessary to deposit the Hamersley banded iron formations. Given the hydrogen and bicarbonate concentrations inferred for the Archean, our data suggest that Fe(II) phototrophy could have been a viable process at this time.", "doi": "10.1111/j.1472-4669.2008.00185.x", "pmcid": "PMC2763526", "issn": "1472-4677", "publisher": "Blackwell Publishing", "publication": "Geobiology", "publication_date": "2009-01", "series_number": "1", "volume": "7", "issue": "1", "pages": "21-24" }, { "id": "authors:m38ej-q1v42", "collection": "authors", "collection_id": "m38ej-q1v42", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130312-105735972", "type": "article", "title": "Redox-Active Antibiotics Control Gene Expression and Community Behavior in Divergent Bacteria", "author": [ { "family_name": "Dietrich", "given_name": "Lars E. P.", "clpid": "Dietrich-L-E-P" }, { "family_name": "Teal", "given_name": "Tracy K.", "clpid": "Teal-T-K" }, { "family_name": "Price-Whelan", "given_name": "Alexa", "orcid": "0000-0003-0872-7098", "clpid": "Price-Whelan-A" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "It is thought that bacteria excrete redox-active pigments as antibiotics to inhibit competitors. In Pseudomonas aeruginosa, the endogenous antibiotic pyocyanin activates SoxR, a transcription factor conserved in Proteo- and Actinobacteria. In Escherichia coli, SoxR regulates the superoxide stress response. Bioinformatic analysis coupled with gene expression studies in P. aeruginosa and Streptomyces coelicolor revealed that the majority of SoxR regulons in bacteria lack the genes required for stress responses, despite the fact that many of these organisms still produce redox-active small molecules, which indicates that redox-active pigments play a role independent of oxidative stress. These compounds had profound effects on the structural organization of colony biofilms in both P. aeruginosa and S. coelicolor, which shows that \"secondary metabolites\" play important conserved roles in gene expression and development.", "doi": "10.1126/science.1160619", "pmcid": "PMC2745639", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2008-08-29", "series_number": "5893", "volume": "321", "issue": "5893", "pages": "1203-1206" }, { "id": "authors:7vtsj-6vf60", "collection": "authors", "collection_id": "7vtsj-6vf60", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130312-094823983", "type": "article", "title": "From iron oxides to infections", "author": [ { "family_name": "Newman", "given_name": "D. K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "I was fortunate to have met Terry Beveridge early during my time in graduate school, when my advisor, Francois Morel (a geochemist), recognized the importance of my having a microbiologist on my PhD advising committee. At the time, I was studying microbial precipitation of arsenic trisulfide (As_2S_3) by Desulfotomaculum auripigmentum and needed the help of a geomicrobiologist to take electron micrographs of my samples (Newman et al., 1997). What better person to ask than Terry Beveridge? Not knowing much about what I was doing, I naively went off to Guelph to spend a week working in Terry's laboratory during the fall of 1994. Little did I know that this would be the start of one of the most inspirational scientific and personal relationships of my career. From that week forward, I turned to Terry whenever I had a question about microbiology, and looked forward to his responses: Terry had a way of making me feel like I had hit upon something profound (when in fact my questions were pretty trivial), and his answers not only were thoughtful and informed, but had the effect of getting me to think about other problems that were much more interesting.", "doi": "10.1111/j.1472-4669.2008.00155.x", "pmcid": "PMC2804855", "issn": "1472-4677", "publisher": "Blackwell Publishing", "publication": "Geobiology", "publication_date": "2008-06", "series_number": "3", "volume": "6", "issue": "3", "pages": "196-200" }, { "id": "authors:vwwff-ycn28", "collection": "authors", "collection_id": "vwwff-ycn28", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130506-090233889", "type": "article", "title": "Redox Reactions of Phenazine Antibiotics with Ferric (Hydr)oxides and Molecular Oxygen", "author": [ { "family_name": "Wang", "given_name": "Yun", "clpid": "Wang-Yun" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Phenazines are small redox-active molecules produced by a variety of bacteria. Beyond merely serving as antibiotics, recent studies suggest that phenazines play important physiological roles, including one in iron acquisition. Here we characterize the ability of four electrochemically reduced natural phenazines\u2014pyocyanin (PYO), phenazine-1-carboxylate (PCA), phenazine-1-carboxamide, and 1-hydroxyphenazine (1-OHPHZ)\u2014to reductively dissolve ferrihydrite and hematite in the pH range 5\u20138. Generally, the reaction rate is higher for a phenazine with a lower reduction potential, with the reaction between PYO and ferrihydrite at pH 5 being an exception; the rate decreases as the pH increases; the rate is higher for poorly crystalline ferrihydrite than for highly crystalline hematite. Ferric (hydr)oxide reduction by reduced phenazines can potentially be inhibited by oxygen, where O_2 competes with Fe(III) as the final oxidant. The reactivity of reduced phenazines with O_2 decreases in the order: PYO > 1-OHPHZ > PCA. Strikingly, reduced PYO, which is the least reactive phenazine with ferrihydrite and hematite at pH 7, is the most reactive phenazine with O_2. These results imply that different phenazines may perform different functions in environments with gradients of iron and O_2.", "doi": "10.1021/es702290a", "pmcid": "PMC2778262", "issn": "0013-936X", "publisher": "American Chemical Society", "publication": "Environmental Science and Technology", "publication_date": "2008-04-01", "series_number": "7", "volume": "42", "issue": "7", "pages": "2380-2386" }, { "id": "authors:fn2h6-cm306", "collection": "authors", "collection_id": "fn2h6-cm306", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:GORpnas08", "type": "article", "title": "DNA binding shifts the redox potential of the transcription factor SoxR", "author": [ { "family_name": "Gorodetsky", "given_name": "Alon A.", "orcid": "0000-0002-3811-552X", "clpid": "Gorodetsky-A-A" }, { "family_name": "Dietrich", "given_name": "Lars E. P.", "clpid": "Dietrich-L-E-P" }, { "family_name": "Lee", "given_name": "Paul E.", "clpid": "Lee-P-E" }, { "family_name": "Demple", "given_name": "Bruce", "clpid": "Demple-B" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "abstract": "Electrochemistry measurements on DNA-modified electrodes are used to probe the effects of binding to DNA on the redox potential of SoxR, a transcription factor that contains a [2Fe-2S] cluster and is activated through oxidation. A DNA-bound potential of +200 mV versus NHE (normal hydrogen electrode) is found for SoxR isolated from Escherichia coli and Pseudomonas aeruginosa. This potential value corresponds to a dramatic shift of +490 mV versus values found in the absence of DNA. Using Redmond red as a covalently bound redox reporter affixed above the SoxR binding site, we also see, associated with SoxR binding, an attenuation in the Redmond red signal compared with that for Redmond red attached below the SoxR binding site. This observation is consistent with a SoxR-binding-induced structural distortion in the DNA base stack that inhibits DNA-mediated charge transport to the Redmond red probe. The dramatic shift in potential for DNA-bound SoxR compared with the free form is thus reconciled based on a high-energy conformational change in the SoxR\u2013DNA complex. The substantial positive shift in potential for DNA-bound SoxR furthermore indicates that, in the reducing intracellular environment, DNA-bound SoxR is primarily in the reduced form; the activation of DNA-bound SoxR would then be limited to strong oxidants, making SoxR an effective sensor for oxidative stress. These results more generally underscore the importance of using DNA electrochemistry to determine DNA-bound potentials for redox-sensitive transcription factors because such binding can dramatically affect this key protein property.", "doi": "10.1073/pnas.0800093105", "pmcid": "PMC2268809", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2008-03-11", "series_number": "10", "volume": "105", "issue": "10", "pages": "3684-3689" }, { "id": "authors:0pk9h-2mg87", "collection": "authors", "collection_id": "0pk9h-2mg87", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:MALjbact08", "type": "article", "title": "Characterization of the Arsenate Respiratory Reductase from Shewanella sp. Strain ANA-3", "author": [ { "family_name": "Malasarn", "given_name": "Davin", "clpid": "Malasarn-Davin" }, { "family_name": "Keeffe", "given_name": "Jennifer R.", "orcid": "0000-0002-5317-6398", "clpid": "Keeffe-J-R" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Microbial arsenate respiration contributes to the mobilization of arsenic from the solid to the soluble phase in various locales worldwide. To begin to predict the extent to which As(V) respiration impacts arsenic geochemical cycling, we characterized the expression and activity of the Shewanella sp. strain ANA-3 arsenate respiratory reductase (ARR), the key enzyme involved in this metabolism. ARR is expressed at the beginning of the exponential phase and persists throughout the stationary phase, at which point it is released from the cell. In intact cells, the enzyme localizes to the periplasm. To purify ARR, a heterologous expression system was developed in Escherichia coli. ARR requires anaerobic conditions and molybdenum for activity. ARR is a heterodimer of ~131 kDa, composed of one ArrA subunit (~95 kDa) and one ArrB subunit (~27 kDa). For ARR to be functional, the two subunits must be expressed together. Elemental analysis of pure protein indicates that one Mo atom, four S atoms associated with a bis-molybdopterin guanine dinucleotide cofactor, and four to five [4Fe-4S] are present per ARR. ARR has an apparent melting temperature of 41\u00b0C, a Km of 5 \u00b5M, and a Vmax of 11,111 \u00b5mol of As(V) reduced min\u20131 mg of protein\u20131 and shows no activity in the presence of alternative electron acceptors such as antimonite, nitrate, selenate, and sulfate. The development of a heterologous overexpression system for ARR will facilitate future structural and/or functional studies of this protein family.", "doi": "10.1128/JB.01110-07", "pmcid": "PMC2223751", "issn": "0021-9193", "publisher": "American Society for Microbiology", "publication": "Journal of Bacteriology", "publication_date": "2008-01", "series_number": "1", "volume": "190", "issue": "1", "pages": "135-142" }, { "id": "authors:w6f73-1qa94", "collection": "authors", "collection_id": "w6f73-1qa94", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:CAIaem07", "type": "article", "title": "Phototrophic Fe(II) Oxidation Promotes Organic Carbon Acquisition by Rhodobacter capsulatus SB1003", "author": [ { "family_name": "Caiazza", "given_name": "Nicky C.", "clpid": "Caiazza-N-C" }, { "family_name": "Lies", "given_name": "Douglas P.", "clpid": "Lies-D-P" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Anoxygenic phototrophic Fe(II) oxidation is usually considered to be a lithoautotrophic metabolism that contributes to primary production in Fe-based ecosystems. In this study, we employed Rhodobacter capsulatus SB1003 as a model organism to test the hypothesis that phototrophic Fe(II) oxidation can be coupled to organic carbon acquisition. R. capsulatus SB1003 oxidized Fe(II) under anoxic conditions in a light-dependent manner, but failed to grow lithoautotrophically on soluble Fe(II). When provided with Fe(II)-citrate, however, growth was observed that was dependent upon microbially catalyzed Fe(II) oxidation, resulting in the formation of Fe(III)-citrate. Subsequent photochemical breakdown of Fe(III)-citrate yielded acetoacetic acid, that supported growth in the light but not the dark. Deletion of genes (RR00247-RR00248) that encode homologs of atoA and atoD, required for acetoacetic acid utilization, severely impaired the ability of R. capsulatus SB1003 to grow on Fe(II)-citrate. The growth yield achieved by R. capsulatus SB1003 in the presence of citrate cannot be explained by lithoautotrophic growth on Fe(II) enabled by indirect effects of the ligand (such as altering the thermodynamics of Fe(II) oxidation or preventing cell encrustation). Together, these results demonstrate that R. capsulatus SB1003 grows photoheterotrophically on Fe(II)-citrate. Nitrilotriacetic acid (NTA) also supported light-dependent growth on Fe(II), suggesting that Fe(II) oxidation may be a general mechanism whereby some Fe(II)-oxidizing bacteria mine otherwise inaccessible organic carbon sources.", "doi": "10.1128/AEM.02830-06", "pmcid": "PMC2074999", "issn": "0099-2240", "publisher": "American Society for Microbiology", "publication": "Applied and Environmental Microbiology", "publication_date": "2007-10", "series_number": "19", "volume": "73", "issue": "19", "pages": "6150-6158" }, { "id": "authors:7e4th-d5711", "collection": "authors", "collection_id": "7e4th-d5711", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:RASpnas07", "type": "article", "title": "Biosynthesis of 2-methylbacteriohopanepolyols by an anoxygenic phototroph", "author": [ { "family_name": "Rashby", "given_name": "Sky E.", "clpid": "Rashby-S-E" }, { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Summons", "given_name": "Roger E.", "orcid": "0000-0002-7144-8537", "clpid": "Summons-R-E" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Sedimentary 2-methyhopanes have been used as biomarker proxies for cyanobacteria, the only known bacterial clade capable of oxygenic photosynthesis and the only group of organisms found thus far to produce abundant 2-methylbacteriohopanepolyols (2-MeBHPs). Here, we report the identification of significant quantities of 2-MeBHP in two strains of the anoxygenic phototroph Rhodopseudomonas palustris. Biosynthesis of 2-MeBHP can occur in the absence of O2, deriving the C-2 methyl group from methionine. The relative abundance of 2-MeBHP varies considerably with culture conditions, ranging from 13.3% of total bacteriohopanepolyol (BHP) to trace levels of methylation. Analysis of intact BHPs reveals the presence of methylated bacteriohopane-32,33,34,35-tetrol but no detectable methylation of 35-aminobacteriohopane-32,33,34-triol. Our results demonstrate that an anoxygenic photoautotroph is capable of generating 2-MeBHPs and show that the potential origins of sedimentary 2-methylhopanoids are more diverse than previously thought.", "doi": "10.1073/pnas.0704912104", "pmcid": "PMC1986619", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2007-09-18", "series_number": "38", "volume": "104", "issue": "38", "pages": "15099-15014" }, { "id": "authors:q0t01-d0319", "collection": "authors", "collection_id": "q0t01-d0319", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:PRIjbact07", "type": "article", "title": "Pyocyanin Alters Redox Homeostasis and Carbon Flux through Central Metabolic Pathways in Pseudomonas aeruginosa PA14", "author": [ { "family_name": "Price-Whelan", "given_name": "Alexa", "orcid": "0000-0003-0872-7098", "clpid": "Price-Whelan-A" }, { "family_name": "Dietrich", "given_name": "Lars E. P.", "clpid": "Dietrich-L-E-P" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "The opportunistic pathogen Pseudomonas aeruginosa produces colorful, redox-active antibiotics called phenazines. Excretion of pyocyanin, the best-studied natural phenazine, is responsible for the bluish tint of sputum and pus associated with P. aeruginosa infections in humans. Although the toxicity of pyocyanin for other bacteria, as well as its role in eukaryotic infection, has been studied extensively, the physiological relevance of pyocyanin metabolism for the producing organism is not well understood. Pyocyanin reduction by P. aeruginosa PA14 is readily observed in standing liquid cultures that have consumed all of the oxygen in the medium. We investigated the physiological consequences of pyocyanin reduction by assaying intracellular concentrations of NADH and NAD+ in the wild-type strain and a mutant defective in phenazine production. We found that the mutant accumulated more NADH in stationary phase than the wild type. This increased accumulation correlated with a decrease in oxygen availability and was relieved by the addition of nitrate. Pyocyanin addition to a phenazine-null mutant also decreased intracellular NADH levels, suggesting that pyocyanin reduction facilitates redox balancing in the absence of other electron acceptors. Analysis of extracellular organic acids revealed that pyocyanin stimulated stationary-phase pyruvate excretion in P. aeruginosa PA14, indicating that pyocyanin may also influence the intracellular redox state by decreasing carbon flux through central metabolic pathways.", "doi": "10.1128/JB.00505-07", "pmcid": "PMC1951912", "issn": "0021-9193", "publisher": "American Society for Microbiology", "publication": "Journal of Bacteriology", "publication_date": "2007-09", "series_number": "17", "volume": "189", "issue": "17", "pages": "6372-6381" }, { "id": "authors:5akny-cs650", "collection": "authors", "collection_id": "5akny-cs650", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130312-102942670", "type": "article", "title": "Extracellular respiration", "author": [ { "family_name": "Gralnick", "given_name": "Jeffrey A.", "orcid": "0000-0001-9250-7770", "clpid": "Gralnick-J-A" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Although it has long been known that microbes can generate energy using diverse strategies, only recently has it become clear that a growing number involve electron transfer to or from extracellular substrates. The best-known example of what we will term 'extracellular respiration' is electron transfer between microbes and minerals, such as iron and manganese (hydr)oxides. This makes sense, given that these minerals are sparingly soluble. What is perhaps surprising, however, is that a number of substrates that might typically be classified as 'soluble' are also respired at the cell surface. There are several reasons why this might be the case: the substrate, in its ecological context, might be associated with a solid surface and thus effectively insoluble; the substrate, while soluble, might simply be too large to transport inside the cell; or the substrate, while benign in one redox state, might become toxic after it is metabolized. In this review, we discuss various examples of extracellular respiration, paying particular attention to what is known about the molecular mechanisms underlying these processes. As will become clear, much remains to be learned about the biochemistry, cell biology and regulation of extracellular respiration, making it a rich field of study for molecular microbiologists.", "doi": "10.1111/j.1365-2958.2007.05778.x", "pmcid": "PMC2804852", "issn": "0950-382X", "publisher": "Blackwell Publishing", "publication": "Molecular Microbiology", "publication_date": "2007-07", "series_number": "1", "volume": "65", "issue": "1", "pages": "1-11" }, { "id": "authors:dke9c-gtn79", "collection": "authors", "collection_id": "dke9c-gtn79", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130417-155449511", "type": "article", "title": "A likely role for anoxygenic photosynthetic microbes in the formation of ancient stromatolites", "author": [ { "family_name": "Bosak", "given_name": "T.", "clpid": "Bosak-T" }, { "family_name": "Greene", "given_name": "S. E.", "clpid": "Greene-S-E" }, { "family_name": "Newman", "given_name": "D. K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Although cyanobacteria are the dominant primary producers in modern stromatolites and other microbialites, the oldest stromatolites pre-date geochemical evidence for oxygenic photosynthesis and cyanobacteria in the rock record. As a step towards the development of laboratory models of stromatolite growth, we tested the potential of a metabolically ancient anoxygenic photosynthetic bacterium to build stromatolites. This organism, Rhodopseudomonas palustris, stimulates the precipitation of calcite in solutions already highly saturated with respect to calcium carbonate, and greatly facilitates the incorporation of carbonate grains into proto-lamina (i.e. crusts). The appreciable stimulation of the growth of proto-lamina by a nonfilamentous anoxygenic microbe suggests that similar microbes may have played a greater role in the formation of Archean stromatolites than previously assumed.", "doi": "10.1111/j.1472-4669.2007.00104.x", "pmcid": "PMC2947360", "issn": "1472-4677", "publisher": "Blackwell Publishing", "publication": "Geobiology", "publication_date": "2007-06", "series_number": "2", "volume": "5", "issue": "2", "pages": "119-126" }, { "id": "authors:8z1js-np959", "collection": "authors", "collection_id": "8z1js-np959", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:JIAjbact07", "type": "article", "title": "The pio Operon Is Essential for Phototrophic Fe(II) Oxidation in Rhodopseudomonas palustris TIE-1", "author": [ { "family_name": "Jiao", "given_name": "Yongqin", "clpid": "Jiao-Yongqin" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Phototrophic Fe(II)-oxidizing bacteria couple the oxidation of ferrous iron [Fe(II)] to reductive CO2 fixation by using light energy, but until recently, little has been understood about the molecular basis for this process. Here we report the discovery, with Rhodopseudomonas palustris TIE-1 as a model organism, of a three-gene operon, designated the pio operon (for phototrophic iron oxidation), that is necessary for phototrophic Fe(II) oxidation. The first gene in the operon, pioA, encodes a c-type cytochrome that is upregulated under Fe(II)-grown conditions. PioA contains a signal sequence and shares homology with MtrA, a decaheme c-type cytochrome from Shewanella oneidensis MR-1. The second gene, pioB, encodes a putative outer membrane beta-barrel protein. PioB is a homologue of MtrB from S. oneidensis MR-1. The third gene, pioC, encodes a putative high potential iron sulfur protein (HiPIP) with a twin-arginine translocation (Tat) signal sequence and is similar to the putative Fe(II) oxidoreductase (Iro) from Acidithiobacillus ferrooxidans. Like PioA, PioB and PioC appear to be secreted proteins. Deletion of the pio operon results in loss of Fe(II) oxidation activity and growth on Fe(II). Complementation studies confirm that the phenotype of this mutant is due to loss of the pio genes. Deletion of pioA alone results in loss of almost all Fe(II) oxidation activity; however, deletion of either pioB or pioC alone results in only partial loss of Fe(II) oxidation activity. Together, these results suggest that proteins encoded by the pio operon are essential and specific for phototrophic Fe(II) oxidation in R. palustris TIE-1.", "doi": "10.1128/JB.00776-06", "pmcid": "PMC1855732", "issn": "0021-9193", "publisher": "American Society for Microbiology", "publication": "Journal of Bacteriology", "publication_date": "2007-03-01", "series_number": "5", "volume": "189", "issue": "5", "pages": "1765-1773" }, { "id": "authors:cd8dg-2zr05", "collection": "authors", "collection_id": "cd8dg-2zr05", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:CROjbact07", "type": "article", "title": "The fox Operon from Rhodobacter Strain SW2 Promotes Phototrophic Fe(II) Oxidation in Rhodobacter capsulatus SB1003", "author": [ { "family_name": "Croal", "given_name": "Laura R.", "clpid": "Croal-L-R" }, { "family_name": "Jiao", "given_name": "Yongqin", "clpid": "Jiao-Yongqin" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Anoxygenic photosynthesis based on Fe(II) is thought to be one of the most ancient forms of metabolism and is hypothesized to represent a transition step in the evolution of oxygenic photosynthesis. However, little is known about the molecular basis of this process because, until recently (Y. Jiao and D. K. Newman, J. Bacteriol. 189:1765-1773, 2007), most phototrophic Fe(II)-oxidizing bacteria have been genetically intractable. In this study, we circumvented this problem by taking a heterologous-complementation approach to identify a three-gene operon (the foxEYZ operon) from Rhodobacter sp. strain SW2 that confers enhanced light-dependent Fe(II) oxidation activity when expressed in its genetically tractable relative Rhodobacter capsulatus SB1003. The first gene in this operon, foxE, encodes a c-type cytochrome with no significant similarity to other known proteins. Expression of foxE alone confers significant light-dependent Fe(II) oxidation activity on SB1003, but maximal activity is achieved when foxE is expressed with the two downstream genes foxY and foxZ. In SW2, the foxE and foxY genes are cotranscribed in the presence of Fe(II) and/or hydrogen, with foxZ being transcribed only in the presence of Fe(II). Sequence analysis predicts that foxY encodes a protein containing the redox cofactor pyrroloquinoline quinone and that foxZ encodes a protein with a transport function. Future biochemical studies will permit the localization and function of the Fox proteins in SW2 to be determined.", "doi": "10.1128/JB.01395-06", "pmcid": "PMC1855712", "issn": "0021-9193", "publisher": "American Society for Microbiology", "publication": "Journal of Bacteriology", "publication_date": "2007-03-01", "series_number": "5", "volume": "189", "issue": "5", "pages": "1774-1782" }, { "id": "authors:0x0m1-6hj83", "collection": "authors", "collection_id": "0x0m1-6hj83", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:TEAaem06", "type": "article", "title": "Spatiometabolic Stratification of Shewanella oneidensis Biofilms", "author": [ { "family_name": "Teal", "given_name": "Tracy K.", "clpid": "Teal-T-K" }, { "family_name": "Lies", "given_name": "Douglas P.", "clpid": "Lies-D-P" }, { "family_name": "Wold", "given_name": "Barbara J.", "orcid": "0000-0003-3235-8130", "clpid": "Wold-B-J" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Biofilms, or surface-attached microbial communities, are both ubiquitous and resilient in the environment. Although much is known about how biofilms form, develop, and detach, very little is understood about how these events are related to metabolism and its dynamics. It is commonly thought that large subpopulations of cells within biofilms are not actively producing proteins or generating energy and are therefore dead. An alternative hypothesis is that within the growth-inactive domains of biofilms, significant populations of living cells persist and retain the capacity to dynamically regulate their metabolism. To test this, we employed unstable fluorescent reporters to measure growth activity and protein synthesis in vivo over the course of biofilm development and created a quantitative routine to compare domains of activity in independently grown biofilms. Here we report that Shewanella oneidensis biofilm structures reproducibly stratify with respect to growth activity and metabolism as a function of size. Within domains of growth-inactive cells, genes typically upregulated under anaerobic conditions are expressed well after growth has ceased. These findings reveal that, far from being dead, the majority of cells in mature S. oneidensis biofilms have actively turned-on metabolic programs appropriate to their local microenvironment and developmental stage.", "doi": "10.1128/AEM.01163-06", "pmcid": "PMC1636161", "issn": "0099-2240", "publisher": "American Society for Microbiology", "publication": "Applied and Environmental Microbiology", "publication_date": "2006-11", "series_number": "11", "volume": "72", "issue": "11", "pages": "7324-7330" }, { "id": "authors:mymrx-9cw34", "collection": "authors", "collection_id": "mymrx-9cw34", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130611-153514379", "type": "article", "title": "Simultaneous Microbial Reduction of Iron(III) and Arsenic(V) in Suspensions of Hydrous Ferric Oxide", "author": [ { "family_name": "Campbell", "given_name": "Kate M.", "clpid": "Campbell-K-M" }, { "family_name": "Malasarn", "given_name": "Davin", "clpid": "Malasarn-D" }, { "family_name": "Saltikov", "given_name": "Chad W.", "clpid": "Saltikov-C-W" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Hering", "given_name": "Janet G.", "clpid": "Hering-J-G" } ], "abstract": "Bacterial reduction of arsenic(V) and iron(III) oxides influences the redox cycling and partitioning of arsenic (As) between solid and aqueous phases in sediment-porewater systems. Two types of anaerobic bacterial incubations were designed to probe the relative order of As(V) and Fe(III) oxide reduction and to measure the effect of adsorbed As species on the rate of iron reduction, using hydrous ferric oxide (HFO) as the iron substrate. In one set of experiments, HFO was pre-equilibrated with As(V) and inoculated with fresh sediment from Haiwee Reservoir (Olancha, CA), an As-impacted field site. The second set of incubations consisted of HFO (without As) and As(III)- and As(V)- equilibrated HFO incubated with Shewanella sp. ANA-3 wild-type (WT) and ANA-3\u0394arrA, a mutant unable to produce the respiratory As(V) reductase. Of the two pathways for microbial As(V) reduction (respiration and detoxification), the respiratory pathway was dominant under these experimental conditions. In addition, As(III) adsorbed onto the surface of HFO enhanced the rate of microbial Fe(III) reduction. In the sediment and ANA-3 incubations, As(V) was reduced simultaneously or prior to Fe(III), consistent with thermodynamic calculations based on the chemical conditions of the ANA-3 WT incubations.", "doi": "10.1021/es0600476", "issn": "0013-936X", "publisher": "American Chemical Society", "publication": "Environmental Science and Technology", "publication_date": "2006-10-01", "series_number": "19", "volume": "40", "issue": "19", "pages": "5950-5955" }, { "id": "authors:rc0te-bqd35", "collection": "authors", "collection_id": "rc0te-bqd35", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:DIEmm06", "type": "article", "title": "The phenazine pyocyanin is a terminal signalling factor in the quorum sensing network of Pseudomonas aeruginosa", "author": [ { "family_name": "Dietrich", "given_name": "Lars E. P.", "clpid": "Dietrich-L-E-P" }, { "family_name": "Price-Whelan", "given_name": "Alexa", "orcid": "0000-0003-0872-7098", "clpid": "Price-Whelan-A" }, { "family_name": "Petersen", "given_name": "Ashley", "clpid": "Petersen-A" }, { "family_name": "Whiteley", "given_name": "Marvin", "clpid": "Whiteley-M" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Certain members of the fluorescent pseudomonads produce and secrete phenazines. These heterocyclic, redox-active compounds are toxic to competing organisms, and the cause of these antibiotic effects has been the focus of intense research efforts. It is largely unknown, however, how pseudomonads themselves respond to \u2013 and survive in the presence of \u2013 these compounds. Using Pseudomonas aeruginosa DNA microarrays and quantitative RT-PCR, we demonstrate that the phenazine pyocyanin elicits the upregulation of genes/operons that function in transport [such as the resistance-nodulation-cell division (RND) efflux pump MexGHI-OpmD] and possibly in redox control (such as PA2274, a putative flavin-dependant monooxygenase), and downregulates genes involved in ferric iron acquisition. Strikingly, mexGHI-opmD and PA2274 were previously shown to be regulated by the PA14 quorum sensing network that controls the production of virulence factors (including phenazines). Through mutational analysis, we show that pyocyanin is the physiological signal for the upregulation of these quorum sensing-controlled genes during stationary phase and that the response is mediated by the transcription factor SoxR. Our results implicate phenazines as signalling molecules in both P. aeruginosa PA14 and PAO1.", "doi": "10.1111/j.1365-2958.2006.05306.x", "issn": "0950-382X", "publisher": "Molecular Microbiology", "publication": "Molecular Microbiology", "publication_date": "2006-09", "series_number": "5", "volume": "61", "issue": "5", "pages": "1308-1321" }, { "id": "authors:shn8g-w9w34", "collection": "authors", "collection_id": "shn8g-w9w34", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130312-133946631", "type": "article", "title": "The co-evolution of life and Earth", "author": [ { "family_name": "Dietrich", "given_name": "Lars E. P.", "clpid": "Dietrich-L-E-P" }, { "family_name": "Tice", "given_name": "Michael M.", "clpid": "Tice-M-M" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "It has long been recognized that deciphering the relationship between the history of life on Earth and the history of the planet is a profound task. Recent technological innovations in both the earth and life sciences have made this task more tractable than ever before, leading to the emergence of the discipline of geobiology \u2014 the study of how organisms have influenced, and been influenced by, the Earth's environment. Along with enthusiasm for this new field, however, has come confusion, as geobiology combines highly specialized and historically separate fields. How does a sedimentologist communicate his/her problems to a cell biologist and vice versa? The fact that geobiology derives from two disparate scientific traditions \u2014 those of natural history and experimental science \u2014 can make identification of appropriate problems challenging. As C.P. Snow [1] recognized nearly a half century ago in his famous lecture 'The Two Cultures', communication between different disciplines often results in \"a gulf of mutual incomprehension\" that can be difficult to ford. Although Snow was referring to the divide that separates the humanities from the sciences, many of his insights can be applied to the divide that until recently has separated biology from geology.\n\nIn this Primer, we shall attempt to illustrate the compelling nature of geobiology by highlighting two geobiological problems. Our goal is to introduce molecular and cell biologists to this discipline, and make it clear just how much their skills can contribute to it and their questions benefit from it. We begin with a brief review of what is known about the geochemical evolution of the Earth. From there, we provide two examples of problems relevant to the co-evolution of life and Earth. The first example illustrates how a better understanding of biology \u2014 specifically, the distribution and function of sterol-like molecules in bacterial membranes \u2014 will inform our understanding of the rise of oxygen, arguably the most important event in the geochemical evolution of the Earth. The second example illustrates the counterpoint: how a better understanding of changes in the Earth's geochemistry over time can affect our interpretations of organelle evolution, specifically, the relationship between hydrogenosomes and mitochondria.", "doi": "10.1016/j.cub.2006.05.017", "issn": "0960-9822", "publisher": "Cell Press", "publication": "Current Biology", "publication_date": "2006-06-06", "series_number": "11", "volume": "16", "issue": "11", "pages": "R395-R400" }, { "id": "authors:4a2k6-m7p09", "collection": "authors", "collection_id": "4a2k6-m7p09", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:GRApnas06b", "type": "article", "title": "Extracellular respiration of dimethyl sulfoxide by Shewanella oneidensis strain MR-1", "author": [ { "family_name": "Gralnick", "given_name": "Jeffrey A.", "orcid": "0000-0001-9250-7770", "clpid": "Gralnick-J-A" }, { "family_name": "Vali", "given_name": "Hojatollah", "clpid": "Vali-H" }, { "family_name": "Lies", "given_name": "Douglas P.", "clpid": "Lies-D-P" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Shewanella species are renowned for their respiratory versatility, including their ability to respire poorly soluble substrates by using enzymatic machinery that is localized to the outside of the cell. The ability to engage in \"extracellular respiration\" to date has focused primarily on respiration of minerals. Here, we identify two gene clusters in Shewanella oneidensis strain MR-1 that each contain homologs of genes required for metal reduction and genes that are predicted to encode dimethyl sulfoxide (DMSO) reductase subunits. Molecular and genetic analyses of these clusters indicate that one (SO1427\u2013SO1432) is required for anaerobic respiration of DMSO. We show that DMSO respiration is an extracellular respiratory process through the analysis of mutants defective in type II secretion, which is required for transporting proteins to the outer membrane in Shewanella. Moreover, immunogold labeling of DMSO reductase subunits reveals that they reside on the outer leaflet of the outer membrane under anaerobic conditions. The extracellular localization of the DMSO reductase in S. oneidensis suggests these organisms may perceive DMSO in the environment as an insoluble compound.", "doi": "10.1073/pnas.0505959103", "pmcid": "PMC1450229", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2006-03-21", "series_number": "12", "volume": "103", "issue": "12", "pages": "4669-4674" }, { "id": "authors:6np8e-7y767", "collection": "authors", "collection_id": "6np8e-7y767", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130312-140213883", "type": "article", "title": "Rethinking 'secondary' metabolism: physiological roles for phenazine antibiotics", "author": [ { "family_name": "Price-Whelan", "given_name": "Alexa", "orcid": "0000-0003-0872-7098", "clpid": "Price-Whelan-A" }, { "family_name": "Dietrich", "given_name": "Lars E. P.", "clpid": "Dietrich-L-E-P" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Microorganisms exist in the environment as multicellular communities that face the challenge of surviving under nutrient-limited conditions. Chemical communication is an essential part of the way in which these populations coordinate their behavior, and there has been an explosion of understanding in recent years regarding how this is accomplished. Much less, however, is understood about the way these communities sustain their metabolism. Bacteria of the genus Pseudomonas are ubiquitous, and are distinguished by their production of colorful secondary metabolites called phenazines. In this article, we suggest that phenazines, which are produced under conditions of high cell density and nutrient limitation, may be important for the persistence of pseudomonads in the environment.", "doi": "10.1038/nchembio764", "issn": "1552-4450", "publisher": "Nature Publishing Group", "publication": "Nature Chemical Biology", "publication_date": "2006-02", "series_number": "2", "volume": "2", "issue": "2", "pages": "71-78" }, { "id": "authors:td9tx-4hj39", "collection": "authors", "collection_id": "td9tx-4hj39", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110803-122522248", "type": "article", "title": "Magnetosomes Are Cell Membrane Invaginations Organized by the Actin-Like Protein MamK", "author": [ { "family_name": "Komeili", "given_name": "Arash", "clpid": "Komeili-A" }, { "family_name": "Li", "given_name": "Zhou", "clpid": "Li-Zhou" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Jensen", "given_name": "Grant J.", "orcid": "0000-0003-1556-4864", "clpid": "Jensen-G-J" } ], "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.", "doi": "10.1126/science.1123231", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2006-01-13", "series_number": "5758", "volume": "311", "issue": "5758", "pages": "242-245" }, { "id": "authors:1zhbn-2hh70", "collection": "authors", "collection_id": "1zhbn-2hh70", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130415-132151408", "type": "article", "title": "Community and cultivation analysis of arsenite oxidizing biofilms at Hot Creek", "author": [ { "family_name": "Salmassi", "given_name": "Tina M.", "clpid": "Salmassi-T-M" }, { "family_name": "Walker", "given_name": "Jeffrey J.", "clpid": "Walker-J-J" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Leadbetter", "given_name": "Jared R.", "orcid": "0000-0002-7033-0844", "clpid": "Leadbetter-J-R" }, { "family_name": "Pace", "given_name": "Norman R.", "clpid": "Pace-N-R" }, { "family_name": "Hering", "given_name": "Janet G.", "clpid": "Hering-J-G" } ], "abstract": "At Hot Creek in California, geothermally derived arsenite is rapidly oxidized to arsenate. This process is mediated by microorganisms colonizing the surfaces of submerged aquatic macrophytes in the creek. Here we describe a multifaceted approach to characterizing this biofilm community and its activity. Molecular techniques were used to describe the community as a function of 16S-rRNA gene diversity. Cultivation-based strategies were used to enumerate and isolate three novel arsenite oxidizers, strains YED1-18, YED6-4 and YED6-21. All three strains are \u03b2-Proteobacteria, of the genus Hydrogenophaga. Because these strains were isolated from the highest (i.e. million-fold) dilutions of disrupted biofilm suspensions, they represent the most numerically significant arsenite oxidizers recovered from this community. One clone (Hot Creek Clone 44) obtained from an inventory of the 16S rDNA sequence diversity present in the biofilm was found to be 99.6% identical to the 16S rDNA sequence of the isolate YED6-21. On the basis of most probable number (MPN) analyses, arsenite-oxidizing bacteria were found to account for 6\u201356% of the cultivated members of the community. Using MPN values, we could estimate an upper bound on the value of V_(max) for the community of 1 \u00d7 10^(\u22129)\u00b5mole arsenite min^(\u22121) cell^(\u22121). This estimate represents the first normalization of arsenite oxidation rates to MPN cell densities for a microbial community in a field incubation experiment.", "doi": "10.1111/j.1462-2920.2005.00862.x", "issn": "1462-2912", "publisher": "Blackwell Publishing", "publication": "Environmental Microbiology", "publication_date": "2006-01", "series_number": "1", "volume": "8", "issue": "1", "pages": "50-59" }, { "id": "authors:rbd5y-cg063", "collection": "authors", "collection_id": "rbd5y-cg063", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130402-132103393", "type": "article", "title": "Influence of a dual-species biofilm on the corrosion of mild steel", "author": [ { "family_name": "Lee", "given_name": "Anthea K.", "clpid": "Lee-A-K" }, { "family_name": "Buehler", "given_name": "Martin G.", "clpid": "Buehler-M-G" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "The effect of a dual-species biofilm on the corrosion of carbon steel was examined using two bacterial species: the iron-reducer, Shewanella oneidensis (MR-1), and the sulfate-reducer, Desulfovibrio desulfuricans (G20). These experiments exploit the fact that the products of their metabolism (ferrous iron or sulfide) affect the corrosion rate of carbon steel in opposite ways. Electrochemical impedance spectroscopy (EIS) shows that over a short time period, co-cultures of MR-1 and G20 protect steel from corrosion. The fact that an iron-reducing bacterium can inhibit corrosion when a corrosion-enhancing bacterium is present warrants future study with respect to its potential applicability to the design of biological corrosion-control measures.", "doi": "10.1016/j.corsci.2004.11.013", "issn": "0010-938X", "publisher": "Elsevier", "publication": "Corrosion Science", "publication_date": "2006-01", "series_number": "1", "volume": "48", "issue": "1", "pages": "165-178" }, { "id": "authors:ms6tm-fba71", "collection": "authors", "collection_id": "ms6tm-fba71", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130415-135410684", "type": "article", "title": "Bacteria Are Beautiful", "author": [ { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "As a microbiologist, I'm appalled when I go to\nbuy soap or dishwashing detergent, because these\ndays it's very hard to find anything that doesn't say\n\"antibacterial\" on it. This is disturbing for a couple\nof reasons. First, there's absolutely no evidence to\nsuggest that these antibacterial versions in any way\nhelp to keep our homes cleaner and us safer from\ndisease-in fact, there's some evidence to suggest\nthese products contribute to the spread of antibiotic\nresistance. And second, it distresses me to\nsee the public given the perception that bacteria are\nbad and need to be eradicated.", "issn": "0013-7812", "publisher": "California Institute of Technology", "publication": "Engineering and Science", "publication_date": "2006", "series_number": "2", "volume": "69", "issue": "2", "pages": "8-15" }, { "id": "authors:nva1x-yqn64", "collection": "authors", "collection_id": "nva1x-yqn64", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:SALjbact05", "type": "article", "title": "Expression Dynamics of Arsenic Respiration and Detoxification in Shewanella sp. Strain ANA-3", "author": [ { "family_name": "Saltikov", "given_name": "Chad W.", "clpid": "Saltikov-C-W" }, { "family_name": "Wildman", "given_name": "Richard A., Jr.", "clpid": "Wildman-R-A-Jr" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Because arsenate [As(V)] reduction by bacteria can significantly enhance arsenic mobility in the environment, it is important to be able to predict when this activity will occur. Currently, two bacterial systems are known that specifically reduce As(V), namely, a respiratory system (encoded by the arr genes) and a detoxification system (encoded by the ars genes). Here we analyze the conditions under which these two systems are expressed in Shewanella sp. strain ANA-3. The ars system is expressed under both aerobic and anaerobic conditions, whereas the arr system is only expressed anaerobically and is repressed by oxygen and nitrate. When cells are grown on As(V), the arr system is maximally induced during exponential growth, with peak expression of the ars system occurring at the beginning of stationary phase. Both the arr and ars systems are specifically induced by arsenite [As(III)], but the arr system is activated by a concentration of As(III) that is 1,000 times lower than that required for the arsC system (\u2264100 nM versus \u2264100 \u00b5M, respectively). A double mutant was constructed that does not reduce As(V) under any growth conditions. In this strain background, As(V) is capable of inducing the arr system at low micromolar concentrations, but it does not induce the ars system. Collectively, these results demonstrate that the two As(V) reductase systems in ANA-3 respond to different amounts and types of inorganic arsenic.", "doi": "10.1128/JB.187.21.7390-7396.2005", "pmcid": "PMC1272973", "issn": "0021-9193", "publisher": "American Society for Microbiology", "publication": "Journal of Bacteriology", "publication_date": "2005-11", "series_number": "21", "volume": "187", "issue": "21", "pages": "7390-7396" }, { "id": "authors:24csj-ef922", "collection": "authors", "collection_id": "24csj-ef922", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130327-084430297", "type": "article", "title": "Deposition of banded iron formations by anoxygenic phototrophic Fe(II)-oxidizing bacteria", "author": [ { "family_name": "Kappler", "given_name": "Andreas", "clpid": "Kappler-A" }, { "family_name": "Pasquero", "given_name": "Claudia", "clpid": "Pasquero-C" }, { "family_name": "Konhauser", "given_name": "Kurt O.", "clpid": "Konhauser-K-O" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "The mechanism of banded iron formation (BIF) deposition is controversial, but classically has been interpreted to reflect ferrous iron [Fe(II)] oxidation by molecular oxygen after cyanobacteria evolved on Earth. Anoxygenic photoautotrophic bacteria can also catalyze Fe(II) oxidation under anoxic conditions. Calculations based on experimentally determined Fe(II) oxidation rates by these organisms under light regimes representative of ocean water at depths of a few hundred meters suggest that, even in the presence of cyanobacteria, anoxygenic phototrophs living beneath a wind-mixed surface layer provide the most likely explanation for BIF deposition in a stratified ancient ocean and the absence of Fe in Precambrian surface waters.", "doi": "10.1130/G21658.1", "issn": "0091-7613", "publisher": "Geological Society of America", "publication": "Geology", "publication_date": "2005-11", "series_number": "11", "volume": "33", "issue": "11", "pages": "865-868" }, { "id": "authors:f0afk-ex528", "collection": "authors", "collection_id": "f0afk-ex528", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130508-105548584", "type": "article", "title": "Fe(III) mineral formation and cell encrustation by the nitrate-dependent Fe(II)-oxidizer strain BoFeN1", "author": [ { "family_name": "Kappler", "given_name": "A.", "clpid": "Kappler-A" }, { "family_name": "Schink", "given_name": "B.", "clpid": "Schink-B" }, { "family_name": "Newman", "given_name": "D. K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Understanding the mechanisms of anaerobic microbial iron cycling is necessary for a full appreciation of present-day biogeochemical cycling of iron and carbon and for drawing conclusions about these cycles on the ancient Earth. Towards that end, we isolated and characterized an anaerobic nitrate-dependent Fe(II)-oxidizing bacterium from a freshwater sediment. The 16SrRNA gene sequence of the isolated bacterium (strain BoFeN1) places it within the \u03b2-Proteobacteria, with Acidovorax sp. strain G8B1 as the closest known relative. During mixotrophic growth with acetate plus Fe(II) and nitrate as electron acceptor, strain BoFeN1 forms Fe(III) mineral crusts around the cells. The amount of the organic cosubstrate acetate present seems to control the rate and extent of Fe(II) oxidation and the viability of the cells. The crystallinity of the mineral products is influenced by nucleation by Fe minerals that are already present in the inoculum.", "doi": "10.1111/j.1472-4669.2006.00056.x", "issn": "1472-4677", "publisher": "Blackwell Publishing", "publication": "Geobiology", "publication_date": "2005-10", "series_number": "4", "volume": "3", "issue": "4", "pages": "235-245" }, { "id": "authors:e0mbe-p8a77", "collection": "authors", "collection_id": "e0mbe-p8a77", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:LIEaem05", "type": "article", "title": "Shewanella oneidensis MR-1 Uses Overlapping Pathways for Iron Reduction at a Distance and by Direct Contact under Conditions Relevant for Biofilms", "author": [ { "family_name": "Lies", "given_name": "Douglas P.", "clpid": "Lies-D-P" }, { "family_name": "Hernandez", "given_name": "Maria E.", "clpid": "Hernandez-M-E" }, { "family_name": "Kappler", "given_name": "Andreas", "clpid": "Kappler-A" }, { "family_name": "Mielke", "given_name": "Randall E.", "clpid": "Mielke-R-E" }, { "family_name": "Gralnick", "given_name": "Jeffrey A.", "orcid": "0000-0001-9250-7770", "clpid": "Gralnick-J-A" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "We developed a new method to measure iron reduction at a distance based on depositing Fe(III) (hydr)oxide within nanoporous glass beads. In this \"Fe-bead\" system, Shewanella oneidensis reduces at least 86.5% of the iron in the absence of direct contact. Biofilm formation accompanies Fe-bead reduction and is observable both macro- and microscopically. Fe-bead reduction is catalyzed by live cells adapted to anaerobic conditions, and maximal reduction rates require sustained protein synthesis. The amount of reactive ferric iron in the Fe-bead system is available in excess such that the rate of Fe-bead reduction is directly proportional to cell density; i.e., it is diffusion limited. Addition of either lysates prepared from anaerobic cells or exogenous electron shuttles stimulates Fe-bead reduction by S. oneidensis, but iron chelators or additional Fe(II) do not. Neither dissolved Fe(III) nor electron shuttling activity was detected in culture supernatants, implying that the mediator is retained within the biofilm matrix. Strains with mutations in omcB or mtrB show about 50% of the wild-type levels of reduction, while a cymA mutant shows less than 20% of the wild-type levels of reduction and a menF mutant shows insignificant reduction. The Fe-bead reduction defect of the menF mutant can be restored by addition of menaquinone, but menaquinone itself cannot stimulate Fe-bead reduction. Because the menF gene encodes the first committed step of menaquinone biosynthesis, no intermediates of the menaquinone biosynthetic pathway are used as diffusible mediators by this organism to promote iron reduction at a distance. CymA and menaquinone are required for both direct and indirect mineral reduction, whereas MtrB and OmcB contribute to but are not absolutely required for iron reduction at a distance.", "doi": "10.1128/AEM.71.8.4414-4426.2005", "pmcid": "PMC1183279", "issn": "0099-2240", "publisher": "American Society for Microbiology", "publication": "Applied and Environmental Microbiology", "publication_date": "2005-08", "series_number": "8", "volume": "71", "issue": "8", "pages": "4414-4426" }, { "id": "authors:t5qmq-7c359", "collection": "authors", "collection_id": "t5qmq-7c359", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:JIAaem05", "type": "article", "title": "Isolation and Characterization of a Genetically Tractable Photoautotrophic Fe(II)-Oxidizing Bacterium, Rhodopseudomonas palustris Strain TIE-1", "author": [ { "family_name": "Jiao", "given_name": "Yongqin", "clpid": "Jiao-Yongqin" }, { "family_name": "Kappler", "given_name": "Andreas", "clpid": "Kappler-A" }, { "family_name": "Croal", "given_name": "Laura R.", "clpid": "Croal-L-R" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "We report the isolation and characterization of a phototrophic ferrous iron [Fe(II)]-oxidizing bacterium named TIE-1 that differs from other Fe(II)-oxidizing phototrophs in that it is genetically tractable. Under anaerobic conditions, TIE-1 grows photoautotrophically with Fe(II), H2, or thiosulfate as the electron donor and photoheterotrophically with a variety of organic carbon sources. TIE-1 also grows chemoheterotrophically in the dark. This isolate appears to be a new strain of the purple nonsulfur bacterial species Rhodopseudomonas palustris, based on physiological and phylogenetic analysis. Fe(II) oxidation is optimal at pH 6.5 to 6.9. The mineral products of Fe(II) oxidation are pH dependent: below pH 7.0 goethite ({alpha}-FeOOH) forms, and above pH 7.2 magnetite (Fe3O4) forms. TIE-1 forms colonies on agar plates and is sensitive to a variety of antibiotics. A hyperactive mariner transposon is capable of random insertion into the chromosome with a transposition frequency of ~10\u20135. To identify components involved in phototrophic Fe(II) oxidation, mutants of TIE-1 were generated by transposon mutagenesis and screened for defects in Fe(II) oxidation in a cell suspension assay. Among approximately 12,000 mutants screened, 6 were identified that are specifically impaired in Fe(II) oxidation. Five of these mutants have independent disruptions in a gene that is predicted to encode an integral membrane protein that appears to be part of an ABC transport system; the sixth mutant has an insertion in a gene that is a homolog of CobS, an enzyme involved in cobalamin (vitamin B12) biosynthesis.", "doi": "10.1128/AEM.71.8.4487-4496.2005", "pmcid": "PMC1183355", "issn": "0099-2240", "publisher": "American Society for Microbiology", "publication": "Applied and Environmental Microbiology", "publication_date": "2005-08", "series_number": "8", "volume": "71", "issue": "8", "pages": "4487-4496" }, { "id": "authors:2phjt-x1d58", "collection": "authors", "collection_id": "2phjt-x1d58", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130313-153823716", "type": "article", "title": "The potential significance of microbial Fe(III) reduction during deposition of Precambrian banded iron formations", "author": [ { "family_name": "Konhauser", "given_name": "K. O.", "clpid": "Konhauser-K-O" }, { "family_name": "Newman", "given_name": "D. K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Kappler", "given_name": "A.", "clpid": "Kappler-A" } ], "abstract": "During deposition of late Archean\u2013early Palaeoproterozoic Precambrian banded iron formations (BIFs) the downward flux of ferric hydroxide (Fe(OH)_3) and phytoplankton biomass should have facilitated microbial Fe(III) reduction. However, quantifying the significance of such a metabolic pathway in the Precambrian is extremely difficult, considering the post-depositional alteration of the rocks and the lack of ideal modern analogues. Consequently, we have very few constraints on the Fe cycle at that time, namely (i) the concentration of dissolved Fe(II) in the ocean waters; (ii) by what mechanisms Fe(II) was oxidized (chemical, photochemical or biological, the latter using either O_2 or light); (iii) where the ferric hydroxide was precipitated (over the shelf vs. open ocean); (iv) the amount of phytoplankton biomass, which relates to the nutrient status of the surface waters; (v) the relative importance of Fe(III) reduction vs. the other types of metabolic pathways utilized by sea floor microbial communities; and (vi) the proportion of primary vs. diagenetic Fe(II) in BIF. Furthermore, although estimates can be made regarding the quantity of reducing equivalents necessary to account for the diagenetic Fe(II) component in Fe-rich BIF layers, those same estimates do not offer any insights into the magnitude of Fe(III) actually generated within the water column, and hence, the efficiency of Fe and C recycling prior to burial. Accordingly, in this study, we have attempted to model the ancient Fe cycle, based simply on conservative experimental rates of photosynthetic Fe(II) oxidation in the euphotic zone. We estimate here that under ideal growth conditions, as much as 70% of the biologically formed Fe(III) could have been recycled back into the water column via fermentation and organic carbon oxidation coupled to microbial Fe(III) reduction. By comparing the potential amount of biomass generated phototrophically with the reducing equivalents required for Fe(III) reduction and magnetite formation, we also hypothesize that another anaerobic metabolic pathway might have been utilized in the surface sediment to oxidize the fermentation by-products. Based on the premise that the deep ocean waters were anoxic, this role could have been fulfilled by methanogens, and maybe even methanotrophs that employed Fe(III) reduction.", "doi": "10.1111/j.1472-4669.2005.00055.x", "issn": "1472-4677", "publisher": "Blackwell Publishing", "publication": "Geobiology", "publication_date": "2005-07", "series_number": "3", "volume": "3", "issue": "3", "pages": "167-177" }, { "id": "authors:49t5a-xne76", "collection": "authors", "collection_id": "49t5a-xne76", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110816-135040019", "type": "article", "title": "Anaerobic regulation by an atypical Arc system in Shewanella oneidensis", "author": [ { "family_name": "Gralnick", "given_name": "Jeffrey A.", "orcid": "0000-0001-9250-7770", "clpid": "Gralnick-J-A" }, { "family_name": "Brown", "given_name": "C. Titus", "orcid": "0000-0001-6001-2677", "clpid": "Brown-C-T" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Shewanella oneidensis strain MR-1 is well known for its respiratory versatility, yet little is understood about how it regulates genes involved in anaerobic respiration. The Arc two-component system plays an important role in this process in Escherichia coli; therefore, we determined its function in S. oneidensis. arcA from S. oneidensis complements an E. coli arcA mutant, but the Arc regulon in S. oneidensis constitutes a different suite of genes. For example, one of the strongest ArcA-regulated gene clusters in E. coli, sdh, is not regulated by the Arc system in S. oneidensis, and the cyd locus, which is induced by ArcA in E. coli under microaerobic conditions, is repressed by ArcA in S. oneidensis under anaerobic conditions. One locus that we identified as being potentially regulated by ArcA in S. oneidensis contains genes predicted to encode subunits of a dimethyl sulphoxide (DMSO) reductase. We demonstrate that these genes encode a functional DMSO reductase, and that an arcA mutant cannot fully induce their expression and is defective in growing on DMSO under anaerobic conditions. While S. oneidensis lacks a highly conserved full-length ArcB homologue, ArcA is partially activated by a small protein homologous to the histidine phosphotransfer domain of ArcB from E. coli, HptA. This protein alone is unable to compensate for the lack of arcB in E. coli, indicating that another protein is required in addition to HptA to activate ArcA in S. oneidensis.", "doi": "10.1111/j.1365-2958.2005.04628.x", "issn": "0950-382X", "publisher": "Blackwell Publishing", "publication": "Molecular Microbiology", "publication_date": "2005-06", "series_number": "5", "volume": "56", "issue": "5", "pages": "1347-1357" }, { "id": "authors:pqd66-ybc67", "collection": "authors", "collection_id": "pqd66-ybc67", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130327-092401068", "type": "article", "title": "Microbial Kinetic Controls on Calcite Morphology in Supersaturated Solutions", "author": [ { "family_name": "Bosak", "given_name": "Tanja", "clpid": "Bosak-T" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Recognizing microbial imprints in the morphology of calcium carbonate minerals that form in very supersaturated solutions containing a high level of dissolved inorganic carbon (DIC) is challenging. To better define criteria for this purpose, we have analyzed the influence of sulfate-reducing bacterium Desulfovibrio desulfuricans strain G20 on the morphology of calcite in such solutions. G20 does not induce large shifts of pH or alkalinity under these conditions, but its uptake of millimolar sulfate and lactate decreases the number of anhedral crystals and stimulates growth of subhedral spar crystals relative to the abiotic controls. In addition, organic compounds associated with the basal growth medium, purified exopolymeric substances produced by G20 and lypopolysaccharide, stimulate the growth of anhedral crystals and crystals with rounded edges at low supersaturation index (SI) of calcite. The effect of organic compounds is reduced at higher SI, where rhombohedral habits dominate. Our results suggest that the local production and uptake of kinetic inhibitors within microbial biofilms may be an important control on calcite morphology in supersaturated solutions.", "doi": "10.2110/jsr.2005.015", "issn": "1527-1404", "publisher": "Society for Sedimentary Geology", "publication": "Journal of Sedimentary Research", "publication_date": "2005-03", "series_number": "2", "volume": "75", "issue": "2", "pages": "190-199" }, { "id": "authors:m6esb-zcw51", "collection": "authors", "collection_id": "m6esb-zcw51", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130327-074631357", "type": "book_section", "title": "What Genetics Offers Geobiology", "book_title": "Molecular Geomicrobiology", "author": [ { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Gralnick", "given_name": "Jeffrey A.", "orcid": "0000-0001-9250-7770", "clpid": "Gralnick-J-A" } ], "contributor": [ { "family_name": "Banfield", "given_name": "Jillian F.", "clpid": "Banfield-J-F" }, { "family_name": "Cervini-Silva", "given_name": "Javiera", "clpid": "Cervini-Silva-J" }, { "family_name": "Nealson", "given_name": "Kenneth H.", "clpid": "Nealson-K-H" } ], "abstract": "For over 50 years, the Parker Brothers' board game \"Clue\" has maintained its position as the classic family detective game. A murder has been committed in the mansion, but we don't know where, by whom, or how. Was it Professor Plum in the study with a knife, or Miss Scarlett in the ballroom with a candlestick? Through rolls of the dice, fragments of information patiently accumulated piece-by-piece, and the application of logic, players construct a case to figure out \"whodunit\". Because there are several potential solutions to the problem, the key challenge is to figure out what happened by understanding how it happened.", "doi": "10.2138/rmg.2005.59.2", "isbn": "9780939950713", "publisher": "Mineralogical Society of America", "place_of_publication": "Chantilly, VA", "publication_date": "2005", "pages": "9-26" }, { "id": "authors:t3jsk-jav05", "collection": "authors", "collection_id": "t3jsk-jav05", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:CROarg04", "type": "article", "title": "The genetics of geochemistry", "author": [ { "family_name": "Croal", "given_name": "Laura R.", "clpid": "Croal-L-R" }, { "family_name": "Gralnick", "given_name": "Jeffrey A.", "orcid": "0000-0001-9250-7770", "clpid": "Gralnick-J-A" }, { "family_name": "Malasarn", "given_name": "Davin", "clpid": "Malasarn-D" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Bacteria are remarkable in their metabolic diversity due to their ability to harvest energy from myriad oxidation and reduction reactions. In some cases, their metabolisms involve redox transformations of metal(loid)s, which lead to the precipitation, transformation, or dissolution of minerals. Microorganism/mineral interactions not only affect the geochemistry of modern environments, but may also have contributed to shaping the near-surface environment of the early Earth. For example, bacterial anaerobic respiration of ferric iron or the toxic metalloid arsenic is well known to affect water quality in many parts of the world today, whereas the utilization of ferrous iron as an electron donor in anoxygenic photosynthesis may help explain the origin of Banded Iron Formations, a class of ancient sedimentary deposits. Bacterial genetics holds the key to understanding how these metabolisms work. Once the genes and gene products that catalyze geochemically relevant reactions are understood, as well as the conditions that trigger their expression, we may begin to predict when and to what extent these metabolisms influence modern geochemical cycles, as well as develop a basis for deciphering their origins and how organisms that utilized them may have altered the chemical and physical features of our planet.", "doi": "10.1146/annurev.genet.38.072902.091138", "issn": "0066-4197", "publisher": "Annual Reviews", "publication": "Annual Review of Genetics", "publication_date": "2004-12", "volume": "38", "pages": "175-202" }, { "id": "authors:kqn3b-93b51", "collection": "authors", "collection_id": "kqn3b-93b51", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130313-141728101", "type": "article", "title": "arrA Is a Reliable Marker for As(V) Respiration", "author": [ { "family_name": "Malasarn", "given_name": "D.", "clpid": "Malasarn-D" }, { "family_name": "Saltikov", "given_name": "C. W.", "clpid": "Saltikov-C-W" }, { "family_name": "Campbell", "given_name": "K. M.", "clpid": "Campbell-K-M" }, { "family_name": "Santini", "given_name": "J. M.", "clpid": "Santini-J-M" }, { "family_name": "Hering", "given_name": "J. G.", "clpid": "Hering-J-G" }, { "family_name": "Newman", "given_name": "D. K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Arsenate [As(V)]-respiring bacteria affect the speciation and mobilization of arsenic in the environment. This can lead to arsenic contamination of drinking water supplies and deleterious consequences for human health. Using molecular genetics, we show that the functional gene for As(V) respiration, arrA, is highly conserved; that it is required for As(V) reduction to arsenite when arsenic is sorbed onto iron minerals; and that it can be used to identify the presence and activity of As(V)-respiring bacteria in arsenic-contaminated iron-rich sediments. The expression of arrA thus can be used to monitor sites in which As(V)-respiring bacteria may be controlling arsenic geochemistry.", "doi": "10.1126/science.1102374", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2004-10-15", "series_number": "5695", "volume": "306", "issue": "5695", "pages": "455-455" }, { "id": "authors:dtevy-ey619", "collection": "authors", "collection_id": "dtevy-ey619", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130313-094545347", "type": "article", "title": "Micrometer-scale porosity as a biosignature in carbonate crusts", "author": [ { "family_name": "Bosak", "given_name": "Tanja", "clpid": "Bosak-T" }, { "family_name": "Souza-Egipsy", "given_name": "Virginia", "clpid": "Souza-Egipsy-V" }, { "family_name": "Corsetti", "given_name": "Frank A.", "clpid": "Corsetti-F-A" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "We formed calcite crusts in the presence and absence of the heterotrophic bacterium Desulfovibrio desulfuricans strain G20 to investigate microbial morphological signatures in fast-accreting carbonate precipitates. Submicrometer- to micrometer-sized pores (micropores) were present and ubiquitous in the G20 crusts but absent in abiotically precipitated crusts. Bacterial micropores resemble inclusions under transmitted light, but have distinct size, biological shapes and patterns (swirling or dendritic) and are distributed differently from common fluid inclusions. We observed similar porosity in both modern and ancient carbonate crusts of putative biotic origin. Our experiments support the microbial origin of micropores and help define specific criteria whereby to recognize these features as biosignatures in the rock record.", "doi": "10.1130/G20681.1", "issn": "0091-7613", "publisher": "Geological Society of America", "publication": "Geology", "publication_date": "2004-09", "series_number": "9", "volume": "32", "issue": "9", "pages": "781-784" }, { "id": "authors:5t78m-stm15", "collection": "authors", "collection_id": "5t78m-stm15", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130424-104406541", "type": "article", "title": "A laboratory model of abiotic peloid formation", "author": [ { "family_name": "Bosak", "given_name": "T.", "clpid": "Bosak-T" }, { "family_name": "Souza-Egipsy", "given_name": "V.", "clpid": "Souza-Egipsy-V" }, { "family_name": "Newman", "given_name": "D. K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Peloids are rounded grains of micritic calcite whose origin has been attributed to various biological and abiotic\nmechanisms. To constrain abiotic parameters that favour the formation of peloids, we precipitated calcite crusts\nin the absence of microorganisms. Clotted opaque fabrics that formed during the initial stages of the experiment\nconsisted of\n\u223c\n10\n\u03bc\nM\npeloids, while compact clear sparitic crusts precipitated in subsequent stages. The increasing\nsupersaturation of the solution in time is responsible for this morphological succession. Initially, peloids form by\nthe radial growth of spar crystals around a small number of nuclei. As the supersaturation increases, more spar\ncrystals nucleate and aggregate nonradially into compact crusts. Rounded clotted precipitates are a consequence\nof the growth in suspension and geopetal settling, and isopachous crusts grow in the absence of these\nprocesses. Although peloids are commonly assumed to have a microbial origin, our results show that very similar\nmorphologies can be created by purely abiotic mechanisms. Thus, the biological origin of rounded micritic calcite\ngrains in the rock record must be verified against the abiotic null-hypothesis in each specific case.", "doi": "10.1111/j.1472-4677.2004.00031.x", "issn": "1472-4677", "publisher": "Blackwell Publishing", "publication": "Geobiology", "publication_date": "2004-07", "series_number": "3", "volume": "2", "issue": "3", "pages": "189-198" }, { "id": "authors:63ajf-4qk57", "collection": "authors", "collection_id": "63ajf-4qk57", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:KOMpnas04", "type": "article", "title": "Magnetosome vesicles are present before magnetite formation, and MamA is required for their activation", "author": [ { "family_name": "Komeili", "given_name": "Arash", "clpid": "Komeili-A" }, { "family_name": "Vali", "given_name": "Hojatollah", "clpid": "Vali-H" }, { "family_name": "Beveridge", "given_name": "Terrance J.", "clpid": "Beveridge-T-J" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Bacterial magnetosomes are intracellular compartments that house highly ordered magnetite crystals. By using Magnetospirillum sp. AMB-1 as a model system, we show that magnetosome vesicles exist in the absence of magnetite, biomineralization of magnetite proceeds simultaneously in multiple vesicles, and biomineralization proceeds from the same location in each vesicle. The magnetosome-associated protein, MamA, is required for the formation of functional magnetosome vesicles and displays a dynamic subcellular localization throughout the growth cycle of magnetotactic bacteria. Together, these results suggest that the magnetosome precisely coordinates magnetite biomineralization and can serve as a model system for the study of organelle biogenesis in noneukaryotic cells.", "doi": "10.1073/pnas.0400391101", "pmcid": "PMC374331", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2004-03-16", "series_number": "11", "volume": "101", "issue": "11", "pages": "3839-3844" }, { "id": "authors:6n6br-rc034", "collection": "authors", "collection_id": "6n6br-rc034", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130416-134701459", "type": "article", "title": "Iron isotope fractionation by Fe(II)-oxidizing photoautotrophic bacteria", "author": [ { "family_name": "Croal", "given_name": "Laura R.", "clpid": "Croal-L-R" }, { "family_name": "Johnson", "given_name": "Clark M.", "clpid": "Johnson-C-M" }, { "family_name": "Beard", "given_name": "Brian L.", "clpid": "Beard-B-L" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Photoautotrophic bacteria that oxidize ferrous iron (Fe[II]) under anaerobic conditions are thought to be ancient in origin, and the ferric (hydr)oxide mineral products of their metabolism are likely to be preserved in ancient rocks. Here, two enrichment cultures of Fe(II)-oxidizing photoautotrophs and a culture of the genus Thiodictyon were studied with respect to their ability to fractionate Fe isotopes. Fe isotope fractionations produced by both the enrichment cultures and the Thiodictyon culture were relatively constant at early stages of the reaction progress, where the ^(56)Fe/^(54)Fe ratios of poorly crystalline hydrous ferric oxide (HFO) metabolic products were enriched in the heavier isotope relative to aqueous ferrous iron (Fe[II]_(aq)) by \u223c1.5 \u00b1 0.2\u2030. This fractionation appears to be independent of the rate of photoautotrophic Fe(II)-oxidation, and is comparable to that observed for Fe isotope fractionation by dissimilatory Fe(III)-reducing bacteria. Although there remain a number of uncertainties regarding how the overall measured isotopic fractionation is produced, the most likely mechanisms include (1) an equilibrium effect produced by biological ligands, or (2) a kinetic effect produced by precipitation of HFO overlaid upon equilibrium exchange between Fe(II) and Fe(III) species. The fractionation we observe is similar in direction to that measured for abiotic oxidation of Fe(II)_(aq) by molecular oxygen. This suggests that the use of Fe isotopes to identify phototrophic Fe(II)-oxidation in the rock record may only be possible during time periods in Earth's history when independent evidence exists for low ambient oxygen contents.", "doi": "10.1016/j.gca.2003.09.011", "issn": "0016-7037", "publisher": "Elsevier", "publication": "Geochimica et Cosmochimica Acta", "publication_date": "2004-03-15", "series_number": "6", "volume": "68", "issue": "6", "pages": "1227-1242" }, { "id": "authors:6s5ts-6mq40", "collection": "authors", "collection_id": "6s5ts-6mq40", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130313-135113949", "type": "article", "title": "Formation of Fe(III)-minerals by Fe(II)-oxidizing photoautotrophic bacteria", "author": [ { "family_name": "Kappler", "given_name": "Andreas", "clpid": "Kappler-A" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "It has been suggested that Fe(II)-oxidizing photoautotrophic bacteria may have catalyzed the precipitation of an ancient class of sedimentary deposits known as Banded Iron Formations. In order to evaluate this claim, it is necessary to define and understand this process at a molecular level so that putative Fe-isotope \"biosignatures\" in ancient rocks can be interpreted. In this report, we characterize the substrates and products of photoautotrophic Fe(II)-oxidation by three phylogenetically distinct Fe(II)-oxidizing bacteria. In every case, dissolved Fe(II) is used as the substrate for oxidation, and there is no evidence for active dissolution of poorly soluble Fe(II)-minerals by biogenic organic ligands. Poorly crystalline Fe(III) (hydr)oxide mineral phases are initially precipitated, and as they age, rapidly convert to the crystalline minerals goethite and lepidocrocite. Although the precipitates appear to associate with the cell wall, they do not cover it entirely, and precipitate-free cells represent a significant portion of the population in aged cultures. Citrate is occasionally detected at nanomolar concentrations in all culture fluids, whereas an unknown organic molecule is always present in two out of the three bacterial cultures. Whether these molecules are released by the cell to bind Fe(III) and prevent the cell from encrustation by Fe(III) (hydr)oxides is uncertain, but seems unlikely if we assume Fe(II)-oxidation occurs at the cell surface. In light of the energetic requirement the cell would face to produce ligands for this purpose, and given the local acidity metabolically generated in the microenvironment surrounding Fe(II)-oxidizing cells, our results suggest that Fe(III) is released in a dissolved form as an inorganic aqueous complex and/or as a colloidal aggregate prior to mineral precipitation. The implication of these results for the interpretation of Fe-isotope fractionation measured for this class of bacteria (Croal et al., 2004) is that equilibrium processes involving free biological ligands do not account for the observed fractionation.", "doi": "10.1016/j.gca.2003.09.006", "issn": "0016-7037", "publisher": "Elsevier", "publication": "Geochimica et Cosmochimica Acta", "publication_date": "2004-03", "series_number": "6", "volume": "68", "issue": "6", "pages": "1217-1226" }, { "id": "authors:xpwve-k6a93", "collection": "authors", "collection_id": "xpwve-k6a93", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:HERaem04", "type": "article", "title": "Phenazines and Other Redox-Active Antibiotics Promote Microbial Mineral Reduction", "author": [ { "family_name": "Hernandez", "given_name": "Maria E.", "clpid": "Hernandez-M-E" }, { "family_name": "Kappler", "given_name": "Andreas", "clpid": "Kappler-A" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Natural products with important therapeutic properties are known to be produced by a variety of soil bacteria, yet the ecological function of these compounds is not well understood. Here we show that phenazines and other redox-active antibiotics can promote microbial mineral reduction. Pseudomonas chlororaphis PCL1391, a root isolate that produces phenazine-1-carboxamide (PCN), is able to reductively dissolve poorly crystalline iron and manganese oxides, whereas a strain carrying a mutation in one of the phenazine-biosynthetic genes (phzB) is not; the addition of purified PCN restores this ability to the mutant strain. The small amount of PCN produced relative to the large amount of ferric iron reduced in cultures of P. chlororaphis implies that PCN is recycled multiple times; moreover, poorly crystalline iron (hydr)oxide can be reduced abiotically by reduced PCN. This ability suggests that PCN functions as an electron shuttle rather than an iron chelator, a finding that is consistent with the observation that dissolved ferric iron is undetectable in culture fluids. Multiple phenazines and the glycopeptidic antibiotic bleomycin can also stimulate mineral reduction by the dissimilatory iron-reducing bacterium Shewanella oneidensis MR1. Because diverse bacterial strains that cannot grow on iron can reduce phenazines, and because thermodynamic calculations suggest that phenazines have lower redox potentials than those of poorly crystalline iron (hydr)oxides in a range of relevant environmental pH (5 to 9), we suggest that natural products like phenazines may promote microbial mineral reduction in the environment.", "doi": "10.1128/AEM.70.2.921-928.2004", "pmcid": "PMC348881", "issn": "0099-2240", "publisher": "American Society for Microbiology", "publication": "Applied and Environmental Microbiology", "publication_date": "2004-02", "series_number": "2", "volume": "70", "issue": "2", "pages": "921-928" }, { "id": "authors:rymn1-w2g21", "collection": "authors", "collection_id": "rymn1-w2g21", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130502-115233969", "type": "book_section", "title": "Isotopic Constraints on Biogeochemical Cycling of Fe", "book_title": "Geochemistry of Non-Traditional Stable Isotopes", "author": [ { "family_name": "Johnson", "given_name": "Clark M.", "clpid": "Johnson-C-M" }, { "family_name": "Beard", "given_name": "Brian L.", "clpid": "Beard-B-L" }, { "family_name": "Roden", "given_name": "Eric E.", "clpid": "Roden-E-E" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Nealson", "given_name": "Kenneth H.", "orcid": "0000-0001-5189-3732", "clpid": "Nealson-K-H" } ], "contributor": [ { "family_name": "Johnson", "given_name": "Clark M.", "clpid": "Johnson-C-M" }, { "family_name": "Beard", "given_name": "Brian L.", "clpid": "Beard-B-L" }, { "family_name": "Albar\u00e8de", "given_name": "Francis", "clpid": "Albar\u00e8de-F" } ], "abstract": "Cycling of redox-sensitive elements such as Fe is affected by not only ambient Eh-pH conditions, but also by a significant biomass that may derive energy through changes in redox state (e.g., Nealson 1983; Lovely et al. 1987; Myers and Nealson 1988; Ghiorse 1989). The evidence now seems overwhelming that biological processing of redox-sensitive metals is likely to be the rule in surface- and near-surface environments, rather than the exception. The Fe redox cycle of the Earth fundamentally begins with tectonic processes, where \"juvenile\" crust (high-temperature metamorphic and igneous rocks) that contains Fe which is largely in the divalent state is continuously exposed on the surface. If the surface is oxidizing, which is likely for the Earth over at least the last two billion years (e.g., Holland 1984), exposure of large quantities of Fe(II) at the surface represents a tremendous redox disequilibrium. Oxidation of Fe(II) early in Earth's history may have occurred through increases in ambient O2 contents through photosynthesis (e.g., Cloud 1965, 1968), UV-photo oxidation (e.g., Braterman and Cairns-Smith 1987), or anaerobic photosynthetic Fe(II) oxidation (e.g., Hartman 1984; Widdel et al. 1993; Ehrenreich and Widdel 1994). Iron oxides produced by oxidation of Fe(II) represent an important sink for Fe released by terrestrial weathering processes, which will generally be quite reactive. In turn, dissimilatory microbial reduction of ferric oxides, coupled to oxidation of organic carbon and/or H2, is an important process by which Fe(III) is reduced in both modern and ancient sedimentary environments (Lovley 1991; Nealson and Saffarini 1994). Recent microbiological evidence (Vargas et al. 1998), together with a wealth of geochemical information, suggests that microbial Fe(III) reduction may have been one of the earliest forms of respiration on Earth. It therefore seems inescapable that biological redox cycling of Fe has occurred for at least several billion years of Earth's history.", "doi": "10.2138/gsrmg.55.1.359", "isbn": "0-939950-67-7", "publisher": "Mineralogical Society of America", "place_of_publication": "Washington, DC", "publication_date": "2004-01", "pages": "359-408" }, { "id": "authors:nzyvs-ktf34", "collection": "authors", "collection_id": "nzyvs-ktf34", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:SALpnas03", "type": "article", "title": "Genetic identification of a respiratory arsenate reductase", "author": [ { "family_name": "Saltikov", "given_name": "Chad W.", "clpid": "Saltikov-C-W" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "For more than a decade, it has been recognized that arsenate [H2AsO41-; As(V)] can be used by microorganisms as a terminal electron acceptor in anaerobic respiration. Given the toxicity of arsenic, the mechanistic basis of this process is intriguing, as is its evolutionary origin. Here we show that a two-gene cluster (arrAB; arsenate respiratory reduction) in the bacterium Shewanella sp. strain ANA-3 specifically confers respiratory As(V) reductase activity. Mutants with in-frame deletions of either arrA or arrB are incapable of growing on As(V), yet both are able to grow on a wide variety of other electron acceptors as efficiently as the wild-type. Complementation by the wild-type sequence rescues the mutants' ability to respire As(V). arrA is predicted to encode a 95.2-kDa protein with sequence motifs similar to the molybdenum containing enzymes of the dimethyl sulfoxide reductase family. arrB is predicted to encode a 25.7-kDa iron-sulfur protein. arrA and arrB comprise an operon that contains a twin arginine translocation (Tat) motif in ArrA (but not in ArrB) as well as a putative anaerobic transcription factor binding site upstream of arrA, suggesting that the respiratory As(V) reductase is exported to the periplasm via the Tat pathway and under anaerobic transcriptional control. These genes appear to define a new class of reductases that are specific for respiratory As(V) reduction.", "doi": "10.1073/pnas.1834303100", "pmcid": "PMC196913", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2003-09-16", "series_number": "19", "volume": "100", "issue": "19", "pages": "10983-10988" }, { "id": "authors:bvgwz-cw242", "collection": "authors", "collection_id": "bvgwz-cw242", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130313-102137541", "type": "article", "title": "Microbial iron respiration: impacts on corrosion processes", "author": [ { "family_name": "Lee", "given_name": "A. K.", "clpid": "Lee-A-K" }, { "family_name": "Newman", "given_name": "D. K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "In this review, we focus on how biofilms comprising iron-respiring bacteria influence steel corrosion. Specifically, we discuss how biofilm growth can affect the chemistry of the environment around the steel at different stages of biofilm development, under static or dynamic fluid regimes. We suggest that a mechanistic understanding of the role of biofilm metabolic activity may facilitate corrosion control.", "doi": "10.1007/s00253-003-1314-7", "issn": "0175-7598", "publisher": "Springer Verlag", "publication": "Applied Microbiology and Biotechnology", "publication_date": "2003-08", "series_number": "2-3", "volume": "62", "issue": "2-3", "pages": "134-139" }, { "id": "authors:k2req-pky63", "collection": "authors", "collection_id": "k2req-pky63", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130326-102905673", "type": "book_section", "title": "Planar Array REDOX Cells and pH Sensors for ISS Water Quality and Microbe Detection", "author": [ { "family_name": "Buehler", "given_name": "Martin G.", "clpid": "Buehler-M-G" }, { "family_name": "Kuhlman", "given_name": "Gregory M.", "clpid": "Kuhlman-G-M" }, { "family_name": "Myung", "given_name": "Nosang V.", "clpid": "Myung-N-V" }, { "family_name": "Keymeulen", "given_name": "Didier", "clpid": "Keymeulen-D" }, { "family_name": "Kounaves", "given_name": "Samuel P.", "clpid": "Kounaves-S-P" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Lies", "given_name": "Douglas", "clpid": "Lies-D-P" } ], "abstract": "This paper describes results acquired from E-Tongue 2 and E-Tongue 3 which are arrays of planar three-element electrochemical cells and pH sensors. The approach uses ASV (Anodic Stripping Voltammery) to achieve a detection limit, which in the case of Pb, is below one \u03bcM which is needed for water quality measurements. The richness of the detectable species is illustrated with Fe where seven species are identified using the Pourbiax diagram. The detection of multiple species is illustrated using Pb and Cu. The apparatus was used to detect the electroactivity of the metabolic-surrogate, PMS (phenazine-methosulphate). Finally, four types of pH sensors were fabricated and characterized for linearity, sensitivity, and responsiveness.", "doi": "10.4271/2003-01-2553", "publisher": "SAE", "publication_date": "2003-07-07" }, { "id": "authors:wmafz-c5t41", "collection": "authors", "collection_id": "wmafz-c5t41", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130313-083421706", "type": "article", "title": "Microbial nucleation of calcium carbonate in the Precambrian", "author": [ { "family_name": "Bosak", "given_name": "Tanja", "clpid": "Bosak-T" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Microbial sulfate reduction is thought to stimulate carbonate precipitation in modern stromatolites, yet whether this metabolism was important in shaping Precambrian stromatolites is unknown. Here we use geochemical modeling to suggest that the influence of sulfate reduction on the saturation index of calcite (SI) is negligible when seawater is in equilibrium with high pCO_2, as is thought for the Precambrian. Our laboratory experiments with heterotrophic bacteria in a medium mimicking Precambrian seawater chemistry show that even if sulfate reduction does not significantly change the SI, the presence of bacteria stimulates calcite precipitation over sterile controls by effectively increasing the SI over a pH range from 7.3 to 7.8. Under our experimental conditions, dead cells stimulate in situ carbonate precipitation equally, if not more, than active sulfate-reducing bacteria. Heterogeneous nucleation of calcite by microbial cell material appears to be the driving mechanism that explains this phenomenon.", "doi": "10.1130/0091-7613(2003)031<0577:MNOCCI>2.0.CO;2", "issn": "0091-7613", "publisher": "Geological Society of America", "publication": "Geology", "publication_date": "2003-07", "series_number": "7", "volume": "31", "issue": "7", "pages": "577-580" }, { "id": "authors:gx61n-fh568", "collection": "authors", "collection_id": "gx61n-fh568", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:SALaem03", "type": "article", "title": "The ars Detoxification System Is Advantageous but Not Required for As(V) Respiration by the Genetically Tractable Shewanella Species Strain ANA-3", "author": [ { "family_name": "Saltikov", "given_name": "Chad W.", "clpid": "Saltikov-C-W" }, { "family_name": "Cifuentes", "given_name": "Ana", "clpid": "Cifuentes-Ana" }, { "family_name": "Venkateswaran", "given_name": "Kasthuri", "clpid": "Venkateswaran-K" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Arsenate [As(V); HAsO42-] respiration by bacteria is poorly understood at the molecular level largely due to a paucity of genetically tractable organisms with this metabolic capability. We report here the isolation of a new As(V)-respiring strain (ANA-3) that is phylogenetically related to members of the genus Shewanella and that also provides a useful model system with which to explore the molecular basis of As(V) respiration. This gram-negative strain stoichiometrically couples the oxidation of lactate to acetate with the reduction of As(V) to arsenite [As(III); HAsO2]. The generation time and lactate molar growth yield (Ylactate) are 2.8 h and 10.0 g of cells mol of lactate-1, respectively, when it is grown anaerobically on lactate and As(V). ANA-3 uses a wide variety of terminal electron acceptors, including oxygen, soluble ferric iron, oxides of iron and manganese, nitrate, fumarate, the humic acid functional analog 2,6-anthraquinone disulfonate, and thiosulfate. ANA-3 also reduces As(V) to As(III) in the presence of oxygen and resists high concentrations of As(III) (up to 10 mM) when grown under either aerobic or anaerobic conditions. ANA-3 possesses an ars operon (arsDABC) that allows it to resist high levels of As(III); this operon also confers resistance to the As-sensitive strains Shewanella oneidensis MR-1 and Escherichia coli AW3110. When the gene encoding the As(III) efflux pump, arsB, is inactivated in ANA-3 by a polar mutation that also eliminates the expression of arsC, which encodes an As(V) reductase, the resulting As(III)-sensitive strain still respires As(V); however, the generation time and the Ylactate value are two- and threefold lower, respectively, than those of the wild type. These results suggest that ArsB and ArsC may be useful for As(V)-respiring bacteria in environments where As concentrations are high, but that neither is required for respiration.", "doi": "10.1128/AEM.69.5.2800-2809.2003", "pmcid": "PMC154534", "issn": "0099-2240", "publisher": "American Society for Microbiology", "publication": "Applied and Environmental Microbiology", "publication_date": "2003-05", "series_number": "5", "volume": "69", "issue": "5", "pages": "2800-2809" }, { "id": "authors:0s493-9rz97", "collection": "authors", "collection_id": "0s493-9rz97", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130313-105838365", "type": "article", "title": "Geomicrobiology: How Molecular-Scale Interactions Underpin Biogeochemical Systems", "author": [ { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Banfield", "given_name": "Jillian F.", "clpid": "Banfield-J-F" } ], "abstract": "Microorganisms populate every habitable environment on Earth and, through their metabolic activity, affect the chemistry and physical properties of their surroundings. They have done this for billions of years. Over the past decade, genetic, biochemical, and genomic approaches have allowed us to document the diversity of microbial life in geologic systems without cultivation, as well as to begin to elucidate their function. With expansion of culture-independent analyses of microbial communities, it will be possible to quantify gene activity at the species level. Genome-enabled biogeochemical modeling may provide an opportunity to determine how communities function, and how they shape and are shaped by their environments.", "doi": "10.1126/science.1010716", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2002-05-10", "series_number": "5570", "volume": "296", "issue": "5570", "pages": "1071-1077" }, { "id": "authors:qh3rw-p8g63", "collection": "authors", "collection_id": "qh3rw-p8g63", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111103-083806661", "type": "article", "title": "Protective Role of tolC in Efflux of the Electron Shuttle Anthraquinone-2,6-Disulfonate", "author": [ { "family_name": "Shyu", "given_name": "J. Bruce H.", "orcid": "0000-0002-2564-3702", "clpid": "Shyu-J-Bruce-H" }, { "family_name": "Lies", "given_name": "Douglas P.", "clpid": "Lies-D-P" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Extracellular electron transfer can play an important role in microbial respiration on insoluble minerals. The humic acid analog anthraquinone-2,6-disulfonate (AQDS) is commonly used as an electron shuttle during studies of extracellular electron transfer. Here we provide genetic evidence that AQDS enters Shewanella oneidensis strain MR-1 and causes cell death if it accumulates past a critical concentration. A tolC homolog protects the cell from toxicity by mediating the efflux of AQDS. Electron transfer to AQDS appears to be independent of the tolC pathway, however, and requires the outer membrane protein encoded by mtrB. We suggest that there may be structural and functional relationships between quinone-containing electron shuttles and antibiotics.", "doi": "10.1128/JB.184.6.1806-1810.2002", "pmcid": "PMC134904", "issn": "0021-9193", "publisher": "American Society for Microbiology", "publication": "Journal of Bacteriology", "publication_date": "2002-03", "series_number": "6", "volume": "184", "issue": "6", "pages": "1806-1810" }, { "id": "authors:gwmeq-4kv97", "collection": "authors", "collection_id": "gwmeq-4kv97", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:DUBaem02", "type": "article", "title": "Microbial Iron Respiration Can Protect Steel from Corrosion", "author": [ { "family_name": "Dubiel", "given_name": "M.", "clpid": "Dubiel-M" }, { "family_name": "Hsu", "given_name": "C. H.", "clpid": "Hsu-C-H" }, { "family_name": "Chien", "given_name": "C. C.", "clpid": "Chien-C-C" }, { "family_name": "Mansfeld", "given_name": "F.", "clpid": "Mansfeld-F" }, { "family_name": "Newman", "given_name": "D. K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Microbiologically influenced corrosion (MC) of steel has been attributed to the activity of biofilms that include anaerobic microorganisms such as iron-respiring bacteria, yet the mechanisms by which these organisms influence corrosion have been unclear. To study this process, we generated mutants of the iron-respiring bacterium Shewanella oneidensis strain MR-1 that were defective in biofilm formation and/or iron reduction. Electrochemical impedance spectroscopy was used to determine changes in the corrosion rate and corrosion potential as a function of time for these mutants in comparison to the wild type. Counter to prevailing theories of MC, our results indicate that biofilms comprising iron-respiring bacteria may reduce rather than accelerate the corrosion rate of steel. Corrosion inhibition appears to be due to reduction of ferric ions to ferrous ions and increased consumption of oxygen, both of which are direct consequences of microbial respiration.", "doi": "10.1128/AEM.68.3.1440-1445.2002", "pmcid": "PMC123774", "issn": "0099-2240", "publisher": "American Society for Microbiology", "publication": "Applied and Environmental Microbiology", "publication_date": "2002-03", "series_number": "3", "volume": "68", "issue": "3", "pages": "1440-1445" }, { "id": "authors:zxwwx-tg619", "collection": "authors", "collection_id": "zxwwx-tg619", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20131127-130752075", "type": "article", "title": "Oxidation of Arsenite by Agrobacterium albertimagni, AOL15, sp. nov., Isolated from Hot Creek, California", "author": [ { "family_name": "Salmassi", "given_name": "Tina M.", "clpid": "Salmassi-T-M" }, { "family_name": "Venkateswaren", "given_name": "Kasthuri", "clpid": "Venkateswaren-K" }, { "family_name": "Satomi", "given_name": "Masataka", "clpid": "Satomi-Masataka" }, { "family_name": "Nealson", "given_name": "Kenneth H.", "orcid": "0000-0001-5189-3732", "clpid": "Nealson-K-H" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Hering", "given_name": "Janet G.", "clpid": "Hering-J-G" } ], "abstract": "An arsenite-oxidizing bacterium, Agrobacterium albertimagni strain AOL15 (ATCC BAA-24), was isolated from the surface of aquatic macrophytes collected in Hot Creek, California. Under laboratory conditions, whole cell suspensions of AOL15 oxidized arsenite with a K_s of 3.4 \u00b1 2.2\u00b5M and a V_(Max) of 1.81 \u00b1 0.58 x 10^(-12) \u00b5mole \u00b7 cell^(-1)\u00b7 min^(-1) (or 0.043 \u00b1 0.017 \u00b5mole \u00b7 mg protein^(-1)\u00b7 min^(-1)). The K_s value for AOL15 is the lowest value to date reported for whole cell suspensions and is comparable to ambient concentrations of arsenic of 2.7 \u00b5M reported for Hot Creek, indicating that AOL15 can oxidize arsenite under ambient conditions. Previous studies at this site revealed a rapid in situ oxidation of geothermally-derived arsenite while field incubation studies demonstrated that this oxidation was bacterially mediated. The isolation of the arsenite oxidizer AOL15 from this environment supports these previous observations. Arsenite does not support chemolithoautotrophic growth of AOL15 and toxicity studies with AOL15 showed that arsenite (at 5 mM) is toxic to AOL15, yet arsenate concentrations as high as 50 mM do not show any toxic effects. These results suggest that the oxidation of arsenite by AOL15 is a detoxification mechanism.", "doi": "10.1080/014904502317246165", "issn": "0149-0451", "publisher": "Taylor & Francis", "publication": "Geomicrobiology Journal", "publication_date": "2002-01", "series_number": "1", "volume": "19", "issue": "1", "pages": "53-66" }, { "id": "authors:b2erc-exn07", "collection": "authors", "collection_id": "b2erc-exn07", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130327-123845559", "type": "book_section", "title": "Bacterial Respiration of Arsenate and Its Significance in the Environment", "book_title": "Environmental Chemistry of Arsenic", "author": [ { "family_name": "Oremland", "given_name": "Ronald S.", "clpid": "Oremland-R-S" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Kail", "given_name": "Brian W.", "clpid": "Kail-B-W" }, { "family_name": "Stolz", "given_name": "John F.", "clpid": "Stolz-J-F" } ], "contributor": [ { "family_name": "Frankenberger", "given_name": "William T.", "clpid": "Frankenberger-W-T" } ], "abstract": "Although arsenic is a trace element in terms of its natural abundance, it nonetheless\nhas a common presence within the earth's crust. Because it is classified as a\ngroup VB element in the periodic table, it shares many chemical and biochemical\nproperties in common with its neighbors phosphorus and nitrogen. Indeed, in the\ncase of this element's most oxidized (+5) oxidation state, arsenate [HAsO_4^(2-) or\nAs (V)], its toxicity is based on its action as an analog of phosphate. Hence,\narsenate ions uncouple the oxidative phosphorylation normally associated with\nthe enzyme glyceraldehyde 3-phosphate dehydrogenase, thereby preventing the\nformation ofphosphoglyceroyl phosphate, a key high-energy intermediate in glycolysis.\nTo guard against this, a number of bacteria possess a detoxifying arsenate\nreductase pathway (the arsC system) whereby cytoplasmic enzymes remove internal\npools of arsenate by achieving its reduction to arsenite [H_2AsO_3- or As\n(III)]. However, because the arsenite product binds with internal sulfhydryl\ngroups that render it even more toxic than the original arsenate, efficient arsenite\nefflux from the cell is also required and is achieved by an active ion ''pumping'' system (1). The details of this bacterial arsenic detoxification phenomenon have\nbeen well established in the literature, and Chapter 10 in this volume provided\na thorough review. Here, we discuss bacterial respiration of arsenate and its significance\nin the environment. As a biological phenomenon, respiratory growth\non arsenate is quite remarkable, given the toxicity of the element. Moreover, the\nconsequences of microbial arsenate respiration may, at times, have a significant\nimpact on environmental chemistry.", "isbn": "9780824706760", "publisher": "Marcel Dekker", "place_of_publication": "New York", "publication_date": "2002", "pages": "273-295" }, { "id": "authors:0rz94-nkh57", "collection": "authors", "collection_id": "0rz94-nkh57", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130313-084219961", "type": "article", "title": "Extracellular electron transfer", "author": [ { "family_name": "Hernandez", "given_name": "M. E.", "clpid": "Hernandez-M-E" }, { "family_name": "Newman", "given_name": "D. K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Results from several laboratories indicate that extracellular electron transfer may be a general mechanism whereby microoorganisms generate energy for cell growth and/or maintenance. Specifically, bacteria can use redox-active organic small molecules, generated outside or inside the cells, to shuttle electrons between reduced and oxidized compounds. Electron shuttling has now been reported for several different bacterial species, and exchanges of shuttling compounds may even syntrophically link diverse organisms in nature. Biofilm systems in both geological and clinical settings are likely to be important environments for metabolisms that employ extracellular electron transfer. Both structural and functional analyses suggest that electron shuttles and some virulence factors may be related to one another.", "doi": "10.1007/PL00000796", "issn": "1420-682X", "publisher": "Springer", "publication": "Cellular and Molecular Life Sciences", "publication_date": "2001-10", "series_number": "11", "volume": "58", "issue": "11", "pages": "1562-1571" }, { "id": "authors:x8fmg-5ye35", "collection": "authors", "collection_id": "x8fmg-5ye35", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130313-134646042", "type": "article", "title": "How Bacteria Respire Minerals", "author": [ { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "abstract": "Some bacteria respire minerals; that is, they harvest energy from minerals through using them as electron acceptors. Many details of this respiration process have remained obscure. In her Perspective, Newman highlights the study by Lower et al., who have used a customized atomic force microscope to observe bacteria during mineral respiration.", "doi": "10.1126/science.1060572", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2001-05-18", "series_number": "5520", "volume": "292", "issue": "5520", "pages": "1312-1313" }, { "id": "authors:e0bmn-2hb90", "collection": "authors", "collection_id": "e0bmn-2hb90", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130313-111011301", "type": "article", "title": "A role for excreted quinones in extracellular electron transfer", "author": [ { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Kolter", "given_name": "Roberto", "clpid": "Kolter-R" } ], "abstract": "Respiratory processes in bacteria are remarkable because of their ability to use a variety of compounds, including insoluble minerals, as terminal electron acceptors. Although much is known about microbial electron transport to soluble electron acceptors, little is understood about electron transport to insoluble compounds such as ferric oxides. In anaerobic environments, humic substances can serve as electron acceptors and also as electron shuttles to ferric oxides. To explore this process, we identified mutants in Shewanella putrefaciens that are unable to respire on humic substances. Here we show that these mutants contain disruptions in a gene that is involved in the biosynthesis of menaquinone. During growth, the wild type releases a menaquinone-related redox-active small molecule into the medium that complements the mutants. This finding raises the possibility that electron transfer to a variety of oxidants, including poorly soluble minerals, may be mediated by microbially excreted quinones that have yet to be identified.", "doi": "10.1038/35011098", "issn": "0028-0836", "publisher": "Nature Publishing Group", "publication": "Nature", "publication_date": "2000-05-04", "series_number": "6782", "volume": "405", "issue": "6782", "pages": "94-97" }, { "id": "authors:gwj0x-nb211", "collection": "authors", "collection_id": "gwj0x-nb211", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130722-145408915", "type": "book_section", "title": "Arsenic", "book_title": "Encyclopedia of Microbiology, 2nd edition", "author": [ { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "contributor": [ { "family_name": "Lederberg", "given_name": "Joshua", "clpid": "Lederberg-J" } ], "abstract": "Arsenic is relatively abundant in the biosphere\nowing to contamination from a variety of anthropogenic\nsources in addition to its natural occurrence in\nminerals. Since the industrial revolution, arsenic has\nbeen discharged into waterways as a waste product\nof sulfuric acid manufacturing, sprayed onto soils as\na pesticide, dispersed into the air during ore smelting,\nand distributed over the Earth through mining activities.\nAlthough human activities are estimated to release 50,000 tons of arsenic per year, simple weathering\nof igneous and sedimentary rocks (including coal)\nnaturally releases nearly an equal amount of arsenic\ninto the environment. The geochemical cycle of arsenic\nis controlled by a variety of chemical reactions, including\noxidation-reduction, precipitation-dissolution,\nadsorption-desorption, and methylation. Strong evidence\nexists that microorganisms play an important\nrole in these reactions. This article will focus primarily\non the microbial contributions to the cycling of inorganic\narsenic.", "isbn": "9780122268007", "publisher": "Academic Press", "place_of_publication": "San Diego, CA", "publication_date": "2000", "pages": "332-338" }, { "id": "authors:vgfvv-j4756", "collection": "authors", "collection_id": "vgfvv-j4756", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130506-152623748", "type": "book_section", "title": "Genetic approaches to study of biofilms", "book_title": "Biofilms", "author": [ { "family_name": "O'Toole", "given_name": "George A.", "clpid": "O'Toole-G-A" }, { "family_name": "Pratt", "given_name": "Leslie A.", "clpid": "Pratt-L-A" }, { "family_name": "Watnick", "given_name": "Paula I.", "clpid": "Watnick-P-I" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Weaver", "given_name": "Valerie B.", "clpid": "Weaver-V-B" }, { "family_name": "Kolter", "given_name": "Roberto", "clpid": "Kolter-R" } ], "contributor": [ { "family_name": "Doyle", "given_name": "Ronald J.", "clpid": "Doyle-R-J" } ], "abstract": "Interest in the study of microbial biofilms has increased greatly in recent\nyears due in large part to the profound impact biofilms have in clinical,\nindustrial, and natural settings. Traditionally, the study of biofilms has\nbeen approached from an ecological or engineering perspective, using a\ncombination of classical microbiology and advanced microscopy. We and\nothers have begun to use genetic approaches to understand the development\nof these complex communities. To begin we must answer the question:\nWhat is a biofilm? This definition, by necessity, may be quite broad because\nit is clear that many organisms can attach to a variety of surfaces under\ndiverse environmental conditions. Therefore, in the context of this article\nwe will operationally define a biofilm as bacteria that are attached to a\nsurface in sufficient numbers to be detected macroscopically.", "doi": "10.1016/S0076-6879(99)10008-9", "isbn": "9780121822118", "publisher": "Academic Press", "place_of_publication": "San Diego, CA", "publication_date": "1999", "pages": "91-109" }, { "id": "authors:mhx7p-s6r75", "collection": "authors", "collection_id": "mhx7p-s6r75", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130506-085017418", "type": "article", "title": "A brief review of microbial arsenate respiration", "author": [ { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Ahmann", "given_name": "Dianne", "clpid": "Ahmann-D" }, { "family_name": "Morel", "given_name": "Fran\u00e7ois M. M.", "orcid": "0000-0002-6311-7826", "clpid": "Morel-F-M-M" } ], "abstract": "In this review, we summarize the important recent findings relating to arsenate respiration by bacteria. A brief discussion of freshwater arsenic cycling is provided, with attention placed on the microbial contributions to this cycle. The basic evidence for microbial growth on arsenate is presented for studies with both consortia and isolates, followed by a summary of the physiology and phytogeny of four arsenate-respiring bacteria: Chrysiogenes arsenatis strain BAL-1T, Desulfotomaculum auripigmentum strain OREX-4, Sulfurospirillum arsenophilus strain MIT-13, and S. barnesii strain SES-3. Drawing on biochemical studies of the arsenate reductasefrom S. barnesii strain SES-3, a preliminary model for growth on arsenate is proposed. We conclude with a discussion of the importance of microbial arsenate reduction in the environment.", "doi": "10.1080/01490459809378082", "issn": "0149-0451", "publisher": "Taylor & Francis", "publication": "Geomicrobiology Journal", "publication_date": "1998-10", "series_number": "4", "volume": "15", "issue": "4", "pages": "255-268" }, { "id": "authors:7sdbq-ekk65", "collection": "authors", "collection_id": "7sdbq-ekk65", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130410-082430372", "type": "article", "title": "Dissimilatory arsenate and sulfate reduction in Desulfotomaculum auripigmentum sp. nov.", "author": [ { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Kennedy", "given_name": "Erin K.", "clpid": "Kennedy-E-K" }, { "family_name": "Coates", "given_name": "John D.", "clpid": "Coates-J-D" }, { "family_name": "Ahmann", "given_name": "Dianne", "clpid": "Ahmann-D" }, { "family_name": "Ellis", "given_name": "Debra J.", "clpid": "Ellis-D-J" }, { "family_name": "Lovley", "given_name": "Derek R.", "clpid": "Lovley-D-R" }, { "family_name": "Morel", "given_name": "Fran\u00e7ois M. M.", "orcid": "0000-0002-6311-7826", "clpid": "Morel-F-M-M" } ], "abstract": "A newly discovered arsenate-reducing bacterium, strain OREX-4, differed significantly from strains MIT-13 and SES-3, the previously described arsenate-reducing isolates, which grew on nitrate but not on sulfate. In contrast, strain OREX-4 did not respire nitrate but grew on lactate, with either arsenate or sulfate serving as the electron acceptor, and even preferred arsenate. Both arsenate and sulfate reduction were inhibited by molybdate. Strain OREX-4, a gram-positive bacterium with a hexagonal S-layer on its cell wall, metabolized compounds commonly used by sulfate reducers. Scorodite (FeAsO_42\u00b7 H_2O) an arsenate-containing mineral, provided micromolar concentrations of arsenate that supported cell growth. Physiologically and phylogenetically, strain OREX-4 was far-removed from strains MIT-13 and SES-3: strain OREX-4 grew on different electron donors and electron acceptors, and fell within the gram-positive group of the Bacteria, whereas MIT-13 and SES-3 fell together in the \u025b-subdivision of the Proteobacteria. Together, these results suggest that organisms spread among diverse bacterial phyla can use arsenate as a terminal electron acceptor, and that dissimilatory arsenate reduction might occur in the sulfidogenic zone at arsenate concentrations of environmental interest. 16S rRNA sequence analysis indicated that strain OREX-4 is a new species of the genus Desulfotomaculum, and accordingly, the name Desulfotomaculum auripigmentum is proposed.", "doi": "10.1007/s002030050512", "issn": "0302-8933", "publisher": "Springer Verlag", "publication": "Archives of Microbiology", "publication_date": "1997-10-01", "series_number": "5", "volume": "168", "issue": "5", "pages": "380-388" }, { "id": "authors:1hdb5-81j62", "collection": "authors", "collection_id": "1hdb5-81j62", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:NEWaem97", "type": "article", "title": "Precipitation of Arsenic Trisulfide by Desulfotomaculum auripigmentum", "author": [ { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Beveridge", "given_name": "Terry J.", "clpid": "Beveridge-T-J" }, { "family_name": "Morel", "given_name": "Francois M. M.", "orcid": "0000-0002-6311-7826", "clpid": "Morel-F-M-M" } ], "abstract": "A newly discovered bacterium, Desulfotomaculum auripigmentum, precipitates arsenic trisulfide (As(inf2)S(inf3)). Precipitation of As(inf2)S(inf3) by this organism results from its reduction of As(V) to As(III) and S(VI) to S(-II). At the As(III) concentration range of interest (0.1 to 1 mM), the stability of As(inf2)S(inf3) is highly sensitive to pH and [S(-II)]. Thus, the relative rates at which D. auripigmentum reduces As(V) and S(VI) are critical to its formation of As(inf2)S(inf3). Other As(V)- or S(VI)-reducing bacteria are unable to precipitate As(inf2)S(inf3) either due to their inability to reduce both As(V) and S(VI) or because they reduce S(VI) too rapidly. Electron microscopy of thin sections showed that the precipitate forms both intra- and extracellularly. Microbial As(inf2)S(inf3) formation nucleates precipitation of the mineral in the bulk milieu, whereas heat-killed cells alone do not serve as templates for its formation. Precipitation of As(inf2)S(inf3) by D. auripigmentum suggests that As(inf2)S(inf3) formation may be important in the biogeochemical cycle of arsenic.", "issn": "0099-2240", "publisher": "Applied and Environmental Microbiology", "publication": "Applied and Environmental Microbiology", "publication_date": "1997-05", "series_number": "5", "volume": "63", "issue": "5", "pages": "2022-2028" } ]