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He C, Li G, Zou S, Zheng P, Song Q, Li G, Yu Q, Yu Y, Zhang Q, Zhang X, Shen Z, Gong J. Spatial and diel variations of bacterioplankton and pico-nanoeukaryote communities and potential biotic interactions during macroalgal blooms. MARINE POLLUTION BULLETIN 2024; 202:116409. [PMID: 38663343 DOI: 10.1016/j.marpolbul.2024.116409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 05/08/2024]
Abstract
We investigated spatial heterogeneity and diel variations in bacterioplankton and pico-nanoeukaryote communities, and potential biotic interactions at the extinction stage of the Ulva prolifera bloom in the Jiaozhou Bay, Yellow Sea. It was found that the presence of Ulva canopies significantly promoted the cell abundance of heterotrophic bacteria, raised evenness, and altered the community structure of bacterioplankton. A diel pattern was solely significant for pico-nanoeukaryote community structure. >50 % of variation in the heterotrophic bacterial abundance was accounted for by the ratio of Bacteroidota to Firmicutes, and dissolved organic nitrogen effectively explained the variations in cell abundances of phytoplankton populations. The factors representing biotic interactions frequently contributed substantially more than environmental factors in explaining the variations in diversity and community structure of both bacterioplankton and pico-nanoeukaryotes. There were higher proportions of eukaryotic pathogens compared to other marine systems, suggesting a higher ecological risk associated with the Ulva blooms.
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Affiliation(s)
- Cui He
- School of Marine Sciences, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, China
| | - Guihao Li
- Zhuhai Doumen Agricultural Technology Extension, Zhuhai, Guangdong, China
| | - Songbao Zou
- Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang, China
| | - Pengfei Zheng
- Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai 536007, China
| | - Qinqin Song
- Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai 536007, China
| | - Guanzhe Li
- School of Marine Sciences, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, China
| | - Qin Yu
- School of Marine Sciences, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China
| | - Yunjun Yu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou 510535, China
| | - Qianqian Zhang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Xiaoli Zhang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Zhuo Shen
- School of Marine Sciences, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China
| | - Jun Gong
- School of Marine Sciences, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, China.
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Vogt LN, Panis G, Schäpers A, Peschek N, Huber M, Papenfort K, Viollier PH, Fröhlich KS. Genome-wide profiling of Hfq-bound RNAs reveals the iron-responsive small RNA RusT in Caulobacter crescentus. mBio 2024; 15:e0315323. [PMID: 38511926 PMCID: PMC11005374 DOI: 10.1128/mbio.03153-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
The alphaproteobacterium Caulobacter crescentus thrives in oligotrophic environments and is able to optimally exploit minimal resources by entertaining an intricate network of gene expression control mechanisms. Numerous transcriptional activators and repressors have been reported to contribute to these processes, but only few studies have focused on regulation at the post-transcriptional level in C. crescentus. Small RNAs (sRNAs) are a prominent class of regulators of bacterial gene expression, and most sRNAs characterized today engage in direct base-pairing interactions to modulate the translation and/or stability of target mRNAs. In many cases, the ubiquitous RNA chaperone, Hfq, contributes to the establishment of RNA-RNA interactions. Although the deletion of the hfq gene is associated with a severe loss of fitness in C. crescentus, the RNA ligands of the chaperone have remained largely unexplored. Here we report on the identification of coding and non-coding transcripts associated with Hfq in C. crescentus and demonstrate Hfq-dependent post-transcriptional regulation in this organism. We show that the Hfq-bound sRNA RusT is transcriptionally controlled by the NtrYX two-component system and induced in response to iron starvation. By combining RusT pulse expression with whole-genome transcriptome analysis, we determine 16 candidate target transcripts that are deregulated, many of which encode outer membrane transporters. We hence suggest RusT to support remodeling of the C. crescentus cell surface when iron supplies are limited.IMPORTANCEThe conserved RNA-binding protein Hfq contributes significantly to the adaptation of bacteria to different environmental conditions. Hfq not only stabilizes associated sRNAs but also promotes inter-molecular base-pairing interactions with target transcripts. Hfq plays a pivotal role for growth and survival, controlling central metabolism and cell wall synthesis in the oligotroph Caulobacter crescentus. However, direct evidence for Hfq-dependent post-transcriptional regulation and potential oligotrophy in C. crescentus has been lacking. Here, we identified sRNAs and mRNAs associated with Hfq in vivo, and demonstrated the requirement of Hfq for sRNA-mediated regulation, particularly of outer membrane transporters in C. crescentus.
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Affiliation(s)
- Laura N. Vogt
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
- Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Gaël Panis
- Department of Microbiology and Molecular Medicine, Faculty of Medicine/Centre Médical Universitaire, University of Geneva, Geneva, Switzerland
| | - Anna Schäpers
- Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Nikolai Peschek
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
- Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Michaela Huber
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
- Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Kai Papenfort
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
- Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, Munich, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany
| | - Patrick H. Viollier
- Department of Microbiology and Molecular Medicine, Faculty of Medicine/Centre Médical Universitaire, University of Geneva, Geneva, Switzerland
| | - Kathrin S. Fröhlich
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
- Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, Munich, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany
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3
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Zappa S, Berne C, Morton RI, De Stercke J, Brun YV. The HmrABCX pathway regulates the transition between motile and sessile lifestyles in Caulobacter crescentus by a HfiA-independent mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571505. [PMID: 38168291 PMCID: PMC10760086 DOI: 10.1101/2023.12.13.571505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Through its cell cycle, the bacterium Caulobacter crescentus switches from a motile, free-living state, to a sessile surface-attached cell. During this coordinated process, cells undergo irreversible morphological changes, such as shedding of their polar flagellum and synthesis of an adhesive holdfast at the same pole. In this work, we used genetic screens to identify genes involved in the regulation of the motile to sessile lifestyle transition. We identified a predicted hybrid histidine kinase that inhibits biofilm formation and activates the motile lifestyle: HmrA (Holdfast and motility regulator A). Genetic screens and genomic localization led to the identification of additional genes that regulate the proportion of cells harboring an active flagellum or a holdfast and that form a putative phosphorelay pathway with HmrA. Further genetic analysis indicates that the Hmr pathway is independent of the holdfast synthesis regulator HfiA and may impact c-di-GMP synthesis through the diguanylate cyclase DgcB pathway. Finally, we provide evidence that the Hmr pathway is involved in the regulation of sessile-to-motile lifestyle as a function of environmental stresses, namely excess copper and non-optimal temperatures.
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Affiliation(s)
- Sébastien Zappa
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Québec, CANADA
| | - Cecile Berne
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Québec, CANADA
| | - Robert I. Morton
- Department of Biology, Indiana University, Bloomington, IN, USA
- Present address: Boston Scientific, Yokneam, Northern, ISRAEL
| | - Jonathan De Stercke
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Québec, CANADA
- Present address: Unité de Recherche en Biologie des Micro-organismes, Université de Namur, 61 rue de Bruxelles, B-5000 Namur, BELGIUM
| | - Yves V. Brun
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Québec, CANADA
- Department of Biology, Indiana University, Bloomington, IN, USA
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4
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Jung E, Kraimps A, Dittmann S, Griesser T, Costafrolaz J, Mattenberger Y, Jurt S, Viollier PH, Sander P, Sievers S, Gademann K. Phenolic Substitution in Fidaxomicin: A Semisynthetic Approach to Antibiotic Activity Across Species. Chembiochem 2023; 24:e202300570. [PMID: 37728121 DOI: 10.1002/cbic.202300570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 09/21/2023]
Abstract
Fidaxomicin (Fdx) is a natural product antibiotic with potent activity against Clostridioides difficile and other Gram-positive bacteria such as Mycobacterium tuberculosis. Only a few Fdx derivatives have been synthesized and examined for their biological activity in the 50 years since its discovery. Fdx has a well-studied mechanism of action, namely inhibition of the bacterial RNA polymerase. Yet, the targeted organisms harbor different target protein sequences, which poses a challenge for the rational development of new semisynthetic Fdx derivatives. We introduced substituents on the two phenolic hydroxy groups of Fdx and evaluated the resulting trends in antibiotic activity against M. tuberculosis, C. difficile, and the Gram-negative model organism Caulobacter crescentus. As suggested by the target protein structures, we identified the preferable derivatisation site for each organism. The derivative ortho-methyl Fdx also exhibited activity against the Gram-negative C. crescentus wild type, a first for fidaxomicin antibiotics. These insights will guide the synthesis of next-generation fidaxomicin antibiotics.
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Affiliation(s)
- Erik Jung
- Department of Chemistry, University of Zurich, 8057, Zürich, Switzerland
| | - Anastassia Kraimps
- Department of Chemistry, University of Zurich, 8057, Zürich, Switzerland
| | - Silvia Dittmann
- Department of Microbial Physiology and Molecular Biology, Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Tizian Griesser
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Jordan Costafrolaz
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Yves Mattenberger
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Simon Jurt
- Department of Chemistry, University of Zurich, 8057, Zürich, Switzerland
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Peter Sander
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Susanne Sievers
- Department of Microbial Physiology and Molecular Biology, Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Karl Gademann
- Department of Chemistry, University of Zurich, 8057, Zürich, Switzerland
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5
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Costafrolaz J, Panis G, Casu B, Ardissone S, Degeorges L, Pilhofer M, Viollier PH. Adaptive β-lactam resistance from an inducible efflux pump that is post-translationally regulated by the DjlA co-chaperone. PLoS Biol 2023; 21:e3002040. [PMID: 38051727 PMCID: PMC10754441 DOI: 10.1371/journal.pbio.3002040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 12/28/2023] [Accepted: 10/19/2023] [Indexed: 12/07/2023] Open
Abstract
The acquisition of multidrug resistance (MDR) determinants jeopardizes treatment of bacterial infections with antibiotics. The tripartite efflux pump AcrAB-NodT confers adaptive MDR in the polarized α-proteobacterium Caulobacter crescentus via transcriptional induction by first-generation quinolone antibiotics. We discovered that overexpression of AcrAB-NodT by mutation or exogenous inducers confers resistance to cephalosporin and penicillin (β-lactam) antibiotics. Combining 2-step mutagenesis-sequencing (Mut-Seq) and cephalosporin-resistant point mutants, we dissected how TipR uses a common operator of the divergent tipR and acrAB-nodT promoter for adaptive and/or potentiated AcrAB-NodT-directed efflux. Chemical screening identified diverse compounds that interfere with DNA binding by TipR or induce its dependent proteolytic turnover. We found that long-term induction of AcrAB-NodT deforms the envelope and that homeostatic control by TipR includes co-induction of the DnaJ-like co-chaperone DjlA, boosting pump assembly and/or capacity in anticipation of envelope stress. Thus, the adaptive MDR regulatory circuitry reconciles drug efflux with co-chaperone function for trans-envelope assemblies and maintenance.
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Affiliation(s)
- Jordan Costafrolaz
- Department of Microbiology and Molecular Medicine, Faculty of Medicine/Centre Médical Universitaire, University of Geneva, Geneva, Switzerland
| | - Gaël Panis
- Department of Microbiology and Molecular Medicine, Faculty of Medicine/Centre Médical Universitaire, University of Geneva, Geneva, Switzerland
| | - Bastien Casu
- Department of Biology, Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Silvia Ardissone
- Department of Microbiology and Molecular Medicine, Faculty of Medicine/Centre Médical Universitaire, University of Geneva, Geneva, Switzerland
| | - Laurence Degeorges
- Department of Microbiology and Molecular Medicine, Faculty of Medicine/Centre Médical Universitaire, University of Geneva, Geneva, Switzerland
| | - Martin Pilhofer
- Department of Biology, Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Patrick H. Viollier
- Department of Microbiology and Molecular Medicine, Faculty of Medicine/Centre Médical Universitaire, University of Geneva, Geneva, Switzerland
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Li T, Wang X, Wang X, Huang J, Shen L. Mechanisms Driving the Distribution and Activity of Mineralization and Nitrification in the Reservoir Riparian Zone. MICROBIAL ECOLOGY 2023; 86:1829-1846. [PMID: 36702929 DOI: 10.1007/s00248-023-02180-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
The riparian zone ecosystems have greater energy flow and elemental cycling than adjacent terrestrial and aquatic ecosystems. Mineralization and nitrification are important initiating processes in the nitrogen cycle, but their distribution and activity under different environmental conditions in the riparian zone and the driving mechanisms are still not clear. We investigated the effects of environmental and microbial factors on mineralization and nitrification activities by analyzing the community of alkaline (apr) and neutral (npr) metallopeptidase, ammonia-oxidizing archaea (AOA), and bacteria (AOB) in soils and sediments under different land-use types in the riparian zone of Miyun Reservoir, as well as measuring potential nitrogen mineralization and ammonia oxidation rates (AOR). The results showed that the mineralization and nitrification activities of soils were greater than those of sediments. AOA and AOB dominate the ammonia oxidation activity of soil and sediment, respectively. NH4+ content was a key factor influencing the ecological niche differentiation between AOA and AOB. The high carbon and nitrogen content of the woodland significantly increased mineralization and nitrification activity. Microbial communities were significantly clustered in the woodland. The land-use type, not the flooding condition, determined the distribution of microbial community structure. The diversity of npr was significantly correlated with potential N mineralization rates, while the transcript abundance of AOA was significantly correlated with ammonia oxidation rates. Our study suggests that environmental changes regulate the distribution and activity of mineralization and nitrification processes in the reservoir riparian zone by affecting the transcript abundance, diversity and community structure of the microbial functional genes.
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Affiliation(s)
- Tingting Li
- College of Resources, Environment and Tourism, Capital Normal University, No. 105, North West Third Ring Road, Haidian District, Beijing, 100048, China
| | - Xiaoyan Wang
- College of Resources, Environment and Tourism, Capital Normal University, No. 105, North West Third Ring Road, Haidian District, Beijing, 100048, China.
| | - Xia Wang
- College of Resources, Environment and Tourism, Capital Normal University, No. 105, North West Third Ring Road, Haidian District, Beijing, 100048, China
| | - Jingyu Huang
- College of Resources, Environment and Tourism, Capital Normal University, No. 105, North West Third Ring Road, Haidian District, Beijing, 100048, China
| | - Lei Shen
- College of Resources, Environment and Tourism, Capital Normal University, No. 105, North West Third Ring Road, Haidian District, Beijing, 100048, China
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Louis G, Cherry P, Michaux C, Rahuel-Clermont S, Dieu M, Tilquin F, Maertens L, Van Houdt R, Renard P, Perpete E, Matroule JY. A cytoplasmic chemoreceptor and reactive oxygen species mediate bacterial chemotaxis to copper. J Biol Chem 2023; 299:105207. [PMID: 37660909 PMCID: PMC10579534 DOI: 10.1016/j.jbc.2023.105207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 08/16/2023] [Accepted: 08/23/2023] [Indexed: 09/05/2023] Open
Abstract
Chemotaxis is a widespread strategy used by unicellular and multicellular living organisms to maintain their fitness in stressful environments. We previously showed that bacteria can trigger a negative chemotactic response to a copper (Cu)-rich environment. Cu ion toxicity on bacterial cell physiology has been mainly linked to mismetallation events and reactive oxygen species (ROS) production, although the precise role of Cu-generated ROS remains largely debated. Here, using inductively coupled plasma optical emission spectrometry on cell fractionates, we found that the cytoplasmic Cu ion content mirrors variations of the extracellular Cu ion concentration. ROS-sensitive fluorescent probe and biosensor allowed us to show that the increase of cytoplasmic Cu ion content triggers a dose-dependent oxidative stress, which can be abrogated by superoxide dismutase and catalase overexpression. The inhibition of ROS production in the cytoplasm not only improves bacterial growth but also impedes Cu chemotaxis, indicating that ROS derived from cytoplasmic Cu ions mediate the control of bacterial chemotaxis to Cu. We also identified the Cu chemoreceptor McpR, which binds Cu ions with low affinity, suggesting a labile interaction. In addition, we demonstrate that the cysteine 75 and histidine 99 within the McpR sensor domain are key residues in Cu chemotaxis and Cu coordination. Finally, we discovered that in vitro both Cu(I) and Cu(II) ions modulate McpR conformation in a distinct manner. Overall, our study provides mechanistic insights on a redox-based control of Cu chemotaxis, indicating that the cellular redox status can play a key role in bacterial chemotaxis.
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Affiliation(s)
- Gwennaëlle Louis
- Research Unit in Biology of Microorganisms (URBM), Department of Biology, Namur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
| | - Pauline Cherry
- Research Unit in Biology of Microorganisms (URBM), Department of Biology, Namur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
| | - Catherine Michaux
- Laboratoire de Chimie Physique des Biomolécules, Namur Research Institute for Life Sciences (NARILIS) and Namur Institute of Structured Matter (NISM), University of Namur, Namur, Belgium
| | | | - Marc Dieu
- MaSUN, Mass Spectrometry Facility, University of Namur, Namur, Belgium
| | - Françoise Tilquin
- Research Unit in Biology of Microorganisms (URBM), Department of Biology, Namur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
| | - Laurens Maertens
- Research Unit in Biology of Microorganisms (URBM), Department of Biology, Namur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium; Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Rob Van Houdt
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Patricia Renard
- MaSUN, Mass Spectrometry Facility, University of Namur, Namur, Belgium
| | - Eric Perpete
- Laboratoire de Chimie Physique des Biomolécules, Namur Research Institute for Life Sciences (NARILIS) and Namur Institute of Structured Matter (NISM), University of Namur, Namur, Belgium
| | - Jean-Yves Matroule
- Research Unit in Biology of Microorganisms (URBM), Department of Biology, Namur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium.
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8
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Kint N, Viollier PH. Extracellular transfer of a conserved polymerization factor for multi-flagellin filament assembly in Caulobacter. Cell Rep 2023; 42:112890. [PMID: 37515768 DOI: 10.1016/j.celrep.2023.112890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 06/15/2023] [Accepted: 07/12/2023] [Indexed: 07/31/2023] Open
Abstract
Unidirectional growth of filamentous protein assemblies including the bacterial flagellum relies on dedicated polymerization factors (PFs). The molecular determinants and structural transitions imposed by PFs on multi-subunit assembly are poorly understood. Here, we unveil FlaY from the polarized α-proteobacterium Caulobacter crescentus as a defining member of an alternative class of specialized flagellin PFs. Unlike the paradigmatic FliD capping protein, FlaY relies on a funnel-like β-propeller fold for flagellin polymerization. FlaY binds flagellin and is secreted by the flagellar secretion apparatus, yet it can also promote flagellin polymerization exogenously when donated from flagellin-deficient cells, serving as a transferable, extracellular public good. While the surge in FlaY abundance precedes bulk flagellin synthesis, FlaY-independent filament assembly is enhanced by mutation of a conserved region in multiple flagellin paralogs. We suggest that FlaYs are (multi-)flagellin PFs that evolved convergently to FliDs yet appropriated the versatile β-propeller fold implicated in human diseases for chaperone-assisted filament assembly.
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Affiliation(s)
- Nicolas Kint
- Department of Microbiology & Molecular Medicine and Geneva Center for Inflammation Research (GCIR), Faculty of Medicine, University of Geneva, Rue Michel Servet 1, 1211 Genève, Switzerland.
| | - Patrick H Viollier
- Department of Microbiology & Molecular Medicine and Geneva Center for Inflammation Research (GCIR), Faculty of Medicine, University of Geneva, Rue Michel Servet 1, 1211 Genève, Switzerland.
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9
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Surveying membrane landscapes: a new look at the bacterial cell surface. Nat Rev Microbiol 2023:10.1038/s41579-023-00862-w. [PMID: 36828896 DOI: 10.1038/s41579-023-00862-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2023] [Indexed: 02/26/2023]
Abstract
Recent studies applying advanced imaging techniques are changing the way we understand bacterial cell surfaces, bringing new knowledge on everything from single-cell heterogeneity in bacterial populations to their drug sensitivity and mechanisms of antimicrobial resistance. In both Gram-positive and Gram-negative bacteria, the outermost surface of the bacterial cell is being imaged at nanoscale; as a result, topographical maps of bacterial cell surfaces can be constructed, revealing distinct zones and specific features that might uniquely identify each cell in a population. Functionally defined assembly precincts for protein insertion into the membrane have been mapped at nanoscale, and equivalent lipid-assembly precincts are suggested from discrete lipopolysaccharide patches. As we review here, particularly for Gram-negative bacteria, the applications of various modalities of nanoscale imaging are reawakening our curiosity about what is conceptually a 3D cell surface landscape: what it looks like, how it is made and how it provides resilience to respond to environmental impacts.
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10
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Synchronized Swarmers and Sticky Stalks: Caulobacter crescentus as a Model for Bacterial Cell Biology. J Bacteriol 2023; 205:e0038422. [PMID: 36715542 PMCID: PMC9945503 DOI: 10.1128/jb.00384-22] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
First isolated and classified in the 1960s, Caulobacter crescentus has been instrumental in the study of bacterial cell biology and differentiation. C. crescentus is a Gram-negative alphaproteobacterium that exhibits a dimorphic life cycle composed of two distinct cell types: a motile swarmer cell and a nonmotile, division-competent stalked cell. Progression through the cell cycle is accentuated by tightly controlled biogenesis of appendages, morphological transitions, and distinct localization of developmental regulators. These features as well as the ability to synchronize populations of cells and follow their progression make C. crescentus an ideal model for answering questions relevant to how development and differentiation are achieved at the single-cell level. This review will explore the discovery and development of C. crescentus as a model organism before diving into several key features and discoveries that have made it such a powerful organism to study. Finally, we will summarize a few of the ongoing areas of research that are leveraging knowledge gained over the last century with C. crescentus to highlight its continuing role at the forefront of cell and developmental biology.
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11
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Berne C, Zappa S, Brun YV. eDNA-stimulated cell dispersion from Caulobacter crescentus biofilms upon oxygen limitation is dependent on a toxin-antitoxin system. eLife 2023; 12:80808. [PMID: 36475544 PMCID: PMC9851616 DOI: 10.7554/elife.80808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
In their natural environment, most bacteria preferentially live as complex surface-attached multicellular colonies called biofilms. Biofilms begin with a few cells adhering to a surface, where they multiply to form a mature colony. When conditions deteriorate, cells can leave the biofilm. This dispersion is thought to be an important process that modifies the overall biofilm architecture and that promotes colonization of new environments. In Caulobacter crescentus biofilms, extracellular DNA (eDNA) is released upon cell death and prevents newborn cells from joining the established biofilm. Thus, eDNA promotes the dispersal of newborn cells and the subsequent colonization of new environments. These observations suggest that eDNA is a cue for sensing detrimental environmental conditions in the biofilm. Here, we show that the toxin-antitoxin system (TAS) ParDE4 stimulates cell death in areas of a biofilm with decreased O2 availability. In conditions where O2 availability is low, eDNA concentration is correlated with cell death. Cell dispersal away from biofilms is decreased when parDE4 is deleted, probably due to the lower local eDNA concentration. Expression of parDE4 is positively regulated by O2 and the expression of this operon is decreased in biofilms where O2 availability is low. Thus, a programmed cell death mechanism using an O2-regulated TAS stimulates dispersal away from areas of a biofilm with decreased O2 availability and favors colonization of a new, more hospitable environment.
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Affiliation(s)
- Cecile Berne
- Département de microbiologie, infectiologie et immunologie, Université de MontréalMontréalCanada
| | - Sébastien Zappa
- Département de microbiologie, infectiologie et immunologie, Université de MontréalMontréalCanada
| | - Yves V Brun
- Département de microbiologie, infectiologie et immunologie, Université de MontréalMontréalCanada
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12
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Shapiro L. A Half Century Defining the Logic of Cellular Life. Annu Rev Genet 2022; 56:1-15. [DOI: 10.1146/annurev-genet-071719-021436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Over more than fifty years, I have studied how the logic that controls and integrates cell function is built into the dynamic architecture of living cells. I worked with a succession of exceptionally talented students and postdocs, and we discovered that the bacterial cell is controlled by an integrated genetic circuit in which transcriptional and translational controls are interwoven with the three-dimensional deployment of key regulatory and morphological proteins. Caulobacter's interconnected genetic regulatory network includes logic that regulates sets of genes expressed at specific times in the cell cycle and mechanisms that synchronize the advancement of the core cyclical circuit with chromosome replication and cytokinesis. Here, I have traced my journey from New York City art student to Stanford developmental biologist.
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Affiliation(s)
- Lucy Shapiro
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
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13
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Next generation sequencing technologies to explore the diversity of germplasm resources: achievements and trends in tomato. Comput Struct Biotechnol J 2022; 20:6250-6258. [PMID: 36420160 PMCID: PMC9676195 DOI: 10.1016/j.csbj.2022.11.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/10/2022] [Accepted: 11/10/2022] [Indexed: 11/14/2022] Open
Abstract
Tomato is one of the major vegetable crops grown worldwide and a model species for genetic and biological research. Progress in genomic technologies made possible the development of forefront methods for high-scale sequencing, providing comprehensive insight into the genetic architecture of germplasm resources. This review revisits next-generation sequencing strategies and applications to investigate the diversity of tomato, describing the common platforms used for SNP genotyping of large collections, de novo sequencing, and whole genome resequencing. Significant findings in evolutionary history are outlined, thus discussing how genomics has provided new hints about the processes behind domestication. Finally, achievement and perspectives on pan-genome construction and graphical pan-genome development toward precise mining of the natural variation to be exploited for breeding purposes are presented.
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14
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New Multidrug Efflux Systems in a Microcystin-Degrading Bacterium Blastomonas fulva and Its Genomic Feature. Int J Mol Sci 2022; 23:ijms231810856. [PMID: 36142771 PMCID: PMC9505733 DOI: 10.3390/ijms231810856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
A microcystin-degrading bacterial strain, Blastomonas fulva T2, was isolated from the culture of a microalgae Microcystis. The strain B. fulva T2 is Gram-stain-negative, non-motile, aerobic, non-spore-forming and phototrophic. The cells of B. fulva T2 are able to grow in ranges of temperature from 15 to 37 °C, with a pH of 6 to 8 and a salinity of 0 to 1% NaCl. Here, we sequenced the complete genome of B. fulva T2, aiming to better understand the evolutionary biology and the function of the genus Blastomonas at the molecular level. The complete genome of B. fulva T2 contained a circular chromosome (3,977,381 bp) with 64.3% GC content and a sizable plasmid (145.829 bp) with 60.7% GC content which comprises about 3.5% of the total genetic content. A total of 3842 coding genes, including 46 tRNAs and 6 rRNAs, were predicted in the genome. The genome contains genes for glycolysis, citric acid cycle, Entner–Doudoroff pathways, photoreaction center and bacteriochlorophylla synthesis. A 7.9 K gene cluster containing mlrA, mlrB, mlrC and mlrD1,2,3,4 of microcystin-degrading enzymes was identified. Notably, eight different efflux pumps categorized into RND, ABC and MFS types have been identified in the genome of strain T2. Our findings should provide new insights of the alternative reaction pathway as well as the enzymes which mediated the degradation of microcystin by bacteria, as well as the evolution, architectures, chemical mechanisms and physiological roles of the new bacterial multidrug efflux system.
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15
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Liu Q, Hao LF, Chen Y, Liu ZC, Xing WW, Zhang C, Fu WL, Xu DG. The Screening and Expression of Polysaccharide Deacetylase from Caulobacter crescentus and Its Function Analysis. Biotechnol Appl Biochem 2022; 70:688-696. [PMID: 35932185 DOI: 10.1002/bab.2390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 07/12/2022] [Indexed: 11/06/2022]
Abstract
The bacterium Caulobacter crescentus secretes an adhesive polysaccharide called holdfast which is the known strongest underwater adhesive in nature. The deacetylase encoded by hfs (holdfast synthesis) H gene is a key factor affecting the adhesion of holdfast. Its structure and function are not yet clear, and whether other polysaccharide deacetylases exist in C. crescentus is still unknown. The screening of both HfsH and its structural analogue as well as their purification from the artificial expression products of E. coli. is the first step to clarify these questions. Here, we determined the conserved domains of HfsH via sequence alignment among Carbohydrate Esterase family 4 enzymes and screened out its structural analogue (CC_2574) in C. crescentus. The recombinant HfsH and CC_2574 were effectively expressed in E. coli. Both of them were purified by chromatography from their corresponding productions in E. coli., and were then functionally analyzed. The results indicated that a high deacetylase activity (61.8 U/mg) was observed in recombinant HfsH but not in CC_2574, which suggesting that HfsH might be the irreplaceable gene mediating adhesion of holdfast in C. crescentus. Moreover, the divalent metal ions Zn2+ , Mg2+ , Mn2+ could promote the activity of recombinant HfsH at the concentration from 0.05mM to 1mM, but inhibit its activity when the concentration exceeds 1mM. In sum, our study firstly realized the artificial production of polysaccharide deacetylase HfsH and its structural analogue, and further explored their functions, both of which laid the foundation for the development of new adhesive materials. Expression of polysaccharide deacetylase HfsH promoting the adhesion of holdfast The effects of various metal ions on the deacetylase activity of recombinant HfsH Functional analysis of recombinant polysaccharide deacetylase Screening of functional analogue of HfsH in Caulobacter crescentus based on ts conserved domains This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Qing Liu
- Beijing Institute of Basic Medical Sciences, Beijing, 100850, China
| | - Li-Fang Hao
- College of Pharmaceutical Sciences, Hebei University, Baoding, Hebei, 071002, China
| | - Yao Chen
- Beijing Institute of Basic Medical Sciences, Beijing, 100850, China
| | - Zhong-Cheng Liu
- College of Pharmaceutical Sciences, Hebei University, Baoding, Hebei, 071002, China
| | - Wei-Wei Xing
- Beijing Institute of Basic Medical Sciences, Beijing, 100850, China
| | - Chao Zhang
- Beijing Institute of Basic Medical Sciences, Beijing, 100850, China
| | - Wen-Liang Fu
- Beijing Institute of Basic Medical Sciences, Beijing, 100850, China
| | - Dong-Gang Xu
- Beijing Institute of Basic Medical Sciences, Beijing, 100850, China
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16
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Padilla-Gómez J, Olea-Ozuna RJ, Contreras-Martínez S, Morales-Tarré O, García-Soriano DA, Sahonero-Canavesi DX, Poggio S, Encarnación-Guevara S, López-Lara IM, Geiger O. Specialized acyl carrier protein used by serine palmitoyltransferase to synthesize sphingolipids in Rhodobacteria. Front Microbiol 2022; 13:961041. [PMID: 35992722 PMCID: PMC9386255 DOI: 10.3389/fmicb.2022.961041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Serine palmitoyltransferase (SPT) catalyzes the first and committed step in sphingolipid biosynthesis condensating L-serine and acyl-CoA to form 3-oxo-sphinganine. Whenever the structural gene for SPT is present in genomes of Rhodobacteria (α-, β-, and γ-Proteobacteria), it co-occurs with genes coding for a putative acyl carrier protein (ACP) and a putative acyl-CoA synthetase (ACS). In the α-proteobacterium Caulobacter crescentus, CC_1162 encodes an SPT, whereas CC_1163 and CC_1165 encode the putative ACP and ACS, respectively, and all three genes are known to be required for the formation of the sphingolipid intermediate 3-oxo-sphinganine. Here we show that the putative ACP possesses a 4'-phosphopantetheine prosthetic group, is selectively acylated by the putative ACS and therefore is a specialized ACP (AcpR) required for sphingolipid biosynthesis in Rhodobacteria. The putative ACS is unable to acylate coenzyme A or housekeeping ACPs, but acylates specifically AcpR. Therefore, it is a specialized acyl-ACP synthetase (AasR). SPTs from C. crescentus, Escherichia coli B, or Sphingomonas wittichii use preferentially acyl-AcpR as thioester substrate for 3-oxo-sphinganine synthesis. Whereas acyl-AcpR from C. crescentus is a good substrate for SPTs from distinct Rhodobacteria, acylation of a specific AcpR is achieved by the cognate AasR from the same bacterium. Rhodobacteria might use this more complex way of 3-oxo-sphinganine formation in order to direct free fatty acids toward sphingolipid biosynthesis.
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Affiliation(s)
- Jonathan Padilla-Gómez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | | | - Orlando Morales-Tarré
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | | | - Sebastian Poggio
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | | | - Isabel M. López-Lara
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Otto Geiger
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
- *Correspondence: Otto Geiger,
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17
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Ely B, Berrios L, Thomas Q. S2B, a Temperate Bacteriophage That Infects Caulobacter Crescentus Strain CB15. Curr Microbiol 2022; 79:98. [PMID: 35150327 DOI: 10.1007/s00284-022-02799-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 02/01/2022] [Indexed: 11/29/2022]
Abstract
The Caulobacter crescentus strain CB15 has been the basis of numerous studies designed to characterize the biphasic life cycle of this bacterium. Here we describe a newly isolated podovirus, designated S2B, which is capable of integrating into the CB15 chromosome by recombining with the 3'-end of a particular tRNA-ser gene. In addition, we show that S2B is a representative of a family of closely related prophages that are present in the genomes of characterized strains from several Alphaproteobacteria genera. In contrast, only distantly related bacteriophage genomes are present in the GenBank database. The 42,846 bp S2B genome includes 262 bp terminal repeats, and it contains 62 genes of which 45 code for proteins of unknown function. Proteins with predicted functions include a T7 DNA polymerase, a T3/T7 RNA polymerase, and a T7 helicase/primase suggesting that S2B is part of the Studiervirinae subfamily of the Autographiviridae family.
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Affiliation(s)
- Bert Ely
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, US.
| | - Louis Berrios
- Department of Biology, Stanford University, Stanford, CA, 94305, US
| | - Quill Thomas
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, US
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18
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Berrios L. The genus Caulobacter and its role in plant microbiomes. World J Microbiol Biotechnol 2022; 38:43. [PMID: 35064419 DOI: 10.1007/s11274-022-03237-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/17/2022] [Indexed: 11/27/2022]
Abstract
Recent omics approaches have revealed the prevalent microbial taxa that constitute the microbiome of various plant species. Across global scales and environmental conditions, strains belonging to the bacterial genus Caulobacter have consistently been found in association with various plant species. Aligned with agroecological relevance and biotechnological advances, many scientific communications have demonstrated that several Caulobacter strains (spanning several Caulobacter species) harbor the potential to enhance plant biomass for various plant species ranging from Arabidopsis to Citrullus and Zea mays. In the past several years, co-occurrence data have driven mechanistically resolved communications about select Caulobacter-plant interactions. Given the long-standing history of Caulobacter as a model organism for cell cycle regulation, genetic studies, and the prevalence of Caulobacter species in various plant microbiomes, the genus Caulobacter offers researchers a unique opportunity to leverage for investigating plant-microbe interactions and realizing targeted biotechnological applications. In this review, recent developments regarding Caulobacter-plant interactions are presented in terms of model utility for future biotechnological investigations.
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Affiliation(s)
- Louis Berrios
- Department of Biology, Stanford University, Stanford, CA, USA.
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19
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Plasmids Bring Additional Capabilities to Caulobacter Isolates. Curr Microbiol 2022; 79:45. [PMID: 34982248 PMCID: PMC8812328 DOI: 10.1007/s00284-021-02742-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 12/06/2021] [Indexed: 01/07/2023]
Abstract
Caulobacter is a well-studied bacterial genus, but little is known about the plasmids that are found in some wild Caulobacter isolates. We used bioinformatic approaches to identify nine plasmids from seven different Caulobacter strains and grouped them based on their size and the similarity of their repABC, parAB, and mobAB genes. Protein pathway analysis of the genes on the K31p1 and K31p2 plasmids showed many metabolic pathways that would enhance the metabolic versatility of the host strain. In contrast, the CB4 plasmid contained 21 heavy metal resistance genes with the majority coding for proteins that enhance copper resistance. Growth assays of C. henricii CB4 demonstrated increased copper resistance and quantitative PCR showed an increase in the expression of eight heavy metal genes when induced with copper.
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20
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Kint N, Unay J, Viollier PH. Specificity and modularity of flagellin nonulosonic acid glycosyltransferases. Trends Microbiol 2021; 30:109-111. [PMID: 34782242 DOI: 10.1016/j.tim.2021.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 12/28/2022]
Abstract
Many bacterial flagella are specifically O-glycosylated with nonulosonic acids, including the sialic acid derivatives, pseudaminic acid or legionaminic acid. Unlike protein glycosyltransferases that are extracytoplasmic, flagellin glycosyltransferases (fGTs) act cytoplasmically with unknown donor or acceptor specificities. The recent reconstitution of fGT-based glycosylation in heterologous hosts enables analyses underpinning such specificity.
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Affiliation(s)
- Nicolas Kint
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Jovelyn Unay
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
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21
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Gogou C, Japaridze A, Dekker C. Mechanisms for Chromosome Segregation in Bacteria. Front Microbiol 2021; 12:685687. [PMID: 34220773 PMCID: PMC8242196 DOI: 10.3389/fmicb.2021.685687] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/19/2021] [Indexed: 11/13/2022] Open
Abstract
The process of DNA segregation, the redistribution of newly replicated genomic material to daughter cells, is a crucial step in the life cycle of all living systems. Here, we review DNA segregation in bacteria which evolved a variety of mechanisms for partitioning newly replicated DNA. Bacterial species such as Caulobacter crescentus and Bacillus subtilis contain pushing and pulling mechanisms that exert forces and directionality to mediate the moving of newly synthesized chromosomes to the bacterial poles. Other bacteria such as Escherichia coli lack such active segregation systems, yet exhibit a spontaneous de-mixing of chromosomes due to entropic forces as DNA is being replicated under the confinement of the cell wall. Furthermore, we present a synopsis of the main players that contribute to prokaryotic genome segregation. We finish with emphasizing the importance of bottom-up approaches for the investigation of the various factors that contribute to genome segregation.
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Affiliation(s)
- Christos Gogou
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Aleksandre Japaridze
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
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22
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Neubauer D, Kolmakova O, Woodhouse J, Taube R, Mangelsdorf K, Gladyshev M, Premke K, Grossart HP. Zooplankton carcasses stimulate microbial turnover of allochthonous particulate organic matter. THE ISME JOURNAL 2021; 15:1735-1750. [PMID: 33462364 PMCID: PMC8163850 DOI: 10.1038/s41396-020-00883-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 12/07/2020] [Accepted: 12/11/2020] [Indexed: 01/04/2023]
Abstract
Carbon turnover in aquatic environments is dependent on biochemical properties of organic matter (OM) and its degradability by the surrounding microbial community. Non-additive interactive effects represent a mechanism where the degradation of biochemically persistent OM is stimulated by the provision of bioavailable OM to the degrading microbial community. Whilst this is well established in terrestrial systems, whether it occurs in aquatic ecosystems remains subject to debate. We hypothesised that OM from zooplankton carcasses can stimulate the degradation of biochemically persistent leaf material, and that this effect is influenced by the daphnia:leaf OM ratio and the complexity of the degrading microbial community. Fresh Daphnia magna carcasses and 13C-labelled maize leaves (Zea mays) were incubated at different ratios (1:1, 1:3 and 1:5) alongside either a complex microbial community (<50 µm) or solely bacteria (<0.8 µm). 13C stable-isotope measurements of CO2 analyses were combined with phospholipid fatty acids (PLFA) analysis and DNA sequencing to link metabolic activities, biomass and taxonomic composition of the microbial community. Our experiments indicated a significantly higher respiration of leaf-derived C when daphnia-derived OM was most abundant (i.e. daphnia:leaf OM ratio of 1:1). This process was stronger in a complex microbial community, including eukaryotic microorganisms, than a solely bacterial community. We concluded that non-additive interactive effects were a function of increased C-N chemodiversity and microbial complexity, with the highest net respiration to be expected when chemodiversity is high and the degrading community complex. This study indicates that identifying the interactions and processes of OM degradation is one important key for a deeper understanding of aquatic and thus global carbon cycle.
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Affiliation(s)
- Darshan Neubauer
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Experimental Limnology, 16775, Stechlin, Germany.
- Institute of Biochemistry and Biology, Potsdam University, 14476, Potsdam, Germany.
| | - Olesya Kolmakova
- Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, Russia
- Siberian Federal University, Institute of Fundamental Biology and Biotechnology, Krasnoyarsk, Russia
| | - Jason Woodhouse
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Experimental Limnology, 16775, Stechlin, Germany
| | - Robert Taube
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Experimental Limnology, 16775, Stechlin, Germany
- Institute of Biochemistry and Biology, Potsdam University, 14476, Potsdam, Germany
| | - Kai Mangelsdorf
- GFZ German Research Centre -for Geosciences, Helmholtz Centre Potsdam, Section 3.2 Organic Geochemistry, 14473, Potsdam, Germany
| | - Michail Gladyshev
- Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, Russia
- Siberian Federal University, Institute of Fundamental Biology and Biotechnology, Krasnoyarsk, Russia
| | - Katrin Premke
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Chemical Analytics and Biogeochemistry, Müggelseedamm 310, 12587, Berlin, Germany
| | - Hans-Peter Grossart
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Experimental Limnology, 16775, Stechlin, Germany.
- Institute of Biochemistry and Biology, Potsdam University, 14476, Potsdam, Germany.
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23
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DeBofsky A, Xie Y, Challis JK, Jain N, Brinkmann M, Jones PD, Giesy JP. Responses of juvenile fathead minnow (Pimephales promelas) gut microbiome to a chronic dietary exposure of benzo[a]pyrene. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 278:116821. [PMID: 33706240 DOI: 10.1016/j.envpol.2021.116821] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 02/10/2021] [Accepted: 02/20/2021] [Indexed: 06/12/2023]
Abstract
The microbiome has been described as an additional host "organ" with well-established beneficial roles. However, the effects of exposures to chemicals on both structure and function of the gut microbiome of fishes are understudied. To determine effects of benzo[a]pyrene (BaP), a model persistent organic pollutant, on structural shifts of gut microbiome in juvenile fathead minnows (Pimephales promelas), fish were exposed ad libitum in the diet to concentrations of 1, 10, 100, or 1000 μg BaP g-1 food, in addition to a vehicle control, for two weeks. To determine the link between exposure to BaP and changes in the microbial community, concentrations of metabolites of BaP were measured in fish bile and 16S rRNA amplicon sequencing was used to evaluate the microbiome. Exposure to BaP only reduced alpha-diversity at the greatest exposure concentrations. However, it did alter community composition assessed as differential abundance of taxa and reduced network complexity of the microbial community in all exposure groups. Results presented here illustrate that environmentally-relevant concentrations of BaP can alter the diversity of the gut microbiome and community network connectivity.
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Affiliation(s)
- Abigail DeBofsky
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yuwei Xie
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
| | - Jonathan K Challis
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Niteesh Jain
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Markus Brinkmann
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada; School of Environment and Sustainability, University of Saskatchewan, Saskatoon, Saskatchewan, Canada; Global Institute for Water Security, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Paul D Jones
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada; School of Environment and Sustainability, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - John P Giesy
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada; Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada; Department of Environmental Science, Baylor University, Waco, TX, USA
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24
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A localized adaptor protein performs distinct functions at the Caulobacter cell poles. Proc Natl Acad Sci U S A 2021; 118:2024705118. [PMID: 33753507 PMCID: PMC8020655 DOI: 10.1073/pnas.2024705118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Asymmetric cell division yields two distinct daughter cells by mechanisms that underlie stem cell behavior and cellular diversity in all organisms. The bacterium Caulobacter crescentus is able to orchestrate this complex process with less than 4,000 genes. This article describes a strategy deployed by Caulobacter where a regulatory protein, PopA, is programed to perform distinct roles based on its subcellular address. We demonstrate that, depending on the availability of a second messenger molecule, PopA adopts either a monomer or dimer form. The two oligomeric forms interact with different partners at the two cell poles, playing a critical role in the degradation of a master transcription factor at one pole and flagellar assembly at the other pole. Asymmetric cell division generates two daughter cells with distinct characteristics and fates. Positioning different regulatory and signaling proteins at the opposing ends of the predivisional cell produces molecularly distinct daughter cells. Here, we report a strategy deployed by the asymmetrically dividing bacterium Caulobacter crescentus where a regulatory protein is programmed to perform distinct functions at the opposing cell poles. We find that the CtrA proteolysis adaptor protein PopA assumes distinct oligomeric states at the two cell poles through asymmetrically distributed c-di-GMP: dimeric at the stalked pole and monomeric at the swarmer pole. Different polar organizing proteins at each cell pole recruit PopA where it interacts with and mediates the function of two molecular machines: the ClpXP degradation machinery at the stalked pole and the flagellar basal body at the swarmer pole. We discovered a binding partner of PopA at the swarmer cell pole that together with PopA regulates the length of the flagella filament. Our work demonstrates how a second messenger provides spatiotemporal cues to change the physical behavior of an effector protein, thereby facilitating asymmetry.
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25
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Cao Y, Jiang G, Li M, Fang X, Zhu D, Qiu W, Zhu J, Yu D, Xu Y, Zhong Z, Zhu J. Glutaredoxins Play an Important Role in the Redox Homeostasis and Symbiotic Capacity of Azorhizobium caulinodans ORS571. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:1381-1393. [PMID: 32970520 DOI: 10.1094/mpmi-04-20-0098-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Glutaredoxin (GRX) plays an essential role in the control of the cellular redox state and related pathways in many organisms. There is limited information on GRXs from the model nitrogen (N2)-fixing bacterium Azorhizobium caulinodans. In the present work, we identified and performed functional analyses of monothiol and dithiol GRXs in A. caulinodans in the free-living state and during symbiosis with Sesbania rostrata. Our data show that monothiol GRXs may be very important for bacterial growth under normal conditions and in response to oxidative stress due to imbalance of the redox state in grx mutants of A. caulinodans. Functional redundancies were also observed within monothiol and dithiol GRXs in terms of different physiological functions. The changes in catalase activity and iron content in grx mutants were assumed to favor the maintenance of bacterial resistance against oxidants, nodulation, and N2 fixation efficiency in this bacterium. Furthermore, the monothiol GRX12 and dithiol GRX34 play a collective role in symbiotic associations between A. caulinodans and Sesbania rostrata. Our study provided systematic evidence that further investigations are required to understand the importance of glutaredoxins in A. caulinodans and other rhizobia.
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Affiliation(s)
- Yajun Cao
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, PR China
| | - Gaofei Jiang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Postdoctoral Station of Agricultural Resources and Environment, Nanjing Agricultural University, 210095 Nanjing, PR China
| | - Mingxu Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, PR China
| | - Xingxing Fang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, PR China
| | - Dan Zhu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, PR China
| | - Wei Qiu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, PR China
| | - Juanjuan Zhu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, PR China
| | - Daogeng Yu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Science, 571737 Danzhou, Hainan, PR China
| | - Yangchun Xu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Postdoctoral Station of Agricultural Resources and Environment, Nanjing Agricultural University, 210095 Nanjing, PR China
| | - Zengtao Zhong
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, PR China
| | - Jun Zhu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, PR China
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Konttinen O, Carmody J, Pathuri S, Anderson K, Zhou X, Reich N. Cell cycle regulated DNA methyltransferase: fluorescent tracking of a DNA strand-separation mechanism and identification of the responsible protein motif. Nucleic Acids Res 2020; 48:11589-11601. [PMID: 33053173 PMCID: PMC7672430 DOI: 10.1093/nar/gkaa844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/10/2020] [Accepted: 09/23/2020] [Indexed: 12/23/2022] Open
Abstract
DNA adenine methylation by Caulobacter crescentus Cell Cycle Regulated Methyltransferase (CcrM) is an important epigenetic regulator of gene expression. The recent CcrM-DNA cocrystal structure shows the CcrM dimer disrupts four of the five base pairs of the (5'-GANTC-3') recognition site. We developed a fluorescence-based assay by which Pyrrolo-dC tracks the strand separation event. Placement of Pyrrolo-dC within the DNA recognition site results in a fluorescence increase when CcrM binds. Non-cognate sequences display little to no fluorescence changes, showing that strand separation is a specificity determinant. Conserved residues in the C-terminal segment interact with the phospho-sugar backbone of the non-target strand. Replacement of these residues with alanine results in decreased methylation activity and changes in strand separation. The DNA recognition mechanism appears to occur with the Type II M.HinfI DNA methyltransferase and an ortholog of CcrM, BabI, but not with DNA methyltransferases that lack the conserved C-terminal segment. The C-terminal segment is found broadly in N4/N6-adenine DNA methyltransferases, some of which are human pathogens, across three Proteobacteria classes, three other phyla and in Thermoplasma acidophilum, an Archaea. This Pyrrolo-dC strand separation assay should be useful for the study of other enzymes which likely rely on a strand separation mechanism.
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Affiliation(s)
- Olivia Konttinen
- Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, CA 93103, USA
| | - Jason Carmody
- Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA 93103, USA
| | - Sarath Pathuri
- Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA 93103, USA
| | - Kyle Anderson
- Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA 93103, USA
| | - Xiaofeng Zhou
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Norbert Reich
- Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, CA 93103, USA
- Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA 93103, USA
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Shyp V, Dubey BN, Böhm R, Hartl J, Nesper J, Vorholt JA, Hiller S, Schirmer T, Jenal U. Reciprocal growth control by competitive binding of nucleotide second messengers to a metabolic switch in Caulobacter crescentus. Nat Microbiol 2020; 6:59-72. [PMID: 33168988 DOI: 10.1038/s41564-020-00809-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 10/02/2020] [Indexed: 12/13/2022]
Abstract
Bacteria use small signalling molecules such as (p)ppGpp or c-di-GMP to tune their physiology in response to environmental changes. It remains unclear whether these regulatory networks operate independently or whether they interact to optimize bacterial growth and survival. We report that (p)ppGpp and c-di-GMP reciprocally regulate the growth of Caulobacter crescentus by converging on a single small-molecule-binding protein, SmbA. While c-di-GMP binding inhibits SmbA, (p)ppGpp competes for the same binding site to sustain SmbA activity. We demonstrate that (p)ppGpp specifically promotes Caulobacter growth on glucose, whereas c-di-GMP inhibits glucose consumption. We find that SmbA contributes to this metabolic switch and promotes growth on glucose by quenching the associated redox stress. The identification of an effector protein that acts as a central regulatory hub for two global second messengers opens up future studies on specific crosstalk between small-molecule-based regulatory networks.
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Affiliation(s)
| | | | - Raphael Böhm
- Biozentrum, University of Basel, Basel, Switzerland
| | - Johannes Hartl
- Institute of Microbiology, ETH Zurich, Zürich, Switzerland
| | - Jutta Nesper
- Biozentrum, University of Basel, Basel, Switzerland
| | | | | | | | - Urs Jenal
- Biozentrum, University of Basel, Basel, Switzerland.
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Ardissone S, Kint N, Petrignani B, Panis G, Viollier PH. Secretion Relieves Translational Co-repression by a Specialized Flagellin Paralog. Dev Cell 2020; 55:500-513.e4. [DOI: 10.1016/j.devcel.2020.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/28/2020] [Accepted: 10/05/2020] [Indexed: 12/12/2022]
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Ardissone S, Kint N, Viollier PH. Specificity in glycosylation of multiple flagellins by the modular and cell cycle regulated glycosyltransferase FlmG. eLife 2020; 9:e60488. [PMID: 33108275 PMCID: PMC7591256 DOI: 10.7554/elife.60488] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 09/24/2020] [Indexed: 12/12/2022] Open
Abstract
How specificity is programmed into post-translational modification of proteins by glycosylation is poorly understood, especially for O-linked glycosylation systems. Here we reconstitute and dissect the substrate specificity underpinning the cytoplasmic O-glycosylation pathway that modifies all six flagellins, five structural and one regulatory paralog, in Caulobacter crescentus, a monopolarly flagellated alpha-proteobacterium. We characterize the biosynthetic pathway for the sialic acid-like sugar pseudaminic acid and show its requirement for flagellation, flagellin modification and efficient export. The cognate NeuB enzyme that condenses phosphoenolpyruvate with a hexose into pseudaminic acid is functionally interchangeable with other pseudaminic acid synthases. The previously unknown and cell cycle-regulated FlmG protein, a defining member of a new class of cytoplasmic O-glycosyltransferases, is required and sufficient for flagellin modification. The substrate specificity of FlmG is conferred by its N-terminal flagellin-binding domain. FlmG accumulates before the FlaF secretion chaperone, potentially timing flagellin modification, export, and assembly during the cell division cycle.
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Affiliation(s)
- Silvia Ardissone
- Department of Microbiology & Molecular Medicine, Faculty of Medicine / CMU, University of GenevaGenèveSwitzerland
| | - Nicolas Kint
- Department of Microbiology & Molecular Medicine, Faculty of Medicine / CMU, University of GenevaGenèveSwitzerland
| | - Patrick H Viollier
- Department of Microbiology & Molecular Medicine, Faculty of Medicine / CMU, University of GenevaGenèveSwitzerland
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Suárez-Esquivel M, Chaves-Olarte E, Moreno E, Guzmán-Verri C. Brucella Genomics: Macro and Micro Evolution. Int J Mol Sci 2020; 21:E7749. [PMID: 33092044 PMCID: PMC7589603 DOI: 10.3390/ijms21207749] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/08/2020] [Accepted: 10/11/2020] [Indexed: 01/25/2023] Open
Abstract
Brucella organisms are responsible for one of the most widespread bacterial zoonoses, named brucellosis. The disease affects several species of animals, including humans. One of the most intriguing aspects of the brucellae is that the various species show a ~97% similarity at the genome level. Still, the distinct Brucella species display different host preferences, zoonotic risk, and virulence. After 133 years of research, there are many aspects of the Brucella biology that remain poorly understood, such as host adaptation and virulence mechanisms. A strategy to understand these characteristics focuses on the relationship between the genomic diversity and host preference of the various Brucella species. Pseudogenization, genome reduction, single nucleotide polymorphism variation, number of tandem repeats, and mobile genetic elements are unveiled markers for host adaptation and virulence. Understanding the mechanisms of genome variability in the Brucella genus is relevant to comprehend the emergence of pathogens.
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Affiliation(s)
- Marcela Suárez-Esquivel
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia 3000, Costa Rica; (M.S.-E.); (E.M.)
| | - Esteban Chaves-Olarte
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José 1180, Costa Rica;
| | - Edgardo Moreno
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia 3000, Costa Rica; (M.S.-E.); (E.M.)
| | - Caterina Guzmán-Verri
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia 3000, Costa Rica; (M.S.-E.); (E.M.)
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José 1180, Costa Rica;
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Jacomini D, Bussler L, Corrêa JM, Kadowaki MK, Maller A, da-Conceição Silva JL, Simão RDCG. Cloning, expression and characterization of C. crescentus xynA2 gene and application of Xylanase II in the deconstruction of plant biomass. Mol Biol Rep 2020; 47:4427-4438. [PMID: 32424521 DOI: 10.1007/s11033-020-05507-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 05/08/2020] [Indexed: 11/24/2022]
Abstract
Biotechnology offers innovative alternatives for industrial bioprocesses mainly because it uses enzymes that biodegrade the hemicellulose releasing fermentable sugars. Caulobacter crescentus (C. crescentus) has seven genes responsible for xylanolytic cleavage, 5 to β-xylosidases (EC 3.2.1.37) and 2 for endoxylanases, like xynA2 (CCNA_03137) that encodes Xylanase II (EC 3.2.1.8) of the glycohydrolases-GH10 group. The xynA2 gene was amplified by PCR, cloned into the pTrcHisA vector e efficiently overexpressed in E. coli providing a His-tag fusion protein. Recombinant xylanase (XynA2) was purified by affinity chromatography using a nickel sepharose column and exhibited a single 43 kDa band on SDS-PAGE gel. XynA2 showed an optimum alkaline pH (8) and stability at alkaline pH for 24 h. Although C. crescentus is mesophilic, XynA2 has optimum temperature of 60 °C and is thermo-resistance at 65 °C. XynA maintains 66% of the enzymatic activity at high temperatures (90 °C) without being denatured.The enzyme displayed a xylanolitic activity free of cellulase to xylan from beechwood and it was not inhibited in the presence of 50 μmol mL-1 of xylose. In addition, dithiothreitol (DTT) induced XynA2 activity, as it improved its kinetic parameters by lowering the KM (5.78 μmol mL-1) and increasing the KCat/KM ratio (1.63 U s-1). Finally, C. crescentus XynA2 efficiently hydrolyzed corn straw with high release of reducing sugars that can be applied in different branches of the industry.
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Affiliation(s)
- Débora Jacomini
- Laboratório de Bioquímica Molecular, Centro de Ciências Exatas e Tecnológicas, Universidade Estadual do Oeste do Paraná, Cascavel,, Paraná, 85814-110, Brazil
| | - Larissa Bussler
- Laboratório de Bioquímica Molecular, Centro de Ciências Exatas e Tecnológicas, Universidade Estadual do Oeste do Paraná, Cascavel,, Paraná, 85814-110, Brazil
| | - Juliana Moço Corrêa
- Laboratório de Bioquímica Molecular, Centro de Ciências Médicas e Farmacêuticas, Universidade Estadual do Oeste do Paraná, Rua Universitária, 2069, Cascavel, PR, 85814-110, Brazil
| | - Marina Kimiko Kadowaki
- Laboratório de Bioquímica Molecular, Centro de Ciências Médicas e Farmacêuticas, Universidade Estadual do Oeste do Paraná, Rua Universitária, 2069, Cascavel, PR, 85814-110, Brazil
| | - Alexandre Maller
- Laboratório de Bioquímica Molecular, Centro de Ciências Médicas e Farmacêuticas, Universidade Estadual do Oeste do Paraná, Rua Universitária, 2069, Cascavel, PR, 85814-110, Brazil
| | - José Luis da-Conceição Silva
- Laboratório de Bioquímica Molecular, Centro de Ciências Médicas e Farmacêuticas, Universidade Estadual do Oeste do Paraná, Rua Universitária, 2069, Cascavel, PR, 85814-110, Brazil
| | - Rita de Cássia Garcia Simão
- Laboratório de Bioquímica Molecular, Centro de Ciências Exatas e Tecnológicas, Universidade Estadual do Oeste do Paraná, Cascavel,, Paraná, 85814-110, Brazil. .,Laboratório de Bioquímica Molecular, Centro de Ciências Médicas e Farmacêuticas, Universidade Estadual do Oeste do Paraná, Rua Universitária, 2069, Cascavel, PR, 85814-110, Brazil.
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Loss of Bacterial Cell Pole Stabilization in Caulobacter crescentus Sensitizes to Outer Membrane Stress and Peptidoglycan-Directed Antibiotics. mBio 2020; 11:mBio.00538-20. [PMID: 32371598 PMCID: PMC7403779 DOI: 10.1128/mbio.00538-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Maintenance of an intact cell envelope is essential for free-living bacteria to protect themselves against their environment. In the case of rod-shaped bacteria, the poles of the cell are potential weak points in the cell envelope due to the high curvature of the layers and the need to break and reform the cell envelope at the division plane as the cells divide. We have found that TipN, a factor required for correct division and cell pole development in Caulobacter crescentus, is also needed for maintaining normal levels of resistance to cell wall-targeting antibiotics such as vancomycin and cefixime, which interfere with peptidoglycan synthesis. Since TipN is normally located at the poles of the cell and at the division plane just before cells complete division, our results suggest that it is involved in stabilization of these weak points of the cell envelope as well as its other roles inside the cell. Rod-shaped bacteria frequently localize proteins to one or both cell poles in order to regulate processes such as chromosome replication or polar organelle development. However, the roles of polar factors in responses to extracellular stimuli have been generally unexplored. We employed chemical-genetic screening to probe the interaction between one such factor from Caulobacter crescentus, TipN, and extracellular stress and found that TipN is required for normal resistance of cell envelope-directed antibiotics, including vancomycin which does not normally inhibit growth of Gram-negative bacteria. Forward genetic screening for suppressors of vancomycin sensitivity in the absence of TipN revealed the TonB-dependent receptor ChvT as the mediator of vancomycin sensitivity. Loss of ChvT improved resistance to vancomycin and cefixime in the otherwise sensitive ΔtipN strain. The activity of the two-component system regulating ChvT (ChvIG) was increased in ΔtipN cells relative to the wild type under some, but not all, cell wall stress conditions that this strain was sensitized to, in particular cefixime and detergent exposure. Together, these results indicate that TipN contributes to cell envelope stress resistance in addition to its roles in intracellular development, and its loss influences signaling through the ChvIG two-component system which has been co-opted as a sensor of cell wall stress in Caulobacter.
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Moore GM, Gitai Z. Both clinical and environmental Caulobacter species are virulent in the Galleria mellonella infection model. PLoS One 2020; 15:e0230006. [PMID: 32163465 PMCID: PMC7067423 DOI: 10.1371/journal.pone.0230006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/18/2020] [Indexed: 01/18/2023] Open
Abstract
The Caulobacter genus, including the widely-studied model organism Caulobacter crescentus, has been thought to be non-pathogenic and thus proposed as a bioengineering vector for various environmental remediation and medical purposes. However, Caulobacter species have been implicated as the causative agents of several hospital-acquired infections, raising the question of whether these clinical isolates represent an emerging pathogenic species or whether Caulobacters on whole possess previously-unappreciated virulence capability. Given the proposed environmental and medical applications for C. crescentus, understanding the potential pathogenicity of this bacterium is crucial. Consequently, we sequenced a clinical Caulobacter isolate to determine if it has acquired novel virulence determinants. We found that the clinical isolate represents a new species, Caulobacter mirare that, unlike C. crescentus, grows well in standard clinical culture conditions. C. mirare phylogenetically resembles both C. crescentus and the related C. segnis, which was also thought to be non-pathogenic. The similarity to other Caulobacters and lack of obvious pathogenesis markers suggested that C. mirare is not unique amongst Caulobacters and that consequently other Caulobacters may also have the potential to be virulent. We tested this hypothesis by characterizing the ability of Caulobacters to infect the model animal host Galleria mellonella. In this context, two different lab strains of C. crescentus proved to be as pathogenic as C. mirare, while lab strains of E. coli were non-pathogenic. Further characterization showed that Caulobacter pathogenesis in the Galleria model is mediated by lipopolysaccharide (LPS), and that differences in LPS chemical composition across species could explain their differential toxicity. Taken together, our findings suggest that many Caulobacter species can be virulent in specific contexts and highlight the importance of broadening our methods for identifying and characterizing potential pathogens.
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Affiliation(s)
- Gabriel M. Moore
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
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Comparative Analysis of Ionic Strength Tolerance between Freshwater and Marine Caulobacterales Adhesins. J Bacteriol 2019; 201:JB.00061-19. [PMID: 30858293 DOI: 10.1128/jb.00061-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 03/08/2019] [Indexed: 11/20/2022] Open
Abstract
Bacterial adhesion is affected by environmental factors, such as ionic strength, pH, temperature, and shear forces. Therefore, marine bacteria must have developed adhesins with different compositions and structures than those of their freshwater counterparts to adapt to their natural environment. The dimorphic alphaproteobacterium Hirschia baltica is a marine budding bacterium in the clade Caulobacterales H. baltica uses a polar adhesin, the holdfast, located at the cell pole opposite the reproductive stalk, for surface attachment and cell-cell adhesion. The holdfast adhesin has been best characterized in Caulobacter crescentus, a freshwater member of the Caulobacterales, and little is known about holdfast compositions and properties in marine Caulobacterales Here, we use H. baltica as a model to characterize holdfast properties in marine Caulobacterales We show that freshwater and marine Caulobacterales use similar genes in holdfast biogenesis and that these genes are highly conserved among the species in the two genera. We determine that H. baltica produces a larger holdfast than C. crescentus and that the holdfasts have different chemical compositions, as they contain N-acetylglucosamine and galactose monosaccharide residues and proteins but lack DNA. Finally, we show that H. baltica holdfasts tolerate higher ionic strength than those of C. crescentus We conclude that marine Caulobacterales holdfasts have physicochemical properties that maximize binding in high-ionic-strength environments.IMPORTANCE Most bacteria spend a large part of their life spans attached to surfaces, forming complex multicellular communities called biofilms. Bacteria can colonize virtually any surface, and therefore, they have adapted to bind efficiently in very different environments. In this study, we compare the adhesive holdfasts produced by the freshwater bacterium C. crescentus and a relative, the marine bacterium H. baltica We show that H. baltica holdfasts have a different morphology and chemical composition and tolerate high ionic strength. Our results show that the H. baltica holdfast is an excellent model to study the effect of ionic strength on adhesion and provides insights into the physicochemical properties required for adhesion in the marine environment.
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Ozaki S. Regulation of replication initiation: lessons from Caulobacter crescentus. Genes Genet Syst 2019; 94:183-196. [PMID: 31495806 DOI: 10.1266/ggs.19-00011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Chromosome replication is a fundamental process in all domains of life. To accurately transmit genetic material to offspring, the initiation of chromosome replication is tightly regulated to ensure that it occurs only once in each cell division cycle. In the model bacterium Caulobacter crescentus, the CtrA response regulator inhibits the origin of replication at the pre-replication stage. Inactivation of CtrA permits the universal DnaA initiator to form an initiation complex at the origin, leading to replication initiation. Subsequently, the initiation complex is inactivated to prevent extra initiation. Whereas DNA replication occurs periodically in exponentially growing cells, replication initiation is blocked under various stress conditions to halt cell cycle progression until the normal condition is restored or the cells adapt to the stress. Thus, regulating the initiation complex plays an important role in not only driving cell cycle progression, but also maintaining cell integrity under stress. Multiple regulatory signaling pathways controlling CtrA and DnaA have been identified and recent studies have advanced our knowledge of the underlying mechanistic and molecular processes. This review focuses on how bacterial cells control replication initiation, highlighting the latest findings that have emerged from studies in C. crescentus.
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Affiliation(s)
- Shogo Ozaki
- Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University
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Role of Caulobacter Cell Surface Structures in Colonization of the Air-Liquid Interface. J Bacteriol 2019; 201:JB.00064-19. [PMID: 31010900 DOI: 10.1128/jb.00064-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/15/2019] [Indexed: 01/17/2023] Open
Abstract
In aquatic environments, Caulobacter spp. can be found at the boundary between liquid and air known as the neuston. I report an approach to study temporal features of Caulobacter crescentus colonization and pellicle biofilm development at the air-liquid interface and have defined the role of cell surface structures in this process. At this interface, C. crescentus initially forms a monolayer of cells bearing a surface adhesin known as the holdfast. When excised from the liquid surface, this monolayer strongly adheres to glass. The monolayer subsequently develops into a three-dimensional structure that is highly enriched in clusters of stalked cells known as rosettes. As this pellicle film matures, it becomes more cohesive and less adherent to a glass surface. A mutant strain lacking a flagellum does not efficiently reach the surface, and strains lacking type IV pili exhibit defects in organization of the three-dimensional pellicle. Strains unable to synthesize the holdfast fail to accumulate at the boundary between air and liquid and do not form a pellicle. Phase-contrast images support a model whereby the holdfast functions to trap C. crescentus cells at the air-liquid boundary. Unlike the holdfast, neither the flagellum nor type IV pili are required for C. crescentus to partition to the air-liquid interface. While it is well established that the holdfast enables adherence to solid surfaces, this study provides evidence that the holdfast has physicochemical properties that allow partitioning of nonmotile mother cells to the air-liquid interface and facilitate colonization of this microenvironment.IMPORTANCE In aquatic environments, the boundary at the air interface is often highly enriched with nutrients and oxygen. Colonization of this niche likely confers a significant fitness advantage in many cases. This study provides evidence that the cell surface adhesin known as a holdfast enables Caulobacter crescentus to partition to and colonize the air-liquid interface. Additional surface structures, including the flagellum and type IV pili, are important determinants of colonization and biofilm formation at this boundary. Considering that holdfast-like adhesins are broadly conserved in Caulobacter spp. and other members of the diverse class Alphaproteobacteria, these surface structures may function broadly to facilitate colonization of air-liquid boundaries in a range of ecological contexts, including freshwater, marine, and soil ecosystems.
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The Two Chemotaxis Clusters in Caulobacter crescentus Play Different Roles in Chemotaxis and Biofilm Regulation. J Bacteriol 2019; 201:JB.00071-19. [PMID: 31109992 DOI: 10.1128/jb.00071-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/16/2019] [Indexed: 02/06/2023] Open
Abstract
The holdfast polysaccharide adhesin is crucial for irreversible cell adhesion and biofilm formation in Caulobacter crescentus Holdfast production is tightly controlled via developmental regulators, as well as via environmental and physical signals. Here, we identify a novel mode of regulation of holdfast synthesis that involves chemotaxis proteins. We characterized the two identified chemotaxis clusters of C. crescentus and showed that only the previously characterized major cluster is involved in the chemotactic response toward different carbon sources. However, both chemotaxis clusters encoded in the C. crescentus genome play a role in biofilm formation and holdfast production by regulating the expression of hfiA, the gene encoding the holdfast inhibitor HfiA. We show that CheA and CheB proteins act in an antagonistic manner, as follows: while the two CheA proteins negatively regulate hfiA expression, the CheB proteins are positive regulators, thus providing a modulation of holdfast synthesis and surface attachment.IMPORTANCE Chemosensory systems constitute major signal transduction pathways in bacteria. These systems are involved in chemotaxis and other cell responses to environment conditions, such as the production of adhesins to enable irreversible adhesion to a surface and surface colonization. The C. crescentus genome encodes two complete chemotaxis clusters. Here, we characterized the second novel chemotaxis-like cluster. While only the major chemotaxis cluster is involved in chemotaxis, both chemotaxis systems modulate C. crescentus adhesion by controlling expression of the holdfast synthesis inhibitor HfiA. Here, we identify a new level in holdfast regulation, providing new insights into the control of adhesin production that leads to the formation of biofilms in response to the environment.
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Fröhlich KS, Förstner KU, Gitai Z. Post-transcriptional gene regulation by an Hfq-independent small RNA in Caulobacter crescentus. Nucleic Acids Res 2019; 46:10969-10982. [PMID: 30165530 PMCID: PMC6237742 DOI: 10.1093/nar/gky765] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 08/21/2018] [Indexed: 12/15/2022] Open
Abstract
Bacterial small RNAs (sRNAs) are a heterogeneous group of post-transcriptional regulators that often act at the heart of large networks. Hundreds of sRNAs have been discovered by genome-wide screens and most of these sRNAs exert their functions by base-pairing with target mRNAs. However, studies addressing the molecular roles of sRNAs have been largely confined to gamma-proteobacteria, such as Escherichia coli. Here we identify and characterize a novel sRNA, ChvR, from the alpha-proteobacterium Caulobacter crescentus. Transcription of chvR is controlled by the conserved two-component system ChvI-ChvG and it is expressed in response to DNA damage, low pH, and growth in minimal medium. Transient over-expression of ChvR in combination with genome-wide transcriptome profiling identified the mRNA of the TonB-dependent receptor ChvT as the sole target of ChvR. Genetic and biochemical analyses showed that ChvR represses ChvT at the post-transcriptional level through direct base-pairing. Fine-mapping of the ChvR-chvT interaction revealed the requirement of two distinct base-pairing sites for full target regulation. Finally, we show that ChvR-controlled repression of chvT is independent of the ubiquitous RNA-chaperone Hfq, and therefore distinct from previously reported mechanisms employed by prototypical bacterial sRNAs. These findings have implications for the mechanism and evolution of sRNA function across bacterial species.
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Affiliation(s)
- Kathrin S Fröhlich
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratories, Princeton, NJ 08544, USA.,Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, D-82152 Martinsried, Germany
| | - Konrad U Förstner
- Core Unit Systems Medicine, University of Würzburg, D-97080 Würzburg, Germany
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratories, Princeton, NJ 08544, USA
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Periyannan GR. Bacterial cellobiose metabolism: An inquiry-driven, comprehensive undergraduate laboratory teaching approach to promote investigative learning. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 47:438-445. [PMID: 30920722 DOI: 10.1002/bmb.21237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 02/06/2019] [Accepted: 03/06/2019] [Indexed: 06/09/2023]
Abstract
Technique-centered biochemistry or molecular biology undergraduate laboratory curricula do not offer significant opportunities for thoughtful, in-depth exploration of the science to foster investigative learning. To demonstrate inclusion of inquiry-driven laboratory experiments into the undergraduate biochemistry and molecular biology curricula, a comprehensive set of laboratory experiments, covering several principles of biochemistry and molecular biology, have been developed under a single theme. The laboratory curriculum described here comprehensively investigates bacterial cellobiose metabolism using multiple biochemical, molecular biological (RNA isolation, RT-PCR, PCR, and enzyme assay), and analytical techniques (High Performance Liquid Chromatography, NMR, spectrophotometry, and thin-layer chromatography) to explore the principles of metabolomics and genomics in a single undergraduate laboratory course setting using Caulobacter crescentus as the model organism. This laboratory module serves as a model for educators to develop easy-to-implement laboratory curricula incorporating contemporary biochemistry and molecular biology concepts and techniques to provide a course-based undergraduate research experiences (CUREs) with defined learning objectives. © 2019 International Union of Biochemistry and Molecular Biology, 47(4):438-445, 2019.
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Affiliation(s)
- Gopal R Periyannan
- Department of Chemistry and Biochemistry, Eastern Illinois University, Charleston, Illinois, 61920
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40
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Attai H, Brown PJB. Isolation and Characterization T4- and T7-Like Phages that Infect the Bacterial Plant Pathogen Agrobacterium tumefaciens. Viruses 2019; 11:v11060528. [PMID: 31181591 PMCID: PMC6630229 DOI: 10.3390/v11060528] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 05/29/2019] [Accepted: 06/04/2019] [Indexed: 01/21/2023] Open
Abstract
In the rhizosphere, bacteria-phage interactions are likely to have important impacts on the ecology of microbial communities and microbe-plant interactions. To better understand the dynamics of Agrobacteria-phage interactions, we have isolated diverse bacteriophages which infect the bacterial plant pathogen, Agrobacterium tumefaciens. Here, we complete the genomic characterization of Agrobacterium tumefaciens phages Atu_ph04 and Atu_ph08. Atu_ph04-a T4-like phage belonging to the Myoviridae family-was isolated from waste water and has a 143,349 bp genome that encodes 223 predicted open reading frames (ORFs). Based on phylogenetic analysis and whole-genome alignments, Atu_ph04 is a member of a newly described T4 superfamily that contains other Rhizobiales-infecting phages. Atu_ph08, a member of the Podoviridae T7-like family, was isolated from waste water, has a 59,034 bp genome, and encodes 75 ORFs. Based on phylogenetic analysis and whole-genome alignments, Atu_ph08 may form a new T7 superfamily which includes Sinorhizobium phage PCB5 and Ochrobactrum phage POI1126. Atu_ph08 is predicted to have lysogenic activity, as we found evidence of an integrase and several transcriptional repressors with similarity to proteins in transducing phage P22. Together, this data suggests that Agrobacterium phages are diverse in morphology, genomic content, and lifestyle.
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Affiliation(s)
- Hedieh Attai
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA.
| | - Pamela J B Brown
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA.
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Caulobacter crescentus Hfq structure reveals a conserved mechanism of RNA annealing regulation. Proc Natl Acad Sci U S A 2019; 116:10978-10987. [PMID: 31076551 PMCID: PMC6561178 DOI: 10.1073/pnas.1814428116] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In many bacteria, the RNA chaperone protein Hfq binds to hundreds of small noncoding RNAs and improves their efficacy by aiding base pairing to target mRNAs. Hfq proteins contain a variable C-terminal domain (CTD), usually structurally disordered, which was recently demonstrated to inhibit Hfq from mediating nonspecific RNA annealing. We obtained a new structure that shows how this inhibition is achieved in Caulobacter crescentus Hfq. The structural data and chaperone assays provide an initial view of the little-known mechanism of small RNA regulation in Caulobacter. In addition, this work demonstrates how the Hfq CTD has evolved to meet the needs for species-specific selectivity in RNA binding and pairing of regulatory RNAs with cognate targets. We have solved the X-ray crystal structure of the RNA chaperone protein Hfq from the alpha-proteobacterium Caulobacter crescentus to 2.15-Å resolution, resolving the conserved core of the protein and the entire C-terminal domain (CTD). The structure reveals that the CTD of neighboring hexamers pack in crystal contacts, and that the acidic residues at the C-terminal tip of the protein interact with positive residues on the rim of Hfq, as has been recently proposed for a mechanism of modulating RNA binding. De novo computational models predict a similar docking of the acidic tip residues against the core of Hfq. We also show that C. crescentus Hfq has sRNA binding and RNA annealing activities and is capable of facilitating the annealing of certain Escherichia coli sRNA:mRNA pairs in vivo. Finally, we describe how the Hfq CTD and its acidic tip residues provide a mechanism to modulate annealing activity and substrate specificity in various bacteria.
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42
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Comparative Genome Characterization of a Petroleum-Degrading Bacillus subtilis Strain DM2. Int J Genomics 2019; 2019:7410823. [PMID: 31205931 PMCID: PMC6530121 DOI: 10.1155/2019/7410823] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/19/2019] [Accepted: 03/24/2019] [Indexed: 12/12/2022] Open
Abstract
The complete genome sequence of Bacillus subtilis strain DM2 isolated from petroleum-contaminated soil on the Tibetan Plateau was determined. The genome of strain DM2 consists of a circular chromosome of 4,238,631 bp for 4458 protein-coding genes and a plasmid of 84,240 bp coding for 103 genes. Thirty-four genomic islands coding for 330 proteins and 5 prophages are found in the genome. The DDH value shows that strain DM2 belongs to B. subtilis subsp. subtilis subspecies, but significant variations of the genome are also present. Comparative analysis showed that the genome of strain DM2 encodes some strain-specific proteins in comparison with B. subtilis subsp. subtilis str. 168, such as carboxymuconolactone decarboxylase family protein, gfo/Idh/MocA family oxidoreductases, GlsB/YeaQ/YmgE family stress response membrane protein, HlyC/CorC family transporters, LLM class flavin-dependent oxidoreductase, and LPXTG cell wall anchor domain-containing protein. Most of the common strain-specific proteins in DM2 and MJ01 strains, or proteins unique to DM2 strain, are involved in the pathways related to stress response, signaling, and hydrocarbon degradation. Furthermore, the strain DM2 genome contains 122 genes coding for developed two-component systems and 138 genes coding for ABC transporter systems. The prominent features of the strain DM2 genome reflect the evolutionary fitness of this strain to harsh conditions and hydrocarbon utilization.
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Karppinen EM, Mamet SD, Stewart KJ, Siciliano SD. The Charosphere Promotes Mineralization of 13C-Phenanthrene by Psychrotrophic Microorganisms in Greenland Soils. JOURNAL OF ENVIRONMENTAL QUALITY 2019; 48:559-567. [PMID: 31180417 DOI: 10.2134/jeq2018.10.0370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
When soil is frozen, biochar promotes petroleum hydrocarbon (PHC) degradation, yet we still do not understand why. To investigate microbial biodegradation activity under frozen conditions, we placed 60-μm mesh bags containing 6% (v/v) biochar created from fishmeal, bonemeal, bone chip, or wood into PHC-contaminated soil, which was then frozen to -5°C. This created three soil niches: biochar particles, the charosphere (biochar-contiguous soil), and bulk soil outside of the bags. After 90 d, C-phenanthrene mineralization reached 55% in bonemeal biochar and 84% in bone chip biochar charosphere soil, compared with only 43% in bulk soil and 13% in bone chip biochar particles. Soil pH remained near neutral in bone chip and bonemeal biochar treatments, unlike wood biochar, which increased alkalinity and likely made phosphate unavailable for microorganisms. Generally, charosphere soil had higher aromatic degradative gene abundances than bulk soil, but gene abundance was not directly linked to C-phenanthrene mineralization. In bone chip biochar-amended soils, phosphate successfully predicted microbial community composition, and abundances of and increased in charosphere soil. Biochar effects on charosphere soil were dependent on feedstock material and suggest that optimizing the charosphere in bone-derived biochars may increase remediation success in northern regions.
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44
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Chemical synthesis rewriting of a bacterial genome to achieve design flexibility and biological functionality. Proc Natl Acad Sci U S A 2019; 116:8070-8079. [PMID: 30936302 PMCID: PMC6475421 DOI: 10.1073/pnas.1818259116] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The fundamental biological functions of a living cell are stored within the DNA sequence of its genome. Classical genetic approaches dissect the functioning of biological systems by analyzing individual genes, yet uncovering the essential gene set of an organism has remained very challenging. It is argued that the rewriting of entire genomes through the process of chemical synthesis provides a powerful and complementary research concept to understand how essential functions are programed into genomes. Understanding how to program biological functions into artificial DNA sequences remains a key challenge in synthetic genomics. Here, we report the chemical synthesis and testing of Caulobacter ethensis-2.0 (C. eth-2.0), a rewritten bacterial genome composed of the most fundamental functions of a bacterial cell. We rebuilt the essential genome of Caulobacter crescentus through the process of chemical synthesis rewriting and studied the genetic information content at the level of its essential genes. Within the 785,701-bp genome, we used sequence rewriting to reduce the number of encoded genetic features from 6,290 to 799. Overall, we introduced 133,313 base substitutions, resulting in the rewriting of 123,562 codons. We tested the biological functionality of the genome design in C. crescentus by transposon mutagenesis. Our analysis revealed that 432 essential genes of C. eth-2.0, corresponding to 81.5% of the design, are equal in functionality to natural genes. These findings suggest that neither changing mRNA structure nor changing the codon context have significant influence on biological functionality of synthetic genomes. Discovery of 98 genes that lost their function identified essential genes with incorrect annotation, including a limited set of 27 genes where we uncovered noncoding control features embedded within protein-coding sequences. In sum, our results highlight the promise of chemical synthesis rewriting to decode fundamental genome functions and its utility toward the design of improved organisms for industrial purposes and health benefits.
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45
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Stankeviciute G, Miguel AV, Radkov A, Chou S, Huang KC, Klein EA. Differential modes of crosslinking establish spatially distinct regions of peptidoglycan in
Caulobacter crescentus. Mol Microbiol 2019; 111:995-1008. [DOI: 10.1111/mmi.14199] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/02/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Gabriele Stankeviciute
- Center for Computational and Integrative Biology Rutgers University‐Camden Camden NJ 08102USA
| | - Amanda V. Miguel
- Department of Bioengineering Stanford University Stanford CA 94305USA
| | - Atanas Radkov
- Department of Biochemistry and Biophysics University of California San Francisco San Francisco CA 94158USA
| | - Seemay Chou
- Department of Biochemistry and Biophysics University of California San Francisco San Francisco CA 94158USA
- Chan Zuckerberg Biohub San Francisco CA 94158USA
| | - Kerwyn Casey Huang
- Department of Bioengineering Stanford University Stanford CA 94305USA
- Chan Zuckerberg Biohub San Francisco CA 94158USA
- Department of Microbiology and Immunology Stanford University School of Medicine Stanford CA 94305USA
| | - Eric A. Klein
- Center for Computational and Integrative Biology Rutgers University‐Camden Camden NJ 08102USA
- Biology Department Rutgers University‐Camden Camden NJ 08102USA
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46
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Menikpurage IP, Barraza D, Meléndez AB, Strebe S, Mera PE. The B12 receptor BtuB alters the membrane integrity of Caulobacter crescentus. MICROBIOLOGY-SGM 2019; 165:311-323. [PMID: 30628887 DOI: 10.1099/mic.0.000753] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Vitamin B12 is one of the most complex biomolecules in nature. Since few organisms can synthesize B12de novo, most bacteria utilize highly sensitive and specialized transporters to scavenge B12 and its precursors. In Gram-negative bacteria, BtuB is the outer membrane TonB-dependent receptor for B12. In the fresh water bacterium Caulobacter crescentus, btuB is among the most highly expressed genes. In this study, we characterized the function of BtuB in C. crescentus and unveiled a potential new function of this receptor involved in cellular fitness. Under standard minimal or rich growth conditions, we found that supplements of vitamin B12 to cultures of C. crescentus provided no significant advantage in growth rate. Using a B12 methionine auxotroph, we showed that BtuB in C. crescentus is capable of transporting B12 at low pico-molar range. A btuB knockout strain displayed higher sensitivity to detergents and to changes in osmotic pressure compared to the wild-type. Electron micrographs of this knockout strain revealed a morphology defect. The sensitivity observed in the btuB knockout strain was not due to changes in membrane permeability or altered S-layer levels. Our results demonstrate that btuB deletion mutants exhibit increased susceptibility to membrane stressors, suggesting a potential role of this receptor in membrane homeostasis. Because we only tested BtuB's function under laboratory conditions, we cannot eliminate the possibility that BtuB also plays a key role as a B12 scavenger in C. crescentus when growing in its highly variable and nutrient-limited natural environment.
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Affiliation(s)
- Inoka P Menikpurage
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM 88003, USA
| | - Daniela Barraza
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM 88003, USA
| | - Ady B Meléndez
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM 88003, USA
| | - Sierra Strebe
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM 88003, USA
| | - Paola E Mera
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM 88003, USA
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47
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Ely B, Wilson K, Ross K, Ingram D, Lewter T, Herring J, Duncan D, Aikins A, Scott D. Genome Comparisons of Wild Isolates of Caulobacter crescentus Reveal Rates of Inversion and Horizontal Gene Transfer. Curr Microbiol 2018; 76:159-167. [PMID: 30483871 DOI: 10.1007/s00284-018-1606-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 11/23/2018] [Indexed: 11/28/2022]
Abstract
Since previous interspecies comparisons of Caulobacter genomes have revealed extensive genome rearrangements, we decided to compare the nucleotide sequences of four C. crescentus genomes, NA1000, CB1, CB2, and CB13. To accomplish this goal, we used PacBio sequencing technology to determine the nucleotide sequence of the CB1, CB2, and CB13 genomes, and obtained each genome sequence as a single contig. To correct for possible sequencing errors, each genome was sequenced twice. The only differences we observed between the two sets of independently determined sequences were random omissions of a single base in a small percentage of the homopolymer regions where a single base is repeated multiple times. Comparisons of these four genomes indicated that horizontal gene transfer events that included small numbers of genes occurred at frequencies in the range of 10-3 to 10-4 insertions per generation. Large insertions were about 100 times less frequent. Also, in contrast to previous interspecies comparisons, we found no genome rearrangements when the closely related NA1000, CB1, and CB2 genomes were compared, and only eight inversions and one translocation when the more distantly related CB13 genome was compared to the other genomes. Thus, we estimate that inversions occur at a rate of one per 10 to 12 million generations in Caulobacter genomes. The inversions seem to be complex events that include the simultaneous creation of indels.
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Affiliation(s)
- Bert Ely
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA.
| | - Kiesha Wilson
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Keshawn Ross
- Department of Biological Sciences, Delaware State University, Dover, DE, 19901, USA
| | - Damyen Ingram
- Department of Biological Sciences, Delaware State University, Dover, DE, 19901, USA
| | - Tajah Lewter
- Department of Biological Sciences, Delaware State University, Dover, DE, 19901, USA
| | - Jasmine Herring
- Department of Biological Sciences, Delaware State University, Dover, DE, 19901, USA
| | - David Duncan
- Department of Biological Sciences, Delaware State University, Dover, DE, 19901, USA
| | - Anthea Aikins
- Department of Biological Sciences, Delaware State University, Dover, DE, 19901, USA
| | - Derrick Scott
- Department of Biological Sciences, Delaware State University, Dover, DE, 19901, USA
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48
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Complete Genome Sequence of a Wild-Type Isolate of Caulobacter vibrioides Strain CB2. Microbiol Resour Announc 2018; 7:MRA01215-18. [PMID: 30533761 PMCID: PMC6256496 DOI: 10.1128/mra.01215-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 10/04/2018] [Indexed: 11/23/2022] Open
Abstract
The complete genome of Caulobacter vibrioides strain CB2 consists of a 4,123,726-bp chromosome, a GC content of 67.2%, and 3,896 coding DNA sequences. It has no rearrangements but numerous indels relative to the reference NA1000 genome. The complete genome of Caulobacter vibrioides strain CB2 consists of a 4,123,726-bp chromosome, a GC content of 67.2%, and 3,896 coding DNA sequences. It has no rearrangements but numerous indels relative to the reference NA1000 genome. This will allow us to study the impact of horizontal gene transfer on caulobacter genomes.
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49
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Mohapatra S, Weisshaar JC. Functional mapping of the
E. coli
translational machinery using single‐molecule tracking. Mol Microbiol 2018; 110:262-282. [DOI: 10.1111/mmi.14103] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2018] [Indexed: 12/22/2022]
Affiliation(s)
| | - James C. Weisshaar
- Department of Chemistry University of Wisconsin‐Madison Madison WI 53706USA
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50
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Wilhelm RC, Singh R, Eltis LD, Mohn WW. Bacterial contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing. ISME JOURNAL 2018; 13:413-429. [PMID: 30258172 PMCID: PMC6331573 DOI: 10.1038/s41396-018-0279-6] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 05/20/2018] [Accepted: 08/11/2018] [Indexed: 11/19/2022]
Abstract
Delignification, or lignin-modification, facilitates the decomposition of lignocellulose in woody plant biomass. The extant diversity of lignin-degrading bacteria and fungi is underestimated by culture-dependent methods, limiting our understanding of the functional and ecological traits of decomposers populations. Here, we describe the use of stable isotope probing (SIP) coupled with amplicon and shotgun metagenomics to identify and characterize the functional attributes of lignin, cellulose and hemicellulose-degrading fungi and bacteria in coniferous forest soils from across North America. We tested the extent to which catabolic genes partitioned among different decomposer taxa; the relative roles of bacteria and fungi, and whether taxa or catabolic genes correlated with variation in lignocellulolytic activity, measured as the total assimilation of 13C-label into DNA and phospholipid fatty acids. We found high overall bacterial degradation of our model lignin substrate, particularly by gram-negative bacteria (Comamonadaceae and Caulobacteraceae), while fungi were more prominent in cellulose-degradation. Very few taxa incorporated 13C-label from more than one lignocellulosic polymer, suggesting specialization among decomposers. Collectively, members of Caulobacteraceae could degrade all three lignocellulosic polymers, providing new evidence for their importance in lignocellulose degradation. Variation in lignin-degrading activity was better explained by microbial community properties, such as catabolic gene content and community structure, than cellulose-degrading activity. SIP significantly improved shotgun metagenome assembly resulting in the recovery of several high-quality draft metagenome-assembled genomes and over 7500 contigs containing unique clusters of carbohydrate-active genes. These results improve understanding of which organisms, conditions and corresponding functional genes contribute to lignocellulose decomposition.
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Affiliation(s)
- Roland C Wilhelm
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Rahul Singh
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Lindsay D Eltis
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - William W Mohn
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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