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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] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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Smith EL, Panis G, Woldemeskel SA, Viollier PH, Chien P, Goley ED. Regulation of the transcription factor CdnL promotes adaptation to nutrient stress in Caulobacter. PNAS Nexus 2024; 3:pgae154. [PMID: 38650860 PMCID: PMC11034885 DOI: 10.1093/pnasnexus/pgae154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024]
Abstract
In response to nutrient deprivation, bacteria activate a conserved stress response pathway called the stringent response (SR). During SR activation in Caulobacter crescentus, SpoT synthesizes the secondary messengers guanosine 5'-diphosphate 3'-diphosphate and guanosine 5'-triphosphate 3'-diphosphate (collectively known as (p)ppGpp), which affect transcription by binding RNA polymerase (RNAP) to down-regulate anabolic genes. (p)ppGpp also impacts the expression of anabolic genes by controlling the levels and activities of their transcriptional regulators. In Caulobacter, a major regulator of anabolic genes is the transcription factor CdnL. If and how CdnL is controlled during the SR and why that might be functionally important are unclear. In this study, we show that CdnL is down-regulated posttranslationally during starvation in a manner dependent on SpoT and the ClpXP protease. Artificial stabilization of CdnL during starvation causes misregulation of ribosomal and metabolic genes. Functionally, we demonstrate that the combined action of SR transcriptional regulators and CdnL clearance allows for rapid adaptation to nutrient repletion. Moreover, cells that are unable to clear CdnL during starvation are outcompeted by wild-type cells when subjected to nutrient fluctuations. We hypothesize that clearance of CdnL during the SR, in conjunction with direct binding of (p)ppGpp and DksA to RNAP, is critical for altering the transcriptome in order to permit cell survival during nutrient stress.
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Affiliation(s)
- Erika L Smith
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Gaël Panis
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Selamawit Abi Woldemeskel
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Peter Chien
- Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst, MA 01003, USA
| | - Erin D Goley
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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3
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Smith EL, Panis G, Woldemeskel SA, Viollier PH, Chien P, Goley ED. Regulation of the transcription factor CdnL promotes adaptation to nutrient stress in Caulobacter. bioRxiv 2023:2023.12.20.572625. [PMID: 38187569 PMCID: PMC10769358 DOI: 10.1101/2023.12.20.572625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
In response to nutrient deprivation, bacteria activate a conserved stress response pathway called the stringent response (SR). During SR activation in Caulobacter crescentus, SpoT synthesizes the secondary messengers (p)ppGpp, which affect transcription by binding RNA polymerase to downregulate anabolic genes. (p)ppGpp also impacts expression of anabolic genes by controlling the levels and activities of their transcriptional regulators. In Caulobacter, a major regulator of anabolic genes is the transcription factor CdnL. If and how CdnL is controlled during the SR and why that might be functionally important is unclear. Here, we show that CdnL is downregulated post-translationally during starvation in a manner dependent on SpoT and the ClpXP protease. Inappropriate stabilization of CdnL during starvation causes misregulation of ribosomal and metabolic genes. Functionally, we demonstrate that the combined action of SR transcriptional regulators and CdnL clearance allows for rapid adaptation to nutrient repletion. Moreover, cells that are unable to clear CdnL during starvation are outcompeted by wild-type cells when subjected to nutrient fluctuations. We hypothesize that clearance of CdnL during the SR, in conjunction with direct binding of (p)ppGpp and DksA to RNAP, is critical for altering the transcriptome in order to permit cell survival during nutrient stress.
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Affiliation(s)
- Erika L. Smith
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205
| | - Gaäl Panis
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland, 1211
| | - Selamawit Abi Woldemeskel
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205
- BlueRock Therapeutics, Cambridge, Massachusetts, 02142 (current)
| | - Patrick H. Viollier
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland, 1211
| | - Peter Chien
- Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst, Massachusetts, 01003
| | - Erin D. Goley
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205
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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] [What about the content of this article? (0)] [Affiliation(s)] [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] [What about the content of this article? (0)] [Affiliation(s)] [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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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Kint N, Dubois T, Viollier PH. Stereoisomer-specific reprogramming of a bacterial flagellin sialyltransferase. EMBO J 2023; 42:e112880. [PMID: 36636824 PMCID: PMC9975948 DOI: 10.15252/embj.2022112880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/02/2022] [Accepted: 12/16/2022] [Indexed: 01/14/2023] Open
Abstract
Glycosylation of surface structures diversifies cells chemically and physically. Nucleotide-activated sialic acids commonly serve as glycosyl donors, particularly pseudaminic acid (Pse) and its stereoisomer legionaminic acid (Leg), which decorate eubacterial and archaeal surface layers or protein appendages. FlmG, a recently identified protein sialyltransferase, O-glycosylates flagellins, the subunits of the flagellar filament. We show that flagellin glycosylation and motility in Caulobacter crescentus and Brevundimonas subvibrioides is conferred by functionally insulated Pse and Leg biosynthesis pathways, respectively, and by specialized FlmG orthologs. We established a genetic glyco-profiling platform for the classification of Pse or Leg biosynthesis pathways, discovered a signature determinant of eubacterial and archaeal Leg biosynthesis, and validated it by reconstitution experiments in a heterologous host. Finally, by rewiring FlmG glycosylation using chimeras, we defined two modular determinants that govern flagellin glycosyltransferase specificity: a glycosyltransferase domain that either donates Leg or Pse and a specialized flagellin-binding domain that identifies the acceptor.
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Affiliation(s)
- Nicolas Kint
- Department of Microbiology & Molecular Medicine and Geneva Center for Inflammation Research (GCIR), Faculty of MedicineUniversity of GenevaGenèveSwitzerland
| | - Thomas Dubois
- University of Lille, CNRS, INRAE, Centrale Lille, UMR 8207‐UMET‐Unité Matériaux et TransformationsLilleFrance
| | - Patrick H Viollier
- Department of Microbiology & Molecular Medicine and Geneva Center for Inflammation Research (GCIR), Faculty of MedicineUniversity of GenevaGenèveSwitzerland
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Fatton M, Filippidou S, Junier T, Cailleau G, Berge M, Poppleton D, Blum TB, Kaminek M, Odriozola A, Blom J, Johnson SL, Abrahams JP, Chain PS, Gribaldo S, Tocheva EI, Zuber B, Viollier PH, Junier P. Cryptosporulation in Kurthia spp. forces a rethinking of asporogenesis in Firmicutes. Environ Microbiol 2022; 24:6320-6335. [PMID: 36530021 PMCID: PMC10086788 DOI: 10.1111/1462-2920.16145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 07/20/2022] [Indexed: 01/12/2023]
Abstract
Endosporulation is a complex morphophysiological process resulting in a more resistant cellular structure that is produced within the mother cell and is called endospore. Endosporulation evolved in the common ancestor of Firmicutes, but it is lost in descendant lineages classified as asporogenic. While Kurthia spp. is considered to comprise only asporogenic species, we show here that strain 11kri321, which was isolated from an oligotrophic geothermal reservoir, produces phase-bright spore-like structures. Phylogenomics of strain 11kri321 and other Kurthia strains reveals little similarity to genetic determinants of sporulation known from endosporulating Bacilli. However, morphological hallmarks of endosporulation were observed in two of the four Kurthia strains tested, resulting in spore-like structures (cryptospores). In contrast to classic endospores, these cryptospores did not protect against heat or UV damage and successive sub-culturing led to the loss of the cryptosporulating phenotype. Our findings imply that a cryptosporulation phenotype may have been prevalent and subsequently lost by laboratory culturing in other Firmicutes currently considered as asporogenic. Cryptosporulation might thus represent an ancestral but unstable and adaptive developmental state in Firmicutes that is under selection under harsh environmental conditions.
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Affiliation(s)
- Mathilda Fatton
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Sevasti Filippidou
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.,AstrobiologyOU, The Open University, Milton Keynes, UK
| | - Thomas Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.,Vital-IT group, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Guillaume Cailleau
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Matthieu Berge
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Daniel Poppleton
- Unité de Biologie Moléculaire du Gène chez les Extrémophiles, Département de Microbiologie, Institut Pasteur, France
| | - Thorsten B Blum
- Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), Villigen, Switzerland
| | - Marek Kaminek
- Institute for Anatomy, University of Bern, Bern, Switzerland
| | | | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Shannon L Johnson
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Jan Pieter Abrahams
- Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), Villigen, Switzerland.,Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland.,Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Patrick S Chain
- Institute for Anatomy, University of Bern, Bern, Switzerland
| | - Simonetta Gribaldo
- Unité de Biologie Moléculaire du Gène chez les Extrémophiles, Département de Microbiologie, Institut Pasteur, France
| | - Elitza I Tocheva
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Benoît Zuber
- Institute for Anatomy, University of Bern, Bern, Switzerland
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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9
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Pióro M, Matusiak I, Gawek A, Łebkowski T, Jaroszek P, Bergé M, Böhm K, Armitage J, Viollier PH, Bramkamp M, Jakimowicz D. Genus-Specific Interactions of Bacterial Chromosome Segregation Machinery Are Critical for Their Function. Front Microbiol 2022; 13:928139. [PMID: 35875543 PMCID: PMC9298525 DOI: 10.3389/fmicb.2022.928139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
Most bacteria use the ParABS system to segregate their newly replicated chromosomes. The two protein components of this system from various bacterial species share their biochemical properties: ParB is a CTPase that binds specific centromere-like parS sequences to assemble a nucleoprotein complex, while the ParA ATPase forms a dimer that binds DNA non-specifically and interacts with ParB complexes. The ParA-ParB interaction incites the movement of ParB complexes toward the opposite cell poles. However, apart from their function in chromosome segregation, both ParAB may engage in genus-specific interactions with other protein partners. One such example is the polar-growth controlling protein DivIVA in Actinomycetota, which binds ParA in Mycobacteria while interacts with ParB in Corynebacteria. Here, we used heterologous hosts to investigate whether the interactions between DivIVA and ParA or ParB are maintained across phylogenic classes. Specifically, we examined interactions of proteins from four bacterial species, two belonging to the Gram positive Actinomycetota phylum and two belonging to the Gram-negative Pseudomonadota. We show that while the interactions between ParA and ParB are preserved for closely related orthologs, the interactions with polarly localised protein partners are not conferred by orthologous ParABs. Moreover, we demonstrate that heterologous ParA cannot substitute for endogenous ParA, despite their high sequence similarity. Therefore, we conclude that ParA orthologs are fine-tuned to interact with their partners, especially their interactions with polarly localised proteins are adjusted to particular bacterial species demands.
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Affiliation(s)
- Monika Pióro
- Faculty of Biotechnology, Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
- *Correspondence: Monika Pióro,
| | - Izabela Matusiak
- Faculty of Biotechnology, Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
| | - Adam Gawek
- Faculty of Biotechnology, Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
| | - Tomasz Łebkowski
- Faculty of Biotechnology, Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
| | - Patrycja Jaroszek
- Faculty of Biotechnology, Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
| | - Matthieu Bergé
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Kati Böhm
- Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Judith Armitage
- Department of Biochemistry, University of Oxford, Oxford,United Kingdom
| | - Patrick H. Viollier
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Marc Bramkamp
- Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Dagmara Jakimowicz
- Faculty of Biotechnology, Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
- Dagmara Jakimowicz,
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10
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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: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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Osorio-Valeriano M, Altegoer F, Das CK, Steinchen W, Panis G, Connolley L, Giacomelli G, Feddersen H, Corrales-Guerrero L, Giammarinaro PI, Hanßmann J, Bramkamp M, Viollier PH, Murray S, Schäfer LV, Bange G, Thanbichler M. The CTPase activity of ParB determines the size and dynamics of prokaryotic DNA partition complexes. Mol Cell 2021; 81:3992-4007.e10. [PMID: 34562373 DOI: 10.1016/j.molcel.2021.09.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/27/2021] [Accepted: 08/31/2021] [Indexed: 01/29/2023]
Abstract
ParB-like CTPases mediate the segregation of bacterial chromosomes and low-copy number plasmids. They act as DNA-sliding clamps that are loaded at parS motifs in the centromere of target DNA molecules and spread laterally to form large nucleoprotein complexes serving as docking points for the DNA segregation machinery. Here, we solve crystal structures of ParB in the pre- and post-hydrolysis state and illuminate the catalytic mechanism of nucleotide hydrolysis. Moreover, we identify conformational changes that underlie the CTP- and parS-dependent closure of ParB clamps. The study of CTPase-deficient ParB variants reveals that CTP hydrolysis serves to limit the sliding time of ParB clamps and thus drives the establishment of a well-defined ParB diffusion gradient across the centromere whose dynamics are critical for DNA segregation. These findings clarify the role of the ParB CTPase cycle in partition complex assembly and function and thus advance our understanding of this prototypic CTP-dependent molecular switch.
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Affiliation(s)
- Manuel Osorio-Valeriano
- Department of Biology, University of Marburg, 35043 Marburg, Germany; Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Florian Altegoer
- Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Chandan K Das
- Theoretical Chemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Wieland Steinchen
- Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Gaël Panis
- Department of Microbiology and Molecular Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Lara Connolley
- Department of Systems & Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Giacomo Giacomelli
- Institute for General Microbiology, Christian Albrechts University, 24118 Kiel, Germany
| | - Helge Feddersen
- Institute for General Microbiology, Christian Albrechts University, 24118 Kiel, Germany
| | | | - Pietro I Giammarinaro
- Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Juri Hanßmann
- Department of Biology, University of Marburg, 35043 Marburg, Germany
| | - Marc Bramkamp
- Institute for General Microbiology, Christian Albrechts University, 24118 Kiel, Germany
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Seán Murray
- Department of Systems & Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Lars V Schäfer
- Theoretical Chemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Gert Bange
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Martin Thanbichler
- Department of Biology, University of Marburg, 35043 Marburg, Germany; Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany.
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12
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Diard M, Bakkeren E, Lentsch V, Rocker A, Bekele NA, Hoces D, Aslani S, Arnoldini M, Böhi F, Schumann-Moor K, Adamcik J, Piccoli L, Lanzavecchia A, Stadtmueller BM, Donohue N, van der Woude MW, Hockenberry A, Viollier PH, Falquet L, Wüthrich D, Bonfiglio F, Loverdo C, Egli A, Zandomeneghi G, Mezzenga R, Holst O, Meier BH, Hardt WD, Slack E. A rationally designed oral vaccine induces immunoglobulin A in the murine gut that directs the evolution of attenuated Salmonella variants. Nat Microbiol 2021; 6:830-841. [PMID: 34045711 PMCID: PMC7611113 DOI: 10.1038/s41564-021-00911-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 04/14/2021] [Indexed: 12/12/2022]
Abstract
The ability of gut bacterial pathogens to escape immunity by antigenic variation-particularly via changes to surface-exposed antigens-is a major barrier to immune clearance1. However, not all variants are equally fit in all environments2,3. It should therefore be possible to exploit such immune escape mechanisms to direct an evolutionary trade-off. Here, we demonstrate this phenomenon using Salmonella enterica subspecies enterica serovar Typhimurium (S.Tm). A dominant surface antigen of S.Tm is its O-antigen: a long, repetitive glycan that can be rapidly varied by mutations in biosynthetic pathways or by phase variation4,5. We quantified the selective advantage of O-antigen variants in the presence and absence of O-antigen-specific immunoglobulin A and identified a set of evolutionary trajectories allowing immune escape without an associated fitness cost in naive mice. Through the use of rationally designed oral vaccines, we induced immunoglobulin A responses blocking all of these trajectories. This selected for Salmonella mutants carrying deletions of the O-antigen polymerase gene wzyB. Due to their short O-antigen, these evolved mutants were more susceptible to environmental stressors (detergents or complement) and predation (bacteriophages) and were impaired in gut colonization and virulence in mice. Therefore, a rationally induced cocktail of intestinal antibodies can direct an evolutionary trade-off in S.Tm. This lays the foundations for the exploration of mucosal vaccines capable of setting evolutionary traps as a prophylactic strategy.
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Affiliation(s)
- Médéric Diard
- Biozentrum, University of Basel, Basel, Switzerland.
| | - Erik Bakkeren
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland.,Department of Zoology, University of Oxford, Oxford, UK
| | - Verena Lentsch
- Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland
| | | | | | - Daniel Hoces
- Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland
| | - Selma Aslani
- Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland
| | - Markus Arnoldini
- Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland
| | - Flurina Böhi
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland.,Department of Molecular Mechanisms of Disease, University of Zürich, Zürich, Switzerland
| | - Kathrin Schumann-Moor
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland.,Division of Surgical Research, University Hospital of Zürich, Zürich, Switzerland
| | - Jozef Adamcik
- Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland
| | - Luca Piccoli
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Beth M Stadtmueller
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nicholas Donohue
- York Biomedical Research Institute, Hull York Medical School, University of York, York, UK.,Department of Orthopedics and Trauma, Medical University of Graz, Graz, Austria
| | - Marjan W van der Woude
- York Biomedical Research Institute, Hull York Medical School, University of York, York, UK
| | - Alyson Hockenberry
- Department of Environmental Microbiology, Eawag, Dubendorf, Switzerland.,Department of Environmental Sciences, ETH Zürich, Zürich, Switzerland
| | - Patrick H Viollier
- Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Laurent Falquet
- Department of Biology, University of Fribourg, Fribourg, Switzerland.,Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Daniel Wüthrich
- Infection Biology, University Hospital of Basel, Basel, Switzerland
| | | | - Claude Loverdo
- Department of Materials, ETH Zürich, Zürich, Switzerland
| | - Adrian Egli
- Infection Biology, University Hospital of Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, Basel, Switzerland
| | | | - Raffaele Mezzenga
- Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland.,Department of Materials, ETH Zürich, Zürich, Switzerland
| | - Otto Holst
- Forschungszentrum Borstel, Borstel, Germany
| | - Beat H Meier
- Institute for Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland.
| | - Emma Slack
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland. .,Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland.
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13
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Yildiz S, Pereira Bonifacio Lopes JP, Bergé M, González-Ruiz V, Baud D, Kloehn J, Boal-Carvalho I, Schaeren OP, Schotsaert M, Hathaway LJ, Rudaz S, Viollier PH, Hapfelmeier S, Francois P, Schmolke M. Respiratory tissue-associated commensal bacteria offer therapeutic potential against pneumococcal colonization. eLife 2020; 9:53581. [PMID: 33287959 PMCID: PMC7723408 DOI: 10.7554/elife.53581] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 11/18/2020] [Indexed: 12/16/2022] Open
Abstract
Under eubiotic conditions commensal microbes are known to provide a competitive barrier against invading bacterial pathogens in the intestinal tract, on the skin or on the vaginal mucosa. Here, we evaluate the role of lung microbiota in Pneumococcus colonization of the lungs. In eubiosis, the lungs of mice were dominantly colonized by Lactobacillus murinus. Differential analysis of 16S rRNA gene sequencing or L. murinus-specific qPCR of DNA from total organ homogenates vs.broncho alveolar lavages implicated tight association of these bacteria with the host tissue. Pure L. murinus conditioned culture medium inhibited growth and reduced the extension of pneumococcal chains. Growth inhibition in vitro was likely dependent on L. murinus-produced lactic acid, since pH neutralization of the conditioned medium aborted the antibacterial effect. Finally, we demonstrate that L. murinus provides a barrier against pneumococcal colonization in a respiratory dysbiosis model after an influenza A virus infection, when added therapeutically.
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Affiliation(s)
- Soner Yildiz
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | - Matthieu Bergé
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Víctor González-Ruiz
- Analytical Sciences, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland.,Swiss Centre for Applied Human Toxicology, Basel, Switzerland
| | - Damian Baud
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Joachim Kloehn
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Inês Boal-Carvalho
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Olivier P Schaeren
- Institute for Infectious Disease (IFIK), University of Bern, Bern, Switzerland.,Graduate School GCB, University of Bern, Bern, Switzerland
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Lucy J Hathaway
- Institute for Infectious Disease (IFIK), University of Bern, Bern, Switzerland
| | - Serge Rudaz
- Analytical Sciences, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland.,Swiss Centre for Applied Human Toxicology, Basel, Switzerland
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | - Patrice Francois
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Mirco Schmolke
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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14
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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] [What about the content of this article? (0)] [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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15
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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: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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Sierra R, Prados J, Panasenko OO, Andrey DO, Fleuchot B, Redder P, Kelley WL, Viollier PH, Renzoni A. Insights into the global effect on Staphylococcus aureus growth arrest by induction of the endoribonuclease MazF toxin. Nucleic Acids Res 2020; 48:8545-8561. [PMID: 32735661 PMCID: PMC7470975 DOI: 10.1093/nar/gkaa617] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 06/18/2020] [Accepted: 07/27/2020] [Indexed: 12/22/2022] Open
Abstract
A crucial bacterial strategy to avoid killing by antibiotics is to enter a growth arrested state, yet the molecular mechanisms behind this process remain elusive. The conditional overexpression of mazF, the endoribonuclease toxin of the MazEF toxin–antitoxin system in Staphylococcus aureus, is one approach to induce bacterial growth arrest, but its targets remain largely unknown. We used overexpression of mazF and high-throughput sequence analysis following the exact mapping of non-phosphorylated transcriptome ends (nEMOTE) technique to reveal in vivo toxin cleavage sites on a global scale. We obtained a catalogue of MazF cleavage sites and unearthed an extended MazF cleavage specificity that goes beyond the previously reported one. We correlated transcript cleavage and abundance in a global transcriptomic profiling during mazF overexpression. We observed that MazF affects RNA molecules involved in ribosome biogenesis, cell wall synthesis, cell division and RNA turnover and thus deliver a plausible explanation for how mazF overexpression induces stasis. We hypothesize that autoregulation of MazF occurs by directly modulating the MazEF operon, such as the rsbUVW genes that regulate the sigma factor SigB, including an observed cleavage site on the MazF mRNA that would ultimately play a role in entry and exit from bacterial stasis.
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Affiliation(s)
- Roberto Sierra
- Service of Infectious Diseases, Department of Medical Specialties, Geneva University Hospitals and Medical School, Geneva 1211, Switzerland.,Department of Microbiology and Molecular Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Julien Prados
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Olesya O Panasenko
- Service of Infectious Diseases, Department of Medical Specialties, Geneva University Hospitals and Medical School, Geneva 1211, Switzerland
| | - Diego O Andrey
- Service of Infectious Diseases, Department of Medical Specialties, Geneva University Hospitals and Medical School, Geneva 1211, Switzerland.,Department of Microbiology and Molecular Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Betty Fleuchot
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Peter Redder
- Centre de Biologie Intégrative, Université de Toulouse III, Toulouse 31400, France
| | - William L Kelley
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Adriana Renzoni
- Service of Infectious Diseases, Department of Medical Specialties, Geneva University Hospitals and Medical School, Geneva 1211, Switzerland.,Department of Microbiology and Molecular Medicine, University of Geneva, Geneva 1211, Switzerland
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17
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Corrales-Guerrero L, He B, Refes Y, Panis G, Bange G, Viollier PH, Steinchen W, Thanbichler M. Molecular architecture of the DNA-binding sites of the P-loop ATPases MipZ and ParA from Caulobacter crescentus. Nucleic Acids Res 2020; 48:4769-4779. [PMID: 32232335 PMCID: PMC7229837 DOI: 10.1093/nar/gkaa192] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/18/2020] [Accepted: 03/17/2020] [Indexed: 12/21/2022] Open
Abstract
The spatiotemporal regulation of chromosome segregation and cell division in Caulobacter crescentus is mediated by two different P-loop ATPases, ParA and MipZ. Both of these proteins form dynamic concentration gradients that control the positioning of regulatory targets within the cell. Their proper localization depends on their nucleotide-dependent cycling between a monomeric and a dimeric state and on the ability of the dimeric species to associate with the nucleoid. In this study, we use a combination of genetic screening, biochemical analysis and hydrogen/deuterium exchange mass spectrometry to comprehensively map the residues mediating the interactions of MipZ and ParA with DNA. We show that MipZ has non-specific DNA-binding activity that relies on an array of positively charged and hydrophobic residues lining both sides of the dimer interface. Extending our analysis to ParA, we find that the MipZ and ParA DNA-binding sites differ markedly in composition, although their relative positions on the dimer surface and their mode of DNA binding are conserved. In line with previous experimental work, bioinformatic analysis suggests that the same principles may apply to other members of the P-loop ATPase family. P-loop ATPases thus share common mechanistic features, although their functions have diverged considerably during the course of evolution.
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Affiliation(s)
| | - Binbin He
- Department of Biology, University of Marburg, D-35043 Marburg, Germany
| | - Yacine Refes
- Department of Biology, University of Marburg, D-35043 Marburg, Germany
| | - Gaël Panis
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, CH-1211 Geneva, Switzerland
| | - Gert Bange
- Center for Synthetic Microbiology, D-35043 Marburg, Germany.,Department of Chemistry, University of Marburg, D-35043 Marburg, Germany
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, CH-1211 Geneva, Switzerland
| | - Wieland Steinchen
- Center for Synthetic Microbiology, D-35043 Marburg, Germany.,Department of Chemistry, University of Marburg, D-35043 Marburg, Germany
| | - Martin Thanbichler
- Department of Biology, University of Marburg, D-35043 Marburg, Germany.,Center for Synthetic Microbiology, D-35043 Marburg, Germany.,Max Planck Fellow Group Bacterial Cell Biology, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
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18
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Delaby M, Panis G, Viollier PH. Bacterial cell cycle and growth phase switch by the essential transcriptional regulator CtrA. Nucleic Acids Res 2020; 47:10628-10644. [PMID: 31598724 PMCID: PMC6847485 DOI: 10.1093/nar/gkz846] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 09/13/2019] [Accepted: 10/05/2019] [Indexed: 11/13/2022] Open
Abstract
Many bacteria acquire dissemination and virulence traits in G1-phase. CtrA, an essential and conserved cell cycle transcriptional regulator identified in the dimorphic alpha-proteobacterium Caulobacter crescentus, first activates promoters in late S-phase and then mysteriously switches to different target promoters in G1-phase. We uncovered a highly conserved determinant in the DNA-binding domain (DBD) of CtrA uncoupling this promoter switch. We also show that it reprograms CtrA occupancy in stationary cells inducing a (p)ppGpp alarmone signal perceived by the RNA polymerase beta subunit. A simple side chain modification in a critical residue within the core DBD imposes opposing developmental phenotypes and transcriptional activities of CtrA and a proximal residue can direct CtrA towards activation of the dispersal (G1-phase) program. Hence, we propose that this conserved determinant in the CtrA primary structure dictates promoter reprogramming during the growth transition in other alpha-proteobacteria that differentiate from replicative cells into dispersal cells.
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Affiliation(s)
- Marie Delaby
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Gaël Panis
- 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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19
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Bergé M, Pezzatti J, González-Ruiz V, Degeorges L, Mottet-Osman G, Rudaz S, Viollier PH. Bacterial cell cycle control by citrate synthase independent of enzymatic activity. eLife 2020; 9:52272. [PMID: 32149608 PMCID: PMC7083601 DOI: 10.7554/elife.52272] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 03/04/2020] [Indexed: 11/17/2022] Open
Abstract
Proliferating cells must coordinate central metabolism with the cell cycle. How central energy metabolism regulates bacterial cell cycle functions is not well understood. Our forward genetic selection unearthed the Krebs cycle enzyme citrate synthase (CitA) as a checkpoint regulator controlling the G1→S transition in the polarized alpha-proteobacterium Caulobacter crescentus, a model for cell cycle regulation and asymmetric cell division. We find that loss of CitA promotes the accumulation of active CtrA, an essential cell cycle transcriptional regulator that maintains cells in G1-phase, provided that the (p)ppGpp alarmone is present. The enzymatic activity of CitA is dispensable for CtrA control, and functional citrate synthase paralogs cannot replace CitA in promoting S-phase entry. Our evidence suggests that CitA was appropriated specifically to function as a moonlighting enzyme to link central energy metabolism with S-phase entry. Control of the G1-phase by a central metabolic enzyme may be a common mechanism of cellular regulation.
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Affiliation(s)
- Matthieu Bergé
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Julian Pezzatti
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, Geneva, Switzerland
| | - Víctor González-Ruiz
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, Geneva, Switzerland.,Swiss Centre for Applied Human Toxicology (SCAHT), Basel, Switzerland
| | - Laurence Degeorges
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Geneviève Mottet-Osman
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Serge Rudaz
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, Geneva, Switzerland.,Swiss Centre for Applied Human Toxicology (SCAHT), Basel, Switzerland
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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20
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Woldemeskel SA, Daitch AK, Alvarez L, Panis G, Zeinert R, Gonzalez D, Smith E, Collier J, Chien P, Cava F, Viollier PH, Goley ED. The conserved transcriptional regulator CdnL is required for metabolic homeostasis and morphogenesis in Caulobacter. PLoS Genet 2020; 16:e1008591. [PMID: 31961855 PMCID: PMC6994171 DOI: 10.1371/journal.pgen.1008591] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 01/31/2020] [Accepted: 01/01/2020] [Indexed: 12/23/2022] Open
Abstract
Bacterial growth and division require regulated synthesis of the macromolecules used to expand and replicate components of the cell. Transcription of housekeeping genes required for metabolic homeostasis and cell proliferation is guided by the sigma factor σ70. The conserved CarD-like transcriptional regulator, CdnL, associates with promoter regions where σ70 localizes and stabilizes the open promoter complex. However, the contributions of CdnL to metabolic homeostasis and bacterial physiology are not well understood. Here, we show that Caulobacter crescentus cells lacking CdnL have severe morphological and growth defects. Specifically, ΔcdnL cells grow slowly in both rich and defined media, and are wider, more curved, and have shorter stalks than WT cells. These defects arise from transcriptional downregulation of most major classes of biosynthetic genes, leading to significant decreases in the levels of critical metabolites, including pyruvate, α-ketoglutarate, ATP, NAD+, UDP-N-acetyl-glucosamine, lipid II, and purine and pyrimidine precursors. Notably, we find that ΔcdnL cells are glutamate auxotrophs, and ΔcdnL is synthetic lethal with other genetic perturbations that limit glutamate synthesis and lipid II production. Our findings implicate CdnL as a direct and indirect regulator of genes required for metabolic homeostasis that impacts morphogenesis through availability of lipid II and other metabolites.
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Affiliation(s)
- Selamawit Abi Woldemeskel
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Allison K. Daitch
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Laura Alvarez
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Gaël Panis
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Rilee Zeinert
- Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, MA, United States of America
| | - Diego Gonzalez
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Switzerland
| | - Erika Smith
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Justine Collier
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Switzerland
| | - Peter Chien
- Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, MA, United States of America
| | - Felipe Cava
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Patrick H. Viollier
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Erin D. Goley
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
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21
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Ellison CK, Kan J, Chlebek JL, Hummels KR, Panis G, Viollier PH, Biais N, Dalia AB, Brun YV. A bifunctional ATPase drives tad pilus extension and retraction. Sci Adv 2019; 5:eaay2591. [PMID: 31897429 PMCID: PMC6920026 DOI: 10.1126/sciadv.aay2591] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 10/21/2019] [Indexed: 06/10/2023]
Abstract
A widespread class of prokaryotic motors powered by secretion motor adenosine triphosphatases (ATPases) drives the dynamic extension and retraction of extracellular fibers, such as type IV pili (T4P). Among these, the tight adherence (tad) pili are critical for surface sensing and biofilm formation. As for most other motors belonging to this class, how tad pili retract despite lacking a dedicated retraction motor ATPase has remained a mystery. Here, we find that a bifunctional pilus motor ATPase, CpaF, drives both activities through adenosine 5'-triphosphate (ATP) hydrolysis. We show that mutations within CpaF result in a correlated reduction in the rates of extension and retraction that directly scales with decreased ATP hydrolysis and retraction force. Thus, a single motor ATPase drives the bidirectional processes of pilus fiber extension and retraction.
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Affiliation(s)
- Courtney K. Ellison
- Department of Biology, Indiana University, 1001 E. 3rd Street, Bloomington, IN 47405, USA
| | - Jingbo Kan
- Biology Department, CUNY Brooklyn College, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- Graduate Center of CUNY, 365 5th Avenue, New York, NY 10016, USA
| | - Jennifer L. Chlebek
- Department of Biology, Indiana University, 1001 E. 3rd Street, Bloomington, IN 47405, USA
| | - Katherine R. Hummels
- Department of Biology, Indiana University, 1001 E. 3rd Street, Bloomington, IN 47405, USA
| | - Gaёl Panis
- 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
| | - Nicolas Biais
- Biology Department, CUNY Brooklyn College, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- Graduate Center of CUNY, 365 5th Avenue, New York, NY 10016, USA
| | - Ankur B. Dalia
- Department of Biology, Indiana University, 1001 E. 3rd Street, Bloomington, IN 47405, USA
| | - Yves V. Brun
- Department of Biology, Indiana University, 1001 E. 3rd Street, Bloomington, IN 47405, USA
- Département de microbiologie, Infectiologie et Immunologie, Université de Montréal, succursale Centre-ville, Montréal, H3C 3J7 Quebec, Canada
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22
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Abstract
Peptidoglycan is the predominant stress-bearing structure in the cell envelope of most bacteria, and also a potent stimulator of the eukaryotic immune system. Obligate intracellular bacteria replicate exclusively within the interior of living cells, an osmotically protected niche. Under these conditions peptidoglycan is not necessarily needed to maintain the integrity of the bacterial cell. Moreover, the presence of peptidoglycan puts bacteria at risk of detection and destruction by host peptidoglycan recognition factors and downstream effectors. This has resulted in a selective pressure and opportunity to reduce the levels of peptidoglycan. In this review we have analysed the occurrence of genes involved in peptidoglycan metabolism across the major obligate intracellular bacterial species. From this comparative analysis, we have identified a group of predicted 'peptidoglycan-intermediate' organisms that includes the Chlamydiae, Orientia tsutsugamushi, Wolbachia and Anaplasma marginale. This grouping is likely to reflect biological differences in their infection cycle compared with peptidoglycan-negative obligate intracellular bacteria such as Ehrlichia and Anaplasma phagocytophilum, as well as obligate intracellular bacteria with classical peptidoglycan such as Coxiella, Buchnera and members of the Rickettsia genus. The signature gene set of the peptidoglycan-intermediate group reveals insights into minimal enzymatic requirements for building a peptidoglycan-like sacculus and/or division septum.
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Affiliation(s)
- Christian Otten
- The Centre for Bacterial Cell BiologyInstitute for Cell and Molecular Biosciences, Newcastle UniversityNewcastle upon TyneNE2 4AXUK
| | - Matteo Brilli
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE)University of Padova. Agripolis ‐ V.le dell'Università, 16 | 35020 Legnaro PadovaItaly
- Present address:
Department of BiosciencesUniversity of Milan, via Celoria 26(MI)Italy
| | - Waldemar Vollmer
- The Centre for Bacterial Cell BiologyInstitute for Cell and Molecular Biosciences, Newcastle UniversityNewcastle upon TyneNE2 4AXUK
| | - Patrick H. Viollier
- Department of Microbiology and Molecular MedicineInstitute of Genetics & Genomics in Geneva (iGE3), University of GenevaGenevaSwitzerland
| | - Jeanne Salje
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global HealthUniversity of OxfordOxfordUK
- Mahidol‐Oxford Tropical Medicine Research UnitMahidol UniversityBangkokThailand
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23
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Bergé M, Viollier PH. End-in-Sight: Cell Polarization by the Polygamic Organizer PopZ. Trends Microbiol 2017; 26:363-375. [PMID: 29198650 DOI: 10.1016/j.tim.2017.11.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 11/02/2017] [Accepted: 11/09/2017] [Indexed: 12/18/2022]
Abstract
Understanding how asymmetries in cellular constituents are achieved and how such positional information directs the construction of structures in a nonrandom fashion is a fundamental problem in cell biology. The recent identification of determinants that self-assemble into macromolecular complexes at the bacterial cell pole provides new insight into the underlying organizational principles in bacterial cells. Specifically, polarity studies in host-associated or free-living α-proteobacteria, a lineage of Gram-negative (diderm) bacteria, reveals that functional and cytological mono- and bipolarity is often conferred by the multivalent polar organizer PopZ, originally identified as a component of a polar chromosome anchor in the cell cycle model system Caulobacter crescentus. PopZ-dependent polarization appears to be widespread and also functional in obligate intracellular pathogens. Here, we discuss how PopZ polarization and the establishment of polar complexes occurs, and we detail the physiological roles of these complexes.
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Affiliation(s)
- Matthieu Bergé
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Rue Michel Servet 1, CH-1211 Geneva, Switzerland.
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Rue Michel Servet 1, CH-1211 Geneva, Switzerland.
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24
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Taylor JA, Panis G, Viollier PH, Marczynski GT. A novel nucleoid-associated protein coordinates chromosome replication and chromosome partition. Nucleic Acids Res 2017; 45:8916-8929. [PMID: 28911105 PMCID: PMC5587793 DOI: 10.1093/nar/gkx596] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 07/05/2017] [Indexed: 11/14/2022] Open
Abstract
We searched for regulators of chromosome replication in the cell cycle model Caulobacter crescentus and found a novel DNA-binding protein (GapR) that selectively aids the initiation of chromosome replication and the initial steps of chromosome partitioning. The protein binds the chromosome origin of replication (Cori) and has higher-affinity binding to mutated Cori-DNA that increases Cori-plasmid replication in vivo. gapR gene expression is essential for normal rapid growth and sufficient GapR levels are required for the correct timing of chromosome replication. Whole genome ChIP-seq identified dynamic DNA-binding distributions for GapR, with the strongest associations at the partitioning (parABS) locus near Cori. Using molecular-genetic and fluorescence microscopy experiments, we showed that GapR also promotes the first steps of chromosome partitioning, the initial separation of the duplicated parS loci following replication from Cori. This separation occurs before the parABS-dependent partitioning phase. Therefore, this early separation, whose mechanisms is not known, coincides with the poorly defined mechanism(s) that establishes chromosome asymmetry: C. crescentus chromosomes are partitioned to distinct cell-poles which develop into replicating and non-replicating cell-types. We propose that GapR coordinates chromosome replication with asymmetry-establishing chromosome separation, noting that both roles are consistent with the phylogenetic restriction of GapR to asymmetrically dividing bacteria.
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Affiliation(s)
- James A Taylor
- Department of Microbiology and Immunology, McGill University, 3775 University St., Montreal, QC H3A 2B4, Canada
| | - Gaël Panis
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland
| | - Gregory T Marczynski
- Department of Microbiology and Immunology, McGill University, 3775 University St., Montreal, QC H3A 2B4, Canada
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25
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Hallez R, Delaby M, Sanselicio S, Viollier PH. Hit the right spots: cell cycle control by phosphorylated guanosines in alphaproteobacteria. Nat Rev Microbiol 2017; 15:137-148. [PMID: 28138140 DOI: 10.1038/nrmicro.2016.183] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The class Alphaproteobacteria includes Gram-negative free-living, symbiotic and obligate intracellular bacteria, as well as important plant, animal and human pathogens. Recent work has established the key antagonistic roles that phosphorylated guanosines, cyclic-di-GMP (c-di-GMP) and the alarmones guanosine tetraphosphate and guanosine pentaphosphate (collectively referred to as (p)ppGpp), have in the regulation of the cell cycle in these bacteria. In this Review, we discuss the insights that have been gained into the regulation of the initiation of DNA replication and cytokinesis by these second messengers, with a particular focus on the cell cycle of Caulobacter crescentus. We explore how the fluctuating levels of c-di-GMP and (p)ppGpp during the progression of the cell cycle and under conditions of stress control the synthesis and proteolysis of key regulators of the cell cycle. As these signals also promote bacterial interactions with host cells, the enzymes that control (p)ppGpp and c-di-GMP are attractive antibacterial targets.
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Affiliation(s)
- Régis Hallez
- Bacterial Cell cycle and Development (BCcD), Unité de recherche en biologie des micro-organismes (URBM), University of Namur, 61 Rue de Bruxelles, Namur 5000, Belgium
| | - Marie Delaby
- Department of Microbiology and Molecular Medicine, Institute of Genetics &Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Stefano Sanselicio
- Department of Microbiology and Molecular Medicine, Institute of Genetics &Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland.,Present address: Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, Institute of Genetics &Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
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26
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Mignolet J, Holden S, Bergé M, Panis G, Eroglu E, Théraulaz L, Manley S, Viollier PH. Functional dichotomy and distinct nanoscale assemblies of a cell cycle-controlled bipolar zinc-finger regulator. eLife 2016; 5. [PMID: 28008851 PMCID: PMC5182063 DOI: 10.7554/elife.18647] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/01/2016] [Indexed: 11/13/2022] Open
Abstract
Protein polarization underlies differentiation in metazoans and in bacteria. How symmetric polarization can instate functional asymmetry remains elusive. Here, we show by super-resolution photo-activated localization microscopy and edgetic mutations that the bitopic zinc-finger protein ZitP implements specialized developmental functions – pilus biogenesis and multifactorial swarming motility – while shaping distinct nanoscale (bi)polar architectures in the asymmetric model bacterium Caulobacter crescentus. Polar assemblage and accumulation of ZitP and its effector protein CpaM are orchestrated in time and space by conserved components of the cell cycle circuitry that coordinate polar morphogenesis with cell cycle progression, and also act on the master cell cycle regulator CtrA. Thus, this novel class of potentially widespread multifunctional polarity regulators is deeply embedded in the cell cycle circuitry. DOI:http://dx.doi.org/10.7554/eLife.18647.001 Living cells become asymmetric for many different reasons and how they do so has been a long-standing question in biology. In some cells, the asymmetry arises because a given protein accumulates at one side of the cell. In particular, this process happens before some cells divide to produce two non-identical daughter cells that then go on to develop in very different ways – which is vital for the development of almost all multicellular organisms. The single-celled bacterium Caulobacter crescentus also undergoes this type of asymmetric division. The polarized Caulobacter cell produces two very different offsprings – a stationary cell and a nomadic cell that swims using a propeller-like structure, called a flagellum, and has projections called pili on its surface. Before it divides asymmetrically, the Caulobacter cell must accumulate specific proteins at its extremities, or poles. Two such proteins are ZitP and CpaM, which appear to have multiple roles and are thought to interact with other factors that regulate cell division. However, little is known about how ZitP and CpaM become organized at the poles at the right time and how they interact with these regulators of cell division. Mignolet et al. explored how ZitP becomes polarized in Caulobacter crescentus using a combination of approaches including biochemical and genetic analyses and very high-resolution microscopy. This revealed that ZitP accumulated via different pathways at the two poles and that it formed distinct structures at each pole. These structures were associated with different roles for ZitP. While ZitP recruited proteins, including CpaM, required for assembly of pili to one of the poles, it acted differently at the opposite pole. By mutating regions of ZitP, Mignolet et al. went on to show that different regions of the protein carry out these roles. Further experiments demonstrated that regulators of the cell division cycle influenced how ZitP and CpaM accumulated and behaved in cells, ensuring that the proteins carry out their roles at the correct time during division. These findings provide more evidence that proteins can have different roles at distinct sites within a cell, in this case at opposite poles of a cell. Future studies will be needed to determine whether this is seen in cells other than Caulobacter including more complex, non-bacterial cells. DOI:http://dx.doi.org/10.7554/eLife.18647.002
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Affiliation(s)
- Johann Mignolet
- Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Seamus Holden
- Laboratory of Experimental Biophysics, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle, United Kingdom
| | - Matthieu Bergé
- Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Gaël Panis
- Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Ezgi Eroglu
- Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Laurence Théraulaz
- Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Suliana Manley
- Laboratory of Experimental Biophysics, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Patrick H Viollier
- Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland
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27
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Bergé M, Campagne S, Mignolet J, Holden S, Théraulaz L, Manley S, Allain FHT, Viollier PH. Modularity and determinants of a (bi-)polarization control system from free-living and obligate intracellular bacteria. eLife 2016; 5. [PMID: 28008852 PMCID: PMC5182065 DOI: 10.7554/elife.20640] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 12/07/2016] [Indexed: 11/24/2022] Open
Abstract
Although free-living and obligate intracellular bacteria are both polarized it is unclear whether the underlying polarization mechanisms and effector proteins are conserved. Here we dissect at the cytological, functional and structural level a conserved polarization module from the free living α-proteobacterium Caulobacter crescentus and an orthologous system from an obligate intracellular (rickettsial) pathogen. The NMR solution structure of the zinc-finger (ZnR) domain from the bifunctional and bipolar ZitP pilus assembly/motility regulator revealed conserved interaction determinants for PopZ, a bipolar matrix protein that anchors the ParB centromere-binding protein and other regulatory factors at the poles. We show that ZitP regulates cytokinesis and the localization of ParB and PopZ, targeting PopZ independently of the previously known binding sites for its client proteins. Through heterologous localization assays with rickettsial ZitP and PopZ orthologs, we document the shared ancestries, activities and structural determinants of a (bi-)polarization system encoded in free-living and obligate intracellular α-proteobacteria. DOI:http://dx.doi.org/10.7554/eLife.20640.001
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Affiliation(s)
- Matthieu Bergé
- Department Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Sébastien Campagne
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Johann Mignolet
- Department Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Seamus Holden
- Laboratory of Experimental Biophysics, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Laurence Théraulaz
- Department Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Suliana Manley
- Laboratory of Experimental Biophysics, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Frédéric H-T Allain
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Patrick H Viollier
- Department Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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28
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de Barsy M, Frandi A, Panis G, Théraulaz L, Pillonel T, Greub G, Viollier PH. Regulatory (pan-)genome of an obligate intracellular pathogen in the PVC superphylum. ISME J 2016; 10:2129-44. [PMID: 26953603 PMCID: PMC4989314 DOI: 10.1038/ismej.2016.23] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 01/19/2016] [Accepted: 01/21/2016] [Indexed: 01/17/2023]
Abstract
Like other obligate intracellular bacteria, the Chlamydiae feature a compact regulatory genome that remains uncharted owing to poor genetic tractability. Exploiting the reduced number of transcription factors (TFs) encoded in the chlamydial (pan-)genome as a model for TF control supporting the intracellular lifestyle, we determined the conserved landscape of TF specificities by ChIP-Seq (chromatin immunoprecipitation-sequencing) in the chlamydial pathogen Waddlia chondrophila. Among 10 conserved TFs, Euo emerged as a master TF targeting >100 promoters through conserved residues in a DNA excisionase-like winged helix-turn-helix-like (wHTH) fold. Minimal target (Euo) boxes were found in conserved developmentally-regulated genes governing vertical genome transmission (cytokinesis and DNA replication) and genome plasticity (transposases). Our ChIP-Seq analysis with intracellular bacteria not only reveals that global TF regulation is maintained in the reduced regulatory genomes of Chlamydiae, but also predicts that master TFs interpret genomic information in the obligate intracellular α-proteobacteria, including the rickettsiae, from which modern day mitochondria evolved.
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Affiliation(s)
- Marie de Barsy
- Institute of Microbiology, University Hospital Center, University of Lausanne, Lausanne, Switzerland
| | - Antonio Frandi
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Gaël Panis
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Laurence Théraulaz
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Trestan Pillonel
- Institute of Microbiology, University Hospital Center, University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University Hospital Center, University of Lausanne, Lausanne, Switzerland
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland
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29
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Kirkpatrick CL, Martins D, Redder P, Frandi A, Mignolet J, Chapalay JB, Chambon M, Turcatti G, Viollier PH. Growth control switch by a DNA-damage-inducible toxin-antitoxin system in Caulobacter crescentus. Nat Microbiol 2016; 1:16008. [PMID: 27572440 DOI: 10.1038/nmicrobiol.2016.8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 01/19/2016] [Indexed: 11/09/2022]
Abstract
Bacterial toxin-antitoxin systems (TASs) are thought to respond to various stresses, often inducing growth-arrested (persistent) sub-populations of cells whose housekeeping functions are inhibited. Many such TASs induce this effect through the translation-dependent RNA cleavage (RNase) activity of their toxins, which are held in check by their cognate antitoxins in the absence of stress. However, it is not always clear whether specific mRNA targets of orthologous RNase toxins are responsible for their phenotypic effect, which has made it difficult to accurately place the multitude of TASs within cellular and adaptive regulatory networks. Here, we show that the TAS HigBA of Caulobacter crescentus can promote and inhibit bacterial growth dependent on the dosage of HigB, a toxin regulated by the DNA damage (SOS) repressor LexA in addition to its antitoxin HigA, and the target selectivity of HigB's mRNA cleavage activity. HigB reduced the expression of an efflux pump that is toxic to a polarity control mutant, cripples the growth of cells lacking LexA, and targets the cell cycle circuitry. Thus, TASs can have outcome switching activity in bacterial adaptive (stress) and systemic (cell cycle) networks.
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Affiliation(s)
- Clare L Kirkpatrick
- Department of Microbiology &Molecular Medicine, Institute of Genetics &Genomics in Geneva (iGE3), Faculty of Medicine/CMU, University of Geneva, Rue Michel-Servet 1, 1211 Genève 4, Switzerland
| | - Daniel Martins
- Department of Microbiology &Molecular Medicine, Institute of Genetics &Genomics in Geneva (iGE3), Faculty of Medicine/CMU, University of Geneva, Rue Michel-Servet 1, 1211 Genève 4, Switzerland
| | - Peter Redder
- Department of Microbiology &Molecular Medicine, Institute of Genetics &Genomics in Geneva (iGE3), Faculty of Medicine/CMU, University of Geneva, Rue Michel-Servet 1, 1211 Genève 4, Switzerland
| | - Antonio Frandi
- Department of Microbiology &Molecular Medicine, Institute of Genetics &Genomics in Geneva (iGE3), Faculty of Medicine/CMU, University of Geneva, Rue Michel-Servet 1, 1211 Genève 4, Switzerland
| | - Johann Mignolet
- Department of Microbiology &Molecular Medicine, Institute of Genetics &Genomics in Geneva (iGE3), Faculty of Medicine/CMU, University of Geneva, Rue Michel-Servet 1, 1211 Genève 4, Switzerland
| | - Julien Bortoli Chapalay
- Biomolecular Screening Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Marc Chambon
- Biomolecular Screening Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Gerardo Turcatti
- Biomolecular Screening Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Patrick H Viollier
- Department of Microbiology &Molecular Medicine, Institute of Genetics &Genomics in Geneva (iGE3), Faculty of Medicine/CMU, University of Geneva, Rue Michel-Servet 1, 1211 Genève 4, Switzerland
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30
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Ardissone S, Viollier PH. Interplay between flagellation and cell cycle control in Caulobacter. Curr Opin Microbiol 2015; 28:83-92. [PMID: 26476805 DOI: 10.1016/j.mib.2015.08.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Revised: 08/09/2015] [Accepted: 08/11/2015] [Indexed: 12/21/2022]
Abstract
The assembly of the flagellum, a sophisticated nanomachine powering bacterial locomotion in liquids and across surfaces, is highly regulated. In the synchronizable α-Proteobacterium Caulobacter crescentus, the flagellum is built at a pre-selected cell pole and flagellar transcript abundance oscillates during the cell cycle. Conserved regulators not only dictate when the transcripts encoding flagellar structural proteins peak, but also those encoding polarization factors. Additionally, post-transcriptional cell cycle cues facilitate flagellar (dis-)assembly at the new cell pole. Because of this regulatory complexity and the power of bacterial genetics, motility is a suitable and simple proxy for dissecting how bacteria implement cell cycle progression and polarity, while also providing clues on how bacteria might decide when and where to display other surface structures.
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Affiliation(s)
- Silvia Ardissone
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Rue Michel Servet 1, 1211 Geneva 4, Switzerland
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Rue Michel Servet 1, 1211 Geneva 4, Switzerland.
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31
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Jacquier N, Frandi A, Viollier PH, Greub G. Disassembly of a Medial Transenvelope Structure by Antibiotics during Intracellular Division. ACTA ACUST UNITED AC 2015; 22:1217-27. [PMID: 26364930 DOI: 10.1016/j.chembiol.2015.08.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 07/28/2015] [Accepted: 08/01/2015] [Indexed: 10/23/2022]
Abstract
Chlamydiales possess a minimal but functional peptidoglycan precursor biosynthetic and remodeling pathway involved in the assembly of the division septum by an atypical cytokinetic machine and cryptic or modified peptidoglycan-like structure (PGLS). How this reduced cytokinetic machine collectively coordinates the invagination of the envelope has not yet been explored in Chlamydiales. In other Gram-negative bacteria, peptidoglycan provides anchor points that connect the outer membrane to the peptidoglycan during constriction using the Pal-Tol complex. Purifying PGLS and associated proteins from the chlamydial pathogen Waddlia chondrophila, we unearthed the Pal protein as a peptidoglycan-binding protein that localizes to the chlamydial division septum along with other components of the Pal-Tol complex. Together, our PGLS characterization and peptidoglycan-binding assays support the notion that diaminopimelic acid is an important determinant recruiting Pal to the division plane to coordinate the invagination of all envelope layers with the conserved Pal-Tol complex, even during osmotically protected intracellular growth.
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Affiliation(s)
- Nicolas Jacquier
- Department of Laboratories, Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne 1011, Switzerland
| | - Antonio Frandi
- Department of Microbiology & Molecular Medicine, Institute of Genetics & Genomics in Geneva (iGE3), Faculty of Medicine/CMU, University of Geneva, Geneva 1211, Switzerland
| | - Patrick H Viollier
- Department of Microbiology & Molecular Medicine, Institute of Genetics & Genomics in Geneva (iGE3), Faculty of Medicine/CMU, University of Geneva, Geneva 1211, Switzerland.
| | - Gilbert Greub
- Department of Laboratories, Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne 1011, Switzerland.
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Pini F, De Nisco NJ, Ferri L, Penterman J, Fioravanti A, Brilli M, Mengoni A, Bazzicalupo M, Viollier PH, Walker GC, Biondi EG. Cell Cycle Control by the Master Regulator CtrA in Sinorhizobium meliloti. PLoS Genet 2015; 11:e1005232. [PMID: 25978424 PMCID: PMC4433202 DOI: 10.1371/journal.pgen.1005232] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 04/21/2015] [Indexed: 01/23/2023] Open
Abstract
In all domains of life, proper regulation of the cell cycle is critical to coordinate genome replication, segregation and cell division. In some groups of bacteria, e.g. Alphaproteobacteria, tight regulation of the cell cycle is also necessary for the morphological and functional differentiation of cells. Sinorhizobium meliloti is an alphaproteobacterium that forms an economically and ecologically important nitrogen-fixing symbiosis with specific legume hosts. During this symbiosis S. meliloti undergoes an elaborate cellular differentiation within host root cells. The differentiation of S. meliloti results in massive amplification of the genome, cell branching and/or elongation, and loss of reproductive capacity. In Caulobacter crescentus, cellular differentiation is tightly linked to the cell cycle via the activity of the master regulator CtrA, and recent research in S. meliloti suggests that CtrA might also be key to cellular differentiation during symbiosis. However, the regulatory circuit driving cell cycle progression in S. meliloti is not well characterized in both the free-living and symbiotic state. Here, we investigated the regulation and function of CtrA in S. meliloti. We demonstrated that depletion of CtrA cause cell elongation, branching and genome amplification, similar to that observed in nitrogen-fixing bacteroids. We also showed that the cell cycle regulated proteolytic degradation of CtrA is essential in S. meliloti, suggesting a possible mechanism of CtrA depletion in differentiated bacteroids. Using a combination of ChIP-Seq and gene expression microarray analysis we found that although S. meliloti CtrA regulates similar processes as C. crescentus CtrA, it does so through different target genes. For example, our data suggest that CtrA does not control the expression of the Fts complex to control the timing of cell division during the cell cycle, but instead it negatively regulates the septum-inhibiting Min system. Our findings provide valuable insight into how highly conserved genetic networks can evolve, possibly to fit the diverse lifestyles of different bacteria. In order to propagate, all living cells must ensure that their genetic material is faithfully copied and properly partitioned into the daughter cells before division. These coordinated processes of DNA replication and cell division are termed the “cell cycle” and are controlled by a complex network of regulatory proteins in all organisms. In the class Alphaproteobacteria, the regulation of the cell cycle is closely linked to cellular differentiation processes that are vital for survival in the environment. In these bacteria, the cell cycle regulator CtrA is thought to serve as the primary link between the coordination of the cell cycle and cellular differentiation. The alphaproteobacterium, Sinorhizobium meliloti, an important model symbiont of alfalfa plants, undergoes a striking cellular differentiation that is vital to the formation of an efficient symbiosis dedicated to the conversion of atmospheric nitrogen to biologically available organic nitrogen. However, the link between cellular differentiation and cell cycle control in S. meliloti has not been made. In this study, we showed that S. meliloti cells without CtrA are similar to the symbiotic form. By the identification of the genes whose expression is directly and indirectly controlled by CtrA, we found that CtrA regulates vital cell cycle processes, including DNA replication and cell division, but through different genetic pathways than in other alphaproteobacteria. We importantly show that the levels of CtrA protein are governed by an essential cell cycle regulated proteolysis, which may also be an important mode of CtrA down-regulation during symbiosis to drive cellular differentiation.
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Affiliation(s)
- Francesco Pini
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576 CNRS—Université de Lille, Villeneuve d'Ascq, France
| | - Nicole J. De Nisco
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Lorenzo Ferri
- Meyer Children Hospital, University of Florence, Firenze, Italy
| | - Jon Penterman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Antonella Fioravanti
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576 CNRS—Université de Lille, Villeneuve d'Ascq, France
| | - Matteo Brilli
- Fondazione Edmund Mach/CRI, Functional genomics, San Michele all'Adige, Italy
| | | | | | - Patrick H. Viollier
- Dept. Microbiology & Molecular Medicine, University of Geneva, Genève, Switzerland
| | - Graham C. Walker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Emanuele G. Biondi
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576 CNRS—Université de Lille, Villeneuve d'Ascq, France
- * E-mail:
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Jacquier N, Viollier PH, Greub G. The role of peptidoglycan in chlamydial cell division: towards resolving the chlamydial anomaly. FEMS Microbiol Rev 2015; 39:262-75. [PMID: 25670734 DOI: 10.1093/femsre/fuv001] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Chlamydiales are obligate intracellular bacteria including some important pathogens causing trachoma, genital tract infections and pneumonia, among others. They share an atypical division mechanism, which is independent of an FtsZ homologue. However, they divide by binary fission, in a process inhibited by penicillin derivatives, causing the formation of an aberrant form of the bacteria, which is able to survive in the presence of the antibiotic. The paradox of penicillin sensitivity of chlamydial cells in the absence of detectable peptidoglycan (PG) was dubbed the chlamydial anomaly, since no PG modified by enzymes (Pbps) that are the usual target of penicillin could be detected in Chlamydiales. We review here the recent advances in this field with the first direct and indirect evidences of PG-like material in both Chlamydiaceae and Chlamydia-related bacteria. Moreover, PG biosynthesis is required for proper localization of the newly described septal proteins RodZ and NlpD. Taken together, these new results set the stage for a better understanding of the role of PG and septal proteins in the division mechanism of Chlamydiales and illuminate the long-standing chlamydial anomaly. Moreover, understanding the chlamydial division mechanism is critical for the development of new antibiotics for the treatment of chlamydial chronic infections.
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Affiliation(s)
- Nicolas Jacquier
- Institute of Microbiology, University Hospital Center and University of Lausanne, CH-1011 Lausanne, Switzerland
| | - Patrick H Viollier
- Department of Microbiology & Molecular Medicine, Institute of Genetics & Genomics in Geneva (iGE3), Faculty of Medicine / CMU, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University Hospital Center and University of Lausanne, CH-1011 Lausanne, Switzerland
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Panis G, Murray SR, Viollier PH. Versatility of global transcriptional regulators in alpha-Proteobacteria: from essential cell cycle control to ancillary functions. FEMS Microbiol Rev 2014; 39:120-33. [PMID: 25793963 DOI: 10.1093/femsre/fuu002] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Recent data indicate that cell cycle transcription in many alpha-Proteobacteria is executed by at least three conserved functional modules in which pairs of antagonistic regulators act jointly, rather than in isolation, to control transcription in S-, G2- or G1-phase. Inactivation of module components often results in pleiotropic defects, ranging from cell death and impaired cell division to fairly benign deficiencies in motility. Expression of module components can follow systemic (cell cycle) or external (nutritional/cell density) cues and may be implemented by auto-regulation, ancillary regulators or other (unknown) mechanisms. Here, we highlight the recent progress in understanding the molecular events and the genetic relationships of the module components in environmental, pathogenic and/or symbiotic alpha-proteobacterial genera. Additionally, we take advantage of the recent genome-wide transcriptional analyses performed in the model alpha-Proteobacterium Caulobacter crescentus to illustrate the complexity of the interactions of the global regulators at selected cell cycle-regulated promoters and we detail the consequences of (mis-)expression when the regulators are absent. This review thus provides the first detailed mechanistic framework for understanding orthologous operational principles acting on cell cycle-regulated promoters in other alpha-Proteobacteria.
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Affiliation(s)
- Gaël Panis
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine/CMU, University of Geneva, Rue Michel Servet 1, 1211 Genève 4, Switzerland
| | - Sean R Murray
- Department of Biology, Center for Cancer and Developmental Biology, Interdisciplinary Research Institute for the Sciences, California State University Northridge, 18111 Nordhoff Street, Northridge, CA 91330-8303, USA
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine/CMU, University of Geneva, Rue Michel Servet 1, 1211 Genève 4, Switzerland
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Ardissone S, Fumeaux C, Bergé M, Beaussart A, Théraulaz L, Radhakrishnan SK, Dufrêne YF, Viollier PH. Cell cycle constraints on capsulation and bacteriophage susceptibility. eLife 2014; 3. [PMID: 25421297 PMCID: PMC4241560 DOI: 10.7554/elife.03587] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 10/21/2014] [Indexed: 12/28/2022] Open
Abstract
Despite the crucial role of bacterial capsules in pathogenesis, it is still unknown if systemic cues such as the cell cycle can control capsule biogenesis. In this study, we show that the capsule of the synchronizable model bacterium Caulobacter crescentus is cell cycle regulated and we unearth a bacterial transglutaminase homolog, HvyA, as restriction factor that prevents capsulation in G1-phase cells. This capsule protects cells from infection by a generalized transducing Caulobacter phage (φCr30), and the loss of HvyA confers insensitivity towards φCr30. Control of capsulation during the cell cycle could serve as a simple means to prevent steric hindrance of flagellar motility or to ensure that phage-mediated genetic exchange happens before the onset of DNA replication. Moreover, the multi-layered regulatory circuitry directing HvyA expression to G1-phase is conserved during evolution, and HvyA orthologues from related Sinorhizobia can prevent capsulation in Caulobacter, indicating that alpha-proteobacteria have retained HvyA activity.
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Affiliation(s)
- Silvia Ardissone
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - Coralie Fumeaux
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - Matthieu Bergé
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - Audrey Beaussart
- Institute of Life Sciences, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Laurence Théraulaz
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - Sunish Kumar Radhakrishnan
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - Yves F Dufrêne
- Institute of Life Sciences, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
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Fumeaux C, Radhakrishnan SK, Ardissone S, Théraulaz L, Frandi A, Martins D, Nesper J, Abel S, Jenal U, Viollier PH. Cell cycle transition from S-phase to G1 in Caulobacter is mediated by ancestral virulence regulators. Nat Commun 2014; 5:4081. [PMID: 24939058 PMCID: PMC4083442 DOI: 10.1038/ncomms5081] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 05/09/2014] [Indexed: 11/10/2022] Open
Abstract
Zinc-finger domain transcriptional regulators regulate a myriad of functions in eukaryotes. Interestingly, ancestral versions (MucR) from Alpha-proteobacteria control bacterial virulence/symbiosis. Whether virulence regulators can also control cell cycle transcription is unknown. Here we report that MucR proteins implement a hitherto elusive primordial S→G1 transcriptional switch. After charting G1-specific promoters in the cell cycle model Caulobacter crescentus by comparative ChIP-seq, we use one such promoter as genetic proxy to unearth two MucR paralogs, MucR1/2, as constituents of a quadripartite and homeostatic regulatory module directing the S→G1 transcriptional switch. Surprisingly, MucR orthologues that regulate virulence and symbiosis gene transcription in Brucella, Agrobacterium or Sinorhizobium support this S→G1 switch in Caulobacter. Pan-genomic ChIP-seq analyses in Sinorhizobium and Caulobacter show that this module indeed targets orthologous genes. We propose that MucR proteins and possibly other virulence regulators primarily control bacterial cell cycle (G1-phase) transcription, rendering expression of target (virulence) genes periodic and in tune with the cell cycle. The bacterium Caulobacter crescentus divides asymmetrically to generate a replicative stalk cell and a quiescent swarmer cell. Fumeaux et al. show that MucR zinc-finger transcription factors, which regulate virulence in other species, also control re-entry into quiescence in Caulobacter.
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Affiliation(s)
- Coralie Fumeaux
- Department Microbiology and Molecular Medicine, Faculty of Medicine/CMU, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Rue Michel Servet 1, 1211 Genève 4, Switzerland
| | - Sunish Kumar Radhakrishnan
- 1] Department Microbiology and Molecular Medicine, Faculty of Medicine/CMU, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Rue Michel Servet 1, 1211 Genève 4, Switzerland [2]
| | - Silvia Ardissone
- Department Microbiology and Molecular Medicine, Faculty of Medicine/CMU, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Rue Michel Servet 1, 1211 Genève 4, Switzerland
| | - Laurence Théraulaz
- Department Microbiology and Molecular Medicine, Faculty of Medicine/CMU, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Rue Michel Servet 1, 1211 Genève 4, Switzerland
| | - Antonio Frandi
- Department Microbiology and Molecular Medicine, Faculty of Medicine/CMU, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Rue Michel Servet 1, 1211 Genève 4, Switzerland
| | - Daniel Martins
- Department Microbiology and Molecular Medicine, Faculty of Medicine/CMU, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Rue Michel Servet 1, 1211 Genève 4, Switzerland
| | - Jutta Nesper
- Biozentrum of the University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Sören Abel
- 1] Biozentrum of the University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland [2]
| | - Urs Jenal
- Biozentrum of the University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Patrick H Viollier
- Department Microbiology and Molecular Medicine, Faculty of Medicine/CMU, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Rue Michel Servet 1, 1211 Genève 4, Switzerland
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Fiebig A, Herrou J, Fumeaux C, Radhakrishnan SK, Viollier PH, Crosson S. A cell cycle and nutritional checkpoint controlling bacterial surface adhesion. PLoS Genet 2014; 10:e1004101. [PMID: 24465221 PMCID: PMC3900383 DOI: 10.1371/journal.pgen.1004101] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 11/19/2013] [Indexed: 11/18/2022] Open
Abstract
In natural environments, bacteria often adhere to surfaces where they form complex multicellular communities. Surface adherence is determined by the biochemical composition of the cell envelope. We describe a novel regulatory mechanism by which the bacterium, Caulobacter crescentus, integrates cell cycle and nutritional signals to control development of an adhesive envelope structure known as the holdfast. Specifically, we have discovered a 68-residue protein inhibitor of holdfast development (HfiA) that directly targets a conserved glycolipid glycosyltransferase required for holdfast production (HfsJ). Multiple cell cycle regulators associate with the hfiA and hfsJ promoters and control their expression, temporally constraining holdfast development to the late stages of G1. HfiA further functions as part of a 'nutritional override' system that decouples holdfast development from the cell cycle in response to nutritional cues. This control mechanism can limit surface adhesion in nutritionally sub-optimal environments without affecting cell cycle progression. We conclude that post-translational regulation of cell envelope enzymes by small proteins like HfiA may provide a general means to modulate the surface properties of bacterial cells.
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Affiliation(s)
- Aretha Fiebig
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (AF); (SC)
| | - Julien Herrou
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Coralie Fumeaux
- Department of Microbiology and Molecular Medicine, Institute of Genetics & Genomics in Geneva (iGE3), University of Geneva Medical School, Geneva, Switzerland
| | - Sunish K. Radhakrishnan
- Department of Microbiology and Molecular Medicine, Institute of Genetics & Genomics in Geneva (iGE3), University of Geneva Medical School, Geneva, Switzerland
| | - Patrick H. Viollier
- Department of Microbiology and Molecular Medicine, Institute of Genetics & Genomics in Geneva (iGE3), University of Geneva Medical School, Geneva, Switzerland
| | - Sean Crosson
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, United States of America
- Committee on Microbiology, University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (AF); (SC)
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Murray SM, Panis G, Fumeaux C, Viollier PH, Howard M. Computational and genetic reduction of a cell cycle to its simplest, primordial components. PLoS Biol 2013; 11:e1001749. [PMID: 24415923 PMCID: PMC3885167 DOI: 10.1371/journal.pbio.1001749] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 11/14/2013] [Indexed: 02/02/2023] Open
Abstract
What are the minimal requirements to sustain an asymmetric cell cycle? Here we use mathematical modelling and forward genetics to reduce an asymmetric cell cycle to its simplest, primordial components. In the Alphaproteobacterium Caulobacter crescentus, cell cycle progression is believed to be controlled by a cyclical genetic circuit comprising four essential master regulators. Unexpectedly, our in silico modelling predicted that one of these regulators, GcrA, is in fact dispensable. We confirmed this experimentally, finding that ΔgcrA cells are viable, but slow-growing and elongated, with the latter mostly due to an insufficiency of a key cell division protein. Furthermore, suppressor analysis showed that another cell cycle regulator, the methyltransferase CcrM, is similarly dispensable with simultaneous gcrA/ccrM disruption ameliorating the cytokinetic and growth defect of ΔgcrA cells. Within the Alphaproteobacteria, gcrA and ccrM are consistently present or absent together, rather than either gene being present alone, suggesting that gcrA/ccrM constitutes an independent, dispensable genetic module. Together our approaches unveil the essential elements of a primordial asymmetric cell cycle that should help illuminate more complex cell cycles.
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Affiliation(s)
- Seán M. Murray
- Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Gaël Panis
- Department of Microbiology & Molecular Medicine, Institute of Genetics & Genomics in Geneva (iGE3), Faculty of Medicine/CMU, University of Geneva, Geneva, Switzerland
| | - Coralie Fumeaux
- Department of Microbiology & Molecular Medicine, Institute of Genetics & Genomics in Geneva (iGE3), Faculty of Medicine/CMU, University of Geneva, Geneva, Switzerland
| | - Patrick H. Viollier
- Department of Microbiology & Molecular Medicine, Institute of Genetics & Genomics in Geneva (iGE3), Faculty of Medicine/CMU, University of Geneva, Geneva, Switzerland
- * E-mail: (P.H.V.); (M.H.)
| | - Martin Howard
- Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
- * E-mail: (P.H.V.); (M.H.)
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Davis NJ, Cohen Y, Sanselicio S, Fumeaux C, Ozaki S, Luciano J, Guerrero-Ferreira RC, Wright ER, Jenal U, Viollier PH. De- and repolarization mechanism of flagellar morphogenesis during a bacterial cell cycle. Genes Dev 2013; 27:2049-62. [PMID: 24065770 PMCID: PMC3792480 DOI: 10.1101/gad.222679.113] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Eukaryotic morphogenesis is seeded with the establishment and subsequent amplification of polarity cues at key times during the cell cycle, often using (cyclic) nucleotide signals. We discovered that flagellum de- and repolarization in the model prokaryote Caulobacter crescentus is precisely orchestrated through at least three spatiotemporal mechanisms integrated at TipF. We show that TipF is a cell cycle-regulated receptor for the second messenger--bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP)--that perceives and transduces this signal through the degenerate c-di-GMP phosphodiesterase (EAL) domain to nucleate polar flagellum biogenesis. Once c-di-GMP levels rise at the G1 → S transition, TipF is activated, stabilized, and polarized, enabling the recruitment of downstream effectors, including flagellar switch proteins and the PflI positioning factor, at a preselected pole harboring the TipN landmark. These c-di-GMP-dependent events are coordinated with the onset of tipF transcription in early S phase and together enable the correct establishment and robust amplification of TipF-dependent polarization early in the cell cycle. Importantly, these mechanisms also govern the timely removal of TipF at cell division coincident with the drop in c-di-GMP levels, thereby resetting the flagellar polarization state in the next cell cycle after a preprogrammed period during which motility must be suspended.
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Affiliation(s)
- Nicole J Davis
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
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Fioravanti A, Fumeaux C, Mohapatra SS, Bompard C, Brilli M, Frandi A, Castric V, Villeret V, Viollier PH, Biondi EG. DNA binding of the cell cycle transcriptional regulator GcrA depends on N6-adenosine methylation in Caulobacter crescentus and other Alphaproteobacteria. PLoS Genet 2013; 9:e1003541. [PMID: 23737758 PMCID: PMC3667746 DOI: 10.1371/journal.pgen.1003541] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2013] [Accepted: 04/16/2013] [Indexed: 01/25/2023] Open
Abstract
Several regulators are involved in the control of cell cycle progression in the bacterial model system Caulobacter crescentus, which divides asymmetrically into a vegetative G1-phase (swarmer) cell and a replicative S-phase (stalked) cell. Here we report a novel functional interaction between the enigmatic cell cycle regulator GcrA and the N6-adenosine methyltransferase CcrM, both highly conserved proteins among Alphaproteobacteria, that are activated early and at the end of S-phase, respectively. As no direct biochemical and regulatory relationship between GcrA and CcrM were known, we used a combination of ChIP (chromatin-immunoprecipitation), biochemical and biophysical experimentation, and genetics to show that GcrA is a dimeric DNA–binding protein that preferentially targets promoters harbouring CcrM methylation sites. After tracing CcrM-dependent N6-methyl-adenosine promoter marks at a genome-wide scale, we show that these marks recruit GcrA in vitro and in vivo. Moreover, we found that, in the presence of a methylated target, GcrA recruits the RNA polymerase to the promoter, consistent with its role in transcriptional activation. Since methylation-dependent DNA binding is also observed with GcrA orthologs from other Alphaproteobacteria, we conclude that GcrA is the founding member of a new and conserved class of transcriptional regulators that function as molecular effectors of a methylation-dependent (non-heritable) epigenetic switch that regulates gene expression during the cell cycle. Methylation of genomic DNA at a specific regulatory site can impact a myriad of processes in eukaryotic cells. In bacteria, methylation at the N6 position of adenosine (m6A) is known to mediate a non-adaptive immunity response to protect cells from foreign DNA. While m6A marks are not known to govern expression of cell cycle genes in Gammaproteobacteria, cell cycle transcription in the model alphaproteobacterium Caulobacter crescentus requires the m6A methyltransferase CcrM that introduces m6A marks at GAnTC sequences and the enigmatic factor GcrA. Investigating if a functional and biochemical relationship exists between CcrM and GcrA, we found that CcrM-dependent m6A marks recruit GcrA to the promoters of cell cycle genes in vitro and in vivo and is required for efficient transcription. GcrA interacts with RNA polymerase, explaining how cell cycle transcription is affected. Importantly, m6A-dependent binding is also seen in GcrA orthologs, indicating that this transcriptional regulatory mechanism by CcrM and GcrA is conserved in Alphaproteobacteria.
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Affiliation(s)
- Antonella Fioravanti
- Interdisciplinary Research Institute USR3078, CNRS–Université Lille Nord de France, Villeneuve d'Ascq, France
| | - Coralie Fumeaux
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Saswat S. Mohapatra
- Interdisciplinary Research Institute USR3078, CNRS–Université Lille Nord de France, Villeneuve d'Ascq, France
| | - Coralie Bompard
- Interdisciplinary Research Institute USR3078, CNRS–Université Lille Nord de France, Villeneuve d'Ascq, France
| | - Matteo Brilli
- Laboratoire de Biométrie et Biologie Evolutive UMR5558, CNRS–Université Lyon 1–INRIA, Villeurbanne, France
| | - Antonio Frandi
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Vincent Castric
- Laboratoire GEPV UMR 8198, CNRS–Université Lille 1–Université Lille Nord de France, Villeneuve d'Ascq, France
| | - Vincent Villeret
- Interdisciplinary Research Institute USR3078, CNRS–Université Lille Nord de France, Villeneuve d'Ascq, France
| | - Patrick H. Viollier
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
- * E-mail: (PH Viollier); (EG Biondi)
| | - Emanuele G. Biondi
- Interdisciplinary Research Institute USR3078, CNRS–Université Lille Nord de France, Villeneuve d'Ascq, France
- * E-mail: (PH Viollier); (EG Biondi)
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Abstract
Spatial and temporal control of cell differentiation and morphogenesis plays a key role in prokaryotes as well as eukaryotes. This is particularly important for bacteria that divide asymmetrically, as they generate two morphologically and functionally distinct daughter cells. Several alpha-proteobacteria, including the aquatic, free-living Caulobacter crescentus, the symbiotic rhizobia and the plant and animal pathogens Agrobacterium and Brucella, have been shown to undergo asymmetrical division. C. crescentus has become a model system for the study of the regulatory networks, in particular the control of the cell cycle, the cytokinetic machinery, the cytoskeleton and the functions required for duplication and differentiation in general. As the bulk of these regulatory networks and functions is conserved in most alpha-proteobacteria, we recapitulate the recent advances in understanding these spatially and temporally controlled processes, focusing on cell cycle progression, DNA replication and partitioning, cell division and regulation of specific phenotypes that vary during the cell cycle or in the case of different lifestyles (like extracellular polysaccharide production) in C. crescentus and other alpha-proteobacteria.
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Affiliation(s)
- Silvia Ardissone
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
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Abstract
Adhesion of bacterial cells to surfaces can be mediated by a wide variety of extracellular structures, which can either recognize specific molecular motifs or adhere in non-specific ways to multiple types of surfaces. The attachment is thought to be highly regulated, but the underlying sensory mechanism(s) are poorly understood. In the α-proteobacterium Caulobacter crescentus, the formation of adhesive organelles is 'hardwired' into the cell cycle regulatory circuitry. In this issue of Molecular Microbiology, Li et al. (2011) employed this model organism to examine the adhesion process and the transition from temporary to permanent attachment using total internal reflection fluorescence (TIRF) microscopy. Surprisingly, they observed that adhesin production was not only under developmental control, but was also stimulated by surface contact. Initial reversible contact of the pili with the surface was followed by flagellum rotation arrest and subsequent induction of the holdfast to allow irreversible surface adhesion. These findings demonstrate that Caulobacter produces its holdfast only at the appropriate time for surface attachment, preventing premature export of the adhesin, which could then be inactivated by 'curing' or be masked by occluding particles. Importantly, their results support the notion that the flagellum serves as a mechanosensor for adhesion.
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Affiliation(s)
- Clare L Kirkpatrick
- Department of Microbiology and Molecular Medicine, University of Geneva, 1 rue Michel-Servet, 1211 Geneva 4, Switzerland
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Abstract
Caulobacter crescentus uses a multi-layered system of oscillating regulators to program different developmental fates into each daughter cell at division. This is achieved by superimposing gene expression, subcellular localization, phosphorylation, and regulated proteolysis to form a complex regulatory network that integrates chromosome replication, segregation, polar differentiation, and cytokinesis. In this review, we outline the current state of research in the field of Caulobacter development, emphasizing new findings that elaborate how the developmental program is modulated by factors such as the environment or the metabolic state of the cell.
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Affiliation(s)
- Clare L Kirkpatrick
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
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Davis NJ, Viollier PH. Probing flagellar promoter occupancy in wild-type and mutant Caulobacter crescentus by chromatin immunoprecipitation. FEMS Microbiol Lett 2011; 319:146-52. [PMID: 21457294 DOI: 10.1111/j.1574-6968.2011.02275.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
In the asymmetric predivisional cell of Caulobacter crescentus, TipF and TipN mark the cellular pole for future flagellar development. TipF is essential for motility and contains a cyclic-di-GMP phosphodiesterase-like (EAL) domain that is necessary for proper function. TipN is localized to the flagellar pole before TipF and is essential for the proper placement of the flagellum in C. crescentus. Using β-galactosidase promoter-probe assays and quantitative chromatin immunoprecipitation, we investigated the influence of the C. crescentus flagellar assembly regulator TipF on flagellar gene transcription. We compared the transcriptional activity of class II-fliF-lacZ, class III-flgE-lacZ, and class IV-fljL-lacZ fusions in a ΔtipF mutant with that of other flagellar mutants and the wild-type strain. We subsequently verified the in vivo occupancy of the fliF, flgE, and fljL flagellar promoters by the flagellar regulators CtrA, FlbD, and FliX in addition to RNA polymerase. We deduce that TipF contributes to proper expression of flagellar genes in C. crescentus by acting both within and outside of the canonical flagellar gene expression hierarchy.
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Affiliation(s)
- Nicole J Davis
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA.
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Abstract
A protective organelle that is essential for viability under most conditions, the cell wall is a dynamic structure that is continuously remodelled with the growth of the bacterial cell. Because the cell wall also moulds the bacterium, the mechanisms of cell wall homeostasis can be deciphered using cell shape as a convenient proxy. In this issue of Molecular Microbiology, Foulquier et al. illuminate a connection between cell shape regulation and metabolism in Bacillus subtilis. They find that the putative NAD(P)-binding enzyme YvcK organizes into helical subcellular structures that exert shape control by directing the cell wall biosynthetic enzyme PBP1 along the cell cylinder and to the septum, a function shared with the MreB actin cytoskeleton. Unlike MreB, however, the role of YvcK in cell shape control is manifested only on certain carbon sources, presumably by way of a previously unknown metabolic feed that taps into cell morphogenesis.
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Affiliation(s)
- Johann Mignolet
- Department of Microbiology and Molecular Medicine, University of Geneva, 1 rue Michel-Servet, 1211 Geneva 4, Switzerland
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46
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Abstract
While polar organelles hold the key to understanding the fundamentals of cell polarity and cell biological principles in general, they have served in the past merely for taxonomical purposes. Here, we highlight recent efforts in unraveling the molecular basis of polar organelle positioning in bacterial cells. Specifically, we detail the role of members of the Ras-like GTPase superfamily and coiled-coil-rich scaffolding proteins in modulating bacterial cell polarity and in recruiting effector proteins to polar sites. Such roles are well established for eukaryotic cells, but not for bacterial cells that are generally considered diffusion-limited. Studies on spatial regulation of protein positioning in bacterial cells, though still in their infancy, will undoubtedly experience a surge of interest, as comprehensive localization screens have yielded an extensive list of (polarly) localized proteins, potentially reflecting subcellular sites of functional specialization predicted for organelles.
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Affiliation(s)
- Clare L Kirkpatrick
- Department of Microbiology and Molecular Medicine, Centre Médicale Universitaire, Faculty of Medicine, University of Geneva, Switzerland
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47
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Abstract
Growth in biofilms provides bacterial species with many advantages over growth in suspension, e.g. colonization of nutrient-rich areas. In the α-proteobacterium Caulobacter crescentus biofilm formation is facilitated through its asymmetric cell division, where one daughter cell becomes a motile flagellated swarmer cell able to colonize new surfaces while the other remains as a stalked cell attached to the substrate through the adhesive holdfast. The Caulobacter biofilm consists of stalked cells arranged either in a monolayer or in a multicellular 'mushroom' structure. In this issue of Molecular Microbiology, Berne et al. demonstrate that extracellular DNA (eDNA) from lysed cells prevents biofilm maturation. eDNA masks the adhesive properties of newly synthesized holdfast to enable the escape of swarmer cells from the biofilm. By contrast, holdfasts on previously attached stalked cells remain unaffected by eDNA. Surprisingly, the inhibitory effect was genus-specific, as only DNA from Caulobacter, but not from other genera, could interfere with biofilm maturation. This study reveals a new role for DNA in biofilms, as a regulatory rather than a structural component, and a novel mechanism to facilitate the escape of cells from biofilms. A compelling case is made for the existence of a new type of genus-specific 'macromolecular language'.
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Affiliation(s)
- Clare L Kirkpatrick
- Department of Microbiology and Molecular Medicine, University of Geneva, 1 rue Michel-Servet, 1211 Geneva 4, Switzerland
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, University of Geneva, 1 rue Michel-Servet, 1211 Geneva 4, Switzerland
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Radhakrishnan SK, Pritchard S, Viollier PH. Coupling prokaryotic cell fate and division control with a bifunctional and oscillating oxidoreductase homolog. Dev Cell 2010; 18:90-101. [PMID: 20152180 DOI: 10.1016/j.devcel.2009.10.024] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2009] [Revised: 08/31/2009] [Accepted: 10/27/2009] [Indexed: 10/19/2022]
Abstract
NAD(H)-binding proteins play important roles in cell-cycle and developmental signaling in eukaryotes. We identified a bifunctional NAD(H)-binding regulator (KidO) that integrates cell-fate signaling with cytokinesis in the bacterium Caulobacter crescentus. KidO stimulates the DivJ kinase and directly acts on the cytokinetic tubulin, FtsZ, to tune cytokinesis with the cell cycle. At the G1-->S transition, DivJ concomitantly signals the ClpXP-dependent degradation of KidO and CtrA, a cell-cycle transcriptional regulator/DNA replication inhibitor. This proteolytic event directs KidO and CtrA into oscillatory cell-cycle abundance patterns that coordinately license replication and cytokinesis. KidO resembles NAD(P)H-dependent oxidoreductases, and conserved residues in the KidO NAD(H)-binding pocket are critical for regulation of FtsZ, but not for DivJ. Since NADPH-dependent regulation by a KidO-like oxidoreductase also occurs in humans, organisms from two domains of life exploit the enzymatic fold of an ancestral oxidoreductase potentially to coordinate cellular or developmental activities with the availability of the metabolic currency, NAD(P)H.
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Affiliation(s)
- Sunish Kumar Radhakrishnan
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
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Radhakrishnan SK, Thanbichler M, Viollier PH. The dynamic interplay between a cell fate determinant and a lysozyme homolog drives the asymmetric division cycle of Caulobacter crescentus. Genes Dev 2008; 22:212-25. [PMID: 18198338 DOI: 10.1101/gad.1601808] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Caulobacter crescentus divides asymmetrically into a swarmer cell and a stalked cell, a process that is governed by the imbalance in phosphorylated levels of the DivK cell fate determinant in the two cellular compartments. The asymmetric polar localization of the DivJ kinase results in its specific inheritance in the stalked daughter cell where it phosphorylates DivK. The mechanism for the polar positioning of DivJ is poorly understood. SpmX, an uncharacterized lysozyme homolog, is shown here to control DivJ localization and activation. In the absence of SpmX, DivJ is delocalized and dysfunctional, resulting in developmental defects caused by an insufficiency in phospho-DivK. While SpmX stimulates DivK phosphorylation in the stalked cell, unphosphorylated DivK in the swarmer cell activates an intricate transcriptional cascade that leads to the production of the spmX message. This event primes the swarmer cell for the impending transition into a stalked cell, a transition that is sparked by the abrupt accumulation and localization of SpmX to the future stalked cell pole. Localized SpmX then recruits and stimulates DivJ, and the resulting phospho-DivK implements the stalked cell fate. The dynamic interplay between SpmX and DivK is at the heart of the molecular circuitry that sustains the Caulobacter developmental cycle.
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Affiliation(s)
- Sunish Kumar Radhakrishnan
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
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