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Wongdontree P, Millan-Oropeza A, Upfold J, Lavergne JP, Halpern D, Lambert C, Page A, Kénanian G, Grangeasse C, Henry C, Fouet A, Gloux K, Anba-Mondoloni J, Gruss A. Oxidative stress is intrinsic to staphylococcal adaptation to fatty acid synthesis antibiotics. iScience 2024; 27:109505. [PMID: 38577105 PMCID: PMC10993138 DOI: 10.1016/j.isci.2024.109505] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/08/2023] [Accepted: 03/13/2024] [Indexed: 04/06/2024] Open
Abstract
Antibiotics inhibiting the fatty acid synthesis pathway (FASII) of the major pathogen Staphylococcus aureus reach their enzyme targets, but bacteria continue growth by using environmental fatty acids (eFAs) to produce phospholipids. We assessed the consequences and effectors of FASII-antibiotic (anti-FASII) adaptation. Anti-FASII induced lasting expression changes without genomic rearrangements. Several identified regulators affected the timing of adaptation outgrowth. Adaptation resulted in decreased expression of major virulence factors. Conversely, stress responses were globally increased and adapted bacteria were more resistant to peroxide killing. Importantly, pre-exposure to peroxide led to faster anti-FASII-adaptation by stimulating eFA incorporation. This adaptation differs from reports of peroxide-stimulated antibiotic efflux, which leads to tolerance. In vivo, anti-FASII-adapted S. aureus killed the insect host more slowly but continued multiplying. We conclude that staphylococcal adaptation to FASII antibiotics involves reprogramming, which decreases virulence and increases stress resistance. Peroxide, produced by the host to combat infection, favors anti-FASII adaptation.
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Affiliation(s)
- Paprapach Wongdontree
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Aaron Millan-Oropeza
- PAPPSO Platform, Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Jennifer Upfold
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Jean-Pierre Lavergne
- Bacterial Pathogens and Protein Phosphorylation, Molecular Microbiology and Structural Biology, UMR 5086 - CNRS / Université de Lyon, Building IBCP, 7 Passage du Vercors, Lyon, France
| | - David Halpern
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Clara Lambert
- Université Paris Cité, Institut Cochin, INSERM, U1016, CNRS, UMR8104, Paris, France
| | - Adeline Page
- Protein Science Facility, SFR BioSciences, CNRS, UMS3444, INSERM US8, Université de Lyon, Lyon, France
| | - Gérald Kénanian
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Christophe Grangeasse
- Bacterial Pathogens and Protein Phosphorylation, Molecular Microbiology and Structural Biology, UMR 5086 - CNRS / Université de Lyon, Building IBCP, 7 Passage du Vercors, Lyon, France
| | - Céline Henry
- PAPPSO Platform, Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Agnès Fouet
- Université Paris Cité, Institut Cochin, INSERM, U1016, CNRS, UMR8104, Paris, France
| | - Karine Gloux
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Jamila Anba-Mondoloni
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Alexandra Gruss
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
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2
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Faure A, Manuse S, Gonin M, Grangeasse C, Jault JM, Orelle C. Daptomycin avoids drug resistance mediated by the BceAB transporter in Streptococcus pneumoniae. Microbiol Spectr 2024; 12:e0363823. [PMID: 38214521 PMCID: PMC10846014 DOI: 10.1128/spectrum.03638-23] [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: 10/12/2023] [Accepted: 12/19/2023] [Indexed: 01/13/2024] Open
Abstract
Drug-resistant bacteria are a serious threat to human health as antibiotics are gradually losing their clinical efficacy. Comprehending the mechanism of action of antimicrobials and their resistance mechanisms plays a key role in developing new agents to fight antimicrobial resistance. The lipopeptide daptomycin is an antibiotic that selectively disrupts Gram-positive bacterial membranes, thereby showing slower resistance development than many classical drugs. Consequently, it is often used as a last resort antibiotic to preserve its use as one of the least potent antibiotics at our disposal. The mode of action of daptomycin has been debated but was recently found to involve the formation of a tripartite complex between undecaprenyl precursors of cell wall biosynthesis and the anionic phospholipid phosphatidylglycerol. BceAB-type ABC transporters are known to confer resistance to antimicrobial peptides that sequester some precursors of the peptidoglycan, such as the undecaprenyl pyrophosphate or lipid II. The expression of these transporters is upregulated by dedicated two-component regulatory systems in the presence of antimicrobial peptides that are recognized by the system. Here, we investigated whether daptomycin evades resistance mediated by the BceAB transporter from the bacterial pathogen Streptococcus pneumoniae. Although daptomycin can bind to the transporter, our data showed that the BceAB transporter does not mediate resistance to the drug and its expression is not induced in its presence. These findings show that the pioneering membrane-active daptomycin has the potential to escape the resistance mechanism mediated by BceAB-type transporters and confirm that the development of this class of compounds has promising clinical applications.IMPORTANCEAntibiotic resistance is rising in all parts of the world. New resistance mechanisms are emerging and dangerously spreading, threatening our ability to treat common infectious diseases. Daptomycin is an antimicrobial peptide that is one of the last antibiotics approved for clinical use. Understanding the resistance mechanisms toward last-resort antibiotics such as daptomycin is critical for the success of future antimicrobial therapies. BceAB-type ABC transporters confer resistance to antimicrobial peptides that target precursors of cell-wall synthesis. In this study, we showed that the BceAB transporter from the human pathogen Streptococcus pneumoniae does not confer resistance to daptomycin, suggesting that this drug and other calcium-dependent lipopeptide antibiotics have the potential to evade the action of this type of ABC transporters in other bacterial pathogens.
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Affiliation(s)
- Agathe Faure
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Sylvie Manuse
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Mathilde Gonin
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Jean-Michel Jault
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Cédric Orelle
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
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3
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Lenoir C, Pelletier A, Manuse S, Millat H, Ducret A, Galinier A, Doan T, Grangeasse C. The morphogenic protein CopD controls the spatio-temporal dynamics of PBP1a and PBP2b in Streptococcus pneumoniae. mBio 2023; 14:e0141123. [PMID: 37728370 PMCID: PMC10653890 DOI: 10.1128/mbio.01411-23] [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: 06/02/2023] [Accepted: 07/25/2023] [Indexed: 09/21/2023] Open
Abstract
IMPORTANCE Penicillin-binding proteins (PBPs) are essential for proper bacterial cell division and morphogenesis. The genome of Streptococcus pneumoniae encodes for two class B PBPs (PBP2x and 2b), which are required for the assembly of the peptidoglycan framework and three class A PBPs (PBP1a, 1b and 2a), which remodel the peptidoglycan mesh during cell division. Therefore, their activities should be finely regulated in space and time to generate the pneumococcal ovoid cell shape. To date, two proteins, CozE and MacP, are known to regulate the function of PBP1a and PBP2a, respectively. In this study, we describe a novel regulator (CopD) that acts on both PBP1a and PBP2b. These findings provide valuable information for understanding bacterial cell division. Furthermore, knowing that ß-lactam antibiotic resistance often arises from PBP mutations, the characterization of such a regulator represents a promising opportunity to develop new strategies to resensitize resistant strains.
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Affiliation(s)
- Cassandra Lenoir
- Molecular Microbiology and Structural Biochemistry, UMR, Université de Lyon, CNRS, Lyon, France
| | - Anaïs Pelletier
- Molecular Microbiology and Structural Biochemistry, UMR, Université de Lyon, CNRS, Lyon, France
| | - Sylvie Manuse
- Molecular Microbiology and Structural Biochemistry, UMR, Université de Lyon, CNRS, Lyon, France
| | - Hugo Millat
- Molecular Microbiology and Structural Biochemistry, UMR, Université de Lyon, CNRS, Lyon, France
| | - Adrien Ducret
- Molecular Microbiology and Structural Biochemistry, UMR, Université de Lyon, CNRS, Lyon, France
| | - Anne Galinier
- Laboratoire de Chimie Bactérienne, UMR, Aix-Marseille Université, CNRS, Marseille, France
| | - Thierry Doan
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires, UMR, Aix-Marseille Université, Marseille, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, UMR, Université de Lyon, CNRS, Lyon, France
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4
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Martinez M, Petit J, Leyva A, Sogues A, Megrian D, Rodriguez A, Gaday Q, Ben Assaya M, Portela MM, Haouz A, Ducret A, Grangeasse C, Alzari PM, Durán R, Wehenkel AM. Eukaryotic-like gephyrin and cognate membrane receptor coordinate corynebacterial cell division and polar elongation. Nat Microbiol 2023; 8:1896-1910. [PMID: 37679597 PMCID: PMC10522489 DOI: 10.1038/s41564-023-01473-0] [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: 12/27/2022] [Accepted: 08/11/2023] [Indexed: 09/09/2023]
Abstract
The order Corynebacteriales includes major industrial and pathogenic Actinobacteria such as Corynebacterium glutamicum or Mycobacterium tuberculosis. These bacteria have multi-layered cell walls composed of the mycolyl-arabinogalactan-peptidoglycan complex and a polar growth mode, thus requiring tight coordination between the septal divisome, organized around the tubulin-like protein FtsZ, and the polar elongasome, assembled around the coiled-coil protein Wag31. Here, using C. glutamicum, we report the discovery of two divisome members: a gephyrin-like repurposed molybdotransferase (Glp) and its membrane receptor (GlpR). Our results show how cell cycle progression requires interplay between Glp/GlpR, FtsZ and Wag31, showcasing a crucial crosstalk between the divisome and elongasome machineries that might be targeted for anti-mycobacterial drug discovery. Further, our work reveals that Corynebacteriales have evolved a protein scaffold to control cell division and morphogenesis, similar to the gephyrin/GlyR system that mediates synaptic signalling in higher eukaryotes through network organization of membrane receptors and the microtubule cytoskeleton.
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Affiliation(s)
- Mariano Martinez
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Julienne Petit
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Alejandro Leyva
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Adrià Sogues
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
- Structural and Molecular Microbiology, VIB-VUB Center for Structural Biology, VIB, Vrije Universiteit Brussel, Brussels, Belgium
| | - Daniela Megrian
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Azalia Rodriguez
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Quentin Gaday
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Mathildeb Ben Assaya
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Maria Magdalena Portela
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Ahmed Haouz
- Plate-forme de cristallographie, C2RT-Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Adrien Ducret
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Université de Lyon, Lyon, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Université de Lyon, Lyon, France
| | - Pedro M Alzari
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Rosario Durán
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay.
| | - Anne Marie Wehenkel
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France.
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5
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Martínez-Caballero S, Freton C, Molina R, Bartual SG, Gueguen-Chaignon V, Mercy C, Gago F, Mahasenan KV, Muñoz IG, Lee M, Hesek D, Mobashery S, Hermoso JA, Grangeasse C. Molecular basis of the final step of cell division in Streptococcus pneumoniae. Cell Rep 2023; 42:112756. [PMID: 37418323 PMCID: PMC10434722 DOI: 10.1016/j.celrep.2023.112756] [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: 02/02/2023] [Revised: 05/13/2023] [Accepted: 06/21/2023] [Indexed: 07/09/2023] Open
Abstract
Bacterial cell-wall hydrolases must be tightly regulated during bacterial cell division to prevent aberrant cell lysis and to allow final separation of viable daughter cells. In a multidisciplinary work, we disclose the molecular dialogue between the cell-wall hydrolase LytB, wall teichoic acids, and the eukaryotic-like protein kinase StkP in Streptococcus pneumoniae. After characterizing the peptidoglycan recognition mode by the catalytic domain of LytB, we further demonstrate that LytB possesses a modular organization allowing the specific binding to wall teichoic acids and to the protein kinase StkP. Structural and cellular studies notably reveal that the temporal and spatial localization of LytB is governed by the interaction between specific modules of LytB and the final PASTA domain of StkP. Our data collectively provide a comprehensive understanding of how LytB performs final separation of daughter cells and highlights the regulatory role of eukaryotic-like kinases on lytic machineries in the last step of cell division in streptococci.
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Affiliation(s)
- Siseth Martínez-Caballero
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano," Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Céline Freton
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université de Lyon, CNRS, Lyon, France
| | - Rafael Molina
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano," Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Sergio G Bartual
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano," Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | | | - Chryslène Mercy
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université de Lyon, CNRS, Lyon, France
| | - Federico Gago
- Department of Biomedical Sciences & Instituto de Química Médica-CSIC Associated Unit, School of Medicine and Health Sciences, University of Alcalá, 28805 Alcalá de Henares, Spain
| | - Kiran V Mahasenan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Inés G Muñoz
- Structural Biology Program, Spanish National Cancer Research Center (CNIO), 28029 Madrid, Spain
| | - Mijoon Lee
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Dusan Hesek
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano," Consejo Superior de Investigaciones Científicas, Madrid, Spain.
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université de Lyon, CNRS, Lyon, France.
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6
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Nikolopoulos N, Matos R, Ravaud S, Courtin P, Akherraz H, Palussiere S, Gueguen-Chaignon V, Salomon-Mallet M, Guillot A, Guerardel Y, Chapot-Chartier MP, Grangeasse C, Leulier F. Structure-function analysis of Lactiplantibacillus plantarum DltE& reveals D-alanylated lipoteichoic acids as direct cues supporting Drosophila juvenile growth. eLife 2023; 12:84669. [PMID: 37042660 DOI: 10.7554/elife.84669] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 04/11/2023] [Indexed: 04/13/2023] Open
Abstract
Metazoans establish mutually beneficial interactions with their resident microorganisms. However, our understanding of the microbial cues contributing to host physiology remains elusive. Previously, we identified a bacterial machinery encoded by the dlt operon involved in Drosophila melanogaster's juvenile growth promotion by Lactiplantibacillus plantarum. Here, using crystallography combined with biochemical and cellular approaches, we investigate the physiological role of an uncharacterized protein (DltE) encoded by this operon. We show that lipoteichoic acids (LTAs) but not wall teichoic acids are D-alanylated in Lactiplantibacillus plantarumNC8 cell envelope and demonstrate that DltE is a D-Ala carboxyesterase removing D-Ala from LTA. Using the mutualistic association of L. plantarumNC8 and Drosophila melanogaster as a symbiosis model, we establish that D-alanylated LTAs (D-Ala-LTAs) are direct cues supporting intestinal peptidase expression and juvenile growth in Drosophila. Our results pave the way to probing the contribution of D-Ala-LTAs to host physiology in other symbiotic models.
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Affiliation(s)
- Nikos Nikolopoulos
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Universite Claude Bernard, Lyon, France
| | - Renata Matos
- Institut de Génomique Fonctionnelle d eLyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Stephanie Ravaud
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Universite Claude Bernard, Lyon, France
| | - Pascal Courtin
- Micalis Institute, Universite Paris-Saclay, INRAE, Jouy-en-Josas, France
| | - Houssam Akherraz
- Institut de Genomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Simon Palussiere
- Micalis Institute, Universite Paris-Saclay, INRAE, Jouy-en-Josas, France
| | | | | | - Alain Guillot
- Micalis Institute, Universite Paris-Saclay, INRAE, Jouy-en-Josas, France
| | - Yann Guerardel
- Unite de Glycobiologie Structurale et Fonctionnelle, Univ Lille, CNRS, UMR 8576, Lille, France
| | | | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Universite Claude Bernard, Lyon, France
| | - François Leulier
- Institut de Génomique Fonctionnelle d eLyon, Ecole Normale Supérieure de Lyon, Lyon, France
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7
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Martinez M, Petit J, Leyva A, Sogues A, Megrian D, Rodriguez A, Gaday Q, Ben Assaya M, Portela M, Haouz A, Ducret A, Grangeasse C, Alzari PM, Durán R, Wehenkel A. Eukaryotic-like gephyrin and cognate membrane receptor coordinate corynebacterial cell division and polar elongation. bioRxiv 2023:2023.02.01.526586. [PMID: 36778425 PMCID: PMC9915583 DOI: 10.1101/2023.02.01.526586] [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] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The order Corynebacteriales includes major industrial and pathogenic actinobacteria such as Corynebacterium glutamicum or Mycobacterium tuberculosis . Their elaborate multi-layered cell wall, composed primarily of the mycolyl-arabinogalactan-peptidoglycan complex, and their polar growth mode impose a stringent coordination between the septal divisome, organized around the tubulin-like protein FtsZ, and the polar elongasome, assembled around the tropomyosin-like protein Wag31. Here, we report the identification of two new divisome members, a gephyrin-like repurposed molybdotransferase (GLP) and its membrane receptor (GLPR). We show that the interplay between the GLPR/GLP module, FtsZ and Wag31 is crucial for orchestrating cell cycle progression. Our results provide a detailed molecular understanding of the crosstalk between two essential machineries, the divisome and elongasome, and reveal that Corynebacteriales have evolved a protein scaffold to control cell division and morphogenesis similar to the gephyrin/GlyR system that in higher eukaryotes mediates synaptic signaling through network organization of membrane receptors and the microtubule cytoskeleton.
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Affiliation(s)
- M. Martinez
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - J. Petit
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - A. Leyva
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - A. Sogues
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - D. Megrian
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - A. Rodriguez
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Q. Gaday
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - M. Ben Assaya
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - M. Portela
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - A. Haouz
- Plate-forme de cristallographie, C2RT-Institut Pasteur, CNRS, UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - A. Ducret
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - C. Grangeasse
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - P. M. Alzari
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - R. Durán
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - A. Wehenkel
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
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8
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Wilhelm L, Ducret A, Grangeasse C. New insights into the Undecaprenol monophosphate recycling pathway of Streptococcus pneumoniae. FEMS Microbiol Lett 2023; 370:fnad109. [PMID: 37849218 DOI: 10.1093/femsle/fnad109] [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: 07/21/2023] [Revised: 10/08/2023] [Accepted: 10/16/2023] [Indexed: 10/19/2023] Open
Abstract
Recycling of undecaprenol pyrophosphate is critical to regenerate the pool of undecaprenol monophosphate required for cell wall biosynthesis. Undecaprenol pyrophosphate is dephosphorylated by membrane-associated undecaprenyl pyrophosphate phosphatases such as UppP or type 2 Phosphatidic Acid Phosphatases (PAP2) and then transferred across the cytoplasmic membrane by Und-P flippases such as PopT (DUF368-containing protein) or UptA (a DedA family protein). While the deletion of uppP in S. pneumoniae has been reported to increase susceptibility to bacitracin and reduce infectivity in a murine infection model, the presence of PAP2 family proteins or Und-P flippases and their potential interplay with UppP in S. pneumoniae remained unknown. In this report, we identified two PAP2 family proteins and a DUF368-containing protein and investigated their roles together with that of UppP in cell growth, cell morphology and susceptibility to bacitracin in S. pneumoniae. Our results suggest that the undecaprenol monophosphate recycling pathway in S. pneumoniae could result from a functional redundancy between UppP, the PAP2-family protein Spr0434 and the DUF368-containing protein Spr0889.
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Affiliation(s)
- Linus Wilhelm
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université de Lyon, CNRS, 69007 Lyon, France
| | - Adrien Ducret
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université de Lyon, CNRS, 69007 Lyon, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université de Lyon, CNRS, 69007 Lyon, France
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9
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Nikolopoulos N, Matos RC, Courtin P, Ayala I, Akherraz H, Simorre JP, Chapot-Chartier MP, Leulier F, Ravaud S, Grangeasse C. DltC acts as an interaction hub for AcpS, DltA and DltB in the teichoic acid D-alanylation pathway of Lactiplantibacillus plantarum. Sci Rep 2022; 12:13133. [PMID: 35907949 PMCID: PMC9338922 DOI: 10.1038/s41598-022-17434-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 04/21/2022] [Accepted: 07/25/2022] [Indexed: 02/04/2023] Open
Abstract
Teichoic acids (TA) are crucial for the homeostasis of the bacterial cell wall as well as their developmental behavior and interplay with the environment. TA can be decorated by different modifications, modulating thus their biochemical properties. One major modification consists in the esterification of TA by d-alanine, a process known as d-alanylation. TA d-alanylation is performed by the Dlt pathway, which starts in the cytoplasm and continues extracellularly after d-Ala transportation through the membrane. In this study, we combined structural biology and in vivo approaches to dissect the cytoplasmic steps of this pathway in Lactiplantibacillus plantarum, a bacterial species conferring health benefits to its animal host. After establishing that AcpS, DltB, DltC1 and DltA are required for the promotion of Drosophila juvenile growth under chronic undernutrition, we solved their crystal structure and/or used NMR and molecular modeling to study their interactions. Our work demonstrates that the suite of interactions between these proteins is ordered with a conserved surface of DltC1 docking sequentially AcpS, DltA and eventually DltB. Altogether, we conclude that DltC1 acts as an interaction hub for all the successive cytoplasmic steps of the TA d-alanylation pathway.
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Affiliation(s)
- Nikos Nikolopoulos
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Université Claude Bernard Lyon 1, Lyon, France
| | - Renata C Matos
- Institut de Génomique Fonctionnelle de Lyon, École Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, Lyon, France
| | - Pascal Courtin
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Isabel Ayala
- Institut de Biologie Structurale, CEA, CNRS UMR 5075, Université Grenoble Alpes, 3800, Grenoble, France
| | - Houssam Akherraz
- Institut de Génomique Fonctionnelle de Lyon, École Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, Lyon, France
| | - Jean-Pierre Simorre
- Institut de Biologie Structurale, CEA, CNRS UMR 5075, Université Grenoble Alpes, 3800, Grenoble, France
| | | | - François Leulier
- Institut de Génomique Fonctionnelle de Lyon, École Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, Lyon, France
| | - Stéphanie Ravaud
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Université Claude Bernard Lyon 1, Lyon, France.
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Université Claude Bernard Lyon 1, Lyon, France.
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10
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Diagne AM, Pelletier A, Durmort C, Faure A, Kanonenberg K, Freton C, Page A, Delolme F, Vorac J, Vallet S, Bellard L, Vivès C, Fieschi F, Vernet T, Rousselle P, Guiral S, Grangeasse C, Jault JM, Orelle C. Identification of a two-component regulatory system involved in antimicrobial peptide resistance in Streptococcus pneumoniae. PLoS Pathog 2022; 18:e1010458. [PMID: 35395062 PMCID: PMC9020739 DOI: 10.1371/journal.ppat.1010458] [Citation(s) in RCA: 8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 04/20/2022] [Accepted: 03/18/2022] [Indexed: 11/24/2022] Open
Abstract
Two-component regulatory systems (TCS) are among the most widespread mechanisms that bacteria use to sense and respond to environmental changes. In the human pathogen Streptococcus pneumoniae, a total of 13 TCS have been identified and many of them have been linked to pathogenicity. Notably, TCS01 strongly contributes to pneumococcal virulence in several infection models. However, it remains one of the least studied TCS in pneumococci and its functional role is still unclear. In this study, we demonstrate that TCS01 cooperates with a BceAB-type ABC transporter to sense and induce resistance to structurally-unrelated antimicrobial peptides of bacterial origin that all target undecaprenyl-pyrophosphate or lipid II, which are essential precursors of cell wall biosynthesis. Even though tcs01 and bceAB genes do not locate in the same gene cluster, disruption of either of them equally sensitized the bacterium to the same set of antimicrobial peptides. We show that the key function of TCS01 is to upregulate the expression of the transporter, while the latter appears the main actor in resistance. Electrophoretic mobility shift assays further demonstrated that the response regulator of TCS01 binds to the promoter region of the bceAB genes, implying a direct control of these genes. The BceAB transporter was overexpressed and purified from E. coli. After reconstitution in liposomes, it displayed substantial ATPase and GTPase activities that were stimulated by antimicrobial peptides to which it confers resistance to, revealing new functional features of a BceAB-type transporter. Altogether, this inducible defense mechanism likely contributes to the survival of the opportunistic microorganism in the human host, in which competition among commensal microorganisms is a key determinant for effective host colonization and invasive path. Streptococcus pneumoniae is a commensal bacterium of the human nasopharynx that can switch to an invasive pathogen causing a variety of diseases, leading to over one million deaths worldwide each year. The sophisticated strategies that allow S. pneumoniae to survive in various environments within the human body are still poorly understood. One of the most widespread tools that enable bacteria to sense environmental changes and to promote adaptative responses by modulating gene expression are two-component regulatory systems (TCS). TCS01 was identified as an important virulence factor, and understanding its biological function is key to comprehend bacterial pathogenesis. In this study, we demonstrated that this TCS upregulates the expression of an ABC transporter that mediates resistance to bacterial antimicrobial peptides targeting cell wall synthesis. Because competition among microorganisms is a key element for host colonization and persistence, our findings contribute to explain the potent role of TCS01 in bacterial survival within the human host.
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Affiliation(s)
- Aissatou Maty Diagne
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Anaïs Pelletier
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Claire Durmort
- Institute of Structural Biology (IBS), UMR 5075 CNRS/University of Grenoble-Alpes, Grenoble, France
| | - Agathe Faure
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Kerstin Kanonenberg
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Céline Freton
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Adeline Page
- Protein Science Facility, SFR BioSciences, CNRS, UMS3444, INSERM US8, University of Lyon, Lyon, France
| | - Frédéric Delolme
- Protein Science Facility, SFR BioSciences, CNRS, UMS3444, INSERM US8, University of Lyon, Lyon, France
| | - Jaroslav Vorac
- Institute of Structural Biology (IBS), UMR 5075 CNRS/University of Grenoble-Alpes, Grenoble, France
| | - Sylvain Vallet
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Laure Bellard
- Institute of Structural Biology (IBS), UMR 5075 CNRS/University of Grenoble-Alpes, Grenoble, France
| | - Corinne Vivès
- Institute of Structural Biology (IBS), UMR 5075 CNRS/University of Grenoble-Alpes, Grenoble, France
| | - Franck Fieschi
- Institute of Structural Biology (IBS), UMR 5075 CNRS/University of Grenoble-Alpes, Grenoble, France
| | - Thierry Vernet
- Institute of Structural Biology (IBS), UMR 5075 CNRS/University of Grenoble-Alpes, Grenoble, France
| | - Patricia Rousselle
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique (LBTI), UMR 5305 CNRS/University of Lyon, Lyon, France
| | - Sébastien Guiral
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Jean-Michel Jault
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Cédric Orelle
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
- * E-mail:
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11
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Nagarajan SN, Lenoir C, Grangeasse C. Recent advances in bacterial signaling by serine/threonine protein kinases. Trends Microbiol 2021; 30:553-566. [PMID: 34836791 DOI: 10.1016/j.tim.2021.11.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 08/02/2021] [Revised: 10/28/2021] [Accepted: 11/01/2021] [Indexed: 11/27/2022]
Abstract
It has been nearly three decades since the discovery of the first bacterial serine/threonine protein kinase (STPK). Since then, a blend of technological advances has led to the characterization of a multitude of STPKs and phosphorylation substrates in several bacterial species that finely regulate intricate signaling cascades. Years of intense research from several laboratories have demonstrated unexpected roles for serine/threonine phosphorylation, regulating not only bacterial growth and cell division but also antibiotic persistence, virulence and infection, metabolism, chromosomal biology, and cellular differentiation. This review aims to provide an account of the most recent and significant developments in this up and growing field in microbiology.
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Affiliation(s)
- Sathya Narayanan Nagarajan
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université de Lyon, CNRS, IBCP building, 7 passage du Vercors, 69367 Lyon Cedex 07, France
| | - Cassandra Lenoir
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université de Lyon, CNRS, IBCP building, 7 passage du Vercors, 69367 Lyon Cedex 07, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université de Lyon, CNRS, IBCP building, 7 passage du Vercors, 69367 Lyon Cedex 07, France.
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12
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Delisle J, Cordier B, Audebert S, Pophillat M, Cluzel C, Espinosa L, Grangeasse C, Galinier A, Doan T. Characterization of TseB: A new actor in cell wall elongation in Bacillus subtilis. Mol Microbiol 2021; 116:1099-1112. [PMID: 34411374 DOI: 10.1111/mmi.14798] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 08/16/2021] [Accepted: 08/16/2021] [Indexed: 11/30/2022]
Abstract
Penicillin-binding proteins (PBPs) are crucial enzymes of peptidoglycan assembly and targets of β-lactam antibiotics. However, little is known about their regulation. Recently, membrane proteins were shown to regulate the bifunctional transpeptidases/glycosyltransferases aPBPs in some bacteria. However, up to now, regulators of monofunctional transpeptidases bPBPs have yet to be revealed. Here, we propose that TseB could be such a PBP regulator. This membrane protein was previously found to suppress tetracycline sensitivity of a Bacillus subtilis strain deleted for ezrA, a gene encoding a regulator of septation ring formation. In this study, we show that TseB is required for B. subtilis normal cell shape, tseB mutant cells being shorter and wider than wild-type cells. We observed that TseB interacts with PBP2A, a monofunctional transpeptidase. While TseB is not required for PBP2A activity, stability, and localization, we show that the overproduction of PBP2A is deleterious in the absence of TseB. In addition, we showed that TseB is necessary not only for efficient cell wall elongation during exponential phase but also during spore outgrowth, as it was also observed for PBP2A. Altogether, our results suggest that TseB is a new member of the elongasome that regulates PBP2A function during cell elongation and spore germination.
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Affiliation(s)
- Jordan Delisle
- Laboratoire de Chimie Bactérienne, UMR 7283, CNRS/Aix-Marseille Univ, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Baptiste Cordier
- Laboratoire de Chimie Bactérienne, UMR 7283, CNRS/Aix-Marseille Univ, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Stéphane Audebert
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, Marseille, France
| | - Matthieu Pophillat
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, Marseille, France
| | - Caroline Cluzel
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique, UMR 5305, CNRS/Université Lyon I, Lyon, France
| | - Leon Espinosa
- Laboratoire de Chimie Bactérienne, UMR 7283, CNRS/Aix-Marseille Univ, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Université Lyon I, Lyon, France
| | - Anne Galinier
- Laboratoire de Chimie Bactérienne, UMR 7283, CNRS/Aix-Marseille Univ, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Thierry Doan
- Laboratoire de Chimie Bactérienne, UMR 7283, CNRS/Aix-Marseille Univ, Institut de Microbiologie de la Méditerranée, Marseille, France
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13
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Garcia PS, Duchemin W, Flandrois JP, Gribaldo S, Grangeasse C, Brochier-Armanet C. A Comprehensive Evolutionary Scenario of Cell Division and Associated Processes in the Firmicutes. Mol Biol Evol 2021; 38:2396-2412. [PMID: 33533884 PMCID: PMC8136486 DOI: 10.1093/molbev/msab034] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The cell cycle is a fundamental process that has been extensively studied in bacteria. However, many of its components and their interactions with machineries involved in other cellular processes are poorly understood. Furthermore, most knowledge relies on the study of a few models, but the real diversity of the cell division apparatus and its evolution are largely unknown. Here, we present a massive in-silico analysis of cell division and associated processes in around 1,000 genomes of the Firmicutes, a major bacterial phylum encompassing models (i.e. Bacillus subtilis, Streptococcus pneumoniae, and Staphylococcus aureus), as well as many important pathogens. We analyzed over 160 proteins by using an original approach combining phylogenetic reconciliation, phylogenetic profiles, and gene cluster survey. Our results reveal the presence of substantial differences among clades and pinpoints a number of evolutionary hotspots. In particular, the emergence of Bacilli coincides with an expansion of the gene repertoires involved in cell wall synthesis and remodeling. We also highlight major genomic rearrangements at the emergence of Streptococcaceae. We establish a functional network in Firmicutes that allows identifying new functional links inside one same process such as between FtsW (peptidoglycan polymerase) and a previously undescribed Penicilin-Binding Protein or between different processes, such as replication and cell wall synthesis. Finally, we identify new candidates involved in sporulation and cell wall synthesis. Our results provide a previously undescribed view on the diversity of the bacterial cell cycle, testable hypotheses for further experimental studies, and a methodological framework for the analysis of any other biological system.
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Affiliation(s)
- Pierre S Garcia
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918 Villeurbanne F-69622, France.,Molecular Microbiology and Structural Biochemistry, UMR 5086, Université Claude Bernard Lyon 1, CNRS, Lyon, France.,Department of Microbiology, Unit "Evolutionary Biology of the Microbial Cell", Institut Pasteur, Paris, France
| | - Wandrille Duchemin
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918 Villeurbanne F-69622, France
| | - Jean-Pierre Flandrois
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918 Villeurbanne F-69622, France
| | - Simonetta Gribaldo
- Department of Microbiology, Unit "Evolutionary Biology of the Microbial Cell", Institut Pasteur, Paris, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université Claude Bernard Lyon 1, CNRS, Lyon, France
| | - Céline Brochier-Armanet
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918 Villeurbanne F-69622, France
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14
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Trouve J, Zapun A, Arthaud C, Durmort C, Di Guilmi AM, Söderström B, Pelletier A, Grangeasse C, Bourgeois D, Wong YS, Morlot C. Nanoscale dynamics of peptidoglycan assembly during the cell cycle of Streptococcus pneumoniae. Curr Biol 2021; 31:2844-2856.e6. [PMID: 33989523 DOI: 10.1016/j.cub.2021.04.041] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 11/02/2020] [Revised: 03/09/2021] [Accepted: 04/16/2021] [Indexed: 12/15/2022]
Abstract
Dynamics of cell elongation and septation are key determinants of bacterial morphogenesis. These processes are intimately linked to peptidoglycan synthesis performed by macromolecular complexes called the elongasome and the divisome. In rod-shaped bacteria, cell elongation and septation, which are dissociated in time and space, have been well described. By contrast, in ovoid-shaped bacteria, the dynamics and relationships between these processes remain poorly understood because they are concomitant and confined to a nanometer-scale annular region at midcell. Here, we set up a metabolic peptidoglycan labeling approach using click chemistry to image peptidoglycan synthesis by single-molecule localization microscopy in the ovoid bacterium Streptococcus pneumoniae. Our nanoscale-resolution data reveal spatiotemporal features of peptidoglycan assembly and fate along the cell cycle and provide geometrical parameters that we used to construct a morphogenesis model of the ovoid cell. These analyses show that septal and peripheral peptidoglycan syntheses first occur within a single annular region that later separates in two concentric regions and that elongation persists after septation is completed. In addition, our data reveal that freshly synthesized peptidoglycan is remodeled all along the cell cycle. Altogether, our work provides evidence that septal peptidoglycan is synthesized from the beginning of the cell cycle and is constantly remodeled through cleavage and insertion of material at its periphery. The ovoid-cell morphogenesis would thus rely on the relative dynamics between peptidoglycan synthesis and cleavage rather than on the existence of two distinct successive phases of peripheral and septal synthesis.
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Affiliation(s)
- Jennyfer Trouve
- Univ. Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France
| | - André Zapun
- Univ. Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France
| | | | - Claire Durmort
- Univ. Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France
| | | | - Bill Söderström
- The ithree institute, University of Technology Sydney, Ultimo, NSW 2007, Australia; Structural Cellular Biology Unit, Okinawa Institute of Science and Technology, 904-0495 Okinawa, Japan
| | - Anais Pelletier
- Molecular Microbiology and Structural Biochemistry (MMSB), CNRS, Univ. Lyon 1, UMR 5086, Lyon 69007, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry (MMSB), CNRS, Univ. Lyon 1, UMR 5086, Lyon 69007, France
| | | | | | - Cecile Morlot
- Univ. Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France.
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15
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Ducret A, Grangeasse C. Recent progress in our understanding of peptidoglycan assembly in Firmicutes. Curr Opin Microbiol 2021; 60:44-50. [PMID: 33588129 DOI: 10.1016/j.mib.2021.01.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/13/2021] [Accepted: 01/27/2021] [Indexed: 02/06/2023]
Abstract
Years of intense research have shown that the assembly of peptidoglycan, the extracellular mesh-like polymer surrounding the bacterial cell, is incredibly complex. It requires a suite of reactions catalyzed by dynamic macromolecular protein complexes whose localization and activity should be finely regulated in space and time. In this review, we focus on the main developments reported over the last five years for the assembly of peptidoglycan in Firmicutes, a bacterial phylum that comprises monoderm bacteria and that encompasses well studied bacterial models with different cell shapes and lifestyles.
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Affiliation(s)
- Adrien Ducret
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Université de Lyon, 7 passage du Vercors, 69367 Lyon, France.
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16
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Hosek T, Bougault CM, Lavergne JP, Martinez D, Ayala I, Fenel D, Restelli M, Morlot C, Habenstein B, Grangeasse C, Simorre JP. Structural features of the interaction of MapZ with FtsZ and membranes in Streptococcus pneumoniae. Sci Rep 2020; 10:4051. [PMID: 32132631 PMCID: PMC7055233 DOI: 10.1038/s41598-020-61036-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 11/13/2019] [Accepted: 02/13/2020] [Indexed: 01/08/2023] Open
Abstract
MapZ localizes at midcell and acts as a molecular beacon for the positioning of the cell division machinery in the bacterium Streptococcus pneumoniae. MapZ contains a single transmembrane helix that separates the C-terminal extracellular domain from the N-terminal cytoplasmic domain. Only the structure and function of the extracellular domain is known. Here, we demonstrate that large parts of the cytoplasmic domain is intrinsically disordered and that there are two regions (from residues 45 to 68 and 79 to 95) with a tendency to fold into amphipathic helices. We further reveal that these regions interact with the surface of liposomes that mimic the Streptococcus pneumoniae cell membrane. The highly conserved and unfolded N-terminal region (from residues 17 to 43) specifically interacts with FtsZ independently of FtsZ polymerization state. Moreover, we show that MapZ phosphorylation at positions Thr67 and Thr68 does not impact the interaction with FtsZ or liposomes. Altogether, we propose a model in which the MapZ-mediated recruitment of FtsZ to mid-cell is modulated through competition of MapZ binding to the cell membrane. The molecular interplay between the components of this tripartite complex could represent a key step toward the complete assembly of the divisome.
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Affiliation(s)
- Tomas Hosek
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, F-38000, Grenoble, France
| | - Catherine M Bougault
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, F-38000, Grenoble, France
| | - Jean-Pierre Lavergne
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Université de Lyon, Lyon, France
| | - Denis Martinez
- Institute of Chemistry and Biology of Membranes and Nano-objects, CBMN-CNRS Université de Bordeaux, Pessac, France
| | - Isabel Ayala
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, F-38000, Grenoble, France
| | - Daphna Fenel
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, F-38000, Grenoble, France
| | - Marine Restelli
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Université de Lyon, Lyon, France
| | - Cecile Morlot
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, F-38000, Grenoble, France
| | - Birgit Habenstein
- Institute of Chemistry and Biology of Membranes and Nano-objects, CBMN-CNRS Université de Bordeaux, Pessac, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Université de Lyon, Lyon, France.
| | - Jean-Pierre Simorre
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, F-38000, Grenoble, France.
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17
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Garcia PS, Jauffrit F, Grangeasse C, Brochier-Armanet C. GeneSpy, a user-friendly and flexible genomic context visualizer. Bioinformatics 2019; 35:329-331. [PMID: 29912383 DOI: 10.1093/bioinformatics/bty459] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 06/12/2018] [Indexed: 11/13/2022] Open
Abstract
Summary The exploration and comparison of genome organization is routinely used in the frame of genomic and phylogenomic analyses. As a consequence, in the past few years, various tools allowing visualizing genomic contexts have been developed. However, their use is often hampered by a lack of flexibility, particularly concerning associated databases input formats and figure customization. Here we present GeneSpy, a graphical user interface that allows the visualization and dynamic exploration of eukaryotic and prokaryotic annotated genomes. GeneSpy relies on user-friendly manageable local databases and allows the easy customization and production of figures in a multitude of formats. Availability and implementation GeneSpy is freely available at https://lbbe.univ-lyon1.fr/GeneSpy/ for Linux, Mac OS and Windows under CeCILL license (http://www.cecill.info/licences/). It is written in Python 2.7 and depends on Matplotlib, Tkinter and Sqlite libraries. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Pierre Simon Garcia
- Univ Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, Villeurbanne, France.,MMSB Molecular Microbiology and Structural Biochemistry, Institut de Biologie et de Chimie des Protéines 7 passage du Vercors, LYON cedex, France
| | - Frédéric Jauffrit
- Univ Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, Villeurbanne, France.,R&D microbiology, Clinical Unit, bioMerieux, Marcy L'Etoile, France
| | - Christophe Grangeasse
- MMSB Molecular Microbiology and Structural Biochemistry, Institut de Biologie et de Chimie des Protéines 7 passage du Vercors, LYON cedex, France
| | - Céline Brochier-Armanet
- Univ Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, Villeurbanne, France
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18
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Pelletier A, Freton C, Gallay C, Trouve J, Cluzel C, Franz-Wachtel M, Macek B, Jault JM, Grangeasse C, Guiral S. The Tyrosine-Autokinase UbK Is Required for Proper Cell Growth and Cell Morphology of Streptococcus pneumoniae. Front Microbiol 2019; 10:1942. [PMID: 31551943 PMCID: PMC6733980 DOI: 10.3389/fmicb.2019.01942] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 06/07/2019] [Accepted: 08/07/2019] [Indexed: 12/11/2022] Open
Abstract
Protein phosphorylation is a key post-translational modification required for many cellular functions of the bacterial cell. Recently, we identified a new protein-kinase, named UbK, in Bacillus subtilis that belongs to a new family of protein-kinases widespread in bacteria. In this study, we analyze the function of UbK in Streptococcus pneumoniae. We show that UbK displays a tyrosine-kinase activity and autophosphorylates on a unique tyrosine in vivo. To get insights into its cellular role, we constructed a set of pneumococcal ubk mutants. Using conventional and electron microscopy, we show that the ubk deficient strain, as well as an ubk catalytic dead mutant, display both severe cell-growth and cell-morphology defects. The same defects are observed with a mutant mimicking permanent phosphorylation of UbK whereas they are not detected for a mutant mimicking defective autophosphorylation of UbK. Moreover, we find that UbK phosphorylation promotes its ability to hydrolyze ATP. These observations show that the hydrolysis of ATP by UbK serves not only for its autophosphorylation but also for a distinct purpose essential for the optimal cell growth and cell-morphogenesis of the pneumococcus. We thus propose a model in which the autophosphorylation/dephosphorylation of UbK regulates its cellular function through a negative feedback loop.
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Affiliation(s)
- Anaïs Pelletier
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université Lyon 1, Lyon, France
| | - Céline Freton
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université Lyon 1, Lyon, France
| | - Clément Gallay
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université Lyon 1, Lyon, France
| | - Jennyfer Trouve
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université Lyon 1, Lyon, France
| | - Caroline Cluzel
- Laboratoire de Biologie Tissulaire et d'Ingénierie Thérapeutique, UMR 5305 CNRS/Université Lyon 1, Lyon, France
| | | | - Boris Macek
- Proteome Center Tübingen, University of Tübingen, Tübingen, Germany
| | - Jean-Michel Jault
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université Lyon 1, Lyon, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université Lyon 1, Lyon, France
| | - Sébastien Guiral
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université Lyon 1, Lyon, France
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19
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Mercy C, Ducret A, Slager J, Lavergne JP, Freton C, Nagarajan SN, Garcia PS, Noirot-Gros MF, Dubarry N, Nourikyan J, Veening JW, Grangeasse C. RocS drives chromosome segregation and nucleoid protection in Streptococcus pneumoniae. Nat Microbiol 2019; 4:1661-1670. [PMID: 31182798 DOI: 10.1038/s41564-019-0472-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 04/26/2019] [Indexed: 11/09/2022]
Abstract
Chromosome segregation in bacteria is poorly understood outside some prominent model strains1-5 and even less is known about how it is coordinated with other cellular processes. This is the case for the opportunistic human pathogen Streptococcus pneumoniae (the pneumococcus)6, which lacks the Min and the nucleoid occlusion systems7, and possesses only an incomplete chromosome partitioning Par(A)BS system, in which ParA is absent8. The bacterial tyrosine kinase9 CpsD, which is required for capsule production, was previously found to interfere with chromosome segregation10. Here, we identify a protein of unknown function that interacts with CpsD and drives chromosome segregation. RocS (Regulator of Chromosome Segregation) is a membrane-bound protein that interacts with both DNA and the chromosome partitioning protein ParB to properly segregate the origin of replication region to new daughter cells. In addition, we show that RocS interacts with the cell division protein FtsZ and hinders cell division. Altogether, this work reveals that RocS is the cornerstone of a nucleoid protection system ensuring proper chromosome segregation and cell division in coordination with the biogenesis of the protective capsular layer.
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Affiliation(s)
- Chryslène Mercy
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Adrien Ducret
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Jelle Slager
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Groningen, The Netherlands
| | - Jean-Pierre Lavergne
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Céline Freton
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Sathya Narayanan Nagarajan
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Pierre Simon Garcia
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Marie-Francoise Noirot-Gros
- Micalis Institute, UMR1319, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.,Biosciences Division, Argonne National Laboratory, Lemont, IL, USA
| | - Nelly Dubarry
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France.,Evotec ID, Marcy l'Etoile, France
| | - Julien Nourikyan
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Jan-Willem Veening
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Groningen, The Netherlands.,Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, Lausanne, Switzerland
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France.
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20
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Manuse S, Fenton A, Grangeasse C. [MacP, a regulator of the cell wall assembly in the human bacterial pathogen Streptococcus pneumoniae]. Med Sci (Paris) 2018; 34:642-645. [PMID: 30230455 DOI: 10.1051/medsci/20183408004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sylvie Manuse
- Unité de microbiologie moléculaire et biochimie structurale, CNRS UMR 5086, université de Lyon, 7, passage du Vercors, F-69007, Lyon, France
| | - Andrew Fenton
- The Florey institute, university of Sheffield, S10 2TN, Sheffield, Royaume-Uni
| | - Christophe Grangeasse
- Unité de microbiologie moléculaire et biochimie structurale, CNRS UMR 5086, université de Lyon, 7, passage du Vercors, F-69007, Lyon, France
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21
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Zucchini L, Mercy C, Garcia PS, Cluzel C, Gueguen-Chaignon V, Galisson F, Freton C, Guiral S, Brochier-Armanet C, Gouet P, Grangeasse C. PASTA repeats of the protein kinase StkP interconnect cell constriction and separation of Streptococcus pneumoniae. Nat Microbiol 2018; 3:197-209. [PMID: 29203882 DOI: 10.1038/s41564-017-0069-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 10/23/2017] [Indexed: 11/09/2022]
Abstract
Eukaryotic-like serine/threonine kinases (eSTKs) with extracellular PASTA repeats are key membrane regulators of bacterial cell division. How PASTA repeats govern eSTK activation and function remains elusive. Using evolution- and structural-guided approaches combined with cell imaging, we disentangle the role of each PASTA repeat of the eSTK StkP from Streptococcus pneumoniae. While the three membrane-proximal PASTA repeats behave as interchangeable modules required for the activation of StkP independently of cell wall binding, they also control the septal cell wall thickness. In contrast, the fourth and membrane-distal PASTA repeat directs StkP localization at the division septum and encompasses a specific motif that is critical for final cell separation through interaction with the cell wall hydrolase LytB. We propose a model in which the extracellular four-PASTA domain of StkP plays a dual function in interconnecting the phosphorylation of StkP endogenous targets along with septal cell wall remodelling to allow cell division of the pneumococcus.
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Affiliation(s)
- Laure Zucchini
- Molecular Microbiology and Structural Biochemistry, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Chryslène Mercy
- Molecular Microbiology and Structural Biochemistry, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Pierre Simon Garcia
- Molecular Microbiology and Structural Biochemistry, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
- Laboratoire de Biométrie et Biologie Evolutive, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Villeurbanne, France
| | - Caroline Cluzel
- Laboratoire de Biologie Tissulaire et d'Ingénierie Thérapeutique, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Virginie Gueguen-Chaignon
- Protein Science Facility, Structure Fédérative de Recherche Biosciences/UMS3444/US8, Université Claude Bernard Lyon 1, Ecole Normale Supérieur de Lyon, INSERM, Centre National de la Recherche Scientifique, Lyon, France
| | - Frédéric Galisson
- Molecular Microbiology and Structural Biochemistry, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Céline Freton
- Molecular Microbiology and Structural Biochemistry, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Sébastien Guiral
- Molecular Microbiology and Structural Biochemistry, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Céline Brochier-Armanet
- Laboratoire de Biométrie et Biologie Evolutive, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Villeurbanne, France
| | - Patrice Gouet
- Molecular Microbiology and Structural Biochemistry, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France.
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22
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Nguyen HA, El Khoury T, Guiral S, Laaberki MH, Candusso MP, Galisson F, Foucher AE, Kesraoui S, Ballut L, Vallet S, Orelle C, Zucchini L, Martin J, Page A, Attieh J, Aghajari N, Grangeasse C, Jault JM. Expanding the Kinome World: A New Protein Kinase Family Widely Conserved in Bacteria. J Mol Biol 2017; 429:3056-3074. [PMID: 28890133 DOI: 10.1016/j.jmb.2017.08.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [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: 04/20/2017] [Revised: 08/20/2017] [Accepted: 08/21/2017] [Indexed: 12/31/2022]
Abstract
Fine tuning of signaling pathways is essential for cells to cope with sudden environmental variations. This delicate balance is maintained in particular by protein kinases that control the activity of target proteins by reversible phosphorylation. In addition to homologous eukaryotic enzymes, bacteria have evolved some specific Ser/Thr/Tyr protein kinases without any structural resemblance to their eukaryotic counterparts. Here, we show that a previously identified family of ATPases, broadly conserved among bacteria, is in fact a new family of protein kinases with a Ser/Thr/Tyr kinase activity. A prototypic member of this family, YdiB from Bacillus subtilis, is able to autophosphorylate and to phosphorylate a surrogate substrate, the myelin basic protein. Two crystal structures of YdiB were solved (1.8 and 2.0Å) that display a unique ATP-binding fold unrelated to known protein kinases, although a conserved HxD motif is reminiscent of that found in Hanks-type protein kinases. The effect of mutations of conserved residues further highlights the unique nature of this new protein kinase family that we name ubiquitous bacterial kinase. We investigated the cellular role of YdiB and showed that a ∆ydiB mutant was more sensitive to paraquat treatment than the wild type, with ~13% of cells with an aberrant morphology. In addition, YdiE, which is known to participate with both YdiC and YdiB in an essential chemical modification of some specific tRNAs, is phosphorylated in vitro by YdiB. These results expand the boundaries of the bacterial kinome and support the involvement of YdiB in protein translation and resistance to oxidative stress in B. subtilis.
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Affiliation(s)
- Hien-Anh Nguyen
- Institut de Biologie Structurale, Université Joseph Fourier Grenoble 1, UMR5075 CNRS/CEA/UJF, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France
| | - Takla El Khoury
- Institut de Biologie Structurale, Université Joseph Fourier Grenoble 1, UMR5075 CNRS/CEA/UJF, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France; University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France; Department of Biology, Faculty of Sciences, University of Balamand, Lebanon
| | - Sébastien Guiral
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Maria-Halima Laaberki
- Institut de Biologie Structurale, Université Joseph Fourier Grenoble 1, UMR5075 CNRS/CEA/UJF, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France
| | - Marie-Pierre Candusso
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Frédéric Galisson
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Anne-Emmanuelle Foucher
- Institut de Biologie Structurale, Université Joseph Fourier Grenoble 1, UMR5075 CNRS/CEA/UJF, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France
| | - Salsabil Kesraoui
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Lionel Ballut
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Sylvain Vallet
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Cédric Orelle
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Laure Zucchini
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Juliette Martin
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Adeline Page
- Protein Science Facility, SFR BioSciences CNRS UMS3444, Inserm US8, UCBL, ENS de Lyon, 50 Avenue Tony Garnier, 69007 Lyon, France
| | - Jihad Attieh
- Department of Biology, Faculty of Sciences, University of Balamand, Lebanon
| | - Nushin Aghajari
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Christophe Grangeasse
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France
| | - Jean-Michel Jault
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry," 7 Passage du Vercors, F-69367 Lyon, France.
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23
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Grangeasse C. Rewiring the Pneumococcal Cell Cycle with Serine/Threonine- and Tyrosine-kinases. Trends Microbiol 2016; 24:713-724. [DOI: 10.1016/j.tim.2016.04.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Revised: 03/23/2016] [Accepted: 04/07/2016] [Indexed: 12/14/2022]
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24
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Mijakovic I, Grangeasse C, Turgay K. Exploring the diversity of protein modifications: special bacterial phosphorylation systems. FEMS Microbiol Rev 2016; 40:398-417. [PMID: 26926353 DOI: 10.1093/femsre/fuw003] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [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: 09/29/2015] [Accepted: 02/02/2016] [Indexed: 12/31/2022] Open
Abstract
Protein modifications not only affect protein homeostasis but can also establish new cellular protein functions and are important components of complex cellular signal sensing and transduction networks. Among these post-translational modifications, protein phosphorylation represents the one that has been most thoroughly investigated. Unlike in eukarya, a large diversity of enzyme families has been shown to phosphorylate and dephosphorylate proteins on various amino acids with different chemical properties in bacteria. In this review, after a brief overview of the known bacterial phosphorylation systems, we focus on more recently discovered and less widely known kinases and phosphatases. Namely, we describe in detail tyrosine- and arginine-phosphorylation together with some examples of unusual serine-phosphorylation systems and discuss their potential role and function in bacterial physiology, and regulatory networks. Investigating these unusual bacterial kinase and phosphatases is not only important to understand their role in bacterial physiology but will help to generally understand the full potential and evolution of protein phosphorylation for signal transduction, protein modification and homeostasis in all cellular life.
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Affiliation(s)
- Ivan Mijakovic
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg 41296, Sweden Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark
| | - Christophe Grangeasse
- Unité Microbiologie Moléculaire et Biochimie Structurale, UMR 5086-CNRS/ Université Lyon 1, Lyon 69367, France
| | - Kürşad Turgay
- Institut für Mikrobiologie, Leibniz Universität Hannover, D-30419 Hannover, Germany
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25
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Manuse S, Fleurie A, Zucchini L, Lesterlin C, Grangeasse C. Role of eukaryotic-like serine/threonine kinases in bacterial cell division and morphogenesis. FEMS Microbiol Rev 2015; 40:41-56. [DOI: 10.1093/femsre/fuv041] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2015] [Indexed: 11/14/2022] Open
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26
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Nourikyan J, Kjos M, Mercy C, Cluzel C, Morlot C, Noirot-Gros MF, Guiral S, Lavergne JP, Veening JW, Grangeasse C. Autophosphorylation of the Bacterial Tyrosine-Kinase CpsD Connects Capsule Synthesis with the Cell Cycle in Streptococcus pneumoniae. PLoS Genet 2015; 11:e1005518. [PMID: 26378458 PMCID: PMC4574921 DOI: 10.1371/journal.pgen.1005518] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 08/21/2015] [Indexed: 01/07/2023] Open
Abstract
Bacterial capsular polysaccharides (CPS) are produced by a multi-protein membrane complex, in which a particular type of tyrosine-autokinases named BY-kinases, regulate their polymerization and export. However, our understanding of the role of BY-kinases in these processes remains incomplete. In the human pathogen Streptococcus pneumoniae, the BY-kinase CpsD localizes at the division site and participates in the proper assembly of the capsule. In this study, we show that the cytoplasmic C-terminal end of the transmembrane protein CpsC is required for CpsD autophosphorylation and localization at mid-cell. Importantly, we demonstrate that the CpsC/CpsD complex captures the polysaccharide polymerase CpsH at the division site. Together with the finding that capsule is not produced at the division site in cpsD and cpsC mutants, these data show that CPS production occurs exclusively at mid-cell and is tightly dependent on CpsD interaction with CpsC. Next, we have analyzed the impact of CpsD phosphorylation on CPS production. We show that dephosphorylation of CpsD induces defective capsule production at the septum together with aberrant cell elongation and nucleoid defects. We observe that the cell division protein FtsZ assembles and localizes properly although cell constriction is impaired. DAPI staining together with localization of the histone-like protein HlpA further show that chromosome replication and/or segregation is defective suggesting that CpsD autophosphorylation interferes with these processes thus resulting in cell constriction defects and cell elongation. We show that CpsD shares structural homology with ParA-like ATPases and that it interacts with the chromosome partitioning protein ParB. Total internal reflection fluorescence microscopy imaging demonstrates that CpsD phosphorylation modulates the mobility of ParB. These data support a model in which phosphorylation of CpsD acts as a signaling system coordinating CPS synthesis with chromosome segregation to ensure that daughter cells are properly wrapped in CPS. Bacteria utilize a multi-protein membrane complex to synthesize and export the polysaccharide capsule that conceals and covers the cell. In bacterial pathogens, the capsule protects the cell form opsonophagocytosis and complement-mediated killing. The mechanisms allowing the bacterial cell to maintain this protective capsule during cell growth and division remain unknown. The capsule assembly machinery encompasses a particular type of tyrosine-kinases found only in bacteria, which are called BY-kinases. These kinases are involved in the regulation of several cellular functions including polysaccharide capsule production. Studying the role of BY-kinase represents thus an interesting approach to decipher the mechanisms of capsule synthesis and export. Here, we study the role of the BY-kinase CpsD in the human pathogen Streptococcus pneumoniae. We show that CpsD plays a dual function in the pneumococcus. Indeed, CpsD captures the capsule assembly machinery at the site of division, but we also show that CpsD coordinates capsule production with the cell cycle by interacting with the chromosome segregation system. These features provide a simple mechanism to cover the complete surface of the pneumococcal daughter cells. This finding further opens a new view of the function of BY-kinases in the bacterial cell notably in localizing protein complexes in subcellular regions over the cell cycle.
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Affiliation(s)
- Julien Nourikyan
- Bases Moléculaires et Structurales des Systèmes Infectieux, UMR5086 CNRS/Université de Lyon 1, Lyon, France
| | - Morten Kjos
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Groningen, the Netherlands
| | - Chryslène Mercy
- Bases Moléculaires et Structurales des Systèmes Infectieux, UMR5086 CNRS/Université de Lyon 1, Lyon, France
| | - Caroline Cluzel
- Laboratoire Biologie Tissulaire et Ingénierie thérapeutique, UMR5305, CNRS/Université de Lyon 1, Lyon, France
| | - Cécile Morlot
- Institut de Biologie Structurale, UMR5075 CNRS/CEA/Université Grenoble Alpes, Grenoble, France
| | | | - Sébastien Guiral
- Bases Moléculaires et Structurales des Systèmes Infectieux, UMR5086 CNRS/Université de Lyon 1, Lyon, France
| | - Jean-Pierre Lavergne
- Bases Moléculaires et Structurales des Systèmes Infectieux, UMR5086 CNRS/Université de Lyon 1, Lyon, France
| | - Jan-Willem Veening
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Groningen, the Netherlands
| | - Christophe Grangeasse
- Bases Moléculaires et Structurales des Systèmes Infectieux, UMR5086 CNRS/Université de Lyon 1, Lyon, France
- * E-mail:
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27
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Grangeasse C, Stülke J, Mijakovic I. Regulatory potential of post-translational modifications in bacteria. Front Microbiol 2015; 6:500. [PMID: 26074895 PMCID: PMC4446998 DOI: 10.3389/fmicb.2015.00500] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 05/06/2015] [Indexed: 11/30/2022] Open
Affiliation(s)
- Christophe Grangeasse
- Bases Moléculaires et Structurales des Systèmes Infectieux, UMR 5086, Centre National de la Recherche Scientifique, University of Lyon Lyon, France
| | - Jörg Stülke
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Göttingen Göttingen, Germany
| | - Ivan Mijakovic
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology Göteborg, Sweden
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28
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Affiliation(s)
- Christophe Grangeasse
- a Bases Moléculaires et Structurales des Systèmes Infectieux; IBCP, Université Lyon 1; CNRS, UMR 5086 ; Lyon , France
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29
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Pompeo F, Foulquier E, Serrano B, Grangeasse C, Galinier A. Phosphorylation of the cell division protein GpsB regulates PrkC kinase activity through a negative feedback loop in Bacillus subtilis. Mol Microbiol 2015; 97:139-50. [PMID: 25845974 DOI: 10.1111/mmi.13015] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2015] [Indexed: 01/12/2023]
Abstract
Although many membrane Ser/Thr-kinases with PASTA motifs have been shown to control bacterial cell division and morphogenesis, inactivation of the Ser/Thr-kinase PrkC does not impact Bacillus subtilis cell division. In this study, we show that PrkC localizes at the division septum. In addition, three proteins involved in cell division/elongation, GpsB, DivIVA and EzrA are required for stimulating PrkC activity in vivo. We show that GpsB interacts with the catalytic subunit of PrkC that, in turn, phosphorylates GpsB. These observations are not made with DivIVA and EzrA. Consistent with the phosphorylated residue previously detected for GpsB in a high-throughput phosphoproteomic analysis of B. subtilis, we show that threonine 75 is the single PrkC-mediated phosphorylation site in GpsB. Importantly, the substitution of this threonine by a phospho-mimetic residue induces a loss of PrkC kinase activity in vivo and a reduced growth under high salt conditions as observed for gpsB and prkC null mutants. Conversely, substitution of threonine 75 by a phospho-ablative residue does not induce such growth and PrkC kinase activity defects. Altogether, these data show that proteins of the divisome control PrkC activity and thereby phosphorylation of PrkC substrates through a negative feedback loop in B. subtilis.
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Affiliation(s)
- Frédérique Pompeo
- Laboratoire de Chimie Bactérienne, UMR 7283, IMM, CNRS, Aix-Marseille Université, 31 Chemin Joseph Aiguier, Marseille, 13009, France
| | - Elodie Foulquier
- Laboratoire de Chimie Bactérienne, UMR 7283, IMM, CNRS, Aix-Marseille Université, 31 Chemin Joseph Aiguier, Marseille, 13009, France
| | - Bastien Serrano
- Laboratoire de Chimie Bactérienne, UMR 7283, IMM, CNRS, Aix-Marseille Université, 31 Chemin Joseph Aiguier, Marseille, 13009, France
| | - Christophe Grangeasse
- Bases Moléculaires et Structurales des Systèmes Infectieux, IBCP, CNRS, UMR, Université Lyon 1, Lyon, 5086, France
| | - Anne Galinier
- Laboratoire de Chimie Bactérienne, UMR 7283, IMM, CNRS, Aix-Marseille Université, 31 Chemin Joseph Aiguier, Marseille, 13009, France
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Shi L, Ji B, Kolar-Znika L, Boskovic A, Jadeau F, Combet C, Grangeasse C, Franjevic D, Talla E, Mijakovic I. Evolution of bacterial protein-tyrosine kinases and their relaxed specificity toward substrates. Genome Biol Evol 2015; 6:800-17. [PMID: 24728941 PMCID: PMC4007543 DOI: 10.1093/gbe/evu056] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [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] [Indexed: 02/04/2023] Open
Abstract
It has often been speculated that bacterial protein-tyrosine kinases (BY-kinases) evolve rapidly and maintain relaxed substrate specificity to quickly adopt new substrates when evolutionary pressure in that direction arises. Here, we report a phylogenomic and biochemical analysis of BY-kinases, and their relationship to substrates aimed to validate this hypothesis. Our results suggest that BY-kinases are ubiquitously distributed in bacterial phyla and underwent a complex evolutionary history, affected considerably by gene duplications and horizontal gene transfer events. This is consistent with the fact that the BY-kinase sequences represent a high level of substitution saturation and have a higher evolutionary rate compared with other bacterial genes. On the basis of similarity networks, we could classify BY kinases into three main groups with 14 subgroups. Extensive sequence conservation was observed only around the three canonical Walker motifs, whereas unique signatures proposed the functional speciation and diversification within some subgroups. The relationship between BY-kinases and their substrates was analyzed using a ubiquitous substrate (Ugd) and some Firmicute-specific substrates (YvyG and YjoA) from Bacillus subtilis. No evidence of coevolution between kinases and substrates at the sequence level was found. Seven BY-kinases, including well-characterized and previously uncharacterized ones, were used for experimental studies. Most of the tested kinases were able to phosphorylate substrates from B. subtilis (Ugd, YvyG, and YjoA), despite originating from very distant bacteria. Our results are consistent with the hypothesis that BY-kinases have evolved relaxed substrate specificity and are probably maintained as rapidly evolving platforms for adopting new substrates.
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Affiliation(s)
- Lei Shi
- INRA-AgroParisTech UMR 1319, Micalis-CBAI, Thiverval-Grignon, France
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Foulquier E, Pompeo F, Freton C, Cordier B, Grangeasse C, Galinier A. PrkC-mediated phosphorylation of overexpressed YvcK protein regulates PBP1 protein localization in Bacillus subtilis mreB mutant cells. J Biol Chem 2014; 289:23662-9. [PMID: 25012659 DOI: 10.1074/jbc.m114.562496] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [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: 12/28/2022] Open
Abstract
The YvcK protein has been shown to be necessary for growth under gluconeogenic conditions in Bacillus subtilis. Amazingly, its overproduction rescues growth and morphology defects of the actin-like protein MreB deletion mutant by restoration of PBP1 localization. In this work, we observed that YvcK was phosphorylated at Thr-304 by the protein kinase PrkC and that phosphorylated YvcK was dephosphorylated by the cognate phosphatase PrpC. We show that neither substitution of this threonine with a constitutively phosphorylated mimicking glutamic acid residue or a phosphorylation-dead mimicking alanine residue nor deletion of prkC or prpC altered the ability of B. subtilis to grow under gluconeogenic conditions. However, we observed that a prpC mutant and a yvcK mutant were more sensitive to bacitracin compared with the WT strain. In addition, the bacitracin sensitivity of strains in which YvcK Thr-304 was replaced with either an alanine or a glutamic acid residue was also affected. We also analyzed rescue of the mreB mutant strain by overproduction of YvcK in which the phosphorylation site was substituted. We show that YvcK T304A overproduction did not rescue the mreB mutant aberrant morphology due to PBP1 mislocalization. The same observation was made in an mreB prkC double mutant overproducing YvcK. Altogether, these data show that YvcK may have two distinct functions: 1) in carbon source utilization independent of its phosphorylation level and 2) in cell wall biosynthesis and morphogenesis through its phosphorylation state.
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Affiliation(s)
- Elodie Foulquier
- From the Laboratoire de Chimie Bactérienne, UMR 7283, Institut de Microbiologie de la Méditerranée, CNRS, Aix-Marseille Université, 13009 Marseille and
| | - Frédérique Pompeo
- From the Laboratoire de Chimie Bactérienne, UMR 7283, Institut de Microbiologie de la Méditerranée, CNRS, Aix-Marseille Université, 13009 Marseille and
| | - Céline Freton
- From the Laboratoire de Chimie Bactérienne, UMR 7283, Institut de Microbiologie de la Méditerranée, CNRS, Aix-Marseille Université, 13009 Marseille and the Bases Moléculaires et Structurales des Systèmes Infectieux, UMR 5086, CNRS, Université de Lyon, 69367 Lyon Cedex 07, France
| | - Baptiste Cordier
- From the Laboratoire de Chimie Bactérienne, UMR 7283, Institut de Microbiologie de la Méditerranée, CNRS, Aix-Marseille Université, 13009 Marseille and
| | - Christophe Grangeasse
- the Bases Moléculaires et Structurales des Systèmes Infectieux, UMR 5086, CNRS, Université de Lyon, 69367 Lyon Cedex 07, France
| | - Anne Galinier
- From the Laboratoire de Chimie Bactérienne, UMR 7283, Institut de Microbiologie de la Méditerranée, CNRS, Aix-Marseille Université, 13009 Marseille and
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Jers C, Soufi B, Grangeasse C, Deutscher J, Mijakovic I. Phosphoproteomics in bacteria: towards a systemic understanding of bacterial phosphorylation networks. Expert Rev Proteomics 2014; 5:619-27. [DOI: 10.1586/14789450.5.4.619] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Morlot C, Bayle L, Jacq M, Fleurie A, Tourcier G, Galisson F, Vernet T, Grangeasse C, Di Guilmi AM. Interaction of Penicillin-Binding Protein 2x and Ser/Thr protein kinase StkP, two key players in Streptococcus pneumoniae R6 morphogenesis. Mol Microbiol 2013; 90:88-102. [PMID: 23899042 DOI: 10.1111/mmi.12348] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2013] [Indexed: 11/30/2022]
Abstract
Bacterial cell growth and division require the co-ordinated action of peptidoglycan biosynthetic enzymes and cell morphogenesis proteins. However, the regulatory mechanisms that allow generating proper bacterial shape and thus preserving cell integrity remain largely uncharacterized, especially in ovococci. Recently, the conserved eukaryotic-like Ser/Thr protein kinase of Streptococcus pneumoniae (StkP) was demonstrated to play a major role in cell shape and division. Here, we investigate the molecular mechanisms underlying the regulatory function(s) of StkP and show that it involves one of the essential actors of septal peptidoglycan synthesis, Penicillin-Binding Protein 2x (PBP2x). We demonstrate that StkP and PBP2x interact directly and are present in the same membrane-associated complex in S. pneumoniae. We further show that they both display a late-division localization pattern at the division site and that the positioning of PBP2x depends on the presence of the extracellular PASTA domains of StkP. We demonstrate that StkP and PBP2x interaction is mediated by their extracellular regions and that the complex formation is inhibited in vitro in the presence of cell wall fragments. These data suggest that the role of StkP in cell division is modulated by an interaction with PBP2x.
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Affiliation(s)
- C Morlot
- Univ. Grenoble Alpes, IBS, F-38027, Grenoble, France; CNRS, IBS, F-38027, Grenoble, France; CEA, IBS, Institut de Biologie Structurale, Pneumococcus Group, F-38027, Grenoble, France
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Temel DB, Dutta K, Alphonse S, Nourikyan J, Grangeasse C, Ghose R. Regulatory interactions between a bacterial tyrosine kinase and its cognate phosphatase. J Biol Chem 2013; 288:15212-28. [PMID: 23543749 DOI: 10.1074/jbc.m113.457804] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The cyclic process of autophosphorylation of the C-terminal tyrosine cluster (YC) of a bacterial tyrosine kinase and its subsequent dephosphorylation following interactions with a counteracting tyrosine phosphatase regulates diverse physiological processes, including the biosynthesis and export of polysaccharides responsible for the formation of biofilms or virulence-determining capsules. We provide here the first detailed insight into this hitherto uncharacterized regulatory interaction at residue-specific resolution using Escherichia coli Wzc, a canonical bacterial tyrosine kinase, and its opposing tyrosine phosphatase, Wzb. The phosphatase Wzb utilizes a surface distal to the catalytic elements of the kinase, Wzc, to dock onto its catalytic domain (WzcCD). WzcCD binds in a largely YC-independent fashion near the Wzb catalytic site, inducing allosteric changes therein. YC dephosphorylation is proximity-mediated and reliant on the elevated concentration of phosphorylated YC near the Wzb active site resulting from WzcCD docking. Wzb principally recognizes the phosphate of its phosphotyrosine substrate and further stabilizes the tyrosine moiety through ring stacking interactions with a conserved active site tyrosine.
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Affiliation(s)
- Deniz B Temel
- Department of Chemistry, City College of New York, New York, New York 10031, USA
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Grangeasse C, Nessler S, Mijakovic I. Bacterial tyrosine kinases: evolution, biological function and structural insights. Philos Trans R Soc Lond B Biol Sci 2012; 367:2640-55. [PMID: 22889913 DOI: 10.1098/rstb.2011.0424] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Reversible protein phosphorylation is a major mechanism in the regulation of fundamental signalling events in all living organisms. Bacteria have been shown to possess a versatile repertoire of protein kinases, including histidine and aspartic acid kinases, serine/threonine kinases, and more recently tyrosine and arginine kinases. Tyrosine phosphorylation is today recognized as a key regulatory device of bacterial physiology, linked to exopolysaccharide production, virulence, stress response and DNA metabolism. However, bacteria have evolved tyrosine kinases that share no resemblance with their eukaryotic counterparts and are unique in exploiting the ATP/GTP-binding Walker motif to catalyse autophosphorylation and substrate phosphorylation on tyrosine. These enzymes, named BY-kinases (for Bacterial tYrosine kinases), have been identified in a majority of sequenced bacterial genomes, and to date no orthologues have been found in Eukarya. The aim of this review was to present the most recent knowledge about BY-kinases by focusing primarily on their evolutionary origin, structural and functional aspects, and emerging regulatory potential based on recent bacterial phosphoproteomic studies.
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Affiliation(s)
- Christophe Grangeasse
- Bases Moléculaires et Structurales des Systèmes Infectieux, IBCP, CNRS, Université de Lyon, UMR 5086, 7 passage du Vercors, 69367 Lyon, France.
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Pompeo F, Freton C, Wicker-Planquart C, Grangeasse C, Jault JM, Galinier A. Phosphorylation of CpgA protein enhances both its GTPase activity and its affinity for ribosome and is crucial for Bacillus subtilis growth and morphology. J Biol Chem 2012; 287:20830-8. [PMID: 22544754 DOI: 10.1074/jbc.m112.340331] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In Bacillus subtilis, the ribosome-associated GTPase CpgA is crucial for growth and proper morphology and was shown to be phosphorylated in vitro by the Ser/Thr protein kinase PrkC. To further understand the function of the Escherichia coli RsgA ortholog, CpgA, we first demonstrated that its GTPase activity is stimulated by its association with the 30 S ribosomal subunit. Then the role of CpgA phosphorylation was analyzed. A single phosphorylated residue, threonine 166, was identified by mass spectrometry. Phosphoablative replacement of this residue in CpgA induces a decrease of both its affinity for the 30 S ribosomal subunit and its GTPase activity, whereas a phosphomimetic replacement has opposite effects. Furthermore, cells expressing a nonphosphorylatable CpgA protein present the morphological and growth defects similar to those of a cpgA-deleted strain. Altogether, our results suggest that CpgA phosphorylation on Thr-166 could modulate its ribosome-induced GTPase activity. Given the role of PrkC in B. subtilis spore germination, we propose that CpgA phosphorylation is a key regulatory process that is essential for B. subtilis development.
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Affiliation(s)
- Frédérique Pompeo
- Laboratoire de Chimie Bactérienne, FR 3479, CNRS, Aix-Marseille Université, 13402 Marseille Cedex 20, France.
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Fleurie A, Cluzel C, Guiral S, Freton C, Galisson F, Zanella-Cleon I, Di Guilmi AM, Grangeasse C. Mutational dissection of the S/T-kinase StkP reveals crucial roles in cell division of Streptococcus pneumoniae. Mol Microbiol 2012; 83:746-58. [DOI: 10.1111/j.1365-2958.2011.07962.x] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Abstract
Bacterial tyrosine-kinases share no resemblance with their eukaryotic counterparts and they have been unified in a new protein family named BY-kinases. These enzymes have been shown to control several biological functions in the bacterial cells. In recent years biochemical studies, sequence analyses and structure resolutions allowed the deciphering of a common signature. However, BY-kinase sequence annotations in primary databases remain incomplete. This prompted us to develop a specialized database of computer-annotated BY-kinase sequences: the Bacterial protein tyrosine-kinase database (BYKdb). BY-kinase sequences are first identified, thanks to a workflow developed in a previous work. A second workflow annotates the UniProtKB entries in order to provide the BYKdb entries. The database can be accessed through a web interface that allows static and dynamic queries and offers integrated sequence analysis tools. BYKdb can be found at http://bykdb.ibcp.fr.
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Affiliation(s)
- Fanny Jadeau
- Unité Bases Moléculaires et Structurales des Systèmes Infectieux, UMR 5086 CNRS - Université Claude Bernard Lyon 1, IBCP FR 3302 - 7, Passage du Vercors, 69367 Lyon CEDEX 07, France
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Gruszczyk J, Fleurie A, Olivares-Illana V, Béchet E, Zanella-Cleon I, Moréra S, Meyer P, Pompidor G, Kahn R, Grangeasse C, Nessler S. Structure analysis of the Staphylococcus aureus UDP-N-acetyl-mannosamine dehydrogenase Cap5O involved in capsular polysaccharide biosynthesis. J Biol Chem 2011; 286:17112-21. [PMID: 21454499 DOI: 10.1074/jbc.m110.216002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Bacterial UDP-sugar dehydrogenases are part of the biosynthesis pathway of extracellular polysaccharides. These compounds act as important virulence factors by protecting the cell from opsonophagocytosis and complement-mediated killing. In Staphylococcus aureus, the protein Cap5O catalyzes the oxidation of UDP-N-acetyl-mannosamine to UDP-N-acetyl-mannosaminuronic acid. Cap5O is crucial for the production of serotype 5 capsular polysaccharide that prevents the interaction of bacteria with both phagocytic and nonphagocytic eukaryotic cells. However, details of its catalytic mechanism remain unknown. We thus crystallized Cap5O and solved the first structure of an UDP-N-acetyl-mannosamine dehydrogenase. This study revealed that the catalytic cysteine makes a disulfide bond that has never been observed in other structurally characterized members of the NDP-sugar dehydrogenase family. Biochemical and mutagenesis experiments demonstrated that the formation of this disulfide bridge regulates the activity of Cap5O. We also identified two arginine residues essential for Cap5O activity. Previous data suggested that Cap5O is activated by tyrosine phosphorylation, so we characterized the phosphorylation site and examined the underlying regulatory mechanism.
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Affiliation(s)
- Jakub Gruszczyk
- Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, CNRS, 91198 Gif sur Yvette, France
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Bechet E, Gruszczyk J, Terreux R, Gueguen-Chaignon V, Vigouroux A, Obadia B, Cozzone AJ, Nessler S, Grangeasse C. Identification of structural and molecular determinants of the tyrosine-kinase Wzc and implications in capsular polysaccharide export. Mol Microbiol 2011; 77:1315-25. [PMID: 20633230 DOI: 10.1111/j.1365-2958.2010.07291.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [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]
Abstract
Capsular polysaccharides are well-established virulence factors of pathogenic bacteria. Their biosynthesis and export are regulated within the transmembrane polysaccharide assembly machinery by the autophosphorylation of atypical tyrosine-kinases, named BY-kinases. However, the accurate functioning of these tyrosine-kinases remains unknown. Here, we report the crystal structure of the non-phosphorylated cytoplasmic domain of the tyrosine-kinase Wzc from Escherichia coli in complex with ADP showing that it forms a ring-shaped octamer. Mutational analysis demonstrates that a conserved EX(2) RX(2) R motif involved in subunit interactions is essential for polysaccharide export. We also elucidate the role of a putative internal regulatory tyrosine and we show that BY-kinases from proteobacteria autophosphorylate on their C-terminal tyrosine cluster via a single-step intermolecular mechanism. This structure-function analysis also allows us to demonstrate that two different parts of a conserved basic region called the RK-cluster are essential for polysaccharide export and for kinase activity respectively. Based on these data, we revisit the dichotomy made between BY-kinases from proteobacteria and firmicutes and we propose a unique process of oligomerization and phosphorylation. We also reassess the function of BY-kinases in the capsular polysaccharide assembly machinery.
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Affiliation(s)
- Emmanuelle Bechet
- Institut de Biologie et Chimie des Protéines, CNRS, Université Lyon 1, Université de Lyon, 69367 Lyon, France
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Kobir A, Shi L, Boskovic A, Grangeasse C, Franjevic D, Mijakovic I. Protein phosphorylation in bacterial signal transduction. Biochim Biophys Acta Gen Subj 2011; 1810:989-94. [PMID: 21266190 DOI: 10.1016/j.bbagen.2011.01.006] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 12/15/2010] [Accepted: 01/18/2011] [Indexed: 11/19/2022]
Abstract
BACKGROUND Protein phosphorylation has emerged as one of the major post translational modifications in bacteria, involved in regulating a myriad of physiological processes. In a complex and dynamic system such as the bacterial cell, connectivity of its components accounts for a number of emergent properties. This article is part of a Special Issue entitled: Systems Biology of Microorganisms. SCOPE OF REVIEW This review focuses on the implications of bacterial protein phosphorylation in cell signaling and regulation and highlights the connections and cross talk between various signaling pathways: bacterial two-component systems and serine/threonine kinases, but also the interference between phosphorylation and other post-translational modifications (methylation and acetylation). MAJOR CONCLUSIONS Recent technical developments in high accuracy mass spectrometry have profoundly transformed proteomics, and today exhaustive site-specific phosphoproteomes are available for a number of bacterial species. Nevertheless, prediction of phosphorylation sites remains the main guide for many researchers, so we discuss the characteristics, limits and advantages of available phosphorylation predictors. GENERAL SIGNIFICANCE The advent of quantitative phosphoproteomics has brought the field on the doorstep of systems biology, but a number of challenges remain before the bacterial phosphorylation networks can be efficiently modeled and their physiological role understood. This article is part of a Special Issue entitled: Systems Biology of Microorganisms.
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Affiliation(s)
- Ahasanul Kobir
- Micalis, AgroParisTech-INRA UMR 1319, Jouy en Josas, France
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Bechet E, Guiral S, Torres S, Mijakovic I, Cozzone AJ, Grangeasse C. Tyrosine-kinases in bacteria: from a matter of controversy to the status of key regulatory enzymes. Amino Acids 2009; 37:499-507. [PMID: 19189200 DOI: 10.1007/s00726-009-0237-8] [Citation(s) in RCA: 37] [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: 10/15/2008] [Accepted: 12/29/2008] [Indexed: 02/05/2023]
Abstract
When considering protein phosphorylation in bacteria, phosphorylation of aspartic acid and histidine residues mediated by the two-component systems is the first to spring to mind. And yet other phosphorylation systems have been described in bacteria in the past 20 years including eukaryotic-like serine/threonine kinases and more recently tyrosine-kinases. Among the latter, a peculiar type is widespread among bacteria, but not in higher organisms. These enzymes possess unique structural features defining thus a new family of enzymes termed Bacterial tyrosine kinases (BY-kinases). BY-kinases have been shown to be mainly involved in polysaccharide production, but their ability to phosphorylate endogenous substrates indicates that they participate in the regulation of other functions of the bacterial cell. Recent advances in mass spectrometry based phosphoproteomics provided lists of many new phosphotyrosine-proteins, indicating that BY-kinases may be involved in regulating a large array of other cellular functions. One may expect that in a near future, tyrosine phosphorylation will turn out to be one of the key regulatory processes in the bacterial cell and will yield new insights into the understanding of its physiology.
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Affiliation(s)
- Emmanuelle Bechet
- Institut de Biologie et Chimie des Protéines, CNRS, Université de Lyon, France
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Petranovic D, Grangeasse C, Macek B, Abdillatef M, Gueguen-Chaignon V, Nessler S, Deutscher J, Mijakovic I. Activation of Bacillus subtilis Ugd by the BY-Kinase PtkA Proceeds via Phosphorylation of Its Residue Tyrosine 70. J Mol Microbiol Biotechnol 2009; 17:83-9. [DOI: 10.1159/000206635] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Olivares-Illana V, Meyer P, Bechet E, Gueguen-Chaignon V, Soulat D, Lazereg-Riquier S, Mijakovic I, Deutscher J, Cozzone AJ, Laprévote O, Morera S, Grangeasse C, Nessler S. Structural basis for the regulation mechanism of the tyrosine kinase CapB from Staphylococcus aureus. PLoS Biol 2008; 6:e143. [PMID: 18547145 PMCID: PMC2422856 DOI: 10.1371/journal.pbio.0060143] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [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: 10/09/2007] [Accepted: 04/28/2008] [Indexed: 12/19/2022] Open
Abstract
Bacteria were thought to be devoid of tyrosine-phosphorylating enzymes. However, several tyrosine kinases without similarity to their eukaryotic counterparts have recently been identified in bacteria. They are involved in many physiological processes, but their accurate functions remain poorly understood due to slow progress in their structural characterization. They have been best characterized as copolymerases involved in the synthesis and export of extracellular polysaccharides. These compounds play critical roles in the virulence of pathogenic bacteria, and bacterial tyrosine kinases can thus be considered as potential therapeutic targets. Here, we present the crystal structures of the phosphorylated and unphosphorylated states of the tyrosine kinase CapB from the human pathogen Staphylococcus aureus together with the activator domain of its cognate transmembrane modulator CapA. This first high-resolution structure of a bacterial tyrosine kinase reveals a 230-kDa ring-shaped octamer that dissociates upon intermolecular autophosphorylation. These observations provide a molecular basis for the regulation mechanism of the bacterial tyrosine kinases and give insights into their copolymerase function. An idiosyncratic new class of bacterial enzymes, bacterial tyrosine-kinases (BY-kinases), has been characterized. These enzymes, which are involved in an increasing number of physiological processes ranging from stress resistance to pathogenicity, share no sequence similarities with eukaryotic kinases, and their function remains largely unknown. They have nevertheless been described to undergo autophosphorylation on a C-terminal tyrosine cluster and to phosphorylate endogenous protein substrates. We describe here the first crystal structure of a bacterial tyrosine kinase, namely CapB from the pathogen Staphylococcus aureus, in complex with the cytoplasmic domain of the transmembrane stimulatory protein CapA. Our data explain the activation mechanism of CapB by CapA and allow us to propose a regulatory mechanism based on intermolecular autophosphorylation. These results also give new insights onto the phosphorylation of the endogenous substrate CapO, an enzyme involved in the synthesis of polysaccharide precursors. CapA and CapB, among others, are involved as copolymerases in the synthesis of extracellular polysaccharides that are thought to be potent virulence factors. Thus, these structural data provide the basis for designing specific inhibitors for these enzymes, which constitute an original and attractive target for the development of new drugs to treat infectious diseases. Structural analysis of a conserved bacterial tyrosine kinase fromStaphylococcus aureus provides the basis for deciphering its regulatory mechanism, leading to a model for its implication in extracellular polysaccharide synthesis.
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Affiliation(s)
| | - Philippe Meyer
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Gif sur Yvette, France
| | - Emmanuelle Bechet
- Institut de Biologie et Chimie des Protéines, CNRS, Université Lyon 1, Université de Lyon, Lyon, France
| | | | - Didier Soulat
- Institut de Biologie et Chimie des Protéines, CNRS, Université Lyon 1, Université de Lyon, Lyon, France
| | | | - Ivan Mijakovic
- Center for Microbial Biotechnology, BioCentrum, Technical University of Denmark, Lyngby, Denmark
| | - Josef Deutscher
- Laboratory of Microbiology and Molecular Genetics, AgroParisTech, CNRS, INRA, Thiverval-Grignon, France
| | - Alain J Cozzone
- Institut de Biologie et Chimie des Protéines, CNRS, Université Lyon 1, Université de Lyon, Lyon, France
| | - Olivier Laprévote
- Institut de Chimie des Substances Naturelles, CNRS, Gif sur Yvette, France
| | - Solange Morera
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Gif sur Yvette, France
| | - Christophe Grangeasse
- Institut de Biologie et Chimie des Protéines, CNRS, Université Lyon 1, Université de Lyon, Lyon, France
- * To whom correspondence should be addressed. E-mail: (CG); (SN)
| | - Sylvie Nessler
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Gif sur Yvette, France
- * To whom correspondence should be addressed. E-mail: (CG); (SN)
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Jadeau F, Bechet E, Cozzone AJ, Deléage G, Grangeasse C, Combet C. Identification of the idiosyncratic bacterial protein tyrosine kinase (BY-kinase) family signature. Bioinformatics 2008; 24:2427-30. [PMID: 18772155 DOI: 10.1093/bioinformatics/btn462] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Most of the protein tyrosine kinases found in bacteria have been recently classified in a new family, termed BY-kinase. Indeed, they share no sequence homology with their eukaryotic counterparts and have no known eukaryotic homologues. They are involved in several biological functions (e.g. capsule biosynthesis, antibiotic resistance, virulence mechanism). Thus, they can be considered interesting therapeutic targets to develop new drugs to treat infectious diseases. However, their identification is rendered difficult due to slow progress in their structural characterization and comes most often from biochemical experiments. Moreover BY-kinase sequences are related to many other bacterial proteins involved in several biological functions (e.g. ParA family proteins). Accordingly, their annotations in generalist databases, sequence analysis and classification remain partial and inhomogeneous and there is no bioinformatics resource dedicated to these proteins. RESULTS The combination of similarity search with sequence-profile alignment, pattern matching and sliding window computation to detect the tyrosine cluster was used to identify BY-kinase sequences in UniProt Knowledgebase. Cross-validations with keywords searches, pattern matching with several patterns and checking of motifs conservation in multiple sequence alignments were performed. Our pipeline identified 640 sequences as BY-kinases and allowed the definition of a PROSITE pattern that is the signature of the BY-kinases. The sequences identified by our pipeline as BY-kinases share a good sequence similarity with BY-kinases that have already been biochemically characterized, and they all bear the characteristic motifs of the catalytic domain, including the three Walker-like motifs followed by a tyrosine cluster. AVAILABILITY http://bykdb.ibcp.fr
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Affiliation(s)
- Fanny Jadeau
- Institut de Biologie et Chimie des Protéines; UMR5086, CNRS, Université Lyon 1, IFR128 BioSciences Lyon-Gerland, 7, passage du Vercors, 69367 Lyon CEDEX 07, France
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Soulat D, Grangeasse C, Vaganay E, Cozzone AJ, Duclos B. UDP-Acetyl-Mannosamine Dehydrogenase Is an Endogenous Protein Substrate of Staphylococcus aureus Protein-Tyrosine Kinase Activity. J Mol Microbiol Biotechnol 2007; 13:45-54. [PMID: 17693712 DOI: 10.1159/000103596] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The in silico analysis of the amino acid sequences deduced from the complete genome sequence of Staphylococcus aureus suggested the presence of two protein tyrosine kinase activities, each split into two distinct polypeptides, respectively Cap5A1/Cap5B1 and Cap5A2/Cap5B2, like in some other Gram-positive bacteria. To check this prediction, the corresponding genes were cloned and overexpressed, and the four corresponding proteins were purified by affinity chromatography and assayed for phosphorylating activity in vitro. Individually, none of them was found to autophosphorylate. However, when Cap5B2 was incubated in the presence of Cap5A2 or, with a larger efficiency, in the presence of Cap5A1, this protein exhibited intensive autokinase activity, occurring selectively at tyrosine residues. On the other hand, whatever the protein combination assayed, Cap5B1 did not present any phosphorylating activity. In search of a possible role for the phosphorylation reaction mediated by Cap5B2, an endogenous substrate of this kinase was characterized. This substrate, termed Cap5O, is the enzyme UDP-acetyl-mannosamine dehydrogenase involved in the cascade of reactions leading to the synthesis of the bacterial capsule. It represents the first endogenous substrate for a tyrosine kinase activity so far identified in S. aureus. The analysis of its dehydrogenase activity showed that it was positively controlled by its phosphorylation at tyrosine.
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Affiliation(s)
- D Soulat
- Institute of Biology and Chemistry of Proteins, University of Lyon/CNRS, Lyon, France
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Soulat D, Jault JM, Geourjon C, Gouet P, Cozzone AJ, Grangeasse C. Tyrosine-kinase Wzc from Escherichia coli possesses an ATPase activity regulated by autophosphorylation. FEMS Microbiol Lett 2007; 274:252-9. [PMID: 17627778 DOI: 10.1111/j.1574-6968.2007.00841.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The catalytic mechanism of bacterial tyrosine-kinases (PTK) is poorly understood. These enzymes possess Walker A and B ATP-binding motifs, which are effectively required for their autophosphorylation whereas these motifs are usually found in ATP-binding proteins but not in eukaryotic protein-kinases. It was previously shown that the PTK Wzc in Escherichia coli undergoes intra- and interphosphorylation. In this work, it is shown that, in addition to its kinase activity, Wzc produces free inorganic phosphate. It is demonstrated that this ATPase activity is increased significantly by intraphosphorylation of Wzc. The fact that intraphosphorylation of Wzc does not affect Wzc affinity for ATP was also demonstrated and it was suggested that it could rather modify the local environment of the ATP molecule in the catalytic site so as to render Wzc more liable to catalyze ATP hydrolysis and interphosphorylation. These results should contribute to better understanding of the catalytic mechanism of this particular class of tyrosine-kinases, which seems, so far, restricted to bacteria.
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Affiliation(s)
- Didier Soulat
- Institute of Microbiology and Immunobiology, University of Vienna, Vienna, Austria
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Grangeasse C, Cozzone AJ, Deutscher J, Mijakovic I. Tyrosine phosphorylation: an emerging regulatory device of bacterial physiology. Trends Biochem Sci 2007; 32:86-94. [PMID: 17208443 DOI: 10.1016/j.tibs.2006.12.004] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2006] [Revised: 11/24/2006] [Accepted: 12/19/2006] [Indexed: 10/23/2022]
Abstract
Tyrosine phosphorylation is a key device in numerous cellular functions in eukaryotes, but in bacteria this protein modification was largely ignored until the mid-1990s. The first conclusive evidence of bacterial tyrosine phosphorylation came only a decade ago. Since then, several tyrosine kinases exhibiting unexpected features have been identified in a variety of bacteria. These enzymes use homologues of Walker motifs of nucleotide-binding proteins for their catalytic mechanism, thus defining an idiosyncratic type of bacterial tyrosine kinases. Recently, bacterial tyrosine kinases have been found to phosphorylate an increasing list of endogenous protein substrates. This discovery contributes to the emerging picture that bacterial tyrosine phosphorylation is an important regulatory arsenal of bacterial physiology in addition to the classical serine/threonine kinases, and the 'two-component' and phosphotransferase systems.
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Affiliation(s)
- Christophe Grangeasse
- Institute of Biology and Chemistry of Proteins, CNRS, University of Lyon, 7 passage du Vercors, 69367 Lyon, France.
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Obadia B, Lacour S, Doublet P, Baubichon-Cortay H, Cozzone AJ, Grangeasse C. Influence of tyrosine-kinase Wzc activity on colanic acid production in Escherichia coli K12 cells. J Mol Biol 2006; 367:42-53. [PMID: 17254603 DOI: 10.1016/j.jmb.2006.12.048] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2006] [Revised: 12/13/2006] [Accepted: 12/18/2006] [Indexed: 11/22/2022]
Abstract
Bacterial tyrosine-kinases have been demonstrated to participate in the regulation of capsule polysaccharides (CPS) and exopolysaccharides (EPS) production and export. However, discrepant data have been reported on the molecular mechanism responsible for this regulation depending on the bacterial species analyzed. Special attention was previously paid to the tyrosine-kinase Wzc(ca) of Escherichia coli K-12, which is involved in the production of the exopolysaccharide, colanic acid, and autophosphorylates by using a cooperative two-step process. In this work, we took advantage of these observations to investigate in further detail the effect of Wzc(ca) phosphorylation on the colanic acid production. First, it is shown that expression of the phosphorylated form of Wzc prevents production of colanic acid whereas expression of the non-phosphorylated form allows biosynthesis of this exopolysaccharide. However, we provide evidence that, in the latter case, the size distribution of the colanic acid polymer is less scattered than in the case of the wild-type strain expressing both phosphorylated and non-phosphorylated forms of Wzc. It is then demonstrated that colanic acid production is not merely regulated by an on/off mechanism and that, instead, both phosphorylated and non-phosphorylated forms of Wzc are required to promote colanic acid synthesis. Moreover, a series of data suggests that besides the involvement of phosphorylated and non-phosphorylated forms of Wzc in the production of colanic acid, two particular regions of this kinase play as such an important role in the synthesis of this exopolysaccharide: a proline-rich domain located in the N-terminal part of Wzc(ca), and a tyrosine cluster present in the C-terminal portion of the enzyme. Furthermore, considering that polysaccharides are known to facilitate bacterial resistance to certain environmental stresses, it is shown that the resistance of E. coli to desiccation is directly connected with the phosphorylation state of Wzc(ca).
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Affiliation(s)
- Brice Obadia
- Institute of Biology and Chemistry of Proteins, University of Lyon, CNRS, 69367 Lyon, France
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Lacour S, Doublet P, Obadia B, Cozzone AJ, Grangeasse C. A novel role for protein-tyrosine kinase Etk from Escherichia coli K-12 related to polymyxin resistance. Res Microbiol 2006; 157:637-41. [PMID: 16814990 DOI: 10.1016/j.resmic.2006.01.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2005] [Revised: 01/23/2006] [Accepted: 01/27/2006] [Indexed: 11/24/2022]
Abstract
The role of protein-tyrosine kinases in bacterial polymyxin resistance was assessed by both genetic and biochemical approaches. Each of the two genes, wzc and etk, encoding protein-tyrosine kinases in Escherichia coli, was knocked out by using the PCR-based method of one-step inactivation of chromosomal genes, and the corresponding mutant strain was assayed in each case for resistance to different concentrations of polymyxin B by measuring the percentage of surviving cells. The resistance of a double knock-out wzc-etk-mutant was also analyzed and complementation experiments were performed by checking the effect of plasmid vectors expressing either Wzc or Etk. Our results concurred in showing that protein-kinase Wzc is not essential for polymyxin resistance, whereas protein-kinase Etk appears to play a key role in such antibiotic resistance. This newly found specific function of Etk reinforces the concept that protein-tyrosine kinases are involved in distinct facets of bacterial physiology.
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Affiliation(s)
- Soline Lacour
- Institute of Biology and Chemistry of Proteins, University of Lyon/CNRS, 7, passage du Vercors 69367 Lyon Cedex 07, France
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