1
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Ukleja M, Kricks L, Torrens G, Peschiera I, Rodrigues-Lopes I, Krupka M, García-Fernández J, Melero R, Del Campo R, Eulalio A, Mateus A, López-Bravo M, Rico AI, Cava F, Lopez D. Flotillin-mediated stabilization of unfolded proteins in bacterial membrane microdomains. Nat Commun 2024; 15:5583. [PMID: 38961085 PMCID: PMC11222466 DOI: 10.1038/s41467-024-49951-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 06/26/2024] [Indexed: 07/05/2024] Open
Abstract
The function of many bacterial processes depends on the formation of functional membrane microdomains (FMMs), which resemble the lipid rafts of eukaryotic cells. However, the mechanism and the biological function of these membrane microdomains remain unclear. Here, we show that FMMs in the pathogen methicillin-resistant Staphylococcus aureus (MRSA) are dedicated to confining and stabilizing proteins unfolded due to cellular stress. The FMM scaffold protein flotillin forms a clamp-shaped oligomer that holds unfolded proteins, stabilizing them and favoring their correct folding. This process does not impose a direct energy cost on the cell and is crucial to survival of ATP-depleted bacteria, and thus to pathogenesis. Consequently, FMM disassembling causes the accumulation of unfolded proteins, which compromise MRSA viability during infection and cause penicillin re-sensitization due to PBP2a unfolding. Thus, our results indicate that FMMs mediate ATP-independent stabilization of unfolded proteins, which is essential for bacterial viability during infection.
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Affiliation(s)
- Marta Ukleja
- Department of Microbiology, National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, 28049, Spain
| | - Lara Kricks
- Department of Microbiology, National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, 28049, Spain
| | - Gabriel Torrens
- Department of Molecular Biology, Umeå University, Umeå, SE-901 87, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS). Umeå Center for Microbial Research (UCMR). Science for Life Laboratory (SciLifeLab), Umeå, SE-901 87, Sweden
| | - Ilaria Peschiera
- Department of Microbiology, National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, 28049, Spain
| | - Ines Rodrigues-Lopes
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504, Coimbra, Portugal
| | - Marcin Krupka
- Department of Microbiology, National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, 28049, Spain
| | - Julia García-Fernández
- Department of Microbiology, National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, 28049, Spain
| | - Roberto Melero
- Department of Structural Biology, National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, 28049, Spain
| | - Rosa Del Campo
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Ramón y Cajal Hospital, 28034, Madrid, Spain
| | - Ana Eulalio
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504, Coimbra, Portugal
- Department of Life Sciences, Center for Bacterial Resistance Biology, Imperial College London, London, SW7 2AZ, United Kingdom
| | - André Mateus
- The Laboratory for Molecular Infection Medicine Sweden (MIMS). Umeå Center for Microbial Research (UCMR). Science for Life Laboratory (SciLifeLab), Umeå, SE-901 87, Sweden
- Department of Chemistry, Umeå University, Umeå, SE-901 87, Sweden
| | - María López-Bravo
- Department of Microbiology, National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, 28049, Spain
| | - Ana I Rico
- Department of Microbiology, National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, 28049, Spain
| | - Felipe Cava
- Department of Molecular Biology, Umeå University, Umeå, SE-901 87, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS). Umeå Center for Microbial Research (UCMR). Science for Life Laboratory (SciLifeLab), Umeå, SE-901 87, Sweden
| | - Daniel Lopez
- Department of Microbiology, National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, 28049, Spain.
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2
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Cordero M, García-Fernández J, Acosta IC, Yepes A, Avendano-Ortiz J, Lisowski C, Oesterreicht B, Ohlsen K, Lopez-Collazo E, Förstner KU, Eulalio A, Lopez D. The induction of natural competence adapts staphylococcal metabolism to infection. Nat Commun 2022; 13:1525. [PMID: 35314690 PMCID: PMC8938553 DOI: 10.1038/s41467-022-29206-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 03/03/2022] [Indexed: 11/26/2022] Open
Abstract
A central question concerning natural competence is why orthologs of competence genes are conserved in non-competent bacterial species, suggesting they have a role other than in transformation. Here we show that competence induction in the human pathogen Staphylococcus aureus occurs in response to ROS and host defenses that compromise bacterial respiration during infection. Bacteria cope with reduced respiration by obtaining energy through fermentation instead. Since fermentation is energetically less efficient than respiration, the energy supply must be assured by increasing the glycolytic flux. The induction of natural competence increases the rate of glycolysis in bacteria that are unable to respire via upregulation of DNA- and glucose-uptake systems. A competent-defective mutant showed no such increase in glycolysis, which negatively affects its survival in both mouse and Galleria infection models. Natural competence foster genetic variability and provides S. aureus with additional nutritional and metabolic possibilities, allowing it to proliferate during infection. Orthologs of natural competence genes are conserved in non-competent bacterial species, suggesting they have a role other than in transformation. Here, the authors show that competence induction in Staphylococcus aureus occurs in response to reactive oxygen species and host defenses that compromise bacterial respiration during infection, leading to increased DNA and glucose uptake and glycolytic flux.
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3
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Liu Q, Li D, Wang N, Guo G, Shi Y, Zou Q, Zhang X. Identification and Application of a Panel of Constitutive Promoters for Gene Overexpression in Staphylococcus aureus. Front Microbiol 2022; 13:818307. [PMID: 35295303 PMCID: PMC8918988 DOI: 10.3389/fmicb.2022.818307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
Staphylococcus aureus is a leading pathogen that is currently the most common cause of infection in hospitalized patients. An in-depth genetic analysis of S. aureus virulence genes contributing to pathogenesis is needed to develop novel antimicrobial therapies. However, tools for genetic manipulation in S. aureus are limited, particularly those for gene expression. Here, 38 highly expressed genes were identified in S. aureus USA300_FPR3757 via RNA-seq. Promoter regions from 30 of these genes were successfully cloned, of which 20 promoters exhibited a wide range of activity. By utilizing these active promoters, 20 S. aureus-Escherichia coli shuttle vectors were constructed and evaluated by expressing an egfp reporter gene. Expression of the egfp gene under the control of different promoters was confirmed and quantified by Western blotting and qPCR, which suggested that the activity of these promoters varied from 18 to 650% of the activity of PsarA, a widely used promoter for gene expression. In addition, our constructed vectors were verified to be highly compatible with gene expression in different S. aureus strains. Furthermore, these vectors were evaluated and used to overexpress two endogenous proteins in S. aureus, namely, catalase and the transcriptional repressor of purine biosynthesis (PurR). Meanwhile, the physiological functions and phenotypes of overexpressed PurR and catalase in S. aureus were validated. Altogether, this evidence indicates that our constructed vectors provide a wide range of promoter activity on gene expression in S. aureus. This set of vectors carrying different constitutive promoters developed here will provide a powerful tool for the direct analysis of target gene function in staphylococcal cells.
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Affiliation(s)
- Qiang Liu
- West China Biopharmaceutical Research Institute, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Qiang Liu,
| | - Daiyu Li
- West China Biopharmaceutical Research Institute, West China Hospital, Sichuan University, Chengdu, China
| | - Ning Wang
- West China Biopharmaceutical Research Institute, West China Hospital, Sichuan University, Chengdu, China
| | - Gang Guo
- West China Biopharmaceutical Research Institute, West China Hospital, Sichuan University, Chengdu, China
| | - Yun Shi
- West China Biopharmaceutical Research Institute, West China Hospital, Sichuan University, Chengdu, China
| | - Quanming Zou
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, China
| | - Xiaokai Zhang
- National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, China
- Xiaokai Zhang,
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4
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Monk IR, Stinear TP. From cloning to mutant in 5 days: rapid allelic exchange in Staphylococcus aureus. Access Microbiol 2021; 3:000193. [PMID: 34151146 PMCID: PMC8209637 DOI: 10.1099/acmi.0.000193] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 12/11/2020] [Indexed: 12/02/2022] Open
Abstract
In the last 10 years, the barriers preventing the uptake of foreign DNA by clinical Staphylococcus aureus isolates have been identified and powerful mutagenesis techniques such as allelic exchange are now possible in most genotypes. However, these targeted approaches can still be cumbersome, and the construction of unmarked deletions/point mutations may take many weeks or months. Here, we introduce a streamlined allelic exchange protocol using IMxxB Escherichia coli and the plasmid pIMAY-Z. With this optimized approach, a site-specific mutation can be introduced into S. aureus in 5 days, from the start of cloning to isolation of genomic DNA for confirmatory whole-genome sequencing. This streamlined protocol considerably reduces the time required to introduce a specific, unmarked mutation in S. aureus and should dramatically improve the scalability of gene-function studies.
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Affiliation(s)
- Ian R. Monk
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
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5
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Ge C, Monk IR, Monard SC, Bedford JG, Braverman J, Stinear TP, Wakim LM. Neutrophils play an ongoing role in preventing bacterial pneumonia by blocking the dissemination of
Staphylococcus aureus
from the upper to the lower airways. Immunol Cell Biol 2020; 98:577-594. [DOI: 10.1111/imcb.12343] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/22/2020] [Accepted: 04/22/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Chenghao Ge
- Department of Microbiology and Immunology The University of Melbourne Peter Doherty Institute for Infection and Immunity Melbourne VIC 3000 Australia
- School of Medicine Tsinghua University Beijing China
| | - Ian R Monk
- Department of Microbiology and Immunology The University of Melbourne Peter Doherty Institute for Infection and Immunity Melbourne VIC 3000 Australia
| | - Sarah C Monard
- Department of Microbiology and Immunology The University of Melbourne Peter Doherty Institute for Infection and Immunity Melbourne VIC 3000 Australia
| | - James G Bedford
- Department of Microbiology and Immunology The University of Melbourne Peter Doherty Institute for Infection and Immunity Melbourne VIC 3000 Australia
| | - Jessica Braverman
- Department of Microbiology and Immunology The University of Melbourne Peter Doherty Institute for Infection and Immunity Melbourne VIC 3000 Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology The University of Melbourne Peter Doherty Institute for Infection and Immunity Melbourne VIC 3000 Australia
| | - Linda M Wakim
- Department of Microbiology and Immunology The University of Melbourne Peter Doherty Institute for Infection and Immunity Melbourne VIC 3000 Australia
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6
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Substrate Interaction with the EssC Coupling Protein of the Type VIIb Secretion System. J Bacteriol 2020; 202:JB.00646-19. [PMID: 31964696 DOI: 10.1128/jb.00646-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 01/08/2020] [Indexed: 01/05/2023] Open
Abstract
Staphylococcus aureus employs the type VIIb secretion system (T7SSb) to secrete effector proteins that either have antibacterial activities or promote bacterial persistence in mouse infection models. Here, we present the crystal structure of the ATPase domain D3 of the EssC coupling protein from S. aureus USA300_FPR3757, an integral component of the T7SSb complex, resolved at a 1.7-Å resolution. EssC-D3 shares structural homology with FtsK/SpoIII-like ATPase domains of T7SSa and T7SSb and exhibits a conserved pocket on the surface with differential amino acid composition. In T7SSa, substrate EsxB interacts with the D3 domain through this pocket. Here, we identify amino acids in this pocket that are essential for effector protein secretion in the T7SSb. Our results reveal that the adjacent ATPase domain D2 is a substrate binding site on EssC and that substrates bound to D2 require domain D3 for further transport. Point mutations in the Walker B motif of domain D3 have diametric effects on secretion activity, either abolishing or boosting it, pointing to a critical role of domain D3 in the substrate transport. Finally, we identify ATPase domain D3 as a virulence determinant of S. aureus USA300_FPR3757 using an invertebrate in vivo infection model.IMPORTANCE The emergence of antibiotic-resistant bacteria poses a rising problem in antibiotic treatment (S. Boyle-Vavra and R. S. Daum, Lab Invest 87:3-9, 2007, https://doi.org/10.1038/labinvest.3700501). We have used the multidrug-resistant S. aureus USA300_FPR3757 as a model organism to study the T7SSb. Effector proteins of this system have been associated with abscess formation and bacterial persistence in mouse models (M. L. Burts, A. C. DeDent, and D. M. Missiakas, Mol Microbiol 69:736-746, 2008, https://doi.org/10.1111/j.1365-2958.2008.06324.x; M. L. Burts, W. A. Williams, K. DeBord, and D. M. Missiakas, Proc Natl Acad Sci U S A 102:1169-1174, 2005, https://doi.org/10.1073/pnas.0405620102). We determined the structure of the essential ATPase domain D3 of the T7SSb at atomic resolution and validated a surface-exposed pocket as a potential drug target to block secretion. Furthermore, our study provides new mechanistic insights into the T7SSb substrate transport.
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7
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Wermser C, Lopez D. Identification of Staphylococcus aureus genes involved in the formation of structured macrocolonies. MICROBIOLOGY-SGM 2018; 164:801-815. [PMID: 29638209 DOI: 10.1099/mic.0.000660] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The human pathogen Staphylococcus aureus causes difficult-to-eradicate biofilm-associated infections that generally become chronic. Understanding the genetic regulation of biofilm formation in S. aureus is central to a precise definition of the conditions and genes involved in development of chronic biofilm-associated infections. Biofilm-related genes have been detected by comparing mutants using the classical submerged biofilm formation assay, in which cells adhere to the bottom of a well containing culture medium. We recently developed an alternative biofilm formation model for S. aureus, based on macrocolony formation on agar plates, comparable to an assay used to study biofilm formation in a few other bacterial species. As organism features are the result of environmental conditions as well as of genes, we used a genome-wide collection of transposon-mapped mutants in this macrocolony assay to seek S. aureus developmental genes and pathways not identified by the classical biofilm formation assay. We identified routes related to glucose and purine metabolism and clarified their regulatory link to macrocolony formation. Our study demonstrates that formation of microbial communities must be correlated to specific growth conditions, and the role of metabolism must be considered in S. aureus biofilm formation and thus, in the development of chronic infections.
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Affiliation(s)
- Charlotte Wermser
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany.,Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Daniel Lopez
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany.,Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany.,National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid 28049, Spain
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8
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Mielich-Süss B, Wagner RM, Mietrach N, Hertlein T, Marincola G, Ohlsen K, Geibel S, Lopez D. Flotillin scaffold activity contributes to type VII secretion system assembly in Staphylococcus aureus. PLoS Pathog 2017; 13:e1006728. [PMID: 29166667 PMCID: PMC5718613 DOI: 10.1371/journal.ppat.1006728] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 12/06/2017] [Accepted: 11/02/2017] [Indexed: 12/13/2022] Open
Abstract
Scaffold proteins are ubiquitous chaperones that promote efficient interactions between partners of multi-enzymatic protein complexes; although they are well studied in eukaryotes, their role in prokaryotic systems is poorly understood. Bacterial membranes have functional membrane microdomains (FMM), a structure homologous to eukaryotic lipid rafts. Similar to their eukaryotic counterparts, bacterial FMM harbor a scaffold protein termed flotillin that is thought to promote interactions between proteins spatially confined to the FMM. Here we used biochemical approaches to define the scaffold activity of the flotillin homolog FloA of the human pathogen Staphylococcus aureus, using assembly of interacting protein partners of the type VII secretion system (T7SS) as a case study. Staphylococcus aureus cells that lacked FloA showed reduced T7SS function, and thus reduced secretion of T7SS-related effectors, probably due to the supporting scaffold activity of flotillin. We found that the presence of flotillin mediates intermolecular interactions of T7SS proteins. We tested several small molecules that interfere with flotillin scaffold activity, which perturbed T7SS activity in vitro and in vivo. Our results suggest that flotillin assists in the assembly of S. aureus membrane components that participate in infection and influences the infective potential of this pathogen. The recently discovered functional membrane microdomains (FMM) of prokaryotic cells contain a protein homologous to the scaffold protein flotillin found in eukaryotic lipid rafts. It remains to be elucidated whether, like their eukaryotic counterparts, flotillin homolog proteins have a scaffold function in bacteria. Here we show that the Staphylococcus aureus flotillin FloA acts as a scaffold protein, to promote more efficient assembly of membrane-associated protein interacting partners of multi-enzyme complexes. In a case study, we provide biochemical evidence that FloA participates in assembly of the Type VII secretion system and thus contributes to S. aureus infective potential. Targeted dispersion of FMM-related processes using anti-FMM molecules opens up new perspectives for microbial therapies to treat persistent S. aureus infections.
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Affiliation(s)
- Benjamin Mielich-Süss
- Research Center for Infectious Diseases ZINF, University of Würzburg, Würzburg, Germany
- Institute for Molecular Infection Biology IMIB, University of Würzburg, Würzburg, Germany
| | - Rabea M. Wagner
- Research Center for Infectious Diseases ZINF, University of Würzburg, Würzburg, Germany
- Institute for Molecular Infection Biology IMIB, University of Würzburg, Würzburg, Germany
- National Center for Biotechnology, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Nicole Mietrach
- Research Center for Infectious Diseases ZINF, University of Würzburg, Würzburg, Germany
- Institute for Molecular Infection Biology IMIB, University of Würzburg, Würzburg, Germany
- Rudolf Virchow Center - DFG Research Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Tobias Hertlein
- Institute for Molecular Infection Biology IMIB, University of Würzburg, Würzburg, Germany
| | - Gabriella Marincola
- Research Center for Infectious Diseases ZINF, University of Würzburg, Würzburg, Germany
- Institute for Molecular Infection Biology IMIB, University of Würzburg, Würzburg, Germany
| | - Knut Ohlsen
- Institute for Molecular Infection Biology IMIB, University of Würzburg, Würzburg, Germany
| | - Sebastian Geibel
- Research Center for Infectious Diseases ZINF, University of Würzburg, Würzburg, Germany
- Institute for Molecular Infection Biology IMIB, University of Würzburg, Würzburg, Germany
- Rudolf Virchow Center - DFG Research Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Daniel Lopez
- Research Center for Infectious Diseases ZINF, University of Würzburg, Würzburg, Germany
- Institute for Molecular Infection Biology IMIB, University of Würzburg, Würzburg, Germany
- National Center for Biotechnology, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
- * E-mail:
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9
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García-Fernández E, Koch G, Wagner RM, Fekete A, Stengel ST, Schneider J, Mielich-Süss B, Geibel S, Markert SM, Stigloher C, Lopez D. Membrane Microdomain Disassembly Inhibits MRSA Antibiotic Resistance. Cell 2017; 171:1354-1367.e20. [PMID: 29103614 PMCID: PMC5720476 DOI: 10.1016/j.cell.2017.10.012] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 09/18/2017] [Accepted: 10/06/2017] [Indexed: 12/21/2022]
Abstract
A number of bacterial cell processes are confined functional membrane microdomains (FMMs), structurally and functionally similar to lipid rafts of eukaryotic cells. How bacteria organize these intricate platforms and what their biological significance is remain important questions. Using the pathogen methicillin-resistant Staphylococcus aureus (MRSA), we show here that membrane-carotenoid interaction with the scaffold protein flotillin leads to FMM formation, which can be visualized using super-resolution array tomography. These membrane platforms accumulate multimeric protein complexes, for which flotillin facilitates efficient oligomerization. One of these proteins is PBP2a, responsible for penicillin resistance in MRSA. Flotillin mutants are defective in PBP2a oligomerization. Perturbation of FMM assembly using available drugs interferes with PBP2a oligomerization and disables MRSA penicillin resistance in vitro and in vivo, resulting in MRSA infections that are susceptible to penicillin treatment. Our study demonstrates that bacteria possess sophisticated cell organization programs and defines alternative therapies to fight multidrug-resistant pathogens using conventional antibiotics. Staphyloxanthin and flotillin preferentially interact and accumulate in FMMs FMMs facilitate efficient oligomerization of multimeric protein complexes PBP2a, which confers β-lactam resistance on S. aureus, is harbored within FMMs FMM disruption disables PBP2a oligomerization and thus, S. aureus antibiotic resistance
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Affiliation(s)
- Esther García-Fernández
- National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), 28049 Madrid, Spain
| | - Gudrun Koch
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, 97080 Würzburg, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, Germany
| | - Rabea M Wagner
- National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), 28049 Madrid, Spain; Research Centre for Infectious Diseases (ZINF), University of Würzburg, 97080 Würzburg, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, Germany
| | - Agnes Fekete
- Julius-von-Sachs-Institute Biocenter, Pharmaceutical Biology, University of Würzburg, 97082 Würzburg, Germany
| | - Stephanie T Stengel
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, 97080 Würzburg, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, Germany
| | - Johannes Schneider
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, 97080 Würzburg, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, Germany
| | - Benjamin Mielich-Süss
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, 97080 Würzburg, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, Germany
| | - Sebastian Geibel
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, 97080 Würzburg, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, Germany
| | - Sebastian M Markert
- Division of Electron Microscopy, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Christian Stigloher
- Division of Electron Microscopy, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Daniel Lopez
- National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), 28049 Madrid, Spain; Research Centre for Infectious Diseases (ZINF), University of Würzburg, 97080 Würzburg, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, Germany; National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Darwin 3, Campus de Cantoblanco, 28049 Madrid, Spain.
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10
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García-Betancur JC, Goñi-Moreno A, Horger T, Schott M, Sharan M, Eikmeier J, Wohlmuth B, Zernecke A, Ohlsen K, Kuttler C, Lopez D. Cell differentiation defines acute and chronic infection cell types in Staphylococcus aureus. eLife 2017; 6. [PMID: 28893374 PMCID: PMC5595439 DOI: 10.7554/elife.28023] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 08/09/2017] [Indexed: 12/13/2022] Open
Abstract
A central question to biology is how pathogenic bacteria initiate acute or chronic infections. Here we describe a genetic program for cell-fate decision in the opportunistic human pathogen Staphylococcus aureus, which generates the phenotypic bifurcation of the cells into two genetically identical but different cell types during the course of an infection. Whereas one cell type promotes the formation of biofilms that contribute to chronic infections, the second type is planktonic and produces the toxins that contribute to acute bacteremia. We identified a bimodal switch in the agr quorum sensing system that antagonistically regulates the differentiation of these two physiologically distinct cell types. We found that extracellular signals affect the behavior of the agr bimodal switch and modify the size of the specialized subpopulations in specific colonization niches. For instance, magnesium-enriched colonization niches causes magnesium binding to S. aureusteichoic acids and increases bacterial cell wall rigidity. This signal triggers a genetic program that ultimately downregulates the agr bimodal switch. Colonization niches with different magnesium concentrations influence the bimodal system activity, which defines a distinct ratio between these subpopulations; this in turn leads to distinct infection outcomes in vitro and in an in vivo murine infection model. Cell differentiation generates physiological heterogeneity in clonal bacterial infections and helps to determine the distinct infection types. While in hospital, patients can be unwittingly exposed to bacteria that can cause disease. These hospital-associated bacteria can lead to potentially life-threatening infections that may also complicate the treatment of the patients’ existing medical conditions. Staphylococcus aureus is one such bacterium, and it can cause several types of infection including pneumonia, blood infections and long-term infections of prosthetic devices. It is thought that S. aureus is able to cause so many different types of infection because it is capable of colonizing distinct tissues and organs in various parts of the body. Understanding the biological processes that drive the different infections is crucial to improving how these infections are treated. S. aureus lives either as an independent, free-swimming cell or as part of a community known as a biofilm. These different lifestyles dictate the type of infection the bacterium can cause, with free-swimming cells producing toxins that contribute to intense, usually short-lived, infections and biofilms promoting longer-term infections that are difficult to eradicate. However, it is not clear how a population of S. aureus cells chooses to adopt a particular lifestyle and whether there are any environmental signals that influence this decision. Here, Garcia-Betancur et al. found that S. aureus populations contain small groups of cells that have already specialized into a particular lifestyle. These groups of cells collectively influence the choice made by other cells in the population. While both lifestyles will be represented in the population, environmental factors influence the numbers of cells that initially adopt each type of lifestyle, which ultimately affects the choice made by the rest of the population. For example, if the bacteria colonize a tissue or organ that contains high levels of magnesium ions, the population is more likely to form biofilms. In the future, the findings of Garcia-Betancur et al. may help us to predict how an infection may develop in a particular patient, which may help to diagnose the infection more quickly and allow it to be treated more effectively.
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Affiliation(s)
- Juan-Carlos García-Betancur
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany.,Research Center for Infectious Diseases, University of Würzburg, Würzburg, Germany
| | - Angel Goñi-Moreno
- School of Computing Science, Newcastle University, Newcastle, United Kingdom
| | - Thomas Horger
- Department of Mathematics, Technical University of Munich, Garching, Germany
| | - Melanie Schott
- Institute of Clinical Biochemistry and Pathobiochemistry, University Hospital Würzburg, Würzburg, Germany
| | - Malvika Sharan
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Julian Eikmeier
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany.,Research Center for Infectious Diseases, University of Würzburg, Würzburg, Germany
| | - Barbara Wohlmuth
- Department of Mathematics, Technical University of Munich, Garching, Germany
| | - Alma Zernecke
- Institute of Clinical Biochemistry and Pathobiochemistry, University Hospital Würzburg, Würzburg, Germany
| | - Knut Ohlsen
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Christina Kuttler
- Department of Mathematics, Technical University of Munich, Garching, Germany
| | - Daniel Lopez
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany.,Research Center for Infectious Diseases, University of Würzburg, Würzburg, Germany.,National Center for Biotechnology, Madrid, Spain
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11
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Koch G, Wermser C, Acosta IC, Kricks L, Stengel ST, Yepes A, Lopez D. Attenuating Staphylococcus aureus Virulence by Targeting Flotillin Protein Scaffold Activity. Cell Chem Biol 2017; 24:845-857.e6. [PMID: 28669526 DOI: 10.1016/j.chembiol.2017.05.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 04/11/2017] [Accepted: 05/30/2017] [Indexed: 01/13/2023]
Abstract
Scaffold proteins are ubiquitous chaperones that bind proteins and facilitate physical interaction of multi-enzyme complexes. Here we used a biochemical approach to dissect the scaffold activity of the flotillin-homolog protein FloA of the multi-drug-resistant human pathogen Staphylococcus aureus. We show that FloA promotes oligomerization of membrane protein complexes, such as the membrane-associated RNase Rny, which forms part of the RNA-degradation machinery called the degradosome. Cells lacking FloA had reduced Rny function and a consequent increase in the targeted sRNA transcripts that negatively regulate S. aureus toxin expression. Small molecules that altered FloA oligomerization also reduced Rny function and decreased the virulence potential of S. aureus in vitro, as well as in vivo, using invertebrate and murine infection models. Our results suggest that flotillin assists in the assembly of protein complexes involved in S. aureus virulence, and could thus be an attractive target for the development of new antimicrobial therapies.
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Affiliation(s)
- Gudrun Koch
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Charlotte Wermser
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Ivan C Acosta
- National Centre for Biotechnology (CNB), Spanish Research Council (CSIC), Darwin 3, Madrid 28049, Spain
| | - Lara Kricks
- National Centre for Biotechnology (CNB), Spanish Research Council (CSIC), Darwin 3, Madrid 28049, Spain
| | - Stephanie T Stengel
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Ana Yepes
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Daniel Lopez
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany; National Centre for Biotechnology (CNB), Spanish Research Council (CSIC), Darwin 3, Madrid 28049, Spain.
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12
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Abstract
A mechanistic understanding of the determination and maintenance of the simplest bacterial cell shape, a sphere, remains elusive compared with that of more complex shapes. Cocci seem to lack a dedicated elongation machinery, and a spherical shape has been considered an evolutionary dead-end morphology, as a transition from a spherical to a rod-like shape has never been observed in bacteria. Here we show that a Staphylococcus aureus mutant (M5) expressing the ftsZG193D allele exhibits elongated cells. Molecular dynamics simulations and in vitro studies indicate that FtsZG193D filaments are more twisted and shorter than wild-type filaments. In vivo, M5 cell wall deposition is initiated asymmetrically, only on one side of the cell, and progresses into a helical pattern rather than into a constricting ring as in wild-type cells. This helical pattern of wall insertion leads to elongation, as in rod-shaped cells. Thus, structural flexibility of FtsZ filaments can result in an FtsZ-dependent mechanism for generating elongated cells from cocci. The mechanisms by which bacteria generate and maintain even the simplest cell shape remain an elusive but fundamental question in microbiology. In the absence of examples of coccus-to-rod transitions, the spherical shape has been suggested to be an evolutionary dead end in morphogenesis. We describe the first observation of the generation of elongated cells from truly spherical cocci, occurring in a Staphylococcus aureus mutant containing a single point mutation in its genome, in the gene encoding the bacterial tubulin homologue FtsZ. We demonstrate that FtsZ-dependent cell elongation is possible, even in the absence of dedicated elongation machinery.
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13
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Abstract
Nearly all bacteria contain a peptidoglycan cell wall. The peptidoglycan precursor molecule is LipidII, containing the basic peptidoglycan building block attached to a lipid. Although the suitability of LipidII as an antibacterial target has long been recognized, progress on elucidating the role(s) of LipidII in bacterial cell biology has been slow. The focus of this review is on exciting new developments, both with respect to antibacterials targeting LipidII as well as the emerging role of LipidII in organizing the membrane and cell wall synthesis. It appears that on both sides of the membrane, LipidII plays crucial roles in organizing cytoskeletal proteins and peptidoglycan synthesis machineries. Finally, the recent discovery of no less than three different categories of LipidII flippases will be discussed.
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Affiliation(s)
- Dirk-Jan Scheffers
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
- * E-mail:
| | - Menno B. Tol
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
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14
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Schneider J, Mielich-Süss B, Böhme R, Lopez D. In vivo characterization of the scaffold activity of flotillin on the membrane kinase KinC of Bacillus subtilis. MICROBIOLOGY-SGM 2015; 161:1871-1887. [PMID: 26297017 DOI: 10.1099/mic.0.000137] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Scaffold proteins are ubiquitous chaperones that bind to proteins and facilitate the physical interaction of the components of signal transduction pathways or multi-enzymic complexes. In this study, we used a biochemical approach to dissect the molecular mechanism of a membrane-associated scaffold protein, FloT, a flotillin-homologue protein that is localized in functional membrane microdomains of the bacterium Bacillus subtilis. This study provides unambiguous evidence that FloT physically binds to and interacts with the membrane-bound sensor kinase KinC. This sensor kinase activates biofilm formation in B. subtilis in response to the presence of the self-produced signal surfactin. Furthermore, we have characterized the mechanism by which the interaction of FloT with KinC benefits the activity of KinC. Two separate and synergistic effects constitute this mechanism: first, the scaffold activity of FloT promotes more efficient self-interaction of KinC and facilitates dimerization into its active form. Second, the selective binding of FloT to KinC prevents the occurrence of unspecific aggregation between KinC and other proteins that may generate dead-end intermediates that could titrate the activity of KinC. Flotillin proteins appear to play an important role in prokaryotes in promoting effective binding of signalling proteins with their correct protein partners.
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Affiliation(s)
- Johannes Schneider
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Benjamin Mielich-Süss
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Richard Böhme
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Daniel Lopez
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
- National Center for Biotechnology (CNB), Spanish Research Council (CSIC), Madrid 28050, Spain
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany
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15
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Mashruwala AA, Pang YY, Rosario-Cruz Z, Chahal HK, Benson MA, Anzaldi-Mike LL, Skaar EP, Torres VJ, Nauseef WM, Boyd JM. Nfu facilitates the maturation of iron-sulfur proteins and participates in virulence in Staphylococcus aureus. Mol Microbiol 2015; 95:383-409. [PMID: 25388433 PMCID: PMC4428306 DOI: 10.1111/mmi.12860] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2014] [Indexed: 01/21/2023]
Abstract
The acquisition and metabolism of iron (Fe) by the human pathogen Staphylococcus aureus is critical for disease progression. S. aureus requires Fe to synthesize inorganic cofactors called iron-sulfur (Fe-S) clusters, which are required for functional Fe-S proteins. In this study we investigated the mechanisms utilized by S. aureus to metabolize Fe-S clusters. We identified that S. aureus utilizes the Suf biosynthetic system to synthesize Fe-S clusters and we provide genetic evidence suggesting that the sufU and sufB gene products are essential. Additional biochemical and genetic analyses identified Nfu as an Fe-S cluster carrier, which aids in the maturation of Fe-S proteins. We find that deletion of the nfu gene negatively impacts staphylococcal physiology and pathogenicity. A nfu mutant accumulates both increased intracellular non-incorporated Fe and endogenous reactive oxygen species (ROS) resulting in DNA damage. In addition, a strain lacking Nfu is sensitive to exogenously supplied ROS and reactive nitrogen species. Congruous with ex vivo findings, a nfu mutant strain is more susceptible to oxidative killing by human polymorphonuclear leukocytes and displays decreased tissue colonization in a murine model of infection. We conclude that Nfu is necessary for staphylococcal pathogenesis and establish Fe-S cluster metabolism as an attractive antimicrobial target.
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Affiliation(s)
- Ameya A. Mashruwala
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901
| | - Yun Y. Pang
- Inflammation Program and Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, and Veterans Administration Medical Center, Iowa City, IA 52240
| | - Zuelay Rosario-Cruz
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901
| | - Harsimranjit K. Chahal
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901
| | - Meredith A. Benson
- Department of Microbiology, NYU Langone Medical Center, New York, NY 10016
| | - Laura L. Anzaldi-Mike
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Eric P. Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Victor J. Torres
- Department of Microbiology, NYU Langone Medical Center, New York, NY 10016
| | - William M. Nauseef
- Inflammation Program and Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, and Veterans Administration Medical Center, Iowa City, IA 52240
| | - Jeffrey M. Boyd
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901
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