1
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Vento JM, Durmusoglu D, Li T, Patinios C, Sullivan S, Ttofali F, van Schaik J, Yu Y, Wang Y, Barquist L, Crook N, Beisel CL. A cell-free transcription-translation pipeline for recreating methylation patterns boosts DNA transformation in bacteria. Mol Cell 2024; 84:2785-2796.e4. [PMID: 38936361 DOI: 10.1016/j.molcel.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 04/10/2024] [Accepted: 06/04/2024] [Indexed: 06/29/2024]
Abstract
The bacterial world offers diverse strains for understanding medical and environmental processes and for engineering synthetic biological chassis. However, genetically manipulating these strains has faced a long-standing bottleneck: how to efficiently transform DNA. Here, we report imitating methylation patterns rapidly in TXTL (IMPRINT), a generalized, rapid, and scalable approach based on cell-free transcription-translation (TXTL) to overcome DNA restriction, a prominent barrier to transformation. IMPRINT utilizes TXTL to express DNA methyltransferases from a bacterium's restriction-modification systems. The expressed methyltransferases then methylate DNA in vitro to match the bacterium's DNA methylation pattern, circumventing restriction and enhancing transformation. With IMPRINT, we efficiently multiplex methylation by diverse DNA methyltransferases and enhance plasmid transformation in gram-negative and gram-positive bacteria. We also develop a high-throughput pipeline that identifies the most consequential methyltransferases, and we apply IMPRINT to screen a ribosome-binding site library in a hard-to-transform Bifidobacterium. Overall, IMPRINT can enhance DNA transformation, enabling the use of sophisticated genetic manipulation tools across the bacterial world.
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Affiliation(s)
- Justin M Vento
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Deniz Durmusoglu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Tianyu Li
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Constantinos Patinios
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Sean Sullivan
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Fani Ttofali
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - John van Schaik
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Yanying Yu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Yanyan Wang
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany; Medical Faculty, University of Würzburg, 97080 Würzburg, Germany; Department of Biology, University of Toronto, Mississauga, ON L5L 1C6, Canada
| | - Nathan Crook
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Chase L Beisel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany; Medical Faculty, University of Würzburg, 97080 Würzburg, Germany.
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2
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Won C, Yim SS. Emerging methylation-based approaches in microbiome engineering. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:96. [PMID: 38987811 PMCID: PMC11238421 DOI: 10.1186/s13068-024-02529-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 06/10/2024] [Indexed: 07/12/2024]
Abstract
Bacterial epigenetics, particularly through DNA methylation, exerts significant influence over various biological processes such as DNA replication, uptake, and gene regulation in bacteria. In this review, we explore recent advances in characterizing bacterial epigenomes, accompanied by emerging strategies that harness bacterial epigenetics to elucidate and engineer diverse bacterial species with precision and effectiveness. Furthermore, we delve into the potential of epigenetic modifications to steer microbial functions and influence community dynamics, offering promising opportunities for understanding and modulating microbiomes. Additionally, we investigate the extensive diversity of DNA methyltransferases and emphasize their potential utility in the context of the human microbiome. In summary, this review highlights the potential of DNA methylation as a powerful toolkit for engineering microbiomes.
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Affiliation(s)
- Changhee Won
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Sung Sun Yim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.
- Graduate School of Engineering Biology, KAIST, Daejeon, Republic of Korea.
- KAIST Institute for BioCentury, KAIST, Daejeon, Republic of Korea.
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.
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3
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Paul S, Todd OA, Eichelberger KR, Tkaczyk C, Sellman BR, Noverr MC, Cassat JE, Fidel PL, Peters BM. A fungal metabolic regulator underlies infectious synergism during Candida albicans-Staphylococcus aureus intra-abdominal co-infection. Nat Commun 2024; 15:5746. [PMID: 38982056 PMCID: PMC11233573 DOI: 10.1038/s41467-024-50058-w] [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: 02/16/2024] [Accepted: 06/26/2024] [Indexed: 07/11/2024] Open
Abstract
Candida albicans and Staphylococcus aureus are two commonly associated pathogens that cause nosocomial infections with high morbidity and mortality. Our prior and current work using a murine model of polymicrobial intra-abdominal infection (IAI) demonstrates that synergistic lethality is driven by Candida-induced upregulation of functional S. aureus α-toxin leading to polymicrobial sepsis and organ damage. In order to determine the candidal effector(s) mediating enhanced virulence, an unbiased screen of C. albicans transcription factor mutants was undertaken revealing that zcf13Δ/Δ fails to drive augmented α-toxin or lethal synergism during co-infection. A combination of transcriptional and phenotypic profiling approaches shows that ZCF13 regulates genes involved in pentose metabolism, including RBK1 and HGT7 that contribute to fungal ribose catabolism and uptake, respectively. Subsequent experiments reveal that ribose inhibits the staphylococcal agr quorum sensing system and concomitantly represses toxicity. Unlike wild-type C. albicans, zcf13Δ/Δ did not effectively utilize ribose during co-culture or co-infection leading to exogenous ribose accumulation and agr repression. Forced expression of RBK1 and HGT7 in the zcf13Δ/Δ mutant fully restores pathogenicity during co-infection. Collectively, our results detail the interwoven complexities of cross-kingdom interactions and highlight how intermicrobial metabolism impacts polymicrobial disease pathogenesis with devastating consequences for the host.
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Affiliation(s)
- Saikat Paul
- Department of Clinical Pharmacy and Translational Science, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Olivia A Todd
- Integrated Program in Biomedical Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Kara R Eichelberger
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christine Tkaczyk
- Early Vaccines and Immune Therapies, AstraZeneca, Gaithersburg, MD, USA
| | - Bret R Sellman
- Early Vaccines and Immune Therapies, AstraZeneca, Gaithersburg, MD, USA
| | - Mairi C Noverr
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA, USA
| | - James E Cassat
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation (VI4), Vanderbilt University Medical Center, Nashville, TN, USA
| | - Paul L Fidel
- Department of Oral and Craniofacial Biology, Louisiana State University Health - School of Dentistry, New Orleans, LA, USA
| | - Brian M Peters
- Department of Clinical Pharmacy and Translational Science, University of Tennessee Health Science Center, Memphis, TN, USA.
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA.
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4
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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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5
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Alves J, Dry I, White JH, Dryden DTF, Lynskey NN. Generation of tools for expression and purification of the phage-encoded Type I restriction enzyme inhibitor, Ocr. MICROBIOLOGY (READING, ENGLAND) 2024; 170. [PMID: 39042422 DOI: 10.1099/mic.0.001465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
DNA manipulation is an essential tool in molecular microbiology research that is dependent on the ability of bacteria to take up and preserve foreign DNA by horizontal gene transfer. This process can be significantly impaired by the activity of bacterial restriction modification systems; bacterial operons comprising paired enzymatic activities that protectively methylate host DNA, while cleaving incoming unmodified foreign DNA. Ocr is a phage-encoded protein that inhibits Type I restriction modification systems, the addition of which significantly improves bacterial transformation efficiency. We recently established an improved and highly efficient transformation protocol for the important human pathogen group A Streptococcus using commercially available recombinant Ocr protein, manufacture of which has since been discontinued. In order to ensure the continued availability of Ocr protein within the research community, we have generated tools and methods for in-house Ocr production and validated the activity of the purified recombinant protein.
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Affiliation(s)
- Joana Alves
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Scotland, EH25 9RG, UK
| | - Inga Dry
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Scotland, EH25 9RG, UK
| | - John H White
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, Edinburgh, EH9 3FJ, UK
| | - David T F Dryden
- Department of Biosciences, University of Durham, South Road, DH1 3LE, UK
| | - Nicola N Lynskey
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Scotland, EH25 9RG, UK
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6
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Schürmann J, Fischer MA, Herzberg M, Reemtsma T, Strommenger B, Werner G, Schuster CF, Layer-Nicolaou F. The genes mgtE and spoVG are involved in zinc tolerance of Staphylococcus aureus. Appl Environ Microbiol 2024; 90:e0045324. [PMID: 38752746 PMCID: PMC11218649 DOI: 10.1128/aem.00453-24] [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: 03/15/2024] [Accepted: 04/16/2024] [Indexed: 06/19/2024] Open
Abstract
Metals are essential for all living organisms, but the type of metal and its concentration determines its action. Even low concentrations of metals may have toxic effects on organisms and therefore exhibit antimicrobial activities. In this study, we investigate the evolutionary adaptation processes of Staphylococcus aureus to metals and common genes for metal tolerance. Laboratory and clinical isolates were treated with manganese, cobalt, zinc, or nickel metal salts to generate growth-adapted mutants. After growth in medium supplemented with zinc, whole-genome sequencing identified, among others, two genes, mgtE (SAUSA300_0910), a putative magnesium transporter and spoVG (SAUSA300_0475), a global transcriptional regulator, as hot spots for stress-induced single-nucleotide polymorphisms (SNPs). SNPs in mgtE were also detected in mutants treated with high levels of cobalt or nickel salts. To investigate the effect of these genes on metal tolerance, deletion mutants and complementation strains in an S. aureus USA300 LAC* laboratory strain were generated. Both, the mgtE and spoVG deletion strains were more tolerant to cobalt, manganese, and zinc. The mgtE mutant was also more tolerant to nickel exposure. Inductively coupled plasma mass spectrometry analysis demonstrated that the mgtE deletion mutant accumulated less intracellular zinc than the wild type, explaining increased tolerance. From these results, we conclude that mgtE gene inactivation increases zinc tolerance presumably due to reduced uptake of zinc. For the SpoVG mutant, no direct effect on the intracellular zinc concentration was detected, indicating toward different pathways to increase tolerance. Importantly, inactivation of these genes offers a growth advantage in environments containing certain metals, pointing toward a common tolerance mechanism. IMPORTANCE Staphylococcus aureus is an opportunistic pathogen causing tremendous public health burden and high mortality in invasive infections. Treatment is becoming increasingly difficult due to antimicrobial resistances. The use of metals in animal husbandry and aquaculture to reduce bacterial growth and subsequent acquisition of metal resistances has been shown to co-select for antimicrobial resistance. Therefore, understanding adaptive mechanisms that help S. aureus to survive metal exposure is essential. Using a screening approach, we were able to identify two genes encoding the transporter MgtE and the transcriptional regulator SpoVG, which conferred increased tolerance to specific metals such as zinc when inactivated. Further testing showed that the deletion of mgtE leads to reduced intracellular zinc levels, suggesting a role in zinc uptake. The accumulation of mutations in these genes when exposed to other metals suggests that inactivation of these genes could be a common mechanism for intrinsic tolerance to certain metals.
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Affiliation(s)
- Jacqueline Schürmann
- Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany
| | - Martin A. Fischer
- Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany
| | - Martin Herzberg
- Department Environmental Analytical Chemistry, Helmholtz-Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Thorsten Reemtsma
- Department Environmental Analytical Chemistry, Helmholtz-Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Birgit Strommenger
- Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany
| | - Guido Werner
- Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany
| | - Christopher F. Schuster
- Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany
| | - Franziska Layer-Nicolaou
- Department of Infectious Diseases, Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany
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7
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Barrault M, Chabelskaya S, Coronel-Tellez RH, Toffano-Nioche C, Jacquet E, Bouloc P. Staphylococcal aconitase expression during iron deficiency is controlled by an sRNA-driven feedforward loop and moonlighting activity. Nucleic Acids Res 2024:gkae506. [PMID: 38869061 DOI: 10.1093/nar/gkae506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/28/2024] [Accepted: 05/31/2024] [Indexed: 06/14/2024] Open
Abstract
Pathogenic bacteria employ complex systems to cope with metal ion shortage conditions and propagate in the host. IsrR is a regulatory RNA (sRNA) whose activity is decisive for optimum Staphylococcus aureus fitness upon iron starvation and for full virulence. IsrR down-regulates several genes encoding iron-containing enzymes to spare iron for essential processes. Here, we report that IsrR regulates the tricarboxylic acid (TCA) cycle by controlling aconitase (CitB), an iron-sulfur cluster-containing enzyme, and its transcriptional regulator, CcpE. This IsrR-dependent dual-regulatory mechanism provides an RNA-driven feedforward loop, underscoring the tight control required to prevent aconitase expression. Beyond its canonical enzymatic role, aconitase becomes an RNA-binding protein with regulatory activity in iron-deprived conditions, a feature that is conserved in S. aureus. Aconitase not only negatively regulates its own expression, but also impacts the enzymes involved in both its substrate supply and product utilization. This moonlighting activity concurrently upregulates pyruvate carboxylase expression, allowing it to compensate for the TCA cycle deficiency associated with iron scarcity. These results highlight the cascade of complex posttranscriptional regulations controlling S. aureus central metabolism in response to iron deficiency.
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Affiliation(s)
- Maxime Barrault
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Svetlana Chabelskaya
- Université de Rennes 1, BRM (Bacterial regulatory RNAs and Medicine) UMR_S 1230, 35000 Rennes, France
| | - Rodrigo H Coronel-Tellez
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Claire Toffano-Nioche
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Eric Jacquet
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR2301, 91198 Gif-sur-Yvette, France
| | - Philippe Bouloc
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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8
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Kengmo Tchoupa A, Elsherbini AMA, Camus J, Fu X, Hu X, Ghaneme O, Seibert L, Lebtig M, Böcker MA, Horlbeck A, Lambidis SP, Schittek B, Kretschmer D, Lämmerhofer M, Peschel A. Lipase-mediated detoxification of host-derived antimicrobial fatty acids by Staphylococcus aureus. Commun Biol 2024; 7:572. [PMID: 38750133 PMCID: PMC11096360 DOI: 10.1038/s42003-024-06278-3] [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: 10/30/2023] [Accepted: 05/02/2024] [Indexed: 05/18/2024] Open
Abstract
Long-chain fatty acids with antimicrobial properties are abundant on the skin and mucosal surfaces, where they are essential to restrict the proliferation of opportunistic pathogens such as Staphylococcus aureus. These antimicrobial fatty acids (AFAs) elicit bacterial adaptation strategies, which have yet to be fully elucidated. Characterizing the pervasive mechanisms used by S. aureus to resist AFAs could open new avenues to prevent pathogen colonization. Here, we identify the S. aureus lipase Lip2 as a novel resistance factor against AFAs. Lip2 detoxifies AFAs via esterification with cholesterol. This is reminiscent of the activity of the fatty acid-modifying enzyme (FAME), whose identity has remained elusive for over three decades. In vitro, Lip2-dependent AFA-detoxification was apparent during planktonic growth and biofilm formation. Our genomic analysis revealed that prophage-mediated inactivation of Lip2 was rare in blood, nose, and skin strains, suggesting a particularly important role of Lip2 for host - microbe interactions. In a mouse model of S. aureus skin colonization, bacteria were protected from sapienic acid (a human-specific AFA) in a cholesterol- and lipase-dependent manner. These results suggest Lip2 is the long-sought FAME that exquisitely manipulates environmental lipids to promote bacterial growth in otherwise inhospitable niches.
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Affiliation(s)
- Arnaud Kengmo Tchoupa
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology Section, University of Tübingen, Tübingen, Germany.
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany.
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany.
| | - Ahmed M A Elsherbini
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology Section, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Justine Camus
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology Section, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Xiaoqing Fu
- Institute of Pharmaceutical Sciences, University of Tübingen, Tübingen, Germany
| | - Xuanheng Hu
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology Section, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Oumayma Ghaneme
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology Section, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Lea Seibert
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology Section, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Marco Lebtig
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology Section, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Marieke A Böcker
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology Section, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Anima Horlbeck
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology Section, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Stilianos P Lambidis
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology Section, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Birgit Schittek
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- Dermatology Department, University Hospital Tübingen, Tübingen, Germany
| | - Dorothee Kretschmer
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology Section, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, University of Tübingen, Tübingen, Germany
| | - Andreas Peschel
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology Section, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
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9
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Nielsen TK, Petersen IB, Xu L, Barbuti MD, Mebus V, Justh A, Alqarzaee AA, Jacques N, Oury C, Thomas V, Kjos M, Henriksen C, Frees D. The Spx stress regulator confers high-level β-lactam resistance and decreases susceptibility to last-line antibiotics in methicillin-resistant Staphylococcus aureus. Antimicrob Agents Chemother 2024:e0033524. [PMID: 38690894 DOI: 10.1128/aac.00335-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/05/2024] [Indexed: 05/03/2024] Open
Abstract
Infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are a leading cause of mortality worldwide. MRSA has acquired resistance to next-generation β-lactam antibiotics through the horizontal acquisition of the mecA resistance gene. Development of high resistance is, however, often associated with additional mutations in a set of chromosomal core genes, known as potentiators, which, through poorly described mechanisms, enhance resistance. The yjbH gene was recently identified as a hot spot for adaptive mutations during severe infections. Here, we show that inactivation of yjbH increased β-lactam MICs up to 16-fold and transformed MRSA cells with low levels of resistance to being homogenously highly resistant to β-lactams. The yjbH gene encodes an adaptor protein that targets the transcriptional stress regulator Spx for degradation by the ClpXP protease. Using CRISPR interference (CRISPRi) to knock down spx transcription, we unambiguously linked hyper-resistance to the accumulation of Spx. Spx was previously proposed to be essential; however, our data suggest that Spx is dispensable for growth at 37°C but becomes essential in the presence of antibiotics with various targets. On the other hand, high Spx levels bypassed the role of PBP4 in β-lactam resistance and broadly decreased MRSA susceptibility to compounds targeting the cell wall or the cell membrane, including vancomycin, daptomycin, and nisin. Strikingly, Spx potentiated resistance independently of its redox-sensing switch. Collectively, our study identifies a general stress pathway that, in addition to promoting the development of high-level, broad-spectrum β-lactam resistance, also decreases MRSA susceptibility to critical antibiotics of last resort.
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Affiliation(s)
- Tobias Krogh Nielsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ida Birkjær Petersen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lijuan Xu
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Maria Disen Barbuti
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Viktor Mebus
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anni Justh
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Abdulelah Ahmed Alqarzaee
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Nicolas Jacques
- Laboratory of Cardiology, GIGA Institute, University of Liège Hospital, Liège, Belgium
| | - Cécile Oury
- Laboratory of Cardiology, GIGA Institute, University of Liège Hospital, Liège, Belgium
| | - Vinai Thomas
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Morten Kjos
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Camilla Henriksen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dorte Frees
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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10
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Mediati DG, Dan W, Lalaouna D, Dinh H, Pokhrel A, Rowell KN, Michie KA, Stinear TP, Cain AK, Tree JJ. The 3' UTR of vigR is required for virulence in Staphylococcus aureus and has expanded through STAR sequence repeat insertions. Cell Rep 2024; 43:114082. [PMID: 38583155 DOI: 10.1016/j.celrep.2024.114082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 01/17/2024] [Accepted: 03/25/2024] [Indexed: 04/09/2024] Open
Abstract
Infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are alarmingly common, and treatment is confined to last-line antibiotics. Vancomycin is the treatment of choice for MRSA bacteremia, and treatment failure is often associated with vancomycin-intermediate S. aureus isolates. The regulatory 3' UTR of the vigR mRNA contributes to vancomycin tolerance and upregulates the autolysin IsaA. Using MS2-affinity purification coupled with RNA sequencing, we find that the vigR 3' UTR also regulates dapE, a succinyl-diaminopimelate desuccinylase required for lysine and peptidoglycan synthesis, suggesting a broader role in controlling cell wall metabolism and vancomycin tolerance. Deletion of the 3' UTR increased virulence, while the isaA mutant is completely attenuated in a wax moth larvae model. Sequence and structural analyses of vigR indicated that the 3' UTR has expanded through the acquisition of Staphylococcus aureus repeat insertions that contribute sequence for the isaA interaction seed and may functionalize the 3' UTR.
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Affiliation(s)
- Daniel G Mediati
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia; Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW, Australia.
| | - William Dan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - David Lalaouna
- Université de Strasbourg, CNRS, ARN UPR 9002, Strasbourg, France
| | - Hue Dinh
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Alaska Pokhrel
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW, Australia; School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Keiran N Rowell
- Structural Biology Facility, University of New South Wales, Sydney, NSW, Australia
| | - Katharine A Michie
- Structural Biology Facility, University of New South Wales, Sydney, NSW, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, Peter Doherty Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Amy K Cain
- School of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Jai J Tree
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
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11
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Schäper S, Brito AD, Saraiva BM, Squyres GR, Holmes MJ, Garner EC, Hensel Z, Henriques R, Pinho MG. Cell constriction requires processive septal peptidoglycan synthase movement independent of FtsZ treadmilling in Staphylococcus aureus. Nat Microbiol 2024; 9:1049-1063. [PMID: 38480900 PMCID: PMC10994846 DOI: 10.1038/s41564-024-01629-6] [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: 06/30/2023] [Accepted: 02/01/2024] [Indexed: 04/06/2024]
Abstract
Bacterial cell division requires recruitment of peptidoglycan (PG) synthases to the division site by the tubulin homologue, FtsZ. Septal PG synthases promote septum growth. FtsZ treadmilling is proposed to drive the processive movement of septal PG synthases and septal constriction in some bacteria; however, the precise mechanisms spatio-temporally regulating PG synthase movement and activity and FtsZ treadmilling are poorly understood. Here using single-molecule imaging of division proteins in the Gram-positive pathogen Staphylococcus aureus, we showed that the septal PG synthase complex FtsW/PBP1 and its putative activator protein, DivIB, move with similar velocity around the division site. Impairing FtsZ treadmilling did not affect FtsW or DivIB velocities or septum constriction rates. Contrarily, PG synthesis inhibition decelerated or stopped directional movement of FtsW and DivIB, and septum constriction. Our findings suggest that a single population of processively moving FtsW/PBP1 associated with DivIB drives cell constriction independently of FtsZ treadmilling in S. aureus.
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Affiliation(s)
- Simon Schäper
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal.
| | - António D Brito
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Bruno M Saraiva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Georgia R Squyres
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Matthew J Holmes
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Ethan C Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Zach Hensel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Ricardo Henriques
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- MRC-Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Mariana G Pinho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal.
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12
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Nong Y, Steinig E, Pollock GL, Taiaroa G, Carter GP, Monk IR, Pang S, Daley DA, Coombs GW, Forde BM, Harris PNA, Sherry NL, Howden BP, Pasricha S, Baines SL, Williamson DA. Emergence and clonal expansion of a qacA-harbouring sequence type 45 lineage of methicillin-resistant Staphylococcus aureus. Commun Biol 2024; 7:349. [PMID: 38514781 PMCID: PMC10957945 DOI: 10.1038/s42003-024-06012-z] [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: 07/10/2023] [Accepted: 03/05/2024] [Indexed: 03/23/2024] Open
Abstract
The past decade has seen an increase in the prevalence of sequence type (ST) 45 methicillin-resistant Staphylococcus aureus (MRSA), yet the underlying drivers for its emergence and spread remain unclear. To better understand the worldwide dissemination of ST45 S. aureus, we performed phylogenetic analyses of Australian isolates, supplemented with a global population of ST45 S. aureus genomes. Our analyses revealed a distinct lineage of multidrug-resistant ST45 MRSA harbouring qacA, predominantly found in Australia and Singapore. Bayesian inference predicted that the acquisition of qacA occurred in the late 1990s. qacA was integrated into a structurally variable region of the chromosome containing Tn552 (carrying blaZ) and Tn4001 (carrying aac(6')-aph(2")) transposable elements. Using mutagenesis and in vitro assays, we provide phenotypic evidence that qacA confers tolerance to chlorhexidine. These findings collectively suggest both antimicrobial resistance and the carriage of qacA may play a role in the successful establishment of ST45 MRSA.
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Affiliation(s)
- Yi Nong
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
| | - Eike Steinig
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Georgina L Pollock
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - George Taiaroa
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Glen P Carter
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Doherty Applied Microbial Genomics, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Ian R Monk
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Stanley Pang
- Antimicrobial Resistance and Infectious Diseases Research Laboratory, Murdoch University, Murdoch, WA, Australia
- Department of Microbiology, PathWest Laboratory Medicine-WA, Fiona Stanley Hospital, Murdoch, WA, Australia
| | - Denise A Daley
- Australian Group on Antimicrobial Resistance, Fiona Stanley Hospital, Murdoch, WA, Australia
| | - Geoffrey W Coombs
- Antimicrobial Resistance and Infectious Diseases Research Laboratory, Murdoch University, Murdoch, WA, Australia
- Department of Microbiology, PathWest Laboratory Medicine-WA, Fiona Stanley Hospital, Murdoch, WA, Australia
| | - Brian M Forde
- The University of Queensland, Faculty of Medicine, UQ Centre for Clinical Research, Brisbane, QLD, Australia
| | - Patrick N A Harris
- The University of Queensland, Faculty of Medicine, UQ Centre for Clinical Research, Brisbane, QLD, Australia
- Central Microbiology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Norelle L Sherry
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Shivani Pasricha
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Sarah L Baines
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Deborah A Williamson
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
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13
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Rondthaler S, Sarker B, Howitz N, Shah I, Andrews LB. Toolbox of Characterized Genetic Parts for Staphylococcus aureus. ACS Synth Biol 2024; 13:103-118. [PMID: 38064657 PMCID: PMC10805105 DOI: 10.1021/acssynbio.3c00325] [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: 05/24/2023] [Revised: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 01/23/2024]
Abstract
Staphylococcus aureus is an important clinical bacterium prevalent in human-associated microbiomes and the cause of many diseases. However, S. aureus has been intractable to synthetic biology approaches due to limited characterized genetic parts for this nonmodel Gram-positive bacterium. Moreover, genetic manipulation of S. aureus has relied on cumbersome and inefficient cloning strategies. Here, we report the first standardized genetic parts toolbox for S. aureus, which includes characterized promoters, ribosome binding sites, terminators, and plasmid replicons from a variety of bacteria for precise control of gene expression. We established a standard relative expression unit (REU) for S. aureus using a plasmid reference and characterized genetic parts in standardized REUs using S. aureus ATCC 12600. We constructed promoter and terminator part plasmids that are compatible with an efficient Type IIS DNA assembly strategy to effectively build multipart DNA constructs. A library of 24 constitutive promoters was built and characterized in S. aureus, which showed a 380-fold activity range. This promoter library was also assayed in Bacillus subtilis (122-fold activity range) to demonstrate the transferability of the constitutive promoters between these Gram-positive bacteria. By applying an iterative design-build-test-learn cycle, we demonstrated the use of our toolbox for the rational design and engineering of a tetracycline sensor in S. aureus using the PXyl-TetO aTc-inducible promoter that achieved 25.8-fold induction. This toolbox greatly expands the growing number of genetic parts for Gram-positive bacteria and will allow researchers to leverage synthetic biology approaches to study and engineer cellular processes in S. aureus.
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Affiliation(s)
- Stephen
N. Rondthaler
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Biprodev Sarker
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Nathaniel Howitz
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Ishita Shah
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Lauren B. Andrews
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
- Molecular
and Cellular Biology Graduate Program, University
of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Biotechnology
Training Program, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
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14
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Reed P, Sorg M, Alwardt D, Serra L, Veiga H, Schäper S, Pinho MG. A CRISPRi-based genetic resource to study essential Staphylococcus aureus genes. mBio 2024; 15:e0277323. [PMID: 38054745 PMCID: PMC10870820 DOI: 10.1128/mbio.02773-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 10/19/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Staphylococcus aureus is an important clinical pathogen that causes a high number of antibiotic-resistant infections. The study of S. aureus biology, and particularly of the function of essential proteins, is of particular importance to develop new approaches to combat this pathogen. We have optimized a clustered regularly interspaced short palindromic repeat interference (CRISPRi) system that allows efficient targeting of essential S. aureus genes. Furthermore, we have used that system to construct a library comprising 261 strains, which allows the depletion of essential proteins encoded by 200 genes/operons. This library, which we have named Lisbon CRISPRi Mutant Library, should facilitate the study of S. aureus pathogenesis and biology.
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Affiliation(s)
- Patricia Reed
- Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Moritz Sorg
- Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Dominik Alwardt
- Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Lúcia Serra
- Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Helena Veiga
- Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Simon Schäper
- Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Mariana G. Pinho
- Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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15
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Sharkey LKR, Guerillot R, Walsh CJ, Turner AM, Lee JYH, Neville SL, Klatt S, Baines SL, Pidot SJ, Rossello FJ, Seemann T, McWilliam HEG, Cho E, Carter GP, Howden BP, McDevitt CA, Hachani A, Stinear TP, Monk IR. The two-component system WalKR provides an essential link between cell wall homeostasis and DNA replication in Staphylococcus aureus. mBio 2023; 14:e0226223. [PMID: 37850732 PMCID: PMC10746227 DOI: 10.1128/mbio.02262-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 10/19/2023] Open
Abstract
IMPORTANCE The opportunistic human pathogen Staphylococcus aureus uses an array of protein sensing systems called two-component systems (TCS) to sense environmental signals and adapt its physiology in response by regulating different genes. This sensory network is key to S. aureus versatility and success as a pathogen. Here, we reveal for the first time the full extent of the regulatory network of WalKR, the only staphylococcal TCS that is indispensable for survival under laboratory conditions. We found that WalKR is a master regulator of cell growth, coordinating the expression of genes from multiple, fundamental S. aureus cellular processes, including those involved in maintaining cell wall metabolism, protein biosynthesis, nucleotide metabolism, and the initiation of DNA replication.
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Affiliation(s)
- Liam K. R. Sharkey
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Romain Guerillot
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Calum J. Walsh
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Adrianna M. Turner
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Jean Y. H. Lee
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Stephanie L. Neville
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Stephan Klatt
- The Florey Institute of Neuroscience and Mental Health, Melbourne Dementia Research Centre, The University of Melbourne, Parkville, Victoria, Australia
| | - Sarah L. Baines
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Fernando J. Rossello
- University of Melbourne Centre for Cancer Research, The University of Melbourne, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
| | - Torsten Seemann
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, Centre for Pathogen Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Hamish E. G. McWilliam
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Ellie Cho
- Biological Optical Microscopy Platform, University of Melbourne, Melbourne, Victoria, Australia
| | - Glen P. Carter
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, Centre for Pathogen Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Christopher A. McDevitt
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Abderrahman Hachani
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, Centre for Pathogen Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Ian R. Monk
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
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16
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Youssouf N, Martin M, Bischoff M, Soubeyran P, Gannoun-Zaki L, Molle V. The secreted tyrosine phosphatase PtpA promotes Staphylococcus aureus survival in RAW 264.7 macrophages through decrease of the SUMOylation host response. Microbiol Spectr 2023; 11:e0281323. [PMID: 37819153 PMCID: PMC10714793 DOI: 10.1128/spectrum.02813-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/04/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE Staphylococcus aureus uses numerous strategies to survive and persist in the intracellular environment of professional phagocytes, including modulation of the SUMOylation process. This study aims to understand how S. aureus alters host SUMOylation to enhance its intracellular survival in professional phagocytes. Our results indicate that S. aureus strain Newman utilizes PtpA-driven phosphorylation to decrease the amount of SUMOylated proteins in murine macrophages to facilitate its survival in this immune cell type.
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Affiliation(s)
- Nadhuma Youssouf
- VBIC, INSERM U1047, Université de Montpellier, Montpellier, France
| | - Marianne Martin
- VBIC, INSERM U1047, Université de Montpellier, Montpellier, France
| | - Markus Bischoff
- Institute for Medical Microbiology and Hygiene, Saarland University, Homburg, Saarland, Germany
| | - Philippe Soubeyran
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR, Aix-Marseille, Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
| | | | - Virginie Molle
- VBIC, INSERM U1047, Université de Montpellier, Montpellier, France
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17
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Yang P, Yang J, Lin T, Liu Q, Yin Y, Chen D, Yang S. Efficient Genome Editing in Most Staphylococcus aureus by Using the Restriction-Modification System Silent CRISPR-Cas9 Toolkit. ACS Synth Biol 2023; 12:3340-3351. [PMID: 37830328 DOI: 10.1021/acssynbio.3c00339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Staphylococcus aureus is a clinically important pathogen that threatens human health due to its strong pathogenicity and drug resistance, leading to meningitis, endocarditis, and skin and soft tissue infections. Genetic manipulation in S. aureus is a powerful approach for characterizing the molecular mechanisms of bacterial drug resistance, pathogenicity, and virulence. However, a strong restriction barrier presents a major obstacle to the extensive utilization of genetic manipulation tools in clinical isolates of S. aureus. Here, we constructed a restriction-modification (RM) system silent CRISPR-Cas9 toolkit that synonymously eliminated the type I RM targets of S. aureus from plasmids, downsized plasmids using minicircle technology, and combined with a plasmid artificial modification (PAM) method to circumvent the type II RM system. The RM-silent CRISPR-Cas9 toolkit enables a significant improvement in transformation (105-106 transformants per microgram plasmid in strains we tested) and high-success efficiency editing for gene deletion (knockout strain obtained in one-round electroporation) in a wide range of S. aureus species including clinical isolates of unknown genetic background. The RM-silent CRISPR-Cas9 toolkits could expedite the process of mutant construction in most S. aureus strains, and this approach could be applied to the design of other genetic toolkit plasmids for utilization in a wider range of S. aureus strains.
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Affiliation(s)
- Ping Yang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Junjie Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ting Lin
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qi Liu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yu Yin
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Daijie Chen
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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18
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Campbell AE, McCready-Vangi AR, Uberoi A, Murga-Garrido SM, Lovins VM, White EK, Pan JTC, Knight SAB, Morgenstern AR, Bianco C, Planet PJ, Gardner SE, Grice EA. Variable staphyloxanthin production by Staphylococcus aureus drives strain-dependent effects on diabetic wound-healing outcomes. Cell Rep 2023; 42:113281. [PMID: 37858460 PMCID: PMC10680119 DOI: 10.1016/j.celrep.2023.113281] [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: 10/21/2022] [Revised: 08/24/2023] [Accepted: 09/28/2023] [Indexed: 10/21/2023] Open
Abstract
Strain-level variation in Staphylococcus aureus is a factor that contributes to disease burden and clinical outcomes in skin disorders and chronic wounds. However, the microbial mechanisms that drive these variable host responses are poorly understood. To identify mechanisms underlying strain-specific outcomes, we perform high-throughput phenotyping screens on S. aureus isolates cultured from diabetic foot ulcers. Isolates from non-healing wounds produce more staphyloxanthin, a cell membrane pigment. In murine diabetic wounds, staphyloxanthin-producing isolates delay wound closure significantly compared with staphyloxanthin-deficient isolates. Staphyloxanthin promotes resistance to oxidative stress and enhances bacterial survival in neutrophils. Comparative genomic and transcriptomic analysis of genetically similar clinical isolates with disparate staphyloxanthin phenotypes reveals a mutation in the sigma B operon, resulting in marked differences in stress response gene expression. Our work illustrates a framework to identify traits that underlie strain-level variation in disease burden and suggests more precise targets for therapeutic intervention in S. aureus-positive wounds.
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Affiliation(s)
- Amy E Campbell
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Amelia R McCready-Vangi
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aayushi Uberoi
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sofía M Murga-Garrido
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Victoria M Lovins
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ellen K White
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jamie Ting-Chun Pan
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Simon A B Knight
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alexis R Morgenstern
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Colleen Bianco
- Division of Infectious Disease, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Paul J Planet
- Division of Infectious Disease, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Departments of Pediatrics and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sue E Gardner
- College of Nursing, University of Iowa, Iowa City, IA 52242, USA
| | - Elizabeth A Grice
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Chen E, Shaffer MG, Bilodeau RE, West RE, Oberly PJ, Nolin TD, Culyba MJ. Clinical rel mutations in Staphylococcus aureus prime pathogen expansion under nutrient stress. mSphere 2023; 8:e0024923. [PMID: 37750686 PMCID: PMC10597345 DOI: 10.1128/msphere.00249-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 07/31/2023] [Indexed: 09/27/2023] Open
Abstract
Persistent infection by Staphylococcus aureus has been linked to the bacterial stringent response (SR), a conserved stress response pathway regulated by the Rel protein. Rel synthesizes (p)ppGpp "alarmones" in response to amino acid starvation, which enables adaptation to stress by modulating bacterial growth and virulence. We previously identified five novel protein-altering mutations in rel that arose in patients with persistent methicillin-resistant S. aureus bacteremia. The mutations mapped to both the enzymatic and regulatory protein domains of Rel. Here, we set out to characterize the phenotype of these mutations to understand how they may have been selected in vivo. After introducing each mutation into S. aureus strain JE2, we analyzed growth, fitness, and antibiotic profiles. Despite being located in different protein domains, we found that all of the mutations converged on the same phenotype. Each shortened the time of lag phase growth and imparted a fitness advantage in nutritionally depleted conditions. Through quantification of intracellular (p)ppGpp, we link this phenotype to increased SR activation, specifically during the stationary phase of growth. In contrast to two previously identified clinical rel mutations, we find that our rel mutations do not cause antibiotic tolerance. Instead, our findings suggest that in vivo selection was due to an augmented SR that primes cells for growth in nutrient-poor conditions, which may be a strategy for evading host-imposed nutritional immunity. Importance Host and pathogen compete for available nutrition during infection. For bacteria, the stringent response (SR) regulator Rel responds to amino acid deprivation by signaling the cell to modulate its growth rate, metabolism, and virulence. In this report, we characterize five rel mutations that arose during cases of persistent methicillin-resistant Staphylococcus aureus bacteremia. We find that all of the mutations augmented SR signaling specifically under nutrient-poor conditions, enabling the cell to more readily grow and survive. Our findings reveal a strategy used by bacterial pathogens to evade the nutritional immunity imposed by host tissues during infection.
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Affiliation(s)
- Edwin Chen
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Marla G. Shaffer
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Robert E. Bilodeau
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Raymond E. West
- Small Molecule Biomarker Core, University of Pittsburgh School of Pharmacy, Pittsburgh, Pennsylvania, USA
| | - Patrick J. Oberly
- Small Molecule Biomarker Core, University of Pittsburgh School of Pharmacy, Pittsburgh, Pennsylvania, USA
| | - Thomas D. Nolin
- Small Molecule Biomarker Core, University of Pittsburgh School of Pharmacy, Pittsburgh, Pennsylvania, USA
| | - Matthew J. Culyba
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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20
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van Dalen R, Elsherbini AMA, Harms M, Alber S, Stemmler R, Peschel A. Secretory IgA impacts the microbiota density in the human nose. MICROBIOME 2023; 11:233. [PMID: 37865781 PMCID: PMC10589987 DOI: 10.1186/s40168-023-01675-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 09/24/2023] [Indexed: 10/23/2023]
Abstract
BACKGROUND Respiratory mucosal host defense relies on the production of secretory IgA (sIgA) antibodies, but we currently lack a fundamental understanding of how sIgA is induced by contact with microbes and how such immune responses may vary between humans. Defense of the nasal mucosal barrier through sIgA is critical to protect from infection and to maintain homeostasis of the microbiome, which influences respiratory disorders and hosts opportunistic pathogens. METHODS We applied IgA-seq analysis to nasal microbiota samples from male and female healthy volunteers, to identify which bacterial genera and species are targeted by sIgA on the level of the individual host. Furthermore, we used nasal sIgA from the same individuals in sIgA deposition experiments to validate the IgA-seq outcomes. CONCLUSIONS We observed that the amount of sIgA secreted into the nasal mucosa by the host varied substantially and was negatively correlated with the bacterial density, suggesting that nasal sIgA limits the overall bacterial capacity to colonize. The interaction between mucosal sIgA antibodies and the nasal microbiota was highly individual with no obvious differences between potentially invasive and non-invasive bacterial species. Importantly, we could show that for the clinically relevant opportunistic pathogen and frequent nasal resident Staphylococcus aureus, sIgA reactivity was in part the result of epitope-independent interaction of sIgA with the antibody-binding protein SpA through binding of sIgA Fab regions. This study thereby offers a first comprehensive insight into the targeting of the nasal microbiota by sIgA antibodies. It thereby helps to better understand the shaping and homeostasis of the nasal microbiome by the host and may guide the development of effective mucosal vaccines against bacterial pathogens. Video Abstract.
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Affiliation(s)
- Rob van Dalen
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany.
- Cluster of Excellence EXC2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany.
- Present Address: Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.
| | - Ahmed M A Elsherbini
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Mareike Harms
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Svenja Alber
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Regine Stemmler
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Andreas Peschel
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany.
- Cluster of Excellence EXC2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany.
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany.
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21
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Cho J, Manna AC, Snelling HS, Cheung AL. GraS signaling in Staphylococcus aureus is regulated by a single D35 residue in the extracellular loop. Microbiol Spectr 2023; 11:e0198223. [PMID: 37728380 PMCID: PMC10581149 DOI: 10.1128/spectrum.01982-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/27/2023] [Indexed: 09/21/2023] Open
Abstract
Bacterial two-component systems are crucial features of bacterial pathogens such as methicillin-resistant Staphylococcus aureus to overcome environmental and antimicrobial stresses by activating regulons to interfere with the bactericidal mechanisms. GraRS is a unique subset of two-component systems belonging to the intramembrane-sensing histidine kinase family (IM-HK) and is responsible for resistance to cationic host defense peptides. However, the precise manner by which the short 9-residue extracellular loop of the membrane sensor GraS detects the antimicrobial peptides and transduces the signal is not comprehensively understood. Here, we show that a single point mutation (D35A) in the extracellular loop of GraS blocked activation of GraRS, but this effect was also abrogated with graS mutations in the N-terminal transmembrane segments without any accompanying effect on GraS protein expression. Additionally, mutations in H120 and T172 in the dimerization/histidine phosphotransfer (DHp) domain of GraS increased activation without any accompanying enhancement in dimerization, likely due to disruption of the H120-T172 interaction that restricts rotational movements of the DHp helices since swapping H120 and T172 did not alter GraS activation. Notably, the enhancing effects of H120 and T172 mutations were abolished with a D35 mutation, highlighting the pivotal role of D35 in the 9-residue extracellular loop of GraS in GraR phosphorylation. In summary, our study delivers the significance of the D35 in the extracellular loop of GraS and ensuing changes in the N-terminal transmembrane helices as a model to illustrate signaling in the IM-HK subset of two-component regulatory systems. IMPORTANCE Methicillin-resistant Staphylococcus aureus (MRSA) is a human pathogen capable of infecting skin, blood, internal organs, and artificial medical devices. Generally, personal hygiene and a robust immune system can limit the spread of this pathogen; however, MRSA possesses an assortment of phenotypic tools to survive the hostile host environment including host defense peptides. More specifically, S. aureus utilizes two-component systems to sense noxious environmental cues to respond to harmful environmental elements. Our study focused on a two-component system called GraRS that S. aureus deploys against host defense peptides. We showed that one single residue in the extracellular loop of GraS and the adjacent membrane segment controlled the activation of GraRS, indicating the importance of a well-tuned-charged residue in the extracellular loop of GraS for sensing activity.
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Affiliation(s)
- Junho Cho
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Adhar C. Manna
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Helah S. Snelling
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Ambrose L. Cheung
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
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22
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Sarosh A, Kwong SM, Jensen SO, Northern F, Walton WG, Eakes TC, Redinbo MR, Firth N, McLaughlin KJ. pSK41/pGO1-family conjugative plasmids of Staphylococcus aureus encode a cryptic repressor of replication. Plasmid 2023; 128:102708. [PMID: 37967733 DOI: 10.1016/j.plasmid.2023.102708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 11/01/2023] [Accepted: 11/09/2023] [Indexed: 11/17/2023]
Abstract
The majority of large multiresistance plasmids of Staphylococcus aureus utilise a RepA_N-type replication initiation protein, the expression of which is regulated by a small antisense RNA (RNAI) that overlaps the rep mRNA leader. The pSK41/pGO1-family of conjugative plasmids additionally possess a small (86 codon) divergently transcribed ORF (orf86) located upstream of the rep locus. The product of pSK41 orf86 was predicted to have a helix-turn-helix motif suggestive of a likely function in transcriptional repression. In this study, we investigated the effect of Orf86 on transcription of thirteen pSK41 backbone promoters. We found that Orf86 only repressed transcription from the rep promoter, and hence now redesignate the product as Cop. Over-expression of Cop in trans reduced the copy number of pSK41 mini-replicons, both in the presence and absence of rnaI. in vitro protein-DNA binding experiments with purified 6 × His-Cop demonstrated specific DNA binding, adjacent to, and partially overlapping the -35 hexamer of the rep promoter. The crystal structure of Cop revealed a dimeric structure similar to other known transcriptional regulators. Cop mRNA was found to result from "read-through" transcription from the strong RNAI promoter that escapes the rnaI terminator. Thus, PrnaI is responsible for transcription of two distinct negative regulators of plasmid copy number; the antisense RNAI that primarily represses Rep translation, and Cop protein that can repress rep transcription. Deletion of cop in a native plasmid did not appear to impact copy number, indicating a cryptic auxiliary role.
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Affiliation(s)
- Alvina Sarosh
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Stephen M Kwong
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Slade O Jensen
- Microbiology and Infectious Diseases, School of Medicine, Western Sydney University, Sydney, New South Wales 2751, Australia; Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Liverpool, New South Wales 2170, Australia
| | - Faith Northern
- Chemistry Department, Vassar College, Poughkeepsie, NY 12604, USA
| | - William G Walton
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Thomas C Eakes
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Matthew R Redinbo
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Biochemistry, Microbiology and Genomics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Neville Firth
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia.
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23
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Li Y, Zhu F, Manna AC, Chen L, Jiang J, Hong JI, Proctor RA, Bayer AS, Cheung AL, Xiong YQ. Gp05, a Prophage-Encoded Virulence Factor, Contributes to Persistent Methicillin-Resistant Staphylococcus aureus Endovascular Infection. Microbiol Spectr 2023; 11:e0060023. [PMID: 37358448 PMCID: PMC10434118 DOI: 10.1128/spectrum.00600-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/24/2023] [Indexed: 06/27/2023] Open
Abstract
Persistent methicillin-resistant Staphylococcus aureus (MRSA) endovascular infections represent a serious public health threat. We recently demonstrated that the presence of a novel prophage ϕSA169 was associated with vancomycin (VAN) treatment failure in experimental MRSA endocarditis. In this study, we assessed the role of a ϕSA169 gene, ϕ80α_gp05 (gp05), in VAN-persistent outcome using gp05 isogenic MRSA strain sets. Of note, Gp05 significantly influences the intersection of MRSA virulence factors, host immune responses, and antibiotic treatment efficacy, including the following: (i) activity of the significant energy-yielding metabolic pathway (e.g., tricarboxylic acid cycle); (ii) carotenoid pigment production; (iii) (p)ppGpp (guanosine tetra- and pentaphosphate) production, which activates the stringent response and subsequent downstream functional factors (e.g., phenol-soluble modulins and polymorphonuclear neutrophil bactericidal activity); and (iv) persistence to VAN treatment in an experimental infective endocarditis model. These data suggest that Gp05 is a significant virulence factor which contributes to the persistent outcomes in MRSA endovascular infection by multiple pathways. IMPORTANCE Persistent endovascular infections are often caused by MRSA strains that are susceptible to anti-MRSA antibiotics in vitro by CLSI breakpoints. Thus, the persistent outcome represents a unique variant of traditional antibiotic resistance mechanisms and a significant therapeutic challenge. Prophage, a critical mobile genetic element carried by most MRSA isolates, provides their bacterial host with metabolic advantages and resistance mechanisms. However, how prophage-encoded virulence factors interact with the host defense system and antibiotics, driving the persistent outcome, is not well known. In the current study, we demonstrated that a novel prophage gene, gp05, significantly impacts tricarboxylic acid cycle activity, stringent response, and pigmentation, as well as vancomycin treatment outcome in an experimental endocarditis model using isogenic gp05 overexpression and chromosomal deletion mutant MRSA strain sets. The findings significantly advance our understanding of the role of Gp05 in persistent MRSA endovascular infection and provide a potential target for development of novel drugs against these life-threatening infections.
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Affiliation(s)
- Yi Li
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Fengli Zhu
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Adhar C. Manna
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Liang Chen
- Center for Discovery and Innovation, Nutley, New Jersey, USA
| | - Jason Jiang
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Jong-In Hong
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Richard A. Proctor
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Arnold S. Bayer
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
- David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Ambrose L. Cheung
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Yan Q. Xiong
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
- David Geffen School of Medicine at UCLA, Los Angeles, California, USA
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Zeden MS, Schuster CF, Gründling A. Allelic Exchange: Construction of an Unmarked In-Frame Deletion in Staphylococcus aureus. Cold Spring Harb Protoc 2023; 2023:107945. [PMID: 37117029 DOI: 10.1101/pdb.top107945] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Here we describe an allelic-exchange procedure for the construction of an unmarked gene deletion in the bacterium Staphylococcus aureus As a practical example, we outline the construction of a tagO gene deletion in S. aureus using the allelic-exchange plasmid pIMAY*. We first present the general principles of the allelic-exchange method, along with information on counterselectable markers. Furthermore, we summarize relevant cloning procedures, such as the splicing by overhang extension (SOE) polymerase chain reaction (PCR) and Gibson assembly methods, and we conclude by giving some general consideration to performing genetic modifications in S. aureus.
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Affiliation(s)
- Merve S Zeden
- Microbiology, School of Biological and Chemical Sciences, University of Galway, Galway H91 TK33, Ireland
| | - Christopher F Schuster
- Center for Pandemic Vaccines and Therapeutics (ZEPAI), Paul-Ehrlich-Institute, 63225 Langen, Germany
| | - Angelika Gründling
- Section of Molecular Microbiology and Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, United Kingdom
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25
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Zeden MS, Schuster CF, Gründling A. Preparation of Electrocompetent Staphylococcus aureus Cells and Plasmid Transformation. Cold Spring Harb Protoc 2023; 2023:107947. [PMID: 37117021 DOI: 10.1101/pdb.prot107947] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
This protocol is part of a series of methodologies for the construction of an in-frame gene deletion in Staphylococcus aureus strain RN4220. Having previously described how an allelic-exchange plasmid containing a desired gene deletion (in this case, pIMAY*-ΔtagO) can be constructed and isolated from Escherichia coli, we now present details of the next steps in this method-the preparation of electrocompetent S. aureus cells and introduction of the tagO mutant plasmid DNA into the S. aureus cells by electroporation. Colonies containing the plasmid can then be selected on chloramphenicol plates at a low temperature permissive for plasmid replication.
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Affiliation(s)
- Merve S Zeden
- Microbiology, School of Biological and Chemical Sciences, University of Galway, Galway, H91 TK33, Ireland
| | - Christopher F Schuster
- Center for Pandemic Vaccines and Therapeutics (ZEPAI), Paul-Ehrlich-Institute, 63225 Langen, Germany
| | - Angelika Gründling
- Section of Molecular Microbiology and Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, Exhibition Road, London, SW7 2AZ, United Kingdom
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26
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Evans DCS, Khamas AB, Marcussen L, Rasmussen KS, Klitgaard JK, Kallipolitis BH, Nielsen J, Otzen DE, Leake MC, Meyer RL. GFP fusions of Sec-routed extracellular proteins in Staphylococcus aureus reveal surface-associated coagulase in biofilms. MICROBIAL CELL (GRAZ, AUSTRIA) 2023; 10:145-156. [PMID: 37395997 PMCID: PMC10311078 DOI: 10.15698/mic2023.07.800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 06/14/2023] [Accepted: 06/19/2023] [Indexed: 07/04/2023]
Abstract
Staphylococcus aureus is a major human pathogen that utilises many surface-associated and secreted proteins to form biofilms and cause disease. However, our understanding of these processes is limited by challenges of using fluorescent protein reporters in their native environment, because they must be exported and fold correctly to become fluorescent. Here, we demonstrate the feasibility of using the monomeric superfolder GFP (msfGFP) exported from S. aureus. By fusing msfGFP to signal peptides for the Secretory (Sec) and Twin Arginine Translocation (Tat) pathways, the two major secretion pathways in S. aureus, we quantified msfGFP fluorescence in bacterial cultures and cell-free supernatant from the cultures. When fused to a Tat signal peptide, we detected msfGFP fluorescence inside but not outside bacterial cells, indicating a failure to export msfGFP. However, when fused to a Sec signal peptide, msfGFP fluorescence was present outside cells, indicating successful export of the msfGFP in the unfolded state, followed by extracellular folding and maturation to the photoactive state. We applied this strategy to study coagulase (Coa), a secreted protein and a major contributor to the formation of a fibrin network in S. aureus biofilms that protects bacteria from the host immune system and increases attachment to host surfaces. We confirmed that a genomically integrated C-terminal fusion of Coa to msfGFP does not impair the activity of Coa or its localisation within the biofilm matrix. Our findings demonstrate that msfGFP is a good candidate fluorescent reporter to consider when studying proteins secreted by the Sec pathway in S. aureus.
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Affiliation(s)
- Dominique C. S. Evans
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
- Department of Physics, University of York, York, UK
| | - Amanda B. Khamas
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - Lisbeth Marcussen
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - Kristian S. Rasmussen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Janne K. Klitgaard
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Birgitte H. Kallipolitis
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Janni Nielsen
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - Daniel E. Otzen
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - Mark C. Leake
- Department of Physics, University of York, York, UK
- Department of Biology, University of York, York, UK
| | - Rikke L. Meyer
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
- Department of Biology, Aarhus University, Aarhus, Denmark
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27
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Fan SH, Proctor RA, Ersoy SC, Manna AC, Cheung AL, Götz F, Chambers HF, Bayer AS. Role of the NaHCO 3 Transporter MpsABC in the NaHCO 3-β-Lactam-Responsive Phenotype in Methicillin-Resistant Staphylococcus aureus. Microbiol Spectr 2023; 11:e0014123. [PMID: 37102972 PMCID: PMC10269494 DOI: 10.1128/spectrum.00141-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/12/2023] [Indexed: 04/28/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) infections are an increasing concern due to their intrinsic resistance to most standard-of-care β-lactam antibiotics. Recent studies of clinical isolates have documented a novel phenotype, termed NaHCO3 responsiveness, in which a substantial proportion of MRSA strains exhibit enhanced susceptibility to β-lactams such as cefazolin and oxacillin in the presence of NaHCO3. A bicarbonate transporter, MpsAB (membrane potential-generating system), was recently found in S. aureus, where it plays a role in concentrating NaHCO3 for anaplerotic pathways. Here, we investigated the role of MpsAB in mediating the NaHCO3 responsiveness phenotype. Radiolabeled NaH14CO3 uptake profiling revealed significantly higher accumulation in NaHCO3-responsive vs nonresponsive MRSA strains when grown in ambient air. In contrast, under 5% CO2 conditions, NaHCO3-responsive (but not nonresponsive) strains exhibited repressed uptake. Oxacillin MICs were measured in four prototype strains and their mpsABC deletion mutants in the presence of NaHCO3 supplementation under 5% CO2 conditions. NaHCO3-mediated reductions in oxacillin MICs were observed in the responsive parental strains but not in mpsABC deletion mutants. No significant impact on oxacillin MICs was observed in the nonresponsive strains under the same conditions. Transcriptional and translational studies were carried out using both quantitative reverse transcription-PCR (qRT-PCR) and mpsA-green fluorescent protein (GFP) fusion constructs; these investigations showed that mpsA expression and translation were significantly upregulated during mid-exponential-phase growth in oxacillin-NaHCO3-supplemented medium in responsive versus nonresponsive strains. Taken together, these data show that the NaHCO3 transporter MpsABC is a key contributor to the NaHCO3-β-lactam responsiveness phenotype in MRSA. IMPORTANCE MRSA infections are increasingly difficult to treat, due in part to their resistance to most β-lactam antibiotics. A novel and relatively common phenotype, termed NaHCO3 responsiveness, has been identified in which MRSA strains show increased susceptibility in vitro and in vivo to β-lactams in the presence of NaHCO3. A recently described S. aureus NaHCO3 transporter, MpsAB, is involved in intracellular NaHCO3 concentration for anaplerotic pathways. We investigated the role of MpsAB in mediating the NaHCO3 responsiveness phenotype in four prototype MRSA strains (two responsive and two nonresponsive). We demonstrated that MpsABC is an important contributor to the NaHCO3-β-lactam responsiveness phenotype. Our study adds to the growing body of well-defined characteristics of this novel phenotype, which could potentially translate to alternative targets for MRSA treatment using β-lactams.
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Affiliation(s)
- Sook-Ha Fan
- The Lundquist Institute, Torrance, California, USA
| | - Richard A. Proctor
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- Department of Medical Microbiology/Immunology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | | | - Adhar C. Manna
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Ambrose L. Cheung
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Friedrich Götz
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Germany
| | | | - Arnold S. Bayer
- The Lundquist Institute, Torrance, California, USA
- Geffen School of Medicine at UCLA, Los Angeles, California, USA
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28
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Leinweber H, Sieber RN, Bojer MS, Larsen J, Ingmer H. Fluoroquinolone resistance does not facilitate phage Φ13 integration or excision in Staphylococcus aureus. Access Microbiol 2023; 5:acmi000583.v4. [PMID: 37424547 PMCID: PMC10323784 DOI: 10.1099/acmi.0.000583.v4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/04/2023] [Indexed: 07/11/2023] Open
Abstract
Prophages of the ΦSa3int family are commonly found in human-associated strains of Staphylococcus aureus where they encode factors for evading the human innate immune system. In contrast, they are usually absent in livestock-associated methicillin-resistant S. aureus (LA-MRSA) strains where the phage attachment site is mutated compared to the human strains. However, ΦSa3int phages have been found in a subset of LA-MRSA strains belonging to clonal complex 398 (CC398), including a lineage that is widespread in pig farms in Northern Jutland, Denmark. This lineage contains amino acid changes in the DNA topoisomerase IV and the DNA gyrase encoded by grlA and gyrA, respectively, which have been associated with fluoroquinolone (FQ) resistance. As both of these enzymes are involved in DNA supercoiling, we speculated that the mutations might impact recombination between the ΦSa3int phage and the bacterial chromosome. To examine this, we introduced the FQ resistance mutations into S. aureus 8325-4attBLA that carry the mutated CC398-like bacterial attachment site for ΦSa3int phages. When monitoring phage integration and release of Φ13, a well-described representative of the ΦSa3int phage family, we did not observe any significant differences between the FQ-resistant mutant and the wild-type strain. Thus our results suggest that mutations in grlA and gyrA do not contribute to the presence of the ΦSa3int phages in LA-MRSA CC398.
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Affiliation(s)
- Helena Leinweber
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Copenhagen, Denmark
| | - Raphael N. Sieber
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Martin S. Bojer
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Copenhagen, Denmark
| | - Jesper Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Copenhagen, Denmark
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29
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Silva KPT, Sundar G, Khare A. Efflux pump gene amplifications bypass necessity of multiple target mutations for resistance against dual-targeting antibiotic. Nat Commun 2023; 14:3402. [PMID: 37296157 PMCID: PMC10256781 DOI: 10.1038/s41467-023-38507-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 05/05/2023] [Indexed: 06/12/2023] Open
Abstract
Antibiotics that have multiple cellular targets theoretically reduce the frequency of resistance evolution, but adaptive trajectories and resistance mechanisms against such antibiotics are understudied. Here we investigate these in methicillin resistant Staphylococcus aureus (MRSA) using experimental evolution upon exposure to delafloxacin (DLX), a novel fluoroquinolone that targets both DNA gyrase and topoisomerase IV. We show that selection for coding sequence mutations and genomic amplifications of the gene encoding a poorly characterized efflux pump, SdrM, leads to high DLX resistance, circumventing the requirement for mutations in both target enzymes. In the evolved populations, sdrM overexpression due to genomic amplifications containing sdrM and two adjacent genes encoding efflux pumps results in high DLX resistance, while the adjacent hitchhiking efflux pumps contribute to streptomycin cross-resistance. Further, lack of sdrM necessitates mutations in both target enzymes to evolve DLX resistance, and sdrM thus increases the frequency of resistance evolution. Finally, sdrM mutations and amplifications are similarly selected in two diverse clinical isolates, indicating the generality of this DLX resistance mechanism. Our study highlights that instead of reduced rates of resistance, evolution of resistance to multi-targeting antibiotics can involve alternate high-frequency evolutionary paths, that may cause unexpected alterations of the fitness landscape, including antibiotic cross-resistance.
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Affiliation(s)
- Kalinga Pavan T Silva
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ganesh Sundar
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Anupama Khare
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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30
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Hachani A, Giulieri SG, Guérillot R, Walsh CJ, Herisse M, Soe YM, Baines SL, Thomas DR, Cheung SD, Hayes AS, Cho E, Newton HJ, Pidot S, Massey RC, Howden BP, Stinear TP. A high-throughput cytotoxicity screening platform reveals agr-independent mutations in bacteraemia-associated Staphylococcus aureus that promote intracellular persistence. eLife 2023; 12:84778. [PMID: 37289634 DOI: 10.7554/elife.84778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 05/23/2023] [Indexed: 06/10/2023] Open
Abstract
Staphylococcus aureus infections are associated with high mortality rates. Often considered an extracellular pathogen, S. aureus can persist and replicate within host cells, evading immune responses, and causing host cell death. Classical methods for assessing S. aureus cytotoxicity are limited by testing culture supernatants and endpoint measurements that do not capture the phenotypic diversity of intracellular bacteria. Using a well-established epithelial cell line model, we have developed a platform called InToxSa (intracellular toxicity of S. aureus) to quantify intracellular cytotoxic S. aureus phenotypes. Studying a panel of 387 S. aureus bacteraemia isolates, and combined with comparative, statistical, and functional genomics, our platform identified mutations in S. aureus clinical isolates that reduced bacterial cytotoxicity and promoted intracellular persistence. In addition to numerous convergent mutations in the Agr quorum sensing system, our approach detected mutations in other loci that also impacted cytotoxicity and intracellular persistence. We discovered that clinical mutations in ausA, encoding the aureusimine non-ribosomal peptide synthetase, reduced S. aureus cytotoxicity, and increased intracellular persistence. InToxSa is a versatile, high-throughput cell-based phenomics platform and we showcase its utility by identifying clinically relevant S. aureus pathoadaptive mutations that promote intracellular residency.
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Affiliation(s)
- Abderrahman Hachani
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Stefano G Giulieri
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Romain Guérillot
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Calum J Walsh
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Marion Herisse
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Ye Mon Soe
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Sarah L Baines
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - David R Thomas
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
- Infection and Immunity Program, Department of Microbiology and Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Shane Doris Cheung
- Biological Optical Microscopy Platform, University of Melbourne, Melbourne, Australia
| | - Ashleigh S Hayes
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Ellie Cho
- Biological Optical Microscopy Platform, University of Melbourne, Melbourne, Australia
| | - Hayley J Newton
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
- Infection and Immunity Program, Department of Microbiology and Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Sacha Pidot
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Ruth C Massey
- School of Microbiology, University College Cork, Cork, Ireland
- School of Medicine, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Benjamin P Howden
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
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31
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Gründling A, Salipante SJ. Introduction of a Recombineering Oligonucleotide and a CRISPR-Cas9 Gene-Targeting Plasmid into Staphylococcus aureus for Generating a Gene-Deletion Strain. Cold Spring Harb Protoc 2023; 2024:pdb.prot107921. [PMID: 37117031 DOI: 10.1101/pdb.prot107921] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Gene deletions can be generated in Staphylococcus aureus using recombineering in combination with a CRISPR-Cas9 counterselection approach. The method involves first designing the recombineering oligonucleotides and generating the relevant plasmids, and then introducing these elements into S. aureus to generate the desired gene deletion. Here, we describe the second part of this workflow; the introduction of the gene-targeting plasmid and the recombineering oligonucleotide(s) into S. aureus to generate the gene-deletion strain. Specifically, we outline the steps to (1) generate the S. aureus recipient strain for the recombineering CRISPR-Cas9 counterselection method by introducing plasmid pCN-EF2132tet, (2) introduce the recombineering oligonucleotide(s) and gene-targeting plasmid into the pCN-EF2132tet plasmid-containing S. aureus strain, (3) confirm the gene deletion in S. aureus by colony PCR and sequencing, and (4) curate the plasmids following successful gene deletion. To illustrate the method, we give a specific example of how to generate a 55-bp deletion in the geh gene of S. aureus strain RN4220. The protocol, however, can be easily adapted to other strain backgrounds and to generate deletions in other genes.
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Affiliation(s)
- Angelika Gründling
- Section of Molecular Microbiology and Medical Research Council Center for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Stephen J Salipante
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, Washington 98195, USA
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32
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Chen YE, Bousbaine D, Veinbachs A, Atabakhsh K, Dimas A, Yu VK, Zhao A, Enright NJ, Nagashima K, Belkaid Y, Fischbach MA. Engineered skin bacteria induce antitumor T cell responses against melanoma. Science 2023; 380:203-210. [PMID: 37053311 DOI: 10.1126/science.abp9563] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Certain bacterial colonists induce a highly specific T cell response. A hallmark of this encounter is that adaptive immunity develops preemptively, in the absence of an infection. However, the functional properties of colonist-induced T cells are not well defined, limiting our ability to understand anticommensal immunity and harness it therapeutically. We addressed both challenges by engineering the skin bacterium Staphylococcus epidermidis to express tumor antigens anchored to secreted or cell-surface proteins. Upon colonization, engineered S. epidermidis elicits tumor-specific T cells that circulate, infiltrate local and metastatic lesions, and exert cytotoxic activity. Thus, the immune response to a skin colonist can promote cellular immunity at a distal site and can be redirected against a target of therapeutic interest by expressing a target-derived antigen in a commensal.
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Affiliation(s)
- Y Erin Chen
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
- Dermatology Service, San Francisco Veterans Administration Health Care System, San Francisco, CA 94121, USA
| | - Djenet Bousbaine
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Alessandra Veinbachs
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Katayoon Atabakhsh
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Alex Dimas
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Victor K Yu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Aishan Zhao
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Nora J Enright
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Kazuki Nagashima
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
| | - Michael A Fischbach
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, Stanford, CA 94305, USA
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33
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Walzl A, Marbach H, Belikova D, Vogl C, Ehling-Schulz M, Heilbronner S, Grunert T. Prevalence of the SigB-Deficient Phenotype among Clinical Staphylococcus aureus Isolates Linked to Bovine Mastitis. Antibiotics (Basel) 2023; 12:699. [PMID: 37107061 PMCID: PMC10135042 DOI: 10.3390/antibiotics12040699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 04/07/2023] Open
Abstract
Phenotypic adaptation has been associated with persistent, therapy-resistant Staphylococcus aureus infections. Recently, we described within-host evolution towards a Sigma factor B (SigB)-deficient phenotype in a non-human host, a naturally infected dairy cow with chronic, persistent mastitis. However, to our knowledge, the prevalence of SigB deficiency among clinical S. aureus isolates remains unknown. In this study, we screened a collection of bovine mastitis isolates for phenotypic traits typical for SigB deficiency: decreased carotenoid pigmentation, increased proteolysis, secretion of α-hemolysin and exoproteins. Overall, 8 out of 77 (10.4%) isolates of our bovine mastitis collection exhibited the SigB-deficient phenotype. These isolates were assigned to various clonal complexes (CC8, CC9, CC97, CC151, CC3666). We further demonstrated a strong positive correlation between asp23-expression (a marker of SigB activity) and carotenoid pigmentation (r = 0.6359, p = 0.0008), underlining the role of pigmentation as a valuable predictor of the functional status of SigB. Sequencing of the sigB operon (mazEF-rsbUVW-sigB) indicated the phosphatase domain of the RsbU protein as a primary target of mutations leading to SigB deficiency. Indeed, by exchanging single nucleotides in rsbU, we could either induce SigB deficiency or restore the SigB phenotype, demonstrating the pivotal role of RsbU for SigB functionality. The data presented highlight the clinical relevance of SigB deficiency, and future studies are needed to exploit its role in staphylococcal infections.
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Affiliation(s)
- Anna Walzl
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine, A-1210 Vienna, Austria
| | - Helene Marbach
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine, A-1210 Vienna, Austria
| | - Darya Belikova
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, D-72076 Tübingen, Germany
| | - Claus Vogl
- Molecular Genetics, Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine, A-1210 Vienna, Austria
| | - Monika Ehling-Schulz
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine, A-1210 Vienna, Austria
| | - Simon Heilbronner
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, D-72076 Tübingen, Germany
| | - Tom Grunert
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine, A-1210 Vienna, Austria
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34
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Leonard AC, Goncheva MI, Gilbert SE, Shareefdeen H, Petrie LE, Thompson LK, Khursigara CM, Heinrichs DE, Cox G. Autolysin-mediated peptidoglycan hydrolysis is required for the surface display of Staphylococcus aureus cell wall-anchored proteins. Proc Natl Acad Sci U S A 2023; 120:e2301414120. [PMID: 36920922 PMCID: PMC10041135 DOI: 10.1073/pnas.2301414120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 02/14/2023] [Indexed: 03/16/2023] Open
Abstract
Peptidoglycan hydrolases, or autolysins, play a critical role in cell wall remodeling and degradation, facilitating bacterial growth, cell division, and cell separation. In Staphylococcus aureus, the so-called "major" autolysin, Atl, has long been associated with host adhesion; however, the molecular basis underlying this phenomenon remains understudied. To investigate, we used the type V glycopeptide antibiotic complestatin, which binds to peptidoglycan and blocks the activity of autolysins, as a chemical probe of autolysin function. We also generated a chromosomally encoded, catalytically inactive variant of the Atl enzyme. Autolysin-mediated peptidoglycan hydrolysis, in particular Atl-mediated daughter cell separation, was shown to be critical for maintaining optimal surface levels of S. aureus cell wall-anchored proteins, including the fibronectin-binding proteins (FnBPs) and protein A (Spa). As such, disrupting autolysin function reduced the affinity of S. aureus for host cell ligands, and negatively impacted early stages of bacterial colonization in a systemic model of S. aureus infection. Phenotypic studies revealed that Spa was sequestered at the septum of complestatin-treated cells, highlighting that autolysins are required to liberate Spa during cell division. In summary, we reveal the hydrolytic activities of autolysins are associated with the surface display of S. aureus cell wall-anchored proteins. We demonstrate that by blocking autolysin function, type V glycopeptide antibiotics are promising antivirulence agents for the development of strategies to control S. aureus infections.
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Affiliation(s)
- Allison C. Leonard
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of Guelph, GuelphONN1G 2W1, Canada
| | - Mariya I. Goncheva
- Department of Microbiology and Immunology, University of Western Ontario, LondonONN6A 5C1, Canada
| | - Stephanie E. Gilbert
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of Guelph, GuelphONN1G 2W1, Canada
| | - Hiba Shareefdeen
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of Guelph, GuelphONN1G 2W1, Canada
| | - Laurenne E. Petrie
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of Guelph, GuelphONN1G 2W1, Canada
| | - Laura K. Thompson
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of Guelph, GuelphONN1G 2W1, Canada
| | - Cezar M. Khursigara
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of Guelph, GuelphONN1G 2W1, Canada
| | - David E. Heinrichs
- Department of Microbiology and Immunology, University of Western Ontario, LondonONN6A 5C1, Canada
| | - Georgina Cox
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of Guelph, GuelphONN1G 2W1, Canada
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35
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A Staphylococcal Glucosaminidase Drives Inflammatory Responses by Processing Peptidoglycan Chains to Physiological Lengths. Infect Immun 2023; 91:e0050022. [PMID: 36715551 PMCID: PMC9933629 DOI: 10.1128/iai.00500-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The peptidoglycan of Staphylococcus aureus is a critical cell envelope constituent and virulence factor that subverts host immune defenses and provides protection against environmental stressors. Peptidoglycan chains of the S. aureus cell wall are processed to characteristically short lengths by the glucosaminidase SagB. It is well established that peptidoglycan is an important pathogen-associated molecular pattern (PAMP) that is recognized by the host innate immune system and promotes production of proinflammatory cytokines, including interleukin-1β (IL-1β). However, how bacterial processing of peptidoglycan drives IL-1β production is comparatively unexplored. Here, we tested the involvement of staphylococcal glucosaminidases in shaping innate immune responses and identified SagB as a mediator of IL-1β production. A ΔsagB mutant fails to promote IL-1β production by macrophages and dendritic cells, and processing of peptidoglycan by SagB is essential for this response. SagB-dependent IL-1β production by macrophages is independent of canonical pattern recognition receptor engagement and NLRP3 inflammasome-mediated caspase activity. Instead, treatment of macrophages with heat-killed cells from a ΔsagB mutant leads to reduced caspase-independent cleavage of pro-IL-1β, resulting in accumulation of the pro form in the macrophage cytosol. Furthermore, SagB is required for virulence in systemic infection and promotes IL-1β production in a skin and soft tissue infection model. Taken together, our results suggest that the length of S. aureus cell wall glycan chains can drive IL-1β production by innate immune cells through a previously undescribed mechanism related to IL-1β maturation.
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36
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Improved Genome Sequence of Australian Methicillin-Resistant Staphylococcus aureus Strain JKD6159. Microbiol Resour Announc 2023; 12:e0112922. [PMID: 36651736 PMCID: PMC9933698 DOI: 10.1128/mra.01129-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Staphylococcus aureus strain JKD6159 represents a prominent community-acquired methicillin-resistant S. aureus (MRSA) clone in Australia. Here, we report an improved assembly of the original S. aureus JKD6159 genome sequence. By using deep sequencing with multiple technologies combined with carefully curated assembly and polishing, we believe the assembly to contain zero errors.
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37
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Huemer M, Mairpady Shambat S, Hertegonne S, Bergada-Pijuan J, Chang CC, Pereira S, Gómez-Mejia A, Van Gestel L, Bär J, Vulin C, Pfammatter S, Stinear TP, Monk IR, Dworkin J, Zinkernagel AS. Serine-threonine phosphoregulation by PknB and Stp contributes to quiescence and antibiotic tolerance in Staphylococcus aureus. Sci Signal 2023; 16:eabj8194. [PMID: 36595572 DOI: 10.1126/scisignal.abj8194] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 12/06/2022] [Indexed: 01/05/2023]
Abstract
Staphylococcus aureus can cause infections that are often chronic and difficult to treat, even when the bacteria are not antibiotic resistant because most antibiotics act only on metabolically active cells. Subpopulations of persister cells are metabolically quiescent, a state associated with delayed growth, reduced protein synthesis, and increased tolerance to antibiotics. Serine-threonine kinases and phosphatases similar to those found in eukaryotes can fine-tune essential bacterial cellular processes, such as metabolism and stress signaling. We found that acid stress-mimicking conditions that S. aureus experiences in host tissues delayed growth, globally altered the serine and threonine phosphoproteome, and increased threonine phosphorylation of the activation loop of the serine-threonine protein kinase B (PknB). The deletion of stp, which encodes the only annotated functional serine-threonine phosphatase in S. aureus, increased the growth delay and phenotypic heterogeneity under different stress challenges, including growth in acidic conditions, the intracellular milieu of human cells, and abscesses in mice. This growth delay was associated with reduced protein translation and intracellular ATP concentrations and increased antibiotic tolerance. Using phosphopeptide enrichment and mass spectrometry-based proteomics, we identified targets of serine-threonine phosphorylation that may regulate bacterial growth and metabolism. Together, our findings highlight the importance of phosphoregulation in mediating bacterial quiescence and antibiotic tolerance and suggest that targeting PknB or Stp might offer a future therapeutic strategy to prevent persister formation during S. aureus infections.
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Affiliation(s)
- Markus Huemer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Srikanth Mairpady Shambat
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sanne Hertegonne
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Judith Bergada-Pijuan
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Chun-Chi Chang
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sandro Pereira
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Alejandro Gómez-Mejia
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Lies Van Gestel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Julian Bär
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Clément Vulin
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sibylle Pfammatter
- Functional Genomics Center Zurich, ETH/University of Zurich, Zurich, Switzerland
| | - Timothy P Stinear
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Ian R Monk
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Jonathan Dworkin
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Annelies S Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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Dietrich A, Gajdiss M, Türck M, Monk I, Bierbaum G. Bacterial Two Component Systems: Overexpression and Purification: In Vitro and In Vivo Inhibitor Screens. Methods Mol Biol 2023; 2601:313-333. [PMID: 36445592 DOI: 10.1007/978-1-0716-2855-3_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Bacterial histidine kinases are promising targets for new antimicrobial agents. In antibacterial therapy, such agents could inhibit bacterial growth by targeting essential two-component regulatory systems or resensitize bacteria to known antibiotics by blocking stress responses upon cell wall or cell membrane damage. However, (i) activity assays using truncated kinase proteins, that is, the cytoplasmic domains containing the conserved histidine residue for phosphorylation, have been shown to produce artifacts, and (ii) the purification of the full-length histidine kinases is complicated. Here, we describe a standard protocol for the recombinant expression and purification of functional full-length histidine kinases and other membrane proteins from Gram-positive bacteria that do not harbor more than two trans-membrane domains in an Escherichia coli host. This guide also presents in vitro and in vivo phosphorylation assays to screen for new antimicrobial compounds that target bacterial histidine kinases, either using a traditional radioactively labeled ATP assay to quantify histidine kinase phosphorylation or Phos-tag acrylamide gel electrophoresis to examine histidine kinase phosphorylation through mobility shift in the polyacrylamide gel. In addition, we describe the use of Phos-tag combined with a western blot approach to visualize the phosphorylation of a response regulator in vivo.
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Affiliation(s)
- Alina Dietrich
- Institute of Medical Microbiology, Immunology and Parasitology, University of Bonn, Bonn, Germany
| | - Mike Gajdiss
- Institute of Medical Microbiology, Immunology and Parasitology, University of Bonn, Bonn, Germany
| | - Michael Türck
- Institute of Medical Microbiology, Immunology and Parasitology, University of Bonn, Bonn, Germany
| | - Ian Monk
- Institute of Medical Microbiology, Immunology and Parasitology, University of Bonn, Bonn, Germany
- Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - Gabriele Bierbaum
- Institute of Medical Microbiology, Immunology and Parasitology, University of Bonn, Bonn, Germany.
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Schiffer CJ, Grätz C, Pfaffl MW, Vogel RF, Ehrmann MA. Characterization of the Staphylococcus xylosus methylome reveals a new variant of type I restriction modification system in staphylococci. Front Microbiol 2023; 14:946189. [PMID: 36970683 PMCID: PMC10030836 DOI: 10.3389/fmicb.2023.946189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 02/13/2023] [Indexed: 03/29/2023] Open
Abstract
Restriction modification (RM) systems are known to provide a strong barrier to the exchange of DNA between and within bacterial species. Likewise, DNA methylation is known to have an important function in bacterial epigenetics regulating essential pathways such as DNA replication and the phase variable expression of prokaryotic phenotypes. To date, research on staphylococcal DNA methylation focused mainly on the two species Staphylococcus aureus and S. epidermidis. Less is known about other members of the genus such as S. xylosus, a coagulase-negative commensal of mammalian skin. The species is commonly used as starter organism in food fermentations but is also increasingly considered to have an as yet elusive function in bovine mastitis infections. We analyzed the methylomes of 14 S. xylosus strains using single-molecular, real-time (SMRT) sequencing. Subsequent in silico sequence analysis allowed identification of the RM systems and assignment of the respective enzymes to the discovered modification patterns. Hereby the presence of type I, II, III and IV RM systems in varying numbers and combinations among the different strains was revealed, clearly distinguishing the species from what is known for other members of the genus so far. In addition, the study characterizes a newly discovered type I RM system, encoded by S. xylosus but also by a variety of other staphylococcal species, with a hitherto unknown gene arrangement that involves two specificity units instead of one (hsdRSMS). Expression of different versions of the operon in E. coli showed proper base modification only when genes encoding both hsdS subunits were present. This study provides new insights into the general understanding of the versatility and function of RM systems as well as the distribution and variations in the genus Staphylococcus.
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Affiliation(s)
- Carolin J. Schiffer
- Chair of Technical Microbiology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- *Correspondence: Carolin J. Schiffer,
| | - Christian Grätz
- Chair of Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Michael W. Pfaffl
- Chair of Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Rudi F. Vogel
- Chair of Technical Microbiology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Matthias A. Ehrmann
- Chair of Technical Microbiology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
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Galarion LH, Clarke JE, Schofield H, O'Neill AJ. Comment on: Identification of a novel tedizolid resistance mutation in rpoB of MRSA after in vitro serial passage. J Antimicrob Chemother 2022; 78:317-318. [PMID: 36416794 DOI: 10.1093/jac/dkac397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Luiza H Galarion
- Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Justin E Clarke
- Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Harry Schofield
- Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Alex J O'Neill
- Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
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Ersoy SC, Gonçalves B, Cavaco G, Manna AC, Sobral RG, Nast CC, Proctor RA, Chambers HF, Cheung A, Bayer AS. Influence of Sodium Bicarbonate on Wall Teichoic Acid Synthesis and β-Lactam Sensitization in NaHCO 3-Responsive and Nonresponsive Methicillin-Resistant Staphylococcus aureus. Microbiol Spectr 2022; 10:e0342222. [PMID: 36377886 PMCID: PMC9769754 DOI: 10.1128/spectrum.03422-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) strains pose major treatment challenges due to their innate resistance to most β-lactams under standard in vitro antimicrobial susceptibility testing conditions. A novel phenotype among MRSA, termed "NaHCO3 responsiveness," where certain strains display increased susceptibility to β-lactams in the presence of NaHCO3, has been identified among a relatively large proportion of MRSA isolates. One underlying mechanism of NaHCO3 responsiveness appears to be related to decreased expression and altered functionality of several genes and proteins involved in cell wall synthesis and maturation. Here, we studied the impact of NaHCO3 on wall teichoic acid (WTA) synthesis, a process intimately linked to peptidoglycan (PG) synthesis and functionality, in NaHCO3-responsive versus -nonresponsive MRSA isolates. NaHCO3 sensitized responsive MRSA strains to cefuroxime, a specific penicillin-binding protein 2 (PBP2)-inhibitory β-lactam known to synergize with early WTA synthesis inhibitors (e.g., ticlopidine). Combining cefuroxime with ticlopidine with or without NaHCO3 suggested that these latter two agents target the same step in WTA synthesis. Further, NaHCO3 decreased the abundance and molecular weight of WTA only in responsive strains. Additionally, NaHCO3 stimulated increased autolysis and aberrant cell division in responsive strains, two phenotypes associated with disruption of WTA synthesis. Of note, studies of key genes involved in the WTA biosynthetic pathway (e.g., tarO, tarG, dltA, and fmtA) indicated that the inhibitory impact of NaHCO3 on WTA biosynthesis in responsive strains likely occurred posttranslationally. IMPORTANCE MRSA is generally viewed as resistant to standard β-lactam antibiotics. However, a NaHCO3-responsive phenotype is observed in a substantial proportion of clinical MRSA strains in vitro, i.e., isolates which demonstrate enhanced susceptibility to standard β-lactam antibiotics (e.g., oxacillin) in the presence of NaHCO3. This phenotype correlates with increased MRSA clearance in vivo by standard β-lactam antibiotics, suggesting that patients with infections caused by such MRSA strains might be amenable to treatment with β-lactams. The mechanism(s) behind this phenotype is not fully understood but appears to involve mecA-PBP2a production and maturation axes. Our study adds significantly to this body of knowledge in terms of additional mechanistic targets of NaHCO3 in selected MRSA strains. This investigation demonstrates that NaHCO3 has direct impacts on S. aureus wall teichoic acid biosynthesis in NaHCO3-responsive MRSA. These findings provide an additional target for new agents being designed to synergistically kill MRSA using β-lactam antibiotics.
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Affiliation(s)
| | - Barbara Gonçalves
- Laboratory of Molecular Microbiology of Bacterial Pathogens, UCIBIO, Applied Molecular Biosciences Unit, Department of Life Sciences, Nova School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Nova School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
| | - Gonçalo Cavaco
- Laboratory of Molecular Microbiology of Bacterial Pathogens, UCIBIO, Applied Molecular Biosciences Unit, Department of Life Sciences, Nova School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Nova School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
| | - Adhar C. Manna
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Rita G. Sobral
- Laboratory of Molecular Microbiology of Bacterial Pathogens, UCIBIO, Applied Molecular Biosciences Unit, Department of Life Sciences, Nova School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Nova School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
| | - Cynthia C. Nast
- Cedars-Sinai Medical Center, Los Angeles, California, USA
- Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Richard A. Proctor
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- Department of Medical Microbiology/Immunology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | | | - Ambrose Cheung
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Arnold S. Bayer
- The Lundquist Institute, Torrance, California, USA
- Geffen School of Medicine at UCLA, Los Angeles, California, USA
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42
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Increased Expression of Efflux Pump norA Drives the Rapid Evolutionary Trajectory from Tolerance to Resistance against Ciprofloxacin in Staphylococcus aureus. Antimicrob Agents Chemother 2022; 66:e0059422. [PMID: 36445128 PMCID: PMC9765010 DOI: 10.1128/aac.00594-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The intensively intermittent use of antibiotics promotes the rapid evolution of tolerance, which may lead to resistance acquisition in the following evolutionary trajectory. In addition to directly exporting antibiotics as an instant resistance strategy, efflux pumps are overexpressed in tolerant strains. To investigate how efflux pumps participate in resistance development from tolerance to resistance, we performed in vitro evolutional experiments against the antibiotic ciprofloxacin in norA efflux pump mutants of Staphylococcus aureus. These experiments demonstrated that overexpression of norA rapidly facilitated the development of ciprofloxacin resistance from tolerance to resistance through elevated spontaneous mutations. The generated resistance mutations were further fixed in the population by increasing survival ability. The observed Ser80Phe and Glu84Lys mutations in the topoisomerase IV ParC (GrlA in S. aureus) may be responsible for tolerant strains to develop resistance to ciprofloxacin since it has been reported that such mutations disrupt the water-metal ion bridge between quinolones and ParC. MepA and Sav1866 are related to the same antibiotic (ciprofloxacin) susceptibility as NorA, and they also contributed to resistance development against ciprofloxacin. MgrA positively regulated NorA expression and the development of ciprofloxacin resistance. Importantly, blocking the evolutionary pathway by coadministering ciprofloxacin with the efflux pump inhibitor reserpine effectively delayed the resistance acquisition in an in vitro experiment. This study illustrated the role of efflux pumps in the evolutionary trajectory from tolerance to resistance. The delayed resistance development caused by the efflux pump inhibitor illuminates a possible strategy for postponing the resistance acquisition from tolerance to resistance by disrupting efflux pumps.
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Molecular Characterization of Clinical Rel Mutations and Consequences for Resistance Expression and Fitness in Staphylococcus aureus. Antimicrob Agents Chemother 2022; 66:e0093822. [PMID: 36346240 PMCID: PMC9764984 DOI: 10.1128/aac.00938-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The stringent response (SR) is a universal stress response that acts as a global regulator of bacterial physiology and virulence, and is a contributor to antibiotic tolerance and resistance. In most bacteria, the SR is controlled by a bifunctional enzyme, Rel, which both synthesizes and hydrolyzes the alarmone (p)ppGpp via two distinct catalytic domains. The balance between these antagonistic activities is fine-tuned to the needs of the cell and, in a "relaxed" state, the hydrolase activity of Rel dominates. We have previously shown that two single amino acid substitutions in Rel (that were identified in clinical isolates from persistent infections) confer elevated basal concentrations of (p)ppGpp and consequent multidrug tolerance in Staphylococcus aureus. Here, we explore the molecular details of how these mutations bring about this increase in cellular (p)ppGpp and investigate the wider cellular consequences in terms of resistance expression, resistance development, and bacterial fitness. Using enzyme assays, we show that both these mutations drastically reduce the hydrolase activity of Rel, thereby shifting the balance of Rel activity in favor of (p)ppGpp synthesis. We also demonstrate that these mutations induce high-level, homogeneous expression of β-lactam resistance and confer a significant fitness advantage in the presence of bactericidal antibiotics (but a fitness cost in the absence of antibiotic). In contrast, these mutations do not appear to accelerate the emergence of endogenous resistance mutations in vitro. Overall, our findings reveal the complex nature of Rel regulation and the multifaceted implications of clinical Rel mutations in terms of antibiotic efficacy and bacteria survival.
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Rodrigues Lopes I, Alcantara LM, Silva RJ, Josse J, Vega EP, Cabrerizo AM, Bonhomme M, Lopez D, Laurent F, Vandenesch F, Mano M, Eulalio A. Microscopy-based phenotypic profiling of infection by Staphylococcus aureus clinical isolates reveals intracellular lifestyle as a prevalent feature. Nat Commun 2022; 13:7174. [PMID: 36418309 PMCID: PMC9684519 DOI: 10.1038/s41467-022-34790-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/08/2022] [Indexed: 11/24/2022] Open
Abstract
Staphylococcus aureus is increasingly recognized as a facultative intracellular pathogen, although the significance and pervasiveness of its intracellular lifestyle remain controversial. Here, we applied fluorescence microscopy-based infection assays and automated image analysis to profile the interaction of 191 S. aureus isolates from patients with bone/joint infections, bacteremia, and infective endocarditis, with four host cell types, at five times post-infection. This multiparametric analysis revealed that almost all isolates are internalized and that a large fraction replicate and persist within host cells, presenting distinct infection profiles in non-professional vs. professional phagocytes. Phenotypic clustering highlighted interesting sub-groups, including one comprising isolates exhibiting high intracellular replication and inducing delayed host death in vitro and in vivo. These isolates are deficient for the cysteine protease staphopain A. This study establishes S. aureus intracellular lifestyle as a prevalent feature of infection, with potential implications for the effective treatment of staphylococcal infections.
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Affiliation(s)
- Ines Rodrigues Lopes
- grid.8051.c0000 0000 9511 4342RNA & Infection Laboratory, Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342Functional Genomics and RNA-based Therapeutics Laboratory, Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
| | - Laura Maria Alcantara
- grid.8051.c0000 0000 9511 4342RNA & Infection Laboratory, Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
| | - Ricardo Jorge Silva
- grid.8051.c0000 0000 9511 4342Functional Genomics and RNA-based Therapeutics Laboratory, Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
| | - Jerome Josse
- grid.15140.310000 0001 2175 9188Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Elena Pedrero Vega
- grid.4711.30000 0001 2183 4846National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, Spain
| | - Ana Marina Cabrerizo
- grid.4711.30000 0001 2183 4846National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, Spain
| | - Melanie Bonhomme
- grid.15140.310000 0001 2175 9188Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Daniel Lopez
- grid.4711.30000 0001 2183 4846National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, Spain
| | - Frederic Laurent
- grid.15140.310000 0001 2175 9188Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France ,grid.413852.90000 0001 2163 3825Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Francois Vandenesch
- grid.15140.310000 0001 2175 9188Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France ,grid.413852.90000 0001 2163 3825Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Miguel Mano
- grid.8051.c0000 0000 9511 4342Functional Genomics and RNA-based Therapeutics Laboratory, Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal ,grid.8051.c0000 0000 9511 4342Department of Life Sciences, University of Coimbra, Coimbra, Portugal ,grid.13097.3c0000 0001 2322 6764British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine & Sciences, King’s College London, London, United Kingdom
| | - Ana Eulalio
- grid.8051.c0000 0000 9511 4342RNA & Infection Laboratory, Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal ,grid.7311.40000000123236065Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal ,grid.7445.20000 0001 2113 8111Department of Life Sciences, Imperial College London, London, United Kingdom
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Characterization of the Secreted Acid Phosphatase SapS Reveals a Novel Virulence Factor of Staphylococcus aureus That Contributes to Survival and Virulence in Mice. Int J Mol Sci 2022; 23:ijms232214031. [PMID: 36430506 PMCID: PMC9692844 DOI: 10.3390/ijms232214031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/07/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Staphylococcus aureus possesses a large arsenal of immune-modulating factors, enabling it to bypass the immune system's response. Here, we demonstrate that the acid phosphatase SapS is secreted during macrophage infection and promotes its intracellular survival in this type of immune cell. In animal models, the SA564 sapS mutant demonstrated a significantly lower bacterial burden in liver and renal tissues of mice at four days post infection in comparison to the wild type, along with lower pathogenicity in a zebrafish infection model. The SA564 sapS mutant elicits a lower inflammatory response in mice than the wild-type strain, while S. aureus cells harbouring a functional sapS induce a chemokine response that favours the recruitment of neutrophils to the infection site. Our in vitro and quantitative transcript analysis show that SapS has an effect on S. aureus capacity to adapt to oxidative stress during growth. SapS is also involved in S. aureus biofilm formation. Thus, this study shows for the first time that SapS plays a significant role during infection, most likely through inhibiting a variety of the host's defence mechanisms.
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Morales-Laverde L, Trobos M, Echeverz M, Solano C, Lasa I. Functional analysis of intergenic regulatory regions of genes encoding surface adhesins in Staphylococcus aureus isolates from periprosthetic joint infections. Biofilm 2022; 4:100093. [PMID: 36408060 PMCID: PMC9667196 DOI: 10.1016/j.bioflm.2022.100093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/31/2022] [Accepted: 11/07/2022] [Indexed: 11/09/2022] Open
Abstract
Staphylococcus aureus is a leading cause of prosthetic joint infections (PJI). Surface adhesins play an important role in the primary attachment to plasma proteins that coat the surface of prosthetic devices after implantation. Previous efforts to identify a genetic component of the bacterium that confers an enhanced capacity to cause PJI have focused on gene content, kmers, or single-nucleotide polymorphisms (SNPs) in coding sequences. Here, using a collection of S. aureus strains isolated from PJI and wounds, we investigated whether genetic variations in the regulatory region of genes encoding surface adhesins lead to differences in their expression levels and modulate the capacity of S. aureus to colonize implanted prosthetic devices. The data revealed that S. aureus isolates from the same clonal complex (CC) contain a specific pattern of SNPs in the regulatory region of genes encoding surface adhesins. As a consequence, each clonal lineage shows a specific profile of surface proteins expression. Co-infection experiments with representative isolates of the most prevalent CCs demonstrated that some lineages have a higher capacity to colonize implanted catheters in a murine infection model, which correlated with a greater ability to form a biofilm on coated surfaces with plasma proteins. Together, results indicate that differences in the expression level of surface adhesins may modulate the propensity of S. aureus strains to cause PJI. Given the high conservation of surface proteins among staphylococci, our work lays the framework for investigating how diversification at intergenic regulatory regions affects the capacity of S. aureus to colonize the surface of medical implants.
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Gerlach D, Sieber RN, Larsen J, Krusche J, De Castro C, Baumann J, Molinaro A, Peschel A. Horizontal transfer and phylogenetic distribution of the immune evasion factor tarP. Front Microbiol 2022; 13:951333. [PMID: 36386695 PMCID: PMC9650247 DOI: 10.3389/fmicb.2022.951333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/12/2022] [Indexed: 11/29/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA), a major human pathogen, uses the prophage-encoded tarP gene as an important immune evasion factor. TarP glycosylates wall teichoic acid (WTA) polymers, major S. aureus surface antigens, to impair WTA immunogenicity and impede host defence. However, tarP phages appear to be restricted to only a few MRSA clonal lineages, including clonal complexes (CC) 5 and 398, for unknown reasons. We demonstrate here that tarP-encoding prophages can be mobilized to lysogenize other S. aureus strains. However, transfer is largely restricted to closely related clones. Most of the non-transducible clones encode tarM, which generates a WTA glycosylation pattern distinct from that mediated by TarP. However, tarM does not interfere with infection by tarP phages. Clonal complex-specific Type I restriction-modification systems were the major reasons for resistance to tarP phage infection. Nevertheless, tarP phages were found also in unrelated S. aureus clones indicating that tarP has the potential to spread to distant clonal lineages and contribute to the evolution of new MRSA clones.
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Affiliation(s)
- David Gerlach
- Interfaculty Institute of Microbiology and Infection Medicine, Infection Biology Section, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Cluster of Excellence EXC2124 Controlling Microbes to Fight Infection, University of Tübingen, Tübingen, Germany
| | | | | | - Janes Krusche
- Interfaculty Institute of Microbiology and Infection Medicine, Infection Biology Section, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Cluster of Excellence EXC2124 Controlling Microbes to Fight Infection, University of Tübingen, Tübingen, Germany
| | | | - Juliane Baumann
- Interfaculty Institute of Microbiology and Infection Medicine, Infection Biology Section, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Cluster of Excellence EXC2124 Controlling Microbes to Fight Infection, University of Tübingen, Tübingen, Germany
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples, Naples, Italy
| | - Andreas Peschel
- Interfaculty Institute of Microbiology and Infection Medicine, Infection Biology Section, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Cluster of Excellence EXC2124 Controlling Microbes to Fight Infection, University of Tübingen, Tübingen, Germany
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Glucose Mediates Niche-Specific Repression of Staphylococcus aureus Toxic Shock Syndrome Toxin-1 through the Activity of CcpA in the Vaginal Environment. J Bacteriol 2022; 204:e0026922. [PMID: 36106854 PMCID: PMC9578429 DOI: 10.1128/jb.00269-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus chronically colonizes up to 30% of the human population on the skin or mucous membranes, including the nasal tract or vaginal canal. While colonization is often benign, this bacterium also has the capability to cause serious infections. Menstrual toxic shock syndrome (mTSS) is a serious toxinosis associated with improper use of tampons, which can induce an environment that is favorable to the production of the superantigen known as toxic shock syndrome toxin-1 (TSST-1). To better understand environmental signaling that influences TSST-1 production, we analyzed expression in the prototype mTSS strain S. aureus MN8. Using transcriptional and protein-based analysis in two niche-related media, we observed that TSST-1 expression was significantly higher in synthetic nasal medium (SNM) than in vaginally defined medium (VDM). One major divergence in medium composition was high glucose concentration in VDM. The glucose-dependent virulence regulator gene ccpA was deleted in MN8, and, compared with wild-type MN8, we observed increased TSST-1 expression in the ΔccpA mutant when grown in VDM, suggesting that TSST-1 is repressed by catabolite control protein A (CcpA) in the vaginal environment. We were able to relieve CcpA-mediated repression by modifying the glucose level in vaginal conditions, confirming that changes in nutritional conditions contribute to the overexpression of TSST-1 that can lead to mTSS. We also compared CcpA-mediated repression to other key regulators of tst, finding that CcpA regulation is dominant compared to other characterized regulatory mechanisms. This study underlines the importance of environmental signaling for S. aureus pathogenesis in the context of mTSS. IMPORTANCE Menstrual toxic shock syndrome (mTSS) is caused by strains of Staphylococcus aureus that overproduce a toxin known as toxic shock syndrome toxin-1 (TSST-1). This work studied how glucose levels in a model vaginal environment could influence the amount of TSST-1 that is produced by S. aureus. We found that high levels of glucose repress TSST-1 production, and this is done by a regulatory protein called catabolite control protein A (CcpA). The research also demonstrated that, compared with other regulatory proteins, the CcpA regulator appears to be the most important for maintaining low levels of TSST-1 in the vaginal environment, and this information helps to understand how changes in the vaginal environmental can lead to mTSS.
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Regulation of the Sae Two-Component System by Branched-Chain Fatty Acids in Staphylococcus aureus. mBio 2022; 13:e0147222. [PMID: 36135382 PMCID: PMC9600363 DOI: 10.1128/mbio.01472-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Staphylococcus aureus is a ubiquitous Gram-positive bacterium and an opportunistic human pathogen. S. aureus pathogenesis relies on a complex network of regulatory factors that adjust gene expression. Two important factors in this network are CodY, a repressor protein responsive to nutrient availability, and the SaeRS two-component system (TCS), which responds to neutrophil-produced factors. Our previous work revealed that CodY regulates the secretion of many toxins indirectly via Sae through an unknown mechanism. We report that disruption of codY results in increased levels of phosphorylated SaeR (SaeR~P) and that codY mutant cell membranes contain a higher percentage of branched-chain fatty acids (BCFAs) than do wild-type membranes, prompting us to hypothesize that changes to membrane composition modulate the activity of the SaeS sensor kinase. Disrupting the lpdA gene encoding dihydrolipoyl dehydrogenase, which is critical for BCFA synthesis, significantly reduced the abundance of SaeR, phosphorylated SaeR, and BCFAs in the membrane, resulting in reduced toxin production and attenuated virulence. Lower SaeR levels could be explained in part by reduced stability. Sae activity in the lpdA mutant could be complemented genetically and chemically with exogenous short- or full-length BCFAs. Intriguingly, lack of lpdA also alters the activity of other TCSs, suggesting a specific BCFA requirement managing the basal activity of multiple TCSs. These results reveal a novel method of posttranscriptional virulence regulation via BCFA synthesis, potentially linking CodY activity to multiple virulence regulators in S. aureus.
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50
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Manna AC, Leo S, Girel S, González-Ruiz V, Rudaz S, Francois P, Cheung AL. Teg58, a small regulatory RNA, is involved in regulating arginine biosynthesis and biofilm formation in Staphylococcus aureus. Sci Rep 2022; 12:14963. [PMID: 36056144 PMCID: PMC9440087 DOI: 10.1038/s41598-022-18815-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 08/19/2022] [Indexed: 12/02/2022] Open
Abstract
Staphylococcus aureus adapts to different environments by sensing and responding to diverse environmental cues. The responses are coordinately regulated by regulatory proteins, and small regulatory RNAs at the transcriptional and translational levels. Here, we characterized teg58, a SarA repressed sRNA, using ChIP-Seq and RNA-Seq analysis of a sarA mutant. Phenotypic and genetic analyses indicated that inactivation of teg58 led to reduced biofilm formation in a process that is independent of SarA, agr, PIA, and PSMs. RNA-Seq analysis of teg58 mutant revealed up-regulation of arginine biosynthesis genes (i.e., argGH) as well as the ability of the mutant to grow in a chemical defined medium (CDM) lacking L-arginine. Exogenous L-arginine or endogenous induction of argGH led to decreased biofilm formation in parental strains. Further analysis in vitro and in vivo demonstrated that the specific interaction between teg58 and the argGH occurred at the post-transcriptional level to repress arginine synthesis. Biochemical and genetic analyses of various arginine catabolic pathway genes demonstrated that the catabolic pathway did not play a significant role in reduced biofilm formation in the teg58 mutant. Overall, results suggest that teg58 is a regulatory sRNA that plays an important role in modulating arginine biosynthesis and biofilm formation in S. aureus.
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Affiliation(s)
- Adhar C Manna
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA.
| | - Stefano Leo
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals and University Medical Center, Rue Michel-Servet 1, 1211, Geneva 4, Switzerland
| | - Sergey Girel
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- University Medical Center, Rue Michel-Servet 1, 1211, Geneva 4, Switzerland
| | - Víctor González-Ruiz
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- University Medical Center, Rue Michel-Servet 1, 1211, Geneva 4, Switzerland
| | - Serge Rudaz
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- University Medical Center, Rue Michel-Servet 1, 1211, Geneva 4, Switzerland
| | - Patrice Francois
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals and University Medical Center, Rue Michel-Servet 1, 1211, Geneva 4, Switzerland
| | - Ambrose L Cheung
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
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