1
|
Jain S, Bhowmick A, Jeong B, Bae T, Ghosh A. Unravelling the physiological roles of mazEF toxin-antitoxin system on clinical MRSA strain by CRISPR RNA-guided cytidine deaminase. J Biomed Sci 2022; 29:28. [PMID: 35524246 PMCID: PMC9077811 DOI: 10.1186/s12929-022-00810-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/22/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Curiosity on toxin-antitoxin modules has increased intensely over recent years as it is ubiquitously present in many bacterial genomes, including pathogens like Methicillin-resistant Staphylococcus aureus (MRSA). Several cellular functions of TA systems have been proposed however, their exact role in cellular physiology remains unresolved. METHODS This study aims to find out the impact of the mazEF toxin-antitoxin module on biofilm formation, pathogenesis, and antibiotic resistance in an isolated clinical ST239 MRSA strain, by constructing mazE and mazF mutants using CRISPR-cas9 base-editing plasmid (pnCasSA-BEC). Transcriptome analysis (RNA-seq) was performed for the mazE antitoxin mutant in order to identify the differentially regulated genes. The biofilm formation was also assessed for the mutant strains. Antibiogram profiling was carried out for both the generated mutants followed by murine experiment to determine the pathogenicity of the constructed strains. RESULTS For the first time our work showed, that MazF promotes cidA mediated cell death and lysis for biofilm formation without playing any significant role in host virulence as suggested by the murine experiment. Interestingly, the susceptibility to oxacillin, daptomycin and vancomycin was reduced significantly by the activated MazF toxin in the mazE mutant strain. CONCLUSIONS Our study reveals that activated MazF toxin leads to resistance to antibiotics like oxacillin, daptomycin and vancomycin. Therefore, in the future, any potential antibacterial drug can be designed to target MazF toxin against the problematic multi-drug resistant bug.
Collapse
Affiliation(s)
- Sonia Jain
- Infectious Disease and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, 700032, India.
| | - Arghya Bhowmick
- Department of Biochemistry, Bose Institute, EN Block, Sector-V, Kolkata, 700091, India
| | - Bohyun Jeong
- Department of Microbiology, Kosin University College of Medicine, Busan, 49267, South Korea
| | - Taeok Bae
- Department of Microbiology and Immunology, Indiana University, School of Medicine-Northwest, Gary, IN, 46408-1197, USA
| | - Abhrajyoti Ghosh
- Department of Biochemistry, Bose Institute, EN Block, Sector-V, Kolkata, 700091, India.
| |
Collapse
|
2
|
Sierra R, Prados J, Panasenko OO, Andrey DO, Fleuchot B, Redder P, Kelley WL, Viollier PH, Renzoni A. Insights into the global effect on Staphylococcus aureus growth arrest by induction of the endoribonuclease MazF toxin. Nucleic Acids Res 2020; 48:8545-8561. [PMID: 32735661 PMCID: PMC7470975 DOI: 10.1093/nar/gkaa617] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 06/18/2020] [Accepted: 07/27/2020] [Indexed: 12/22/2022] Open
Abstract
A crucial bacterial strategy to avoid killing by antibiotics is to enter a growth arrested state, yet the molecular mechanisms behind this process remain elusive. The conditional overexpression of mazF, the endoribonuclease toxin of the MazEF toxin–antitoxin system in Staphylococcus aureus, is one approach to induce bacterial growth arrest, but its targets remain largely unknown. We used overexpression of mazF and high-throughput sequence analysis following the exact mapping of non-phosphorylated transcriptome ends (nEMOTE) technique to reveal in vivo toxin cleavage sites on a global scale. We obtained a catalogue of MazF cleavage sites and unearthed an extended MazF cleavage specificity that goes beyond the previously reported one. We correlated transcript cleavage and abundance in a global transcriptomic profiling during mazF overexpression. We observed that MazF affects RNA molecules involved in ribosome biogenesis, cell wall synthesis, cell division and RNA turnover and thus deliver a plausible explanation for how mazF overexpression induces stasis. We hypothesize that autoregulation of MazF occurs by directly modulating the MazEF operon, such as the rsbUVW genes that regulate the sigma factor SigB, including an observed cleavage site on the MazF mRNA that would ultimately play a role in entry and exit from bacterial stasis.
Collapse
Affiliation(s)
- Roberto Sierra
- Service of Infectious Diseases, Department of Medical Specialties, Geneva University Hospitals and Medical School, Geneva 1211, Switzerland.,Department of Microbiology and Molecular Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Julien Prados
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Olesya O Panasenko
- Service of Infectious Diseases, Department of Medical Specialties, Geneva University Hospitals and Medical School, Geneva 1211, Switzerland
| | - Diego O Andrey
- Service of Infectious Diseases, Department of Medical Specialties, Geneva University Hospitals and Medical School, Geneva 1211, Switzerland.,Department of Microbiology and Molecular Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Betty Fleuchot
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Peter Redder
- Centre de Biologie Intégrative, Université de Toulouse III, Toulouse 31400, France
| | - William L Kelley
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Adriana Renzoni
- Service of Infectious Diseases, Department of Medical Specialties, Geneva University Hospitals and Medical School, Geneva 1211, Switzerland.,Department of Microbiology and Molecular Medicine, University of Geneva, Geneva 1211, Switzerland
| |
Collapse
|
3
|
Khemici V, Prados J, Petrignani B, Di Nolfi B, Bergé E, Manzano C, Giraud C, Linder P. The DEAD-box RNA helicase CshA is required for fatty acid homeostasis in Staphylococcus aureus. PLoS Genet 2020; 16:e1008779. [PMID: 32730248 PMCID: PMC7392221 DOI: 10.1371/journal.pgen.1008779] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/15/2020] [Indexed: 01/05/2023] Open
Abstract
Staphylococcus aureus is an opportunistic pathogen that can grow in a wide array of conditions: on abiotic surfaces, on the skin, in the nose, in planktonic or biofilm forms and can cause many type of infections. Consequently, S. aureus must be able to adapt rapidly to these changing growth conditions, an ability largely driven at the posttranscriptional level. RNA helicases of the DEAD-box family play an important part in this process. In particular, CshA, which is part of the degradosome, is required for the rapid turnover of certain mRNAs and its deletion results in cold-sensitivity. To understand the molecular basis of this phenotype, we conducted a large genetic screen isolating 82 independent suppressors of cold growth. Full genome sequencing revealed the fatty acid synthesis pathway affected in many suppressor strains. Consistent with that result, sublethal doses of triclosan, a FASII inhibitor, can partially restore growth of a cshA mutant in the cold. Overexpression of the genes involved in branched-chain fatty acid synthesis was also able to suppress the cold-sensitivity. Using gas chromatography analysis of fatty acids, we observed an imbalance of straight and branched-chain fatty acids in the cshA mutant, compared to the wild-type. This imbalance is compensated in the suppressor strains. Thus, we reveal for the first time that the cold sensitive growth phenotype of a DEAD-box mutant can be explained, at least partially, by an improper membrane composition. The defect correlates with an accumulation of the pyruvate dehydrogenase complex mRNA, which is inefficiently degraded in absence of CshA. We propose that the resulting accumulation of acetyl-CoA fuels straight-chained fatty acid production at the expense of the branched ones. Strikingly, addition of acetate into the medium mimics the cshA deletion phenotype, resulting in cold sensitivity suppressed by the mutations found in our genetic screen or by sublethal doses of triclosan. DEAD-box RNA helicases are highly conserved proteins found in all domains of life. By acting on RNA secondary structures they determine the fate of RNA from transcription to degradation. Bacterial DEAD-box RNA helicases are not essential under laboratory conditions but are required for fitness and under stress conditions. Whereas many DEAD-box protein mutants display a cold sensitive phenotype, the underlying mechanisms have been studied only in few cases and found to be associated with ribosome biogenesis. We aimed here to elucidate the cold sensitivity of a cshA mutant in the Gram-positive opportunist pathogen Staphylococcus aureus. Our study revealed for the first time that part of the cold sensitivity is related to the inability of the bacterium to adapt the cytoplasmic membrane to lower temperatures. We propose that straight-chain fatty acid synthesis, reduced to sustain growth at lower temperature, is maintained due to inefficient turn-over of the pyruvate dehydrogenase mRNA, leading to elevated acetyl-CoA levels. This study allowed us to unravel at least in part the cold sensitive phenotype and to show that the pyruvate dehydrogenase activity plays an important function in the regulation of fatty acid composition of the membrane, a process that remains poorly understood in Gram-positive bacteria.
Collapse
Affiliation(s)
- Vanessa Khemici
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Julien Prados
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Bianca Petrignani
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Benjamin Di Nolfi
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Elodie Bergé
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Caroline Manzano
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Caroline Giraud
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Patrick Linder
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- * E-mail:
| |
Collapse
|
4
|
Wood A, Irving SE, Bennison DJ, Corrigan RM. The (p)ppGpp-binding GTPase Era promotes rRNA processing and cold adaptation in Staphylococcus aureus. PLoS Genet 2019; 15:e1008346. [PMID: 31465450 PMCID: PMC6738653 DOI: 10.1371/journal.pgen.1008346] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 09/11/2019] [Accepted: 08/05/2019] [Indexed: 12/15/2022] Open
Abstract
Ribosome assembly cofactors are widely conserved across all domains of life. One such group, the ribosome-associated GTPases (RA-GTPase), act as molecular switches to coordinate ribosome assembly. We previously identified the Staphylococcus aureus RA-GTPase Era as a target for the stringent response alarmone (p)ppGpp, with binding leading to inhibition of GTPase activity. Era is highly conserved throughout the bacterial kingdom and is essential in many species, although the function of Era in ribosome assembly is unclear. Here we show that Era is not essential in S. aureus but is important for 30S ribosomal subunit assembly. Protein interaction studies reveal that Era interacts with the 16S rRNA endonuclease YbeY and the DEAD-box RNA helicase CshA. We determine that both Era and CshA are required for growth at suboptimal temperatures and rRNA processing. Era and CshA also form direct interactions with the (p)ppGpp synthetase RelSau, with RelSau positively impacting the GTPase activity of Era but negatively affecting the helicase activity of CshA. We propose that in its GTP-bound form, Era acts as a hub protein on the ribosome to direct enzymes involved in rRNA processing/degradation and ribosome subunit assembly to their site of action. This activity is impeded by multiple components of the stringent response, contributing to the slowed growth phenotype synonymous with this stress response pathway. The bacterial ribosome is an essential cellular component and as such is the target for a number of currently used antimicrobials. Correct assembly of this complex macromolecule requires a number of accessory enzymes, the functions of which are poorly characterised. Here we examine the function of Era, a GTPase enzyme involved in 30S ribosomal subunit biogenesis in the important human pathogen S. aureus. We uncover that Era is not an essential enzyme in S. aureus, as it is in many other species, but is important for correct ribosome assembly. In a bid to determine a function for this enzyme in ribosomal assembly, we identify a number of protein interaction partners with roles in ribosomal RNA maturation or degradation, supporting the idea that Era acts as a hub protein facilitating ribosomal biogenesis. We also uncover a link between Era and the (p)ppGpp synthetase RelSau, revealing an additional level of control of rRNA processing by the stringent response. With this study we elaborate on the functions of GTPases in ribosomal assembly, processes that are controlled at multiple points by the stringent response.
Collapse
Affiliation(s)
- Alison Wood
- The Florey Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Sophie E. Irving
- The Florey Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Daniel J. Bennison
- The Florey Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Rebecca M. Corrigan
- The Florey Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
- * E-mail:
| |
Collapse
|
5
|
Donegan NP, Manna AC, Tseng CW, Liu GY, Cheung AL. CspA regulation of Staphylococcus aureus carotenoid levels and σ B activity is controlled by YjbH and Spx. Mol Microbiol 2019; 112:532-551. [PMID: 31074903 DOI: 10.1111/mmi.14273] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2019] [Indexed: 01/06/2023]
Abstract
Staphyloxanthin, a carotenoid in S. aureus, is a powerful antioxidant against oxidative stresses. The crtOPQMN operon driving pigment synthesis is under the control of σB . CspA, a cold shock protein, is known to control σB activity. To ascertain genes that regulate cspA, we screened a transposon library that exhibited reduced cspA expression and pigmentation. We found that the adaptor protein YjbH activates cspA expression. Spx, the redox-sensitive transcriptional regulator and a proteolytic target for YjbH and ClpXP, complexes with αCTD of RNAP prior to binding the cspA promoter to repress cspA activity. Increased cspA expression in trans in the inactive spx C10A mutant of JE2 did not enhance pigment production while it did in JE2, suggesting that cspA is downstream to Spx in pigmentation control. As the staphyloxanthin pigment is critical to S. aureus survival in human hosts, we demonstrated that the cspA and yjbH mutants survived less well than the parent in whole blood killing assay. Collectively, our studies suggest a pathway wherein YjbH and ClpXP proteolytically cleave Spx, a repressor of cspA transcription, to affect σB -dependent carotenoid expression, thus providing a critical link between intracellular redox sensing by Spx and carotenoid production to improve S. aureus survival during infections.
Collapse
Affiliation(s)
- Niles P Donegan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Adhar C Manna
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Ching Wen Tseng
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - George Y Liu
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Ambrose L Cheung
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| |
Collapse
|
6
|
Sierra R, Viollier P, Renzoni A. Linking toxin-antitoxin systems with phenotypes: A Staphylococcus aureus viewpoint. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:742-751. [PMID: 30056132 DOI: 10.1016/j.bbagrm.2018.07.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 07/04/2018] [Accepted: 07/17/2018] [Indexed: 10/28/2022]
Abstract
Toxin-antitoxin systems (TAS) are genetic modules controlling different aspects of bacterial physiology. They operate with versatility in an incredibly wide range of mechanisms. New TA modules with unexpected functions are continuously emerging from genome sequencing projects. Their discovery and functional studies have shed light on different characteristics of bacterial metabolism that are now applied to understanding clinically relevant questions and even proposed as antimicrobial treatment. Our main source of knowledge of TA systems derives from Gram-negative bacterial studies, but studies in Gram-positives are becoming more prevalent and provide new insights to TA functional mechanisms. In this review, we present an overview of the present knowledge of TA systems in the clinical pathogen Staphylococcus aureus, their implications in bacterial physiology and discuss relevant aspects that are driving TAS research. "This article is part of a Special Issue entitled: Dynamic gene expression, edited by Prof. Patrick Viollier".
Collapse
Affiliation(s)
- Roberto Sierra
- Geneva University Hospital, Service of Infectious Diseases, Geneva, Switzerland; Department of Microbiology and Molecular Medicine, University of Geneva, Switzerland
| | - Patrick Viollier
- Department of Microbiology and Molecular Medicine, University of Geneva, Switzerland
| | - Adriana Renzoni
- Geneva University Hospital, Service of Infectious Diseases, Geneva, Switzerland.
| |
Collapse
|
7
|
Small RNA teg49 Is Derived from a sarA Transcript and Regulates Virulence Genes Independent of SarA in Staphylococcus aureus. Infect Immun 2018; 86:IAI.00635-17. [PMID: 29133345 DOI: 10.1128/iai.00635-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 10/30/2017] [Indexed: 01/08/2023] Open
Abstract
Expression of virulence factors in Staphylococcus aureus is regulated by a wide range of transcriptional regulators, including proteins and small RNAs (sRNAs), at the level of transcription and/or translation. The sarA locus consists of three overlapping transcripts generated from three distinct promoters, all containing the sarA open reading frame (ORF). The 5' untranslated regions (UTRs) of these transcripts contain three separate regions ∼711, 409, and 146 nucleotides (nt) upstream of the sarA translation start, the functions of which remain unknown. Recent transcriptome-sequencing (RNA-Seq) analysis and subsequent characterization indicated that two sRNAs, teg49 and teg48, are processed and likely produced from the sarA P3 and sarA P1 transcripts of the sarA locus, respectively. In this report, we utilized a variety of sarA promoter mutants and cshA and rnc mutants to ascertain the contributions of these factors to the generation of teg49. We also defined the transcriptional regulon of teg49, including virulence genes not regulated by SarA. Phenotypically, teg49 did not impact biofilm formation or affect overall SarA expression significantly. Comparative analyses of RNA-Seq data between the wild-type, teg49 mutant, and sarA mutant strains indicated that ∼133 genes are significantly upregulated while 97 are downregulated in a teg49 deletion mutant in a sarA-independent manner. An abscess model of skin infection indicated that the teg49 mutant exhibited a reduced bacterial load compared to the wild-type S. aureus Overall, these results suggest that teg49 sRNA has a regulatory role in target gene regulation independent of SarA. The exact mechanism of this regulation is yet to be dissected.
Collapse
|
8
|
Kato F, Yabuno Y, Yamaguchi Y, Sugai M, Inouye M. Deletion of mazF increases Staphylococcus aureus biofilm formation in an ica-dependent manner. Pathog Dis 2017; 75:3063887. [DOI: 10.1093/femspd/ftx026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 03/07/2017] [Indexed: 11/12/2022] Open
|
9
|
Schuster CF, Bertram R. Toxin-Antitoxin Systems of Staphylococcus aureus. Toxins (Basel) 2016; 8:E140. [PMID: 27164142 PMCID: PMC4885055 DOI: 10.3390/toxins8050140] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 04/21/2016] [Accepted: 04/25/2016] [Indexed: 01/02/2023] Open
Abstract
Toxin-antitoxin (TA) systems are small genetic elements found in the majority of prokaryotes. They encode toxin proteins that interfere with vital cellular functions and are counteracted by antitoxins. Dependent on the chemical nature of the antitoxins (protein or RNA) and how they control the activity of the toxin, TA systems are currently divided into six different types. Genes comprising the TA types I, II and III have been identified in Staphylococcus aureus. MazF, the toxin of the mazEF locus is a sequence-specific RNase that cleaves a number of transcripts, including those encoding pathogenicity factors. Two yefM-yoeB paralogs represent two independent, but auto-regulated TA systems that give rise to ribosome-dependent RNases. In addition, omega/epsilon/zeta constitutes a tripartite TA system that supposedly plays a role in the stabilization of resistance factors. The SprA1/SprA1AS and SprF1/SprG1 systems are post-transcriptionally regulated by RNA antitoxins and encode small membrane damaging proteins. TA systems controlled by interaction between toxin protein and antitoxin RNA have been identified in S. aureus in silico, but not yet experimentally proven. A closer inspection of possible links between TA systems and S. aureus pathophysiology will reveal, if these genetic loci may represent druggable targets. The modification of a staphylococcal TA toxin to a cyclopeptide antibiotic highlights the potential of TA systems as rather untapped sources of drug discovery.
Collapse
Affiliation(s)
- Christopher F Schuster
- Section of Microbiology & MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK.
| | - Ralph Bertram
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Lehrbereich Mikrobielle Genetik, University of Tübingen, 72076 Tübingen, Germany.
- Klinikum Nürnberg Medical School GmbH, Research Department, Paracelsus Medical University, 90419 Nuremberg, Germany.
| |
Collapse
|