1
|
Pivard M, Bastien S, Macavei I, Mouton N, Rasigade JP, Couzon F, Youenou B, Tristan A, Carrière R, Moreau K, Lemoine J, Vandenesch F. Targeted proteomics links virulence factor expression with clinical severity in staphylococcal pneumonia. Front Cell Infect Microbiol 2023; 13:1162617. [PMID: 37077532 PMCID: PMC10106754 DOI: 10.3389/fcimb.2023.1162617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
IntroductionThe bacterial pathogen Staphylococcus aureus harbors numerous virulence factors that impact infection severity. Beyond virulence gene presence or absence, the expression level of virulence proteins is known to vary across S. aureus lineages and isolates. However, the impact of expression level on severity is poorly understood due to the lack of high-throughput quantification methods of virulence proteins.MethodsWe present a targeted proteomic approach able to monitor 42 staphylococcal proteins in a single experiment. Using this approach, we compared the quantitative virulomes of 136 S. aureus isolates from a nationwide cohort of French patients with severe community-acquired staphylococcal pneumonia, all requiring intensive care. We used multivariable regression models adjusted for patient baseline health (Charlson comorbidity score) to identify the virulence factors whose in vitro expression level predicted pneumonia severity markers, namely leukopenia and hemoptysis, as well as patient survival.ResultsWe found that leukopenia was predicted by higher expression of HlgB, Nuc, and Tsst-1 and lower expression of BlaI and HlgC, while hemoptysis was predicted by higher expression of BlaZ and HlgB and lower expression of HlgC. Strikingly, mortality was independently predicted in a dose-dependent fashion by a single phage-encoded virulence factor, the Panton-Valentine leucocidin (PVL), both in logistic (OR 1.28; 95%CI[1.02;1.60]) and survival (HR 1.15; 95%CI[1.02;1.30]) regression models.DiscussionThese findings demonstrate that the in vitro expression level of virulence factors can be correlated with infection severity using targeted proteomics, a method that may be adapted to other bacterial pathogens.
Collapse
Affiliation(s)
- Mariane Pivard
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), UMR5308, École Normale Supérieure (ENS) de Lyon, Lyon, France
| | - Sylvère Bastien
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), UMR5308, École Normale Supérieure (ENS) de Lyon, Lyon, France
| | - Iulia Macavei
- Institut des Sciences Analytiques, Université de Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), UMR 5280, Villeurbanne, France
| | - Nicolas Mouton
- Institut des Sciences Analytiques, Université de Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), UMR 5280, Villeurbanne, France
| | - Jean-Philippe Rasigade
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), UMR5308, École Normale Supérieure (ENS) de Lyon, Lyon, France
- Centre National de Référence des Staphylocoques, Institut des agents infectieux, Hospices Civils de Lyon, Lyon, France
| | - Florence Couzon
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), UMR5308, École Normale Supérieure (ENS) de Lyon, Lyon, France
| | - Benjamin Youenou
- Centre National de Référence des Staphylocoques, Institut des agents infectieux, Hospices Civils de Lyon, Lyon, France
| | - Anne Tristan
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), UMR5308, École Normale Supérieure (ENS) de Lyon, Lyon, France
- Centre National de Référence des Staphylocoques, Institut des agents infectieux, Hospices Civils de Lyon, Lyon, France
| | - Romain Carrière
- Institut des Sciences Analytiques, Université de Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), UMR 5280, Villeurbanne, France
| | - Karen Moreau
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), UMR5308, École Normale Supérieure (ENS) de Lyon, Lyon, France
| | - Jérôme Lemoine
- Institut des Sciences Analytiques, Université de Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), UMR 5280, Villeurbanne, France
| | - François Vandenesch
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), UMR5308, École Normale Supérieure (ENS) de Lyon, Lyon, France
- Centre National de Référence des Staphylocoques, Institut des agents infectieux, Hospices Civils de Lyon, Lyon, France
- *Correspondence: François Vandenesch,
| |
Collapse
|
2
|
Menard G, Silard C, Suriray M, Rouillon A, Augagneur Y. Thirty Years of sRNA-Mediated Regulation in Staphylococcus aureus: From Initial Discoveries to In Vivo Biological Implications. Int J Mol Sci 2022; 23:ijms23137346. [PMID: 35806357 PMCID: PMC9266662 DOI: 10.3390/ijms23137346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/20/2022] [Accepted: 06/28/2022] [Indexed: 01/27/2023] Open
Abstract
Staphylococcus aureus is a widespread livestock and human pathogen that colonizes diverse microenvironments within its host. Its adaptation to the environmental conditions encountered within humans relies on coordinated gene expression. This requires a sophisticated regulatory network, among which regulatory RNAs (usually called sRNAs) have emerged as key players over the last 30 years. In S. aureus, sRNAs regulate target genes at the post-transcriptional level through base–pair interactions. The functional characterization of a subset revealed that they participate in all biological processes, including virulence, metabolic adaptation, and antibiotic resistance. In this review, we report 30 years of S. aureus sRNA studies, from their discovery to the in-depth characterizations of some of them. We also discuss their actual in vivo contribution, which is still lagging behind, and their place within the complex regulatory network. These shall be key aspects to consider in order to clearly uncover their in vivo biological functions.
Collapse
Affiliation(s)
- Guillaume Menard
- CHU Rennes, INSERM, BRM (Bacterial Regulatory RNAs and Medicine), SB2H (Service de Bactériologie Hygiène-Hospitalière), University Rennes, UMR_S 1230, F-35000 Rennes, France; (G.M.); (M.S.)
| | - Chloé Silard
- INSERM, BRM (Bacterial Regulatory RNAs and Medicine), University Rennes, UMR_S 1230, F-35000 Rennes, France; (C.S.); (A.R.)
| | - Marie Suriray
- CHU Rennes, INSERM, BRM (Bacterial Regulatory RNAs and Medicine), SB2H (Service de Bactériologie Hygiène-Hospitalière), University Rennes, UMR_S 1230, F-35000 Rennes, France; (G.M.); (M.S.)
| | - Astrid Rouillon
- INSERM, BRM (Bacterial Regulatory RNAs and Medicine), University Rennes, UMR_S 1230, F-35000 Rennes, France; (C.S.); (A.R.)
| | - Yoann Augagneur
- INSERM, BRM (Bacterial Regulatory RNAs and Medicine), University Rennes, UMR_S 1230, F-35000 Rennes, France; (C.S.); (A.R.)
- Correspondence: ; Tel.: +33-223234631
| |
Collapse
|
3
|
Abstract
Bacterial small RNAs (sRNAs) contribute to a variety of regulatory mechanisms that modulate a wide range of pathways, including metabolism, virulence, and antibiotic resistance. We investigated the involvement of sRNAs in rifampicin resistance in the opportunistic pathogen Staphylococcus aureus. Using a competition assay with an sRNA mutant library, we identified 6S RNA as being required for protection against low concentrations of rifampicin, an RNA polymerase (RNAP) inhibitor. This effect applied to rifabutin and fidaxomicin, two other RNAP-targeting antibiotics. 6S RNA is highly conserved in bacteria, and its absence in two other major pathogens, Salmonella enterica and Clostridioides difficile, also impaired susceptibility to RNAP inhibitors. In S. aureus, 6S RNA is produced from an autonomous gene and accumulates in stationary phase. In contrast to what was reported for Escherichia coli, S. aureus 6S RNA does not appear to play a critical role in the transition from exponential to stationary phase but affects σB-regulated expression in prolonged stationary phase. Nevertheless, its protective effect against rifampicin is independent of alternative sigma factor σB activity. Our results suggest that 6S RNA helps maintain RNAP-σA integrity in S. aureus, which could in turn help bacteria withstand low concentrations of RNAP inhibitors.
Collapse
|
4
|
Buchad H, Nair M. The small RNA SprX regulates the autolysin regulator WalR in Staphylococcus aureus. Microbiol Res 2021; 250:126785. [PMID: 34000511 DOI: 10.1016/j.micres.2021.126785] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 10/21/2022]
Abstract
Pathogenesis of Staphylococcus aureus is attributed to its remarkable adaptation to changes in the environment, mediated by the arsenal of virulence factors, which are regulated by intricate mechanisms that include small RNAs (sRNAs) as important regulatory molecules. The sRNA SprX was previously described to be involved in the regulation of S. aureus pathogenicity, by modifying the expression of surface-associated clumping factor B and the secreted delta haemolysin. This study describes the regulation by SprX, of expression of multiple autolysins, which play an essential role in cell wall metabolism and function as important virulence factors that facilitate adhesion, internalization, and immune evasion during S. aureus colonization and pathogenesis. SprX acts by positively regulating the expression of autolysin regulator WalR. Overexpression of SprX resulted in differential regulation of autolysins IsaA, and LytM, while WalR levels were unchanged. SprX knockdown strain exhibited down-regulation of multiple autolytic bands corresponding to the major autolysin AtlA and its process intermediates in cell wall degradation zymography, and 0.2 to 0.1 fold reduction of lytM, atlA, isaA, and walR transcripts in qRT-PCRs. Down-regulation of SprX resulted in altered phenotype with high cell aggregation as analyzed by SEM, decrease in biofilm formation and higher resistance to Triton X-100-induced lysis, all of which indicate that SprX is essential for expression of autolysins. A putative RNA-RNA interaction was indicated in silico between SprX and walR mRNA and further confirmed by in vitro RNA-RNA interaction in electrophoretic mobility shift assays. These findings elucidate a new mechanism in which SprX modulates the S. aureus pathogenicity by regulating the regulator of autolysins in cell wall metabolism and as virulence factors.
Collapse
Affiliation(s)
- Hasmatbanu Buchad
- Department of Microbiology and Biotechnology Centre, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, 390002, India.
| | - Mrinalini Nair
- Department of Microbiology and Biotechnology Centre, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, 390002, India.
| |
Collapse
|
5
|
Ménard G, Rouillon A, Ghukasyan G, Emily M, Felden B, Donnio PY. Galleria mellonella Larvae as an Infection Model to Investigate sRNA-Mediated Pathogenesis in Staphylococcus aureus. Front Cell Infect Microbiol 2021; 11:631710. [PMID: 33954118 PMCID: PMC8089379 DOI: 10.3389/fcimb.2021.631710] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/26/2021] [Indexed: 11/30/2022] Open
Abstract
Small regulatory RNAs (sRNAs) are key players in bacterial regulatory networks. Monitoring their expression inside living colonized or infected organisms is essential for identifying sRNA functions, but few studies have looked at sRNA expression during host infection with bacterial pathogens. Insufficient in vivo studies monitoring sRNA expression attest to the difficulties in collecting such data, we therefore developed a non-mammalian infection model using larval Galleria mellonella to analyze the roles of Staphylococcus aureus sRNAs during larval infection and to quickly determine possible sRNA involvement in staphylococcal virulence before proceeding to more complicated animal testing. We began by using the model to test infected larvae for immunohistochemical evidence of infection as well as host inflammatory responses over time. To monitor sRNA expression during infection, total RNAs were extracted from the larvae and invading bacteria at different time points. The expression profiles of the tested sRNAs were distinct and they fluctuated over time, with expression of both sprD and sprC increased during infection and associated with mortality, while rnaIII expression remained barely detectable over time. A strong correlation was observed between sprD expression and the mortality. To confirm these results, we used sRNA-knockout mutants to investigate sRNA involvement in Staphylococcus aureus pathogenesis, finding that the decrease in death rates is delayed when either sprD or sprC was lacking. These results demonstrate the relevance of this G. mellonella model for investigating the role of sRNAs as transcriptional regulators involved in staphylococcal virulence. This insect model provides a fast and easy method for monitoring sRNA (and mRNA) participation in S. aureus pathogenesis, and can also be used for other human bacterial pathogens.
Collapse
Affiliation(s)
- Guillaume Ménard
- Univ Rennes, CHU Rennes, INSERM, BRM [Bacterial Regulatory RNAs and Medicine], SB2H (service de Bactériologie Hygiène-Hospitalière), UMR_S 1230, F-35000, Rennes, France
| | - Astrid Rouillon
- Univ Rennes, INSERM, BRM (Bacterial Regulatory RNAs and Medicine), UMR_S 1230, F-35000, Rennes, France
| | - Gevorg Ghukasyan
- Univ Rennes, CNRS, INSERM, BIOSIT (Biologie, Santé, Innovation Technologique de Rennes), UMS 3480, US_S018, F-35000, Rennes, France
| | - Mathieu Emily
- Institut Agro, CNRS, Univ Rennes, IRMAR (Institut de recherche Mathématique de Rennes), UMR 6625, F-35000, Rennes, France
| | - Brice Felden
- Univ Rennes, INSERM, BRM (Bacterial Regulatory RNAs and Medicine), UMR_S 1230, F-35000, Rennes, France
| | - Pierre-Yves Donnio
- Univ Rennes, CHU Rennes, INSERM, BRM [Bacterial Regulatory RNAs and Medicine], SB2H (service de Bactériologie Hygiène-Hospitalière), UMR_S 1230, F-35000, Rennes, France
| |
Collapse
|
6
|
Staphylococcus aureus Responds to Physiologically Relevant Temperature Changes by Altering Its Global Transcript and Protein Profile. mSphere 2021; 6:6/2/e01303-20. [PMID: 33731473 PMCID: PMC8546721 DOI: 10.1128/msphere.01303-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Staphylococcus aureus is an opportunistic pathogen that colonizes the anterior nares of 30 to 50% of the population. Colonization is most often asymptomatic; however, self-inoculation can give rise to potentially fatal infections of the deeper tissues and blood. Like all bacteria, S. aureus can sense and respond to environmental cues and modify gene expression to adapt to specific environmental conditions. The transition of S. aureus from the nares to the deeper tissues and blood is accompanied by changes in environmental conditions, such as nutrient availability, pH, and temperature. In this study, we perform transcriptomics and proteomics on S. aureus cultures growing at three physiologically relevant temperatures, 34°C (nares), 37°C (body), and 40°C (pyrexia), to determine if small scale, biologically meaningful alterations in temperature impact S. aureus gene expression. Results show that small but definite temperature changes elicit a large-scale restructuring of the S. aureus transcriptome and proteome in a manner that, most often, inversely correlates with increasing temperature. We also provide evidence that a large majority of these changes are modulated at the posttranscriptional level, possibly by sRNA regulatory elements. Phenotypic analyses were also performed to demonstrate that these changes have physiological relevance. Finally, we investigate the impact of temperature-dependent alterations in gene expression on S. aureus pathogenesis and demonstrate decreased intracellular invasion of S. aureus grown at 34°C. Collectively, our results demonstrate that small but biologically meaningful alterations in temperature influence S. aureus gene expression, a process that is likely a major contributor to the transition from a commensal to pathogen. IMPORTANCE Enteric bacterial pathogens, like Escherichia coli, are known to experience large temperature differences as they are transmitted through the fecal oral route. This change in temperature has been demonstrated to influence bacterial gene expression and facilitate infection. Staphylococcus aureus is a human-associated pathogen that can live as a commensal on the skin and nares or cause invasive infections of the deeper tissues and blood. Factors influencing S. aureus nasal colonization are not fully understood; however, individuals colonized with S. aureus are at increased risk of invasive infections through self-inoculation. The transition of S. aureus from the nose (colonization) to the body (infection) is accompanied by a modest but definite temperature increase, from 34°C to 37°C. In this study, we investigate whether these host-associated small temperature changes can influence S. aureus gene expression. Results show widespread changes in the bacterial transcriptome and proteome at three physiologically relevant temperatures (34°C, 37°C, and 40°C).
Collapse
|
7
|
Joshi B, Singh B, Nadeem A, Askarian F, Wai SN, Johannessen M, Hegstad K. Transcriptome Profiling of Staphylococcus aureus Associated Extracellular Vesicles Reveals Presence of Small RNA-Cargo. Front Mol Biosci 2021; 7:566207. [PMID: 33521050 PMCID: PMC7838569 DOI: 10.3389/fmolb.2020.566207] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 12/14/2020] [Indexed: 12/13/2022] Open
Abstract
Bacterial extracellular vesicles (EVs) have a vital role in bacterial pathogenesis. However, to date, the small RNA-cargo of EVs released by the opportunistic pathogen Staphylococcus aureus has not been characterized. Here, we shed light on the association of small RNAs with EVs secreted by S. aureus MSSA476 cultured in iron-depleted bacteriologic media supplemented with a subinhibitory dosage of vancomycin to mimic infection condition. Confocal microscopy analysis on intact RNase-treated EVs indicated that RNA is associated with EV particles. Transcriptomic followed by bioinformatics analysis of EV-associated RNA revealed the presence of potential gene regulatory small RNAs and high levels of tRNAs. Among the EV-associated enriched small RNAs were SsrA, RsaC and RNAIII. Our finding invites new insights into the potential role of EV-associated RNA as a modulator of host-pathogen interaction.
Collapse
Affiliation(s)
- Bishnu Joshi
- Department of Medical Biology, Research Group for Host-Microbe Interactions, UiT The Arctic University of Norway, Tromsø, Norway
| | - Bhupender Singh
- Department of Medical Biology, Research Group for Host-Microbe Interactions, UiT The Arctic University of Norway, Tromsø, Norway
| | - Aftab Nadeem
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Fatemeh Askarian
- Department of Medical Biology, Research Group for Host-Microbe Interactions, UiT The Arctic University of Norway, Tromsø, Norway.,Faculty of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Sun Nyunt Wai
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Mona Johannessen
- Department of Medical Biology, Research Group for Host-Microbe Interactions, UiT The Arctic University of Norway, Tromsø, Norway
| | - Kristin Hegstad
- Department of Medical Biology, Research Group for Host-Microbe Interactions, UiT The Arctic University of Norway, Tromsø, Norway.,Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North-Norway, Tromsø, Norway
| |
Collapse
|
8
|
Liu S, Li H, Guo Z, Guan J, Sun Y, Zhang K. Insight into the Effect of Small RNA srn225147 on Mutacin IV in Streptococcus mutans. Indian J Microbiol 2019; 59:445-450. [PMID: 31762507 DOI: 10.1007/s12088-019-00820-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 08/22/2019] [Indexed: 12/11/2022] Open
Abstract
Streptococcus mutans (S. mutans) is a serious microbe causing dental caries. Mutacin IV is an effective bacteriocin produced by S. mutans to antagonize numerous non-mutans streptococcal species. However, the posttranscriptional regulation of mutacin IV remains unclear. This study aimed to analyze the effect of small RNA srn225147 on mutacin IV. The functional prediction suggested that srn225147 is involved in the production of mutacin IV, an important secondary metabolite. According to RNAhybrid and RNAPredator prediction, the mutacin IV formation-associated gene comD is a target of srn225147. We further analyzed the roles of srn225147 and comD in 20 S. mutans clinical strains with high production of mutacin IV (High-IV group) and lacking mutacin IV (None-IV group). Levels of comD expression were significantly higher in the High-IV group, whereas the Non-IV group showed relatively higher expression of srn225147, with a negative correlation observed between srn225147 and comD. Moreover, compared to the mimic negative control (NC) group, comD expression was decreased at 400-fold srn225147 overexpression but increased at approximately 1400-fold overexpression. Although the production of mutacin IV in the 1400-fold change srn225147 mimic group was larger than that in the 400-fold change mimic group, there was no significant difference in the production of mutacin IV between the srn225147 mimic group and mimic NC group. These results indicate that srn225147 has a two-way regulation effect on the expression of comD but that its regulation in the production of mutacin IV is weak.
Collapse
Affiliation(s)
- Shanshan Liu
- 1Department of Stomatology, The First Affiliated Hospital of Bengbu Medical College, 287 Chang Huai Road, Bengbu, 233004 China
| | - Huihui Li
- 2Department of Microbiology and Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, 2600 Dong Hai Avenue, Bengbu, 233030 China
| | - Zhenfei Guo
- 1Department of Stomatology, The First Affiliated Hospital of Bengbu Medical College, 287 Chang Huai Road, Bengbu, 233004 China
| | - Junchang Guan
- 2Department of Microbiology and Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, 2600 Dong Hai Avenue, Bengbu, 233030 China
| | - Yu Sun
- 3Department of Biochemistry and Molecular Biology, Bengbu Medical College, 2600 Dong Hai Avenue, Bengbu, 233030 China
| | - Kai Zhang
- 1Department of Stomatology, The First Affiliated Hospital of Bengbu Medical College, 287 Chang Huai Road, Bengbu, 233004 China
| |
Collapse
|
9
|
Abstract
Regulatory RNAs, present in many bacterial genomes and particularly in pathogenic bacteria such as Staphylococcus aureus, control the expression of genes encoding virulence factors or metabolic proteins. They are extremely diverse and include noncoding RNAs (sRNA), antisense RNAs, and some 5' or 3' untranslated regions of messenger RNAs that act as sensors for metabolites, tRNAs, or environmental conditions (e.g., temperature, pH). In this review we focus on specific examples of sRNAs of S. aureus that illustrate how numerous sRNAs and associated proteins are embedded in complex networks of regulation. In addition, we discuss the CRISPR-Cas systems defined as an RNA-interference-like mechanism, which also exist in staphylococcal strains.
Collapse
|
10
|
Zhao X, Zhang Y, Huang X. Pathogenicity-island-encoded regulatory RNAs regulate bacterial virulence and pathogenesis. Microb Pathog 2018; 125:196-204. [PMID: 30227229 DOI: 10.1016/j.micpath.2018.09.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 08/16/2018] [Accepted: 09/14/2018] [Indexed: 02/07/2023]
Abstract
Bacterial regulatory RNAs (regRNAs) have been widely studied for decades and shown to be involved in various aspects of bacterial survival, including their virulence and pathogenesis. Recently, many regRNAs have been found to be encoded within bacterial pathogenicity islands (PAIs). These PAI-encoded regRNAs also play important regulatory roles in bacterial virulence and pathogenesis. In this review, we introduce the reported PAI-encoded regRNAs individually, focusing on their types, target genes, regulatory roles, regulatory mechanisms and significance. We also summarize the virulence and pathogenesis of the pathogens concerned.
Collapse
Affiliation(s)
- Xin Zhao
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China.
| | - Ying Zhang
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China.
| | - Xinxiang Huang
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China.
| |
Collapse
|
11
|
Ivain L, Bordeau V, Eyraud A, Hallier M, Dreano S, Tattevin P, Felden B, Chabelskaya S. An in vivo reporter assay for sRNA-directed gene control in Gram-positive bacteria: identifying a novel sRNA target in Staphylococcus aureus. Nucleic Acids Res 2017; 45:4994-5007. [PMID: 28369640 PMCID: PMC5416835 DOI: 10.1093/nar/gkx190] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 03/11/2017] [Indexed: 12/15/2022] Open
Abstract
Bacterial small regulatory RNAs (sRNAs) play a major role in the regulation of various cellular functions. Most sRNAs interact with mRNA targets via an antisense mechanism, modifying their translation and/or degradation. Despite considerable progresses in discovering sRNAs in Gram-positive bacteria, their functions, for the most part, are unknown. This is mainly due to difficulties in identifying their targets. To aid in the identification of sRNA targets in Gram-positive bacteria, we set up an in vivo method for fast analysis of sRNA-mediated post-transcriptional control at the 5΄ regions of target mRNAs. The technology is based on the co-expression of an sRNA and a 5΄ sequence of an mRNA target fused to a green fluorescent protein (GFP) reporter. The system was challenged on Staphylococcus aureus, an opportunistic Gram-positive pathogen. We analyzed several established sRNA–mRNA interactions, and in addition, we identified the ecb mRNA as a novel target for SprX2 sRNA. Using our in vivo system in combination with in vitro experiments, we demonstrated that SprX2 uses an antisense mechanism to prevent ecb mRNA translation initiation. Furthermore, we used our reporter assay to validate sRNA regulations in other Gram-positive organisms, Bacillus subtilis and Listeria monocytogenes. Overall, our method is broadly applicable to challenge the predicted sRNA–mRNA interactions in Gram-positive bacteria.
Collapse
Affiliation(s)
- Lorraine Ivain
- Université de Rennes 1, Inserm U1230-UPRES EA 2311, Biochimie Pharmaceutique, Regulatory RNA and Medicine (RMM), 2 avenue du Prof. Léon Bernard, 35043 Rennes, France
| | - Valérie Bordeau
- Université de Rennes 1, Inserm U1230-UPRES EA 2311, Biochimie Pharmaceutique, Regulatory RNA and Medicine (RMM), 2 avenue du Prof. Léon Bernard, 35043 Rennes, France
| | - Alex Eyraud
- Université de Rennes 1, Inserm U1230-UPRES EA 2311, Biochimie Pharmaceutique, Regulatory RNA and Medicine (RMM), 2 avenue du Prof. Léon Bernard, 35043 Rennes, France
| | - Marc Hallier
- Université de Rennes 1, Inserm U1230-UPRES EA 2311, Biochimie Pharmaceutique, Regulatory RNA and Medicine (RMM), 2 avenue du Prof. Léon Bernard, 35043 Rennes, France
| | - Stéphane Dreano
- Université de Rennes 1, CNRS UMR 6290 IGDR, BIOSIT, Molecular Bases of Tumorigenesis: VHL Disease Team, 35043 Rennes, France
| | - Pierre Tattevin
- Université de Rennes 1, Inserm U1230-UPRES EA 2311, Biochimie Pharmaceutique, Regulatory RNA and Medicine (RMM), 2 avenue du Prof. Léon Bernard, 35043 Rennes, France
| | - Brice Felden
- Université de Rennes 1, Inserm U1230-UPRES EA 2311, Biochimie Pharmaceutique, Regulatory RNA and Medicine (RMM), 2 avenue du Prof. Léon Bernard, 35043 Rennes, France
| | - Svetlana Chabelskaya
- Université de Rennes 1, Inserm U1230-UPRES EA 2311, Biochimie Pharmaceutique, Regulatory RNA and Medicine (RMM), 2 avenue du Prof. Léon Bernard, 35043 Rennes, France
| |
Collapse
|
12
|
An outbreak in intravenous drug users due to USA300 Latin-American variant community-acquired methicillin-resistant Staphylococcus aureus in France as early as 2007. Eur J Clin Microbiol Infect Dis 2017; 36:2495-2501. [DOI: 10.1007/s10096-017-3092-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/09/2017] [Indexed: 12/25/2022]
|