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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.
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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
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Desgranges E, Barrientos L, Herrgott L, Marzi S, Toledo-Arana A, Moreau K, Vandenesch F, Romby P, Caldelari I. The 3'UTR-derived sRNA RsaG coordinates redox homeostasis and metabolism adaptation in response to glucose-6-phosphate uptake in Staphylococcus aureus. Mol Microbiol 2021; 117:193-214. [PMID: 34783400 DOI: 10.1111/mmi.14845] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 11/08/2021] [Accepted: 11/11/2021] [Indexed: 01/28/2023]
Abstract
Staphylococcus aureus RsaG is a 3'-untranslated region (3'UTR) derived sRNA from the conserved uhpT gene encoding a glucose-6-phosphate (G6P) transporter expressed in response to extracellular G6P. The transcript uhpT-RsaG undergoes degradation from 5'- to 3'-end by the action of the exoribonucleases J1/J2, which are blocked by a stable hairpin structure at the 5'-end of RsaG, leading to its accumulation. RsaG together with uhpT is induced when bacteria are internalized into host cells or in the presence of mucus-secreting cells. Using MS2-affinity purification coupled with RNA sequencing, several RNAs were identified as targets including mRNAs encoding the transcriptional factors Rex, CcpA, SarA, and the sRNA RsaI. Our data suggested that RsaG contributes to the control of redox homeostasis and adjusts metabolism to changing environmental conditions. RsaG uses different molecular mechanisms to stabilize, degrade, or repress the translation of its mRNA targets. Although RsaG is conserved only in closely related species, the uhpT 3'UTR of the ape pathogen S. simiae harbors an sRNA, whose sequence is highly different, and which does not respond to G6P levels. Our results hypothesized that the 3'UTRs from UhpT transporter encoding mRNAs could have rapidly evolved to enable adaptation to host niches.
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Affiliation(s)
- Emma Desgranges
- Architecture et Réactivité de l'ARN, UPR9002, CNRS, Université de Strasbourg, Strasbourg, France
| | - Laura Barrientos
- Architecture et Réactivité de l'ARN, UPR9002, CNRS, Université de Strasbourg, Strasbourg, France
| | - Lucas Herrgott
- Architecture et Réactivité de l'ARN, UPR9002, CNRS, Université de Strasbourg, Strasbourg, France
| | - Stefano Marzi
- Architecture et Réactivité de l'ARN, UPR9002, CNRS, Université de Strasbourg, Strasbourg, France
| | | | - Karen Moreau
- CIRI, Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Hospices Civils de Lyon, Université de Lyon, Lyon, France
| | - François Vandenesch
- CIRI, Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Hospices Civils de Lyon, Université de Lyon, Lyon, France
| | - Pascale Romby
- Architecture et Réactivité de l'ARN, UPR9002, CNRS, Université de Strasbourg, Strasbourg, France
| | - Isabelle Caldelari
- Architecture et Réactivité de l'ARN, UPR9002, CNRS, Université de Strasbourg, Strasbourg, France
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Abstract
SarA, a transcriptional regulator of Staphylococcus aureus, is a major global regulatory system that coordinates the expression of target genes involved in its pathogenicity. Various studies have identified a large number of SarA target genes, but an in-depth characterization of the sarA regulon, including small regulatory RNAs (sRNAs), has not yet been done. In this study, we utilized transcriptome sequencing (RNA-Seq) and chromatin immunoprecipitation sequencing (ChIP-Seq) to determine a comprehensive list of SarA-regulated targets, including both mRNAs and sRNAs. RNA-Seq analysis indicated 390 mRNAs and 51 sRNAs differentially expressed in a ΔsarA mutant, while ChIP-Seq revealed 354 mRNAs and 55 sRNA targets in the S. aureus genome. We confirmed the authenticity of several novel SarA targets by Northern blotting and electrophoretic mobility shift assays. Among them, we characterized repression of sprG2, a gene that encodes the toxin of a type I toxin-antitoxin system, indicating a multilayer lockdown of toxin expression by both SarA and its cognate antitoxin, SprF2. Finally, a novel SarA consensus DNA binding sequence was generated using the upstream promoter sequences of 15 novel SarA-regulated sRNA targets. A genome-wide scan with a deduced SarA motif enabled the discovery of new potential SarA target genes which were not identified in our RNA-Seq and ChIP-Seq analyses. The strength of this new consensus was confirmed with one predicted sRNA target. The RNA-Seq and ChIP-Seq combinatory analysis gives a snapshot of the regulation, whereas bioinformatic analysis reveals a permanent view of targets based on sequence. Altogether these experimental and in silico methodologies are effective to characterize transcriptional factor (TF) regulons and functions. IMPORTANCEStaphylococcus aureus, a commensal and opportunist pathogen, is responsible for a large number of human and animal infections, from benign to severe. Gene expression adaptation during infection requires a complex network of regulators, including transcriptional factors (TF) and sRNAs. TF SarA influences virulence, metabolism, biofilm formation, and resistance to some antibiotics. SarA directly regulates expression of around 20 mRNAs and a few sRNAs. Here, we combined high-throughput expression screening methods combined with binding assays and bioinformatics for an in-depth investigation of the SarA regulon. This combinatory approach allowed the identification of 85 unprecedented mRNAs and sRNAs targets, with at least 14 being primary. Among novel SarA direct targets, we characterized repression of sprG2, a gene that encodes the toxin of a toxin-antitoxin system, indicating a multilayer lockdown of toxin expression by both SarA and its cognate antitoxin, SprF2.
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Barrientos L, Mercier N, Lalaouna D, Caldelari I. Assembling the Current Pieces: The Puzzle of RNA-Mediated Regulation in Staphylococcus aureus. Front Microbiol 2021; 12:706690. [PMID: 34367109 PMCID: PMC8334554 DOI: 10.3389/fmicb.2021.706690] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/30/2021] [Indexed: 01/16/2023] Open
Abstract
The success of the major opportunistic human Staphylococcus aureus relies on the production of numerous virulence factors, which allow rapid colonization and dissemination in any tissues. Indeed, regulation of its virulence is multifactorial, and based on the production of transcriptional factors, two-component systems (TCS) and small regulatory RNAs (sRNAs). Advances in high-throughput sequencing technologies have unveiled the existence of hundreds of potential RNAs with regulatory functions, but only a fraction of which have been validated in vivo. These discoveries have modified our thinking and understanding of bacterial physiology and virulence fitness by placing sRNAs, alongside transcriptional regulators, at the center of complex and intertwined regulatory networks that allow S. aureus to rapidly adapt to the environmental cues present at infection sites. In this review, we describe the recently acquired knowledge of characterized regulatory RNAs in S. aureus that are associated with metal starvation, nutrient availability, stress responses and virulence. These findings highlight the importance of sRNAs for the comprehension of S. aureus infection processes while raising questions about the interplay between these key regulators and the pathways they control.
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Affiliation(s)
- Laura Barrientos
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France
| | - Noémie Mercier
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France
| | - David Lalaouna
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France
| | - Isabelle Caldelari
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France
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Fu W, He W, Ren Y, Li Z, Liu J, Liu Y, Xie Z, Xu J, Bi Q, Kong M, Lee CC, Daiss JL, Muthukrishnan G, Owen JR, Kates SL, Peng J, Xie C. Distinct expression trend of signature antigens of Staphylococcus aureus osteomyelitis correlated with clinical outcomes. J Orthop Res 2021; 39:265-273. [PMID: 33336817 PMCID: PMC7946439 DOI: 10.1002/jor.24961] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/08/2020] [Accepted: 12/14/2020] [Indexed: 02/04/2023]
Abstract
The major limitations of clinical outcome predictions of osteomyelitis mediated by Staphylococcus aureus (S. aureus) are not specific and definitive. To this end, current studies aim to investigate host immune responses of trend changes of the iron-regulated surface determinant (Isd) of IsdA, IsdB, IsdH, cell wall-modifying proteins of amidase (Amd) and glucosaminidase (Gmd), and secreted virulence factor of chemotaxis inhibitory protein S. aureus (CHIPS) and staphylococcal complement inhibitor (SCIN) longitudinally to discover their correlationship with clinical outcomes. A total of 55 patients with confirmed S. aureus infection of the long bone by clinical and laboratory methods were recruited for the study. Whole blood was collected at 0, 6, 12 months for the serum that was used to test IsdA, IsdB, IsdH, Gmd, Amd, CHIPS, and SCIN using a customized Luminex assay after clinical standard care parameters were collected. The patients were then divided into two groups: (1) infection controlled versus (2) adverse outcome based on clinical criteria for statistical analysis. We found that standard clinical parameters were unable to distinguish therapeutic outcomes. Significant overexpression of all antigens was confirmed in infection patients at 0-, 6-, and 12-month time points. A distinct expression trend and dynamic changes of IsdB, Amd, Gmd, and CHIPS were observed between infection controlled and adverse outcome patients, while the IsdA, IsdH, SCIN remained demonstrated no statistical significance. We conclude that dynamic changes of specific antigens could predict clinical outcomes of S. aureus osteomyelitis. Clinical Relevance: The trend changes of host immune responses to S. aureus specific antigens of IsdB, Gmd, Amd, and CHIPS could predict clinical outcomes of S. aureus osteomyelitis.
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Affiliation(s)
- Wei Fu
- Department of Orthopaedics, Joint Orthopaedic Research Center of Zunyi Medical University & University of Rochester Medical Center (JORC – ZMU&URMC), First Affiliated Hospital of Zunyi Medical University, Zunyi, 563003 China,Joint Orthopaedic, Research Center of Zunyi Medical University & University of Rochester Medical Center (JORC – ZMU&URMC), First Affiliated Hospital of Zunyi Medical University, Zunyi, 563003 China,The authors contributed equally
| | - Wenbin He
- Department of Orthopaedics, Joint Orthopaedic Research Center of Zunyi Medical University & University of Rochester Medical Center (JORC – ZMU&URMC), First Affiliated Hospital of Zunyi Medical University, Zunyi, 563003 China,Joint Orthopaedic, Research Center of Zunyi Medical University & University of Rochester Medical Center (JORC – ZMU&URMC), First Affiliated Hospital of Zunyi Medical University, Zunyi, 563003 China,The authors contributed equally
| | - Youliang Ren
- Department of Orthopaedics, Joint Orthopaedic Research Center of Zunyi Medical University & University of Rochester Medical Center (JORC – ZMU&URMC), First Affiliated Hospital of Zunyi Medical University, Zunyi, 563003 China,Joint Orthopaedic, Research Center of Zunyi Medical University & University of Rochester Medical Center (JORC – ZMU&URMC), First Affiliated Hospital of Zunyi Medical University, Zunyi, 563003 China
| | - Zhengdao Li
- Department of Orthopaedics, Joint Orthopaedic Research Center of Zunyi Medical University & University of Rochester Medical Center (JORC – ZMU&URMC), First Affiliated Hospital of Zunyi Medical University, Zunyi, 563003 China,Joint Orthopaedic, Research Center of Zunyi Medical University & University of Rochester Medical Center (JORC – ZMU&URMC), First Affiliated Hospital of Zunyi Medical University, Zunyi, 563003 China
| | - Jinyue Liu
- Department of Orthopaedics, Joint Orthopaedic Research Center of Zunyi Medical University & University of Rochester Medical Center (JORC – ZMU&URMC), First Affiliated Hospital of Zunyi Medical University, Zunyi, 563003 China,Joint Orthopaedic, Research Center of Zunyi Medical University & University of Rochester Medical Center (JORC – ZMU&URMC), First Affiliated Hospital of Zunyi Medical University, Zunyi, 563003 China
| | - Yi Liu
- Department of Orthopaedics, Joint Orthopaedic Research Center of Zunyi Medical University & University of Rochester Medical Center (JORC – ZMU&URMC), First Affiliated Hospital of Zunyi Medical University, Zunyi, 563003 China,Joint Orthopaedic, Research Center of Zunyi Medical University & University of Rochester Medical Center (JORC – ZMU&URMC), First Affiliated Hospital of Zunyi Medical University, Zunyi, 563003 China
| | - Zhao Xie
- Department of Orthopaedic, Joint Orthopaedic Research Center of Southwest Hospital of Third Military Medical University & University of Rochester Medical Center (JORC – SHTMMU &URMC), Southwest Hospital of Third Military Medical University, Chongqing, 400038 China,Joint Orthopaedic, Research Center of Southwest Hospital of Third Military Medical University & University of Rochester Medical Center (JORC – SHTMMU &URMC), Southwest Hospital of Third Military Medical University, Chongqing, 400038 China
| | - Jianzhong Xu
- Department of Orthopaedic, Joint Orthopaedic Research Center of Southwest Hospital of Third Military Medical University & University of Rochester Medical Center (JORC – SHTMMU &URMC), Southwest Hospital of Third Military Medical University, Chongqing, 400038 China,Joint Orthopaedic, Research Center of Southwest Hospital of Third Military Medical University & University of Rochester Medical Center (JORC – SHTMMU &URMC), Southwest Hospital of Third Military Medical University, Chongqing, 400038 China
| | - Qing Bi
- Department of Orthopaedic, Joint Orthopaedic Research Center of Zhejiang Provincial People’s Hospital & University of Rochester Medical Center (JORC – ZPPH &URMC), Zhejiang Provincial Hospital, Hangzhou, 310024 China,Joint Orthopaedic, Research Center of Zhejiang Provincial People’s Hospital & University of Rochester Medical Center (JORC – ZPPH &URMC), Zhejiang Provincial Hospital, Hangzhou, 310024 China
| | - Mingxiang Kong
- Department of Orthopaedic, Joint Orthopaedic Research Center of Zhejiang Provincial People’s Hospital & University of Rochester Medical Center (JORC – ZPPH &URMC), Zhejiang Provincial Hospital, Hangzhou, 310024 China,Joint Orthopaedic, Research Center of Zhejiang Provincial People’s Hospital & University of Rochester Medical Center (JORC – ZPPH &URMC), Zhejiang Provincial Hospital, Hangzhou, 310024 China
| | - Charles C. Lee
- Center for Musculoskeletal Research, Department of Orthopaedics, University of Rochester Medical Center, Rochester, NY 14642,Department of Orthopaedics, University of Rochester Medical Center, Rochester, NY 14642
| | - John L. Daiss
- Center for Musculoskeletal Research, Department of Orthopaedics, University of Rochester Medical Center, Rochester, NY 14642,Department of Orthopaedics, University of Rochester Medical Center, Rochester, NY 14642
| | - Gowrishankar Muthukrishnan
- Center for Musculoskeletal Research, Department of Orthopaedics, University of Rochester Medical Center, Rochester, NY 14642,Department of Orthopaedics, University of Rochester Medical Center, Rochester, NY 14642
| | - John R. Owen
- Department of Orthopaedic Surgery, Virginia Commonwealth University, Richmond, VA 23298
| | - Stephen L. Kates
- Joint Orthopaedic, Research Center of Zunyi Medical University & University of Rochester Medical Center (JORC – ZMU&URMC), First Affiliated Hospital of Zunyi Medical University, Zunyi, 563003 China,Department of Orthopaedic Surgery, Virginia Commonwealth University, Richmond, VA 23298
| | - Jiachen Peng
- Department of Orthopaedics, Joint Orthopaedic Research Center of Zunyi Medical University & University of Rochester Medical Center (JORC – ZMU&URMC), First Affiliated Hospital of Zunyi Medical University, Zunyi, 563003 China,Joint Orthopaedic, Research Center of Zunyi Medical University & University of Rochester Medical Center (JORC – ZMU&URMC), First Affiliated Hospital of Zunyi Medical University, Zunyi, 563003 China,To whom correspondence should be addressed: Dr. Chao Xie, The Center for Musculoskeletal Research, Department of Orthopaedics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 665, Rochester, NY 14642, Phone 585-275-0818, FAX 585-276-2177, or Dr. Jiachen Peng, Department of Orthopaedics First Affiliated Hospital of Zunyi Medical University Zunyi, 563003 China,
| | - Chao Xie
- Joint Orthopaedic, Research Center of Zunyi Medical University & University of Rochester Medical Center (JORC – ZMU&URMC), First Affiliated Hospital of Zunyi Medical University, Zunyi, 563003 China,Center for Musculoskeletal Research, Department of Orthopaedics, University of Rochester Medical Center, Rochester, NY 14642,Department of Orthopaedics, University of Rochester Medical Center, Rochester, NY 14642,To whom correspondence should be addressed: Dr. Chao Xie, The Center for Musculoskeletal Research, Department of Orthopaedics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 665, Rochester, NY 14642, Phone 585-275-0818, FAX 585-276-2177, or Dr. Jiachen Peng, Department of Orthopaedics First Affiliated Hospital of Zunyi Medical University Zunyi, 563003 China,
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