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Regulatory Rnas in Staphylococcus Aureus: Function and Mechanism

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Regulatory Rnas in Staphylococcus Aureus: Function and Mechanism Regulatory RNAs in Staphylococcus aureus : Function and Mechanism Thao Nguyen Le Lam To cite this version: Thao Nguyen Le Lam. Regulatory RNAs in Staphylococcus aureus : Function and Mechanism. Agri- cultural sciences. Université Paris Sud - Paris XI, 2015. English. NNT : 2015PA112216. tel- 01424170 HAL Id: tel-01424170 https://tel.archives-ouvertes.fr/tel-01424170 Submitted on 2 Jan 2017 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. UNIVERSITÉ PARIS SACLAY - UNIVERSITÉ PARIS SUD UFR SCIENTIFIQUE D’ORSAY - ÉCOLE DOCTORALE STRUCTURE ET DYNAMIQUE DES SYSTÈMES VIVANTS Thèse Présentée pour obtenir le grade de DOCTEUR EN SCIENCES DE L’UNIVERSITÉ PARIS SUD Le 24 septembre 2015 Characterization of regulatory RNAs in Staphylococcus aureus Thao Nguyen LE LAM Directeur de thèse : Dr. Philippe BOULOC Laboratoire d’accueil : Signalisation et Réseaux de Régulations Bactériens Institute for Integrative Biology of the Cell (I2BC) CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Orsay, France Composition du jury : Président du jury Pr. Nicolas BAYAN Rapporteur Dr. Maude GUILLIER Rapporteur Dr. Francis REPOILA Examinateur Pr. Brice FELDEN Examinateur Dr. Nara FIGUEROA-BOSSI Directeur de thèse Dr. Philippe BOULOC 1 2 TABLE OF CONTENTS FIGURES AND TABLES .......................................................................................................... 5 ABBREVIATIONS .................................................................................................................. 7 INTRODUCTION ................................................................................................................... 9 I. Staphylococcus aureus ...................................................................................................... 11 1. General features .............................................................................................................. 11 2. Role in disease ................................................................................................................. 12 3. Antibiotic resistance ........................................................................................................ 14 II. Overview of adaptation and virulence in S. aureus ...................................................... 15 1. Some examples in adaptation ......................................................................................... 15 2. Host-pathogen interaction .............................................................................................. 25 III. Overview of bacterial competitive fitness ................................................................... 27 IV. Overview of regulatory RNAs in S. aureus ................................................................... 31 1. Identification of regulatory RNAs by various approaches ............................................... 31 2. Classification .................................................................................................................... 36 2.1 Regulatory small RNAs targeting mRNAs ................................................................ 36 2.2 Cis-regulatory elements .......................................................................................... 39 2.3 Protein-targeting RNAs ........................................................................................... 42 3. Role of regulatory RNAs in S. aureus ............................................................................... 43 4. Proteins involved in S. aureus sRNA functions ................................................................ 51 4.1 RNA chaperone Hfq: a controversial factor ............................................................ 51 4.2 Main RNases in S. aureus ........................................................................................ 53 V. Selected samples of regulatory RNAs in some Firmicutes species ................................. 61 1. sRNA in the pathogenesis of Streptococcus .................................................................... 61 2. sRNA in the pathogenesis of Clostridium ........................................................................ 62 3. sRNA in the pathogenesis of Listeria monocytogenes .................................................... 63 4. sRNA in the pathogenesis of Bacillus subtilis .................................................................. 67 5. sRNAs in the pathogenesis of Enterococcus faecalis....................................................... 68 AIM OF THE THESIS ............................................................................................................ 71 CHAPTER A1 ...................................................................................................................... 73 CHAPTER A2 .................................................................................................................... 125 CHAPTER B ...................................................................................................................... 149 CHAPTER C ...................................................................................................................... 217 DISCUSSION & PERSPECTIVES ........................................................................................... 249 BIBLIOGRAPHY ................................................................................................................ 263 3 4 FIGURES AND TABLES Figure 1: Staphylococcus aureus also known “the golden Staph”. .......................................... 11 Figure 2: Sites of infection and diseases caused by S. aureus. ................................................ 13 Figure 3: Model of SrrAB system. ............................................................................................ 17 Figure 4: Model for the NreBC sensor and regulation system in staphylococci. .................... 18 Figure 5: The CtsR, HrcA regulon of S. aureus......................................................................... 21 Figure 6: Mechanism of acid resistance of Gram-positive bacteria ........................................ 23 Figure 7: Human lines of defense against pathogens .............................................................. 26 Figure 8: Mechanisms by which S. aureus subverts host innate immune defense ................. 27 Figure 9: Scheme of a competitive fitness assay. .................................................................... 28 Figure 10: Signature-tagged mutagenesis in Salmonella. ........................................................ 30 Figure 11: Example of cis-encoded antisense RNAs (asRNAs). ................................................ 36 Figure 12: Antisense regulation of plasmid pT181 replication. ............................................... 37 Figure 13: Gene arrangement and regulatory functions of sRNAs. ......................................... 38 Figure 14: C-rich box conserved motif in S. aureus sRNAs and an example of example sRNA/mRNA base pairing. ........................................................................................................ 39 Figure 15: Diversity of riboswitches and mechanisms of gene control in bacteria. ................ 40 Figure 16: Model of a regulatory cascade for methionine biosynthesis operon control ........ 41 Figure 17: RNA polymerase interacts with 6S sRNA in E.coli ................................................... 43 Figure 18: The accessory gene regulator (agr) quorum sensing system of S. aureus ............. 44 Figure 19: Regulatory circuits involved in virulence gene expression ..................................... 46 Figure 20: RsaE controls metabolic pathways. ........................................................................ 48 Figure 21: RsaA and its regulatory circuits. .............................................................................. 49 Figure 22: Base-pair association of SprD with sbi mRNA. ........................................................ 51 Figure 23: Effect of hfq deletion on pigmentation in different S. aureus strains. ................... 51 Figure 24: Examples of regulatory RNAs and their mechanism of action in S. aureus. ........... 53 Figure 25: Examples of RNase III functions. ............................................................................. 57 Figure 26: Schematic representation of the saePQRS operon ................................................ 58 Figure 27: S. aureus hemolysin production via RNA stability control by RNase Y and PNPase.. .................................................................................................................................................. 60 Figure 28: Regulatory mechanism of FasX with the ska mRNA. .............................................. 62 Figure 29: Examples of regulatory RNAs in Clostridium. ......................................................... 63 Figure 30: Regulatory mechanism of LhrA and chiA mRNA. .................................................... 64 Figure 31: Interplay between a metabolite-sensing riboswitch and
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