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Pagliuso A, Tham TN, Allemand E, Robertin S, Dupuy B, Bertrand Q, Bécavin C, Koutero M, Najburg V, Nahori MA, Tangy F, Stavru F, Bessonov S, Dessen A, Muchardt C, Lebreton A, Komarova AV, Cossart P. An RNA-Binding Protein Secreted by a Bacterial Pathogen Modulates RIG-I Signaling. Cell Host Microbe 2019; 26:823-835.e11. [PMID: 31761719 PMCID: PMC6907008 DOI: 10.1016/j.chom.2019.10.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 08/21/2019] [Accepted: 10/07/2019] [Indexed: 01/20/2023]
Abstract
RNA-binding proteins (RBPs) perform key cellular activities by controlling the function of bound RNAs. The widely held assumption that RBPs are strictly intracellular has been challenged by the discovery of secreted RBPs. However, extracellular RBPs have been described in eukaryotes, while secreted bacterial RBPs have not been reported. Here, we show that the bacterial pathogen Listeria monocytogenes secretes a small RBP that we named Zea. We show that Zea binds a subset of L. monocytogenes RNAs, causing their accumulation in the extracellular medium. Furthermore, during L. monocytogenes infection, Zea binds RIG-I, the non-self-RNA innate immunity sensor, potentiating interferon-β production. Mouse infection studies reveal that Zea affects L. monocytogenes virulence. Together, our results unveil that bacterial RNAs can be present extracellularly in association with RBPs, acting as “social RNAs” to trigger a host response during infection. L. monocytogenes secretes an RNA-binding protein, Zea Zea binds and protects L. monocytogenes RNA, resulting in extracellular RNA accumulation During infection, Zea binds RIG-I and modulates RIG-I-dependent IFN response Zea plays a role in L. monocytogenes virulence in mice
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Affiliation(s)
- Alessandro Pagliuso
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, Paris, France; U604 Inserm, Paris, France; USC2020 INRA, Paris, France.
| | - To Nam Tham
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, Paris, France; U604 Inserm, Paris, France; USC2020 INRA, Paris, France
| | - Eric Allemand
- Unité de régulation épigénétique, Institut Pasteur, UMR3738 CNRS, Paris, France
| | - Stevens Robertin
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, Paris, France; U604 Inserm, Paris, France; USC2020 INRA, Paris, France
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Paris, Université de Paris, Paris, France
| | - Quentin Bertrand
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Bacterial Pathogenesis Group, Grenoble, France
| | - Christophe Bécavin
- Hub de bioinformatique et biostatistique - Centre de Bioinformatique, Biostatistique et Biologie Intégrative, Unité mixte de Service et Recherche 3756 Institut Pasteur - Centre National de la Recherche Scientifique, Paris 75015, France
| | - Mikael Koutero
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, Paris, France; U604 Inserm, Paris, France; USC2020 INRA, Paris, France
| | - Valérie Najburg
- Unité de Génomique Virale et Vaccination, Institut Pasteur, Paris 75015, France; CNRS UMR-3569, Paris, France
| | - Marie-Anne Nahori
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, Paris, France; U604 Inserm, Paris, France; USC2020 INRA, Paris, France
| | - Frédéric Tangy
- Unité de Génomique Virale et Vaccination, Institut Pasteur, Paris 75015, France; CNRS UMR-3569, Paris, France
| | - Fabrizia Stavru
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, Paris, France; U604 Inserm, Paris, France; USC2020 INRA, Paris, France
| | - Sergey Bessonov
- Department I of Internal Medicine, University Hospital Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Department of Translational Epigenetics and Tumor Genetics, University Hospital Cologne, Cologne, Germany
| | - Andréa Dessen
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Bacterial Pathogenesis Group, Grenoble, France; Brazilian Biosciences National Laboratory (LNBio), CNPEM, Campinas, SP, Brazil
| | - Christian Muchardt
- Unité de régulation épigénétique, Institut Pasteur, UMR3738 CNRS, Paris, France
| | - Alice Lebreton
- Équipe Infection et Devenir de l'ARN, Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, Inserm, PSL Université Paris, Paris 75005, France; INRA, IBENS, 75005 Paris, France
| | - Anastassia V Komarova
- Unité de Génomique Virale et Vaccination, Institut Pasteur, Paris 75015, France; CNRS UMR-3569, Paris, France
| | - Pascale Cossart
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, Paris, France; U604 Inserm, Paris, France; USC2020 INRA, Paris, France.
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2
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Identification and functional characterization of bacterial small non-coding RNAs and their target: A review. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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3
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Tomasini A, Moreau K, Chicher J, Geissmann T, Vandenesch F, Romby P, Marzi S, Caldelari I. The RNA targetome of Staphylococcus aureus non-coding RNA RsaA: impact on cell surface properties and defense mechanisms. Nucleic Acids Res 2017; 45:6746-6760. [PMID: 28379505 PMCID: PMC5499838 DOI: 10.1093/nar/gkx219] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 03/24/2017] [Indexed: 01/08/2023] Open
Abstract
The virulon of Staphyloccocus aureus is controlled by intricate connections between transcriptional and post-transcriptional regulators including proteins and small non-coding RNAs (sRNAs). Many of the sRNAs regulate gene expression through base-pairings with mRNAs. However, characterization of the direct sRNA targets in Gram-positive bacteria remained a difficult challenge. Here, we have applied and adapted the MS2-affinity purification approach coupled to RNA sequencing (MAPS) to determine the targetome of RsaA sRNA of S. aureus, known to repress the synthesis of the transcriptional regulator MgrA. Several mRNAs were enriched with RsaA expanding its regulatory network. Besides mgrA, several of these mRNAs encode a family of SsaA-like enzymes involved in peptidoglycan metabolism and the secreted anti-inflammatory FLIPr protein. Using a combination of in vivo and in vitro approaches, these mRNAs were validated as direct RsaA targets. Quantitative differential proteomics of wild-type and mutant strains corroborated the MAPS results. Additionally, it revealed that RsaA indirectly activated the synthesis of surface proteins supporting previous data that RsaA stimulated biofilm formation and favoured chronic infections. All together, this study shows that MAPS could also be easily applied in Gram-positive bacteria for identification of sRNA targetome.
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Affiliation(s)
- Arnaud Tomasini
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000 Strasbourg, France
| | - Karen Moreau
- CIRI, International Center for Infectiology Research, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Hospices Civils de Lyon, University of Lyon, F-69008, Lyon, France
| | | | - Thomas Geissmann
- CIRI, International Center for Infectiology Research, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Hospices Civils de Lyon, University of Lyon, F-69008, Lyon, France
| | - François Vandenesch
- CIRI, International Center for Infectiology Research, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Hospices Civils de Lyon, University of Lyon, F-69008, Lyon, France
| | - Pascale Romby
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000 Strasbourg, France
| | - Stefano Marzi
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000 Strasbourg, France
| | - Isabelle Caldelari
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000 Strasbourg, France
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4
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Duval M, Marenna A, Chevalier C, Marzi S. Site-Directed Chemical Probing to map transient RNA/protein interactions. Methods 2016; 117:48-58. [PMID: 28027957 DOI: 10.1016/j.ymeth.2016.12.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 12/11/2016] [Accepted: 12/21/2016] [Indexed: 12/24/2022] Open
Abstract
RNA-protein interactions are at the bases of many biological processes, forming either tight and stable functional ribonucleoprotein (RNP) complexes (i.e. the ribosome) or transitory ones, such as the complexes involving RNA chaperone proteins. To localize the sites where a protein interacts on an RNA molecule, a common simple and inexpensive biochemical method is the footprinting technique. The protein leaves its footprint on the RNA acting as a shield to protect the regions of interaction from chemical modification or cleavages obtained with chemical or enzymatic nucleases. This method has proven its efficiency to study in vitro the organization of stable RNA-protein complexes. Nevertheless, when the protein binds the RNA very dynamically, with high off-rates, protections are very often difficult to observe. For the analysis of these transient complexes, we describe an alternative strategy adapted from the Site Directed Chemical Probing (SDCP) approach and we compare it with classical footprinting. SDCP relies on the modification of the RNA binding protein to tether an RNA probe (usually Fe-EDTA) to specific protein positions. Local cleavages on the regions of interaction can be used to localize the protein and position its domains on the RNA molecule. This method has been used in the past to monitor stable complexes; we provide here a detailed protocol and a practical example of its application to the study of Escherichia coli RNA chaperone protein S1 and its transitory complexes with mRNAs.
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Affiliation(s)
- Mélodie Duval
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Alessandra Marenna
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Clément Chevalier
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Stefano Marzi
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France.
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5
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Mollerup MS, Ross JA, Helfer AC, Meistrup K, Romby P, Kallipolitis BH. Two novel members of the LhrC family of small RNAs in Listeria monocytogenes with overlapping regulatory functions but distinctive expression profiles. RNA Biol 2016; 13:895-915. [PMID: 27400116 DOI: 10.1080/15476286.2016.1208332] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Multicopy small RNAs (sRNAs) have gained recognition as an important feature of bacterial gene regulation. In the human pathogen Listeria monocytogenes, 5 homologous sRNAs, called LhrC1-5, control gene expression by base pairing to target mRNAs though 3 conserved UCCC motifs common to all 5 LhrCs. We show here that the sRNAs Rli22 and Rli33-1 are structurally and functionally related to LhrC1-5, expanding the LhrC family to 7 members, which makes it the largest multicopy sRNA family reported so far. Rli22 and Rli33-1 both contain 2 UCCC motifs important for post-transcriptional repression of 3 LhrC target genes. One such target, oppA, encodes a virulence-associated oligo-peptide binding protein. Like LhrC1-5, Rli22 and Rli33-1 employ their UCCC motifs to recognize the Shine-Dalgarno region of oppA mRNA and prevent formation of the ribosomal complex, demonstrating that the 7 sRNAs act in a functionally redundant manner. However, differential expression profiles of the sRNAs under infection-relevant conditions suggest that they might also possess non-overlapping functions. Collectively, this makes the LhrC family a unique case for studying the purpose of sRNA multiplicity in the context of bacterial virulence.
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Affiliation(s)
- Maria Storm Mollerup
- a Department of Biochemistry and Molecular Biology , University of Southern Denmark , Odense , Denmark
| | - Joseph Andrew Ross
- a Department of Biochemistry and Molecular Biology , University of Southern Denmark , Odense , Denmark
| | - Anne-Catherine Helfer
- b Architecture et Réactivité de l´ARN, Université de Strasbourg, CNRS, IBMC , Strasbourg , France
| | - Kristine Meistrup
- a Department of Biochemistry and Molecular Biology , University of Southern Denmark , Odense , Denmark
| | - Pascale Romby
- b Architecture et Réactivité de l´ARN, Université de Strasbourg, CNRS, IBMC , Strasbourg , France
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6
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Lioliou E, Fechter P, Caldelari I, Jester BC, Dubrac S, Helfer AC, Boisset S, Vandenesch F, Romby P, Geissmann T. Various checkpoints prevent the synthesis of Staphylococcus aureus peptidoglycan hydrolase LytM in the stationary growth phase. RNA Biol 2016; 13:427-40. [PMID: 26901414 DOI: 10.1080/15476286.2016.1153209] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
In Staphylococcus aureus, peptidoglycan metabolism plays a role in the host inflammatory response and pathogenesis. Transcription of the peptidoglycan hydrolases is activated by the essential 2-component system WalKR at low cell density. During stationary growth phase, WalKR is not active and transcription of the peptidoglycan hydrolase genes is repressed. In this work, we studied regulation of expression of the glycylglycine endopeptidase LytM. We show that, in addition to the transcriptional regulation mediated by WalKR, the synthesis of LytM is negatively controlled by a unique mechanism at the stationary growth phase. We have identified 2 different mRNAs encoding lytM, which vary in the length of their 5' untranslated (5'UTR) regions. LytM is predominantly produced from the WalKR-regulated mRNA transcript carrying a short 5'UTR. The lytM mRNA is also transcribed as part of a polycistronic operon with the upstream SA0264 gene and is constitutively expressed. Although SA0264 protein can be synthesized from the longer operon transcript, lytM cannot be translated because its ribosome-binding site is sequestered into a translationally inactive secondary structure. In addition, the effector of the agr system, RNAIII, can inhibit translation of lytM present on the operon without altering the transcript level but does not have an effect on the translation of the upstream gene. We propose that this dual regulation of lytM expression, at the transcriptional and post-transcriptional levels, contributes to prevent cell wall damage during the stationary phase of growth.
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Affiliation(s)
- Efthimia Lioliou
- a Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC , 15 rue René Descartes, Strasbourg , France
| | - Pierre Fechter
- a Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC , 15 rue René Descartes, Strasbourg , France
| | - Isabelle Caldelari
- a Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC , 15 rue René Descartes, Strasbourg , France
| | - Brian C Jester
- b Institute of Systems and Synthetic Biology, University of Evry-Val-d'Essonne, CNRS FRE3561 , Evry , France
| | - Sarah Dubrac
- c Unité de Biologie des Bactéries pathogènes à Gram-positif, Institut Pasteur , 28 rue du Dr Roux, Paris , France
| | - Anne-Catherine Helfer
- a Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC , 15 rue René Descartes, Strasbourg , France
| | - Sandrine Boisset
- d CIRI, Center International de Recherche en Infectiologie - Inserm U1111 - Université Lyon 1 - Ecole Normale Supérieure de Lyon - CNRS UMR5308 , 21 Avenue Tony Garnier, LYON cedex 07 , France
| | - François Vandenesch
- d CIRI, Center International de Recherche en Infectiologie - Inserm U1111 - Université Lyon 1 - Ecole Normale Supérieure de Lyon - CNRS UMR5308 , 21 Avenue Tony Garnier, LYON cedex 07 , France
| | - Pascale Romby
- a Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC , 15 rue René Descartes, Strasbourg , France
| | - Thomas Geissmann
- d CIRI, Center International de Recherche en Infectiologie - Inserm U1111 - Université Lyon 1 - Ecole Normale Supérieure de Lyon - CNRS UMR5308 , 21 Avenue Tony Garnier, LYON cedex 07 , France
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7
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Fechter P, Parmentier D, Wu Z, Fuchsbauer O, Romby P, Marzi S. Traditional Chemical Mapping of RNA Structure In Vitro and In Vivo. Methods Mol Biol 2016; 1490:83-103. [PMID: 27665595 DOI: 10.1007/978-1-4939-6433-8_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Chemical probing is often used to gain knowledge on the secondary and tertiary structures of RNA molecules either free or engaged in complexes with ligands. The method monitors the reactivity of each nucleotide towards chemicals of various specificities reflecting the hydrogen bonding environment of each nucleotide within the RNA molecule. In addition, information can be obtained on the binding site of a ligand (noncoding RNAs, protein, metabolites), and on RNA conformational changes that accompanied ligand binding or perturbation of the environmental cues. The detection of the modifications can be obtained either by using end-labeled RNA molecules or by primer extension using reverse transcriptase. The goal of this chapter is to provide the reader with an experimental guide to probe the structure of RNA in vitro and in vivo with the most suitable chemical probes.
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Affiliation(s)
- Pierre Fechter
- Biotechnologie et Signalisation Cellulaire, CNRS-INSERM, ESBS, Université de Strasbourg, 300 boulevard Sebastien Brant, Illkirch, 67412, France
| | - Delphine Parmentier
- Architecture et Réactivité de l'ARN, CNRS, IBMC, Université de Strasbourg, 15 rue René Descartes, 67084, Strasbourg, France
| | - ZongFu Wu
- College of Veterinary Medicine, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Olivier Fuchsbauer
- Architecture et Réactivité de l'ARN, CNRS, IBMC, Université de Strasbourg, 15 rue René Descartes, 67084, Strasbourg, France
| | - Pascale Romby
- Architecture et Réactivité de l'ARN, CNRS, IBMC, Université de Strasbourg, 15 rue René Descartes, 67084, Strasbourg, France.
| | - Stefano Marzi
- Architecture et Réactivité de l'ARN, CNRS, IBMC, Université de Strasbourg, 15 rue René Descartes, 67084, Strasbourg, France
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8
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Durand S, Braun F, Lioliou E, Romilly C, Helfer AC, Kuhn L, Quittot N, Nicolas P, Romby P, Condon C. A nitric oxide regulated small RNA controls expression of genes involved in redox homeostasis in Bacillus subtilis. PLoS Genet 2015; 11:e1004957. [PMID: 25643072 PMCID: PMC4409812 DOI: 10.1371/journal.pgen.1004957] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 12/15/2014] [Indexed: 11/18/2022] Open
Abstract
RsaE is the only known trans-acting small regulatory RNA (sRNA) besides the ubiquitous 6S RNA that is conserved between the human pathogen Staphylococcus aureus and the soil-dwelling Firmicute Bacillus subtilis. Although a number of RsaE targets are known in S. aureus, neither the environmental signals that lead to its expression nor its physiological role are known. Here we show that expression of the B. subtilis homolog of RsaE is regulated by the presence of nitric oxide (NO) in the cellular milieu. Control of expression by NO is dependent on the ResDE two-component system in B. subtilis and we determined that the same is true in S. aureus. Transcriptome and proteome analyses revealed that many genes with functions related to oxidative stress and oxidation-reduction reactions were up-regulated in a B. subtilis strain lacking this sRNA. We have thus renamed it RoxS. The prediction of RoxS-dependent mRNA targets also suggested a significant enrichment for mRNAs related to respiration and electron transfer. Among the potential direct mRNA targets, we have validated the ppnKB mRNA, encoding an NAD+/NADH kinase, both in vivo and in vitro. RoxS controls both translation initiation and the stability of this transcript, in the latter case via two independent pathways implicating RNase Y and RNase III. Furthermore, RNase Y intervenes at an additional level by processing the 5′ end of the RoxS sRNA removing about 20 nucleotides. Processing of RoxS allows it to interact more efficiently with a second target, the sucCD mRNA, encoding succinyl-CoA synthase, thus expanding the repertoire of targets recognized by this sRNA. Bacteria have evolved various strategies to continually monitor the redox state of the internal and external environments to prevent cell damage and/or to protect them from host defense mechanisms. These signals modify the expression of genes, allowing bacteria to adapt to altered redox environments and to maintain homeostasis. Studies in Enterobacteriaceae have shown that sRNAs play central roles in adaptation to oxidative stress. We show here that the conserved sRNA, RoxS is induced by the presence of nitric oxide (NO) in the medium, through the ResDE and SrrAB two-component systems of Bacillus subtilis and Staphylococcus aureus, respectively. B. subtilis RoxS regulates functions related to oxidation-reduction reactions and acts as an antisense RNA to control translation initiation and the degradation of ppnKB mRNA, encoding an NAD+/NADH kinase. Interestingly, RNase Y processes the 5′ end of the RoxS sRNA leading to a truncated sRNA that in turn interacts more efficiently with a second target, the sucCD mRNA, encoding succinyl-CoA synthase. Taken together this work shows that RoxS is part of a complex regulatory network that allows the cell to sense and respond to redox perturbations, and revealed a novel process that allows an expansion of the repertoire of sRNA targets.
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Affiliation(s)
- Sylvain Durand
- CNRS FRE 3630 (affiliated with Univ. Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris, France
| | - Frédérique Braun
- CNRS FRE 3630 (affiliated with Univ. Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris, France
| | - Efthimia Lioliou
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
| | - Cédric Romilly
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
| | - Anne-Catherine Helfer
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
| | - Laurianne Kuhn
- Plateforme Protéomique Esplanade, IBMC, Strasbourg, France
| | - Noé Quittot
- Mathématique Informatique et Génome, INRA UR1077, Jouy en Josas, France
| | - Pierre Nicolas
- Mathématique Informatique et Génome, INRA UR1077, Jouy en Josas, France
| | - Pascale Romby
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
- * E-mail: (CC); (PR)
| | - Ciarán Condon
- CNRS FRE 3630 (affiliated with Univ. Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, Paris, France
- * E-mail: (CC); (PR)
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9
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Ellis MJ, Trussler RS, Ross JA, Haniford DB. Probing Hfq:RNA interactions with hydroxyl radical and RNase footprinting. Methods Mol Biol 2015; 1259:403-15. [PMID: 25579599 DOI: 10.1007/978-1-4939-2214-7_24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
RNA footprinting and structure probing techniques are used to characterize the interaction between RNA-binding proteins and RNAs in vitro. Hydroxyl radical footprinting results in the identification of protein binding site(s) in an RNA. Ribonuclease (RNase) structure probing is a complementary technique that also provides information about protein binding sites, as well as RNA structure and possible protein-directed RNA remodeling. Here we provide a comprehensive protocol for studying the interaction between Hfq and an mRNA or sRNA of interest using a combination of RNase A, T1, and V1 as well as hydroxyl radical footprinting techniques. Detailed protocols for in vitro synthesis of (32)P-labeled RNA; formation of Hfq:RNA binary complex(es), RNase, and hydroxyl radical footprinting; preparation and running of sequencing gels; and data analysis are provided.
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Affiliation(s)
- Michael J Ellis
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, 1151 Richmond St., London, ON, Canada, N6A 5C1
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10
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Romilly C, Lays C, Tomasini A, Caldelari I, Benito Y, Hammann P, Geissmann T, Boisset S, Romby P, Vandenesch F. A non-coding RNA promotes bacterial persistence and decreases virulence by regulating a regulator in Staphylococcus aureus. PLoS Pathog 2014; 10:e1003979. [PMID: 24651379 PMCID: PMC3961350 DOI: 10.1371/journal.ppat.1003979] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 01/21/2014] [Indexed: 11/19/2022] Open
Abstract
Staphylococcus aureus produces a high number of RNAs for which the functions are poorly understood. Several non-coding RNAs carry a C-rich sequence suggesting that they regulate mRNAs at the post-transcriptional level. We demonstrate that the Sigma B-dependent RsaA RNA represses the synthesis of the global transcriptional regulator MgrA by forming an imperfect duplex with the Shine and Dalgarno sequence and a loop-loop interaction within the coding region of the target mRNA. These two recognition sites are required for translation repression. Consequently, RsaA causes enhanced production of biofilm and a decreased synthesis of capsule formation in several strain backgrounds. These phenotypes led to a decreased protection of S. aureus against opsonophagocytic killing by polymorphonuclear leukocytes compared to the mutant strains lacking RsaA. Mice animal models showed that RsaA attenuates the severity of acute systemic infections and enhances chronic catheter infection. RsaA takes part in a regulatory network that contributes to the complex interactions of S. aureus with the host immune system to moderate invasiveness and favour chronic infections. It is the first example of a conserved small RNA in S. aureus functioning as a virulence suppressor of acute infections. Because S. aureus is essentially a human commensal, we propose that RsaA has been positively selected through evolution to support commensalism and saprophytic interactions with the host. Staphylococcus aureus is a commensal and an opportunistic pathogen that causes a large range of community and hospital-acquired infections. The bacteria produce an array of virulence factors, the expression of which is regulated by a set of regulators including proteins and RNAs. In recent years, a large number of small non-coding RNAs encoded by the S. aureus genome have been identified but determination of their function is still lagging behind. This study shows that RsaA, a staphylococcal conserved non-coding RNA, operates at the post-transcriptional level by repressing the translation of the master regulatory protein MgrA. The repression is based on a direct interaction of RsaA with the ribosome binding site of mgrA mRNA. Through MgrA regulation, RsaA activates biofilm formation and inhibits capsule synthesis. Using appropriate animal models, we showed that RsaA acts as a suppressor of virulence because the deletion of its gene increases the invasiveness of S. aureus in the mice sepsis model. RsaA is thus part of complex regulatory network that modify the interactions of S. aureus with the eukaryotic immune system. These findings illustrate how small RNAs can have a major impact in bacterial biology.
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Affiliation(s)
- Cédric Romilly
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
| | - Claire Lays
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France
- Inserm U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Arnaud Tomasini
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
| | - Isabelle Caldelari
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
| | - Yvonne Benito
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France
- Inserm U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Lyon, France
- CNRS, UMR5308, Lyon, France
- Hospices Civils de Lyon, Lyon, France
| | | | - Thomas Geissmann
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France
- Inserm U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Sandrine Boisset
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France
- Inserm U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Lyon, France
- CNRS, UMR5308, Lyon, France
- Hospices Civils de Lyon, Lyon, France
| | - Pascale Romby
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
- * E-mail: (PR); (FV)
| | - François Vandenesch
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France
- Inserm U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Lyon 1, Lyon, France
- CNRS, UMR5308, Lyon, France
- Hospices Civils de Lyon, Lyon, France
- * E-mail: (PR); (FV)
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11
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Sesto N, Touchon M, Andrade JM, Kondo J, Rocha EPC, Arraiano CM, Archambaud C, Westhof É, Romby P, Cossart P. A PNPase dependent CRISPR System in Listeria. PLoS Genet 2014; 10:e1004065. [PMID: 24415952 PMCID: PMC3886909 DOI: 10.1371/journal.pgen.1004065] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 11/12/2013] [Indexed: 12/26/2022] Open
Abstract
The human bacterial pathogen Listeria monocytogenes is emerging as a model organism to study RNA-mediated regulation in pathogenic bacteria. A class of non-coding RNAs called CRISPRs (clustered regularly interspaced short palindromic repeats) has been described to confer bacterial resistance against invading bacteriophages and conjugative plasmids. CRISPR function relies on the activity of CRISPR associated (cas) genes that encode a large family of proteins with nuclease or helicase activities and DNA and RNA binding domains. Here, we characterized a CRISPR element (RliB) that is expressed and processed in the L. monocytogenes strain EGD-e, which is completely devoid of cas genes. Structural probing revealed that RliB has an unexpected secondary structure comprising basepair interactions between the repeats and the adjacent spacers in place of canonical hairpins formed by the palindromic repeats. Moreover, in contrast to other CRISPR-Cas systems identified in Listeria, RliB-CRISPR is ubiquitously present among Listeria genomes at the same genomic locus and is never associated with the cas genes. We showed that RliB-CRISPR is a substrate for the endogenously encoded polynucleotide phosphorylase (PNPase) enzyme. The spacers of the different Listeria RliB-CRISPRs share many sequences with temperate and virulent phages. Furthermore, we show that a cas-less RliB-CRISPR lowers the acquisition frequency of a plasmid carrying the matching protospacer, provided that trans encoded cas genes of a second CRISPR-Cas system are present in the genome. Importantly, we show that PNPase is required for RliB-CRISPR mediated DNA interference. Altogether, our data reveal a yet undescribed CRISPR system whose both processing and activity depend on PNPase, highlighting a new and unexpected function for PNPase in “CRISPRology”. CRISPR-Cas systems confer to bacteria and archaea an adaptive immunity that protects them against invading bacteriophages and plasmids. In this study, we characterize a CRISPR (RliB-CRISPR) that is present in all L. monocytogenes strains at the same genomic locus but is never associated with a cas operon. It is an unusual CRISPR that, as we demonstrate, has a secondary structure consisting of basepair interactions between the repeat sequence and the adjacent spacer. We show that the RliB-CRISPR is processed by the endogenously encoded polynucleotide phosphorylase enzyme (PNPase). In addition, we show that the RliB-CRISPR system requires PNPase and presence of trans encoded cas genes of a second CRISPR-Cas system, to mediate DNA interference directed against a plasmid carrying a matching protospacer. Altogether, our data reveal a novel type of CRISPR system in bacteria that requires endogenously encoded PNPase enzyme for its processing and interference activity.
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Affiliation(s)
- Nina Sesto
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, Paris, France ; INSERM, U604, Paris, France ; INRA, USC2020, Paris, France
| | - Marie Touchon
- Unité de Génomique Evolutive des Microbes, Institut Pasteur, Paris, France ; CNRS, UMR3525, Paris, France
| | - José Marques Andrade
- Control of Gene Expression, Instituto de Tecnologia Química e Biológica, Oeiras, Portugal
| | - Jiro Kondo
- Architecture et Réactivité de l'ARN Université de Strasbourg, CNRS, Strasbourg, France
| | - Eduardo P C Rocha
- Unité de Génomique Evolutive des Microbes, Institut Pasteur, Paris, France ; CNRS, UMR3525, Paris, France
| | - Cecilia Maria Arraiano
- Control of Gene Expression, Instituto de Tecnologia Química e Biológica, Oeiras, Portugal
| | - Cristel Archambaud
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, Paris, France ; INSERM, U604, Paris, France ; INRA, USC2020, Paris, France
| | - Éric Westhof
- Architecture et Réactivité de l'ARN Université de Strasbourg, CNRS, Strasbourg, France
| | - Pascale Romby
- Architecture et Réactivité de l'ARN Université de Strasbourg, CNRS, Strasbourg, France
| | - Pascale Cossart
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, Paris, France ; INSERM, U604, Paris, France ; INRA, USC2020, Paris, France
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12
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Duval M, Korepanov A, Fuchsbauer O, Fechter P, Haller A, Fabbretti A, Choulier L, Micura R, Klaholz BP, Romby P, Springer M, Marzi S. Escherichia coli ribosomal protein S1 unfolds structured mRNAs onto the ribosome for active translation initiation. PLoS Biol 2013; 11:e1001731. [PMID: 24339747 PMCID: PMC3858243 DOI: 10.1371/journal.pbio.1001731] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 10/25/2013] [Indexed: 11/24/2022] Open
Abstract
Regulation of translation initiation is well appropriate to adapt cell growth in response to stress and environmental changes. Many bacterial mRNAs adopt structures in their 5' untranslated regions that modulate the accessibility of the 30S ribosomal subunit. Structured mRNAs interact with the 30S in a two-step process where the docking of a folded mRNA precedes an accommodation step. Here, we used a combination of experimental approaches in vitro (kinetic of mRNA unfolding and binding experiments to analyze mRNA-protein or mRNA-ribosome complexes, toeprinting assays to follow the formation of ribosomal initiation complexes) and in vivo (genetic) to monitor the action of ribosomal protein S1 on the initiation of structured and regulated mRNAs. We demonstrate that r-protein S1 endows the 30S with an RNA chaperone activity that is essential for the docking and the unfolding of structured mRNAs, and for the correct positioning of the initiation codon inside the decoding channel. The first three OB-fold domains of S1 retain all its activities (mRNA and 30S binding, RNA melting activity) on the 30S subunit. S1 is not required for all mRNAs and acts differently on mRNAs according to the signals present at their 5' ends. This work shows that S1 confers to the ribosome dynamic properties to initiate translation of a large set of mRNAs with diverse structural features.
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Affiliation(s)
- Mélodie Duval
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire-CNRS, Strasbourg, France
| | - Alexey Korepanov
- CNRS UPR9073, University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - Olivier Fuchsbauer
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire-CNRS, Strasbourg, France
| | - Pierre Fechter
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire-CNRS, Strasbourg, France
| | - Andrea Haller
- Institute of Organic Chemistry and Center for Molecular Biosciences, Leopold Franzens University, Innsbruck, Austria
| | - Attilio Fabbretti
- Laboratory of Genetics, Department of Biology MCA, University of Camerino, Camerino, Italy
| | - Laurence Choulier
- CNRS UMR 7213, Université de Strasbourg, Faculté de pharmacie, Illkirch, France
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences, Leopold Franzens University, Innsbruck, Austria
| | - Bruno P. Klaholz
- Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, UMR 7104-CNRS, U964-INSERM, Illkirch, France; and Université de Strasbourg, Strasbourg, France
| | - Pascale Romby
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire-CNRS, Strasbourg, France
| | - Mathias Springer
- CNRS UPR9073, University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Stefano Marzi
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire-CNRS, Strasbourg, France
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13
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Kaito C, Saito Y, Ikuo M, Omae Y, Mao H, Nagano G, Fujiyuki T, Numata S, Han X, Obata K, Hasegawa S, Yamaguchi H, Inokuchi K, Ito T, Hiramatsu K, Sekimizu K. Mobile genetic element SCCmec-encoded psm-mec RNA suppresses translation of agrA and attenuates MRSA virulence. PLoS Pathog 2013; 9:e1003269. [PMID: 23592990 PMCID: PMC3617227 DOI: 10.1371/journal.ppat.1003269] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 02/08/2013] [Indexed: 01/02/2023] Open
Abstract
Community acquired-methicillin resistant Staphylococcus aureus (CA-MRSA) is a socially problematic pathogen that infects healthy individuals, causing severe disease. CA-MRSA is more virulent than hospital associated-MRSA (HA-MRSA). The underlying mechanism for the high virulence of CA-MRSA is not known. The transcription product of the psm-mec gene, located in the mobile genetic element SCCmec of HA-MRSA, but not CA-MRSA, suppresses the expression of phenol-soluble modulin α (PSMα), a cytolytic toxin of S. aureus. Here we report that psm-mec RNA inhibits translation of the agrA gene encoding a positive transcription factor for the PSMα gene via specific binding to agrA mRNA. Furthermore, 25% of 325 clinical MRSA isolates had a mutation in the psm-mec promoter that attenuated transcription, and 9% of the strains had no psm-mec. In most of these psm-mec-mutated or psm-mec-deleted HA-MRSAs, PSMα expression was increased compared with strains carrying intact psm-mec, and some mutated strains produced high amounts of PSMα comparable with that of CA-MRSA. Deletion of psm-mec from HA-MRSA strains carrying intact psm-mec increased the expression of AgrA protein and PSMα, and virulence in mice. Thus, psm-mec RNA suppresses MRSA virulence via inhibition of agrA translation and the absence of psm-mec function in CA-MRSA causes its high virulence property. Methicillin-resistant Staphylococcus aureus (MRSA) is resistant to various antibiotics, including β-lactams, thus causing serious clinical problems. Hospital-associated (HA)-MRSA infects immunocompromised patients in hospitals. Community-acquired (CA)-MRSA causes serious diseases in healthy people who have not had contact with hospitals in the United States, Canada, or Europe. CA-MRSA produces higher amounts of extracellular toxins and has higher virulence than HA-MRSA, although the reason for this is unclear. SCCmec is a foreign DNA integrated into the MRSA chromosome that contains several genes including the mecA gene that confers resistance against methicillin. The SCCmec of CA-MRSA does not contain the psm-mec gene that exists in the HA-MRSA SCCmec. In the present study, we found that the transcription product of psm-mec inhibits translation of the agrA gene encoding a positive transcription factor for many extracellular toxins by direct binding to the agrA mRNA, resulting in decreased extracellular toxin production. Furthermore, some HA-MRSA strains carry mutated psm-mec or no psm-mec and produce higher amounts of extracellular toxins than HA-MRSA strains carrying intact psm-mec. These findings suggest that psm-mec RNA negatively regulates agrA and mutation or absence of psm-mec leads to a high virulence capacity of MRSA.
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Affiliation(s)
- Chikara Kaito
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
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14
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Probing the sequence and structure of in vitro synthesized antisense and target RNAs from the replication control system of plasmid pMV158. Plasmid 2013; 70:94-103. [PMID: 23541653 DOI: 10.1016/j.plasmid.2013.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 02/21/2013] [Accepted: 02/28/2013] [Indexed: 12/30/2022]
Abstract
Antisense RNAII is a replication control element encoded by promiscuous plasmid pMV158. RNAII binds to its complementary sequence in the copG-repB mRNA, thus inhibiting translation of the replication initiator repB gene. In order to initiate the biochemical characterization of the pMV158 antisense RNA-mediated control system, conditions for in vitro transcription by T7RNA polymerase were set up that yielded large amounts of antisense and target run-off products able to bind to each other. The run-off antisense transcript was expected, and confirmed, to span the entire RNAII as synthesized by the bacterial RNA polymerase, including the intrinsic transcription terminator at its 3'-terminus. On the other hand, two different target transcripts, mRNA₆₀ and mRNA₈₀, were produced, characterized and tested for efficient binding to the antisense product. The mRNA₆₀ and mRNA₈₀ run-off transcripts supposedly spanned 60 and 80 nucleotides, respectively, on the copG-repB mRNA and lacked terminator-like structures at their 3'-termini. Probing of the sequence and conformation of the main products, along with modeling of their secondary structures, showed that both target transcripts were actually longer-than-expected, and contained a 3'-terminal hairpin wherein the extra nucleotides base-paired to the expected 3'-terminus of the corresponding run-off transcript. These longer products were proposed to arise from the RNA-dependent polymerizing activity of T7RNA polymerase on correct run-off transcripts primed by extremely short 3'-selfcomplementarity. Seizing of the target mRNA sequence complementary to the 5'-terminus of RNAII in a stable 3'-terminal hairpin generated by this activity seemed to cause a 3-fold decrease in the efficiency of binding to the antisense RNA.
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15
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Lioliou E, Sharma CM, Caldelari I, Helfer AC, Fechter P, Vandenesch F, Vogel J, Romby P. Global regulatory functions of the Staphylococcus aureus endoribonuclease III in gene expression. PLoS Genet 2012; 8:e1002782. [PMID: 22761586 PMCID: PMC3386247 DOI: 10.1371/journal.pgen.1002782] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2011] [Accepted: 05/09/2012] [Indexed: 11/18/2022] Open
Abstract
RNA turnover plays an important role in both virulence and adaptation to stress in the Gram-positive human pathogen Staphylococcus aureus. However, the molecular players and mechanisms involved in these processes are poorly understood. Here, we explored the functions of S. aureus endoribonuclease III (RNase III), a member of the ubiquitous family of double-strand-specific endoribonucleases. To define genomic transcripts that are bound and processed by RNase III, we performed deep sequencing on cDNA libraries generated from RNAs that were co-immunoprecipitated with wild-type RNase III or two different cleavage-defective mutant variants in vivo. Several newly identified RNase III targets were validated by independent experimental methods. We identified various classes of structured RNAs as RNase III substrates and demonstrated that this enzyme is involved in the maturation of rRNAs and tRNAs, regulates the turnover of mRNAs and non-coding RNAs, and autoregulates its synthesis by cleaving within the coding region of its own mRNA. Moreover, we identified a positive effect of RNase III on protein synthesis based on novel mechanisms. RNase III–mediated cleavage in the 5′ untranslated region (5′UTR) enhanced the stability and translation of cspA mRNA, which encodes the major cold-shock protein. Furthermore, RNase III cleaved overlapping 5′UTRs of divergently transcribed genes to generate leaderless mRNAs, which constitutes a novel way to co-regulate neighboring genes. In agreement with recent findings, low abundance antisense RNAs covering 44% of the annotated genes were captured by co-immunoprecipitation with RNase III mutant proteins. Thus, in addition to gene regulation, RNase III is associated with RNA quality control of pervasive transcription. Overall, this study illustrates the complexity of post-transcriptional regulation mediated by RNase III. Control of mRNA stability is crucial for bacteria to survive and rapidly adapt to environmental changes and stress conditions. The molecular players and the degradation pathways involved in these adaptive processes are poorly understood in Staphylococcus aureus. The universally conserved double-strand-specific endoribonuclease III (RNase III) in S. aureus is known to repress the synthesis of several virulence factors and was recently implicated in genome-wide mRNA processing mediated by antisense transcripts. We present here the first global map of direct RNase III targets in S. aureus. Deep sequencing was used to identify RNAs associated with epitope-tagged wild-type RNase III and two catalytically impaired but binding-competent mutant proteins in vivo. Experimental validation revealed an unexpected variety of structured RNA transcripts as novel RNase III substrates. In addition to rRNA operon maturation, autoregulation, degradation of structured RNAs, and antisense regulation, we propose novel mechanisms by which RNase III increases mRNA translation. Overall, this study shows that RNase III has a broad function in gene regulation of S. aureus. We can now address more specifically the roles of this universally conserved enzyme in gene regulation in response to stress and during host infection.
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Affiliation(s)
- Efthimia Lioliou
- Architecture et Réactivité de l′ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
| | | | - Isabelle Caldelari
- Architecture et Réactivité de l′ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
| | - Anne-Catherine Helfer
- Architecture et Réactivité de l′ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
| | - Pierre Fechter
- Architecture et Réactivité de l′ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
| | - François Vandenesch
- Inserm U851, Centre National de Référence des Staphylocoques, Université de Lyon, Lyon, France
| | - Jörg Vogel
- Institut für Molekulare Infektionsbiologie, Würzburg, Germany
- * E-mail: (JV); (PR)
| | - Pascale Romby
- Architecture et Réactivité de l′ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
- * E-mail: (JV); (PR)
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16
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Fourmy D, Yoshizawa S. Protein-RNA footprinting: an evolving tool. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 3:557-66. [PMID: 22566372 DOI: 10.1002/wrna.1119] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
As more RNA molecules with important cellular functions are discovered, there is a strong need to characterize their structures, functions, and interactions. Chemical and enzymatic footprinting methods are used to map RNA secondary and tertiary structure, to monitor ligand interactions and conformational changes, and in the study of protein-RNA interactions. These methods provide data at single-nucleotide resolution that nicely complements the structural information available from X-ray diffraction, nuclear magnetic resonance spectroscopy (NMR), or cryo-electron microscopy. Footprinting methods also complement the dynamic information derived from single-molecule Förster resonance energy transfer. RNA footprinting tools have been used for decades, but we have recently seen spectacular advances, for instance, the use in combination with massive parallel sequencing techniques. Large libraries of RNA molecules (small or large in size) can now be probed in high-throughput manner when RNA footprinting methods are combined with fluorescent probe technologies and automation. In this article, after a brief historical overview, we summarize recent advances in RNA-protein footprinting methodologies that now integrate tools for massive parallel analysis.
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Affiliation(s)
- Dominique Fourmy
- Centre de Génétique Moléculaire UPR 3404, CNRS, Université Paris-Sud, Gif-sur-Yvette, France.
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17
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Vockenhuber MP, Suess B. Streptomyces coelicolor sRNA scr5239 inhibits agarase expression by direct base pairing to the dagA coding region. MICROBIOLOGY-SGM 2011; 158:424-435. [PMID: 22075028 DOI: 10.1099/mic.0.054205-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Transcriptional regulation of primary and secondary metabolism is well-studied in Streptomyces coelicolor, a model organism for antibiotic production and cell differentiation. In contrast, little is known about post-transcriptional regulation and the potential functions of small non-coding RNAs (sRNAs) in this Gram-positive, GC-rich soil bacterium. Here, we report the identification and characterization of scr5239, an sRNA highly conserved in the genus Streptomyces. The sRNA is 159 nt long, composed of five stem-loops, and encoded in the intergenic region between SCO5238 and SCO5239. scr5239 expression is constitutive under several stress and growth conditions but dependent on the nitrogen supply. scr5239 decreases the production of the antibiotic actinorhodin, and represses expression of the extracellular agarase dagA at the post-transcriptional level by direct base pairing to the coding region 33 nt downstream of the ribosome-binding site.
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Affiliation(s)
- Michael-Paul Vockenhuber
- Institut für Molekulare Biowissenschaften, Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Beatrix Suess
- Institut für Molekulare Biowissenschaften, Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
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18
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Sharma CM, Papenfort K, Pernitzsch SR, Mollenkopf HJ, Hinton JCD, Vogel J. Pervasive post-transcriptional control of genes involved in amino acid metabolism by the Hfq-dependent GcvB small RNA. Mol Microbiol 2011; 81:1144-65. [PMID: 21696468 DOI: 10.1111/j.1365-2958.2011.07751.x] [Citation(s) in RCA: 166] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
GcvB is one of the most highly conserved Hfq-associated small RNAs in Gram-negative bacteria and was previously reported to repress several ABC transporters for amino acids. To determine the full extent of GcvB-mediated regulation in Salmonella, we combined a genome-wide experimental approach with biocomputational target prediction. Comparative pulse expression of wild-type versus mutant sRNA variants revealed that GcvB governs a large post-transcriptional regulon, impacting ~1% of all Salmonella genes via its conserved G/U-rich domain R1. Complementary predictions of C/A-rich binding sites in mRNAs and gfp reporter fusion experiments increased the number of validated GcvB targets to more than 20, and doubled the number of regulated amino acid transporters. Unlike the previously described targeting via the single R1 domain, GcvB represses the glycine transporter CycA by exceptionally redundant base-pairing. This novel ability of GcvB is focused upon the one target that could feedback-regulate the glycine-responsive synthesis of GcvB. Several newly discovered mRNA targets involved in amino acid metabolism, including the global regulator Lrp, question the previous assumption that GcvB simply acts to limit unnecessary amino acid uptake. Rather, GcvB rewires primary transcriptional control circuits and seems to act as a distinct regulatory node in amino acid metabolism.
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Affiliation(s)
- Cynthia M Sharma
- Institute for Molecular Infection Biology, Research Centre of Infectious Diseases, University of Würzburg, Germany
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19
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Kortmann J, Sczodrok S, Rinnenthal J, Schwalbe H, Narberhaus F. Translation on demand by a simple RNA-based thermosensor. Nucleic Acids Res 2010; 39:2855-68. [PMID: 21131278 PMCID: PMC3074152 DOI: 10.1093/nar/gkq1252] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Structured RNA regions are important gene control elements in prokaryotes and eukaryotes. Here, we show that the mRNA of a cyanobacterial heat shock gene contains a built-in thermosensor critical for photosynthetic activity under stress conditions. The exceptionally short 5′-untranslated region is comprised of a single hairpin with an internal asymmetric loop. It inhibits translation of the Synechocystis hsp17 transcript at normal growth conditions, permits translation initiation under stress conditions and shuts down Hsp17 production in the recovery phase. Point mutations that stabilized or destabilized the RNA structure deregulated reporter gene expression in vivo and ribosome binding in vitro. Introduction of such point mutations into the Synechocystis genome produced severe phenotypic defects. Reversible formation of the open and closed structure was beneficial for viability, integrity of the photosystem and oxygen evolution. Continuous production of Hsp17 was detrimental when the stress declined indicating that shutting-off heat shock protein production is an important, previously unrecognized function of RNA thermometers. We discovered a simple biosensor that strictly adjusts the cellular level of a molecular chaperone to the physiological need.
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Affiliation(s)
- Jens Kortmann
- Lehrstuhl für Biologie der Mikroorganismen, Ruhr-Universität Bochum, 44780 Bochum, Germany
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20
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Sobczak K, Michlewski G, de Mezer M, Krol J, Krzyzosiak WJ. Trinucleotide repeat system for sequence specificity analysis of RNA structure probing reagents. Anal Biochem 2010; 402:40-6. [PMID: 20302838 DOI: 10.1016/j.ab.2010.03.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Revised: 03/11/2010] [Accepted: 03/13/2010] [Indexed: 10/19/2022]
Abstract
Chemical and enzymatic structural probes have been used for decades to obtain rapid and comprehensive information regarding the molecular architecture of various RNAs. Despite their widespread use, the sequence specificity of these RNA structural probing reagents has not yet been thoroughly characterized. In this study, we revisited the properties of commonly used structural probes such as Pb(II) ions, ribonuclease V1, ribonuclease T2, and the S1 and mung bean nucleases by testing them on highly regular triplet repeat sequences representing phosphodiester bonds with every possible combination of 3' and 5' adjacent nucleotides. We show that Pb(II) ions preferentially cleave after pyrimidines and that S1 nuclease possesses a previously overlooked specificity toward phosphodiester bonds following G residues. We also observed that mung bean nuclease shows a preference for cleaving ApN bonds and that RNase V1 mainly recognizes U residues in both single- and double-stranded RNAs. These data are important for accurate interpretation of the results of structure probing experiments and for assignment of the correct structure to individual RNA molecules. The triplet repeat transcript system described here may be considered as a reliable platform for determining the sequence specificity of other reagents used to probe RNA structure.
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Affiliation(s)
- Krzysztof Sobczak
- Laboratory of Cancer Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego St. 12/14, 61-704 Poznan, Poland
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21
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Sharma CM, Vogel J. Experimental approaches for the discovery and characterization of regulatory small RNA. Curr Opin Microbiol 2009; 12:536-46. [PMID: 19758836 DOI: 10.1016/j.mib.2009.07.006] [Citation(s) in RCA: 162] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Revised: 07/23/2009] [Accepted: 07/28/2009] [Indexed: 01/27/2023]
Abstract
Following the pioneering screens for small regulatory RNAs (sRNAs) in Escherichia coli in 2001, sRNAs are now being identified in almost every branch of the eubacterial kingdom. Experimental strategies have become increasingly important for sRNA discovery, thanks to increased availability of tiling arrays and fast progress in the development of high-throughput cDNA sequencing (RNA-Seq). The new technologies also facilitate genome-wide discovery of potential target mRNAs by sRNA pulse-expression coupled to transcriptomics, and immunoprecipitation with RNA-binding proteins such as Hfq. Moreover, the staggering rate of new sRNAs demands mechanistic analysis of target regulation. We will also review the available toolbox for wet lab-based research, including in vivo and in vitro reporter systems, genetic methods and biochemical co-purification of sRNA interaction partners.
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Affiliation(s)
- Cynthia Mira Sharma
- RNA Biology Group, Max Planck Institute for Infection Biology, Charitéplatz 1, D-10117 Berlin, Germany
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Serganov A, Patel DJ. Amino acid recognition and gene regulation by riboswitches. BIOCHIMICA ET BIOPHYSICA ACTA 2009; 1789:592-611. [PMID: 19619684 PMCID: PMC3744886 DOI: 10.1016/j.bbagrm.2009.07.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Revised: 07/08/2009] [Accepted: 07/09/2009] [Indexed: 01/06/2023]
Abstract
Riboswitches specifically control expression of genes predominantly involved in biosynthesis, catabolism and transport of various cellular metabolites in organisms from all three kingdoms of life. Among many classes of identified riboswitches, two riboswitches respond to amino acids lysine and glycine to date. Though these riboswitches recognize small compounds, they both belong to the largest riboswitches and have unique structural and functional characteristics. In this review, we attempt to characterize molecular recognition principles employed by amino acid-responsive riboswitches to selectively bind their cognate ligands and to effectively perform a gene regulation function. We summarize up-to-date biochemical and genetic data available for the lysine and glycine riboswitches and correlate these results with recent high-resolution structural information obtained for the lysine riboswitch. We also discuss the contribution of lysine riboswitches to antibiotic resistance and outline potential applications of riboswitches in biotechnology and medicine.
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Affiliation(s)
- Alexander Serganov
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.
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