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A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation

Geissmann, Thomas ; Chevalier, Clément ; Cros, Marie-Josée ; Boisset, Sandrine ; Fechter, Pierre ; Noirot, Céline ; Schrenzel, Jacques ; François, Patrice ; Vandenesch, François ; Gaspin, Christine ; Romby, Pascale

In: Nucleic Acids Research, 2009, vol. 37, no. 21, p. 7239-7257

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    Titre
    • A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation
    Auteur
    • Geissmann, Thomas. Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, F-67084 Strasbourg, INRA, UR 875, F-31320 Castanet-Tolosan, INSERM U851, Centre National de Référence des Staphylocoques, Université de Lyon I, F-69008 Lyon, France and Genomic Research Laboratory, Service of Infectious Diseases, University of Geneva Hospitals, Rue Micheli-du-Crest, 24, CH-1211 Geneva 14, Switzerland
    • Chevalier, Clément. Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, F-67084 Strasbourg, INRA, UR 875, F-31320 Castanet-Tolosan, INSERM U851, Centre National de Référence des Staphylocoques, Université de Lyon I, F-69008 Lyon, France and Genomic Research Laboratory, Service of Infectious Diseases, University of Geneva Hospitals, Rue Micheli-du-Crest, 24, CH-1211 Geneva 14, Switzerland
    • Cros, Marie-Josée. Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, F-67084 Strasbourg, INRA, UR 875, F-31320 Castanet-Tolosan, INSERM U851, Centre National de Référence des Staphylocoques, Université de Lyon I, F-69008 Lyon, France and Genomic Research Laboratory, Service of Infectious Diseases, University of Geneva Hospitals, Rue Micheli-du-Crest, 24, CH-1211 Geneva 14, Switzerland
    • Boisset, Sandrine. Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, F-67084 Strasbourg, INRA, UR 875, F-31320 Castanet-Tolosan, INSERM U851, Centre National de Référence des Staphylocoques, Université de Lyon I, F-69008 Lyon, France and Genomic Research Laboratory, Service of Infectious Diseases, University of Geneva Hospitals, Rue Micheli-du-Crest, 24, CH-1211 Geneva 14, Switzerland
    • Fechter, Pierre. Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, F-67084 Strasbourg, INRA, UR 875, F-31320 Castanet-Tolosan, INSERM U851, Centre National de Référence des Staphylocoques, Université de Lyon I, F-69008 Lyon, France and Genomic Research Laboratory, Service of Infectious Diseases, University of Geneva Hospitals, Rue Micheli-du-Crest, 24, CH-1211 Geneva 14, Switzerland
    • Noirot, Céline. Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, F-67084 Strasbourg, INRA, UR 875, F-31320 Castanet-Tolosan, INSERM U851, Centre National de Référence des Staphylocoques, Université de Lyon I, F-69008 Lyon, France and Genomic Research Laboratory, Service of Infectious Diseases, University of Geneva Hospitals, Rue Micheli-du-Crest, 24, CH-1211 Geneva 14, Switzerland
    • Schrenzel, Jacques. Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, F-67084 Strasbourg, INRA, UR 875, F-31320 Castanet-Tolosan, INSERM U851, Centre National de Référence des Staphylocoques, Université de Lyon I, F-69008 Lyon, France and Genomic Research Laboratory, Service of Infectious Diseases, University of Geneva Hospitals, Rue Micheli-du-Crest, 24, CH-1211 Geneva 14, Switzerland
    • François, Patrice. Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, F-67084 Strasbourg, INRA, UR 875, F-31320 Castanet-Tolosan, INSERM U851, Centre National de Référence des Staphylocoques, Université de Lyon I, F-69008 Lyon, France and Genomic Research Laboratory, Service of Infectious Diseases, University of Geneva Hospitals, Rue Micheli-du-Crest, 24, CH-1211 Geneva 14, Switzerland
    • Vandenesch, François. Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, F-67084 Strasbourg, INRA, UR 875, F-31320 Castanet-Tolosan, INSERM U851, Centre National de Référence des Staphylocoques, Université de Lyon I, F-69008 Lyon, France and Genomic Research Laboratory, Service of Infectious Diseases, University of Geneva Hospitals, Rue Micheli-du-Crest, 24, CH-1211 Geneva 14, Switzerland
    • Gaspin, Christine. Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, F-67084 Strasbourg, INRA, UR 875, F-31320 Castanet-Tolosan, INSERM U851, Centre National de Référence des Staphylocoques, Université de Lyon I, F-69008 Lyon, France and Genomic Research Laboratory, Service of Infectious Diseases, University of Geneva Hospitals, Rue Micheli-du-Crest, 24, CH-1211 Geneva 14, Switzerland
    • Romby, Pascale. Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, F-67084 Strasbourg, INRA, UR 875, F-31320 Castanet-Tolosan, INSERM U851, Centre National de Référence des Staphylocoques, Université de Lyon I, F-69008 Lyon, France and Genomic Research Laboratory, Service of Infectious Diseases, University of Geneva Hospitals, Rue Micheli-du-Crest, 24, CH-1211 Geneva 14, Switzerland
    Type de document
    • Postprint
    Langue
    • Inglese
    Publié dans
    • Nucleic Acids Research, 2009, vol. 37, no. 21, p. 7239-7257. Oxford University Press
    Autre version électronique
    Classification
    • Santé
    Mots clés
    Identifiant OAI-PMH
    • oai:doc.rero.ch:303828
    Summary
    Bioinformatic analysis of the intergenic regions of Staphylococcus aureus predicted multiple regulatory regions. From this analysis, we characterized 11 novel noncoding RNAs (RsaA‐K) that are expressed in several S. aureus strains under different experimental conditions. Many of them accumulate in the late-exponential phase of growth. All ncRNAs are stable and their expression is Hfq-independent. The transcription of several of them is regulated by the alternative sigma B factor (RsaA, D and F) while the expression of RsaE is agrA-dependent. Six of these ncRNAs are specific to S. aureus, four are conserved in other Staphylococci, and RsaE is also present in Bacillaceae. Transcriptomic and proteomic analysis indicated that RsaE regulates the synthesis of proteins involved in various metabolic pathways. Phylogenetic analysis combined with RNA structure probing, searches for RsaE‐mRNA base pairing, and toeprinting assays indicate that a conserved and unpaired UCCC sequence motif of RsaE binds to target mRNAs and prevents the formation of the ribosomal initiation complex. This study unexpectedly shows that most of the novel ncRNAs carry the conserved C−rich motif, suggesting that they are members of a class of ncRNAs that target mRNAs by a shared mechanism