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Nucleic Acids Research Advance Access published online on September 28, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp668
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

RNA

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

Thomas Geissmann1, Clément Chevalier1, Marie-Josée Cros2, Sandrine Boisset3, Pierre Fechter1, Céline Noirot2, Jacques Schrenzel4, Patrice François4, François Vandenesch3, Christine Gaspin2 and Pascale Romby1,*

1Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, F-67084 Strasbourg, 2INRA, UR 875, F-31320 Castanet-Tolosan, 3INSERM U851, Centre National de Référence des Staphylocoques, Université de Lyon I, F-69008 Lyon, France and 4Genomic Research Laboratory, Service of Infectious Diseases, University of Geneva Hospitals, Rue Micheli-du-Crest, 24, CH-1211 Geneva 14, Switzerland

*To whom correspondence should be addressed. Tel: 33 3 88417051; Fax: 33 3 88602218; Email: p.romby{at}ibmc.u-strasbg.fr Correspondence may also be addressed to Christine Gaspin. Email: gaspin{at}toulouse.inra.fr Correspondence may also be addressed to François Vandenesch. Email: denesch{at}univ-lyon1.fr

Received May 22, 2009. Revised July 24, 2009. Accepted July 29, 2009.

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.

Present address: Thomas Geissmann, INSERM U851, Centre National de Référence des Staphylocoques, Université de Lyon I, F-69008 Lyon, France.


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