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

Geissmann, Thomas
Chevalier, Clement
Cros, Marie-Josee
Boisset, Sandrine
Fechter, Pierre
Noirot, Celine
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Published in Nucleic Acids Research. 2009, vol. 37, no. 21, p. 7239-7257
Abstract 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.
Keywords Bacillus subtilis/genetics/metabolismBase SequenceComputational BiologyConserved SequenceGene Expression Profiling*Gene Expression Regulation, BacterialMolecular Sequence DataProteomicsRNA StabilityRNA, Messenger/metabolismRNA, Untranslated/*chemistry/genetics/metabolismStaphylococcus aureus/*geneticsTranscription, Genetic
PMID: 19786493
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Research group Analyse génomique et fonctionnelle du staphylocoque doré (604)
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GEISSMANN, Thomas et al. A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation. In: Nucleic Acids Research, 2009, vol. 37, n° 21, p. 7239-7257. doi: 10.1093/nar/gkp668 https://archive-ouverte.unige.ch/unige:19828

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Deposited on : 2012-04-23

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