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

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 t...

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Bibliographic Details
Published in:Nucleic acids research 2009-11, Vol.37 (21), p.7239-7257
Main Authors: Geissmann, Thomas, Chevalier, Clément, Cros, Marie-Josée, Boisset, Sandrine, Fechter, Pierre, Noirot, Céline, Schrenzel, Jacques, François, Patrice, Vandenesch, François, Gaspin, Christine, Romby, Pascale
Format: Article
Language:English
Subjects:
Bacillaceae
Bacillus subtilis
Bacillus subtilis - genetics
Bacillus subtilis - metabolism
Base Sequence
Biochemistry, Molecular Biology
Cellular Biology
Computational Biology
Conserved Sequence
Gene Expression Profiling
Gene Expression Regulation, Bacterial
Life Sciences
Molecular Sequence Data
Proteomics
RNA
RNA Stability
RNA, Messenger
RNA, Messenger - metabolism
RNA, Untranslated
RNA, Untranslated - chemistry
RNA, Untranslated - genetics
RNA, Untranslated - metabolism
Staphylococcus aureus
Staphylococcus aureus - genetics
Transcription, Genetic
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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.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkp668