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; Schrenzel, Jacques; Francois, Patrice; Vandenesch, François; Gaspin, Christine; Romby, Pascale

doi:10.1093/nar/gkp668

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Title		A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation
Authors		Geissmann, Thomas Chevalier, Clement Cros, Marie-Josee Boisset, Sandrine Fechter, Pierre Noirot, Celine Schrenzel, Jacques Francois, Patrice Vandenesch, François Gaspin, Christine Romby, Pascale show all authors [1 - 11]
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/metabolism — Base Sequence — Computational Biology — Conserved Sequence — Gene Expression Profiling — Gene Expression Regulation, Bacterial — Molecular Sequence Data — Proteomics — RNA Stability — RNA, Messenger/metabolism — RNA, Untranslated/chemistry/genetics/metabolism — Staphylococcus aureus/*genetics — Transcription, Genetic
Identifiers		DOI: 10.1093/nar/gkp668 PMID: 19786493
Full text		Article - Limited access to UNIGE
Structures		Faculté de médecine / Section de médecine clinique / Département de médecine
Research group		Analyse génomique et fonctionnelle du staphylocoque doré (604)
Citation (ISO format)		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