Genomics

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


ABSTRACT: Analysis of the intergenic regions of Staphylococcus aureus by bioinformatics predicted multiple regulatory regions. From this analysis, we also 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 factor B (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 additionally 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.

ORGANISM(S): Staphylococcus aureus subsp. aureus COL Staphylococcus aureus subsp. aureus N315 Staphylococcus aureus subsp. aureus Mu50 Staphylococcus aureus subsp. aureus MRSA252 Staphylococcus aureus Staphylococcus aureus subsp. aureus NCTC 8325 Staphylococcus aureus subsp. aureus USA300 Staphylococcus aureus subsp. aureus MW2 Staphylococcus aureus subsp. aureus MSSA476

PROVIDER: GSE17135 | GEO | 2009/12/10

SECONDARY ACCESSION(S): PRJNA119821

REPOSITORIES: GEO

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