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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. Total RNA of the strain Staphylococcus aureus RN6390 (wild type) was co-hybridized in duplicate with the RsaX15 mutant strain (Staphylococcus aureus Lug1430). cDNA of RN6390 was labeled with Cy-5 ; cDNA of RN6390 was labeled with Cy-3. Hybridization, performed in Agilent proprietary buffer was performed for 17H at 60°C. Slides were then scanned in the Agilent scanner and extracted with Feature Extraction software. Background subtracted data were normalized for unequal incorporation or loading (LOWESS).

ORGANISM(S): Staphylococcus aureus

SUBMITTER: Marie-Josée Cros 

PROVIDER: E-GEOD-17135 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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

Geissmann Thomas T   Chevalier Clément C   Cros Marie-Josée MJ   Boisset Sandrine S   Fechter Pierre P   Noirot Céline C   Schrenzel Jacques J   François Patrice P   Vandenesch François F   Gaspin Christine C   Romby Pascale P  

Nucleic acids research 20091101 21


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)  ...[more]

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