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| Status |
Public on Dec 10, 2009 |
| Title |
A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation. |
| Platform organisms |
Staphylococcus aureus; Staphylococcus aureus subsp. aureus NCTC 8325; Staphylococcus aureus subsp. aureus COL; Staphylococcus aureus subsp. aureus Mu50; Staphylococcus aureus subsp. aureus N315; Staphylococcus aureus subsp. aureus MW2; Staphylococcus aureus subsp. aureus MRSA252; Staphylococcus aureus subsp. aureus MSSA476; Staphylococcus aureus subsp. aureus USA300 |
| Sample organism |
Staphylococcus aureus |
| Experiment type |
Non-coding RNA profiling by array
|
| Summary |
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.
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| Overall design |
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).
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| Contributor(s) |
Geissmann T, Chevalier C, Cros M, Boisset S, Fechter P, Noirot C, Schrenzel J, Francois P, Vandenesch F, Gaspin C, Romby P |
| Citation(s) |
19786493 |
| |
| Submission date |
Jul 16, 2009 |
| Last update date |
Mar 21, 2012 |
| Contact name |
FRANCOIS Patrice |
| E-mail(s) |
[email protected]
|
| Phone |
+41 (0)22 372 93 37
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| Organization name |
Genomic Research Laboratory
|
| Department |
Service of Infectious Diseases
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| Lab |
Genomic Research Lab
|
| Street address |
Rue Gabrielle-Perret-Gentil, 4
|
| City |
Geneva |
| State/province |
Ge 4 |
| ZIP/Postal code |
1211 |
| Country |
Switzerland |
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| Platforms (1) |
| GPL7137 |
Agilent-017903 Staphylococcus aureus V5 Bis 15K (basic) |
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| Samples (2) |
| GSM428997 |
Staphylococcus aureus Lug1430 (RsaX15 Mutant) / RN6390 (wild type) - Replicate #1 |
| GSM428998 |
Staphylococcus aureus Lug1430 (RsaX15 Mutant) / RN6390 (wild type) - Replicate #2 |
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| Relations |
| BioProject |
PRJNA119821 |
