Rsa RNA

Rsa RNAs are non-coding RNAs found in the bacterium Staphylococcus aureus. The shared name comes from their discovery, and does not imply homology. Bioinformatics scans identified the 16 Rsa RNA families named RsaA-K and RsaOA-OG.[1][2] Others, RsaOH-OX, were found thanks to an RNomic approach.[3] Although the RNAs showed varying expression patterns, many of the newly discovered RNAs were shown to be Hfq-independent and most carried a C-rich motif (UCCC).[1]

RsaE

The consensus secondary structure of RsaI (later renamed RsaOG) showing its pseudoknot. Boundaries were determined by RACE mapping in Staphylococcus aureus N315. Taken from Marchais et al., 2010 [4] created in Varna.[5]

RsaE is found in other members of the Staphylococcus genus such as Staphylococcus epidermidis and Staphylococcus saprophyticus and is the only Rsa RNA to be found outside of this genus, in Macrococcus caseolyticus and Bacillus. In Bacillus subtilis, RsaE had previously been identified as ncr22.[6][7] RsaE is also consistently found downstream of PepF which codes for oligoendopeptidase F. The function of RsaE was discovered using gene knockout analysis and gene overexpression - it was found to regulate the expression of several enzymes involved in metabolism via antisense binding of their mRNA.[1][3]

RsaF

In S.aureus species RsaF is located in the same intergenic region as RsaE and overlaps with 3' end of RsaE by approximately 20bp. In contrast to RsaE, RsaF and its upstream gene have only been identified in S.aureus species.[1]

RsaK

RsaK is found in the leader sequence of glcA mRNA which encodes an enzyme involved in the glucose-specific phosphotransferase system. RsaK also contains a conserved ribonucleic antiterminator system, as recognised by GclT protein.[8]

RsaI

RsaOG[2] also renamed RsaI[1] is thought to fine-tune the regulation of toxin or invasion mechanisms in S. aureus via trans-acting mechanisms. Its secondary structure contains a pseudoknot formed between two highly conserved unpaired sequences.[4]

Expression patterns

RsaD, E H and I were found to be highly expressed in S. aureus. Expression levels of other Rsa RNAs varied under various environmental conditions, for example RsaC was induced by cold shock and RsaA is induced in response to osmotic stress.[1][2][3]

RsaE and RsaF genes overlap in S.aureus species but appear to have opposite expression patterns.[1] Transcriptional interference due to an overlap between a σA recognition motif and a potential σB binding site is proposed as a mechanism causing the differential expression of the two transcripts [1][9]

See also

References

  1. 1 2 3 4 5 6 7 8 Geissmann T, Chevalier C, Cros MJ, et al. (November 2009). "A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation". Nucleic Acids Res. 37 (21): 7239–57. doi:10.1093/nar/gkp668. PMC 2790875Freely accessible. PMID 19786493. Retrieved 2010-08-24.
  2. 1 2 3 Marchais A, Naville M, Bohn C, et al. (June 2009). "Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles". Genome Res. 19 (6): 1084–92. doi:10.1101/gr.089714.108. PMC 2694484Freely accessible. PMID 19237465.
  3. 1 2 3 Bohn C, Rigoulay C, Chabelskaya S, et al. (2010). "Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism". Nucleic Acids Res. 38 (19): 6620–6636. doi:10.1093/nar/gkq462. PMC 2965222Freely accessible. PMID 20511587.
  4. 1 2 Marchais A, Bohn C, Bouloc P, Gautheret D (March 2010). "RsaOG, a new staphylococcal family of highly transcribed non-coding RNA". RNA Biol. 7 (2): 116–9. doi:10.4161/rna.7.2.10925. PMID 20200491. Retrieved 2010-08-27.
  5. ↑ Darty K, Denise A, Ponty Y (August 2009). "VARNA: Interactive drawing and editing of the RNA secondary structure". Bioinformatics. 25 (15): 1974–5. doi:10.1093/bioinformatics/btp250. PMC 2712331Freely accessible. PMID 19398448. Retrieved 2010-07-12.
  6. ↑ Rasmussen S, Nielsen HB, Jarmer H (September 2009). "The transcriptionally active regions in the genome of Bacillus subtilis". Mol. Microbiol. 73 (6): 1043–57. doi:10.1111/j.1365-2958.2009.06830.x. PMC 2784878Freely accessible. PMID 19682248. Retrieved 2010-09-24.
  7. ↑ Irnov I, Sharma CM, Vogel J, Winkler WC (June 2010). "Identification of regulatory RNAs in Bacillus subtilis". Nucleic Acids Res. 38 (19): 6637–6651. doi:10.1093/nar/gkq454. PMC 2965217Freely accessible. PMID 20525796. Retrieved 2010-09-24.
  8. ↑ Langbein I, Bachem S, Stülke J (November 1999). "Specific interaction of the RNA-binding domain of the bacillus subtilis transcriptional antiterminator GlcT with its RNA target, RAT". J. Mol. Biol. 293 (4): 795–805. doi:10.1006/jmbi.1999.3176. PMID 10543968. Retrieved 2010-08-27.
  9. ↑ Shearwin KE, Callen BP, Egan JB (June 2005). "Transcriptional interference--a crash course". Trends Genet. 21 (6): 339–45. doi:10.1016/j.tig.2005.04.009. PMC 2941638Freely accessible. PMID 15922833.

Further reading

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