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]

RsaA

Represses the translation of the transcriptional regulator MgrA by binding to its mRNA, enhances biofilm formation and decreases bacterial virulence. ^[4] Other mRNAs: including SsaA-like enzymes involved in peptidoglycan metabolism and the secreted anti-inflammatory FLIPr protein were validated as direct targets of RsaA. ^[5]

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 created in Varna.

RsaE is found in other members of the genus Staphylococcus 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. ^{[8] [9]} 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] [10]}

RsaE was shown to be regulated by the presence of nitric oxide (NO). In Bacillus subtilis it controls expression of genes with functions related to oxidative stress and oxidation-reduction reactions and it was renamed RoxS (for related to oxidative stress). ^[11]

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. ^[12]

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. ^[6]

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 σ^A recognition motif and a potential σ^B binding site is proposed as a mechanism causing the differential expression of the two transcripts ^{[1] [13]}

See also

• RsaOG

References

1. Geissmann T, Chevalier C, Cros MJ, Boisset S, Fechter P, Noirot C, Schrenzel J, François P, Vandenesch F, Gaspin C, Romby P (November 2009). "A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation". Nucleic Acids Research. 37 (21): 7239–7257. doi:10.1093/nar/gkp668. PMC   2790875 . PMID   19786493.
2. Marchais A, Naville M, Bohn C, Bouloc P, Gautheret D (June 2009). "Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles". Genome Research. 19 (6): 1084–1092. doi:10.1101/gr.089714.108. PMC   2694484 . PMID   19237465.
3. Bohn C, Rigoulay C, Chabelskaya S, Sharma CM, Marchais A, Skorski P, Borezée-Durant E, Barbet R, Jacquet E, Jacq A, Gautheret D, Felden B, Vogel J, Bouloc P (October 2010). "Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism". Nucleic Acids Research. 38 (19): 6620–6636. doi:10.1093/nar/gkq462. PMC   2965222 . PMID   20511587.
4. Romilly C, Lays C, Tomasini A, Caldelari I, Benito Y, Hammann P, Geissmann T, Boisset S, Romby P, Vandenesch F (March 2014). "A non-coding RNA promotes bacterial persistence and decreases virulence by regulating a regulator in Staphylococcus aureus". PLOS Pathogens. 10 (3): e1003979. doi: 10.1371/journal.ppat.1003979 . PMC   3961350 . PMID   24651379.
5. Tomasini A, Moreau K, Chicher J, Geissmann T, Vandenesch F, Romby P, Marzi S, Caldelari I (June 2017). "The RNA targetome of Staphylococcus aureus non-coding RNA RsaA: impact on cell surface properties and defense mechanisms". Nucleic Acids Research. 45 (11): 6746–6760. doi:10.1093/nar/gkx219. PMC   5499838 . PMID   28379505.
6. Marchais A, Bohn C, Bouloc P, Gautheret D (March 2010). "RsaOG, a new staphylococcal family of highly transcribed non-coding RNA" . RNA Biology. 7 (2): 116–119. doi: 10.4161/rna.7.2.10925 . PMID   20200491.
7. Darty K, Denise A, Ponty Y (August 2009). "VARNA: Interactive drawing and editing of the RNA secondary structure". Bioinformatics. 25 (15): 1974–1975. doi:10.1093/bioinformatics/btp250. PMC   2712331 . PMID   19398448.
8. Rasmussen S, Nielsen HB, Jarmer H (September 2009). "The transcriptionally active regions in the genome of Bacillus subtilis". Molecular Microbiology. 73 (6): 1043–1057. doi:10.1111/j.1365-2958.2009.06830.x. PMC   2784878 . PMID   19682248.
9. Irnov I, Sharma CM, Vogel J, Winkler WC (October 2010). "Identification of regulatory RNAs in Bacillus subtilis". Nucleic Acids Research. 38 (19): 6637–6651. doi:10.1093/nar/gkq454. PMC   2965217 . PMID   20525796.
10. Rochat T, Bohn C, Morvan C, Le Lam TN, Razvi F, Pain A, Toffano-Nioche C, Ponien P, Jacq A, Jacquet E, Fey PD, Gautheret D, Bouloc P (September 2018). "The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus". Nucleic Acids Research. 46 (17): 8803–8816. doi:10.1093/nar/gky584. PMC   6158497 . PMID   29986060.
11. Durand S, Braun F, Lioliou E, Romilly C, Helfer AC, Kuhn L, Quittot N, Nicolas P, Romby P, Condon C (February 2015). "A nitric oxide regulated small RNA controls expression of genes involved in redox homeostasis in Bacillus subtilis". PLOS Genetics. 11 (2): e1004957. doi: 10.1371/journal.pgen.1004957 . PMC   4409812 . PMID   25643072.
12. 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". Journal of Molecular Biology. 293 (4): 795–805. doi:10.1006/jmbi.1999.3176. PMID   10543968.
13. Shearwin KE, Callen BP, Egan JB (June 2005). "Transcriptional interference—a crash course". Trends in Genetics. 21 (6): 339–345. doi:10.1016/j.tig.2005.04.009. PMC   2941638 . PMID   15922833.

Further reading

• Pichon C, Felden B (October 2005). "Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains". Proceedings of the National Academy of Sciences of the United States of America. 102 (40): 14249–14254. doi: 10.1073/pnas.0503838102 . PMC   1242290 . PMID   16183745.
• Altuvia S (June 2007). "Identification of bacterial small non-coding RNAs: experimental approaches". Current Opinion in Microbiology. 10 (3): 257–261. doi:10.1016/j.mib.2007.05.003. PMID   17553733.
• Morfeldt E, Taylor D, von Gabain A, Arvidson S (September 1995). "Activation of alpha-toxin translation in Staphylococcus aureus by the trans-encoded antisense RNA, RNAIII". The EMBO Journal. 14 (18): 4569–4577. doi:10.1002/j.1460-2075.1995.tb00136.x. PMC   394549 . PMID   7556100.
• Roberts C, Anderson KL, Murphy E, Projan SJ, Mounts W, Hurlburt B, Smeltzer M, Overbeek R, Disz T, Dunman PM (April 2006). "Characterizing the effect of the Staphylococcus aureus virulence factor regulator, SarA, on log-phase mRNA half-lives". Journal of Bacteriology. 188 (7): 2593–2603. doi:10.1128/JB.188.7.2593-2603.2006. PMC   1428411 . PMID   16547047.
• Anderson KL, Roberts C, Disz T, Vonstein V, Hwang K, Overbeek R, Olson PD, Projan SJ, Dunman PM (October 2006). "Characterization of the Staphylococcus aureus heat shock, cold shock, stringent, and SOS responses and their effects on log-phase mRNA turnover". Journal of Bacteriology. 188 (19): 6739–6756. doi:10.1128/JB.00609-06. PMC   1595530 . PMID   16980476.
• Huntzinger E, Boisset S, Saveanu C, Benito Y, Geissmann T, Namane A, Lina G, Etienne J, Ehresmann B, Ehresmann C, Jacquier A, Vandenesch F, Romby P (February 2005). "Staphylococcus aureus RNAIII and the endoribonuclease III coordinately regulate spa gene expression". The EMBO Journal. 24 (4): 824–835. doi:10.1038/sj.emboj.7600572. PMC   549626 . PMID   15678100.
• Novick RP, Ross HF, Projan SJ, Kornblum J, Kreiswirth B, Moghazeh S (October 1993). "Synthesis of staphylococcal virulence factors is controlled by a regulatory RNA molecule". The EMBO Journal. 12 (10): 3967–3975. doi:10.1002/j.1460-2075.1993.tb06074.x. PMC   413679 . PMID   7691599.
• Bohn C, Rigoulay C, Bouloc P (February 2007). "No detectable effect of RNA-binding protein Hfq absence in Staphylococcus aureus". BMC Microbiology. 7: 10. doi: 10.1186/1471-2180-7-10 . PMC   1800855 . PMID   17291347.