DsrA RNA

DsrA RNA is a non-coding RNA that regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein,[1] and translation, by promoting efficient translation of the stress sigma factor, RpoS.[2][3] These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation. The structures of DsrA and DsrA/rpoS complex were studied by NMR. The study concluded that the sRNA contains a dynamic conformational equilibrium for its second stem–loop which might be an important mechanism for DsrA to regulate the translations of its multiple target mRNAs.[4]

DsrA RNA
Predicted secondary structure and sequence conservation of DsrA
Identifiers
SymbolDsrA
RfamRF00014
Other data
RNA typeGene; sRNA
Domain(s)Bacteria
SOSO:0000378
PDB structuresPDBe

There is evidence that DsrA RNA can self-assemble into nanostructures through antisense interactions of three self-complementary regions.[5][6]

Targets of DsrA

There is experimental evidence to suggest that DsrA interacts with the protein-coding genes hns,[7][8][9] rbsD,[7] argR,[7] ilvI[7] and rpoS[10][11][12][13] via an anti-sense mechanism.

DsrA folds into a structure with three hairpins. The second of these (nucleotides 23–60) binds to Hfq.[14]

References
  1. Sledjeski, D; Gottesman S (1995). "A small RNA acts as an antisilencer of the H-NS-silenced rcsA gene of Escherichia coli". Proc Natl Acad Sci USA. 92 (6): 2003–2007. Bibcode:1995PNAS...92.2003S. doi:10.1073/pnas.92.6.2003. PMC 42411. PMID 7534408.
  2. Majdalani, N; Cunning C; Sledjeski D; Elliott T; Gottesman S (1998). "DsrA RNA regulates translation of RpoS message by an anti-antisense mechanism, independent of its action as an antisilencer of transcription". Proc Natl Acad Sci USA. 95 (21): 12462–12467. Bibcode:1998PNAS...9512462M. doi:10.1073/pnas.95.21.12462. PMC 22853. PMID 9770508.
  3. Gottesman, S (2005). "Micros for microbes: non-coding regulatory RNAs in bacteria". Trends Genet. 21 (7): 399–404. CiteSeerX 10.1.1.391.8944. doi:10.1016/j.tig.2005.05.008. PMID 15913835.
  4. Wu, Pengzhi; Liu, Xiaodan; Yang, Lingna; Sun, Yitong; Gong, Qingguo; Wu, Jihui; Shi, Yunyu (2017-09-19). "The important conformational plasticity of DsrA sRNA for adapting multiple target regulation". Nucleic Acids Research. 45 (16): 9625–9639. doi:10.1093/nar/gkx570. ISSN 1362-4962. PMC 5766208. PMID 28934467.
  5. Cayrol B, Nogues C, Dawid A, Sagi I, Silberzan P, Isambert H (2009). "A Nanostructure Made of a Bacterial Noncoding RNA". J Am Chem Soc. 131 (47): 17270–17276. doi:10.1021/ja906076e. PMID 19821568.
  6. Cayrol B, Geinguenaud F, Lacoste J, Busi F, Le Dérout J, Piétrement O, Le Cam E, Régnier P, Lavelle C, Arluison V (2009). "Auto-assembly of E. coli DsrA small noncoding RNA: Molecular characteristics and functional consequences." RNA Biol. 6 (4): 434–445. doi:10.4161/rna.6.4.8949. PMID 19535898.
  7. Lease RA, Cusick ME, Belfort M (1998). "Riboregulation in Escherichia coli: DsrA RNA acts by RNA:RNA interactions at multiple loci". Proc Natl Acad Sci U S A. 95 (21): 12456–12461. Bibcode:1998PNAS...9512456L. doi:10.1073/pnas.95.21.12456. PMC 22852. PMID 9770507.
  8. Urban JH, Vogel J (2007). "Translational control and target recognition by Escherichia coli small RNAs in vivo". Nucleic Acids Res. 35 (3): 1018–1037. doi:10.1093/nar/gkl1040. PMC 1807950. PMID 17264113.
  9. Lease RA Belfort M (2000). "A trans-acting RNA as a control switch in Escherichia coli: DsrA modulates function by forming alternative structures". Proc Natl Acad Sci U S A. 97 (18): 9919–9924. Bibcode:2000PNAS...97.9919L. doi:10.1073/pnas.170281497. PMC 27626. PMID 10954740.
  10. Majdalani N, Cunning C, Sledjeski D, Elliott T, Gottesman S (1998). "DsrA RNA regulates translation of RpoS message by an anti-antisense mechanism, independent of its action as an antisilencer of transcription". Proc Natl Acad Sci U S A. 95 (21): 12462–12467. Bibcode:1998PNAS...9512462M. doi:10.1073/pnas.95.21.12462. PMC 22853. PMID 9770508.
  11. Majdalani N, Chen S, Murrow J, St John K, Gottesman S (2001). "Regulation of RpoS by a novel small RNA: the characterization of RprA". Mol Microbiol. 39 (5): 1382–1394. doi:10.1111/j.1365-2958.2001.02329.x. PMID 11251852.
  12. Sledjeski DD, Gupta A, Gottesman S (1996). "The small RNA, DsrA, is essential for the low temperature expression of RpoS during exponential growth in Escherichia coli". EMBO J. 15 (15): 3993–4000. doi:10.1002/j.1460-2075.1996.tb00773.x. PMC 452119. PMID 8670904.
  13. Sledjeski DD, Whitman C, Zhang A (2001). "Hfq is necessary for regulation by the untranslated RNA DsrA". J Bacteriol. 183 (6): 1997–2005. doi:10.1128/JB.183.6.1997-2005.2001. PMC 95095. PMID 11222598.
  14. Brescia, CC; Mikulecky, PJ; Feig, AL; Sledjeski, DD (Jan 2003). "Identification of the Hfq-binding site on DsrA RNA: Hfq binds without altering DsrA secondary structure". RNA. 9 (1): 33–43. doi:10.1261/rna.2570803. PMC 1370368. PMID 12554874.

Further reading
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