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RybB RNA

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RNA family
RybB RNA
Predicted secondary structure and sequence conservation of RybB
Identifiers
SymbolRybB
RfamRF00110
Other data
RNA typeGene; sRNA
Domain(s)Bacteria
SOSO:0000655
PDB structuresPDBe

RybB is a small non-coding RNA was identified in a large scale screen of Escherichia coli. The function of this short RNA has been studied using a transcriptomic approach and kinetic analyses of target mRNA decay in vivo. RybB was identified as a factor that selectively accelerates the decay of multiple major omp mRNAs upon induction of the envelope stress response. This RNA has been shown to bind to the Hfq protein.

In Salmonella, direct interactions for RybB with the following targets have been verified experimentally: STM2391 (fadL), STM1070 (ompA), STM2267 (ompC), STM1572 (ompD), STM0999 (ompF), STM1473 (ompN), STM1995 (ompS), STM1732 (ompW), STM0413 (tsx), STM0687 (ybfM, chiP) and STM1530.

In Escherichia coli, direct interactions for RybB with the following targets have been verified experimentally: b0805 (fiu), b0721 (sdhC), b2215 (ompC), b1256 (ompW), b2594 (rluD) and b0081 (mraZ).

See also

References

  1. Wassarman, KM; Repoila F; Rosenow C; Storz G; Gottesman S (2001). "Identification of novel small RNAs using comparative genomics and microarrays". Genes Dev. 15 (13): 1637–1651. doi:10.1101/gad.901001. PMC 312727. PMID 11445539.
  2. Papenfort, K; Pfeiffer V; Mika F; Lucchini S; Hinton JC; Vogel J (2006). "SigmaE-dependent small RNAs of Salmonella respond to membrane stress by accelerating global omp mRNA decay". Mol. Microbiol. 62 (6): 1674–1688. doi:10.1111/j.1365-2958.2006.05524.x. PMC 1804206. PMID 17427289.
  3. Papenfort K, Bouvier M, Mika F, Sharma CM, Vogel J (2010). "Evidence for an autonomous 5′ target recognition domain in an Hfq-associated small RNA". Proc Natl Acad Sci U S A. 107 (47): 20435–20440. Bibcode:2010PNAS..10720435P. doi:10.1073/pnas.1009784107. PMC 2996696. PMID 21059903.
  4. Bouvier M, Sharma CM, Mika F, Nierhaus KH, Vogel J (2008). "Small RNA binding to 5′ mRNA coding region inhibits translational initiation". Mol Cell. 32 (6): 827–837. doi:10.1016/j.molcel.2008.10.027. PMID 19111662.
  5. Balbontín R, Fiorini F, Figueroa-Bossi N, Casadesús J, Bossi L (2010). "Recognition of heptameric seed sequence underlies multi-target regulation by RybB small RNA in Salmonella enterica". Mol Microbiol. 78 (2): 380–394. doi:10.1111/j.1365-2958.2010.07342.x. PMID 20979336. S2CID 43670213.
  6. Wright, PR (2012). hIntaRNA - Comparative prediction of sRNA targets in prokaryotes (Diploma). Albert-Ludwigs-Universität Freiburg.
  7. Gogol EB, Rhodius VA, Papenfort K, Vogel J, Gross CA (2011). "Small RNAs endow a transcriptional activator with essential repressor functions for single-tier control of a global stress regulon". Proc Natl Acad Sci U S A. 108 (31): 12875–12880. Bibcode:2011PNAS..10812875G. doi:10.1073/pnas.1109379108. PMC 3150882. PMID 21768388.
  8. Desnoyers G, Massé E (2012). "Noncanonical repression of translation initiation through small RNA recruitment of the RNA chaperone Hfq". Genes Dev. 26 (7): 726–739. doi:10.1101/gad.182493.111. PMC 3323883. PMID 22474262.
  9. Johansen J, Rasmussen AA, Overgaard M, Valentin-Hansen P (2006). "Conserved small non-coding RNAs that belong to the sigmaE regulon: role in down-regulation of outer membrane proteins". J Mol Biol. 364 (1): 1–8. doi:10.1016/j.jmb.2006.09.004. PMID 17007876.
  10. Wright PR, Richter AS, Papenfort K, Mann M, Vogel J, Hess WR, Backofen R, Georg J (2013). "Comparative genomics boosts target prediction for bacterial small RNAs". Proc Natl Acad Sci U S A. 110 (37): E3487 – E3496. Bibcode:2013PNAS..110E3487W. doi:10.1073/pnas.1303248110. PMC 3773804. PMID 23980183.

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