RybB RNA explained

RybB RNA
Symbol:	RybB
Rfam:	RF00110
Rna Type:	Gene sRNA
Tax Domain:	Bacteria

RybB is a small non-coding RNA was identified in a large scale screen of Escherichia coli.^[1] 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.^[2] 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.^{[3] [4] [5] [6]}

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).^{[7] [8] [9] [10]}

See also

• RyfA RNA
• RydB RNA
• RydC RNA
• MicA RNA

Notes and 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 . 1637–1651 . 11445539 . 10.1101/gad.901001 . 13 . 312727.
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 . 1674–1688 . 17427289 . 10.1111/j.1365-2958.2006.05524.x . 6 . 1804206 .
3. Papenfort K, Bouvier M, Mika F, Sharma CM, Vogel J . 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. 2010 . 21059903 . 10.1073/pnas.1009784107 . 2996696. 2010PNAS..10720435P . free .
4. Bouvier M, Sharma CM, Mika F, Nierhaus KH, Vogel J . Small RNA binding to 5′ mRNA coding region inhibits translational initiation. . Mol Cell . 32. 6. 827–837. 2008 . 19111662 . 10.1016/j.molcel.2008.10.027. free .
5. Balbontín R, Fiorini F, Figueroa-Bossi N, Casadesús J, Bossi L . Recognition of heptameric seed sequence underlies multi-target regulation by RybB small RNA in Salmonella enterica. . Mol Microbiol . 78. 2. 380–394. 2010 . 20979336 . 10.1111/j.1365-2958.2010.07342.x. 43670213 .
6. Diploma . PR . Wright . hIntaRNA - Comparative prediction of sRNA targets in prokaryotes. . Albert-Ludwigs-Universität Freiburg . 2012.
7. Gogol EB, Rhodius VA, Papenfort K, Vogel J, Gross CA . 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. 2011 . 21768388 . 10.1073/pnas.1109379108 . 3150882. 2011PNAS..10812875G . free .
8. Desnoyers G, Massé E . Noncanonical repression of translation initiation through small RNA recruitment of the RNA chaperone Hfq. . Genes Dev . 26. 7. 726–739. 2012 . 22474262 . 10.1101/gad.182493.111 . 3323883.
9. Johansen J, Rasmussen AA, Overgaard M, Valentin-Hansen P . 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. 2006 . 17007876 . 10.1016/j.jmb.2006.09.004.
10. Wright PR, Richter AS, Papenfort K, Mann M, Vogel J, Hess WR, Backofen R, Georg J . Comparative genomics boosts target prediction for bacterial small RNAs. . Proc Natl Acad Sci U S A . 110. 37. E3487–E3496. 2013 . 23980183 . 10.1073/pnas.1303248110 . 3773804. 2013PNAS..110E3487W . free .