RybB RNA

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.

RybB RNA
Predicted secondary structure and sequence conservation of RybB
Identifiers
SymbolRybB
RfamRF00110
Other data
RNA typeGene; sRNA
Domain(s)Bacteria
SO0000655
PDB structuresPDBe

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

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. 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.
  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. 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. doi:10.1073/pnas.1303248110. PMC 3773804. PMID 23980183.
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