Biology:RybB RNA
| RybB RNA | |
|---|---|
 Predicted secondary structure and sequence conservation of RybB | |
| Identifiers | |
| Symbol | RybB |
| Rfam | RF00110 |
| Other data | |
| RNA type | Gene; sRNA |
| Domain(s) | Bacteria |
| SO | 0000655 |
| PDB structures | PDBe |
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
References
- ↑ 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. PMID 11445539.
- ↑ 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. PMID 17427289.
- ↑ "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. doi:10.1073/pnas.1009784107. PMID 21059903. Bibcode: 2010PNAS..10720435P.
- ↑ "Small RNA binding to 5′ mRNA coding region inhibits translational initiation.". Mol Cell 32 (6): 827–837. 2008. doi:10.1016/j.molcel.2008.10.027. PMID 19111662.
- ↑ "Recognition of heptameric seed sequence underlies multi-target regulation by RybB small RNA in Salmonella enterica.". Mol Microbiol 78 (2): 380–394. 2010. doi:10.1111/j.1365-2958.2010.07342.x. PMID 20979336.
- ↑ Wright, PR (2012). hIntaRNA - Comparative prediction of sRNA targets in prokaryotes (Diploma). Albert-Ludwigs-Universität Freiburg.
- ↑ "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. doi:10.1073/pnas.1109379108. PMID 21768388. Bibcode: 2011PNAS..10812875G.
- ↑ "Noncanonical repression of translation initiation through small RNA recruitment of the RNA chaperone Hfq.". Genes Dev 26 (7): 726–739. 2012. doi:10.1101/gad.182493.111. PMID 22474262.
- ↑ "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. doi:10.1016/j.jmb.2006.09.004. PMID 17007876.
- ↑ "Comparative genomics boosts target prediction for bacterial small RNAs.". Proc Natl Acad Sci U S A 110 (37): E3487–E3496. 2013. doi:10.1073/pnas.1303248110. PMID 23980183. Bibcode: 2013PNAS..110E3487W.
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