RybB RNA
{{Infobox rfam
| Name = RybB RNA
| image = RF00110.jpg
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| caption = Predicted secondary structure and sequence conservation of RybB
| Symbol = RybB
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| Rfam = RF00110
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| Tax_domain = Bacteria
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| SO = {{SO|0000655}}
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RybB is a small non-coding RNA was identified in a large scale screen of Escherichia coli.{{cite journal | last = Wassarman | first = KM |author2=Repoila F |author3=Rosenow C |author4=Storz G |author5=Gottesman S | year = 2001 | title = Identification of novel small RNAs using comparative genomics and microarrays | journal = Genes Dev | volume = 15 | pages = 1637–1651 | pmid = 11445539 | doi = 10.1101/gad.901001 | issue = 13 | pmc = 312727}} 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.{{cite journal | last = Papenfort | first = K |author2=Pfeiffer V |author3=Mika F |author4=Lucchini S |author5=Hinton JC |author6=Vogel J | year = 2006 | title = SigmaE-dependent small RNAs of Salmonella respond to membrane stress by accelerating global omp mRNA decay | journal = Mol. Microbiol. | volume = 62 | pages = 1674–1688 | pmid = 17427289 | doi = 10.1111/j.1365-2958.2006.05524.x | issue = 6 | pmc = 1804206 }} 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.{{cite journal |vauthors=Papenfort K, Bouvier M, Mika F, Sharma CM, Vogel J |title=Evidence for an autonomous 5′ target recognition domain in an Hfq-associated small RNA. |journal=Proc Natl Acad Sci U S A |volume=107|issue=47|pages=20435–20440|year=2010 |pmid=21059903 |doi=10.1073/pnas.1009784107 |pmc=2996696|bibcode=2010PNAS..10720435P |doi-access=free }}{{cite journal |vauthors=Bouvier M, Sharma CM, Mika F, Nierhaus KH, Vogel J |title=Small RNA binding to 5′ mRNA coding region inhibits translational initiation. |journal=Mol Cell |volume=32|issue=6|pages=827–837|year=2008 |pmid=19111662 |doi=10.1016/j.molcel.2008.10.027|doi-access=free }}{{cite journal |vauthors=Balbontín R, Fiorini F, Figueroa-Bossi N, Casadesús J, Bossi L |title=Recognition of heptameric seed sequence underlies multi-target regulation by RybB small RNA in Salmonella enterica. |journal=Mol Microbiol |volume=78|issue=2|pages=380–394|year=2010 |pmid=20979336 |doi=10.1111/j.1365-2958.2010.07342.x|s2cid=43670213 |doi-access= }}{{cite thesis |type=Diploma |first=PR |last=Wright |title=hIntaRNA - Comparative prediction of sRNA targets in prokaryotes. |publisher=Albert-Ludwigs-Universität Freiburg |year=2012}}
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).{{cite journal |vauthors=Gogol EB, Rhodius VA, Papenfort K, Vogel J, Gross CA |title=Small RNAs endow a transcriptional activator with essential repressor functions for single-tier control of a global stress regulon. |journal=Proc Natl Acad Sci U S A |volume=108|issue=31|pages=12875–12880|year=2011 |pmid=21768388 |doi=10.1073/pnas.1109379108 |pmc=3150882|bibcode=2011PNAS..10812875G |doi-access=free }}{{cite journal |vauthors=Desnoyers G, Massé E |title=Noncanonical repression of translation initiation through small RNA recruitment of the RNA chaperone Hfq. |journal=Genes Dev |volume=26|issue=7|pages=726–739|year=2012 |pmid=22474262 |doi=10.1101/gad.182493.111 |pmc=3323883}}{{cite journal |vauthors=Johansen J, Rasmussen AA, Overgaard M, Valentin-Hansen P |title=Conserved small non-coding RNAs that belong to the sigmaE regulon: role in down-regulation of outer membrane proteins. |journal=J Mol Biol |volume=364|issue=1|pages=1–8|year=2006 |pmid=17007876 |doi=10.1016/j.jmb.2006.09.004}}{{cite journal |vauthors=Wright PR, Richter AS, Papenfort K, Mann M, Vogel J, Hess WR, Backofen R, Georg J |title=Comparative genomics boosts target prediction for bacterial small RNAs. |journal=Proc Natl Acad Sci U S A |volume= 110|issue= 37|pages=E3487–E3496|year=2013 |pmid=23980183 |doi=10.1073/pnas.1303248110 |pmc=3773804|bibcode=2013PNAS..110E3487W |doi-access=free }}
See also
References
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