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'''RybB''' is a small [[non-coding RNA]] was identified in a large scale screen of ''[[Escherichia coli]]''.<ref>{{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}}</ref> 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.<ref>{{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 }}</ref> This RNA has been shown to bind to the [[Hfq protein]].
'''RybB''' is a small [[non-coding RNA]] was identified in a large scale screen of ''[[Escherichia coli]]''.<ref>{{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}}</ref> 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.<ref>{{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 }}</ref> 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.<ref name="pmid21059903">{{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 }}</ref><ref name="pmid19111662">{{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 }}</ref><ref name="pmid20979336">{{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=free }}</ref><ref name="thesisprw">{{cite thesis |type=Diploma |first=PR |last=Wright |title=hIntaRNA - Comparative prediction of sRNA targets in prokaryotes. |publisher=Albert-Ludwigs-Universität Freiburg |year=2012}}</ref>
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.<ref name="pmid21059903">{{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 }}</ref><ref name="pmid19111662">{{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 }}</ref><ref name="pmid20979336">{{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= }}</ref><ref name="thesisprw">{{cite thesis |type=Diploma |first=PR |last=Wright |title=hIntaRNA - Comparative prediction of sRNA targets in prokaryotes. |publisher=Albert-Ludwigs-Universität Freiburg |year=2012}}</ref>


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'').<ref name="pmid21768388">{{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 }}</ref><ref name="pmid22474262">{{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}}</ref><ref name="pmid17007876">{{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}}</ref><ref name="pmid23980183">{{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 }}</ref>
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'').<ref name="pmid21768388">{{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 }}</ref><ref name="pmid22474262">{{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}}</ref><ref name="pmid17007876">{{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}}</ref><ref name="pmid23980183">{{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 }}</ref>

Latest revision as of 11:54, 3 December 2023

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.[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

[edit]

References

[edit]
  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.
[edit]
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