Prediction of CsrA-regulating small RNAs in bacteria and their experimental verification in Vibrio fischeri

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dc.contributor.authorKulkarni, Prajna R.en
dc.contributor.authorCui, Xiaohuien
dc.contributor.authorWilliams, Joshua W.en
dc.contributor.authorStevens, Ann M.en
dc.contributor.authorKulkarni, Rahul V.en
dc.contributor.departmentBiological Sciencesen
dc.contributor.departmentPhysicsen
dc.date.accessioned2019-04-23T13:29:24Zen
dc.date.available2019-04-23T13:29:24Zen
dc.date.issued2006-01-01en
dc.description.abstractThe role of small RNAs as critical components of global regulatory networks has been highlighted by several recent studies. An important class of such small RNAs is represented by CsrB and CsrC of Escherichia coli, which control the activity of the global regulator CsrA. Given the critical role played by CsrA in several bacterial species, an important problem is the identification of CsrA-regulating small RNAs. In this paper, we develop a computer program (CSRNA_FIND) designed to locate potential CsrA-regulating small RNAs in bacteria. Using CSRNA_FIND to search the genomes of bacteria having homologs of CsrA, we identify all the experimentally known CsrA-regulating small RNAs and also make predictions for several novel small RNAs. We have verified experimentally our predictions for two CsrA-regulating small RNAs in Vibrio fischeri. As more genomes are sequenced, CSRNA_FIND can be used to locate the corresponding small RNAs that regulate CsrA homologs. This work thus opens up several avenues of research in understanding the mode of CsrA regulation through small RNAs in bacteria.en
dc.description.sponsorshipNIGMS NIH HHS [R01 GM066786, GM066786]en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1093/nar/gkl439en
dc.identifier.eissn1362-4962en
dc.identifier.issn0305-1048en
dc.identifier.issue11en
dc.identifier.pmid16822857en
dc.identifier.urihttp://hdl.handle.net/10919/89092en
dc.identifier.volume34en
dc.language.isoen_USen
dc.rightsCreative Commons Attribution-NonCommercial 2.0 Genericen
dc.rights.urihttp://creativecommons.org/licenses/by-nc/2.0/en
dc.subjectpseudomonas-fluorescens cha0en
dc.subjectescherichia-colien
dc.subjectgene-expressionen
dc.subjectextracellular enzymesen
dc.subjectglobal regulationen
dc.subjectaeruginosa pao1en
dc.subjectencoding genesen
dc.subjectcell-divisionen
dc.subjectmolecule csrben
dc.subjectprotein csraen
dc.titlePrediction of CsrA-regulating small RNAs in bacteria and their experimental verification in Vibrio fischerien
dc.title.serialNucleic Acids Researchen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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