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Article: Computational prediction of RpoS and RpoD regulatory sites in Geobacter sulfurreducens using sequence and gene expression information

TitleComputational prediction of RpoS and RpoD regulatory sites in Geobacter sulfurreducens using sequence and gene expression information
Authors
KeywordsBinding site
Operon
Regulation
RNA polymerase sigma factor
Transcription
Issue Date2006
PublisherElsevier BV. The Journal's web site is located at http://www.elsevier.com/locate/gene
Citation
Gene, 2006, v. 384 n. 1-2, p. 73-95 How to Cite?
AbstractRpoS, the sigma S subunit of RNA polymerase, is vital during the growth and survival of Geobacter sulfurreducens under conditions typically encountered in its native subsurface environments. We investigated the conservation of sites that may be important for RpoS function in G. sulfurreducens. We also employed sequence information and expression microarray data to predict G. sulfurreducens genome sites that may be related to RpoS regulation. Hierarchical clustering identified three clusters of significantly downregulated genes in the rpoS deletion mutant. The search for conserved overrepresented motifs in co-regulated operons identified likely - 35 and - 10 promoter elements upstream of a number of functionally important G. sulfurreducens operons that were downregulated in the rpoS deletion mutant. Putative - 35/- 10 promoter elements were also identified in the G. sulfurreducens genome using sequence similarity searches to matrices of - 35/- 10 promoter elements found in G. sulfurreducens and in Escherichia coli. Due to a sufficient degree of sequence similarity between - 35/- 10 promoter elements for RpoS, RpoD, and other sigma factors, both the sequence similarity searches and the search for conserved overrepresented motifs using microarray data may identify promoter elements for both RpoS and other sigma factors.
Persistent Identifierhttp://hdl.handle.net/10722/231148
ISSN
2015 Impact Factor: 2.319
2015 SCImago Journal Rankings: 1.043

 

DC FieldValueLanguage
dc.contributor.authorYan, B-
dc.contributor.authorNúñez, C-
dc.contributor.authorUeki, T-
dc.contributor.authorEsteve-Núñez, A-
dc.contributor.authorPuljic, M-
dc.contributor.authorAdkins, RM-
dc.contributor.authorMethé, BA-
dc.contributor.authorLovley, DR-
dc.contributor.authorKrushkal, J-
dc.date.accessioned2016-09-20T04:47:31Z-
dc.date.available2016-09-20T04:47:31Z-
dc.date.issued2006-
dc.identifier.citationGene, 2006, v. 384 n. 1-2, p. 73-95-
dc.identifier.issn0378-1119-
dc.identifier.urihttp://hdl.handle.net/10722/231148-
dc.description.abstractRpoS, the sigma S subunit of RNA polymerase, is vital during the growth and survival of Geobacter sulfurreducens under conditions typically encountered in its native subsurface environments. We investigated the conservation of sites that may be important for RpoS function in G. sulfurreducens. We also employed sequence information and expression microarray data to predict G. sulfurreducens genome sites that may be related to RpoS regulation. Hierarchical clustering identified three clusters of significantly downregulated genes in the rpoS deletion mutant. The search for conserved overrepresented motifs in co-regulated operons identified likely - 35 and - 10 promoter elements upstream of a number of functionally important G. sulfurreducens operons that were downregulated in the rpoS deletion mutant. Putative - 35/- 10 promoter elements were also identified in the G. sulfurreducens genome using sequence similarity searches to matrices of - 35/- 10 promoter elements found in G. sulfurreducens and in Escherichia coli. Due to a sufficient degree of sequence similarity between - 35/- 10 promoter elements for RpoS, RpoD, and other sigma factors, both the sequence similarity searches and the search for conserved overrepresented motifs using microarray data may identify promoter elements for both RpoS and other sigma factors.-
dc.languageeng-
dc.publisherElsevier BV. The Journal's web site is located at http://www.elsevier.com/locate/gene-
dc.relation.ispartofGene-
dc.rightsPosting accepted manuscript (postprint): © <year>. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/-
dc.subjectBinding site-
dc.subjectOperon-
dc.subjectRegulation-
dc.subjectRNA polymerase sigma factor-
dc.subjectTranscription-
dc.titleComputational prediction of RpoS and RpoD regulatory sites in Geobacter sulfurreducens using sequence and gene expression information-
dc.typeArticle-
dc.identifier.emailYan, B: yanbin14@hku.hk-
dc.identifier.authorityYan, B=rp01940-
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1016/j.gene.2006.06.025-
dc.identifier.pmid17014972-
dc.identifier.scopuseid_2-s2.0-33750957661-
dc.identifier.volume384-
dc.identifier.issue1-2-
dc.identifier.spage73-
dc.identifier.epage95-
dc.publisher.placeNetherlands-

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