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Article: Genome-wide similarity search for transcription factors and their binding sites in a metal-reducing prokaryote Geobacter sulfurreducens

TitleGenome-wide similarity search for transcription factors and their binding sites in a metal-reducing prokaryote Geobacter sulfurreducens
Authors
KeywordsEscherichia coli
Geobacter sulfurreducens
Operon
Transcription factor binding site
Transcription regulation
Issue Date2007
PublisherElsevier Ireland Ltd. The Journal's web site is located at http://www.elsevier.com/locate/biosystems
Citation
BioSystems, 2007, v. 90 n. 2, p. 421-441 How to Cite?
AbstractThe knowledge obtained from understanding individual elements involved in gene regulation is important for reconstructing gene regulatory networks, a key for understanding cellular behavior. To study gene regulatory interactions in a model microorganism, Geobacter sulfurreducens, which participates in metal reduction and energy harvesting, we investigated the presence of 59 known Escherichia coli transcription factors and predicted transcription regulatory sites in its genome. The supplementary material, available at http://www.geobacter.org/research/genomescan/, provides the results of similarity comparisons that identified regulatory proteins of G. sulfurreducens and the genome locations of the predicted regulatory sites, including the list of putative regulatory elements in the upstream regions of every predicted operon and singleton open reading frame. Regulatory sequence elements, predicted using genome similarity searches to matrices of established transcription regulatory elements from E. coli, provide an initial insight into regulation of genes and operons in G. sulfurreducens. The predicted regulatory elements were predominantly located in the upstream regions of operons and singleton open reading frames. The validity of the predictions was examined using a permutation approach. Sequence similarity searches indicate that E. coli transcription factors ArgR, CytR, DeoR, FlhCD (both FlhC and FlhD subunits), FruR, GalR, GlpR, H-NS, LacI, MetJ, PurR, TrpR, and Tus are likely missing from G. sulfurreducens. Phylogenetic analysis suggests that one HU subunit is present in G. sulfurreducens as compared to two subunits in E. coli, while each of the two E. coli IHF subunits, HimA and HimD, have two homologs in G. sulfurreducens. The closest homolog of E. coli RpoE in G. sulfurreducens may be more similar to FecI than to RpoE. These findings represent the first step in the understanding of the regulatory relationships in G. sulfurreducens on the genome scale.
Persistent Identifierhttp://hdl.handle.net/10722/233706
ISSN
2015 Impact Factor: 1.495
2015 SCImago Journal Rankings: 0.623

 

DC FieldValueLanguage
dc.contributor.authorYan, B-
dc.contributor.authorLovley, DR-
dc.contributor.authorKrushkal, J-
dc.date.accessioned2016-09-20T06:13:50Z-
dc.date.available2016-09-20T06:13:50Z-
dc.date.issued2007-
dc.identifier.citationBioSystems, 2007, v. 90 n. 2, p. 421-441-
dc.identifier.issn0303-2647-
dc.identifier.urihttp://hdl.handle.net/10722/233706-
dc.description.abstractThe knowledge obtained from understanding individual elements involved in gene regulation is important for reconstructing gene regulatory networks, a key for understanding cellular behavior. To study gene regulatory interactions in a model microorganism, Geobacter sulfurreducens, which participates in metal reduction and energy harvesting, we investigated the presence of 59 known Escherichia coli transcription factors and predicted transcription regulatory sites in its genome. The supplementary material, available at http://www.geobacter.org/research/genomescan/, provides the results of similarity comparisons that identified regulatory proteins of G. sulfurreducens and the genome locations of the predicted regulatory sites, including the list of putative regulatory elements in the upstream regions of every predicted operon and singleton open reading frame. Regulatory sequence elements, predicted using genome similarity searches to matrices of established transcription regulatory elements from E. coli, provide an initial insight into regulation of genes and operons in G. sulfurreducens. The predicted regulatory elements were predominantly located in the upstream regions of operons and singleton open reading frames. The validity of the predictions was examined using a permutation approach. Sequence similarity searches indicate that E. coli transcription factors ArgR, CytR, DeoR, FlhCD (both FlhC and FlhD subunits), FruR, GalR, GlpR, H-NS, LacI, MetJ, PurR, TrpR, and Tus are likely missing from G. sulfurreducens. Phylogenetic analysis suggests that one HU subunit is present in G. sulfurreducens as compared to two subunits in E. coli, while each of the two E. coli IHF subunits, HimA and HimD, have two homologs in G. sulfurreducens. The closest homolog of E. coli RpoE in G. sulfurreducens may be more similar to FecI than to RpoE. These findings represent the first step in the understanding of the regulatory relationships in G. sulfurreducens on the genome scale.-
dc.languageeng-
dc.publisherElsevier Ireland Ltd. The Journal's web site is located at http://www.elsevier.com/locate/biosystems-
dc.relation.ispartofBioSystems-
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.subjectEscherichia coli-
dc.subjectGeobacter sulfurreducens-
dc.subjectOperon-
dc.subjectTranscription factor binding site-
dc.subjectTranscription regulation-
dc.titleGenome-wide similarity search for transcription factors and their binding sites in a metal-reducing prokaryote Geobacter sulfurreducens-
dc.typeArticle-
dc.identifier.emailYan, B: yanbin14@hku.hk-
dc.identifier.authorityYan, B=rp01940-
dc.identifier.doi10.1016/j.biosystems.2006.10.006-
dc.identifier.pmid17184904-
dc.identifier.scopuseid_2-s2.0-34548415488-
dc.identifier.volume90-
dc.identifier.issue2-
dc.identifier.spage421-
dc.identifier.epage441-
dc.publisher.placeIreland-

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