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- Publisher Website: 10.1016/j.jtbi.2004.04.022
- Scopus: eid_2-s2.0-3242725955
- PMID: 15276006
- WOS: WOS:000223521400012
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Article: Computational prediction of conserved operons and phylogenetic footprinting of transcription regulatory elements in the metal-reducing bacterial family Geobacteraceae
Title | Computational prediction of conserved operons and phylogenetic footprinting of transcription regulatory elements in the metal-reducing bacterial family Geobacteraceae |
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Authors | |
Keywords | Geobacter metallireducens Geobacter sulfurreducens Operon Promoter |
Issue Date | 2004 |
Publisher | Academic Press. The Journal's web site is located at http://www.elsevier.com/locate/yjtbi |
Citation | Journal of Theoretical Biology, 2004, v. 230 n. 1, p. 133-144 How to Cite? |
Abstract | Members of the family Geobacteraceae are an important group of microorganisms from the delta subdivision of Proteobacteria that couple the oxidation of organic compounds to metal reduction. In order to uncover transcription regulatory interactions in these organisms, we used computational methods to identify conserved operons and putative cis-regulatory transcription elements. We identified 26 putative operons with gene order and function conserved among two species of Geobacteraceae, Geobacter sulfurreducens and Geobacter metallireducens. Most of these operons were also conserved in Desulfovibrio vulgaris, an additional metal reducing organism from family Desulfovibrionaceae of the delta subdivision of Proteobacteria. The predicted conserved operons were investigated for the presence of transcription factor binding sites by two different methods, (i) comparison of non-coding regions in conserved operons, and (ii) neural network promoter prediction. Predicted motifs were screened to identify most likely transcription factor binding sites and ribosome-binding sites. We provide information on motifs in Geobacteraceae similar to known transcription factor binding sites in Escherichia coli, conserved motifs in other bacterial species, putative palindromic sites, and predicted ribosome-binding sites. These predictions will aid in further elucidation of regulatory networks of gene interactions in Geobacteraceae. © 2004 Elsevier Ltd. All rights reserved. |
Persistent Identifier | http://hdl.handle.net/10722/231147 |
ISSN | 2023 Impact Factor: 1.9 2023 SCImago Journal Rankings: 0.553 |
ISI Accession Number ID |
DC Field | Value | Language |
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dc.contributor.author | Yan, B | - |
dc.contributor.author | Methé, BA | - |
dc.contributor.author | Lovley, DR | - |
dc.contributor.author | Krushkal, J | - |
dc.date.accessioned | 2016-09-20T04:40:05Z | - |
dc.date.available | 2016-09-20T04:40:05Z | - |
dc.date.issued | 2004 | - |
dc.identifier.citation | Journal of Theoretical Biology, 2004, v. 230 n. 1, p. 133-144 | - |
dc.identifier.issn | 0022-5193 | - |
dc.identifier.uri | http://hdl.handle.net/10722/231147 | - |
dc.description.abstract | Members of the family Geobacteraceae are an important group of microorganisms from the delta subdivision of Proteobacteria that couple the oxidation of organic compounds to metal reduction. In order to uncover transcription regulatory interactions in these organisms, we used computational methods to identify conserved operons and putative cis-regulatory transcription elements. We identified 26 putative operons with gene order and function conserved among two species of Geobacteraceae, Geobacter sulfurreducens and Geobacter metallireducens. Most of these operons were also conserved in Desulfovibrio vulgaris, an additional metal reducing organism from family Desulfovibrionaceae of the delta subdivision of Proteobacteria. The predicted conserved operons were investigated for the presence of transcription factor binding sites by two different methods, (i) comparison of non-coding regions in conserved operons, and (ii) neural network promoter prediction. Predicted motifs were screened to identify most likely transcription factor binding sites and ribosome-binding sites. We provide information on motifs in Geobacteraceae similar to known transcription factor binding sites in Escherichia coli, conserved motifs in other bacterial species, putative palindromic sites, and predicted ribosome-binding sites. These predictions will aid in further elucidation of regulatory networks of gene interactions in Geobacteraceae. © 2004 Elsevier Ltd. All rights reserved. | - |
dc.language | eng | - |
dc.publisher | Academic Press. The Journal's web site is located at http://www.elsevier.com/locate/yjtbi | - |
dc.relation.ispartof | Journal of Theoretical Biology | - |
dc.rights | Posting 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.subject | Geobacter metallireducens | - |
dc.subject | Geobacter sulfurreducens | - |
dc.subject | Operon | - |
dc.subject | Promoter | - |
dc.title | Computational prediction of conserved operons and phylogenetic footprinting of transcription regulatory elements in the metal-reducing bacterial family Geobacteraceae | - |
dc.type | Article | - |
dc.identifier.email | Yan, B: yanbin14@hku.hk | - |
dc.identifier.authority | Yan, B=rp01940 | - |
dc.description.nature | link_to_subscribed_fulltext | - |
dc.identifier.doi | 10.1016/j.jtbi.2004.04.022 | - |
dc.identifier.pmid | 15276006 | - |
dc.identifier.scopus | eid_2-s2.0-3242725955 | - |
dc.identifier.volume | 230 | - |
dc.identifier.issue | 1 | - |
dc.identifier.spage | 133 | - |
dc.identifier.epage | 144 | - |
dc.identifier.isi | WOS:000223521400012 | - |
dc.publisher.place | United Kingdom | - |
dc.identifier.issnl | 0022-5193 | - |