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- Publisher Website: 10.1089/omi.2007.0043
- Scopus: eid_2-s2.0-40349089020
- PMID: 18266557
- WOS: WOS:000254066800003
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Article: Characterizing regulation of metabolism in Geobacter sulfurreducens through genome-wide expression data and sequence analysis
Title | Characterizing regulation of metabolism in Geobacter sulfurreducens through genome-wide expression data and sequence analysis |
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Authors | |
Issue Date | 2008 |
Publisher | Mary Ann Liebert Inc.. |
Citation | OMICS A Journal of Integrative Biology, 2008, v. 12 n. 1, p. 33-59 How to Cite? |
Abstract | Geobacteraceae are a family of metal reducing bacteria with important applications in bioremediation and electricity generation. G. sulfurreducens is a representative of Geobacteraceae that has been extensively studied with the goal of extending the understanding of this family of organisms for optimizing their practical applications. Here, we have analyzed gene expression data from 10 experiments involving environmental and genetic perturbations and have identified putative transcription factor binding sites (TFBS) involved in regulating key aspects of metabolism. Specifically, we considered data from both a subset of 10 microarray experiments (7 of 10) and all 10 experiments. The expression data from these two sets were independently clustered, and the upstream regions of genes and operons from the clusters in both sets were used to identify TFBS using the AlignACE program. This analysis resulted in the identification of motifs upstream of several genes involved in central metabolism, sulfate assimilation, and energy metabolism, as well as genes potentially encoding acetate permease. Further, similar TFBS were identified from the analysis of both sets, suggesting that these TFBS are significant in the regulation of metabolism in G. sulfurreducens. In addition, we have utilized microarray data to derive condition specific constraints on the capacity of key enzymes in central metabolism. We have incorporated these constraints into the metabolic model of G. sulfurreducens and simulated Fe(II)-limited growth. The resulting prediction was consistent with data, suggesting that regulatory constraints are important for simulating growth phenotypes in nonoptimal environments. |
Persistent Identifier | http://hdl.handle.net/10722/231146 |
ISSN | 2021 Impact Factor: 3.978 2020 SCImago Journal Rankings: 0.811 |
ISI Accession Number ID |
DC Field | Value | Language |
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dc.contributor.author | Mahadevan, R | - |
dc.contributor.author | Yan, B | - |
dc.contributor.author | Postier, B | - |
dc.contributor.author | Nevin, KP | - |
dc.contributor.author | Woodard, TL | - |
dc.contributor.author | O'Neil, R | - |
dc.contributor.author | Coppi, MV | - |
dc.contributor.author | Methé, BA | - |
dc.contributor.author | Krushkal, J | - |
dc.date.accessioned | 2016-09-20T04:33:20Z | - |
dc.date.available | 2016-09-20T04:33:20Z | - |
dc.date.issued | 2008 | - |
dc.identifier.citation | OMICS A Journal of Integrative Biology, 2008, v. 12 n. 1, p. 33-59 | - |
dc.identifier.issn | 1536-2310 | - |
dc.identifier.uri | http://hdl.handle.net/10722/231146 | - |
dc.description.abstract | Geobacteraceae are a family of metal reducing bacteria with important applications in bioremediation and electricity generation. G. sulfurreducens is a representative of Geobacteraceae that has been extensively studied with the goal of extending the understanding of this family of organisms for optimizing their practical applications. Here, we have analyzed gene expression data from 10 experiments involving environmental and genetic perturbations and have identified putative transcription factor binding sites (TFBS) involved in regulating key aspects of metabolism. Specifically, we considered data from both a subset of 10 microarray experiments (7 of 10) and all 10 experiments. The expression data from these two sets were independently clustered, and the upstream regions of genes and operons from the clusters in both sets were used to identify TFBS using the AlignACE program. This analysis resulted in the identification of motifs upstream of several genes involved in central metabolism, sulfate assimilation, and energy metabolism, as well as genes potentially encoding acetate permease. Further, similar TFBS were identified from the analysis of both sets, suggesting that these TFBS are significant in the regulation of metabolism in G. sulfurreducens. In addition, we have utilized microarray data to derive condition specific constraints on the capacity of key enzymes in central metabolism. We have incorporated these constraints into the metabolic model of G. sulfurreducens and simulated Fe(II)-limited growth. The resulting prediction was consistent with data, suggesting that regulatory constraints are important for simulating growth phenotypes in nonoptimal environments. | - |
dc.language | eng | - |
dc.publisher | Mary Ann Liebert Inc.. | - |
dc.relation.ispartof | OMICS A Journal of Integrative Biology | - |
dc.title | Characterizing regulation of metabolism in Geobacter sulfurreducens through genome-wide expression data and sequence analysis | - |
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 | 10.1089/omi.2007.0043 | - |
dc.identifier.pmid | 18266557 | - |
dc.identifier.scopus | eid_2-s2.0-40349089020 | - |
dc.identifier.volume | 12 | - |
dc.identifier.issue | 1 | - |
dc.identifier.spage | 33 | - |
dc.identifier.epage | 59 | - |
dc.identifier.isi | WOS:000254066800003 | - |
dc.publisher.place | US | - |
dc.identifier.issnl | 1536-2310 | - |