Comparisons of Shewanella strains based on genome annotations, modeling, and experiments

Persistent Link:
http://hdl.handle.net/10150/610105
Title:
Comparisons of Shewanella strains based on genome annotations, modeling, and experiments
Author:
Ong, Wai; Vu, Trang; Lovendahl, Klaus; Llull, Jenna; Serres, Margrethe; Romine, Margaret; Reed, Jennifer
Affiliation:
University of Wisconsin-Madison, Madison, USA; Marine Biological Laboratory, Woods Hole, USA; Pacific Northwest National Laboratory, Richland, USA
Issue Date:
2014
Publisher:
BioMed Central
Citation:
Ong et al. BMC Systems Biology 2014, 8:31 http://www.biomedcentral.com/1752-0509/8/31
Journal:
BMC Systems Biology
Rights:
© 2014 Ong et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
Abstract:
BACKGROUND:Shewanella is a genus of facultatively anaerobic, Gram-negative bacteria that have highly adaptable metabolism which allows them to thrive in diverse environments. This quality makes them an attractive bacterial target for research in bioremediation and microbial fuel cell applications. Constraint-based modeling is a useful tool for helping researchers gain insights into the metabolic capabilities of these bacteria. However, Shewanella oneidensis MR-1 is the only strain with a genome-scale metabolic model constructed out of 21 sequenced Shewanella strains.RESULTS:In this work, we updated the model for Shewanella oneidensis MR-1 and constructed metabolic models for three other strains, namely Shewanella sp. MR-4, Shewanella sp. W3-18-1, and Shewanella denitrificans OS217 which span the genus based on the number of genes lost in comparison to MR-1. We also constructed a Shewanella core model that contains the genes shared by all 21 sequenced strains and a few non-conserved genes associated with essential reactions. Model comparisons between the five constructed models were done at two levels - for wildtype strains under different growth conditions and for knockout mutants under the same growth condition. In the first level, growth/no-growth phenotypes were predicted by the models on various carbon sources and electron acceptors. Cluster analysis of these results revealed that the MR-1 model is most similar to the W3-18-1 model, followed by the MR-4 and OS217 models when considering predicted growth phenotypes. However, a cluster analysis done based on metabolic gene content revealed that the MR-4 and W3-18-1 models are the most similar, with the MR-1 and OS217 models being more distinct from these latter two strains. As a second level of comparison, we identified differences in reaction and gene content which give rise to different functional predictions of single and double gene knockout mutants using Comparison of Networks by Gene Alignment (CONGA). Here, we showed how CONGA can be used to find biomass, metabolic, and genetic differences between models.CONCLUSIONS:We developed four strain-specific models and a general core model that can be used to do various in silico studies of Shewanella metabolism. The developed models provide a platform for a systematic investigation of Shewanella metabolism to aid researchers using Shewanella in various biotechnology applications.
EISSN:
1752-0509
DOI:
10.1186/1752-0509-8-31
Keywords:
Constraint-based model; Electron acceptors; Phenotype; FBA
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1752-0509/8/31

Full metadata record

DC FieldValue Language
dc.contributor.authorOng, Waien
dc.contributor.authorVu, Trangen
dc.contributor.authorLovendahl, Klausen
dc.contributor.authorLlull, Jennaen
dc.contributor.authorSerres, Margretheen
dc.contributor.authorRomine, Margareten
dc.contributor.authorReed, Jenniferen
dc.date.accessioned2016-05-20T08:58:41Z-
dc.date.available2016-05-20T08:58:41Z-
dc.date.issued2014en
dc.identifier.citationOng et al. BMC Systems Biology 2014, 8:31 http://www.biomedcentral.com/1752-0509/8/31en
dc.identifier.doi10.1186/1752-0509-8-31en
dc.identifier.urihttp://hdl.handle.net/10150/610105-
dc.description.abstractBACKGROUND:Shewanella is a genus of facultatively anaerobic, Gram-negative bacteria that have highly adaptable metabolism which allows them to thrive in diverse environments. This quality makes them an attractive bacterial target for research in bioremediation and microbial fuel cell applications. Constraint-based modeling is a useful tool for helping researchers gain insights into the metabolic capabilities of these bacteria. However, Shewanella oneidensis MR-1 is the only strain with a genome-scale metabolic model constructed out of 21 sequenced Shewanella strains.RESULTS:In this work, we updated the model for Shewanella oneidensis MR-1 and constructed metabolic models for three other strains, namely Shewanella sp. MR-4, Shewanella sp. W3-18-1, and Shewanella denitrificans OS217 which span the genus based on the number of genes lost in comparison to MR-1. We also constructed a Shewanella core model that contains the genes shared by all 21 sequenced strains and a few non-conserved genes associated with essential reactions. Model comparisons between the five constructed models were done at two levels - for wildtype strains under different growth conditions and for knockout mutants under the same growth condition. In the first level, growth/no-growth phenotypes were predicted by the models on various carbon sources and electron acceptors. Cluster analysis of these results revealed that the MR-1 model is most similar to the W3-18-1 model, followed by the MR-4 and OS217 models when considering predicted growth phenotypes. However, a cluster analysis done based on metabolic gene content revealed that the MR-4 and W3-18-1 models are the most similar, with the MR-1 and OS217 models being more distinct from these latter two strains. As a second level of comparison, we identified differences in reaction and gene content which give rise to different functional predictions of single and double gene knockout mutants using Comparison of Networks by Gene Alignment (CONGA). Here, we showed how CONGA can be used to find biomass, metabolic, and genetic differences between models.CONCLUSIONS:We developed four strain-specific models and a general core model that can be used to do various in silico studies of Shewanella metabolism. The developed models provide a platform for a systematic investigation of Shewanella metabolism to aid researchers using Shewanella in various biotechnology applications.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1752-0509/8/31en
dc.rights© 2014 Ong et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)en
dc.subjectConstraint-based modelen
dc.subjectElectron acceptorsen
dc.subjectPhenotypeen
dc.subjectFBAen
dc.titleComparisons of Shewanella strains based on genome annotations, modeling, and experimentsen
dc.typeArticleen
dc.identifier.eissn1752-0509en
dc.contributor.departmentUniversity of Wisconsin-Madison, Madison, USAen
dc.contributor.departmentMarine Biological Laboratory, Woods Hole, USAen
dc.contributor.departmentPacific Northwest National Laboratory, Richland, USAen
dc.identifier.journalBMC Systems Biologyen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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