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Constraint-based modeling analysis of the metabolism of two Pelobacter species

BACKGROUND: Pelobacter species are commonly found in a number of subsurface environments, and are unique members of the Geobacteraceae family. They are phylogenetically intertwined with both Geobacter and Desulfuromonas species. Pelobacter species likely play important roles in the fermentative degr...

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Autores principales: Sun, Jun, Haveman, Shelley A, Bui, Olivia, Fahland, Tom R, Lovley, Derek R
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3022650/
https://www.ncbi.nlm.nih.gov/pubmed/21182788
http://dx.doi.org/10.1186/1752-0509-4-174
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author Sun, Jun
Haveman, Shelley A
Bui, Olivia
Fahland, Tom R
Lovley, Derek R
author_facet Sun, Jun
Haveman, Shelley A
Bui, Olivia
Fahland, Tom R
Lovley, Derek R
author_sort Sun, Jun
collection PubMed
description BACKGROUND: Pelobacter species are commonly found in a number of subsurface environments, and are unique members of the Geobacteraceae family. They are phylogenetically intertwined with both Geobacter and Desulfuromonas species. Pelobacter species likely play important roles in the fermentative degradation of unusual organic matters and syntrophic metabolism in the natural environments, and are of interest for applications in bioremediation and microbial fuel cells. RESULTS: In order to better understand the physiology of Pelobacter species, genome-scale metabolic models for Pelobacter carbinolicus and Pelobacter propionicus were developed. Model development was greatly aided by the availability of models of the closely related Geobacter sulfurreducens and G. metallireducens. The reconstructed P. carbinolicus model contains 741 genes and 708 reactions, whereas the reconstructed P. propionicus model contains 661 genes and 650 reactions. A total of 470 reactions are shared among the two Pelobacter models and the two Geobacter models. The different reactions between the Pelobacter and Geobacter models reflect some unique metabolic capabilities such as fermentative growth for both Pelobacter species. The reconstructed Pelobacter models were validated by simulating published growth conditions including fermentations, hydrogen production in syntrophic co-culture conditions, hydrogen utilization, and Fe(III) reduction. Simulation results matched well with experimental data and indicated the accuracy of the models. CONCLUSIONS: We have developed genome-scale metabolic models of P. carbinolicus and P. propionicus. These models of Pelobacter metabolism can now be incorporated into the growing repertoire of genome scale models of the Geobacteraceae family to aid in describing the growth and activity of these organisms in anoxic environments and in the study of their roles and interactions in the subsurface microbial community.
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spelling pubmed-30226502011-01-20 Constraint-based modeling analysis of the metabolism of two Pelobacter species Sun, Jun Haveman, Shelley A Bui, Olivia Fahland, Tom R Lovley, Derek R BMC Syst Biol Research Article BACKGROUND: Pelobacter species are commonly found in a number of subsurface environments, and are unique members of the Geobacteraceae family. They are phylogenetically intertwined with both Geobacter and Desulfuromonas species. Pelobacter species likely play important roles in the fermentative degradation of unusual organic matters and syntrophic metabolism in the natural environments, and are of interest for applications in bioremediation and microbial fuel cells. RESULTS: In order to better understand the physiology of Pelobacter species, genome-scale metabolic models for Pelobacter carbinolicus and Pelobacter propionicus were developed. Model development was greatly aided by the availability of models of the closely related Geobacter sulfurreducens and G. metallireducens. The reconstructed P. carbinolicus model contains 741 genes and 708 reactions, whereas the reconstructed P. propionicus model contains 661 genes and 650 reactions. A total of 470 reactions are shared among the two Pelobacter models and the two Geobacter models. The different reactions between the Pelobacter and Geobacter models reflect some unique metabolic capabilities such as fermentative growth for both Pelobacter species. The reconstructed Pelobacter models were validated by simulating published growth conditions including fermentations, hydrogen production in syntrophic co-culture conditions, hydrogen utilization, and Fe(III) reduction. Simulation results matched well with experimental data and indicated the accuracy of the models. CONCLUSIONS: We have developed genome-scale metabolic models of P. carbinolicus and P. propionicus. These models of Pelobacter metabolism can now be incorporated into the growing repertoire of genome scale models of the Geobacteraceae family to aid in describing the growth and activity of these organisms in anoxic environments and in the study of their roles and interactions in the subsurface microbial community. BioMed Central 2010-12-23 /pmc/articles/PMC3022650/ /pubmed/21182788 http://dx.doi.org/10.1186/1752-0509-4-174 Text en Copyright ©2010 Sun et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<url>http://creativecommons.org/licenses/by/2.0</url>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Sun, Jun
Haveman, Shelley A
Bui, Olivia
Fahland, Tom R
Lovley, Derek R
Constraint-based modeling analysis of the metabolism of two Pelobacter species
title Constraint-based modeling analysis of the metabolism of two Pelobacter species
title_full Constraint-based modeling analysis of the metabolism of two Pelobacter species
title_fullStr Constraint-based modeling analysis of the metabolism of two Pelobacter species
title_full_unstemmed Constraint-based modeling analysis of the metabolism of two Pelobacter species
title_short Constraint-based modeling analysis of the metabolism of two Pelobacter species
title_sort constraint-based modeling analysis of the metabolism of two pelobacter species
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3022650/
https://www.ncbi.nlm.nih.gov/pubmed/21182788
http://dx.doi.org/10.1186/1752-0509-4-174
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