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iRsp1095: A genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network

BACKGROUND: Rhodobacter sphaeroides is one of the best studied purple non-sulfur photosynthetic bacteria and serves as an excellent model for the study of photosynthesis and the metabolic capabilities of this and related facultative organisms. The ability of R. sphaeroides to produce hydrogen (H(2))...

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Autores principales: Imam, Saheed, Yilmaz, Safak, Sohmen, Ugur, Gorzalski, Alexander S, Reed, Jennifer L, Noguera, Daniel R, Donohue, Timothy J
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3152904/
https://www.ncbi.nlm.nih.gov/pubmed/21777427
http://dx.doi.org/10.1186/1752-0509-5-116
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author Imam, Saheed
Yilmaz, Safak
Sohmen, Ugur
Gorzalski, Alexander S
Reed, Jennifer L
Noguera, Daniel R
Donohue, Timothy J
author_facet Imam, Saheed
Yilmaz, Safak
Sohmen, Ugur
Gorzalski, Alexander S
Reed, Jennifer L
Noguera, Daniel R
Donohue, Timothy J
author_sort Imam, Saheed
collection PubMed
description BACKGROUND: Rhodobacter sphaeroides is one of the best studied purple non-sulfur photosynthetic bacteria and serves as an excellent model for the study of photosynthesis and the metabolic capabilities of this and related facultative organisms. The ability of R. sphaeroides to produce hydrogen (H(2)), polyhydroxybutyrate (PHB) or other hydrocarbons, as well as its ability to utilize atmospheric carbon dioxide (CO(2)) as a carbon source under defined conditions, make it an excellent candidate for use in a wide variety of biotechnological applications. A genome-level understanding of its metabolic capabilities should help realize this biotechnological potential. RESULTS: Here we present a genome-scale metabolic network model for R. sphaeroides strain 2.4.1, designated iRsp1095, consisting of 1,095 genes, 796 metabolites and 1158 reactions, including R. sphaeroides-specific biomass reactions developed in this study. Constraint-based analysis showed that iRsp1095 agreed well with experimental observations when modeling growth under respiratory and phototrophic conditions. Genes essential for phototrophic growth were predicted by single gene deletion analysis. During pathway-level analyses of R. sphaeroides metabolism, an alternative route for CO(2 )assimilation was identified. Evaluation of photoheterotrophic H(2 )production using iRsp1095 indicated that maximal yield would be obtained from growing cells, with this predicted maximum ~50% higher than that observed experimentally from wild type cells. Competing pathways that might prevent the achievement of this theoretical maximum were identified to guide future genetic studies. CONCLUSIONS: iRsp1095 provides a robust framework for future metabolic engineering efforts to optimize the solar- and nutrient-powered production of biofuels and other valuable products by R. sphaeroides and closely related organisms.
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spelling pubmed-31529042011-08-10 iRsp1095: A genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network Imam, Saheed Yilmaz, Safak Sohmen, Ugur Gorzalski, Alexander S Reed, Jennifer L Noguera, Daniel R Donohue, Timothy J BMC Syst Biol Research Article BACKGROUND: Rhodobacter sphaeroides is one of the best studied purple non-sulfur photosynthetic bacteria and serves as an excellent model for the study of photosynthesis and the metabolic capabilities of this and related facultative organisms. The ability of R. sphaeroides to produce hydrogen (H(2)), polyhydroxybutyrate (PHB) or other hydrocarbons, as well as its ability to utilize atmospheric carbon dioxide (CO(2)) as a carbon source under defined conditions, make it an excellent candidate for use in a wide variety of biotechnological applications. A genome-level understanding of its metabolic capabilities should help realize this biotechnological potential. RESULTS: Here we present a genome-scale metabolic network model for R. sphaeroides strain 2.4.1, designated iRsp1095, consisting of 1,095 genes, 796 metabolites and 1158 reactions, including R. sphaeroides-specific biomass reactions developed in this study. Constraint-based analysis showed that iRsp1095 agreed well with experimental observations when modeling growth under respiratory and phototrophic conditions. Genes essential for phototrophic growth were predicted by single gene deletion analysis. During pathway-level analyses of R. sphaeroides metabolism, an alternative route for CO(2 )assimilation was identified. Evaluation of photoheterotrophic H(2 )production using iRsp1095 indicated that maximal yield would be obtained from growing cells, with this predicted maximum ~50% higher than that observed experimentally from wild type cells. Competing pathways that might prevent the achievement of this theoretical maximum were identified to guide future genetic studies. CONCLUSIONS: iRsp1095 provides a robust framework for future metabolic engineering efforts to optimize the solar- and nutrient-powered production of biofuels and other valuable products by R. sphaeroides and closely related organisms. BioMed Central 2011-07-21 /pmc/articles/PMC3152904/ /pubmed/21777427 http://dx.doi.org/10.1186/1752-0509-5-116 Text en Copyright ©2011 Imam et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Imam, Saheed
Yilmaz, Safak
Sohmen, Ugur
Gorzalski, Alexander S
Reed, Jennifer L
Noguera, Daniel R
Donohue, Timothy J
iRsp1095: A genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network
title iRsp1095: A genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network
title_full iRsp1095: A genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network
title_fullStr iRsp1095: A genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network
title_full_unstemmed iRsp1095: A genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network
title_short iRsp1095: A genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network
title_sort irsp1095: a genome-scale reconstruction of the rhodobacter sphaeroides metabolic network
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3152904/
https://www.ncbi.nlm.nih.gov/pubmed/21777427
http://dx.doi.org/10.1186/1752-0509-5-116
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