iRsp1095: A genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network
1 Program in Cellular and Molecular Biology, University of Wisconsin - Madison, USA
2 Department of Civil and Environmental Engineering, University of Wisconsin - Madison, USA
3 Department of Bacteriology, University of Wisconsin - Madison, 5159 Microbial Sciences Building, 1550 Linden Drive, Madison, WI 53706, USA
4 Chemical and Biological Engineering Department, University of Wisconsin - Madison, USA
5 DOE Great Lakes Bioenergy Research Center, University of Wisconsin - Madison, USA
6 BACTER Institute, University of Wisconsin - Madison, USA
BMC Systems Biology 2011, 5:116 doi:10.1186/1752-0509-5-116Published: 21 July 2011
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 (H2), polyhydroxybutyrate (PHB) or other hydrocarbons, as well as its ability to utilize atmospheric carbon dioxide (CO2) 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.
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 CO2 assimilation was identified. Evaluation of photoheterotrophic H2 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.
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.