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

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.Photosynthetic organisms perform many functions of significance to the planet and society. Plants and photosynthetic microbes are responsible for harvesting solar energy, evolving oxygen and sequestering atmospheric carbon dioxide [1]. In addition, algae, cyanobacteria and photosynthetic bacteria are either naturally able to or have been modified to evolve hydrogen (H2), accumulate oils and hydrocarbons, or produce alcohols or other compounds that can reduce society's dependence on fossil fuels [2,3]. The ability to understand, capitalize on or improve these activities is limited by our knowledge of the metabolic blueprint of photosynthetic organisms. To fill this knowledge gap, we are modeling the flow of carbon and reducing power in the well-studied photosynthetic bacterium Rhodobacter sphaeroides