title: iRsp1095: a genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network.
abstract: 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 (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.
  
  
  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 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.
  
  
  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.
authors.affiliation: Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Saheed
authors.initials: S
authors.lastname: Imam
authors.forename: Safak
authors.initials: S
authors.lastname: Yilmaz
authors.forename: Ugur
authors.initials: U
authors.lastname: Sohmen
authors.forename: Alexander S
authors.initials: AS
authors.lastname: Gorzalski
authors.forename: Jennifer L
authors.initials: JL
authors.lastname: Reed
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Noguera
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Donohue
mesh_terms: D000332:Aerobiosis; D052818:Autotrophic Processes; D001692:Biological Transport; D018533:Biomass; D001711:Biotransformation; D005798:Genes, Bacterial / Q000235:genetics; D023281:Genomics / Q000379:methods*; D006859:Hydrogen / Q000378:metabolism; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D015203:Reproducibility of Results; D012242:Rhodobacter sphaeroides / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*
chemical_list: D006859:Hydrogen