Abstract
BackgroundRhodobacter 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.ResultsHere 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.ConclusionsiRsp1095 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.
Highlights
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 R. sphaeroides model was further analyzed for stoichiometrically balanced cycles (SBCs) - internal network loops that carry flux in a closed system with no net production or consumption of metabolites [20,27]
Sensitivity analysis Further analyses were conducted to evaluate the effects of biomass objective function (BOF) composition, light uptake and P/O ratio on growth and metabolite production rates in iRsp1095. These analyses showed that: (i) growth rate predictions are not significantly affected by changes in BOF composition, the production rate of certain metabolites (e.g., H2) can be affected; (ii) the predicted growth rate and production rates for PHB and H2 increased with increasing light until they reached a plateau, while the predicted CO2 production decreased with light uptake, presumably reflecting improved carbon assimilation as biomass increased; and (iii) the P/O ratio can have a significant impact on growth rate, as seen in other metabolic models [38]
Summary
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 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. This facultative bacterium is capable of either aerobic or anaerobic respiration, depending on the availability of oxygen (O2) or alternative electron acceptors. R. sphaeroides is capable of autotrophic or heterotrophic growth using either carbon dioxide (CO2) or organic carbon sources [4,5] It provides an ideal system for studying the details of each lifestyle and the mechanisms of transition between these various metabolic states
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