Flux Balance Analysis of Cyanobacterial Metabolism: The Metabolic Network of Synechocystis sp. PCC 6803

Abstract

Cyanobacteria are versatile unicellular phototrophic microorganisms that are highly abundant in many environments. Owing to their capability to utilize solar energy and atmospheric carbon dioxide for growth, cyanobacteria are increasingly recognized as a prolific resource for the synthesis of valuable chemicals and various biofuels. To fully harness the metabolic capabilities of cyanobacteria necessitates an in-depth understanding of the metabolic interconversions taking place during phototrophic growth, as provided by genome-scale reconstructions of microbial organisms. Here we present an extended reconstruction and analysis of the metabolic network of the unicellular cyanobacterium Synechocystis sp. PCC 6803. Building upon several recent reconstructions of cyanobacterial metabolism, unclear reaction steps are experimentally validated and the functional consequences of unknown or dissenting pathway topologies are discussed. The updated model integrates novel results with respect to the cyanobacterial TCA cycle, an alleged glyoxylate shunt, and the role of photorespiration in cellular growth. Going beyond conventional flux-balance analysis, we extend the computational analysis to diurnal light/dark cycles of cyanobacterial metabolism. Phototrophic microorganisms hold great promises as a resource to generate high-value products and biofuels using only atmospheric carbon dioxide, light, and some minerals. In particular cyanobacteria, the only known prokaryotes capable of oxygen-evolving photosynthesis, have attracted recent attention as a possible chassis for the generation of third generation biofuels. Rational engineering of microorganisms is increasingly guided by large-scale reconstructions of the metabolic network of the respective organism. Such reconstructions then serve as an integrated knowledge base for all metabolic interconversions taking place during cellular growth. Here, we present and analyze such a genome-scale reconstruction for the unicellular cyanobacterium Synechocystis sp. PCC 6803. Taking into account several recent reconstructions, the functional consequences of unclear and dissenting pathway annotations are discussed. The model is supplemented with experimental data to validate specific reactions steps. As a specific feature of phototrophic organisms, the re-organization of metabolism in alternating diurnal light/dark cycles is studied.