Flux balance analysis of cyanobacterial metabolism: the metabolic network of Synechocystis sp. PCC 6803

PLoS Comput Biol. 2013;9(6):e1003081. doi: 10.1371/journal.pcbi.1003081. Epub 2013 Jun 27.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Citric Acid Cycle
  • Darkness
  • Glyoxylates / metabolism
  • Metabolic Networks and Pathways*
  • Phototrophic Processes
  • Ribulose-Bisphosphate Carboxylase / metabolism
  • Synechocystis / enzymology
  • Synechocystis / growth & development
  • Synechocystis / metabolism*


  • Glyoxylates
  • Ribulose-Bisphosphate Carboxylase
  • glyoxylic acid

Grant support

This work was funded by the European Commission FP7-ENERGY-2010-1, under grant agreement no 256808 (DirectFuel). HK, WL, YZ and RS were supported by the German ministry of education and research (BMBF) program FORSYS-Partner (Foerderkennzeichen: 0315274B, 2008–2012). RS is part of the project “Local Team and International Consortium for Computational Modelling of a Cyanobacterial Cell,” Reg. No. CZ.1.07/2.3.00/20.0256. The funding bodies had no role in study design, analysis, interpretation of data and the decision to submit the manuscript.