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.

Inference and prediction of metabolic network fluxes

“…PCC 6803 (Knoop et al, 2013). Similarly, FBA models of Chlamydomonas reinhardtii (Boyle and Morgan, 2009;Chang et al, 2011) included biomass functions for both photoautotrophic and mixotrophic growth.…”

“…FBA modeling techniques have been developed that can handle multiple time points, including dynamic FBA, in which each time step is solved separately, with the outputs of one time step forming the inputs of the next (Knoop et al, 2013;Kleessen et al, 2015), as well as global methods, in which the different phases are handled simultaneously by the model optimization algorithms (Cheung et al, 2014;de Oliveira Dal'Molin et al, 2015). Accounting for the expansion phase of cell growth will require a consideration of the appropriate experimental measures that can be used as constraints.…”

Finding novel relationships with integrated gene-gene association network analysis of Synechocystis sp. PCC 6803 using species-independent text-mining

“…A part of the metabolic flux through the carbon fixing Cuu cycle has been measured to pass through the oxidative branch of PPP (oxPPP) (Young et al 2011) though the optimal solution for biomass flux in stoichiometric models did not incorporate any oxPPP flux (Knoop et al 2013). We were curious about the metabolic role that key-enzymes responsible for NADP + -reduction in fermentative microorganisms may have in an autotrophic system and how they are regulated.…”

Agriculture-independent, sustainable, fail-safe and efficient food production by autotrophic single-cell protein

“…It is noteworthy that cyanobacteria do have oxygenic photosynthesis and also provide effective physiological adaptations allowing BNF to be driven by either o-PS or the Knallgas reaction [39,40]. However, cyanobacteria fix CO 2 with CBB and do not assimilate acetate well [41,42]. Above all, a multitude of cyanobacteria are known to form cyanotoxins such as microcystins, anatoxins, saxitoxins, hepatotoxic cyclic peptides [43,44] and β-N-methylamino-L-alanine [45,46].…”