Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium

Abstract

Background: Synechocystis sp. PCC6803 is a cyanobacterium considered as a candidate photo-biological production platform--an attractive cell factory capable of using CO2 and light as carbon and energy source, respectively. In order to enable efficient use of metabolic potential of Synechocystis sp. PCC6803, it is of importance to develop tools for uncovering stoichiometric and regulatory principles in the Synechocystis metabolic network.

Results: We report the most comprehensive metabolic model of Synechocystis sp. PCC6803 available, iSyn669, which includes 882 reactions, associated with 669 genes, and 790 metabolites. The model includes a detailed biomass equation which encompasses elementary building blocks that are needed for cell growth, as well as a detailed stoichiometric representation of photosynthesis. We demonstrate applicability of iSyn669 for stoichiometric analysis by simulating three physiologically relevant growth conditions of Synechocystis sp. PCC6803, and through in silico metabolic engineering simulations that allowed identification of a set of gene knock-out candidates towards enhanced succinate production. Gene essentiality and hydrogen production potential have also been assessed. Furthermore, iSyn669 was used as a transcriptomic data integration scaffold and thereby we found metabolic hot-spots around which gene regulation is dominant during light-shifting growth regimes.

Conclusions: iSyn669 provides a platform for facilitating the development of cyanobacteria as microbial cell factories.

Figure 1

Selected reactions in iSyn669 network that display flux changes across the four studied growth modes. Flux values (in mmol g_DW^-1 h^-1) for selected reactions in the Synechocystis sp. PCC6803 metabolism. These reactions mark changes across four growth modes, viz., autotrophy, mixotrophy and light and dark heterotrophy. Corresponding flux ranges can be found in Table 4 and in Additional file 4 for all the reactions in iSyn669.

Figure 2

Overview of the flux adjustments between different growth conditions. Comparison of flux variability between autotrophy vs. mixotrophy, autotrophy vs. dark heterotrophy and autotrophy vs. light-activated heterotrophy. Minimum and maximum flux ranges were compared for each reaction, 378 reactions were found blocked in all the studied conditions.

Figure 3

Essential genes in Synechocystis sp. PCC6803. Distribution of gene knock-out results for three model organisms, simulated by using FBA and MOMA algorithm, classified as wild-type growth, constrained growth and no growth.

Figure 4

Reporter metabolites under light/dark regime. a) Reporter metabolites for all time points set of arrays depicted on the iSyn669 network. b) Light/dark-shift profiles and localization of the genome arrays for the work from Gill et al. [47].