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

Arnau Montagud,Kiran Raosaheb Patil,Javier F Urchueguía,Emilio Navarro,Pedro Fernández De Córdoba

doi:10.1186/1752-0509-4-156

Abstract

BackgroundSynechocystis 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.ResultsWe 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.ConclusionsiSyn669 provides a platform for facilitating the development of cyanobacteria as microbial cell factories.

Highlights

Genome-scale metabolic network reconstruction A complete literature examination, including databases, biochemistry textbooks and the annotated genome sequence, was needed in order to extract the current state of the art on known metabolic reactions within the metabolic network of Synechocystis sp
From the annotation publicly available, our metabolic network includes 882 metabolic reactions and 790 metabolites, as well as the information from 669 genes that have some relationship with the metabolic reactions
PCC6803 to date, which has its potential as the photosynthetic model organism

Summary

Introduction

PCC6803, it is of importance to develop tools for uncovering stoichiometric and regulatory principles in the Synechocystis metabolic network. All cyanobacteria combine the ability to perform an oxygenic photosynthesis (resembling that of chloroplasts) with typical prokaryotic features, like performing anoxygenic photosynthesis by using hydrogen sulfide (H2S) as the electron donor or fixing atmospheric dinitrogen (N2) into ammonia (NH3). Relevance of this phylum covers from evolutionary studies [4] to biotechnological applications, including biofuel production [5].

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