Metabolic modelling to support synthetic biology in C1net organisms

PI: Andrezj Kierzek, University of Surrey. CoI: Mark Poolman, Oxford Brookes University

The aim of this short C1net Proof of Concept project was to create a genome-scale metabolic model of a C1 gas fermenting microorganism and demonstrate the applicability of predictive modelling to the design of new strains of interest to C1net. We selected the methanotroph Methylococcus capsulatus (Bath) as the target organism, though in parallel we provided advice and guidance to the University of Nottingham in the construction of a model of Clostridium autoethanogenum. The draft model of M. capsulatus has been completed starting from the gene-enzyme-reaction mapping in the organism's BioCyc database. It is fully mass-balanced for C, N, S and P and accounts for 965 reactions and 896 internal metabolites. The 63 external metabolites include 38 biomass precursors, and the rest are nutrients and metabolic products. Flux balance analysis of the model confirms that it is energetically consistent, in that it cannot show production of ATP or reduced cofactors in the absence of mass flow. The model can account for aerobic oxidation of substrates including glucose and methane to CO2, and anaerobic conversion of glucose to acetate and CO2, as well as production of biomass precursors (i.e. growth). Other products that can be formed form both glucose and methane include pyruvate, ethanol and succinate, and nitrate can be used as an oxidant.

The model was initially generated with the ScrumPy package. It is available to C1net members on request both as a ScrumPy source file (a human-readable text file) and in SBML format for import into other metabolic modelling packages. Email Mark Poolman, mgpoolman(at)brookes.ac.uk, or David Fell, dfell(at)brookes.ac.uk to request it.

The slides from the project report submitted to the C1net conference in Nottingham in July 2016 are available from this link.

Funding: