Genome scale metabolic reconstruction and hypothesis testing in the methanogenic archaeon Methanosarcina acetivorans C2A

Methanosarcina acetivorans strain C2A is a marine methanogenic archaeon notable for its substrate utilization, genetic tractability, and novel energy conservation mechanisms. To help probe the implications of this organism’s unique metabolism, we have constructed and manually curated a genome-scale metabolic model, iMB744, accounting for 744 of the 4540 predicted protein coding genes (16%) in the M. acetivorans genome. The reconstruction effort has identified key knowledge gaps and differences in the peripheral metabolism and central metabolism between methanogenic species. Using flux balance analysis, the model quantitatively predicts wild type phenotypes and is 96% accurate in knockout lethality predictions compared to currently available experimental data. Flux balance analysis was used to probe the mechanisms and energetics of byproduct formation and growth on carbon monoxide, and the nature of the reaction catalyzed by the soluble heterodisulfide reductase HdrABC in M. acetivorans. This work highlights the great utility of constraint-based modeling for identifying feasible solutions to biological questions and provides insights into the workings of the cell at the genome scale