Ab initio Whole Cell Kinetic Model of Desulfovibrio desulfuricans L4 (ddsAAR26)

Desulfovibrio desulfuricans is a Gram-negative, anaerobic sulfate-reducing bacterium with applications in bioremediation and is likely to involve metabolic engineering and synthetic biology. Metabolic engineering and synthetic biology approaches are often guided by mathematical models. To date, no whole-cell kinetic model has been reported for this organism. In this study, we present an Ab initio whole-cell kinetic model of D. desulfuricans L4, ddsAAR26, comprising of 701 metabolites, 275 enzymes with associated transcription and translation processes and 573 enzymatic reactions, formulated as a system of ordinary differential equations. Enzymatic reactions are represented using Michaelis-Menten kinetics with median kinetic values. This establishes computational framework for future model refinement and extension.