Applying asymptotic methods to synthetic biology: Modelling the reaction kinetics of the mevalonate pathway

摘要

Highlights ? We investigate a kinetic model for the mevalonate pathway which includes inhibition effects and a sink of acetyl-CoA. ? Of the enzymes in the pathway, upregulating HMG-CoA reductase has the most significant positive effect on improving pathway efficiency. ? Upregulating pyruvate dehydrogenase complex and HMG-CoA synthase can also help, but only in conjunction with the upregulation of HMG-CoA reductase. ? We confirm our theoretical predictions by introducing the mevalonate pathway into Cupriavidus necator. Abstract The mevalonate pathway is normally found in eukaryotes, and allows for the production of isoprenoids, a useful class of organic compounds. This pathway has been successfully introduced to Escherichia coli , enabling a biosynthetic production route for many isoprenoids. In this paper, we develop and solve a mathematical model for the concentration of metabolites in the mevalonate pathway over time, accounting for the loss of acetyl-CoA to other metabolic pathways. Additionally, we successfully test our theoretical predictions experimentally by introducing part of the pathway into Cupriavidus necator . In our model, we exploit the natural separation of time scales as well as of metabolite concentrations to make significant asymptotic progress in understanding the system. We confirm that our asymptotic results agree well with numerical simulations, the former enabling us to predict the most important reactions to increase isopentenyl diphosphate production whilst minimizing the levels of HMG-CoA, which inhibits cell growth. Thus, our mathematical model allows us to recommend the upregulation of certain combinations of enzymes to improve production through the mevalonate pathway.