The Genetic Landscape of a Metabolic Interaction

Abstract

Enzyme abundance, catalytic activity, and ultimately sequence are all shaped by the need of growing cells to maintain metabolic flux while minimizing accumulation of deleterious intermediates. To quantify how variation in the activity of one enzyme constrains the biochemical parameters and sequence of another, we focused on dihydrofolate reductase (DHFR) and thymidylate synthase (TYMS), a pair of enzymes catalyzing consecutive reactions in folate metabolism. We used deep mutational scanning to quantify the growth rate effect of 2,696 DHFR single mutations in 3 TYMS backgrounds and show that our data are well-described by a relatively simple enzyme velocity to growth rate model. From the data and model we estimate the approximate effects of all single mutations on DHFR catalytic power. Together our data provide a comprehensive view of epistasis between mutations in a biochemically linked enzyme pair, reveal the structural distribution of positions tuning DHFR catalysis, and establish a foundation for the design of multi-enzyme systems.