A two-enzyme adaptive unit in bacterial folate metabolism

Abstract

Metabolic enzyme function and evolution is influenced by the larger context of a biochemical pathway - deleterious mutations or perturbations in one enzyme can often be compensated by mutations to others. To explore strategies for mapping adaptive dependencies between enzymes, we used a combination of comparative genomics and experiments to examine interactions with the model metabolic enzyme Dihydrofolate Reductase (DHFR). Biochemically, DHFR shares a metabolic intermediate with numerous folate metabolic enzymes. In contrast, comparative genomics analyses of synteny and gene co-occurrence indicate a sparse pattern of evolutionary couplings in which DHFR is coupled to the enzyme thymidylate synthase (TYMS), but is relatively independent from the rest of folate metabolism. To test this apparent modularity, we used quantitative growth rate measurements and forward evolution in E. coli to demonstrate that the two enzymes are coupled to one another, and can adapt independently from the remainder of the genome. Mechanistically, the coupling between DHFR and TYMS is driven by a constraint wherein TYMS activity must not greatly exceed that of DHFR - both to avoid depletion of reduced folates and prevent accumulation of the metabolic intermediate dihydrofolate. Extending our comparative genomics analyses genome-wide reveals over 200 gene pairs with statistical signatures similar to DHFR/TYMS, suggesting the possibility that cellular pathways might be decomposed into small adaptive units.