A two-enzyme adaptive unit in bacterial folate metabolism

The activity of a gene may be influenced or modified by other genes in the genome. Here, we show that co-evolution can be used to identify quasi-independent gene groups inside of larger cellular systems. Using folate metabolism as a case study, we show that co-evolution indicates a sparse architecture of interactions, with three small groups of genes co-evolving in the midst of others that evolve independently. For one such module - dihydrofolate reductase (DHFR) and thymidylate synthase (TYMS) - we use epistasis measurements and forward evolution to demonstrate both internal functional coupling and independence from the remainder of the genome. Mechanistically, the coupling is driven by a constraint on their relative activities, which must be balanced to prevent accumulation of a metabolic intermediate. Applying co-evolution analyses genome-wide reveals a number of other gene pairs with statistical signatures similar to DHFR/TYMS, suggesting that small adaptive units are a general feature of cellular systems.