An evolutionary module in central metabolism. Escherichia coli strain:K-12 MG1655

The ability to understand and predict cell behavior is complicated by a yet unknown pattern of functional interdependence among genes. Here, we use the conservation of gene proximity across species (synteny) to infer functional couplings between genes. For the folate metabolic pathway, we observe a sparse, modular architecture of interactions, with two small groups of genes coevolving in the midst of others that evolve independently. For one such module - dihydrofolate reductase and thymidylate synthase – 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. The results indicate an organization of cellular systems that is not apparent from inspection of biochemical pathways or physical complexes, and support the strategy of using evolutionary information to decompose cellular systems into functional units.