Context-Dependent Flux Coupling via Conserved Small-Molecule Regulatory Structures

Small-molecule regulation modulates enzyme activity and is widespread in metabolic networks. However, the organization of small-molecule regulatory networks and its generalized role is not well understood. We analyze the structure of the genome-wide Escherichia coli small-molecule regulatory network (SMRN) to reveal that it optimizes controllability in the metabolic network. This is achieved by conserved, highly overabundant incoherent feedforward loops. Using multi-omics data, we characterize loop examples in central carbon metabolism. These use signals from hypothesized flux-sensing metabolites phosphoenolpyruvate, -ketoglutarate, citrate, and malate to distinguish between glycolysis, gluconeogenesis, and glyoxylate shunt activity to differentially couple fluxes across these major modes of metabolism. Our results suggest that coupling of fluxes by direct modulation of enzyme activity is an emergent property of the SMRN that depends heavily on both regulatory structure and metabolic context via the metabolome, and further that flux sensing and coupling may be a global property of the metabolic network.