Co-substrate induced nonlinear flux switching at branch-points can explain overflow metabolism

Metabolic behaviours of cells, such as metabolic overflow, involve regulation of metabolic fluxes across different pathways. Two well-established concepts in flux regulation are the transcriptional regulation, involving changes in enzyme levels through gene regulation, and allosteric regulation, involving changes in enzyme catalytic activities through metabolite binding. Here, we describe an additional mechanism arising through co-substrate usage around metabolic branch points. We find that asymmetric usage of a given co-substrate by reactions at and around a branch point introduces nonlinear flux switching at that branch point with increasing influx. This provides cells with an ‘inherent self-regulation’ embedded in the architecture of metabolic pathways. Using models of different branch point motifs, we explain this regulation mechanism and provide parameter ranges under which it can operate. We then develop a specific model of the yeast pyruvate branch point and NADH usage around it to show that co-substrate based flux switching can explain experimental data obtained during yeast metabolic overflow. Furthermore, the model captures observed effects of altering NADH dynamics on the metabolic overflow initiation point. We conclude that co-substrate dynamics around branch points provides an inherent regulatory mechanism that could explain observed relations between co-substrate dynamics and metabolic behaviors. Additionally, the presented theory offers a quantitative approach to manipulation of co-substrate dynamics for metabolic engineering.