Cross-regulation between proteome reallocation and metabolic flux redistribution governs bacterial growth transition kinetics.

Bacteria need to adjust their metabolism and protein synthesis simultaneously to adapt to changing nutrient conditions. It's still a grand challenge to predict how cells coordinate such adaptation due to the cross-regulation between the metabolic fluxes and the protein synthesis. Here we developed a dynamic Constrained Allocation Flux Balance Analysis method (dCAFBA), which integrates flux-controlled proteome allocation and protein limited flux balance analysis. This framework can predict the redistribution dynamics of metabolic fluxes without requiring detailed enzyme parameters. We reveal that during nutrient up-shifts, the calculated metabolic fluxes change in agreement with experimental measurements of enzyme protein dynamics. During nutrient down-shifts, we uncover a switch of metabolic bottleneck from carbon uptake proteins to metabolic enzymes, which disrupts the coordination between metabolic flux and their enzyme abundance. Our method provides a quantitative framework to investigate cellular metabolism under varying environments and reveals insights into bacterial adaptation strategies. • A dynamic model integrating protein allocation with flux balance analysis. • Model can predict transition kinetics of metabolic fluxes without enzymatic details. • Enzyme protein dynamics determine metabolic fluxes kinetics during nutrient upshift. • Switch of metabolic bottleneck during nutrient downshift. [ABSTRACT FROM AUTHOR]