Protein-Level Control of Metabolism: Design Principles and Prospects from a Representative System

Abstract

Abstract: Significant evidence suggests protein-level or metabolic control is widespread and important in metabolic networks. However, the biophysical interactions responsible for flux control at the metabolic level are not nearly as well-characterized as those which are responsible for control at other biological levels, such as transcriptional regulation. This knowledge gap is a limiting factor in the application of engineered protein-level regulation in Metabolic Engineering for the rational and sensitive control of pathway flux. Here we apply an in silico dynamic numerical optimization approach to a representative branched pathway to understand how engineered allosteric regulation could be used to control flux. We consider inhibition sensitivity as a hypothetical tunable parameter to demonstrate that integration of allosteric and transcriptional regulation is necessary to stably achieve arbitrary targets for both downstream metabolite concentrations. We further show that the steady-state ratio of these metabolites can be controlled by tuning the sensitivity of allostery at the branch point. Finally, we demonstrate that system dynamics dictate which type of engineered control is optimal. This work has implications for the co-optimization of transcriptional and allosteric regulatory systems in metabolic networks and provides a framework for the design of allosteric regulation in engineered metabolisms.