Towards Constraint-Based Burden-Aware Models for Metabolic Engineering

Abstract

Over the years, hundreds of applications have proved the effectiveness of constraint-based methods to validate the definition of metabolic networks, determine the robustness of metabolic models, and analyze the flow of metabolites through a network. However, stoichiometric models do not include information on flux capacity via enzymatic activity. Methods combining biological data from genome to metabolome have been developed to obtain improved flux predictions and constrain the range of possible flux distributions. Yet, these models still lack relevant information to design de novo metabolic pathways. Expressing the exogenous enzymes induces a cell burden due to competition for cell resources between the exogenous genes and the endogenous host ones, compromising the performance of the designed pathway. Thus, optimal selection of the expression strength of the pathway enzymes is still a challenge. Host-aware models have been developed to tackle cell burden in the context of designing increasingly complex synthetic genetic circuits in synthetic biology. This paper suggests a method to integrate host-aware gene expression models with constraint-based modeling to maximize the flux through an exogenous pathway by optimizing promoter and ribosome binding site strengths, crucial parameters that define the required transcription and translation strengths of the pathway enzymes’ genes. This study considers the formation of p-coumaric acid, shows promising results, and paves the way for further investigations.