Construction of kinetic models for metabolic reaction networks: Lessons learned in analysing short-term stimulus response data

Abstract

Construction of dynamic models of large-scale metabolic networks is one of the central issues in the engineering of living cells. However, construction of such models is often hampered by a number of challenges, for example, data availability, compartmentalization and parameter identification coupled with design of in vivo perturbations. As a solution to the latter, short-term perturbation experiments are proposed and are proven to be a useful experimental method to obtain insights into the in vivo kinetic properties of the metabolic pathways. The aim of this work is to construct a kinetic model using the available experimental data obtained by short-term perturbation experiments, where the steady state of a glucose-limited anaerobic chemostat culture of Saccharomyces cerevisiae was perturbed. In constructing the model, we first determined the steady-state flux distribution using the data before the glucose pulse and the known stoichiometry. For the rate expressions, we used approximative linlog kinetics, which allows the enzyme–metabolite kinetic interactions to be represented by an elasticity matrix. We performed a priori model reduction based on timescale analysis and parameter identifiability analysis allowing the information content of the experimental data to be assessed. The final values of the elasticities are estimated by fitting the model to the available short-term kinetic response data. The final model consists of 16 metabolites and 14 reactions. With 25 parameters, the model adequately describes the short-term response of the cells to the glucose perturbation, pointing to the fact that the assumed kinetic interactions in the model are sufficient to account for the observed response.