Prediction of Rate-Limiting Reactions for Growth-Associated Production Using a Constraint-Based Approach

Identification of a rate-limiting step in pathways is a key challenge in metabolic engineering. Although the prediction of rate-limiting steps using a kinetic model is a powerful approach, there are several technical hurdles for developing a kinetic model. In this study, an in silico screening algorithm of key enzyme for metabolic engineering is developed to identify the possible rate-limiting reactions for the growth-coupled target production using a stoichiometric model without any experimental data and kinetic parameters. In this method, for each reaction, an upper-bound flux constraint is imposed and the target production is predicted by linear programming. When the constraint decreases the target production at the optimal growth state, the reaction is thought to be a possible rate-limiting step. For validation, this method is applied to the production of succinate or 1,4-butanediol (1,4-BDO) in Escherichia coli, in which the experimental engineering for eliminating rate-limiting steps has been previously reported. In succinate production from glycerol, nine reactions including phosphoenolpyruvate carboxylase are predicted as the rate-limiting steps. In 1,4-BDO production from glucose, eight reactions including pyruvate dehydrogenase are predicted as the rate-limiting steps. These predictions include experimentally identified rate-limiting steps, which would contribute to metabolic engineering as a practical tool for screening candidates of rate-limiting reactions.