Model reduction of genome-scale metabolic models as a basis for targeted kinetic models

Metab Eng. 2021 Mar:64:74-84. doi: 10.1016/j.ymben.2021.01.008. Epub 2021 Jan 22.

Abstract

Constraint-based, genome-scale metabolic models are an essential tool to guide metabolic engineering. However, they lack the detail and time dimension that kinetic models with enzyme dynamics offer. Model reduction can be used to bridge the gap between the two methods and allow for the integration of kinetic models into the Design-Built-Test-Learn cycle. Here we show that these reduced size models can be representative of the dynamics of the original model and demonstrate the automated generation and parameterisation of such models. Using these minimal models of metabolism could allow for further exploration of dynamic responses in metabolic networks.

Keywords: DBTL cycle; Metabolic engineering; Model optimisation; Model reduction; Model-driven design; Synthetic biology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Genome
  • Kinetics
  • Metabolic Engineering
  • Metabolic Networks and Pathways* / genetics
  • Models, Biological*