Genome-Scale Metabolic Modeling of Escherichia coli and Its Chassis Design for Synthetic Biology Applications

Methods Mol Biol. 2021:2189:217-229. doi: 10.1007/978-1-0716-0822-7_16.


Genome-scale metabolic modeling is and will continue to play a central role in computational systems metabolic engineering and synthetic biology applications for the productions of chemicals and antibiotics. To that end, a survey and workflows of methods used for the development of high-quality genome-scale metabolic models (GEMs) and chassis design for synthetic biology are described here. The chapter consists of two parts (a) the methods of development of GEMs (Escherichia coli as a case study) and (b) E. coli chassis design for synthetic production of 1,4-butanediol (BDO). The methods described here can guide existing and future development of GEMs coupled with host chassis design for synthetic productions of novel antibiotics.

Keywords: 1,4-butanediol; Antibiotics; Chassis design; Escherichia coli GEMs; In silico modeling; Synthetic biology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Escherichia coli* / genetics
  • Escherichia coli* / metabolism
  • Genome, Bacterial*
  • Metabolic Engineering*
  • Models, Biological*
  • Synthetic Biology*