Basic and applied uses of genome‐scale metabolic network reconstructions of Escherichia coli

Molecular Systems Biology

Douglas McCloskey¹  Bernhard Ø Palsson¹ 

[1] Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA

关键词: constraint‐based modeling;    Escherichia coli;    metabolic engineering;    metabolism;    network reconstruction;   

DOI  :  10.1038/msb.2013.18

来源: Wiley

【 摘 要 】

Abstract

The genome-scale model (GEM) of metabolism in the bacterium Escherichia coli K-12 has been in development for over a decade and is now in wide use. GEM-enabled studies of E. coli have been primarily focused on six applications: (1) metabolic engineering, (2) model-driven discovery, (3) prediction of cellular phenotypes, (4) analysis of biological network properties, (5) studies of evolutionary processes, and (6) models of interspecies interactions. In this review, we provide an overview of these applications along with a critical assessment of their successes and limitations, and a perspective on likely future developments in the field. Taken together, the studies performed over the past decade have established a genome-scale mechanistic understanding of genotype–phenotype relationships in E. coli metabolism that forms the basis for similar efforts for other microbial species. Future challenges include the expansion of GEMs by integrating additional cellular processes beyond metabolism, the identification of key constraints based on emerging data types, and the development of computational methods able to handle such large-scale network models with sufficient accuracy.

【 授权许可】

CC BY-NC-SA   
Copyright © 2013 EMBO and Macmillan Publishers Limited

Creative Commons Attribution License, which permits distribution, and reproduction in any medium, provided the original author and source are credited. This license does not permit commercial exploitation without specific permission.