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

TitleBasic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli.
Publication TypeJournal Article
Year of Publication2013
AuthorsMcCloskey D, Palsson BØ, Feist AM
JournalMol Syst Biol
Volume9
Pagination661
PubMed Date2013-5-2
ISSN1744-4292
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.

Alternate JournalMol. Syst. Biol.
PubMed ID23632383
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