A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information

Adam M. Feist, Christopher S. Henry, Jennifer L. Reed, Markus Krummenacker, Andrew R. Joyce, Peter D. Karp, Linda J. Broadbelt, Vassily Hatzimanikatis, Bernhard Palsson*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

1010 Scopus citations

Abstract

An updated genome-scale reconstruction of the metabolic network in Escherichia coli K-12 MG1655 is presented. This updated metabolic reconstruction includes: (1) an alignment with the latest genome annotation and the metabolic content of EcoCyc leading to the inclusion of the activities of 1260 ORFs, (2) characterization and quantification of the biomass components and maintenance requirements associated with growth of E. coli and (3) thermodynamic information for the included chemical reactions. The conversion of this metabolic network reconstruction into an in silico model is detailed. A new step in the metabolic reconstruction process, termed thermodynamic consistency analysis, is introduced, in which reactions were checked for consistency with thermodynamic reversibility estimates. Applications demonstrating the capabilities of the genome-scale metabolic model to predict high-throughput experimental growth and gene deletion phenotypic screens are presented. The increased scope and computational capability using this new reconstruction is expected to broaden the spectrum of both basic biology and applied systems biology studies of E. coli metabolism.

Original languageEnglish (US)
Article number121
JournalMolecular Systems Biology
Volume3
DOIs
StatePublished - 2007

Keywords

  • Computational biology
  • Group contribution method
  • Systems biology
  • Thermodynamics

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Agricultural and Biological Sciences(all)
  • Applied Mathematics

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