Genome-scale thermodynamic analysis of Escherichia coli metabolism

Christopher S. Henry, Matthew D. Jankowski, Linda J. Broadbelt, Vassily Hatzimanikatis*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

153 Scopus citations

Abstract

Genome-scale metabolic models are an invaluable tool for analyzing metabolic systems as they provide a more complete picture of the processes of metabolism.Wehave constructed a genome-scale metabolic model of Escherichia coli based on the iJR904 model developed by the Palsson Laboratory at the University of California at San Diego. Group contribution methods were utilized to estimate the standard Gibbs free energy change of every reaction in the constructed model. Reactions in the model were classified based on the activity of the reactions during optimal growth on glucose in aerobic media. The most thermodynamically unfavorable reactions involved in the production of biomass in E. coli were identified as ATP phosphoribosyltransferase, ATPsynthase, methylene-tetra-hydrofolate dehydrogenase, and tryptophanase. The effect of a knockout of these reactions on the production of biomass and the production of individual biomass precursors was analyzed. Changes in the distribution of fluxes in the cell after knockout of these unfavorable reactions were also studied. The methodologies and results discussed can be used to facilitate the refinement of the feasible ranges for cellular parameters such as species concentrations and reaction rate constants.

Original languageEnglish (US)
Pages (from-to)1453-1461
Number of pages9
JournalBiophysical Journal
Volume90
Issue number4
DOIs
StatePublished - Feb 2006

ASJC Scopus subject areas

  • Biophysics

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