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Biophys. J. BioFAST: First Published November 18, 2005. doi:10.1529/biophysj.105.071720
© 2005 by the Biophysical Society.

A more recent version of this article appeared on February 15, 2006.
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Christopher S. Henry
Matthew D. Jankowski
Linda J. Broadbelt
Vassily Hatzimanikatis
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BIOENERGETICS

Genome-scale Thermodynamic Analysis of E. coli Metabolism

Christopher S. Henry 1, Matthew D. Jankowski 1, Linda J. Broadbelt 1 and Vassily Hatzimanikatis 1*

1 Northwestern University

* To whom correspondence should be addressed. E-mail: vassily{at}northwestern.edu.

Submitted on August 2, 2005
Revised on October 25, 2005
Accepted on 28 October 2005


  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. We have constructed a genome-scale metabolic model of E. coli based on the iJR904 model developed by the Palsson Laboratory at UCSD (29). 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, ATP synthase, methylenetetrahydrofolate 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.

Key Words: E. coli, genome scale, group contribution, metabolic flux analysis, metabolism, thermodynamics




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Copyright © 2005 by the Biophysical Society.