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PMID: 16738551 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S.

Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri.

Molecular systems biology ·Vol. 2 ·2006-00-00 ·Pages 2006.0004

Feist AM, Scholten JC, Palsson BØ, Brockman FJ, Ideker T

Abstract

We present a genome-scale metabolic model for the archaeal methanogen Methanosarcina barkeri. We characterize the metabolic network and compare it to reconstructions from the prokaryotic, eukaryotic and archaeal domains. Using the model in conjunction with constraint-based methods, we simulate the metabolic fluxes and resulting phenotypes induced by different environmental and genetic conditions. This represents the first large-scale simulation of either a methanogen or an archaeal species. Model predictions are validated by comparison to experimental growth measurements and phenotypes of M. barkeri on different substrates. The predicted growth phenotypes for wild type and mutants of the methanogenic pathway have a high level of agreement with experimental findings. We further examine the efficiency of the energy-conserving reactions in the methanogenic pathway, specifically the Ech hydrogenase reaction, and determine a stoichiometry for the nitrogenase reaction. This work demonstrates that a reconstructed metabolic network can serve as an analysis platform to predict cellular phenotypes, characterize methanogenic growth, improve the genome annotation and further uncover the metabolic characteristics of methanogenesis.

MeSH Terms
Genome, Bacterial Metabolism/genetics Methane/biosynthesis Methanosarcina barkeri/metabolism Models, Biological Nitrogenase/metabolism Oxidoreductases/metabolism
Chemicals
Oxidoreductases Ech hydrogenase Nitrogenase Methane
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Feist Adam M
Department of Bioengineering, University of California--San Diego, La Jolla, CA 92092-0412, USA.
Scholten Johannes C M
Palsson Bernhard Ø
Brockman Fred J
Ideker Trey
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Article Info
Journal
Molecular systems biology
Abbr.
Mol Syst Biol
ISSN
1744-4292
DOI
10.1038/msb4100046
Published
2006-00-00
Epub
2006-00-31
Pages
2006.0004
Language
English
Region
England
NLM ID
101235389
PMCID
PMC1681478
Subset
IM
External Links
PubMed source DOI: 10.1038/msb4100046 PMC Full Text View journal details
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