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

TitleModeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri.
Publication TypeJournal Article
Year of Publication2006
AuthorsFeist AM, Scholten JCM, Palsson BØ, Brockman FJ, Ideker T
JournalMolecular systems biology
Volume2
Pagination2006.0004
PubMed Date2006
ISSN1744-4292
KeywordsGenome, Bacterial, Metabolism, Methane, Methanosarcina barkeri, Models, Biological, Nitrogenase, Oxidoreductases
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.

Alternate JournalMol. Syst. Biol.
PubMed ID16738551

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