Genomically and biochemically accurate metabolic reconstruction of Methanosarcina barkeri Fusaro, iMG746

Matthew C. Gonnerman, Matthew N. Benedict, Adam Feist, William W. Metcalf, Nathan D. Price

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

Methanosarcina barkeri is an Archaeon that produces methane anaerobically as the primary byproduct of its metabolism. M. barkeri can utilize several substrates for ATP and biomass production including methanol, acetate, methyl amines, and a combination of hydrogen and carbon dioxide. In 2006, a metabolic reconstruction of M. barkeri, iAF692, was generated based on a draft genome annotation. The iAF692 reconstruction enabled the first genome-Scale simulations for Archaea. Since the publication of the first metabolic reconstruction of M. barkeri, additional genomic, biochemical, and phenotypic data have clarified several metabolic pathways. We have used this newly available data to improve the M. barkeri metabolic reconstruction. Modeling simulations using the updated model, iMG746, have led to increased accuracy in predicting gene knockout phenotypes and simulations of batch growth behavior. We used the model to examine knockout lethality data and make predictions about metabolic regulation under different growth conditions. Thus, the updated metabolic reconstruction of M. barkeri metabolism is a useful tool for predicting cellular behavior, studying the methanogenic lifestyle, guiding experimental studies, and making predictions relevant to metabolic engineering applications. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Original languageEnglish
JournalBiotechnology Journal
Volume8
Issue number9
Pages (from-to)1070-1079
ISSN1860-6768
DOIs
Publication statusPublished - 2013
Externally publishedYes

Keywords

  • Carbon dioxide
  • Forecasting
  • Genes
  • Methane
  • Microbiology
  • Microorganisms
  • Models
  • Physiology
  • Metabolism

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