Neisseria meningitidis

Volume 799 of the series Methods in Molecular Biology pp 107-126


Genome-Scale Metabolic Models: Reconstruction and Analysis

  • Gino J. E. BaartAffiliated withVIB Department of Plant Systems Biology/Department of Biology, Protistology and Aquatic Ecology, Ghent University Email author 
  • , Dirk E. MartensAffiliated withBioprocess Engineering Group, Wageningen University

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Metabolism can be defined as the complete set of chemical reactions that occur in living organisms in order to maintain life. Enzymes are the main players in this process as they are responsible for catalyzing the chemical reactions. The enzyme–reaction relationships can be used for the reconstruction of a network of reactions, which leads to a metabolic model of metabolism. A genome-scale metabolic network of chemical reactions that take place inside a living organism is primarily reconstructed from the information that is present in its genome and the literature and involves steps such as functional annotation of the genome, identification of the associated reactions and determination of their stoichiometry, assignment of localization, determination of the biomass composition, estimation of energy requirements, and definition of model constraints. This information can be integrated into a stoichiometric model of metabolism that can be used for detailed analysis of the metabolic potential of the organism using constraint-based modeling approaches and hence is valuable in understanding its metabolic capabilities.

Key words

Genome-scale metabolic network reconstruction Metabolic networks Metabolic flux analysis Flux balance analysis Constraint-based modeling