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Genome-Scale Metabolic Models: Reconstruction and Analysis

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Neisseria meningitidis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 799))

Abstract

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.

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Acknowledgments

We are grateful to The Netherlands Vaccine Institute (NVI) for supporting this work.

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Authors and Affiliations

  1. VIB Department of Plant Systems Biology/Department of Biology, Protistology and Aquatic Ecology, Ghent University, Ghent, Belgium

    Gino J. E. Baart

  2. Bioprocess Engineering Group, Wageningen University, Wageningen, The Netherlands

    Dirk E. Martens

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  1. Gino J. E. Baart
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  2. Dirk E. Martens
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Correspondence to Gino J. E. Baart .

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Editors and Affiliations

  1. Medical School, Molecular Microbiology and Infection, University of Southampton, Tremona Road, Southampton, SO16 6YD, Hampshire, United Kingdom

    Myron Christodoulides

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Baart, G.J.E., Martens, D.E. (2012). Genome-Scale Metabolic Models: Reconstruction and Analysis. In: Christodoulides, M. (eds) Neisseria meningitidis. Methods in Molecular Biology, vol 799. Humana, Totowa, NJ. https://doi.org/10.1007/978-1-61779-346-2_7

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  • DOI: https://doi.org/10.1007/978-1-61779-346-2_7

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