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Genome-Scale Models of Plant Metabolism

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Plant Metabolism

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1083))

Abstract

A genome-scale model (GSM) is an in silico metabolic model comprising hundreds or thousands of chemical reactions that constitute the metabolic inventory of a cell, tissue, or organism. A complete, accurate GSM, in conjunction with a simulation technique such as flux balance analysis (FBA), can be used to comprehensively predict cellular metabolic flux distributions for a given genotype and given environmental conditions. Apart from enabling a user to quantitatively visualize carbon flow through metabolic pathways, these flux predictions also facilitate the hypothesis of new network properties. By simulating the impacts of environmental stresses or genetic interventions on metabolism, GSMs can aid the formulation of nontrivial metabolic engineering strategies. GSMs for plants and other eukaryotes are significantly more complicated than those for prokaryotes due to their extensive compartmentalization and size. The reconstruction of a GSM involves creating an initial model, curating the model, and then rendering the model ready for FBA. Model reconstruction involves obtaining organism-specific reactions from the annotated genome sequence or organism-specific databases. Model curation involves determining metabolite protonation status or charge, ensuring that reactions are stoichiometrically balanced, assigning reactions to appropriate subcellular compartments, deleting generic reactions or creating specific versions of them, linking dead-end metabolites, and filling of pathway gaps to complete the model. Subsequently, the model requires the addition of transport, exchange, and biomass synthesis reactions to make it FBA-ready. This cycle of editing, refining, and curation has to be performed iteratively to obtain an accurate model. This chapter outlines the reconstruction and curation of GSMs with a focus on models of plant metabolism.

Margaret N. Simons, Ashish Misra, and Ganesh Sriram conceived the chapter. Margaret N. Simons wrote an initial draft of the chapter; Ashish Misra and Ganesh Sriram critically edited it; Ganesh Sriram prepared the final version. All authors approved the final version.

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Acknowledgments

This work was funded by the US National Science Foundation (Award IOS-0922650).

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Authors and Affiliations

  1. University of Maryland, College Park, MD, USA

    Margaret Simons & Ashish Misra

  2. Pennsylvania State University, State College, PA, USA

    Margaret Simons

  3. Center for Energy Biosciences, Institute of Chemical Technology, Mumbai, India

    Ashish Misra

  4. Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, USA

    Ganesh Sriram

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  1. Margaret Simons
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  2. Ashish Misra
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  3. Ganesh Sriram
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Editors and Affiliations

  1. Engineering, University of Maryland Dept. Chemical & Biomolecular, College Park, Maryland, USA

    Ganesh Sriram

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Simons, M., Misra, A., Sriram, G. (2014). Genome-Scale Models of Plant Metabolism. In: Sriram, G. (eds) Plant Metabolism. Methods in Molecular Biology, vol 1083. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-661-0_13

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  • DOI: https://doi.org/10.1007/978-1-62703-661-0_13

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-660-3

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