Stoichiometric Representation of Gene–Protein–Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction

Daniel Machado, Markus Herrgard, Isabel Rocha

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Abstract

Genome-scale metabolic reconstructions are currently available for hundreds of organisms. Constraint-based modeling enables the analysis of the phenotypic landscape of these organisms, predicting the response to genetic and environmental perturbations. However, since constraint-based models can only describe the metabolic phenotype at the reaction level, understanding the mechanistic link between genotype and phenotype is still hampered by the complexity of gene-protein-reaction associations. We implement a model transformation that enables constraint-based methods to be applied at the gene level by explicitly accounting for the individual fluxes of enzymes (and subunits) encoded by each gene. We show how this can be applied to different kinds of constraint-based analysis: flux distribution prediction, gene essentiality analysis, random flux sampling, elementary mode analysis, transcriptomics data integration, and rational strain design. In each case we demonstrate how this approach can lead to improved phenotype predictions and a deeper understanding of the genotype-to-phenotype link. In particular, we show that a large fraction of reaction-based designs obtained by current strain design methods are not actually feasible, and show how our approach allows using the same methods to obtain feasible gene-based designs. We also show, by extensive comparison with experimental 13C-flux data, how simple reformulations of different simulation methods with gene-wise objective functions result in improved prediction accuracy. The model transformation proposed in this work enables existing constraint-based methods to be used at the gene level without modification. This automatically leverages phenotype analysis from reaction to gene level, improving the biological insight that can be obtained from genome-scale models.
Original languageEnglish
Article numbere1005140
JournalP L o S Computational Biology (Online)
Volume12
Issue number10
Number of pages24
ISSN1553-7358
DOIs
Publication statusPublished - 2016

Bibliographical note

© 2016 Machado et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Projects

DD-DeCaF: Bioinformatics Services for Data-Driven Design of Cell Factories and Communities

Herrgard, M., Sonnenschein, N., Kutuzova, S., Redestig, N. H., Beber, M. E., Dannaher, D., Lopez Benito, A., Kaafarani, A., Lieven, C., Lohmann, R., Rasmussen, B. K., Kjiproski, D. & Beck Knudsen, E.

Horizon 2020

01/03/201629/02/2020

Project: Research

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