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Reconstruction of Danio rerio Metabolic Model Accounting for Subcellular Compartmentalisation

Plant and microbial metabolic engineering is commonly used in the production of functional foods and quality trait improvement. Computational model-based approaches have been used in this important endeavour. However, to date, fish metabolic models have only been scarcely and partially developed, in...

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Autor principal: Bekaert, Michaël
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3498201/
https://www.ncbi.nlm.nih.gov/pubmed/23166792
http://dx.doi.org/10.1371/journal.pone.0049903
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author Bekaert, Michaël
author_facet Bekaert, Michaël
author_sort Bekaert, Michaël
collection PubMed
description Plant and microbial metabolic engineering is commonly used in the production of functional foods and quality trait improvement. Computational model-based approaches have been used in this important endeavour. However, to date, fish metabolic models have only been scarcely and partially developed, in marked contrast to their prominent success in metabolic engineering. In this study we present the reconstruction of fully compartmentalised models of the Danio rerio (zebrafish) on a global scale. This reconstruction involves extraction of known biochemical reactions in D. rerio for both primary and secondary metabolism and the implementation of methods for determining subcellular localisation and assignment of enzymes. The reconstructed model (ZebraGEM) is amenable for constraint-based modelling analysis, and accounts for 4,988 genes coding for 2,406 gene-associated reactions and only 418 non-gene-associated reactions. A set of computational validations (i.e., simulations of known metabolic functionalities and experimental data) strongly testifies to the predictive ability of the model. Overall, the reconstructed model is expected to lay down the foundations for computational-based rational design of fish metabolic engineering in aquaculture.
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spelling pubmed-34982012012-11-19 Reconstruction of Danio rerio Metabolic Model Accounting for Subcellular Compartmentalisation Bekaert, Michaël PLoS One Research Article Plant and microbial metabolic engineering is commonly used in the production of functional foods and quality trait improvement. Computational model-based approaches have been used in this important endeavour. However, to date, fish metabolic models have only been scarcely and partially developed, in marked contrast to their prominent success in metabolic engineering. In this study we present the reconstruction of fully compartmentalised models of the Danio rerio (zebrafish) on a global scale. This reconstruction involves extraction of known biochemical reactions in D. rerio for both primary and secondary metabolism and the implementation of methods for determining subcellular localisation and assignment of enzymes. The reconstructed model (ZebraGEM) is amenable for constraint-based modelling analysis, and accounts for 4,988 genes coding for 2,406 gene-associated reactions and only 418 non-gene-associated reactions. A set of computational validations (i.e., simulations of known metabolic functionalities and experimental data) strongly testifies to the predictive ability of the model. Overall, the reconstructed model is expected to lay down the foundations for computational-based rational design of fish metabolic engineering in aquaculture. Public Library of Science 2012-11-14 /pmc/articles/PMC3498201/ /pubmed/23166792 http://dx.doi.org/10.1371/journal.pone.0049903 Text en © 2012 Michaël Bekaert http://creativecommons.org/licenses/by/4.0/ 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 properly credited.
spellingShingle Research Article
Bekaert, Michaël
Reconstruction of Danio rerio Metabolic Model Accounting for Subcellular Compartmentalisation
title Reconstruction of Danio rerio Metabolic Model Accounting for Subcellular Compartmentalisation
title_full Reconstruction of Danio rerio Metabolic Model Accounting for Subcellular Compartmentalisation
title_fullStr Reconstruction of Danio rerio Metabolic Model Accounting for Subcellular Compartmentalisation
title_full_unstemmed Reconstruction of Danio rerio Metabolic Model Accounting for Subcellular Compartmentalisation
title_short Reconstruction of Danio rerio Metabolic Model Accounting for Subcellular Compartmentalisation
title_sort reconstruction of danio rerio metabolic model accounting for subcellular compartmentalisation
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3498201/
https://www.ncbi.nlm.nih.gov/pubmed/23166792
http://dx.doi.org/10.1371/journal.pone.0049903
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