Please use this identifier to cite or link to this item: http://hdl.handle.net/1893/11535
Appears in Collections:Aquaculture Journal Articles
Peer Review Status: Refereed
Title: Reconstruction of Danio rerio Metabolic Model Accounting for Subcellular Compartmentalisation
Authors: Bekaert, Michaël
Contact Email: michael.bekaert@stir.ac.uk
Issue Date: Nov-2012
Publisher: Public Library of Science
Citation: Bekaert M (2012) Reconstruction of Danio rerio Metabolic Model Accounting for Subcellular Compartmentalisation, PLoS ONE, 7 (11), p. e49903.
Abstract: 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.
Type: Journal Article
URI: http://hdl.handle.net/1893/11535
DOI Link: http://dx.doi.org/10.1371/journal.pone.0049903
Rights: 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.
Affiliation: Aquaculture

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