Reconstruction of Danio rerio metabolic model accounting for subcellular compartmentalisation

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.

FAIRDOMHub ID: https://seek.sysmo-db.org/publications/241

PubMed ID: 23166792

Projects: GenoSysFat

Journal: PLoS One

Citation: PLoS One. 2012;7(11):e49903. doi: 10.1371/journal.pone.0049903. Epub 2012 Nov 14.

Date Published: 14th Nov 2012

Author: M. Bekaert

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Created: 19th Oct 2015 at 10:23

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