reconstruction of danio rerio metabolic model accounting for subcellular compartmentalisation重建鲐鱼类代谢模型占亚细胞上.pdfVIP

Reconstruction of Danio rerio Metabolic Model Accounting for Subcellular Compartmentalisation ¨ Michael Bekaert* Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom 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. Citation: Bekaert M (2012) Reconstruction of Danio rerio Metabolic Model Accounting for Subcellular Compartmentalisation. PLoS One 7(11): e49903. doi:10.1371/journal.pone.0049903 Editor: Ramani Ramchandran, Medical College of Wisconsin, United States of America Received July 8, 2012; Accepted October 16, 2012;