Reconstruction of Danio rerio Metabolic Model Accounting for Subcellular Compartmentalisation 英文参考文献.docVIP

ReconstructionofDaniorerioMetabolicModel AccountingforSubcellularCompartmentalisation Michae¨lBekaert* InstituteofAquaculture,UniversityofStirling,Stirling,Scotland,UnitedKingdom Abstract Plant and microbial metabolic engineering is commonly used in the production of functional foods and quality trait improvement.Computationalmodel-basedapproacheshavebeenusedinthisimportantendeavour.However,todate,fish metabolic models have only been scarcely and partially developed, in marked contrast to their prominent success in metabolicengineering.InthisstudywepresentthereconstructionoffullycompartmentalisedmodelsoftheDaniorerio (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 accountsfor4,988genescodingfor2,406gene-associatedreactionsandonly418non-gene-associatedreactions.Asetof computationalvalidations(i.e.,simulationsofknownmetabolicfunctionalitiesandexperimentaldata)stronglytestifiesto the predictive ability of the model. Overall, the reconstructed model is expected to lay down the foundations for computational-basedrationaldesignoffishmetabolicengineeringinaquaculture. 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:RamaniRamchandran,MedicalCollegeofWisconsin,UnitedStatesofAmerica ReceivedJuly8,2012;AcceptedOctober16,2012;PublishedNovember14,2012 Copyright: ?2012 Michae¨lBekaert.This is anopen-access article distributed under the terms ofthe Creative Commons Attribution License, which permits unrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited. Funding: This work was supported by the Marine