A new metabolic model ofDrosophila melanogasterand the integrative analysis of Parkinson’s disease

Abstract

High conservation of the disease-associated genes between flies and humans facilitates the common use ofDrosophila melanogasterto study metabolic disorders under controlled laboratory conditions. However, metabolic modeling studies are highly limited for this organism. We here report a comprehensively curated genome-scale metabolic network model ofDrosophilausing an orthology-based approach. The gene coverage and metabolic information of the draft model derived from a reference human model were expanded viaDrosophila-specific KEGG and MetaCyc databases, with several curation steps to avoid metabolic redundancy and stoichiometric inconsistency. Furthermore, we performed literature-based curations to improve gene–reaction associations, subcellular metabolite locations, and various metabolic pathways. The performance of the resultingDrosophilamodel (8,230 reactions, 6,990 metabolites, and 2,388 genes), iDrosophila1 (https://github.com/SysBioGTU/iDrosophila), was assessed using flux balance analysis in comparison with the other currently available fly models leading to superior or comparable results. We also evaluated the transcriptome-based prediction capacity of iDrosophila1, where differential metabolic pathways during Parkinson’s disease could be successfully elucidated. Overall, iDrosophila1 is promising to investigate system-level metabolic alterations in response to genetic and environmental perturbations.