title: Integrative identification of Arabidopsis mitochondrial proteome and its function exploitation through protein interaction network.
abstract: Mitochondria are major players on the production of energy, and host several key reactions involved in basic metabolism and biosynthesis of essential molecules. Currently, the majority of nucleus-encoded mitochondrial proteins are unknown even for model plant Arabidopsis. We reported a computational framework for predicting Arabidopsis mitochondrial proteins based on a probabilistic model, called Naive Bayesian Network, which integrates disparate genomic data generated from eight bioinformatics tools, multiple orthologous mappings, protein domain properties and co-expression patterns using 1,027 microarray profiles. Through this approach, we predicted 2,311 candidate mitochondrial proteins with 84.67% accuracy and 2.53% FPR performances. Together with those experimental confirmed proteins, 2,585 mitochondria proteins (named CoreMitoP) were identified, we explored those proteins with unknown functions based on protein-protein interaction network (PIN) and annotated novel functions for 26.65% CoreMitoP proteins. Moreover, we found newly predicted mitochondrial proteins embedded in particular subnetworks of the PIN, mainly functioning in response to diverse environmental stresses, like salt, draught, cold, and wound etc. Candidate mitochondrial proteins involved in those physiological acitivites provide useful targets for further investigation. Assigned functions also provide comprehensive information for Arabidopsis mitochondrial proteome.
authors.affiliation: College of Life Sciences, Center for Bioinformatics and Institute of Biomedical Sciences, East China Normal University, Shanghai, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Cui
authors.forename: Jinghua
authors.initials: J
authors.lastname: Liu
authors.forename: Yuhua
authors.initials: Y
authors.lastname: Li
authors.forename: Tieliu
authors.initials: T
authors.lastname: Shi
mesh_terms: D017360:Arabidopsis / Q000737:chemistry / Q000502:physiology*; D029681:Arabidopsis Proteins / Q000032:analysis / Q000502:physiology*; D001499:Bayes Theorem; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D024101:Mitochondrial Proteins / Q000032:analysis* / Q000502:physiology; D020543:Proteome / Q000032:analysis*; D013312:Stress, Physiological
chemical_list: D029681:Arabidopsis Proteins; D024101:Mitochondrial Proteins; D020543:Proteome