title: The Trypanosoma brucei MitoCarta and its regulation and splicing pattern during development.
abstract: It has long been known that trypanosomes regulate mitochondrial biogenesis during the life cycle of the parasite; however, the mitochondrial protein inventory (MitoCarta) and its regulation remain unknown. We present a novel computational method for genome-wide prediction of mitochondrial proteins using a support vector machine-based classifier with ∼90% prediction accuracy. Using this method, we predicted the mitochondrial localization of 468 proteins with high confidence and have experimentally verified the localization of a subset of these proteins. We then applied a recently developed parallel sequencing technology to determine the expression profiles and the splicing patterns of a total of 1065 predicted MitoCarta transcripts during the development of the parasite, and showed that 435 of the transcripts significantly changed their expressions while 630 remain unchanged in any of the three life stages analyzed. Furthermore, we identified 298 alternatively splicing events, a small subset of which could lead to dual localization of the corresponding proteins.
authors.affiliation: Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, Jiangsu 210016 China.
authors.forename: Xiaobai
authors.initials: X
authors.lastname: Zhang
authors.forename: Juan
authors.initials: J
authors.lastname: Cui
authors.forename: Daniel
authors.initials: D
authors.lastname: Nilsson
authors.forename: Kapila
authors.initials: K
authors.lastname: Gunasekera
authors.forename: Astrid
authors.initials: A
authors.lastname: Chanfon
authors.forename: Xiaofeng
authors.initials: X
authors.lastname: Song
authors.forename: Huinan
authors.initials: H
authors.lastname: Wang
authors.forename: Ying
authors.initials: Y
authors.lastname: Xu
authors.forename: Torsten
authors.initials: T
authors.lastname: Ochsenreiter
mesh_terms: D017398:Alternative Splicing; D001185:Artificial Intelligence; D002460:Cell Line; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D024101:Mitochondrial Proteins / Q000032:analysis / Q000235:genetics* / Q000378:metabolism; D015800:Protozoan Proteins / Q000032:analysis / Q000235:genetics* / Q000378:metabolism; D014346:Trypanosoma brucei brucei / Q000235:genetics* / Q000378:metabolism
chemical_list: D024101:Mitochondrial Proteins; D015800:Protozoan Proteins