The Trypanosoma brucei MitoCarta and its regulation and splicing pattern during development

Xiaobai Zhang, Juan Cui, Daniel Nilsson, Kapila Gunasekera, Astrid Chanfon, Xiaofeng Song, Huinan Wang, Ying Xu, Torsten Ochsenreiter

Research output: Contribution to journalArticle

44 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)7378-7387
Number of pages10
JournalNucleic acids research
Volume38
Issue number21
DOIs
StatePublished - Nov 1 2010

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Trypanosoma brucei brucei
Mitochondrial Proteins
Parasites
Proteins
Trypanosomiasis
Organelle Biogenesis
Life Cycle Stages
Genome
Technology
Equipment and Supplies

ASJC Scopus subject areas

  • Genetics

Cite this

Zhang, X., Cui, J., Nilsson, D., Gunasekera, K., Chanfon, A., Song, X., ... Ochsenreiter, T. (2010). The Trypanosoma brucei MitoCarta and its regulation and splicing pattern during development. Nucleic acids research, 38(21), 7378-7387. https://doi.org/10.1093/nar/gkq618

The Trypanosoma brucei MitoCarta and its regulation and splicing pattern during development. / Zhang, Xiaobai; Cui, Juan; Nilsson, Daniel; Gunasekera, Kapila; Chanfon, Astrid; Song, Xiaofeng; Wang, Huinan; Xu, Ying; Ochsenreiter, Torsten.

In: Nucleic acids research, Vol. 38, No. 21, 01.11.2010, p. 7378-7387.

Research output: Contribution to journalArticle

Zhang, X, Cui, J, Nilsson, D, Gunasekera, K, Chanfon, A, Song, X, Wang, H, Xu, Y & Ochsenreiter, T 2010, 'The Trypanosoma brucei MitoCarta and its regulation and splicing pattern during development', Nucleic acids research, vol. 38, no. 21, pp. 7378-7387. https://doi.org/10.1093/nar/gkq618
Zhang, Xiaobai ; Cui, Juan ; Nilsson, Daniel ; Gunasekera, Kapila ; Chanfon, Astrid ; Song, Xiaofeng ; Wang, Huinan ; Xu, Ying ; Ochsenreiter, Torsten. / The Trypanosoma brucei MitoCarta and its regulation and splicing pattern during development. In: Nucleic acids research. 2010 ; Vol. 38, No. 21. pp. 7378-7387.
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