The mitochondrial proteome of diplonemids: from conventional pathways to eccentric RNA editing and transcript processing.

backgroundDiplonemids constitute an abundant and geographically widespread but little-studied group of marine protists. A hallmark of this lineage, the kinetoplastid sister group within Euglenozoa, is a mitochondrial genome comprising numerous small circular DNA molecules that carry fragments of mitochondrial genes. Complex RNA processing of the corresponding transcripts involves numerous ligation and RNA editing steps in the production of mature RNA species. To assess the diplonemid mitochondrial proteome and, in particular, to search for proteins that might mediate RNA processing, we undertook a comprehensive in silico analysis to predict candidate mitochondrial proteins in the type species Diplonema papillatum.

resultsUsing sequence similarity searches in conjunction with a mitochondrial targeting pipeline, we identified at least 1878 candidate nucleus-encoded mitochondrial proteins in addition to 16 mitochondrion-encoded proteins described previously. Despite the highly unconventional nature of the mitochondrial genome in D. papillatum, its mitochondrial proteome (mitoproteome) contains virtually all the functionally most important proteins that are ubiquitous among aerobic mitochondria, and several novel proteins that have been recruited in the euglenozoan last common ancestor to augment complexes involved in coupled electron transport oxidative phosphorylation and mitochondrial ribosome formation. Notably, we identified several individual proteins and multi-protein families that are candidates for RNA ligation and editing enzymes.

conclusionsThis first comprehensive mitoproteome data for a diplonemid, together with published mitoproteome data for other members of Discoba, allows us to make inferences about marked changes in mitochondrial structure and function that have occurred since the divergence of diplonemids and other euglenozoans from the last common discobid ancestor.