Mitochondrial proteome of the apicomplexan Babesia divergens

Babesia are tick-transmitted apicomplexan parasites of widespread medical and veterinary importance. Although atovaquone, a first-line therapy for human babesiosis, targets one of the three proteins encoded by mitochondrial DNA, a full characterization of the nuclear-encoded mitochondrial proteome is lacking. Here, we combined organelle immunoprecipitation and density gradient separation to enrich mitochondria from Babesia divergens . Using protein mass spectrometry and protein correlation profiling, we generated B. divergens MitoCarta (BdMitoCarta), a high-confidence inventory of 525 mitochondrial proteins. The B. divergens mitoproteome is broadly conserved across Apicomplexa, which, as a clade, have undergone reductive evolution. As seen in other apicomplexans, metabolite transport and the TCA cycle have diverged, with loss of the pyruvate dehydrogenase complex, presence of malate:quinone oxidoreductase, and a class I fumarate hydratase. Specific to Babesia is the presence of two mitochondrial isocitrate dehydrogenase homologs. Using isolated mitochondria, we performed blue native PAGE complexome analysis and detected previously uncharacterized proteins co-migrating with the ATP synthase and mitochondrial ribosome. Our work has yielded the first mitochondrial proteome and complexome for Babesia , which we expect to be a valuable resource for understanding the evolution of apicomplexan parasites for future therapeutic development.