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.