Genetic screens have been used extensively to probe interactions betweennuclear genes and their impact on phenotypes. Probing interactions betweenmitochondrial genes and their phenotypic outcome, however, has not beenpossible due to a lack of tools to map the responsible polymorphisms. Here,using a toolkit we previously established in Drosophila, we isolate over 300recombinant mitochondrial genomes and map a naturally occurring polymorphism at the cytochrome c oxidase III residue 109 (CoIII109) that fully rescues the lethality and other defects associated with a point mutation incytochrome c oxidase I (CoIT300I). Through lipidomics profiling, biochemicalassays and phenotypic analyses, we show that the CoIII109 polymorphismmodulates cardiolipin binding to prevent complex IV instability caused by theCoIT300I mutation. This study demonstrates the feasibility of genetic interactionscreens in animal mitochondrial DNA. It unwraps the complex intra-genomicinterplays underlying disorders linked to mitochondrial DNA and how theyinfluence disease expression
