Mitochondrial fragmentation drives selective removal of deleterious mtDNA in the germline

Mitochondria contain their own genomes, and unlike nuclear genomes, mitochondrial genomes are inherited maternally. With a high mutation rate and little recombination, special selection mechanisms exist in the female germline to prevent the accumulation of deleterious mutations(1–5). The molecular mechanisms underpinning selection remain poorly understood(6). Here, using an allele-specific fluorescent in situ-hybridization approach to distinguish wildtype from mutant mtDNA, we have visualized germline selection for the first time. Selection first manifests in the early stages of Drosophila oogenesis, triggered by reduction of the pro-fusion protein Mitofusin. This leads to the physical separation of mitochondrial genomes into different mitochondrial fragments, preventing the mixing of genomes and their products, and thereby reducing complementation. Once fragmentated, mitochondria harboring mutant genomes are less able to make ATP, which marks them for selection through a process requiring the mitophagy proteins Atg1 and BNIP3. Surprisingly, a reduction in Atg1 or BNIP3 decreases the amount of wildtype mtDNA, suggesting a link between mitochondrial turnover and mtDNA replication. Remarkably, fragmentation is not only necessary for selection in germline tissues, but also sufficient to induce selection in somatic tissues where selection is normally absent. Our studies posit a generalizable mechanism to select against deleterious mtDNA mutations that may allow the development of strategies for treatment of mtDNA disorders.