Heme oxygenase-1 (HO-1) and ATPase inhibitory factor (ATPIF) 1 is often overexpressed in different types of cancer cells. To gain a physiological significance, we treated the synthetic flavonoids in colon cancer cells, HT29 and HCT116 cells and confirmed that overexpression of both HO-1 and ATPIF1 was critical for tumor cell death with an impaired mitochondrial energetics. It would provide a strategy for developing selective anti-tumor candidates. A transgene-based model of a heteroplasmic lethal mtDNA deletion (mtDNAΔ) in adult Drosophila muscle. Stimulation of autophagy, activation of the PINK1/parkin pathway or decreased levels of mitofusin result in a selective decrease in mtDNAΔ. Decreased levels of mitofusin and increased levels of ATPIF1, an inhibitor of ATP synthase reversal-dependent mitochondrial repolarization, result in a further decrease in mtDNAΔ levels. The loss of ATPIF1 strongly protects against antimycin-induced ETC dysfunction and cell death by allowing for the maintenance of mitochondrial membrane potential. Inhibition of ATPIF1 ameliorates complex III blockade in primary hepatocytes, a cell type afflicted in severe mitochondrial disease, that inhibition of ATPIF1 can ameliorate severe ETC dysfunction in mitochondrial pathology.