Whole genome duplication uncouples cell volume scaling from mitochondrial homeostasis

Whole genome duplication, or polyploidy, increases cell size and nuclear volume, yet how cells maintain cytonuclear balance and metabolic fitness following ploidy expansion remains unclear. Using isogenic series of Saccharomyces cerevisiae strains ranging from haploid (1N) to tetraploid (4N), and isogenic human diploid and tetraploid cell lines, we investigated the impact of polyploidy on mitochondrial homeostasis and metabolic adaptation. Quantitative proteomics uncovered a sub-linear scaling of mitochondrial proteins with increasing ploidy, with pronounced depletion of respiratory chain components, mitochondrial DNA maintenance factors, and redox homeostasis proteins. These changes were highly conserved, indicating a conserved consequence of genome expansion. Impaired mitochondrial scaling reduced respiratory growth, membrane potential and oxygen consumption, and elevated oxidative stress. In budding yeast, the mitochondrial dysfunction triggered reactive oxygen species (ROS) accumulation and an unconventional activation of stress-responsive signaling pathways, including the Hog1 and cell integrity MAPK networks, which converged on Rtg2-dependent retrograde signaling to promote mitochondrial metabolism despite chronic dysfunction. Our findings identify defective mitochondrial scaling as a key consequence of polyploidy and establish ROS- and stress signaling-dependent retrograde response as a key adaptive mechanism linking genome duplication to mitochondrial homeostasis and cellular fitness.