Two Genomes, One Metabolome: Mitonuclear Incompatibility Remodels Developmental Metabolism and Fitness in Drosophila

Mitochondrial-nuclear (hereafter mitonuclear) genetic variation can alter cellular bioenergetics and metabolism via jointly encoding the subunits of oxidative phosphorylation (OXPHOS) system. Here we tested whether genetic variation in biochemical and bioenergetic phenotype can scale up across higher levels of biological organization to affect organismal development. We used a panel of (mtDNA); nDNA genotypes created by asymmetric substitution of divergent mtDNA between Drosophila melanogaster and its sister species D. simulans . Two genotypes – (ore); OreR and (ore); Aut – carry coevolved mitonuclear genomes from D. melanogaster , whereas the other two – (w ⁵⁰¹ ); Aut and (w ⁵⁰¹ ); OreR – harbor D. simulans mitochondrial DNA introgressed onto D. melanogaster nuclear backgrounds. We utilized untargeted metabolomics to track down the comprehensive biochemical footprint of the joint genomic architecture in the metabolome of these genotypes. We show that in (w ⁵⁰¹ ); OreR larvae with mitonuclear genome incompatibility there is extensive and coordinated metabolic remodeling of carbon, nitrogen, and redox balance, characterized by increased glycolysis, limited TCA cycle, amino acid scarcity, reduced nucleic acid balance, lipid remodeling, with compensatory activation of antioxidant pathways and possible epigenetic modulation by metabolites. This biochemical rewiring puts a physiological constraint that prioritizes maintenance metabolism over larval growth, leading to reduced body size, slow locomotion and delayed development, despite a compensatory increase in feeding in these larvae. These findings underscore the context dependency of mitonuclear interactions, which can uniquely scale up to influence organismal energy budget trade-offs, fitness and life-history evolution.