Mitochondria are particularly susceptible to increased formation of reactive oxygen and nitrogen species in the cell that can occur in response to pathological and xenobiotic stimuli. Proteomics can give insights into both mechanism of pathology and adaptation to stress. Herein we report the use of proteomics to evaluate alterations in the levels of mitochondrial proteins following chronic ethanol exposure in an animal model. Forty-three proteins showed differential expression, 13 increased and 30 decreased, as a consequence of chronic ethanol. Of these proteins, 25 were not previously known to be affected by chronic ethanol emphasizing the power of proteomic approaches in revealing global responses to stress. Both nuclear and mitochondrially encoded gene products of the oxidative phosphorylation complexes in mitochondria from ethanol-fed rats were decreased suggesting an assembly defect in this integrated metabolic pathway. Moreover mtDNA damage was increased by ethanol demonstrating that the effects of ethanol consumption extend beyond the proteome to encompass mtDNA. Taken together, we have demonstrated that chronic ethanol consumption extends to a modification of the mitochondrial proteome far broader than realized previously. These data also suggest that the response of mitochondria to stress may not involve non-discriminate changes in the proteome but is restricted to those metabolic pathways that have a direct role in a specific pathology.Chronic ethanol consumption causes liver damage by a complex process thought to involve oxidative and nitrosative stress, hypoxia, up-regulation of proinflammatory cytokines, and defects in energy metabolism (1-3). As both a source for the formation and target of modifications mediated by reactive oxygen and nitrogen species, the mitochondrion is recognized as a site critical in the cellular stress response induced by chronic ethanol exposure. Increased mitochondrial production of reactive oxygen species (4 -6), oxidation of mitochondrial proteins (7-10), depressed oxidative phosphorylation activity (11-13), and disrupted fatty acid metabolism (14 -16) occur following consumption of alcohol, indicating that ethanol induces significant changes in mitochondria physiology. These responses are also accompanied by a profound increase in the sensitivity of the respiratory chain to inhibition by NO, which we propose plays a key role in contributing to the hypoxia associated with ethanol-dependent hepatotoxicity (17). While mechanisms responsible for ethanol-induced mitochondrial dysfunction have been investigated, the impact of chronic ethanol consumption on the overall content of mitochondrial proteins, the "mitochondrial proteome," has not been studied. Earlier studies by Cunningham and colleagues (18,19) have demonstrated that ethanol consumption decreases the synthesis of the 13 mitochondrially encoded proteins that comprise respiratory complexes I, III, and IV and the ATP synthase. It is proposed that the inhibition of mitochondrial protein synthesis following chronic etha...