A large fraction (30-50%) of the various proteins synthesized within isolated rat liver mitochondria were degraded to amino acids within 60 min after synthesis. Incomplete mitochondrial polypeptides resulting from the incorporation of puromycin were degraded even more extensively (80% per hr). Protein breakdown was measured by the appearance of acid-soluble radioactivity and by the disappearance of labeled polypeptides detected on NaDodSO4/polyacrylamide gel electrophoresis. The amino acids generated by proteolysis were transported rapidly out of the mitochondria and no peptide intermediates accumulated in the organelle. This degradative process did not involve lysosomes or lysosomal enzymes and was markedly stimulated by ATP either generated within the mitochondria or supplied exogenously. An inhibitor of respiration (cyanide) or uncouplers of oxidative phosphorylation (oligomycin, dinitrophenol) reduced proteolysis when mitochondria were provided substrates for ATP generation. When exogenous ATP was provided, these agents did not affect proteolysis, but degradation was then sensitive to atractyloside, an inhibitor of adenine nucleotide transport. Vanadate, an inhibitor of various ATPases, blocked proteolysis even in the presence of ATP and caused a marked stabilization of nearly all polypeptide bands. Thus, mitochondria-like bacteria or the cytosol of animal cells-contain a pathway for complete degradation of proteins which seems to selectively remove polypeptides with abnormal structures. Within this organelle, ATP hydrolysis appears necessary for an initial step in this degradative process.The proteins comprising the mitochondria, like other proteins in mammalian cells, are subject to continual turnover (1). It has generally been assumed that mitochondria are degraded within the lysosome (2-5), and under certain conditions whole mitochondria or mitochondrial enzymes have been demonstrated within autophagic vacuoles (2-4). However, different mitochondrial proteins turn over at distinct rates. Outer membrane proteins tend to be degraded at a faster rate than those of the inner membrane (6). Furthermore, individual proteins within the same mitochondrial compartment can also have different turnover rates. In the matrix, several enzymes have tl/2 ranging from 70 min to 1-2 days, whereas the bulk of mitochondrial proteins turn over with a tl/2 of 3-5 days (6-8). Such observations cannot be explained by indiscriminate degradation of this organelle within the lysosome.One possible explanation for this heterogeneity in degradative rates is that proteins may be excreted by the mitochondria for degradation in the cytoplasm or lysosome. Another possibility is that there exists within mitochondria a proteolytic system that selectively hydrolyzes the short-lived enzymes. Several groups have reported proteases associated with the mitochondrial fraction of mammalian cells (9-14). However, an intramitochondrial localization has not been demonstrated definitively for any of these enzymes. The presence in the mitochon...