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Mitochondrial DNA (mtDNA) deletions occur sporadically in zygotic and somatic tissues and reach their highest concentration in substantia nigra. Previously, we noted the increase of the adenosine monophosphate (AMP)-activated protein kinase (AMPK) transcript by microarray in multiple cells and tissues bearing deletions. In this work, we demonstrate that the induction of AMPK transcript is dependent on deletions by quantitative polymerase chain reaction, and also demonstrate a deficiency in adenosine triphosphate (ATP) synthesis in the same cells. Consistent with AMPK induction, its known targets SREBF1 (sterol regulatory element binding protein-1) and ATG12 were inhibited and induced, respectively. AMPK induction is known to decrease secretory processes in some cells, and the secretion of both osteoprotegerin (OPG) and fibronectin (FN) proteins to the extracellular space was significantly deficient. Deletions caused a defect in the adenosine diphosphate (ADP)-ribosylation factor-like 2 (ARL2) transcript, which is known to be important in secretion and interacts with protein phosphatase 2A (PP2A) and thus AMPK. The deletion-dependent dysfunctions occurred even in cells bearing less than 30% deletions, suggesting that the concept of a high biological ‘threshold’ for deletions should be further revised downward. The defects in ATP synthesis, induction of the AMPK and SREBF1 transcripts, and decreased expression of ARL2 and secretion of OPG and FN were recapitulated by low doses of rotenone, demonstrating that they were a specific consequence of electron transport chain inhibition. Thus, mtDNA deletions result in cellular energy depletion, which causes the induction of AMPK and its regulated targets, and inhibit secretion of some proteins. We integrate these observations into a pathophysiological model for how mitochondrial deletions cause disease.