Inactivation of the mitochondrial protease Afg3l2 results in severely diminished respiratory chain activity and widespread defects in mitochondrial gene expression

The m-AAA proteases plays a critical role in the proteostasis of the inner mitochondrial membrane proteins, and mutations in the genes encoding these proteases cause severe incurable neurological diseases. To further explore the biological role of the m-AAA proteases and the pathological consequences of their deficiency, we used a genetic approach in the fruit fly Drosophila melanogaster to inactivate the ATPase family gene 3-like 2 (AFG3L2) gene, which encodes a component of the m-AAA proteases. We found that null alleles of Drosophila AFG3L2 die early in development, but partial inactivation of AFG3L2 using RNAi extended viability to the late pupal and adult stages of development. Flies with partial inactivation of Afg3l2 exhibited marked behavioral defects, neurodegeneration, mitochondrial morphological alterations, and diminished respiratory chain (RC) activity. Further work revealed that reduced RC activity was a consequence of widespread defects in mitochondrial gene expression, including diminished mitochondrial transcription, translation and impaired mitochondrial ribosome biogenesis. These defects were accompanied by the compensatory activation of the mitochondrial unfolded protein response (mito-UPR) and accumulation of unfolded mitochondrial proteins, including proteins involved in transcription. Overexpression of the mito-UPR components partially rescued the Afg3l2-deficient phenotypes, indicating that sequestration of essential components of the mitochondrial gene expression into aggregates partly accounts for these defects. However, Afg3l2 also co-sediments with the mitochondrial ribosome biogenesis machinery, suggesting an additional novel role for Afg3l2 in ribosome biogenesis. Our work suggests that strategies designed to modify mitochondrial stress pathways and mitochondrial gene expression could be therapeutic in the diseases caused by mutations in AFG3L2. Author Summary Mitochondria produce virtually all of the cellular energy through the actions of the respiratory chain (RC) complexes. However, both the assembly of the RC complexes, and their biological functions come at a cost. Biogenesis of the RC complexes depends on the coordinated expression of nuclear and mitochondrially encoded subunits and an imbalance in this process can cause protein aggregation. Moreover, the RC complexes produce highly damaging reactive oxygen species as a side product of their activity. The Mitochondrial AAA+ family of proteases are believed to provide the first line of defense against these insults. The importance of this protease family is best exemplified by the severe neurodegenerative diseases that are caused by mutations in their respective genes. To better understand the biological roles of the AAA+ proteases, and the physiological consequences of their inactivation we used a genetic approach in Drosophila to study the Afg3l2 AAA+ protease. Unexpectedly, we found that Afg3l2 deficiency profoundly impaired mitochondrial gene expression, including transcription, translation and ribosome biogenesis. These phenotypes were accompanied by accumulation of insoluble mitochondrial proteins, and compensatory activation of mito-UPR and autophagy. Our work indicates Afg3l2 plays critical roles in degrading unfolded mitochondrial proteins and regulating mitochondrial gene expression.