13The m-AAA proteases plays a critical role in the proteostasis of the inner mitochondrial 14 membrane proteins, and mutations in the genes encoding these proteases cause severe incurable 15 neurological diseases. To further explore the biological role of the m-AAA proteases and the 16 pathological consequences of their deficiency, we used a genetic approach in the fruit fly 17 Drosophila melanogaster to inactivate the ATPase family gene 3-like 2 (AFG3L2) gene, which 18 encodes a component of the m-AAA proteases. We found that null alleles of Drosophila 19 AFG3L2 die early in development, but partial inactivation of AFG3L2 using RNAi extended 20 viability to the late pupal and adult stages of development. Flies with partial inactivation of 21 Afg3l2 exhibited marked behavioral defects, neurodegeneration, mitochondrial morphological 22 alterations, and diminished respiratory chain (RC) activity. Further work revealed that reduced 23 RC activity was a consequence of widespread defects in mitochondrial gene expression, 24 including diminished mitochondrial transcription, translation and impaired mitochondrial 25 ribosome biogenesis. These defects were accompanied by the compensatory activation of the 26 mitochondrial unfolded protein response (mito-UPR) and accumulation of unfolded 27 mitochondrial proteins, including proteins involved in transcription. Overexpression of the mito-28 UPR components partially rescued the Afg3l2-deficient phenotypes, indicating that sequestration 29 of essential components of the mitochondrial gene expression into aggregates partly accounts for 30 these defects. However, Afg3l2 also co-sediments with the mitochondrial ribosome biogenesis 31 machinery, suggesting an additional novel role for Afg3l2 in ribosome biogenesis. Our work 32 suggests that strategies designed to modify mitochondrial stress pathways and mitochondrial 33 gene expression could be therapeutic in the diseases caused by mutations in AFG3L2. 34 35 3 Author Summary 36 Mitochondria produce virtually all of the cellular energy through the actions of the respiratory 37 chain (RC) complexes. However, both the assembly of the RC complexes, and their biological 38 functions come at a cost. Biogenesis of the RC complexes depends on the coordinated expression 39 of nuclear and mitochondrially encoded subunits and an imbalance in this process can cause 40 protein aggregation. Moreover, the RC complexes produce highly damaging reactive oxygen 41 species as a side product of their activity. The Mitochondrial AAA + family of proteases are 42 believed to provide the first line of defense against these insults. The importance of this protease 43 family is best exemplified by the severe neurodegenerative diseases that are caused by mutations 44 in their respective genes. To better understand the biological roles of the AAA + proteases, and 45 the physiological consequences of their inactivation we used a genetic approach in Drosophila to 46 study the Afg3l2 AAA + protease. Unexpectedly, we found that Afg3l2 deficiency profoundly...