The iAAA protease is an ATP-dependent proteolytic complex in the mitochondrial inner membrane and belongs to the highly conserved family of AAA proteins. In the yeast Saccharomyces cerevisiae, the iAAA protease is a homo-oligomeric complex composed of Yme1p subunits which are active in the intermembrane space and mediate protein quality control. Yeast cells lacking Yme1p are characterized by pleiotropic phenotypes including a respiratory deficiency at elevated temperature and an aberrant mitochondrial morphology. However, the molecular basis of the different yeast yme1 phenotypes has not been completely understood. Human YME1L was shown to be the ortholog of the yeast Yme1p, but its functions within mammalian mitochondria and specific substrate proteins have not been identified so far. In order to define the roles of the mammalian iAAA protease two main approaches were carried out: (1) down regulation studies in mammalian cells using RNA interference, and (2) inducible overexpression of YME1L and several mutant variants in the mammalian system. The present study reports the functional conservation of the mammalian YME1L by showing its involvement in the proteolysis of prohibitin 1 whose homolog is also degraded by the iAAA protease in yeast. Furthermore, it demonstrates that YME1L has a role in the maintenance of the tubular mitochondrial morphology and in the constitutive processing of OPA1, a component of the mitochondrial fusion machinery. Moreover, the degradation of TIM23, a core subunit of the translocase of the inner membrane, in caspase-independent apoptosis depends on YME1L identifying a novel substrate for the mammalian iAAA protease and a new pathway it is involved in. The overexpression of YME1L mutants has no dominant negative effect on the iAAA protease. Its functions in mitochondrial proteolysis, import, and mitochondrial morphology remain unaltered. Taken together, this study reveals versatile roles of mammalian YME1L in protein quality control, mitochondrial morphology and apoptosis, thus demonstrating its importance for both the cellular viability and death
