Biochemical and functional analysis of the YME1 gene product, an ATP and zinc-dependent mitochondrial protease from S. cerevisiae.

Abstract

Inactivation of YME1 in yeast causes several distinct phenotypes: an increased rate of DNA escape from mitochondria, temperature-sensitive growth on nonfermentable carbon sources, extremely slow growth when mitochondrial DNA is completely absent from the cell, and altered morphology of the mitochondrial compartment. The protein encoded by YME1, Ymelp, contains two highly conserved sequence elements, one implicated in the binding and hydrolysis of ATP, and the second characteristic of active site residues found in neutral, zinc-dependent proteases. Both the putative ATPase and zinc-dependent protease elements are necessary for the function of Ymelp as genes having mutations in critical residues of either of these motifs are unable to suppress any of the phenotypes exhibited by ymel deletion strains. Ymelp co-fractionates with proteins associated with the mitochondrial inner membrane, is tightly associated with this membrane, and is oriented with the bulk of the protein facing the matrix. Unassembled subunit II of cytochrome oxidase is stabilized in ymel yeast strains. The data support a model in which Ymelp is an ATP and zinc-dependent protease associated with the matrix side of the inner mitochondrial membrane. Subunit II of cytochrome oxidase, when not assembled into a higher order complex, is a likely substrate of Ymelp.

Proteomic Analysis of the Mouse Liver Mitochondrial Inner Membrane

“…Interestingly, sequence analysis shows that the closest homologue of TOB3 in yeast is YME1, a mitochondrial I-AAA protease (Table II). YME1 plays an essential role in the degradation of unassembled or misassembled subunits of cytochrome c oxidase (16). YME1 gene disruption led to several dysfunctions, including a reduced activity of the respiration chain complexes, slow growth, and lethality when the mutation is expressed in a Ϫ mitochondrial background (17).…”

The Evolution of the Conserved ATPase Domain (CAD): Reconstructing the History of an Ancient Protein Module

“…Both the ATPase activity and Zn-binding activity are required for the correct functioning of these proteins (Weber et al 1996). Members of this protein group have been shown to degrade transcription factors such as 32 (Tomoyasu et al 1995;Herman et al 1995) and phage cII (Arlt et al 1996) protein and probably participate in a number of other cellular functions as well.…”

The role of protein degradation in mitochondrial function and biogenesis

“…However, their physiological functions remain to be established. Identification of the 372 Weber et al (1996), however, reported an orientation towards the matrix side. See Table 2 and text for details on the different proteases corresponding genes will be an important step towards that end.…”

“…The latter appears to be degraded by Yme1p. Mutation of YME1 has been found to attenuate degradation of CoxII in the absence of CoxIV (Nakai et al 1995;Weber et al 1996), and a stabilizing effect of YME1-inactivation on both CoxII and CoxIII has been observed in a strain lacking cytochrome c (Pearce and Sherman 1995a). The presence of ATP-and zinc-binding motifs typical of metalloproteases in Yme1p, Rca1p and Afg3p supports the notion that these three proteins are indeed responsible for the degradation of mitochondrial translation products destined for the inner membrane, which, as described above, is both ATP-and divalent metal ion-dependent.…”

“…All these phenotypes are thought to result from a morphologically altered inner membrane . Whether this can be fully attributed to the accumulation of membrane proteins that are degraded by Yme1p or indeed involves another function of Yme1p, is still a matter of speculation (Nakai et al 1995;Weber et al 1996).…”