Two cDNA Clones Encoding Isoforms of the [beta]-Subunit of the General Mitochondrial Processing Peptidase from Potato

The general MPP removes the amino-terminal extensions of nuclear-encoded mitochondrial proteins. It consists of two nonidentical subunits termed a-MPP and p-MPP, which are supposed to form a heterodimer (Kalousek et al., 1993). Although the enzyme is localized in the matrix space of fungal and mammalian mitochondria, it was shown to reside in the inner mitochondrial membrane in plants (Braun et al., 1992; Glaser et al., 1992). Interestingly, in potato and wheat the complete protease forms part of the Cyt bc, complex (also known as Cyt c reductase or complex 111) of the respiratory chain (Braun et al., 1992; Emmermann et al., 1993a, 1993b; Braun et al., 1995). There are also indications that it forms part of this protein complex in spinach (Eriksson et al., 1994). The complex has been termed Cyt c reductase/processing peptidase complex and is extraordinarily stable (Emmermann et al., 1993a). The complex-integrated processing enzyme exhibits severa1 unique physiological features in comparison with the soluble protease from fungi and mammals (Emmermann and Schmitz, 1993). Here we report the primary structure of two cDNA clones encoding the P-subunit of MPP from potato (Table I). Extensive protein sequencing of a11 subunits of the Cyt bc, complex from potato (Braun et al., 1994) revealed the integration of the processing peptidase into the complex and was the basis for the design of oligonucleotide mixtures for the isolation of cDNA clones. Positively reacting clones were identified and isolated with radiolabeled oligonucleotides. The DNA inserts of two clones designated pp-I MPP and pp-I1 MPP share 71% sequence identity at the nucleotide level and 70% at the protein level. The open reading frame of clone pp-I1 MPP contains a11 61 possible codons. The amino acid sequence of the encoded protein is identical with the peptides sequenced from subunit I1 of the Cyt bc, complex. Similarly, pp-I MPP corresponds to subunit I of this protein complex. Both proteins are more similar to the P-subunits of the general mitochondrial processing peptidase than to subunits I and I1 of fungal and mammalian Cyt bc, complexes. Still, there is around 25% sequence identity with the high mo1 wt subunits of the complex, indi-