The mobile group I intron 3 alpha of the yeast mitochondrial COXI gene encodes a 35-kDa processed protein that is an endonuclease but not a maturase.

Three mitochondrial mutants were characterized that block the splicing of aI3 alpha, a mobile group I intron of the COXI gene of yeast mtDNA. Mutant C1085 alters helical structures known to be important for splicing of group I introns. M44 and C1072 are point mutants in exon 3 that block correct splicing but allow some splicing at cryptic 5'-splice sites. M44 alters the P1 helix needed for 5'-splice site definition, while the mutation in C1072 is a new kind of mutation because it is located upstream of the exon sequence involved in the P1 helix. All three mutants accumulate novel proteins of 35 and 44 kDa (p35 and p44, respectively) detected both by labeling of mitochondrial translation products and by Western blotting. Partial protease digestions indicate that p44 and p35 are closely related, probably as precursor and processed protein. The level of the intron-encoded endonuclease activity, I-SceIII, is elevated approximately 10-fold in the mutants. Partial purification of I-SceIII from the mutants showed that most, if not all, of the activity is associated with p35. Finally, because aI3 alpha splices accurately in a petite mutant, we conclude that aI3 alpha splicing does not depend on a mtDNA-encoded maturase.