Functional domains in introns. RNA processing intermediates in cis- and trans-acting mutants in the penultimate intron of the mitochondrial gene for cytochrome b.

The penultimate intron of the split mitochondrial gene (cob) for apocytochrome b of Saccharomyces cerevisiae is of particular interest; it contains a long unassigned reading frame, is present in both long form (six exons) and short form (three exons) of the gene, and a product expressed from it is required for the removal of its transcript and that of an intron in the transcript of the oxi3 gene. Complementation analysis shows mutants in this intron to be either cis-dominant or transrecessive. Cis-dominant mutants are located in the first third (approximately 350 base pairs) of the open and near the 3'-end of the closed reading frame, while trans-recessive mutants are scattered throughout the remaining two-thirds (approximately 750 base pairs) of the open frame. Mutants in both classes exhibit the same pattern of splicing defects in their transcripts, but for different reasons. Those in the trans-recessive class lack a functional maturase (probably a protein of Mr = 27,000) encoded wholly within the 3'-terminal segment of the intron, and for this reason also fail to express oxi3. In contrast, cis-dominant mutants are incapable of providing the splicing complex with a substrate of appropriate 2 degrees structure. They also accumulate a novel transcript, 1900 nucleotides long, which contains the intron fused to the downstream (3') exons. This may reflect an inability of the splicing complex to complete the normal sequence of cleavage of the intron at its downstream junction and the ligation of the two exonic moieties.