Mutational evidence for competition between the P1 and the P10 helices of a mitochondrial group I intron

A guanosine to cytosine transversion at position 2 of the fifth intron of the mitochondrial gene COB blocks the ligation step of splicing. This mutation prevents the formation of a base pair within the P1 helix of this group I intron—the RNA duplex formed between the 3 ' end of the upstream exon and the internal guide sequence. The mutation also reduces the rate of the first step of splicing (guanosine addition at the 5 ' splice junction) while stimulating hydrolysis at the 3 intron-exon boundary. Consequently, the ligation of exons is blocked because the 3 ' exon is removed prior to cleavage at the 5 ' splice junction. The lesion can be suppressed by second-site mutations that preserve the potential for base-pairing at this position. Because the P1 duplex and the P10 duplex (between the guide sequence and the 3 ' exon) overlap at the affected position, these results imply that the P1 and P10 pairings represent alternative structures that do not, indeed cannot, form simultaneously