FUNCTION OF A PSEUDOKNOT IN THE SUPPRESSION OF AN ALTERNATIVE SPLICING EVENT IN A GROUP-I INTRON

Like most mitochondrial group I introns with a free-standing open read ing frame (ORF) located downstream of their catalytic core, the Sd.cob ,1 intron in the gene coding for the cytochrome b of Saccharomyces dou glasii mitochondria possesses a putative proximal 3' splice site. Howe ver, incubation of Sd.cob, 1 preRNA transcripts under optimal in vitro splicing conditions essentially results in splicing at the authentic, distal 3' splice junction. The mechanism by which the proximal splici ng event is suppressed in vitro involves formation of a tertiary inter action which is only found in the Sd.cob,1 intron. Core nucleotides lo cated in loop L5 block proximal splicing by forming Watson-Crick base pairs with the nucleotide sequence of the proximal 3' splice site. Thi s tertiary base pairing, also important for the folding of the intron into an active conformation, may be regarded as equivalent to the L9/P 5, GNRA-loop/helix interaction found in more than one-third of known g roup I introns.