Mechanism of recognition of the 5′ splice site in self-splicing group I introns

Abstract

Group I introns include many mitochondrial ribosomal RNA and messenger RNA introns and the nuclear rRNA introns of Tetrahymena and Physarum^1–6. The splicing of precursor RNAs containing these introns is a two-step reaction. Cleavage at the 5′ splice site precedes cleavage at the 3′ splice site, the latter cleavage being coupled with exon ligation^7–9. Following the first cleavage, the 5′ exon must somehow be held in place for ligation. We have now tested the reactivity of two self-splicing group I RNAs, the Tetrahymena pre-rRNA and the intron 1 portion of the Neurospora mitochondrial cytochrome b (cob) pre-mRNA, in the inter-molecular exon ligation reaction (splicing in trans) described by Inoue et al.¹⁰. The different sequence specificity of the reactions supports the idea that the nucleotides immediately upstream from the 5′ splice site are base-paired to an internal, 5′ exon-binding site, in agreement with RNA structure models proposed by Davies and co-workers^2,3 and others^4,5,11. The internal binding site is proposed to be involved in the formation of a structure that specifies the 5′ splice site and, following the first step of splicing, to hold the 5′ exon in place for exon ligation.