Group II intron splicing pathways. (A) Branching pathway. Following transcription of the interrupted gene, the 2′-OH residue of the branch-point nucleotide (A) performs the first nucleophilic attack at the exon 1–intron junction (step 1). This transesterification reaction connects the 5′ end of the intron to the branch point and relesases exon 1 that remains associated to the intron through base-pairing interactions (EBS–IBS interactions, vertical lines). The liberated 3′-OH at the end of exon 1 then initiates a second nucleophilic attack at the intron–exon 2 junction (step 2), ligating the two exons and releasing the intron as a lariat. (B) Hydrolytic pathway. A water molecule or a hydroxyl ion initiates the first nucleophilic attack at the exon 1–intron junction (step 1). The second nucleophilic attack at the intron–exon 2 junction is initiated by the liberated 3′-OH at the end of exon 1 (step 2) which ligates the two exons and releases a linear intron. (C) Circularization pathway. The first nucleophilic attack at the intron–exon 2 junction is initiated by the 3′-OH of a free exon 1 (step 1). The 2′-OH of the last intron residue is thought to initiate the second nucleophilic reaction at the exon 1–intron junction (step 2) resulting in intron circularization and the release of free exon 1. A potential source of free exon 1 is the spliced exon reopening (SER) reaction where both excised lariats and linear introns can recognize and hydrolyze ligated exons at the splice junction. An alternative pathway for intron circle formation is the potential circularization of an excised linear intron by a host-encoded RNA ligase.
