Structural insights into intron catalysis and dynamics during splicing

Abstract

The group II intron ribonucleoprotein is an archetypal splicing system with numerous mechanistic parallels to the spliceosome, including excision of lariat introns1,2. Despite the importance of branching in RNA metabolism, structural understanding of this process has remained elusive. Here we present a comprehensive analysis of three single-particle cryogenic electron microscopy structures captured along the splicing pathway. They reveal the network of molecular interactions that specifies the branchpoint adenosine and positions key functional groups to catalyse lariat formation and coordinate exon ligation. The structures also reveal conformational rearrangements of the branch helix and the mechanism of splice site exchange that facilitate the transition from branching to ligation. These findings shed light on the evolution of splicing and highlight the conservation of structural components, catalytic mechanism and dynamical strategies retained through time in premessenger RNA splicing machines.

Cryo-EM sample preparation for high-resolution structure studies

“…Common strategies, as already discussed above, are also useful for achieving different and, if you are lucky, more diverse orientation distributions. If different grid-preparation methods lead to differing preferred orientation issues, combining data from grids prepared using multiple strategies can be useful (Klebl et al, 2020;Xu et al, 2023).…”

Intron-lariat spliceosomes convert lariats to true circles: implications for intron transposition

“…Ideas that explain the birth and persistence of introns and the spliceosome in eukaryotic genomes commonly invoke an ancient self-splicing transposable group II intron that spreads itself as (or before) it fragments during its evolution into the modern spliceosome (Lambowitz and Belfort 2015;Lynch and Richardson 2002). This hypothesis has become ever more cemented by the near superimposability of high resolution structures for the spliceosome and group II introns at various steps in forward splicing (Haack et al 2024;Xu et al 2023). If group II introns and the spliceosome shared a common ancestor, they each must have retained, acquired, or lost different abilities as their evolution proceeded along divergent paths.…”