The RES complex core subunits Snu17 and Bud13 buffer the spliceosome against intrinsically weak splicing signals in budding yeast

Abstract

Eukaryotic pre-mRNA splicing by the spliceosome requires a series of orchestrated rearrangements to promote formation of a catalytically active spliceosome. The Retention and Splicing (RES) complex, which contains Snu17p, Bud13p and Pml1p, assembles onto the B-complex and facilitates removal of the U4 snRNP while preventing premature catalytic activation of the spliceosome by Prp2p. To better understand the roles of each subunit of the RES complex in vivo, we analyzed splicing through RNA sequencing in snu17{Delta}, bud13{Delta}, and pml1{Delta} yeast mutants, with and without inactivation of nonsense-mediated decay. Inactivation of Snu17p and Bud13p led to a major decrease in splicing efficiency for many intron-containing genes, while inactivation of Pml1p affected only a very minor subset. Snu17p and Bud13p are particularly critical for promoting splicing of inefficiently spliced non-ribosomal protein genes with small introns, non-consensus 5' splice sites or branchpoints, or without well-defined poly(U) tracts, suggesting a role for these elements in early intron recognition. The loss of these two core RES subunits therefore does not appear to cause splicing defects but rather exacerbate existing ones, such that transcripts with intrinsically high splicing efficiency remain unaffected by inactivation of RES. Cells lacking Pml1p also show growth phenotypes that are clearly distinct from those observed in snu17{Delta} and bud13{Delta} cells. These results show that Snu17p and Bud13p act as the core subcomplex of RES for efficient splicing of poorly spliced introns in vivo, while Pml1p may play accessory functions in linking the spliceosome to other processes.