# Prp16 enables efficient splicing of introns with diverse exonic consensus elements in the short-intron rich Cryptococcus neoformans transcriptome

## TL;DR

This study explores how the splicing helicase Prp16 helps process short introns in the fungus Cryptococcus neoformans, revealing its role in efficient splicing.

## Contribution

The study identifies Prp16's specific role in splicing short introns with diverse exonic consensus elements in C. neoformans.

## Key findings

- Prp16's splicing functions depend on conserved helicase motifs I and II.
- Short and ultrashort introns are more sensitive to Prp16 knockdown than longer introns.
- Introns spliced without Prp16 have exonic sequences with stronger U5 loop 1 affinity.

## Abstract

DEAH box splicing helicase Prp16 in budding yeast governs spliceosomal remodelling from the branching conformation (C complex) to the exon ligation conformation (C* complex). In this study, we examined the genome-wide functions of Prp16 in the short intron-rich genome of the basidiomycete yeast Cryptococcus neoformans. The presence of multiple introns per transcript with intronic features that are more similar to those of higher eukaryotes makes it a promising model for studying spliceosomal splicing. Using a promoter-shutdown conditional Prp16 knockdown strain, we uncovered genome-wide but substrate-specific roles in C. neoformans splicing. The splicing functions of Prp16 are dependent on helicase motifs I and II, which are conserved motifs for helicase activity. A small subset of introns spliced independent of Prp16 activity was investigated to discover that exonic sequences at the 5’ splice site (5’SS) and 3’ splice site (3’SS) with stronger affinity for U5 loop 1 are a common feature in these introns. Furthermore, short (60–100nts) and ultrashort introns (<60nts) prevalent in the C. neoformans transcriptome were more sensitive to Prp16 knockdown than longer introns, indicating that Prp16 is required for the efficient splicing of short and ultrashort introns. We propose that stronger U5 snRNA-pre-mRNA interactions enable efficient transition of the spliceosome from the first to the second catalytic confirmation in Prp16 knockdown, particularly for short introns and introns with suboptimal features. This study provides insights into fine-tuning spliceosomal helicase function with variations in cis-element features.