Deep evolutionary origin of nematode SL2 trans-splicing revealed by genome-wide analysis of the Trichinella spiralis transcriptome

Abstract

Spliced leader trans-splicing is intimately associated with the presence of eukaryotic operons, allowing the processing of polycistronic RNAs into individual mRNAs. Most of our understanding of spliced leader trans-splicing as it relates to operon gene expression comes from studies in C. elegans. In this organism, two distinct spliced leader trans-splicing events are recognised: SL1, which is used to replace the 5' ends of pre-mRNAs that have a nascent monomethyl guanosine cap; and SL2, which provides the 5' end to uncapped pre-mRNAs derived from polycistronic RNAs. Limited data on operons and spliced leader trans-splicing in other nematodes suggested that SL2-type trans-splicing is a relatively recent innovation, associated with increased efficiency of polycistronic processing, and confined to only one of the five major nematode clades, Clade V. We have conducted the first transcriptome-wide analysis of spliced leader trans-splicing in a nematode species, Trichinella spiralis, which belongs to a clade distantly related to Clade V. Our work identifies a set of T. spiralis SL2type spliced leaders that are specifically used to process polycistronic RNAs, the first examples of specialised spliced leaders that have been found outside of Clade V. These T. spiralis spliced leader RNAs possess a perfectly conserved stem-loop motif previously shown to be essential for polycistronic RNA processing in C. elegans. We show that this motif is found in specific sets of spliced leader RNAs broadly distributed across the nematode phylum. This work substantially revises our understanding of the evolution of nematode spliced leader trans-splicing, showing that the machinery for SL2 trans-splicing evolved much earlier during nematode evolution than was previously appreciated, and has been conserved throughout the radiation of the nematode phylum.