Trans-splicing enhances translational efficiency in C. elegans

Abstract

Translational efficiency is subject to extensive regulation. However, the factors influencing such regulation are poorly understood. In , 62% of genes arespliced to a specific spliced leader (SL1), which replaces part of the native 5' untranslated region (5' UTR). Given the pivotal role the 5' UTR plays in the regulation of translational efficiency, we hypothesized that SL1 splicing functions to regulate translational efficiency. With genome-wide analysis on Ribo-seq data, polysome profiling experiments, and CRISPR-Cas9-based genetic manipulation ofsplicing sites, we found four lines of evidence in support of this hypothesis. First, SL1 spliced genes have higher translational efficiencies than non-spliced genes. Second, SL1 spliced genes have higher translational efficiencies than non-spliced orthologous genes in other nematode species. Third, an SL1 spliced isoform has higher translational efficiency than the non-spliced isoform of the same gene. Fourth, deletion of -splicing sites of endogenous genes leads to reduced translational efficiency. Importantly, we demonstrated that SL1splicing plays a key role in enhancing translational efficiencies of essential genes. We further discovered that SL1 splicing likely enhances translational efficiency by shortening the native 5' UTRs, hence reducing the presence of upstream start codons (uAUG) and weakening mRNA secondary structures. Taken together, our study elucidates the global function ofsplicing in enhancing translational efficiency in nematodes, paving the way for further understanding the genomic mechanisms of translational regulation.

Dietary restriction induces post-transcriptional regulation of longevity genes

“…SL sequences in nematodes bear trimethylguanosine caps (m 2,2,7 G; Liou and Blumenthal 1990), in contrast to native 5' UTRs, which contain a monomethylguanosine (m 7 G) cap (Sonenberg, 2000). Under well fed conditions, we found that trans-spliced mRNA was translated better than mRNA with the native 5' UTR, supporting previous analysis (Yang et al, 2017). While this pattern was maintained under DR, it was modestly but significantly attenuated for SL1 spliced genes ( Figure 3B).…”

“…Using annotations of SL1 and SL2 spliced genes from Allen et al (2011), we calculated the average fold change in translational regulation of genes with trans-spliced or native 5' UTRs. Under AL, our analysis confirmed that both SL1 and SL2 trans-spliced messages tend to be better translated than transcripts with native 5' UTRs ( Figure 3B), as previously reported (Yang et al, 2017). DR led to translational suppression of SL1 spliced genes compared to AL conditions (p=1.4e-7, Wilcoxon rank sum test with continuity correction).…”

Heterodera glycines utilizes promiscuous spliced leaders and demonstrates a unique preference for a species-specific spliced leader over C. elegans SL1

“…However, operon resolution is not the sole function of SLTS in C. elegans , as only 17% of C. elegans transcripts originate from operons 15,18 . It has been hypothesized that SLTS is involved in many translational regulation mechanisms, including the replacement of deleterious sequences in the 5′-untranslated region, addition of translational motifs from within the SL sequence, or by replacing a transcript’s 5′-monomethylated cap with a 5′-hypermodified cap structure 18–24 .…”

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

“…The first to be discovered, SL1, is acquired by mRNAs through a trans-splicing reaction that removes the 5' UTR, also known as the 'outron', of capped pre-mRNAs derived from monocistronic genes and the first genes in operons. SL1 trans-splicing serves to sanitise the 5' ends of mRNAs, and thus impacts their translational efficiency (Yang et al 2017). The other spliced leader type, SL2, is added to mRNAs encoded by downstream operonic genes, which are otherwise uncapped and thus cannot be translated without SL2 trans-splicing (Spieth et al 1993).…”