<em>Trans</em>-splicing enhances translational efficiency in <em>C. elegans</em>

Abstract

Although proteins are the major macromolecules performing cellular activities, their relative concentrations are largely unknown (Tyers and Mann 2003; Altelaar et al. 2013). Instead, mRNA concentrations are often used as a proxy for protein concentrations in genome-wide studies. This assumes negligible variation of translational efficiencies among genes. With quantitative proteomic data becoming more widely available (Bantscheff et al. 2012; Bensimon et al. 2012), it was surprisingly found that protein and mRNA concentrations are only moderately correlated. For example, only 32% of the variance in protein concentrations in the budding yeast Saccharomyces cerevisiae could be explained by mRNA concentration (Ghaemmaghami et al. 2003). Similar phenomena were observed in mice (Schwanhausser et al. 2011) and humans (Wilhelm et al. 2014), in which the proportion of explained variance varied from 0.10 to 0.41 across different tissues. In prokaryotes, where operons are pervasive in the genome, the disparity between mRNA and protein concentrations can become extreme. This is because genes in an operon are transcribed together, yet different protein concentrations may be required to maintain the stoichiometric relationship in protein complexes. Indeed, it was discovered that in Escherichia coli, the protein concentration variation in an operon cannot be explained by mRNA concentration (Quax et al. 2013; Li et al. 2014), implying regulation at the level of translation. Furthermore, mRNA concentration differences between haploid and diploid yeast are not an accurate predictor of the differences at the protein level (de Godoy et al. 2008), suggesting the presence of post-transcriptional regulation. Finally, the expression divergence among species is usually smaller at the protein level than that at the mRNA level (Khan et al. 2013), which also suggests the existence of extensive translational regulation (Artieri and Fraser 2014b; McManus et al. 2014).

The process of translation is comprised of three steps: initiation, elongation, and termination (Scheper et al. 2007). Initiation is generally considered the rate-determining step in endogenous genes (Andersson and Kurland 1990; Bulmer 1991; Plotkin and Kudla 2011; Shah et al. 2013; Chu et al. 2014). The 5′ UTR and the 5′ terminus of coding sequences have both been reported to be the main targets for translational regulation (Hall et al. 1982; de Smit and van Duin 1990; Babendure et al. 2006; Kudla et al. 2009; Dvir et al. 2013). Consistently, sequence motifs involved in translational regulation have been identified in the 5′ UTR. Examples include the Kozak sequence (Kozak 1987; Dvir et al. 2013)—the consensus sequence around the start codon AUG—and upstream open reading frame (uORF) (Ingolia et al. 2009; Dvir et al. 2013).

Trans-splicing edits 5′ UTR sequences in nematodes, trypanosomes, dinoflagellates, flatworms, and hydra, among many other species (Blumenthal 2004; Lasda and Blumenthal 2011), and thus may be involved in the regulation of translational efficiency. In Caenorhabditis elegans, the majority of genes are spliced leader (SL) trans-spliced (Blumenthal 2005; Allen et al. 2011). In this process, an SL RNA trims the 5′ UTR of pre-mRNA and then attaches a short (∼22 nucleotide [nt]) sequence to the 5′ terminus (Krause and Hirsh 1987; Hastings 2005). After SL trans-splicing, ∼49% of transcripts retain less than 10 nt of the 5′ UTR sequence of the pre-mRNAs (Lall et al. 2004). SL trans-splicing can be classified into two types based on the sequence of the spliced leader: SL1 and SL2, affecting 62% and 12% of genes, respectively (Allen et al. 2011). SL2 trans-splicing is related to eukaryotic operons. In C. elegans, more than 17% of genes are localized in operons, where they are transcribed into a single nonfunctional polycistronic pre-mRNA (Blumenthal et al. 2002; Blumenthal and Gleason 2003; Blumenthal 2004; Allen et al. 2011; Saito et al. 2013). SL2 trans-splicing is used by downstream genes in operons to generate functional monocistronic mRNAs from the pre-mRNA (Spieth et al. 1993; Zorio et al. 1994; Blumenthal et al. 2002). In contrast, SL1 trans-splicing is used by the first genes in operons and genes that are not in operons. Although SL1 trans-splicing is more prevalent, the function of it is not yet fully understood (Blumenthal 2005). Since SL1 trans-splicing modifies the 5′ UTRs of genes, we hypothesized that it functions to regulate translational efficiency (number of proteins made per mRNA per unit time).

Acknowledgments

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