Aliens — as we know them

Cis-spliced acceptors can be converted to trans-splicing acceptors if the donor site upstream is mutated, and similarly an SL addition site will be cis-spliced if a donor site is inserted upstream. What is the function of SL trans-splicing? SL addition provides the cell with an alternative way of capping mRNAs, a modification required for mRNA stability, transport and translation. The standard capping machinery is typically recruited by RNA polymerase II at the beginning of transcription to cap the growing RNA. In trypanosomes, SL addition is used to cap a subset of pre-mRNAs transcribed by RNA polymerase I, which does not recruit the capping machinery. In a wider range of eukaryotes, SL addition allows the formation of operons — adjacent genes that are transcribed as a single primary transcript. The cleavage reaction that precedes polyadenylation of each gene effectively chops the transcript into smaller pieces. Since only the message from the 5′ end retains the transcript's original cap, SL trans-splicing is needed to cap the remaining fragments. Addition of an SL has also been shown to affect the translation rate of some genes, add missing start codons and trim off outron sequences. But while the role of SL addition in these processes is well established, the benefit of transcription by polymerase I, inclusion in an operon, translational regulation, substitution of a start codon and outron removal is not immediately obvious for most trans-spliced genes. How is it phylogenetically distributed? The complete phylogenetic distribution of SL trans-splicing is not currently known. To date, SL trans-splicing has been found in six diverse groups of eukaryotes: nematodes, flatworms, cnidarians, ascidians, rotifers and euglenozoans. But it has not been detected in other well-studied eukaryotic taxa, such as fungi, plants, vertebrates and arthropods. How did it evolve? There are two competing hypotheses describing the origin of SL trans-splicing. The 'SL trans-splicing early' hypothesis proposes that SL trans-splicing was present in the ancestral eukaryote and subsequently lost in most phyla. This hypothesis is supported in part by the continuing discovery of SL trans-splicing in an expanding range of eukaryotes. The 'SL trans-splicing late' hypothesis proposes that the process has emerged several times independently, and that features unique to SL addition — the SL RNA, trans-spliceosome-specific proteins, SL-specific translation enhancer proteins, operons, and so on — are also independently derived in these lineages. This hypothesis is supported by the observation that the few unique components shown to be …