Viral RNA Trans-Splicing: Chance Event or Product of Evolution?

Abstract

EditorialOne year after the discovery of exons and introns in the adenoviral hexon gene by the teams of Roberts and Sharp [1,2], Walther Gilbert suggested that the employment of different exons of a single gene could lead to the generation of various mRNA isoforms [3], a process that is today known as alternative splicing. Alternative splicing implies a number of distinct mechanisms including exon skipping, intron retention, mutually exclusive exons, alternative splice site selection as well as alternative promoter usage and alternative polyadenylation. Constitutive and alternative splicing isn't mutually exclusive which solves the former problem that for a steady evolutionary process, essential genes don't need to duplicate before one version can mutate to a new gene function. Alternative splicing generates new functions by creating new exons within existing genes and can relax the negative selection pressure against evolutionary changes in functional genes. Thus, alternative splicing might open nearly neutral paths for evolutionary changes.For most viruses, economy in genome size is a common theme. To express a maximum number of proteins, viruses use multiple promoters, translational frame shifting, alternative open reading frames, stop codon read-through; for regulation of gene expression, viruses further use antisense transcription and virus-encoded miRNAs. Alternative splicing represents a key mechanism that is recruited by most DNA viruses, and nuclear replicating RNA viruses to generate the full repertoire of protein functions [4].RNA trans-splicing represents a special form of alternative splicing in which sequences of distinct pre-mRNA transcripts are joined in trans. Thus, like alternative cis-splicing, trans-splicing contributes to the diversification of genotypes and phenotypes. Naturally occurring RNA trans-splicing was first described in 1986 in trypanosomes and one year later also in the nematode Caenorhabditis elegans. In these organisms a species-specific non-coding small RNA with a singular 5' splice donor site, the socalled small leader RNA (SL RNA), is spliced to variable 3' splice acceptor sites on separate pre-mRNA molecules. SL RNA transsplicing differs from regular cis-splicing, as the U1 small nuclear ribonucleoprotein (snRNP) containing the U1 small nuclear (sn) RNA is replaced by the SL snRNP, which carries the SL RNA. SL RNA trans-splicing was also detected in other nematodes, flatworms, and in tunicates, primitive chordates. The hypothesis it might also occur in vertebrates has not been confirmed yet. In the mid-90s first experimental evidence was obtained showing that mammalian cells can combine natural pre-mRNAs to new mRNA via RNA trans-splicing [5,6]. The mammalian RNA transsplicing, however, is independent of SL RNA but instead mediated by the spliceosome of the cell. Computational analyses of cDNAs from a gene databank indicated one percent of all sequenced mRNAs to be chimeric [7], some of which might be synthesized by RNA trans-splicing. Up to date several examples of natural...

Homologous SV40 RNA trans-splicing: Special case or prime example of viral RNA trans-splicing?

“…SV40 trans -splicing was confirmed by the systematic exclusion of alternative mechanisms that might trigger the generation of the observed chimeric RNA, such as direct coding from integrated rearranged SV40 DNA and alternative RNA cis -splicing of a long pre-mRNA transcript that might originate from genomic SV40 tandem integration, using southern hybridization and PCR. The coincidence of various trans -splicing helper functions led us to the conclusion that SV40 RNA trans -splicing is certainly not a chance event but instead a mechanism that is intrinsic to the virus leading to the diversification of viral gene expression [6] .…”