A spliceosomal twin intron (stwintron) participates in both exon skipping and evolutionary exon loss

Abstract

Spliceosomal twin introns (stwintrons) are introns where any of the three consensus sequences involved in splicing is interrupted by another intron (internal intron). In Aspergillus nidulans , a donor-disrupted stwintron (intron-1) is extant in the transcript encoding a reticulon-like protein. The orthologous transcript of Aspergillus niger can be alternatively spliced; the exon downstream the stwintron could be skipped by excising a sequence that comprises this stwintron, the neighbouring intron-2, and the exon bounded by these. This process involves the use of alternative 3′ splice sites for the internal intron, the resulting alternative intervening sequence being a longer 3′-extended stwintron. In 29 species of Onygenales , a multi-step splicing process occurs in the orthologous transcript, in which a complex intervening sequence including the stwintron and neigbouring intron-2, generates by three splicing reactions a “second order intron” which must then be excised with a fourth splicing event. The gene model in two species can be envisaged as one canonical intron (intron-1) evolved from this complex intervening sequence of nested canonical introns found elsewhere in Onygenales . Postulated splicing intermediates were experimentally verified in one or more species. This work illustrates a role of stwintrons in both alternative splicing and the evolution of intron structure.

Complex intron generation in the yeast genus Lipomyces

“…Evolution of the intron-exon structure of the transcript of the genes for a reticulon-like protein in the genus Lipomyces. The conservation of intron positions in multiple species of Taphrinomycotina and in the family of the Lipomycetaceae (Saccharomycotina) is consistent with their reticulon-like genes being genuine orthologues of the one in Aspergillus nidulans (rtnA) and in other Pezizomycotina 11 . Figure 3a shows the monophyletic cluster of the Lipomyces genus (nine species) drawn from an extensive maximum likelihood tree of the reticulon-like protein in all Ascomycota (see Methods section for details).…”

“…Additional homologues were found in the Saccharomycotina and Taphrinomycotina subphyla of the Ascomycota, the Blastocladiomycota, the Glomeromycota, the Mucoromycotina and the Mortierellomycotina (Supplementary Table S1). Although most genome-sequenced ascomycete yeasts have intronless genes for the reticulon-like protein (Rtn), quite some taxa, including species from the Cephaloascaceae, Alloascoideaceae, Pichiaceae and Debaryomycetaceae families, retained one standard intron at the position corresponding to the fifth intron in the orthologous Aspergillus nidulans rtnA gene 11 . This position conservation suggests that the Ascomycota genes are phylogenetically related.…”

“…In fungi, spliceosomal introns are generally quite small -often <100 nucleotide (nt). Nevertheless, one of the fungal stwintrons we have described is crucial to an authentic alternative splicing event 11 .…”

“…Intervening sequences of any of the three main classes -group I, group II and spliceosomal -can be made up of more than one functional intron unit [4][5][6] . Previously, we have described a particular class of nested U2 introns, the stwintron, for which the excision of the internal intron is required to accomplish the subsequent excision of the external intron because the former interrupts one of the three conserved intron splicing elements of the latter, the 5'-donor, the sequence element around the lariat branch point adenosine, or the 3'-acceptor [7][8][9][10][11] (Fig. 1).…”

“…In a previous paper 11 , we identified a [D5,6] stwintron in the gene encoding a reticulon-like protein in the Pezizomycotina, one of the three Ascomycota subphyla. The gene product is a "protein of unknown function which associates with the endoplasmic reticulum" (protein family PF02453).…”