Spliceosome twin introns in fungal nuclear transcripts

Abstract

The spliceosome is an RNA/protein complex, responsible for intron excision from eukaryotic nuclear transcripts. In bacteria, mitochondria and plastids, intron excision does not involve the spliceosome, but occurs through mechanisms dependent on intron RNA secondary and tertiary structure. For group II/III chloroplast introns, "twintrons" (introns within introns) have been described. The excision of the external intron, and thus proper RNA maturation, necessitates prior removal of the internal intron, which interrupts crucial sequences of the former. We have here predicted analogous instances of spliceosomal twintrons ("stwintrons") in filamentous fungi. In two specific cases, where the internal intron interrupts the donor of the external intron after the first or after the second nucleotide, respectively, we show that intermediates with the sequence predicted by the "stwintron" hypothesis, are produced in the splicing process. This implies that two successive rounds of RNA scanning by the spliceosome are necessary to produce the mature mRNA. The phylogenetic distributions of the stwintrons we have identified suggest that they derive from "late" events, subsequent to the appearance of the host intron. They may well not be limited to fungal nuclear transcripts, and their generation and eventual disappearance in the evolutionary process are relevant to hypotheses of intron origin and alternative splicing.

Complex intron generation in the yeast genus Lipomyces

“…To excise these [D7,8] CIS, two standard splicing reactions are necessary. This intron nesting does not constitute a [D] stwintron in sensu stricto as previously defined 7 , since the internal intron does not interrupt the donor element of the external intron; the two canonical donor elements are actually one nt apart from each other. In the primary transcript of the gene for the reticulon-like protein in L. suomiensis, the primary selected 5'-and 3'-splice sites are clearly those that define the smallest possible internal intron (intron definition).…”

“…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).…”

From lignocellulosic metagenomes to lignocellulolytic genes: trends, challenges and future prospects

“…Divergences in codon usage, promoter regulation/activation and RNA processing/translation inherently limit the effective functional expression of eukaryotic genes in prokaryotic systems. In addition, essential post‐translational modifications such as glycosylation of eukaryotic cellulases and xylanases to facilitate secretion is deficient in prokaryotic hosts . It is therefore not surprising perhaps that if one analyzes lignocellulolytic enzymes characterized to date from mDNA, the vast majority belong to prokaryotic proteins …”

Convergent evolution of twintron-like configurations: One is never enough

“…[2][3][4][5][6][7] Later other twintron variations were noted such as group I introns within group I introns, 8,9 group II introns within group I introns, 9 lariat capping twin ribozyme introns, 10 tRNA introns within tRNA introns 11 and various combinations of spliceosomal introns embedded within spliceosomal introns. [12][13][14][15][16] In addition there are composite intron arrangements such as spliceosomal type introns inserted within a group I introns. 8 With regards to twintrons composed of group I and group II introns (i.e.…”

“…13 An internal intron disrupts the splice donor sequence of the external intron and therefore has to be removed in order to allow for the reconstitution of a functional splicing sequence in order to permit the external intron to be spliced out (Fig. 2D).…”