Complex intron generation in the yeast genus Lipomyces

Abstract

In primary transcripts of eukaryotic nuclear genes, coding sequences are often interrupted by U2-type introns. Such intervening sequences can constitute complex introns excised by consecutive splicing reactions. The origin of spliceosomal introns is a vexing problem. Sequence variation existent across fungal taxa provides means to study their structure and evolution. In one class of complex introns called [D] stwintrons, an (internal) U2 intron is nested within the 5'-donor element of another (external) U2 intron. In the gene for a reticulon-like protein in species of the ascomycete yeast genus Lipomyces, the most 5' terminal intron position is occupied by one of three complex intervening sequences consistent of differently nested U2 intron units, as demonstrated in L. lipofer, L. suomiensis, and L. starkeyi. In L. starkeyi, the donor elements of the constituent introns are abutting and the complex intervening sequence can be excised alternatively either with one standard splicing reaction or, as a [D] stwintron, by two consecutive reactions. Our work suggests how [D] stwintrons could emerge by the appearance of new functional splice sites within an extant intron. The stepwise stwintronisation mechanism may involve duplication of the functional intron donor element of the ancestor intron.

Unique and Repeated Stwintrons (Spliceosomal Twin Introns) in the Hypoxylaceae

“…Usually, the internal U2 intron disrupts the continuity of either the consensus 5 -donor [D], branch point (BP) sequence element [L] or 3acceptor [A] of the external U2 intron. In addition, we have described functional stwintrons where the internal U2 intron is integrated into the external intron next to, rather than within, the latter's consensus 5 -donor [20]. In a [D1,2] stwintron (Figure 1b), the internal intron is located in the 5 -donor sequence of the external intron between the first and the second nucleotides (nts) (5 -G 1 |U 2 RWGY) [18,21].…”

Internally Symmetrical Stwintrons and Related Canonical Introns in Hypoxylaceae Species

“…Intervening sequences may include more than one canonical intron unit [ 9 , 10 ]. We have described a class of nested U2 introns in ascomycete fungi, the stwintrons ( s pliceosomal tw in introns ) [ 11 , 12 , 13 , 14 , 15 , 16 ]. Stwintrons are removed from pre-mRNAs by two consecutive standard U2 splicing reactions ( Figure 1 a).…”

“…These characteristics enabled the design of a simple motif search algorithm to predict potential stwintrons in fungal genomes in the absence of high-throughput transcription data [ 13 , 14 , 15 ]. By these means, we illustrated two mechanisms by which fungal (stw)introns are formed: by intronisation of bordering exonic sequences and by the formation of a new intron within an extant intron [ 14 , 15 , 16 ].…”