Intron sliding or intron gain ?

The exon/intron organisation of homologous nuclear genes was compared in several yeast species. CLUSTALX multiple alignments were performed to verify the degree of conservation of the homologues and to reconstruct a virtual (scaffold) gene, exhibiting the probable ancestral intron arrangement. Intron position was defined at the nucleotide level making it possible to determine whether the intron is at an identical position (same codon and same phase) or not in the homologues.

In the cases herein illustrated, some intron positions were found divergent in homologues sharing a high degree of sequence conservation, suggesting that these positions may result either from intron sliding or intron gain events [Bon et al., 2003].

Intron sliding is defined as the relocation of a pre-existing intron over short distances in the course of gene evolution [Rogozin et al., 2000, Trends Genet., 16, 430-432]. Although it is now admitted that intron sliding by one or two bases is a real phenomenon, it remains relatively rare and probably occurs in less than 5% of all introns [Stoltzfus et al., 1997, Proc. Natl. Acad. Sci. USA, 94, 10739-10744; Rogozin et al., 2000; Boudet et al., 2001, Genome Res., 11, 2101-2114].

This implies that most of these discordant intron positions should be attributed to independent intron insertion events rather than intron sliding events [Bon et al., 2003].

Intron sliding or hot spot of intron insertions?

Divergent intron positions or alignment artefacts ?

The YFL037w / TUB2 case

The YFL037w scaffold gene contains 6 introns of which i2 position is absent in the S. pombe YFL037w gene, but present in C. albicans and P. sorbitophila.

Different scenario were proposed to explain the absence of this intron position in S. pombe:

  1. One possibility is that i2 may have been lost in S. pombe unlike i1, i3, i4, i5 and i6 positions. A short distance separates i2 and i3 positions (Δ = 14 nt) and both are located within a very highly conserved region. This would imply the existence of very accurate and reliable mechanism, distinct from the Fink system previously cited, capable of spotting an intron in the ORF sequence, and of removing it without introducing frame reading errors.
  2. An other one is that i2 position would result from an intron gain in the common ancestor of C. albicans and P. sorbitophila, just after the divergence from S. pombe.
  3. The last one is that i3 position may result from the sliding of i2 to a novel position, 14 nt upstream.

SC: S. cerevisiae; CA: C. albicans; PA: P. angusta and SP: S. pombe.

Last modified: Tue Feb 10 11:12:28 CET 2004