7.3 Splicing in east 135present in the exon definition complex, interacting with the U2 snRNP by base
pairing between the U2 and U6 snRNAs [24]. Such complexes can then be
directly converted to precatalytic B-like complexes, without prior formation of
the cross-intron A complex [24].
Splicing mainly occurs co-transcriptional (see Section 7.5.4) with a 5′ to 3′
directionality. Exceptions to this rule include introns flanking alternatively
spliced exons with the excision being delayed or even happening posttranscrip-
tionally [25, 26].
7.3 Splicing in Yeast
7.3.1 Organization and Distribution of Yeast Introns
From an evolutionary perspective, yeasts are a highly diverse group of single-
celled microorganisms within the kingdom of fungi. The budding yeast (also
“true yeast”), including the well-known Saccharomyces cerevisiae, belongs to the
phylum Ascomycota. Other yeasts, like the fission yeast Schizosaccharomyces
pombe, belong to the phylum Basidiomycota. Both S. cerevisiae and S. pombe are
eukaryotic model organisms.
The genome of S. pombe was sequenced in 2002 [27]. It contains ~4800 genes
with ~43% of the genes containing up to 15 introns. The average intron size is 81
nucleotides. With regard to splicing factors and 3′ splice site selection, splicing in
S. pombe is considered to be more similar mechanistically to mammals than in
S. cerevisiae [28, 29]. We will still focus exclusively on budding yeast in the
following sections, as S. cerevisiae is the more widely studied eukaryotic model
organism.
In contrast to mammals (and fission yeast), very few genes in budding yeast
code for introns. Only 5% of the ~5800 genes contain introns [30]. In addition,
most genes contain only one intronic sequence; a mere 10 genes code for 2
introns. Why does S. cerevisiae have such an intron-poor genome? In general,
unicellular eukaryotes seem to be under pressure to loose introns. A correlation
exists between the intron density of a genome and the logarithm of the genera-
tion time of an organism: organisms with a short generation time tend to have
fewer introns when compared with more slowly growing organisms [31]. This
observation could be explained by selection for smaller genomes and for faster
protein production, for example, in response to stress conditions.
Intron boundaries in S. cerevisiae are well defined, with a 6 bp sequence at
the 5′ splice site and a 7 bp sequence at the branch site required for efficient
splicing (see Figure 7.1) [32–34]. The average distance between the branch
point and 3′ splice site is 30 nucleotides and this region also contains a poly(U)
tract (see Figure 7.1) [30, 35]. Introns tend to be short, with an average length
of 154 nucleotides in non-ribosomal and 408 nucleotides in ribosomal
proteins.
Introns are not equally distributed in the S. cerevisiae genome, but are highly
enriched in ribosomal proteins. Eighty nine of the 137 ribosomal proteins (>60%)
code for at least one intron, whereas only 198 of the remaining genes (<1%)