7.7 Splicing egulation y i ossitches 1477.6.3 Function of Splicing in S. cerevisiae
In contrast to the finding that introns seem to be beneficial for high gene expres-
sion, most of them can be deleted without affecting growth in rich medium [219,
220]. Also, multiple deletions of introns in one strain, for example, all 16 introns
within the 15 intron-containing cytoskeleton-related genes, showed no impact
on growth under standard laboratory conditions. Only the deletion of introns in
RNA-binding proteins caused growth defects in rich medium. There, introns
seem to be important for gene expression by the endogenous promoter, as heter-
ologous expression of the genes from an act1 promoter restored cell growth.
Introns also seem to be important for fine-tuning gene expression and growth
under stress conditions. Parenteau et al. systematically deleted the introns of all
ribosomal proteins and investigated their impact on gene expression, rRNA
maturation, and growth under stress conditions [219]. They found that 21% of
the intron deletions inhibited growth in the presence of staurosporine and 37%
affected growth during at least one of five stress conditions tested. Furthermore,
intron deletions did not only alter the expression of the respective gene but also
affected pre-rRNA processing and expression of the paralog in duplicated
genes [219]. This shows that, albeit in most cases, the few remaining introns in
S. cerevisiae are not important for cell survival per se, but they do play a role in
posttranscriptional gene regulation and therefore might not be readily expelled
from the genome in future evolution.
Recently, a novel role for the spliceosome in the regulation of intronless genes
has been discovered [221]. Intronless genes containing consensus 5′ splice sites
and branch point sequences are bound by the spliceosome and spliced (at least
the first step of splicing is performed). The incorrectly spliced pre-mRNA is sub-
sequently degraded, leading to the downregulation of gene expression. The
authors suggest that the expression of ~1% of the intronless genes in S. cerevisiae
is regulated by this so-called spliceosome-mediated decay (SMD) mechanism.
The advancement of novel high-throughput sequencing methods allows for an
unprecedented in-depth analysis of expressed isoform variants. Consequently,
several recent transcriptomic studies discovered novel introns and usage of alter-
native splice sites in S. cerevisiae, significantly expanding the role of splicing in
this “intron-poor” eukaryote [222–224].
7.7 Splicing Regulation by Riboswitches
A decade ago, a novel RNA-based regulatory mechanism was discovered. The
so-called riboswitches are structured RNA elements usually residing in the 5′
UTR of bacterial genes [225]. Riboswitches consist of two domains: an aptamer
domain and an expression platform. These aptamer domain senses the amount
of a small molecule ligand. Its binding leads to a structural rearrangement, which
is translated to the expression platform, subsequently modulating gene expres-
sion. Most bacterial riboswitches regulate gene expression by either transcrip-
tional termination or translational repression. They are found predominantly in
genes related to the metabolic pathways of their cognate ligand.