6.3 Natural Yeast Promoters 113position of these sequences along promoters have a direct effect on nucleosome
occupancy and by consequence on transcription initiation efficiency [45].
Besides sequences stimulating transcription initiation, some yeast promot-
ers also carry upstream elements that inhibit the process. These are called
upstream repression sequences (URSs) and contain TFBSs that bind transcrip-
tion repressors [12]. Some mechanisms of repression are also based on recruit-
ment. Here, the binding of the repressor attracts corepressors to the promoter,
which block transcription initiation by recruiting chromatin remodelers to
make DNA less accessible for PIC assembly or by preventing the transcrip-
tional machinery from starting [46].
6.3 Natural Yeast Promoters
We can distinguish two classes of natural promoters: regulated and constitutive.
A wide selection of these promoters is used today to control gene expression.
Although natural promoters are popular, their use is frequently limited to special
genetic backgrounds and/or growth conditions. Nevertheless, the lessons learned
from nature are essential to create synthetic systems more suitable for biotech-
nology or synthetic biology applications.
6.3.1 Regulated Promoters
The activity of a regulated promoter is, in terms of both timing and intensity,
specifically dependent on a well‐characterized stimulus, for example, chemical
or physical agent. In many cases the stimulus operates a single specific
TFBS. The promoters depending on galactose, inorganic phosphate, or copper
described below are interesting examples.
The most used regulated promoters belong to the GAL genes, involved in
galactose catabolism. The mechanism of their regulation is well characterized
and involves several players (reviewed in [47]). GAL4 is the main regulator of the
GAL circuit and encodes a transcription activator. In the absence of galactose,
the inhibitor Gal80 binds Gal4, preventing its activity. In the presence of galac-
tose, Gal4 is released, as Gal80 is sequestered in the cytoplasm. This triggers the
transcription of the Gal4 targets, which include GAL1, GAL7, and GAL10,
encoding the enzymes of the Leloir pathway, and regulators of the circuit, such
as GAL80, GAL2, and GAL3. The autocatalytic nature of the GAL circuit gives a
switch‐like response to galactose. The interruption of the positive feedback loop
controlling the expression of the galactose permease GAL2 results in a linear
response of GAL genes to increasing amounts of galactose. This allows the induc-
tion of GAL promoters at intermediate levels [48]. Some yeast strains carry an
extensive deletion in the TRP1 locus resulting in the truncation of the adjacent
GAL3 promoter [49]. In this background, induction of the GAL genes is not fast
and efficient, because the levels of Gal3 are low [50].
Galactose induces transcription of GAL1 and GAL10 by more than 1000‐fold
[51, 52]. GAL1 and GAL10 are in close proximity on the genome and diverge in
their orientation [52, 53]. Deletion analysis of the DNA sequence lying between