Coordinated regulation of gene expression by E ... - Jacobs University

INTRODUCTION
can also influence elongation and termination [Lim et al., 2003]. Variations in
promoter’s core sequence combined with a range of negative supercoiling bring in an
opportunity for a very wide transcriptional response.
Promoters respond distinctly to supercoiling changes. The in vitro response of
promoters of fis (encoding chromatin protein FIS) and bla (beta lactamase) genes to
varying supercoiling is shown in Figure 4. The two promoters are quite different in their
architecture. The fis promoter has a non-consensus -35 hexamer sequence and a GC rich
discriminator which makes it more strictly dependent on supercoiling. Even promoters
that are quite similar, for example, ‘stringent’ promoters of fis and tyrT (tyrosyl tRNA)
genes deviate in their response to supercoiling. The core promoter sequences of tyrT
also comprise a non-consensus -35 hexamer and a GC rich discriminator, but the
distinction is due to the requirement of UP element and the upstream activating
sequence (UAS) in the case of tyrT promoter [Auner et al., 2003]. The activating
protein binding at the UAS (FIS in the case of tyrT) essentially wraps the DNA around
itself to buffer the promoter against any variations in the global superhelical density
[Maurer et al., 2006]. This superhelical density that is fostered at the local promoter
region through binding of protein is described as ‘effective supercoiling’ [Travers,
2005b], which is a local parameter that is recognized by the polymerase. Effective
supercoiling can be considerably different from the ‘global supercoiling’ prevailing at a
particular instant.
Figure 4: In vitro transcription from fis & bla promoters at different superhelical densities
[Modified with permission from Schneider, 2000].
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