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

INTRODUCTION
[Rimsky et al., 2001]. At similar superhelical density HU and H-NS can exert opposite
effect on the transcription. HU binds and bends DNA resulting in a decrease in pitch
angle (the angle between two adjacent major grooves), while H-NS binding leads to an
increase in pitch angle. Replacing HU by H-NS on a plectonemic DNA would lead to
over twisting of the DNA rendering it less transcriptionally active [Travers &
Muskhelishvili, 2007].
The transcription of stable RNA genes is one of the determining elements of
growth rate. The promoters of tyrT and rrnA P1 (exemplary stable RNA promoters) are
an excellent model systems to fathom the intricacies of the interactions among the
global regulators on a miniaturized location. The unique promoter architecture
involving a GC rich discriminator confers ‘stringent response’ and ‘growth-rate control’
[Travers, 1980] imposing a need for negative superhelicity for promoter activity
[Pemberton et al., 2000]. During stringent response, a result of amino acid starvation,
the regulatory nucleotide ppGpp accumulates and inhibits the synthesis of rRNA
operons by blocking the RNAP at the initiation step. Growth-rate control is essentially a
phenomenon of balanced exponential growth controlled by a combination of promoter
elements (a suboptimal spacer region and -35 hexamer sequences) and a need for UAS
bound by activator protein, FIS. Binding of H-NS counteracts activation by FIS
[Tippner et al., 1994]. Thus it appears that the NAPs on binding DNA exert both global
and local effects. It was of interest therefore to investigate, whether the growth phasedependent
patterns of transcription are associated with NAP-dependent changes in
distributions of effective superhelicity.
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