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

INTRODUCTION
formed as a repercussion of active transcription from highly transcribed gene by
removing any previously established DNA attachments would generate barriers near the
transcription terminus [Deng et al., 2005]. Barrier formation is also altered by abnormal
activities of gyrase and topoisomerase IV enzymes [Staczek & Higgins, 1998].
Scattered binding sites for NAPs in the genome may also act as regions where proteins
bind to prevent the diffusion of supercoiling.
DNA supercoiling itself might act as a principal coordinator of global gene
expression [Balke & Gralla, 1987; Dorman, 1996; Tse-Dinh et al., 1997; Cheung et al.,
2003; Travers & Muskhelishvili, 2005b]. Recent enumeration of number of supercoiling
sensitive genes in the E.coli genome found only 8% of the total genes to be associated
with supercoiling [Peter et al., 2004]. However the observed role of supercoiling in
many distinct processes such as sigma factor recognition, transcription termination,
sensing of stress and nutritional status appeal to a much wider influence of supercoiling.
Furthermore, recent study of the experimental evolution of E.coli populations identified
supercoiling as a key target for evolution and mutations in topA & fis genes were found
to conferred increased fitness [Crozat et al., 2005].
The supercoiling transitions during growth are tightly coupled to the changing
NAP composition and abundance. During early exponential phase the nucleoid is
composed of FIS, HUα2 and H-NS proteins, to be succeeded by HUαβ and H-NS in the
transition between exponential and stationary phase, and finally by IHF and Dps in late
stationary phase. Among these FIS, HU, HNS constrain different amounts of
supercoiling [Travers & Muskhelishvili, 2005a], resulting in a change of plasmid DNA
supercoiling when the constraining proteins are eliminated [Schneider et al., 1997;
Berger M et al., unpublished; Blot et al., 2006]. FIS binds to the DNA as a dimer and
can bend DNA by 50-90 o [Pan et al., 1996]. Low amount of FIS binding has a distinct
effect on the architecture of DNA compared to multiple FIS binding. Low amounts of
FIS lead to the formation of branches on the supercoiled DNA, while binding in large
amounts it compacts the DNA [Schneider et al., 2001]. HU present in comparable
amounts to FIS binds non-specifically to supercoiled DNA and to structurally distorted
DNA [Pontiggia et al., 1993]. H-NS present in 20,000 copies binds patches of DNA
with a preference for A/T rich tracts and functions as a general repressor of transcription
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