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

INTRODUCTION
Figure 6: Graphical representation of global DNA topology changing with growth.
The dotted line traces the typical growth curve of E.coli in batch culture. Electron microscopy pictures of
plasmids with different supercoiling are shown. ME, TS and LS stands for phases of growth - mid
exponential, transition to stationary and late stationary phase respectively.
1.2.5 The nucleoid associated proteins – major players in global
gene expression regulation
Histones are the predominant structural proteins of the eukaryotic chromatin, while in
E.coli there are a dozen so-called “histone-like” proteins involved in spatial
organization of the nucleoid. About half of them are considered to be important in
shaping the nucleoid based on their abundance. The difference between the core group
of NAPs and the other proteins that bind to DNA is in the lack of clear consensus
binding sequence for the NAPs. Some of the NAPs do have a reasonable consensus
binding sequence, while binding of the others is dependent on inexplicit sequence
organization combined with topological parameter, like bent/curved DNA. In addition
to providing spatial organization of the nucleoid, NAPs also contribute to DNA
transactions such as replication, recombination and transcription.
The regulatory roles of nucleoid proteins in DNA functions thus include
modulation of the genome conformation as a whole but also more direct effect on the
local conformation of specific DNA regions or even direct interaction with other protein
components. For instance, the three FIS dimers binding at the tyrT promoter, may act as
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