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

RESULTS
furthermore the colour of the line shows the mode of regulation (activated / repressed
and sensitive to hypernegative / relaxed DNA conditions) of the particular gene. A line
coloured by two colours is a gene (will be referred to as ‘double coded’) which was
associated with more than one regulatory condition (for example, a gene repressed at
hypernegative supercoiling can be seen as line coloured yellow and blue).
The genomic wheel representation allows visualization of growth phase
dependent transcription of genes together with corresponding supercoiling sensitivity.
Figure 13 A and B, show respectively the effect of fis and hns on the spatiotemporal
organization of transcription throughout the growth cycle (compare the outer circle to
inner circle for differences between wild-type & mutant during each growth phase). The
fis mutation most clearly affects the distribution of transcripts in the domains of the
origin and terminus of replication during the exponential and stationary phases. Effect
of hns as a global repressor is evident from the high proportion of repressed genes
throughout the growth (see below). Both FIS & H-NS are proteins most abundant
during early exponential growth [Ali Azam et al., 1999]. Afterwards the FIS
concentration drops sharply, whereas H-NS is present at relatively high levels
throughout the growth cycle. From the genomic wheels it can be seen that strong effects
of FIS and H-NS on transcription are observed even in stationary phase. It is important
to note that FIS is capable of exerting an effect on transcription either by direct binding
to the promoters or by modulating the global topology of DNA. The latter effect could
be the basis for regulation by FIS during the later stages of growth. About 50% of the fis
and hns regulated genes were found to be sensitive to supercoiling (see below),
suggesting a central role of supercoiling in organizing the growth phase dependent
transcription. The observed changing genomic patterns of supercoiling sensitivity (seen
as cluster of blue [Hyp] or red [Rel]coloured lines) agree with the previous findings of
fluid short range [Postow et al., 2004; Stein et al., 2005] and long range domains of
transcription [Jeong et al., 2004].
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