## 5 Interdependence of the Network Elements
The cultures were grown in a fermenter under constant pH 7.4 and high aeration (5 L air per min) at 37 \({}^{\circ}\)C. The cells were harvested during exponential phase at O.D\({}_{600}\) of 0.5 (early), at O.D\({}_{600}\) of 2.0 during transition to stationary phase (mid) and at O.D\({}_{600}\) of 4.0 in stationary phase (late). The relative NAP amounts in the “stringent” RNAP mutants were normalized to those in the wild type cells. NAP proteins were detected using mouse monoclonal antibodies raised against FIS, H-NS, IHF and Dps. Bars indicate the standard errors of two biological replicates (for experimental details, see the appended Master Thesis of [PERSON] [PERSON] in the Supplementary data file). Importantly, the increase of the RNAP \(\sigma^{S}/\sigma^{70}\) ratio in _rpoZ_ cells where DNA is relaxed, coordinately changes both the global DNA topology and the average thermodynamic stability (GC-content) of the transcribed sequences, indicating that under conditions of DNA relaxation, sequences with lower GC-content are utilized preferentially (Figure 4A,B). This finding is in keeping with previous observations [13]. Corresponding decrease in GC-content of transcribed sequences is observed on transition of cells from exponential growth to stationary phase (Figure 4C,D), characterized by transition from the predominance of RNAP\(\sigma^{70}\) holoenzyme to that of RNAP\(\sigma^{S}\) and from high to low levels of global negative superhelicity, respectively [98]. It is noteworthy, that the more and the less GC-rich sequences are respectively enriched around the origin (OriC) and terminus (Ter) of chromosomal replication, such that ultimately, the genomic sequence organization underpins the sequential transcription of chromosomal ends [30]. Taken together, all these observations support the notion of structural coupling between DNA topology, NAP-dependent chromatin architecture and the transcription machinery composition as a fundamental device coordinating the spatiotemporal genomic transcription [38; 39; 3]. Understanding of this coordinating effect can be facilitated by analyses of the joint impacts of the NAPs and transcription machinery components on genomic transcription. \begin{table}
\begin{tabular}{c c c c c} \hline
**Strain,** & **CF1943 Wild** & **CF2790 _rpoZ_ & **CF2790 _rpoZ_ +** & **CF2790 _rpoZ_ +** & **CF2790 _rpoZ_ \\
**Condition** & **Type** & & & _rpoD_ * & \\ \hline Impacts of NAPs \& global TFs & FIS, IHF & CRP & IHF, CRP, Fnr & H-NS, FIS, Lrp \\ \hline Impacts of \& RNAP sigma subunits & RpoD & RpoS & RpoD & RpoS \\ \hline Regulons up & & RpoS & CRP, Fnr & RpoS \\ \hline Couplons up & H-NS/RpoS & & CRP/RpoD & CRP/RpoS \\  & & Fnr/RpoD & & Lrp/RpoS \\  & & & IHF/RpoS \\  & & & Fnr/RpoS \\ \hline \end{tabular}  
* CF2790 _rpoZ_ mutant strain grown with episomal _rpoD_ overexpression.  
\end{table} 
Table 2: Impacts of NAPs/global TFs and the RNAP sigma factors in the transcript profiles of growing cells (data from [39]). The first two columns compare the relative impacts in the profiles of wild-type and _rpoZ_ mutants, the next two columns compare those in _rpoZ_ mutant with and without _rpoD_ overexpression.