## 10 NAPs versus Global TFs? Whereas expression of the NAP genes positively correlates with, and most likely defines, the temporal patterns of NAP/RpoD but not that of NAP/RpoS couplons, the expression patterns of the latter appear defined primarily by that of _rpoS_ gene. Among the studied NAPs, only IHF does not conform to this rule--there is no such sigma factor-dependent difference of IHF impact (compare Figures 7B and 8A) and in that sense, IHF shows similarity to the global TFs, CRP and Fnr. This difference between IHF and the other NAPs is interesting and merits some elaboration. It is noteworthy that except IHF, all the NAPs examined here affect the global DNA topology by constraining DNA supercoils and stabilizing higher-order nucleoprotein structures, while IHF is apparently incapable of oligomerization. On binding DNA, IHF stabilizes planar bends rather than writhed coils [115] and affects local DNA trajectory, rather than global DNA topology [112; 116]. The sequence-specificity of IHF binding is almost entirely determined by structural features of the DNA and not by direct readout of the base sequence [117], yet similar to the global TFs, IHF recognizes a relatively well-defined sequence motif [118] introducing sharp bends (U-turns) in the DNA. Stabilization of such tightly bent structures could explain, why IHF in contrast to other NAPs, is primarily affecting the directionality (leading/lagging strand bias) of genomic transcription with associated transcription-coupled supercoil diffusion [112]. Put another way, IHF exerts its primary effect at that level of genomic organization (mutual orientation of transcription units), for which the promoter sigma factor specificity is, most probably, immaterial. Figure 11: Modulation of the expression of NAP genes affects the temporal patterns of corresponding regulons and couplons. (**A**). Expression patterns of _lrp_ gene Lrp regulon and Lrp couplons in wild type (wt) cells (color-code indicated in the inset). Numbers in round brackets indicate the number of genes involved in the respective regulon or couplon. The different curves were normalized to [0;1] to compare them in one plot. The envelopes of the curves indicate the standard deviation at 10% random remapping of the expression patterns to genes. (**B**). The same as in (**A**) but in the _fs_ mutant cells. (**C**). Expression patterns of _lns_ gene, H-NS regulon and H-NS couplons in wild type cells. (**D**). The same as in (**C**) but in the _fs_ mutant cells. Note that mutation of _fs_ gene alters the expression pattern of _lrp_ and _lns_ genes (grey dashed lines) as well as the patterns of Lrp and H-NS couplons (data from [29]). The experimental procedure was as described in the legend to Figure 6.  
The global TFs, CRP and Fnr, are structurally closely related sequence-specific DNA binding proteins [119] not known to constrain supercoils or form long-range nucleoprotein structures characteristic of NAPs, although DNA bending by CRP may assist in wrapping of DNA by RNAP--a characteristic associated with \(\sigma^{70}\) holoenzyme [66; 120; 121; 122]. The debated difference between the NAPs and other global TFs [123] may lie by and large, in the prominent capacity of the former to constrain supercoils and stabilize long-range nucleoprotein structures, that is to say, in prevalence of analog over the digital mode of transcriptional control [5]. Notably, specific CRP binding activity strictly depends on cAMP levels [124], whereas Fnr utilizes iron-sulfur clusters as cofactors and is activated strictly under conditions of anaerbiosis [125]. It is conceivable that this strict dependence of specific binding effects of CRP and Fnr on physiological conditions would require tight coupling with ASFs in coordinating functional responses to physiological stress. Interestingly, among the analyzed regulators, the _rpoH_ and _rpoE_ gene expression show no correlation with the expression patterns of corresponding regulons (Figure 9).