## 4 Role of DNA Topology and Homeostatic Regulation of Supercoiling Response  
Compositional variation in the transcription machinery during the _E. coli_ growth cycle is paralleled by variation of spatial distribution of RNAP in the nucleoid, likely determined by the changes of NAP composition, DNA topology and overall nucleoid configuration [61; 62]. Notably, while the direct communications of metabolic enzymes with RNAP could relate the extant state of particular physiological function(s) to transcription machinery, the topoisomerases relay the cellular energy charge to the global supercoiling level of chromosomal DNA [18; 19; 55] and also, facilitate the translocation of RNAP along the DNA template by relieving the supercoiling imbalance resultant from the [PERSON]/Wang twin supercoil domain effect, manifest in accumulation of positive and negative supercoils respectively ahead and behind of the translocating RNAP [63; 64]. Furthermore and perhaps most importantly, the superhelical density of the DNA modulates the promoter recognition and transcription initiation by RNAP holoenzyme [1]. Binding of RNAP at the strong stable RNA promoters lead to constraint of writhed microloops storing torque, which subsequently can be utilized for promoter opening via topological writhe to twist transition [65; 66]. The RNAP holoenzyme and DNA topology thus act conjointly as major analog factors harnessing and channeling the torque for facilitated promoter opening and transcription initiation [38]. Dynamic changes in DNA supercoiling and NAP composition in vivo determine both how DNA is packaged and how it is accessed for transcription initiation and other DNA transactions [65]. At the same time, changes in DNA superhelical density concertedly alter the expression of the networked genes of NAPs, RNAP sigma initiation factors, transcription elongation and termination factors and RNAP secondary channel modulators [3]. Accordingly, gene expression analyses of the wild type _E. coli_ cells and its mutant derivatives lacking the NAPs (either FIS or H-NS, or both) grown under conditions of nonfloxacin-induced hypernegative DNA supercoiling (\(-\sigma\)-0.09) and DNA relaxation (\(-\sigma\)-0.03) reveal specific patterns of up-regulated genes (Table 1), consistent with the homeostatic network regulating DNA supercoiling [67; 55; 68]. DNA hypernegative superhelicity induced by the addition of the TopoIV and gyrase inhibitor norfloxacin to the _E. coli_ LZ54 WT strain (and its derivatives lacking the NAPs) encoding nonfloxacin-resistant gyrase (i.e., TopoIV is inhibited, whereas gyrase is not), activates the _yrdD_ and _parC/parE_ genes encoding DNA relaxing topoisomerase. Interestingly, under the same conditions activation of the _crl_ gene, the product of which facilitates the assembly of RNAPoS halogenzyme, is observed [69; 70; 71]. In addition, the _rpoZ_ gene, encoding the RNAP \(\omega\) subunit, which stabilises the \(\sigma^{70}\) holoenzyme assembly [72], as well as the _rpoE_, _musG_ and _rho_ genes respectively encoding RpoE initiation, NusG elongation and Rho termination factors, are up-regulated. Transcription elongation factor NusG enhances the elongation rate [73] and links transcription to translation [74; 75] by forming a bridge with ribosomal protein S10 (aka NusE). NusG thus stabilizes the RNAP-ribosome interaction in the expressosome complex, albeit dependent on the length of the mRNA spacer between the RNAP and the P site of the ribosome active-center [76]. However, the RNAP-ribosome contact likely precedes the association of NusG with the complex, suggesting that recruitment of NusG depends on translation [77]. The termination factor Rho can resolve clashes between transcription and replication machineries [78], is crucial for maintaining the transcriptional boundaries in the genome and, being supported by NusG and NusA, exerts a silencing effect on transcription of AT-rich DNA [79] which may undergo undesirable spontaneous unwinding under conditions of high negative superhelicity.