## 9 Role for Changing Chromosome Configuration in Organizing Genomic Transcription  
The bacterial growth cycle appears as an intrinsically ordered process following a \"programmed\" as it were, passage of the population through successive, physiologically distinct states or \"growth phases\" associated with transitions in nucleoid structure [35; 113; 114; 115]. Notwithstanding the existence of evolutionarily pre-programmed phase transitions in nucleoid structure, this sequential order during the bacterial growth cycle could also be produced by the continuous adjustment of the physiological state to changing growth environments and thus, be largely determined, or better to say, triggered by the latter. What we touch upon here is essentially a \"nature versus nurture\" issue. In this respect, a relevant observation is that environmental factors can be crucial in determining the genetic capacity of _E. coli_ to vary traits qualitatively [116]. However, the question we ask here is how the environmental change is translated into physiological alteration and, first and foremost, into an adequate transcriptional response. Spatiotemporal organization of the transcription \"program\" governing the growth in _E. coli_ has been described previously in considerable detail [6; 12; 117]. Briefly, during the _E. coli_ growth cycle, the transcriptional activation of the chromosomal OriC and Ter poles occurs consecutively [12]. A similar, yet more nuanced pattern was observed in _Salmonella enterica_[118]. On nutritional shift-up, under conditions of high negative superhelicity, the transcription of the relatively G/C-rich chromosomal OriC pole is activated, whereas that of the Ter pole is repressed [12]. Conversely, on the transition to the stationary phase associated with the global relaxation of the DNA, the relatively A/T-rich Ter pole is activated, whereas the OriC pole is repressed. Since it is assumed, as mentioned above, that the chromosome configuration and genomic transcription are interdependent [6; 15; 16; 119; 120], the successive activation of OriC and Ter poles likely reflects the coordinately changing configuration and genetic activity of the chromosome, which is associated with the global redistribution of RNAP in the nucleoid [118; 121]. In this regard, the non-random distribution of the binding sites of the NAPs and especially of the DNA gyrase and major RNAP sigma factors along the OriC-Ter axis that were observed in the _E. coli_ genome [6; 14], are suggestive. This gross transition of chromosome configuration during the growth cycle was proposed to act as a topological device governing the \"growth program\" by converting the available metabolic energy into the growth-phase-dependent gene expression pattern, which seems connected via the metabolites to replication [2; 6; 122]. Ultimately, it appears that the spatial organization of DNA thermodynamic stability in bacterial genomes serves the purpose of the temporal coordination of chromosome structural dynamics and genetic response [107]. Coupling of DNA Topology, NAP Binding Effects, and Holoenzyme Sigma-Factor Composition: Major Regulatory Events during the _E. coli_ Growth Cycle  
On nutritional shift-up, the expression of the _gyrA_ and _gyrB_ genes encoding DNA gyrase--an enzyme introducing negative supercells into the DNA in an ATP-dependent manner,--increases [123; 124] concomitantly with an increase in the ATP/ADP ratio [125; 126; 127]. It is likely that at the chromosomal OriC pole negative superhelicity rapidly attains high densities of \(\sigma\)--\(0.07\) to \(-0.08\), consistent with both the enrichment of the OriC pole for the gyrase binding sites and the preferential binding of gyrase downstream of the strongly transcribed genes organized predominantly around OriC including the exceptionally strong rRNA operons [66; 128].