## 16 Is Ribonucleotide Reductase an Essential Constituent of the Initiation Hyperstructure? The initiation and elongation steps of chromosome replication are tightly coordinated and mutually dependent in all organisms: the inhibition of initiation results in an increase in elongation rates and vice versa [119; 120; 121; 122; 123]. The observation of a negative correlation between initiation and elongation suggests that either directly or indirectly, initiation of DNA replication and elongation of DNA synthesis are interdependent. In eukaryotes, under physiological conditions, a clear negative correlation has been observed between replicon size (length of DNA replicated bidirectionally) and DNA replication fork rates, while inhibiting elongation at replication forks induces the activation of additional replication origins termed \"dormant origins\" [124]. Could this interrelationship between DNA replication initiation and elongation involve ribonucleoside diphosphate reductase (RNR), which supplies the deoxyribonucleotides (dNTPs) that are essential for replication? Could there be a relationship between the oscillations in ATP during cell growth [109], the oscillations in the speed of the replisome with its pauses at ribosomal genes [107], and the activity of RNR--indeed, could a need to divert ribonucleotides into dNTPs be one explanation for why there is no transcription during the S phase in eukaryotes?The pool of available dNTPs is critical for successful replication since, with a defective supply, the DNA is likely to be damaged. Decreases in the size of the dNTP pool result in increases in the C period and _vice versa_, consistent with a major role for this pool in replication speed [125; 126; 127; 128]. It would make no apparent sense then for initiation of replication to occur without the availability of this pool--and without the ability of RNR to supply dNTPs continuously at the right rate. Localisation of RNR is consistent with this enzyme being part of a replication hyperstructure [129; 130] and, importantly, only a very small pool of dNTPs accumulates in the cell, which would allow for no more than one half minute of replication [131; 132]. This would suggest the need for ribonucleotide reductase to be present and active at or near the replication forks both at the time of initiation and during elongation. The question then is whether RNR must be functioning for initiation to occur--and, possibly, functioning in the right place? Put differently, could RNR act as a sensor--or allow the initiation hyperstructure to act as a sensor--in order to couple metabolism and cell growth with replication? If so, could the very activity of RNR determine its presence in the initiation hyperstructure and the ability of this hyperstructure to trigger replication, as proposed for functioning-dependent structures [133]? The rate of replication fork movement in all organisms depends on the activity of the enzyme RNR, which controls the level and balance of dNTP pool sizes during DNA synthesis (the S phase in eukaryotes and the C period in bacteria). The rate of replication fork movement also depends on a number of other factors, including the lagging strand DNA polymerase DnaE in _B. subtilis_[134] and the replication elongation factor DnaX in _E. coli_[135]. Consistent with an initiation-elongation regulatory circuit, it has been found in _E. coli_ that DnaA regulates the _nrdAB_ gene, which encodes RNR [136; 137; 138; 139]. Low levels/concentrations of DnaA-ATP stimulate _nrdAB_ expression (presumably prior to initiation), whereas high levels inhibit _nrdAB_ expression (presumably at the time of initiation). Various studies have shown that DnaA-ATP modulates the level of _nrdAB_ transcription and RNR activity, such that the active DnaA-ATP form of the protein correlates with both the number of replication forks and dNTP levels [138; 139]. Genetic evidence for the existence of such a regulatory circuit has been established with the identification of suppressors of elongation mutants (_dnaX_2016) in _E.