Since DNA replication needs a supply of guanine nucleotides, there must be some co-ordination between the DNA replication machinery and the gua operon. One method through which this happens is the DnaA protein. DnaA is a protein which recognises the origin of replication, promotes a local unwinding of an AT rich DNA region and finally guides the helicase DnaB to its entry site. DnaA is the replication initiation factor which causes DNA replication if present in sufficient concentration.
When replication happens, the origin of replication creates a "sink" for DnaA proteins. So genes which are negatively modulated by DnaA, like those of the gua operon are derepressed. Two potential DnaA binding sites, one on the gua promoter and another 200 bp downstream of the IMP dehydrogenase initiation codon on the guaB gene exist. It is thought that both the former and the latter sequences play a part, the latter part being vital and DNA binding at these sequences negatively affect transcription of the gene.
While growing on media in which growth rates are low, cAMP binds to a cAMP receptor protein forming a complex which has regulatory properties. This complex binds to a region 100 bp upstream of the guaB transcription start site which then represses the gua operon. It is a matter of debate of how this complex interacts with RNA polymerase from as long as around 100 bit/s away. One view suggests the involvement of an unknown regulatory factor. In any case, the complex confers growth rate dependent control to the promoter region of the operon.
The repressor purR encoded by purR genes controls the synthesis of enzymes involved in purine biosynthesis. A putative 16 bp pur operator was found in the gua promoter. The purR repressor works with other co-repressors, for example guanine which is a co-repressor in E. coli.
The gua mRNA leader has the potential for forming a stable stem-loop secondary structure incorporating the first 37 nucleotides of the transcript. As the ribosome binding site is sequestered in the stem loop, this structure may be involved in translational regulation.
The gua promoter lies back-to-back with the xseA promoter (encoding the mismatch repair enzyme exonuclease VII). Such close spacing of promoters may have regulatory significance and will lead to steric hindrance as the RNA polymerase molecules try to bind simultaneously. Inactivation of one promoter will naturally lead to greater expression of the other promoter. Other mechanisms include FIS (factor for inversion stimulation) which sterically hinders RNA polymerase binding. But the role of FIS is not yet properly investigated.