Expression of master regulators
In the preceding sections, we have emphasised the hierarchical organisation as well as important local structural variations in E. coli transcriptional network. In the subsequent section, we consider the expression of a TF as a function of its position in the regulatory hierarchy. Although it is difficult to address this at the protein level because of the current relative scarcity of proteomic data, this question can be readily addressed at the level of transcription. Therefore, we have analysed the levels of mRNA reported by two independent experiments on E. coli cells grown on minimal medium + glucose.63–65 In summary, the mean mRNA levels of global TFs such as CRP, FNR, ArcA and IHF are significantly higher than those of more specialised regulators (Fig. 2b). This result supports the contention that the master regulators are continuously required at high levels to bind to numerous DNA sites across the genome, whereas downstream, specialised TFs can be expressed or not depending on the environmental conditions. Indeed, in conditions favourable to planktonic growth (as in the condition for mRNA quantification mentioned above), TFs controlling the final stages of biofilm/motility development are lowly expressed. Similarly, the TFs controlling specific sugar catabolism regulons show much lower mean concentration compared to CRP, suggesting that these TFs are sporadically required, depending on the metabolic state of the cell. A similar tendency has been recently observed by measuring the fluorescence of 15 different TF–green fluorescent protein gene fusions.66