Figure 1

Schematic representations of E. coli zinc homeostasis system and the in vitro sub-processes. (a) A schematic graph depicts the Zn²⁺ homeostasis system in Escherichia coli. Extracellular Zn²⁺ enters the cytoplasm through ZnuABC and ZupT [7, 19]. In the presence of zinc, Zur binds to the znu operator and represses the transcription of znuACB gene cluster [8, 20]. Excess intracellular zinc ions are exported by ZntA and ZitB [16, 17, 21]. Intracellular zinc can bind with protein ZntR and convert it into a strong transcriptional activator of the zntA gene [8, 14, 29]. The cytoplasmic zinc trafficking may involve chaperone-like proteins [22]. Abbreviations used in this graph are as follows: Zur* (active Zur); ZntR* (active ZntR); C? (zinc chaperone whose existence is still under debate) [2, 22]. (b) A schematic graph depicts the main sub-processes which we need to model for simulating in vitro transcriptional response: (i) Zn²⁺-sensing by Zur, (ii) Transcriptional repression of znuC gene by Zur, (iii) Zn²⁺-sensing by ZntR and (iv) Transcriptional activation of zntA gene by ZntR (Please note that here we only model the transcription of znuC gene rather than of the whole znuACB gene cluster because we only have reported data for znuC transcripts available for comparison) [22].