Figure 3
From: Simulating in vitro transcriptional response of zinc homeostasis system in Escherichia coli
Transient curves of simulated Zur transcription assay and data comparison (I). (a) The green, purple and red curves denote the simulated transient curves of Zn2Zur (Py), Zn4Zur (Py1), RNA polymerase (Rw) concentrations as a function of t, respectively. (b) The green, purple and red curves denote the simulated transient curves of free znuC DNA (Dw), znuC transcription initiation complex (Qw1) and Zn4Zur-DNA complex (Qw2) concentrations as a function of t, respectively. (c) The simulated concentration of the mRNA of ZnuC (Mw(t)) is depicted as a function of t. (d) Data comparison for Zur and ZntR transcription assays. Big red dots for the Zur transcription assay and big blue dots for the ZntR transcription assay (I) are reconstructed from the reported data in the original figure (Fig. 4 in [22]) using image analysis method. The purple curve and the green curve are the corresponding simulated normalized final concentrations of the mRNA of ZnuC (Mw (t = td 0+ t d )) and the mRNA of ZntA (Mz (t = td 0+ t d )) as a function of the logarithm of Zn (also denoted as [Zn] free ), respectively. The three small purple dots on the purple curve are simulated data points for Zn = 10-5 nM, 10-6 nM, 10-7 nM, respectively. The three small green dots on the green curve are simulated data points for Zn = 10-5 nM, 10-6 nM, 10-7 nM, respectively (please note that the simulated transient curves of Zur and ZntR transcription assays for Zn = 10-5 nM are shown in Fig. 3a-c and Fig. 4, respectively. More simulated transient curves for Zn = 10-6 nM, 10-7 nM are shown in Additional file 2: MoreTransientCurves.doc). The area highlighted in gray is the range of Zn between the half maximal induction points on the two simulated curves.