Figure 3

Experimental and theoretical dynamics of the mar circuit.

(A,C) Normalized YFP expression upon induction with salicylate [0.5 mM in (A), and 5 mM in (C)] at the population level (blue circles; error bars correspond to the mean and standard deviations of three independent replicates; fluorescence values normalized by the maximum, which is the steady state value). Red circles correspond to promoter activity (normalized by the maximum) calculated from the generalized exponential model inferred from the experimental data (blue circles). Solid blue/red lines correspond to a model simulation of the mar circuit (blue for MarR, red for MarA) starting from the uninduced steady state. Dashed blue line correspond to a model simulation starting from [MarR] = [MarA] = 0. (B,D) Two-dimensional phase space associated to (MarA, MarR) dynamics (ss refers to steady state). Nullclines (black curves; solid for induced and dashed for uninduced situations) represent the trajectories in this space where only the concentration of MarR (d[MarA]/dt = 0 nullcline) or MarA (d[MarR]/dt = 0 nullcline) changes. Steady states (black points) are given by the intersection of these curves. A trajectory upon induction [0.5 mM in (B), and 5 mM in (D)] from the uninduced state (0 mM) is represented; blue solid line is the simulation and blue circles the experimental data. Blue arrows represent direction and strength of change (the bigger the arrow the faster the change). Black arrows represent direction of change in the nullclines of the induced situation.