Fig 3. Spatio-temporal dynamics of tetracycline action on E. coli colonies.

(A-C) Schematic of tetracycline response from diffusion at a colony scale to transport at a single-cell scale to regulation of gene expression at a molecular scale. (D) Snapshots of a representative colony simulation after addition of tetracycline at the MIC (1.5 mg/L). The color of each cell represents the log₂ fold change of instantaneous growth rate compared to the average instantaneous growth rate of cells in a representative baseline glucose simulation. The cell lineage ending with cell 0011111 was outlined in blue and also plotted as blue traces in Panels E-K. (E) Per-cell dry mass starting with a single cell grown in M9 minimal medium with 1mM glucose and no tetracycline for about 3.2 hours (11550 seconds), at which point tetracycline was added at the MIC and the simulation continued for approximately 4 more hours (14550 seconds). (F-H) Per-cell concentration of, from left to right, periplasmic tetracycline, cytoplasmic tetracycline, and active ribosomes in the minutes surrounding tetracycline addition. (I-K) Per-cell concentration of, from left to right, micF-ompF RNA duplexes, ompF mRNA, and OmpF monomers for the entire 7.2-hour (26000 seconds) simulation. (L) Whole colony mass for representative simulations run across six different concentrations of tetracycline (MIC in blue). Data from these same simulations was also used to create Panel M. (M) Average active ribosome concentration and instantaneous doubling rate for all cells over the first (left) and fourth (right) hour of tetracycline exposure, with color corresponding to different tetracycline concentrations (MIC in blue). Marginal kernel density estimates were normalized such that the area under each colored curve is 1. Note: All data shown is from simulations run with seed 0 initialized with a snapshot 3.2 hours (11550 seconds) into a baseline glucose simulation (also seed 0) before being continued for an additional four hours (14550 seconds) with varying levels of external tetracycline.