Fig. 4.

An overview of transcription regulation following analogue and digital expression dynamics. (A) A hypothetical transcription activity dynamics plot is depicted. Faint green and red lines represent transcription activity (activation and repression, respectively) subject to linear/analogue dynamics. Dark green and red curves represent activation and repression subject to step-change/digital dynamics, respectively. Individual points represent one hypothetical measurement of transcription activity. Concentrations of hypothetical activator or repressor ligands increase from left to right on the horizontal axis, and transcription activity increases from the bottom to the top of the vertical axis. (B) An example of a system subject to linear/analogue dynamics. This model is modified from the work of Daniel et al. [25]. Activator (gold ovals) fused to Reporter 1 (blue suns) is produced from a gene expressed from a low copy plasmid and subject to a positive feedback (auto-activation) loop at P_Activator (green arrow). Activator (bound to inducer) also binds target sites on a high copy number plasmid activating reporter2, again at P_Activator, and simultaneously titrates Activator from the low copy plasmid above. Based on inducer concentration, this model allows for log-linear titration of Reporter 2 (green suns) levels [25]. (C) A digital AND logic gate (engineered from two NOR gates and a NOT gate) is symbolically represented along with the associated truth table. The depicted model is modified from the work of Tamsir et al. [18]. This circuit is distributed among three co-cultured cells (pale brown, blue, and purple circles), and the scenario depicted represents the ON output state, when Reporter (green suns) is produced (1 and a green box in the truth table). Both inducer 1 (brown diamond) and inducer 2 (blue pentagon) are present (1 and a green box in the truth table) and bound to Regulators 1 and 2, respectively. These regulators bind P_Inducer1 and P_Inducer2, respectively, activating repressor (green arrow). Repressor is subsequently produced and represses inducer3 (red crossbar), the gene encoding the producer of inducer 3 (purple hexagon), at P_Repress. Inducer 3 is not secreted (red arrow with a cross), and Regulator 3 (without inducer 3 bound) binds P_Inducer3 repressing repressor. Subsequently, Repressor does not repress reporter, at P_Repress, leading to reporter expression and Reporter production. In the absence of either or both inducers 1 and 2 (0 and red boxes in the truth table) inducer3 is not repressed, which leads to inducer 3 secretion. Regulator 3 (with inducer 3 bound) activates repressor, at P_Repress. Repressor subsequently represses reporter, blocking Reporter production (0 and a red box in the truth table).