Figure 1

Gene circuit modules and their interface process. (A) The repressilator (Module 1) [30] regulates multiple copies of a downstream module (Module 2). The multiple copies can be realized by placing the downstream module in a plasmid. TetR repressors (output of Module 1) regulate their specific downstream-module promoters (input of Module 2). A module interface process (MIP) defines the collection of the processes of tetR-transcription and translation and its specific downstream-module regulation. As the number of the downstream-module promoter (P _T ) increases, the amplitude of the oscillation in the repressilator can be changed significantly (B and C). A repressilator model was obtained from the BioModels Database BIOMD0000000012 [50]. The model was modified to lower the expression levels (by changing translation efficiency to 10 and K _M to 10 molecules per cell and the maximum transcription rate to 3 molecules per min per cell) and to add promoter binding-unbinding reactions for TetR repressors (for the detailed model description, refer to Additional File 1).