Autoregulatory gene circuits can be physically encoded within the genome in a number of different configurations. By physical encoding, we mean the orientation and relative proximity of the genes within the circuit. In this work, we quantified the behaviour of an inducible, negatively autoregulated gene circuit arranged in different transcriptional configurations using the tetRA circuit from Tn10 as our basis. Mathematical modelling predicted that circuits arranged in configurations where the expression of the transcription factor is decoupled from its target genes afforded more flexibility relative to configurations where expression is coupled. We found that these decoupled configurations reduced the concentration of transcription factor needed to regulate inducible expression from the circuit. As lower concentrations of transcription factor were required, these decoupled configurations could also be activated at much lower concentrations of the inducer. We experimentally validated these predictions in Escherichia coli by comparing the response of synthetic circuits based on the tetRA circuit arranged in different configurations. Collectively, these results provide one example of how the arrangement of a gene circuit within the genome can affect its behaviour.
