Model guided design of enhanced bi-stable controllers to effectively switch cellular states

Abstract

1AbstractBi-stable gene regulatory motifs are found in a wide variety of natural gene regulatory networks and typically effect transcriptional switching between stable phenotypic states in cells. In synthetic gene regulatory circuits, these architectures can be used to dynamically switch between distinct metabolic states for metabolic engineering and therapeutic applications. Though it has been over two decades since the first synthetic bi-stable switch was developed, the lack of modularity and predictability of these motifs in varying environments has limited widespread application, especially since the factors that affect switching characteristics are still unclear. In this work, we develop a mathematical model describing a bi-stable gene regulatory element using mass action kinetics. Using this model and a newly developed dynamical modeling and continuity analysis framework, we identify the changes in switching characteristics shown by the bi-stable motif over a range of biologically relevant model parameter values. Interestingly, there appears to be a trade-off between the robustness of the motif - the parameter ranges over which it retains bi-stable function, and the speed at which it effects a phenotypic change. Further, using E. coli as a model host, we constructed a large library of transcriptional switches that show a wide range of switching speeds, to experimentally demonstrate the presence of this trade-off. The presence of this trade-off has significant implications on the design of transcriptional switches for diverse applications and could potentially explain the circuit architecture of natural transcriptional switches as well. Additionally, we anticipate that our diverse library of bi-stable switches will be valuable to effect phenotypic changes with differing switching speed requirements for metabolic engineering applications.