An integrative circuit-host modelling framework for predicting synthetic gene network behaviours

One fundamental challenge in synthetic biology is the lack of quantitative tools that accurately describe and predict the behaviours of engineered gene circuits. This challenge arises from multiple factors, among which the complex interdependence of circuits and their host is a leading cause. Here we present a gene circuit modelling framework that explicitly integrates circuit behaviours with host physiology through bidirectional circuit-host coupling. The framework consists of a coarse-grained but mechanistic description of host physiology that involves dynamic resource partitioning, multilayered circuit-host coupling including both generic and system-specific interactions, and a detailed kinetic module of exogenous circuits. We showed that, following training, the framework was able to capture and predict a large set of experimental data concerning the host and its foreign gene overexpression. To demonstrate its utility, we applied the framework to examine a growth-modulating feedback circuit whose dynamics is qualitatively altered by circuit-host interactions. Using an extended version of the framework, we further systematically revealed the behaviours of a toggle switch across scales from single-cell dynamics to population structure and to spatial ecology. This work advances our quantitative understanding of gene circuit behaviours and also benefits the rational design of synthetic gene networks.