Winner-takes-all resource competition redirects cascading cell fate transitions

Abstract

Failure of modularity remains a significant challenge for assembling synthetic gene circuits with tested modules as they often do not function as expected. Competition over shared limited gene expression resources is a crucial underlying reason. It was reported that resource competition makes two seemingly separate genes connect in a graded linear manner. Here we unveil nonlinear resource competition within synthetic gene circuits. We first build a synthetic cascading bistable switches (Syn-CBS) circuit in a single strain with two coupled self-activation modules to achieve two successive cell fate transitions. Interestingly, we find that the in vivo transition path was redirected as the activation of one switch always prevails against the other, contrary to the theoretically expected coactivation. This qualitatively different type of resource competition between the two modules follows a ‘winner-takes-all’ rule, where the winner is determined by the relative connection strength between the modules. To decouple the resource competition, we construct a two-strain circuit, which achieves successive activation and stable coactivation of the two switches. These results illustrate that a highly nonlinear hidden interaction between the circuit modules due to resource competition may cause counterintuitive consequences on circuit functions, which can be controlled with a division of labor strategy.

Predicting Composition of Genetic Circuits with Resource Competition: Demand and Sensitivity

“…However, modules with large resource demand will cause other modules to experience more significant changes in their behavior due to resource competition. Additionally, unexpected changes in behavior may occur due to resource competition, such as a change in the number of equilibria of a system ( 32, 33 ). The method assumes that disturbances due to resource competition are small enough such that these qualitative changes do not occur.…”

Context-Dependent Stability and Robustness of Genetic Toggle Switches with Leaky Promoters

“…To promote modularity and predictable system-level performance, sources of contextdependence need to be incorporated into the design of genetic modules [10]. Considering the prominent and versatile role that multistable genetic switches play in systems and synthetic biology [74], it is crucial to characterize how tunable biophysical parameters affect their stability and robustness properties, especially since they display particularly strong dependence on their context [23,40,41]. To address this issue, in this paper we considered a reduced order mechanistic model describing the dynamics of genetic switches, explicitly accounting for the limited availability of shared transcriptional/translational resources and yielding accurate predictions both in vivo [16] and in vitro [50], in addition to explaining counter-intuitive experimental phenomena [13].…”

“…As the behavior of genetic switches displays strong dependence on their context [23,40,41], here we explore how loading from the context affects their stability and robustness properties. Since the rescalings α ← α/(1 + β c ) and β ← β/(1 + β c ) transform the dynamics in (1) as if the switch was isolated (i.e., as if β c was zero), revealing the effects of the context is straightforward, using results presented in earlier sections.…”

“…Considering the central role that multistable switches play in both natural and synthetic gene systems [37][38][39], it is especially troubling that their behavior displays particularly strong dependence on their context [40,41]. While some variants fail to function as a memory module upon changes to their genetic context as a result of competition for shared resources (Figure 1A), others preserve this critical functionality (Figure 1B), although their robustness to noise decreases (Figure 1C).…”

“…Therefore, core properties of the toggle switch are not only context-dependent but seemingly identical realizations can react fundamentally differently to burden-related perturbations (Figure 1). [40,41]. (A) In the absence of loading from its context, trajectories of toggle switch #1 converge to one of two metastable states (red and green).…”