Zhang Rong, Goetz Hanah, Melendez-Alvarez Juan, Li Jiao, Ding Tian, Wang Xiao, Tian Xiao-Jun
School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA.
Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang, China.
Nat Commun. 2021 Feb 8;12(1):853. doi: 10.1038/s41467-021-21125-3.
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.
模块化失败仍然是使用经过测试的模块组装合成基因电路的一个重大挑战,因为这些模块往往无法按预期发挥作用。对共享的有限基因表达资源的竞争是一个关键的根本原因。据报道,资源竞争使两个看似独立的基因以分级线性方式连接。在这里,我们揭示了合成基因电路中的非线性资源竞争。我们首先在单个菌株中构建了一个合成级联双稳开关(Syn-CBS)电路,该电路带有两个耦合的自激活模块,以实现两个连续的细胞命运转变。有趣的是,我们发现体内转变路径被重新定向,因为一个开关的激活总是胜过另一个开关,这与理论上预期的共同激活相反。这两个模块之间这种性质不同的资源竞争遵循“赢家通吃”规则,其中赢家由模块之间的相对连接强度决定。为了解耦资源竞争,我们构建了一个双菌株电路,该电路实现了两个开关的连续激活和稳定共同激活。这些结果表明,由于资源竞争,电路模块之间高度非线性的隐藏相互作用可能会对电路功能产生违反直觉的后果,而这可以通过分工策略来控制。