Entrainment of a Bacterial Synthetic Gene Oscillator through Proteolytic Queueing

Internal
chemical oscillators (chemical clocks) direct the behavior
of numerous biological systems, and maintenance of a given period
and phase among many such oscillators may be important for their proper
function. However, both environmental variability and fundamental
molecular noise can cause biochemical oscillators to lose coherence.
One solution to maintaining coherence is entrainment, where an external
signal provides a cue that resets the phase of the oscillators. In
this work, we study the entrainment of gene networks by a queueing
interaction established by competition between proteins for a common
proteolytic pathway. Principles of queueing entrainment are investigated
for an established synthetic oscillator in Escherichia
coli. We first explore this theoretically using a
standard chemical reaction network model and a map-based model, both
of which suggest that queueing entrainment can be achieved through
pulsatile production of an additional protein competing for a common
degradation pathway with the oscillator proteins. We then use a combination
of microfluidics and fluorescence microscopy to verify that pulse
trains modulating the production rate of a fluorescent protein targeted
to the same protease (ClpXP) as the synthetic oscillator can entrain
the oscillator.

胞内化学振荡器（chemical oscillators，又称化学时钟）调控诸多生物系统的行为，而在众多此类振荡器中维持特定的周期与时相，对其正常功能至关重要。然而，环境扰动与固有分子噪声均可导致生化振荡器丧失相干性。维持相干性的一种解决方案是振同步（entrainment）：即通过外部信号提供重置振荡器时相的调控提示。本研究探讨了蛋白质竞争共同蛋白水解通路所形成的队列相互作用，对基因网络振同步的调控机制。我们以大肠杆菌（Escherichia coli）中已构建的合成振荡器为模型，探究队列牵引（queueing entrainment）的作用原理。首先，我们通过标准化学反应网络模型与基于映射的模型开展理论分析，结果均表明：队列牵引可通过脉冲式合成额外蛋白质实现——该蛋白质与振荡器蛋白竞争共同的降解通路。随后我们结合微流控技术与荧光显微镜技术开展实验验证：靶向与该合成振荡器共用的蛋白酶（ClpXP）的荧光蛋白，其表达速率受脉冲序列调控时，可实现对该振荡器的振同步。