Kernel Architecture of the Genetic Circuitry of the Arabidopsis Circadian System

A wide range of organisms features molecular machines, circadian clocks, which generate endogenous oscillations with ~24 h periodicity and thereby synchronize biological processes to diurnal environmental fluctuations. Recently, it has become clear that plants harbor more complex gene regulatory circuits within the core circadian clocks than other organisms, inspiring a fundamental question: are all these regulatory interactions between clock genes equally crucial for the establishment and maintenance of circadian rhythms? Our mechanistic simulation for Arabidopsis thaliana demonstrates that at least half of the total regulatory interactions must be present to express the circadian molecular profiles observed in wild-type plants. A set of those essential interactions is called herein a kernel of the circadian system. The kernel structure unbiasedly reveals four interlocked negative feedback loops contributing to circadian rhythms, and three feedback loops among them drive the autonomous oscillation itself. Strikingly, the kernel structure, as well as the whole clock circuitry, is overwhelmingly composed of inhibitory, rather than activating, interactions between genes. We found that this tendency underlies plant circadian molecular profiles which often exhibit sharply-shaped, cuspidate waveforms. Through the generation of these cuspidate profiles, inhibitory interactions may facilitate the global coordination of temporally-distant clock events that are markedly peaked at very specific times of day. Our systematic approach resulting in experimentally-testable predictions provides insights into a design principle of biological clockwork, with implications for synthetic biology.诸多生物均拥有分子机器——生物钟（circadian clock），这类装置可产生约24小时周期的内源性振荡，从而将生物过程与昼夜环境波动同步。近期研究明确，植物核心生物钟内的基因调控回路相较于其他生物更为复杂，由此引出一项基础性问题：生物钟基因间的所有调控互作，对于节律的建立与维持是否都同等重要？ 本研究针对拟南芥（Arabidopsis thaliana）开展的机制性模拟显示，若要复现野生型植物中观测到的生物钟分子特征，至少需要保留总调控互作数量的一半。本文将此类必需调控互作的集合定义为生物钟系统的核心组（kernel）。该核心组的结构无偏向性地揭示了4个相互联锁的负反馈环路参与调控生物钟节律，其中3个环路可自主驱动振荡过程。 值得注意的是，无论是核心组还是整个生物钟调控网络，其构成均以基因间的抑制性互作为主，而非激活型互作。本研究发现，这种偏好性正是植物生物钟分子特征常呈现尖锐尖峰波形的成因。通过生成此类尖峰分子特征，抑制性互作可助力全局协调时序上相隔较远的生物钟事件——这类事件往往在一天中的特定时刻达到显著峰值。 本研究采用的系统性方法可生成可实验验证的预测，为解析生物生物钟的设计原则提供了新的理论视角，同时对合成生物学研究具有重要参考价值。