Structural Flexibility Mediates Circadian Adaptation in Diverse Organisms

项目摘要： 生物钟已经进化到使生物体生理学与环境条件同步。的核心 它们的功能是能够适应独特的环境生态位，以保持24小时的日常循环， 有机体适应性尽管生物体的昼夜节律网络各不相同，但昼夜节律网络的两个特征 1）由转录-翻译反馈环（TTFL）组成的中央振荡器， 和2）将TTFL带入内源性和环境线索的感觉元件。昼夜节律检查 跨不同生物体的网络拓扑结构揭示了两个蛋白质结构域家族被广泛用于整合 环境刺激进入昼夜节律网络。这些是光-氧-电压（LOV：真菌和 隐花色素（Cryptochromes，CRY：植物和动物）。不同生物体的结果表明，尽管 这些蛋白质的机制和作用可以有很大的不同。LOV和CRY蛋白是如何 能够适应信号传播的幅度和模式以适应环境条件是未知的。 基于最近对植物、真菌和动物中LOV和CRY系统的计算和生物物理研究， 我们假设LOV/CRY系统利用动态构象景观， 整合物种和/或环境特定的环境变量。通过了解 这些复杂的景观，我们可以：1）预测密切相关的生物如何调整昼夜节律反应， 最大化健身。2)制定策略来操纵生物体生理学，以纠正有害（疾病） 导致）错误或鼓励有益的适应。在此，我们开发了一个平台，可用于 本科研究人员，整合生物，生物物理和计算方法。我们专注于 二是验证昼夜节律网络的可塑性。我们特别关注保留变构的系统， 类似于哺乳动物中发现的机制，从而使我们能够开发新的策略来影响 人类疾病目的1：利用最近的计算和结构数据，我们将直接评估变构 改变LOV蛋白构象的开关残基。具体重点将放在残留物上 允许密切相关的植物和真菌物种改变环境特异性的信号动力学， 方式我们将展示这些信令网络的可调谐性，从而开发新的方法， 操纵生物体的生理机能目标2：利用最近的化学和结构研究， 脊椎动物的CRY，我们将证明类似的结构可塑性存在于基于神经网络的系统， 生物改变构象反应的大小和方向。利用结构和生物化学 我们将开发一种能够操纵哺乳动物昼夜节律网络的光遗传学工具。的 结合的方法使我们能够识别用于调节昼夜节律网络的自然机制，从而 允许设计新的遗传和化学机制来操纵生物体的适应性。

Project Summary: Circadian clocks have evolved to synchronize organism physiology with environmental conditions. Central to their function is the ability to adapt to unique environmental niches to maintain a 24-hour daily cycle to optimize organism fitness. Although circadian networks differ in various organisms, two hallmarks of circadian networks are conserved across phyla: 1) A central oscillator composed of a transcription-translation feedback loop (TTFL), and 2) Sensory elements that entrain the TTFL to endogenous and environmental cues. Examination of circadian network topology across diverse organisms reveals two protein domain families are widely employed to integrate environmental stimuli into circadian networks. These are members of the Light-Oxygen-Voltage (LOV: fungi and plants) and Cryptochromes (CRY: plants and animals). Results in diverse organisms demonstrate that despite conservation, the mechanisms and roles of these proteins can differ considerably. How LOV and CRY proteins are able to adapt the magnitude and mode of signal propagation to adapt to environmental conditions is unknown. Based on recent computational and biophysical studies of LOV and CRY systems in plants, fungi, and animals, we hypothesize that LOV/CRY systems leverage a dynamic conformational landscape to enable integration of environmental variables that are species and/or environment specific. By understanding these complex landscapes, we can: 1) Predict how closely related organisms tune circadian responses to maximize fitness. 2) Develop strategies to manipulate organism physiology to rectify either deleterious (disease causing) errors or encourage beneficial adaptations. Herein, we develop a platform, amendable to undergraduate researchers, that integrates biological, biophysical, and computational approaches. We focus on two aims to verify plasticity in circadian networks. We specifically focus on systems that retain allosteric mechanisms analogous to those found in mammals, thereby allowing us to develop new strategies to impact human disease. Aim 1: Leveraging recent computational and structural data we will directly evaluate allosteric switch residues that alter the conformational landscape of LOV proteins. Specific focus will be on residues allowing closely related plant and fungal species to alter signaling dynamics in an environmentally specific manner. We will demonstrate tunability of these signaling networks, thereby developing new methodologies to manipulate organism physiology. Aim 2: Leveraging recent chemical and structural studies of a photoactive vertebrate CRY, we will demonstrate that analogous structural plasticity exists in CRY-based systems allowing organisms to alter the magnitude and direction of conformational responses. Using structural and biochemical approaches we will develop an optogenetic tool capable of manipulating mammalian circadian networks. The combined approach enables us to identify natural mechanisms employed to tune circadian networks, thereby allowing the design of new genetic and chemical mechanisms to manipulate organism fitness.