A comparative proteomic approach to understand animal circadian clock

这个项目的总体目标是深入了解产生生命节奏的机制。生物钟是一种内源性计时系统，存在于从细菌到动物的所有生命王国中。它的主要功能是整合环境信号和代谢状态，以确保生物体在一天中的生物有利时间执行必要的任务。已知蛋白质-蛋白质相互作用在生物体内昼夜节律定时信息的转导中是重要的。 虽然已经在动物中鉴定了构成昼夜节律计时系统中的核心振荡器的许多关键保守蛋白，但是振荡器蛋白模块接收输入时间线索并随后转导该计时信息以产生生理节律的机制还不清楚。在这个项目中，蛋白质网络分析集中在三种昆虫的振荡器蛋白模块与不同的时钟设计将进行基于质谱的分析在一个昼夜节律的时间框架。将开发算法来模拟振荡器和细胞蛋白质复合物之间的网络连接的动态变化，相对于昼夜节律以及进化时间。该项目将揭示以前未知的蛋白质相互作用，并揭示正确定时生物活动所必需的动态蛋白质网络重新布线。该项目将为研究生、本科生、高中教师和K-12级学生提供培训机会和职业发展。展示昆虫昼夜节律的展览将在加州大学戴维斯分校的博哈特昆虫学博物馆举办。将组织实验室讲习班，提供实验室经验，使高中教师和学生受益。本项目的目的是对构成果蝇（Drosophila melanogaster）、黑脉金斑蝶（Danaus plexippus）和意大利蜜蜂（Apis mellifera）这三种昆虫的昼夜节律振荡器的核心转录因子进行时间调节和动态蛋白质网络的分析和建模。这些相对密切相关的昆虫物种与不同的时钟设计之间的Interactomic比较将是有价值的，不仅在确定保守的和可能重要的细胞蛋白模块的钟表，但也在突出网络重新布线和差异的相互作用，可以反映固有的灵活性和适应性的时钟网络。该项目的结果将为测试有关动物钟表机构的新假设和预测时钟系统对扰动的反应奠定基础。由于蛋白质网络是组织和细胞类型特异性的，因此将测试一种新的框架，以克服质谱灵敏度的当前限制，并使用反式组学方法从更广泛的组织样品组装的网络数据中建模细胞类型特异性蛋白质网络。该项目将开发蛋白质组学方法以及生物信息学工具，以了解动态和振荡的生物系统，所有这些都将对科学界有价值。

The overall goal of this project is to gain insight into the mechanisms that generate the rhythms of life. The circadian clock is an endogenous timing system that exists in all kingdoms of life, from bacteria to animals. Its main function is to enable the integration of environmental signals and metabolic status to ensure that organisms perform necessary tasks at biologically advantageous times of day. It is known that protein-protein interactions are important in the transduction of circadian timing information within an organism. Although a number of key conserved proteins that make up the core oscillator in the circadian timing system have been identified in animals, the mechanisms by which the oscillator protein module receives input time cues and subsequently transduces this timing information to generate physiological rhythms are not well understood. In this project, protein network analysis centering on the oscillator protein module in three insect species with distinct clock designs will be conducted using mass spectrometry-based analyses over a circadian timeframe. Algorithms will be developed to model the dynamic changes in the network connections between the oscillator and cellular protein complexes with respect to circadian as well as evolutionary time. This project will uncover previously unknown protein interactions and shed light on the dynamic protein network rewiring necessary for properly timed biological activities. This project will provide training opportunities and career development for graduate students, undergraduates, high school teachers and students from K-12 levels. Exhibits showcasing insect circadian rhythms will be organized at the Bohart Museum of Entomology at UC Davis. Laboratory workshops providing hands on laboratory experience will be organized to benefit high school teachers and students. Video training tools will be developed as resources for laboratory workshops and for training students involved in this project.This project aims to profile and model temporally-regulated and dynamic protein networks centered on core transcription factors that make up the circadian oscillators in three insect species, Drosophila melanogaster, the Monarch butterfly Danaus plexippus, and the honeybee Apis mellifera. Interactomic comparisons between these relatively closely related insect species with distinct clock designs will be valuable not only in identifying conserved and likely important cellular protein modules for clockworks, but also in highlighting network rewiring and differential interactions that can reflect inherent flexibility and adaptability of the clock network. Results from this project will lay the foundation for testing new hypotheses regarding animal clockwork and predicting the behavior of the clock system in response to perturbations. Since protein networks are tissue and cell-type specific, a novel framework to overcome current limits of mass spectroscopy sensitivity and model cell-type specific protein networks from network data assembled from broader tissue samples using a trans-omics approach will be tested. This project will develop proteomic methods as well as bioinformatic tools for understanding a dynamic and oscillating biological system, all of which will be valuable to the scientific community.