Evolutionary Dynamics of Post-translational Regulatory Networks

描述(申请人提供)：由重复事件重组和点突变产生的遗传变异是自然选择在物种进化过程中发挥作用的原材料。为了充分了解生物系统，我们必须了解进化过程，以及这种变异是如何转化为对适应性有可测量影响的表型变化的。基因组研究和比较基因组学对研究基因组进化、识别功能DNA元件至关重要，并引导我们建立了更复杂的转录基因调控模型。最近，质谱学的进步揭示了转录后调控的复杂世界，并正在挑战我们目前对信号系统的看法。现在，每项研究中经常发现数千个不同的翻译后修饰(PTM)位点，并且不同类型的丰富的PTM的列表正在增加(例如，磷酸化、乙酰化、泛素化、SUMO化等)。这些技术发展提出了一个功能定性的问题，这是本提案旨在解决的一个问题。加州大学旧金山分校为开展这项研究提供了一个充满活力和协作精神的理想环境，以及包含最后一代MS仪器的优秀质谱学设施。自从来到加州大学旧金山分校以来，在HFSP奖学金的支持下，我与这个机构合作进行了蛋白质磷酸化的跨物种MS研究。这项初步研究表明，在进化过程中，蛋白质磷酸化的调节可能会迅速分化，尽管目前尚不清楚这些变化在多大程度上具有功能后果。这项工作强调了跨物种研究的重要性，以及开发蛋白质调控网络正式模型的迫切需要。我们应该利用从基因组研究中学到的经验教训，并将其应用于转录后调控网络的研究。考虑到这一点，本提案的主要目标是1)使用比较蛋白质组学方法来编目和确定功能上重要的PTM；2)开发能够根据它们的功能对PTM进行分类的预测器；以及3)为不同物种建立这些调控网络的模型。除了提高我们对细胞相互作用网络的信号和进化动力学的理解外，从这些模式生物中学到的经验教训将被应用于人类遗传变异的研究。 公共卫生相关性：了解进化过程是生物学研究中的一个基本问题。这个项目特别关注于研究调控细胞内蛋白质功能的重要的转录后调控网络。这些网络将在不同的真菌中进行比较，使我们第一次了解这些网络在进化过程中是如何变化的。研究DNA水平的变化如何导致表型差异，从而影响适应能力，将有助于我们理解为什么一些特定的突变会导致疾病，以及为什么不同的物种对不同的药物或环境条件反应不同。

DESCRIPTION (provided by applicant): Genetic variation, created by duplication events recombination and point mutations serves as the raw material for natural selection to act upon during the evolution of species. To fully understand biological systems we must understand the evolutionary process and how this variation is translated into changes in phenotypes that have a measurable impact on fitness. Genome research and comparative genomics in particular have been crucial to study genome evolution, to identify functional DNA elements and has led us to ever more sophisticated models of transcriptional gene regulation. More recently, progress in mass-spectrometry is unveiling a complex world of post-transcriptional regulation and is challenging our current view of signaling systems. Thousands of different post-translational modification (PTM) sites are now routinely identified per study and the list of different types of abundant PTMs is growing (e.g. phosphorylation, acetylation, ubiquitylation, sumoylation, etc). These technological developments raise a problem of functional characterization, an issue this proposal aims to address. UCSF provides an ideal environment to conduct this research with a vibrant and collaborative spirit and an excellent Mass-Spectrometry facility containing last-generation MS instrumentation. Since arriving at UCSF, with the support of a HFSP fellowship, I have collaborated with this facility to perform a cross-species MS study of protein phosphorylation. This initial study revealed that the regulation by protein phosphorylation can diverge quickly during evolution although it is not yet clear to what extent these changes have a functional consequence. This work underscores the importance of cross-species studies and the crucial need to develop formal models of protein regulatory networks. We should make use of the lessons learned from genome research and applied them to the study of post- transcriptional regulatory networks. With this in mind, the main objectives of this proposal are to 1) use a comparative proteomics approach to catalog and identify functionally important PTMs; 2) to develop predictors that can classify PTMs according to their function and 3) create models of these regulatory networks for different species. Besides improving our understanding signaling and of the evolutionary dynamics of cellular interaction networks, lessons learned from these model organisms will then be applied to the study of human genetic variation. PUBLIC HEALTH RELEVANCE: Understanding the evolutionary process is a fundamental problem in biological research. This project focuses specifically on the study of if the important post-transcriptional regulatory networks that regulate protein function inside the cell. These networks will be compared across different fungi allowing us for the first time to understand how these networks change during evolution. Studying how changes at the level of DNA result in a phenotypic difference with impact on fitness will help us understand why some specific mutations result in disease and why different species react differently to different drugs or environmental conditions.