Development of Yeast Prionomics

智力优势：自组装的纤维蛋白聚集体（淀粉样蛋白）可能代表一种古老的蛋白质折叠。淀粉样蛋白的种子聚合为淀粉样蛋白状态的潜在感染性或遗传性提供了基础。事实上，最近的证据表明，形成可传播的淀粉样蛋白（朊病毒）的能力在酵母蛋白中广泛存在，可能在其他生物体的蛋白质中也存在。忽略朊病毒在遗传和进化中的潜在输入是不可能的。然而，对酵母朊病毒生物学作用的了解仍处于初级水平，部分原因是缺乏与序列和表型无关的朊病毒检测和监测方法。本研究的总体目标是构建酵母朊病毒组，即能够在其天然状态下形成朊病毒的蛋白质目录，并评估对酵母生物学和进化的影响。这将有助于确定酵母菌株的朊病毒谱是否以与基因型模式相同的方式由自然选择驱动。为此，人们正在开发与菌株基因型无关的、适用于高通量分析和朊病毒谱分析的朊病毒检测方法。具体的研究目标如下：1)优化与序列无关的快速检测朊病毒的生化方法；2)鉴定新的候选朊病毒。对基于蛋白质的遗传这一迅速兴起的主题的重视（这一主题仍未得到充分研究，可能会显著改变我们对生物进化的理解），推动了知识价值的提升。人们正在开发新的无偏倚的朊病毒检测生化工具，并将其应用于重要的生物学问题，如鉴定新的朊病毒，表征其作用，确定酵母菌株的完整朊病毒谱。更广泛的影响：用于检测淀粉样蛋白和朊病毒的生化方法和工具可能适用于高通量分析，并可应用于酵母和其他生物在其自然环境中的朊酶体特征。这将为环境“朊经济学”开辟一个全新的领域，为环境基因组学提供补充，并可能对理解淀粉样蛋白的生物学作用和被假设涉及朊蛋白样开关的过程具有深远的意义，如记忆、应激保护和细胞内结构的组装。在这个项目中开发的新的淀粉样蛋白检测工具，以及关于糖利用和朊病毒之间联系的数据，可能对生物技术工业感兴趣。该项目高度依赖于学生的参与，并将通过提供博士论文的研究主题以及本科和研究生课程的教学，与教育过程紧密结合。PI的实验室参与了以大分子组装和分子进化为重点的跨学科中心，这些中心将从项目的成功中显著受益。

Intellectual Merit: Self-assembled fibrous protein aggregates (amyloids) probably represent an ancient protein fold. Seeded polymerization of an amyloid provides a basis for potential infectivity or heritability of an amyloid state. Indeed, recent evidence demonstrates that ability to form transmissible amyloids (prions) is widespread among yeast proteins, and likely among the proteins from other organisms. It is no longer possible to ignore the potential input of prions in inheritance and evolution. However, understanding of the biological roles of yeast prions remains at rudimentary levels, in part due to the lack of sequence- and phenotype-independent approaches for prion detection and monitoring. Overall goal of this research is to compose the yeast prionome, that is, a catalogue of proteins capable of forming prions in their native state, and to assess impact on yeast biology and evolution. This will help to determine if prion profiles of the yeast strains are driven by natural selection in the same way as genotypic patterns are. For this purpose, approaches for prion detection are being developed that are independent of strain genotype and applicable to the high throughput analysis and prion profiling. Specific research objectives are as follows: 1) to optimize the sequence-independent biochemical approaches for rapid prion detection; 2) to characterize new prion candidates. Intellectual merit is driven by the emphasis on a rapidly emerging topic of protein-based inheritance (that is still grossly understudied and may significantly change our understanding of biological evolution). New unbiased biochemical tools for prion detection are being developed and applied to important biological questions, such as identification of new prions, characterization of their effects, and determining of the complete prion profiles of the yeast strains. Broader Impacts: Biochemical approaches and tools for detection of amyloids and prions are potentially amenable to high throughput analysis and can be applied to characterizing prionomes of yeast and other organisms in their natural environments. This will open a whole new area of environmental "prionomics", providing a complement to environmental genomics, and may have far-reaching implications for understanding the biological roles of amyloids and the processes that have been hypothesized to involve prion-like switches, such as memory, protection from stresses, and assembly of intracellular structures. New amyloid detection tools, developed in the course of this project, and data on the connection between the sugar utilization and prions could be of interest to the biotechnological industry. This project heavily relies on participation of students and will be tightly integrated with the educational process by providing subjects of study for Ph.D. dissertations and for teaching undergraduate and graduate courses. The PI's lab participates in the interdisciplinary centers focused on macromolecular assemblies and molecular evolution, and these centers will significantly benefit from the success of the project.