Evolution of silencing proteins in yeast

新的DNA测序技术的出现和丰富的基因组测序已经加强了开发从这些数据中提取功能见解的创新方法的需求。虽然同源性是一个有用的原则，但同源蛋白有时在物种间具有不同的功能，这些差异可以重新配置控制生物体如何应对环境变化的调节途径。因此，从模式物种推断函数可能会产生误导。为了了解蛋白质如何获得新功能以及这些变化的生物学后果，该项目将重点放在一组名为Sir2脱乙酰酶的蛋白质上，这些蛋白质在所有生命领域中都有发现。这些酶被提议协调生命周期的转变与营养的可用性。重要的是，Sir2去乙酰化酶表现出不同的作用模式，并可能使物种对营养条件产生特异性反应。本项目采用基因组规模和经典功能研究相结合的方法来研究遗传易感酵母物种中Sir2的进化史。该项目的第一部分研究了Sir2同源基因是如何通过获得与多种抑制基因表达的蛋白质复合物的相互作用而进化出新的功能的，第二部分探索了这些变化与细胞生理学相关的后果。为了阐明Sir2在酿酒酵母中获得功能的步骤，我们将在与酿酒酵母处于适当进化距离的物种中，即假丝酵母菌（Candida lusitaniae）和酵母菌（Kluyveromyces lactis）中比较Sir2同源基因的功能。由于这些物种在生理的特定方面对营养水平有不同的反应，因此该项目有可能阐明Sir2在这些反应中的作用。该项目将为两名研究生、几名进行独立研究的杜克大学本科生和参加两个旨在鼓励弱势学生从事科学事业的项目的暑期学生提供培训机会。杜克大学夏季研究机会计划（SROP）的目标是本科生，而北卡罗来纳部分项目SEED计划则支持高中生。此外，该项目将通过支持研究生和首席研究员的职业发展，促进女性科学家的招聘和保留。最后，其他酵母菌物种的发展，如K. lactis和C. lusitaniae，作为模式生物，将极大地促进未来的分子进化研究，使研究人员能够使用多个实验可处理的酵母菌物种来测试他们的假设，这些物种经过数亿年的进化而分离。

Intellectual Merit The advent of new DNA sequencing technologies and a wealth of sequenced genomes have intensified the need to develop innovative approaches for extracting functional insights from these data. Although homology is a useful principle, homologous proteins sometimes have different functions across species, and these differences can reconfigure regulatory pathways governing how organisms respond to environmental changes. Consequently, extrapolating function from model species can be misleading. To understand how proteins acquire new functions and the biological consequences of these changes, this project focuses on a group of proteins named Sir2 deacetylases, which are found in all kingdoms of life. These enzymes are proposed to coordinate life-cycle transitions with nutrient availability. Importantly, Sir2 deacetylases display varied modes of action and may enable species-specific responses to nutritional conditions. This project employs a combination of genome-scale and classical functional studies to investigate the evolutionary history of Sir2 in genetically tractable yeast species. The first part of the project examines how Sir2 orthologs have evolved new functions by acquiring interactions with a variety of protein complexes that repress gene expression, and the second part explores the consequences of such changes as they relate to the physiology of cells. To elucidate the steps by which Sir2 acquired its function in Saccharomyces cerevisiae, the functions of Sir2 orthologs will be compared in species at appropriate evolutionary distances from S. cerevisiae, namely in Candida lusitaniae, a representative species of the Candida clade, and in the yeast Kluyveromyces lactis. As these species have different responses to nutrient levels in terms of specific aspects of their physiology, this project has the potential to elucidate the roles of Sir2 in such responses.Broader Impact This project will provide training opportunities for two graduate students, several Duke undergraduate students conducting independent studies, and summer students participating in two programs designed to encourage disadvantaged students to pursue careers in science. The Duke Summer Research Opportunity Program (SROP) targets undergraduates, and the North Carolina Section Project SEED program supports high school students. In addition, this project will promote the recruitment and retention of female scientists by supporting the careers of a graduate student and the principal investigator, who are both women. Finally, the development of additional yeast species, such as K. lactis and C. lusitaniae, as model organisms will greatly facilitate future studies in molecular evolution by enabling researchers to test their hypotheses using multiple experimentally tractable yeast species that are separated by hundreds of millions of years of evolution.