Sirtuins as rewiring points to evolve new responses to low NAD+ stress in yeast

这个项目研究如何通过在压力下激活的一组基因的变化来创造新的特征。它将揭示分子进化的基本原理，解释生物如何在短期内适应环境变化，以及物种如何在长期内适应环境变化。该项目的重点是一种名为烟酰胺腺嘌呤二核苷酸或NAD+的分子，它是从营养素中提取能量所必需的。细胞中的NAD+水平随着代谢条件的变化而波动，而这种波动是由一种被称为sirtuins的广泛的蛋白质家族感受到的。当NAD+水平不足时，sirtuins允许特定基因变得活跃，从而产生一种反应，允许有机体适应低NAD+水平。这个项目检验了这样一种假设，即当新的基因受到sirtuins的控制时，可以对低NAD+压力产生新的反应。除了促进对分子进化过程的理解外，该项目还将通过三种方式培训下一代科学家，从而加强科学基础设施。首先，实验将由两名博士生进行。通过他们的工作，学生们将学习分析、实验室和计算技能。其次，该项目将为四名本科生提供暑期研究机会。这些本科生将被介绍给实验科学，并发现研究职业是否适合他们。第三，该项目将加强布法罗大学的遗传学本科教育。PI将为本科生遗传学课程开发互动教学模块。这些活动将通过帮助学生认识到遗传学与他们的生活和职业的相关性来增加学生的参与度和学术成功。尽管科学家们长期以来一直在研究sirtuins的脱乙酰基如何调节细胞过程，但很少考虑sirtuin靶标的变化对进化的影响。这个项目通过研究含有sirtuin的酵母复合体SUM1C如何对表型变异和适应性进化做出贡献来解决这个问题。SuM1C由sirtuin脱乙酰酶和DNA结合蛋白组成，DNA结合蛋白针对脱乙酰酶的特定基因组位置。中心假设是，SUM1C作为一个重联点，允许酵母物种通过将新基因带到依赖于NAD+的脱乙酰酶的控制下，对低NAD+胁迫进化出不同的反应。这个项目将使用RNA-Seq和CHIP-Seq相结合的方法在八个系统发育分布的酵母物种中鉴定SUM1C靶基因。这些数据将被用来(I)研究SUM1C如何调节细胞内[NAD+]的转录输出，以及(Ii)确定SUM1C靶点改变的功能后果。通过这样做，这项工作将提供新的见解，以了解广泛保守的sirtuin脱乙酰酶如何在短期内促进表型变化，并在长期内促进适应性进化。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

This project investigates how new traits are created through changes in the set of genes that are activated upon stress. It will uncover basic principles of molecular evolution that explain how organisms adapt to environmental changes in the short term and how species adapt to environmental changes in the long term. The project focuses on a molecule called nicotinamide adenine dinucleotide, or NAD+, which is required to extract energy from nutrients. NAD+ levels in cells fluctuate with metabolic conditions, and these fluctuations are sensed by a widespread family of proteins called sirtuins. When NAD+ levels are insufficient, sirtuins allow particular genes to become active, which produces a response that allows the organism to adjust to the low NAD+. This project examines the hypothesis that new responses to low NAD+ stress can arise when new genes come under the control of sirtuins. In addition to advancing the understanding of molecular evolutionary processes, this project will enhance the scientific infrastructure by training the next generation of scientists in three ways. First, the experiments will be conducted by two PhD students. Through their work, the students will learn analytical, laboratory, and computational skills. Second, the project will provide summer research opportunities for four undergraduates. These undergraduates will be introduced to experimental science and discover whether a research career is a good fit. Third, the project will enhance undergraduate education in genetics at the University at Buffalo. The PI will develop interactive teaching modules for an undergraduate genetics course. These activities will increase student engagement and academic success by helping them appreciate the relevance of genetics to their lives and careers. Although scientists have long studied how deacetylation by sirtuins modulates cellular processes, there has been little consideration of the evolutionary implications of changes in sirtuin targets. This project addresses the issue by investigating how the yeast sirtuin-containing complex SUM1C contributes to phenotypic variation and adaptive evolution. SUM1C is composed of a sirtuin deacetylase and a DNA-binding protein that targets the deacetylase to particular genomic locations. The central hypothesis is that SUM1C serves as a rewiring point that allows yeast species to evolve distinct responses to low NAD+ stress by bringing new genes under the control of an NAD+-dependent deacetylase. This project will identify SUM1C target genes in eight phylogenetically distributed yeast species using a combination of RNA-Seq and ChIP-Seq. These data will be used to (i) investigate how SUM1C tunes transcriptional output to intracellular [NAD+] and (ii) determine the functional consequences of changes in the set of SUM1C targets. In so doing, this work will provide new insights into how sirtuin deacetylases, which are broadly conserved across the tree of life, contribute to phenotypic variation in the short term and adaptive evolution in the long-term.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.