Collaborative Research: RoL: The Evolution of the Genotype-Phenotype Map across Budding Yeasts

合作研究：RoL：出芽酵母基因型-表型图谱的演变

基本信息

批准号：
2110403
负责人：
Christopher Hittinger
金额：
$ 125万
依托单位：
University of Wisconsin-Madison
依托单位国家：
美国
项目类别：
Continuing Grant
财政年份：
2021
资助国家：
美国
起止时间：
2021-07-15 至 2026-06-30
项目状态：
未结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=2110403&HistoricalAwards=false
关键词：
Collaborative Research RoL Evolution Genotype

项目摘要

How organisms’ external characteristics or traits are encoded in their genomes and how they change over time represent important and largely unanswered biological questions. This project will address these questions by studying the metabolisms and genomes of the more than 1,000 known species of budding yeasts and their evolution. Some of these yeast species are important opportunistic pathogens, while others are of great industrial relevance as producers of foods, beverages, medicines, and biofuels. This project will span multiple scales of biological organization (from molecules to cells, species, and beyond) and ~400 million years of evolution to yield fundamental insights into how traits are encoded in genomes, how new functions evolve, and how the relationship between traits and genomes itself evolves. The project will support the Wild YEAST and Computational Genomics Programs, two established and highly successful educational and training programs that immerse early-stage undergraduate students, including those from underrepresented backgrounds, in authentic, discovery-driven research.Using draft genomes for nearly all known budding yeast species and state-of-the-art genome-editing tools that are broadly active in diverse species, this project will predict the connection of every metabolic gene in every yeast species’ genome to its function(s), as well as examine the evolution of every known metabolic gene, pathway, and trait across the budding yeast subphylum Saccharomycotina. Through genome-scale evolutionary analyses and targeted functional experiments on key representative taxa spanning budding yeast genomic and metabolic diversity, this project will functionally characterize how between-taxa variation at the level of genotypes gives rise to variation at the level of phenotypes. In particular, the project will chart how variation at the level of DNA, RNA, proteins, and metabolites sequentially transforms genetic variation into biochemical functions and physiological traits with an emphasis on functionally characterizing gaps and correcting discrepancies in the predicted Genotype-Phenotype Map.This project is jointly funded by the Evolutionary Processes program in the Division of Environmental Biology and the Genetic Mechanisms program in the Division of Molecular and Cellular Biosciences of the Directorate for Biological Sciences.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.

生物体的外部特征或性状如何在其基因组中编码，以及它们如何随时间变化是重要且很大程度上尚未解答的生物学问题，该项目将通过研究 1,000 多种已知芽殖酵母及其它们的新陈代谢和基因组来解决这些问题。其中一些酵母物种是重要的机会病原体，而另一些则作为食品、饮料、药品和生物燃料的生产者具有重要的工业相关性。该项目将跨越生物组织的多个尺度。细胞、物种等）和约 4 亿年的进化，以深入了解性状如何在基因组中编码、新功能如何进化以及性状与基因组本身之间的关系如何进化。该项目将支持野生酵母。和计算基因组学项目，这是两个已建立且非常成功的教育和培训项目，使早期本科生（包括来自代表性不足的背景的学生）沉浸在真实的、发现驱动的研究中。对几乎所有已知的芽殖酵母使用基因组草案物种和在不同物种中广泛活跃的最先进的基因组编辑工具，该项目将预测每个酵母物种基因组中的每个代谢基因与其功能的联系，并检查进化通过对跨越芽殖酵母基因组目标和代谢多样性的关键代表性分类群进行基因组规模的进化分析和功能实验，该项目将在功能上表征分类群之间的变异。这基因型水平引起表型水平的变异特别是，该项目将绘制DNA、RNA、蛋白质和代谢物水平的变异如何依次将遗传变异转化为生化功能和生理特征的图表，重点是功能表征。差距并纠正预测的基因型-表型图谱中的差异。该项目由环境生物学司的进化过程计划和分子和细胞司的遗传机制计划共同资助生物科学理事会的生物科学。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

期刊论文数量（17）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Crabtree/Warburg-like aerobic xylose fermentation by engineered Saccharomyces cerevisiae

DOI：
10.1016/j.ymben.2021.09.008
发表时间：
2021-10-04
期刊：
METABOLIC ENGINEERING
影响因子：
8.4
作者：
Lee, Sae-Byuk;Tremaine, Mary;Sato, Trey K.
通讯作者：
Sato, Trey K.

Contrasting modes of macro and microsynteny evolution in a eukaryotic subphylum

DOI：
10.1016/j.cub.2022.10.025
发表时间：
2022-12-19
期刊：
CURRENT BIOLOGY
影响因子：
9.2
作者：
Li, Yuanning;Liu, Hongyue;Rokas, Antonis
通讯作者：
Rokas, Antonis

Yeasts from temperate forests

DOI：
10.1002/yea.3699
发表时间：
2022-02-17
期刊：
YEAST
影响因子：
2.6
作者：
Mozzachiodi, Simone;Bai, Feng-Yan;Boynton, Primrose
通讯作者：
Boynton, Primrose

Comparative functional genomics identifies an iron-limited bottleneck in a Saccharomyces cerevisiae strain with a cytosolic-localized isobutanol pathway.

DOI：
10.1016/j.synbio.2022.02.007
发表时间：
2022-06
期刊：
Synthetic and systems biotechnology
影响因子：
4.8
作者：
Gambacorta FV;Wagner ER;Jacobson TB;Tremaine M;Muehlbauer LK;McGee MA;Baerwald JJ;Wrobel RL;Wolters JF;Place M;Dietrich JJ;Xie D;Serate J;Gajbhiye S;Liu L;Vang-Smith M;Coon JJ;Zhang Y;Gasch AP;Amador-Noguez D;Hittinger CT;Sato TK;Pfleger BF
通讯作者：
Pfleger BF

The Brazilian Amazonian rainforest harbors a high diversity of yeasts associated with rotting wood, including many candidates for new yeast species