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特征如何在其基因组中编码以及它们随着时间的变化如何代表重要且在很大程度上没有解决的生物学问题。该项目将通过研究1,000多种已知的萌芽酵母菌及其进化的代谢和基因组来解决这些问题。这些酵母菌中的一些是重要的机会性病原体，而另一些酵母菌物种则是食品，卧室，药品和生物燃料的生产者的重要工业意义。该项目将跨越生物组织的多个尺度（从分子到细胞，物种及以后），并进行了约4亿年的进化，以产生基本的见解，以了解基因组中的特征如何编码，新功能如何发展以及特征和基因组本身之间的关系如何发展。 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 almost all known budding yeast species and state-of-the-art genome-editing tools that are broadly active in divers species, this project will predict the connection of every metabolic gene in every yeast species’基因组具有其功能，并检查了贯穿芽的酵母亚晶状体糖果cotina的每个已知代谢基因，途径和性状的演变。通过基因组尺度的进化分析和针对代表跨越酵母基因组和代谢多样性的分类单元的靶向功能实验，该项目将在功能上表征基因型水平上的托法变异如何在表型水平上产生变化。特别是，该项目将列出DNA，RNA，蛋白质和代谢物的变化如何将遗传变异转化为生物化学功能和物理性状，并强调差距在功能上表征差距并纠正预测的基因类型图中的遗传学机构，并纠正了遗传学的遗传机构。该奖项反映了NSF的法定任务，并通过基金会的知识分子优点和更广泛的影响审查标准来诚实地支持NSF的法定任务。

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