TRTech-PGR: Establishing a one-stop-shop for plant metabolism annotations and launching a plant enzyme function consortium

TRTech-PGR：建立植物代谢注释一站式服务并启动植物酶功能联盟

• 批准号: 2312181
• 负责人: Seung Rhee
• 金额: $ 299.95万
• 依托单位: Michigan State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-10-01 至 2027-09-30
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2312181&HistoricalAwards=false
• 关键词: TRTech; PGR; Establishing; stop; shop

Surging human population and climate change have placed unprecedented stress on agriculture. Meeting the world’s evolving food needs necessitates the development of resilient, nutritious, and bountiful crops. Collaborative and innovative approaches to plant science, combined with outreach initiatives for STEM education and recruitment, are needed to meet these challenges. This project will expand the Plant Metabolic Network (PMN), a collection of databases used to study the metabolism of plants and how their genomes relate to metabolism. This expansion will grow the databases in the PMN from 126 to over 1000 species. An expanded PMN will provide researchers access to a rich, evolving suite of tools to rapidly accelerate fundamental and translational plant science research and applications to meet real-world demands. The expansion of the PMN will also create a valuable educational tool for those in secondary- and post-secondary education. Educational resources about plant genetics, biochemistry, and metabolism will be produced and distributed, including video tutorials for PMN and lesson plans demonstrating how plants produce various chemicals useful to humans. In universities, a pilot Course-based Undergraduate Research Experience (CURE) will be established to provide undergraduate students with cutting-edge, experiential opportunities in genome and metabolism research. An advisory board of schoolteachers will guide engagement efforts in middle- and high-school audiences, focusing on student bodies predominantly composed of underrepresented minorities. This project offers ample opportunities for increased collaboration and advancement across the plant sciences, as well as initiatives to inspire and guide students who identify with underrepresented groups to pursue STEM education.To expand the PMN databases, this project will retool the existing PMN pipeline to operate at scale, packaging it into a containerized app and automating much of the process of running it. The retooled pipeline will be used to rapidly create new PMN databases from 1000 plant genomes taken from GenBank, 10KP, and other sources. This project aims to expand the contents and improve the accuracy of the databases by experimentally determining and integrating enzyme biochemical data to enhance computational prediction of plant metabolism. As a project component, an enzyme consortium will be established to conduct prediction-guided enzyme function studies at scale, targeting enzyme classes that perform poorly in computational annotations, and integrate the biochemical data into PMN. We will focus on terpene synthases, cytochrome P450s, and aminoacyltransferases in this initial consortium. To effectively incorporate these data in PMN, improvements will be made to the PMN enzyme prediction software to better identify differentiating features among enzyme family members, including enzyme classes with few existing members. The scope of information available in PMN will be expanded to include new cell-type and tissue-specific databases. Workshops will be organized at major plant biology conferences to introduce users to PMN’s capabilities. Workshops at phytochemistry and plant metabolism conferences will focus on distributing the data generated by the consortium. These conferences are poised to recruit scientists to expand the consortium beyond the enzyme families targeted in this proposal.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.

人口激增和气候变化已经给农业带来了前所未有的压力。满足世界不断发展的食物需要有必要的韧性，营养和丰富的农作物的发展。需要解决这些挑战的植物科学的协作和创新方法，再加上STEM教育和招募的外展计划。该项目将扩大植物代谢网络（PMN），该数据库的集合用于研究植物的代谢及其基因组与代谢的关系。这种扩展将使PMN的数据库从126种增加到1000多种。扩大的PMN将为研究人员提供一系列不断发展的工具，以迅速加速基本和翻译的植物科学研究和应用，以满足现实世界的需求。 PMN的扩展还将为中学和大专教育的人们创造出宝贵的教育工具。将生产和分发有关植物遗传学，生物化学和代谢的教育资源，包括用于PMN的视频教程和课程计划，展示了植物如何产生对人类有用的各种化学物质。在大学中，将建立基于试验课程的本科研究经验（CURE），以为本科生提供基因组和代谢研究的尖端，专家机会。学校老师的顾问委员会将指导中学和高中受众的参与工作，重点是由代表人数不足的少数群体组成的学生身体。该项目为植物科学的协作和进步提供了足够的机会，以及激发和指导与代表性不足的团体认同STEM教育的学生的举措。为了扩展PMN数据库，该项目将重新使用现有的PMN管道，以便按规模运行，将其包装到一个容器化的应用程序中，并将其包装到运行的过程中。重新处理的管道将用于快速创建从GenBank，10KP和其他来源的1000个植物基因组中创建新的PMN数据库。该项目旨在通过实验确定和整合酶生化数据来增强植物代谢的计算预测，以扩大内容并提高数据库的准确性。作为一个项目成分，将建立一个酶联盟，以大规模进行预测引导的酶功能研究，靶向在计算注释中表现较差的酶类别，并将生化数据整合到PMN中。我们将重点关注该初始财团中的萜烯合酶，细胞色素P450和氨基酰基转移酶。为了有效地将这些数据纳入PMN，将对PMN酶预测软件进行改进，以更好地识别酶家庭成员之间的区别特征，包括酶类，少数现有成员。 PMN中可用的信息范围将扩大，包括新的细胞类型和组织特异性数据库。研讨会将在主要的植物生物学会议上组织，以向用户介绍PMN的功能。植物化学和植物代谢会议的讲习班将集中于分布财团产生的数据。这些会议被毒死以招募科学家，以将财团扩展到本提案中针对的酶家族之外。该奖项反映了NSF的法定任务，并使用基金会的知识分子优点和更广泛的影响审查标准，通过评估被认为是宝贵的支持。