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

人口激增和气候变化给农业带来了前所未有的压力。要满足世界不断变化的粮食需求，就必须发展具有抗灾能力、营养丰富和产量丰富的作物。应对这些挑战需要植物科学的协作和创新方法，以及STEM教育和招聘的外展举措。该项目将扩展植物代谢网络（PMN），这是一个用于研究植物代谢及其基因组如何与代谢相关的数据库集合。这一扩展将使PMN的数据库从126种增加到1000多种。扩展后的PMN将为研究人员提供丰富的、不断发展的工具套件，以快速加速基础和转化植物科学研究和应用，以满足现实世界的需求。PMN的扩大也将为接受中等和高等教育的人创造一个宝贵的教育工具。将制作和分发有关植物遗传学、生物化学和新陈代谢的教育资源，包括PMN的视频教程和课程计划，展示植物如何产生对人类有用的各种化学物质。在大学，将建立一个基于课程的本科生研究体验（CURE）试点项目，为本科生提供基因组和代谢研究的前沿体验机会。一个由教师组成的咨询委员会将指导初中和高中学生的参与工作，重点关注主要由代表性不足的少数民族组成的学生群体。该项目为加强植物科学领域的合作和进步提供了充足的机会，也为那些认同代表性不足群体的学生提供了激励和指导，让他们接受STEM教育。为了扩展PMN数据库，该项目将重新配置现有的PMN管道以进行大规模操作，将其打包到容器化应用程序中，并自动化运行它的大部分过程。重组后的管道将用于从GenBank、10KP和其他来源获取的1000个植物基因组快速创建新的PMN数据库。本项目旨在通过实验测定和整合酶生化数据，扩大数据库的内容，提高数据库的准确性，以增强对植物代谢的计算预测。作为项目组成部分，将建立一个酶联盟，针对在计算注释中表现不佳的酶类，进行大规模的预测指导酶功能研究，并将生化数据整合到PMN中。我们将重点研究萜烯合成酶、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，以更好地识别酶家族成员之间的差异特征，包括现有成员很少的酶类。PMN中可用的信息范围将扩大到包括新的细胞类型和组织特异性数据库。将在主要的植物生物学会议上组织讲习班，向用户介绍PMN的功能。植物化学和植物代谢会议的研讨会将集中讨论由该联盟产生的数据的分发。这些会议准备招募科学家来扩大联盟，超越本提案所针对的酶家族。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

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.