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，就必须发展富有弹性、营养丰富的作物。为了应对这些挑战，需要对植物科学采取协作和创新的方法，并结合STEM教育和招聘的外联倡议。该项目将扩展植物新陈代谢网络(PMN)，这是一个用于研究植物新陈代谢及其基因组与新陈代谢相关的数据库集合。这一扩展将使PMN中的数据库从126个物种增加到1000多个物种。一个扩展的PMN将为研究人员提供一套丰富的、不断发展的工具，以快速加快基础和翻译植物科学研究和应用，以满足现实世界的需求。PMN的扩大还将为中学和中学后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的视频教程和演示植物如何产生对人类有用的各种化学物质的教案。在大学，将建立以试点课程为基础的本科生研究体验(CURE)，为本科生提供在基因组和新陈代谢研究方面的前沿经验机会。一个由学校教师组成的顾问委员会将指导初中和高中观众的参与努力，重点是主要由代表性不足的少数族裔组成的学生团体。这个项目提供了大量的机会来加强在植物科学领域的合作和进步，以及鼓励和引导那些认同代表不足群体的学生进行STEM教育。为了扩大PMN数据库，这个项目将重新装备现有的PMN管道以进行规模化操作，将其打包到一个集装箱应用程序中，并使其运行的大部分过程自动化。重组后的管道将用于从GenBank、10kp和其他来源的1000个植物基因组中快速创建新的PMN数据库。本项目旨在通过实验测定和整合酶生化数据来扩大数据库的内容和提高数据库的准确性，以增强对植物代谢的计算预测。作为一个项目组成部分，将建立一个酶联盟，在规模上进行预测引导的酶功能研究，针对在计算注释方面表现不佳的酶类，并将生化数据整合到PMN中。在这个最初的联合体中，我们将重点关注萜烯合成酶、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区别特征，包括现有成员很少的酶类。PMN提供的信息范围将扩大到包括新的细胞类型和特定组织数据库。将在主要的植物生物学会议上组织研讨会，向用户介绍PMN的能力。植物化学和植物新陈代谢会议的研讨会将侧重于分发该联盟产生的数据。这些会议准备招募科学家，以扩大该联盟的范围，使其超越本提案中所针对的酶家族。这一奖项反映了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。

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.