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，就必须发展适应力强、营养丰富和邦蒂富尔的作物。为了应对这些挑战，需要对植物科学采取合作和创新的方法，并结合STEM教育和招聘的外联举措。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与代谢关系的数据库集合。这一扩展将使PMN中的数据库从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，满足现实世界的需求。扩大中学网还将为中学和中学后教育的学生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课程计划。在大学中，将建立一个试点课程为基础的本科生研究经验（CURE），为本科生提供基因组和代谢研究方面的尖端体验机会。一个学校教师咨询委员会将指导在初中和高中受众中开展的参与工作，重点是主要由代表性不足的少数群体组成的学生团体。该项目为植物科学领域的合作和进步提供了充足的机会，并鼓励和引导那些认同代表性不足的群体的学生接受STEM教育。为了扩大PMN数据库，该项目将重组现有的PMN管道，以大规模运作，将其打包成一个容器化的应用程序，并自动化运行它的大部分过程。重组后的管道将用于从1000个植物基因组中快速创建新的PMN数据库。GenBank，10KP和其他来源。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并提高准确性，以增强植物代谢的计算预测。作为项目的一部分，将建立一个酶联盟，以进行大规模的预测指导酶功能研究，针对在计算注释中表现不佳的酶类别，并将生化数据整合到PMN中。我们将集中在萜烯脱氢酶，细胞色素P450，和氨酰转移酶在这个最初的财团。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别。PMN中可用信息的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研讨会，向用户介绍PMN的功能。在植物化学和植物代谢会议上举办的讲习班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，以扩大联盟以外的酶家族的目标在这个建议。这个奖项反映了NSF的法定使命，并已被认为是值得的支持，通过评估使用基金会的知识价值和更广泛的影响审查标准。

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.