RESEARCH-PGR: How do plants produce so many diverse metabolites: A computational and experimental comparative genomics investigation in the Solanaceae

RESEARCH-PGR：植物如何产生如此多不同的代谢物：茄科的计算和实验比较基因组学研究

• 批准号: 1546617
• 负责人: Robert Last
• 金额: $ 526.69万
• 依托单位: Michigan State University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-08-15 至 2022-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1546617&HistoricalAwards=false
• 关键词: RESEARCH; PGR; How; do; plants

Part 1: Non-technical abstractPlants are master chemists, producing thousands of small molecules of varied structures and activities. Some of these specialized metabolites have well established roles, including protection from diseases and insects and attraction of beneficial partner organisms. Some are used by humans as medicines and environmentally safe pesticides. The metabolic pathways for only a small fraction of these compounds are well understood, leaving much to learn about how plants produce this enormous diversity of products. This research will focus on specialized metabolism in the Solanaceae (nightshade) family, which includes the important crops tomato, potato, peppers and eggplant and in which a great diversity of natural products is documented. The overarching goal is to develop computational and experimental approaches to discover new plant chemicals and to find the genes that plants use to make small molecules that are valuable for agriculture and human wellbeing. The project outcomes will expand the understanding of the biochemical and genetic mechanisms by which plants produce different classes of specialized metabolites. This research will support breeding and transgenic approaches to improve specialized metabolite synthesis in crop plants to increase resistance to disease and insects and enhance crop value; it will also develop new methods for combining computational and experimental approaches in the study of metabolism. The project outreach activities include summer research for undergraduates from under-represented groups, training of faculty for primarily undergraduate institutions with substantial minority enrollments, and a summer program for science outreach to adults.Part 2: Technical abstractThe identification of genes involved in specialized metabolism is of great importance, since changes in these genes provide a basis for lineage-specific chemical diversity. This project will provide quantitative assessments of the differences between specialized metabolism genes and other genes. The predicted portion of the genome devoted to specialized metabolism within the Solanaceae will be tested using hypothesis-driven experimental approaches. This analysis of the Solanaceae family, which includes important crops as well as models in plant ecology and evolution, will establish a paradigm for computationally predicting and experimentally validating specialized metabolism-related genes across the plant kingdom. The project will take advantage of the rapidly increasing plant genome and transcriptome resources in the Solanaceae to define computationally the characteristics of genes encoding specialized metabolic enzymes. The computational approaches will be coupled with analytical chemical methods, including mass spectrometry and nuclear magnetic resonance spectroscopy, to discover specialized metabolites and to guide the identification of candidate genes encoding enzymes that produce novel metabolites. In vitro protein biochemistry and functional genomics methods will be employed to validate gene candidate functions, and to improve the accuracy of the computational methods. The project outreach activities include summer research for undergraduates from under-represented groups, training of faculty for primarily undergraduate institutions with substantial minority enrollments, and a summer program for science outreach to adults.

第一部分：非技术抽象植物是化学大师，能产生成千上万种不同结构和活性的小分子。其中一些专门的代谢物具有良好的作用，包括保护免受疾病和昆虫的伤害，以及吸引有益的伙伴生物体。一些被人类用作药物和环境安全的杀虫剂。这些化合物中只有一小部分的代谢途径已经被很好地理解了，关于植物如何产生如此巨大的多样性的产品，留下了很多需要了解的东西。这项研究将集中在茄科(茄科)中的特殊代谢，包括重要的作物番茄、马铃薯、辣椒和茄子，其中有大量的天然产物被记录在案。首要目标是开发计算和实验方法，以发现新的植物化学物质，并找到植物用来制造对农业和人类福祉有价值的小分子的基因。该项目的成果将扩大对植物产生不同类别专门代谢物的生化和遗传机制的理解。这项研究将支持育种和转基因方法，以改善作物中专门的代谢物合成，以提高对病虫害的抵抗力和提高作物价值；它还将开发新的方法，将计算和实验方法结合在代谢研究中。该项目的外展活动包括为来自代表性不足群体的本科生进行暑期研究，为主要有大量少数族裔入学的本科生机构培训教师，以及针对成年人的暑期科学外展计划。第二部分：技术摘要识别与专门化新陈代谢有关的基因非常重要，因为这些基因的变化为特定血统的化学多样性提供了基础。该项目将对特定新陈代谢基因和其他基因之间的差异进行定量评估。将使用假说驱动的实验方法来测试基因组中专门用于茄科专门化新陈代谢的预测部分。这种对茄科家族的分析，包括重要的农作物以及植物生态学和进化的模型，将建立一个范例，用于在整个植物界通过计算预测和实验验证与特定代谢相关的基因。该项目将利用茄科迅速增长的植物基因组和转录组资源，通过计算确定编码专门代谢酶的基因的特征。计算方法将与分析化学方法相结合，包括质谱学和核磁共振波谱，以发现专门的代谢物，并指导识别编码产生新代谢物的酶的候选基因。体外蛋白质生物化学和功能基因组学方法将被用来验证基因候选功能，并提高计算方法的准确性。该项目的外展活动包括为来自代表性不足群体的本科生进行暑期研究，为主要为招收大量少数族裔学生的本科院校培训教师，以及一个面向成年人的暑期科学外展项目。

项目成果

Defining Functional Genic Regions in the Human Genome through Integration of Biochemical, Evolutionary, and Genetic Evidence

• DOI: 10.1093/molbev/msx101
• 发表时间: 2017-07
• 期刊: Molecular Biology and Evolution
• 影响因子: 10.7
• 作者: Z. Tsai;J. P. Lloyd;Shin-Han Shiu

Optimising the use of gene expression data to predict plant metabolic pathway memberships

优化基因表达数据的使用来预测植物代谢途径成员资格

• DOI: 10.1111/nph.17355
• 发表时间: 2021
• 期刊: New Phytologist
• 影响因子: 9.4
• 作者: Wang, Peipei;Moore, Bethany M.;Uygun, Sahra;Lehti‐Shiu, Melissa D.;Barry, Cornelius S.;Shiu, Shin‐Han
• 通讯作者: Shiu, Shin‐Han

Regulatory Divergence in Wound-Responsive Gene Expression between Domesticated and Wild Tomato

• DOI: 10.1105/tpc.18.00194
• 发表时间: 2018-07-01
• 期刊: PLANT CELL
• 影响因子: 11.6
• 作者: Liu, Ming-Jung;Sugimoto, Koichi;Shiu, Shin-Han
• 通讯作者: Shiu, Shin-Han