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

植物是化学大师，产生成千上万的具有不同结构和活性的小分子。这些特殊代谢物中的一些具有明确的作用，包括防止疾病和昆虫以及吸引有益的伴侣生物。有些被人类用作药物和对环境安全的杀虫剂。这些化合物中只有一小部分的代谢途径得到了很好的理解，关于植物如何产生如此巨大的产品多样性，还有很多需要了解的。本研究将集中研究茄科（茄科）的特殊代谢，茄科包括重要的作物番茄、土豆、辣椒和茄子，其中有大量的天然产物被记录下来。总体目标是开发计算和实验方法来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健康有价值的小分子的基因。该项目的成果将扩大对生物化学和遗传机制的理解，通过这些机制，植物产生不同种类的特殊代谢物。这项研究将支持育种和转基因方法，以改善作物中特殊代谢物的合成，从而增强对疾病和昆虫的抵抗力，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。项目外展活动包括针对代表性不足群体的本科生的暑期研究，针对少数族裔学生较多的主要本科院校的师资培训，以及针对成年人的暑期科学外展项目。鉴定参与特化代谢的基因非常重要，因为这些基因的变化为谱系特异性化学多样性提供了基础。该项目将对特化代谢基因与其他基因之间的差异进行定量评估。预测的部分基因组致力于在茄科的特殊代谢将使用假设驱动的实验方法进行测试。对茄科植物的分析，包括重要的作物以及植物生态学和进化模型，将为计算预测和实验验证植物界的特殊代谢相关基因建立一个范例。该项目将利用茄科快速增长的植物基因组和转录组资源，通过计算来定义编码特殊代谢酶的基因特征。计算方法将与分析化学方法相结合，包括质谱法和核磁共振波谱法，以发现专门的代谢物，并指导鉴定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用于验证基因候选功能，并提高计算方法的准确性。项目外展活动包括针对代表性不足群体的本科生的暑期研究，针对少数族裔学生较多的主要本科院校的师资培训，以及针对成年人的暑期科学外展项目。

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.