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

植物是大师级的化学家，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明确的作用，包括保护免受疾病和昆虫的侵害以及吸引有益的伙伴生物。有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是很好理解的，留下了很多关于植物如何产生这种巨大多样性的产品的知识。这项研究将侧重于茄科（茄属）家族的专门代谢，其中包括重要的作物番茄、马铃薯、辣椒和茄子，并记录了各种各样的天然产物。总体目标是开发计算和实验方法，以发现新的植物化学物质，并找到植物用于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的专门代谢物的生物化学和遗传机制的理解。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，提高对疾病和昆虫的抗性，并提高作物价值;它还将开发新的方法，将计算和实验方法结合起来，研究代谢。该项目的推广活动包括夏季研究的本科生从代表性不足的群体，教师的培训，主要是本科院校与大量的少数民族招生，和夏季计划的科学推广到adult.Part 2：技术摘要识别基因参与专门的新陈代谢是非常重要的，因为这些基因的变化提供了一个基础，特定的谱系化学多样性。该项目将提供专门的代谢基因和其他基因之间的差异的定量评估。预测的部分基因组专门在茄科代谢将使用假设驱动的实验方法进行测试。对茄科（Solanaceae）家族的分析，包括重要的作物以及植物生态学和进化模型，将建立一个计算预测和实验验证植物王国中与代谢相关的专门基因的范例。该项目将利用迅速增加的茄科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，包括质谱法和核磁共振光谱法，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。将采用体外蛋白质生物化学和功能基因组学方法验证候选基因的功能，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的群体的本科生进行夏季研究，为主要是本科院校的少数民族学生进行教师培训，以及为成人提供科学外展的夏季计划。

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.