RESEARCH-PGR: Combining machine learning and experimental analysis to define trichome and root-specific gene regulatory networks in cultivated tomato and related Solanaceae species

植物专门化代谢物是一种独特的化学物质，只由某些物种产生，通常存在于植物的特定部位。一些专门的代谢物对植物害虫是有毒的，而另一些则吸引有益的昆虫或微生物。许多专门的代谢物对人类来说是美味的，例如罗勒、薄荷和生姜中的代谢物，而其他一些代谢物则具有药用价值，如抗癌药物紫杉醇和抗疟疾青蒿素。西红柿会产生一种叫做酰基糖的特殊代谢物，这种物质像苍蝇纸胶一样粘稠，可以抵御害虫。酰基糖只在番茄的两个部分中产生：1)叶表面微小的毛状结构，称为毛状体；2)根。了解西红柿如何控制酰基糖的产生时间和地点，将教会生物技术专家如何修改甚至设计植物，以便在特定发育阶段的指定植物部位产生专门的代谢物。我们的第一个目标是将试验台实验和计算分析相结合，以揭示控制毛状体和根中酰糖生产的DNA序列和蛋白质。接下来，我们将比较番茄近缘的DNA和蛋白质，以揭示毛状体和根中的酰糖生产是如何进化的。除了研究，我们的团队还将领导两项活动，让公众了解我们的科学方法和发现：一项是为中小学生练习计算思维而设计的《Codes-Like-A-Girl》，另一项是向参与者介绍植物的特殊代谢物--《植物为什么这么难闻？》。特定的代谢物是在特定的细胞或组织中合成的，表明它们受到严格的监管。然而，调控特定代谢基因的组织和细胞类型特异性表达的顺式调控序列和DNA结合的转录因子通常是未知的。由于番茄酰基糖是在毛状体和根中特异合成的，我们的目标是利用酰基糖途径作为一个模型：(1)识别调控代谢基因空间特异性表达的顺式/反式机制；(2)评估调控进化对代谢多样性的贡献。这些目标将使用茄科物种来解决，重点是栽培番茄茄子及其野生近亲S.pennellii。该项目将生成毛状体和根基因调控网络，描述每个物种中转录因子、它们结合的顺式调控序列和它们的目标基因之间的全基因组联系。通过比较茄科不同物种的酰基糖调节成分，将揭示毛状体和根特异表达进化的分子变化。这些发现将提供关于顺式/反式调控创新如何影响空间表达模式并最终有助于特定代谢物的适应功能的新细节。这个项目为跨学科的科学培训提供了一个天然的平台，因为它包括生物化学、计算生物学、进化生物学、遗传学和基因组学方面的专家。此外，该项目每年夏天将接待来自PlantGenology@MSU REU计划的本科生，为期10周的研究密集型体验，包括计算生物学培训、每周的STEM职业研讨会、每周的研讨会，让学生参与不同的研究主题、职业发展机会和口头/海报演示。该奖项反映了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。

Plant specialized metabolites are distinct chemicals, only made by certain species, often in specific plant parts. Some specialized metabolites are poisonous to plant pests, while others attract beneficial insects or microbes. Many specialized metabolites are flavorful to humans, for example those in basil, mint, and ginger root, while others have medicinal properties, such as the anti-cancer drug taxol and the antimalarial artemisinin. Tomatoes produce specialized metabolites called acylsugars, which are sticky like fly paper glue and protect against pests. Acylsugars are only made in two parts of the tomato: 1) tiny hair-like structures on the leaf surface called trichomes and 2) roots. Understanding how tomatoes control when and where acylsugars are produced will teach biotechnologists how to modify or even design plants to make specialized metabolites in designated plant parts at certain developmental stages. Our first goal is to combine bench experiments and computational analyses to uncover the DNA sequences and proteins that control acylsugar production in trichomes and roots. Next, we will compare DNA and proteins across tomato relatives to reveal how acylsugar production has evolved in trichomes and roots. Beyond research, our team will lead two activities to engage the public about our scientific approaches and findings: “Code-Like-A-Girl'', designed for elementary and middle school girls to practice computational thinking, and “Why are Plants So Smelly?”, which introduces participants to plant specialized metabolites. Specialized metabolites are synthesized in specific cells or tissues, indicating they are under tight regulatory control. However, the cis-regulatory sequences and DNA-binding transcription factors regulating tissue- and cell type-specific expression of specialized metabolism genes are often unknown. Because tomato acylsugars are synthesized specifically in trichomes and roots, our goals are to utilize the acylsugar pathway as a model to: (1) identify the cis/trans mechanisms regulating spatially-specific expression of metabolic genes and (2) assess the contribution of regulatory evolution to metabolic diversity. These goals will be addressed using Solanaceae species, focusing on the cultivated tomato, Solanum lycopersicum, and its wild relative, S. pennellii. This project will generate trichome and root gene regulatory networks, describing genome-wide connections between transcription factors, the cis-regulatory sequences they bind, and their target genes in each species. Comparison of acylsugar regulatory components across Solanaceae species will reveal the molecular changes underlying trichome- and root-specific expression evolution. These findings will provide new details on how cis/trans regulatory innovations influence spatial expression patterns and ultimately contribute to adaptive functions of specialized metabolites. This project provides a natural platform for interdisciplinary scientific training because it includes experts in biochemistry, computational biology, evolutionary biology, genetics, and genomics. In addition, the project will host undergraduates each summer from the PlantGenomics@MSU REU program, a 10-week research-intensive experience including computational biology training, a weekly STEM career workshop, a weekly seminar engaging students on diverse research themes, professional development opportunities, and oral/poster presentations.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.