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

RESEARCH-PGR：结合机器学习和实验分析来定义栽培番茄和相关茄科物种中的毛状体和根特异性基因调控网络

• 批准号: 2218206
• 负责人: Shin-Han Shiu
• 金额: $ 180万
• 依托单位: Michigan State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-01-01 至 2025-12-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2218206&HistoricalAwards=false
• 关键词: RESEARCH; PGR; Combining; machine; learning

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.

植物专用代谢物是不同的化学物质，仅由某些物种制成，通常是在特定植物部分中。一些专门的代谢产物对植物有毒是有毒的，而另一些则吸引有益的昆虫或微生物。许多专门的代谢产物对人类味道鲜美，例如罗勒，薄荷和生姜根，而其他人则具有药用特性，例如抗癌药物紫杉醇和抗疟temisinin。西红柿产生的专门代谢产物称为酰基糖，它们像飞纸一样粘稠并防止害虫。酰基糖仅在番茄的两个部分中制成：1）叶片表面上的微型头发状结构，称为毛状体和2）根。了解西红柿如何控制酰基糖的何时何地，将教会生物技术医生如何修改甚至设计植物以在某些发育阶段在指定的植物部分中制作专门的代谢物。我们的第一个目标是结合基准实验和计算分析，以揭示控制丝粒和根中酰基糖产生的DNA序列和蛋白质。接下来，我们将比较跨番茄亲戚的DNA和蛋白质，以揭示酰基糖产量如何在毛状体和根中进化。除了研究之外，我们的团队还将领导两项活动，以使我们的科学方法和发现与公众吸引：“像代码一样的女孩”，专为小学和中学女孩设计，以练习计算思维，“为什么植物如此臭？”，参与者介绍了植物专用代谢物的参与者。专门的代谢物是在特定的细胞或组织中合成的。 DNA-binding transcription factors regulatory tissue- and cell type-specific expression Because tomato acylsugars 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 regulatory spatially-specific expression of metabolic genes and (2) assess the contribution of regulatory代谢多样性的进化将使用卵巢科来解决，重点是培养的番茄，茄列氏菌及其野生亲戚S. pennellii。该项目将生成毛状基因调节网络，描述转录因子之间的全基因组连接，它们结合的顺式调节序列以及每个物种中的靶基因。比较茄科种类的酰基糖调节成分将揭示毛毛毛虫和根特异性表达演化的分子变化。这些发现将提供有关顺式/反式调节创新如何影响空间表达模式的新细节，并最终有助于专门代谢物的适应性功能。该项目为跨学科科学培训提供了自然平台，因为它包括生物化学，计算生物学，进化生物学，遗传学和基因组学专家。 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 semi-engaging students on divers research themes, professional development opportunities, and oral/poster presentations.This award reflects NSF's statutory mission and has been deemed precious of support through evaluation using the Foundation's intellectual merit and broader impacts review 标准。

项目成果

Effect of wastewater collection and concentration methods on assessment of viral diversity

废水收集和浓缩方法对病毒多样性评估的影响

• DOI: 10.1016/j.scitotenv.2023.168128
• 发表时间: 2023
• 期刊: Science of The Total Environment
• 影响因子: 9.8
• 作者: Li, Yabing;Miyani, Brijen;Childs, Kevin L.;Shiu, Shin-Han;Xagoraraki, Irene
• 通讯作者: Xagoraraki, Irene

Challenges and opportunities to build quantitative self-confidence in biologists

• DOI: 10.1093/biosci/biad015
• 发表时间: 2023-04-29
• 期刊: BIOSCIENCE
• 影响因子: 10.1
• 作者: Cuddington，Kim;Abbott，Karen C.;White，Easton R.
• 通讯作者: White，Easton R.

Plant Science Knowledge Graph Corpus: a gold standard entity and relation corpus for the molecular plant sciences

植物科学知识图谱语料库：分子植物科学的黄金标准实体和关系语料库

• DOI: 10.1093/insilicoplants/diad021
• 发表时间: 2023
• 期刊: in silico Plants
• 影响因子: 3.1
• 作者: Lotreck, Serena;Segura Abá, Kenia;Lehti-Shiu, Melissa D.;Seeger, Abigail;Brown, Brianna N. I.;Ranaweera, Thilanka;Schumacher, Ally;Ghassemi, Mohammad;Shiu, Shin-Han;Marshall-Colon, ed., Amy
• 通讯作者: Marshall-Colon, ed., Amy

Lignin Biosynthesis Gene Expression Is Associated with Age-related Resistance of Winter Squash to Phytophthora capsici

• DOI: 10.21273/jashs05317-23
• 发表时间: 2023-09
• 期刊: J. Amer. Soc. Hort. Sci.
• 作者: S. Alzohairy;Bethany M. Moore;Raymond Hammerschmidt;Shin-Han Shiu;M. Hausbeck