Network-Based Discovery of Brassinosteroid Regulation of Plant Growth and Stress Responses in Arabidopsis

油菜素内酯（BRs）是一种调节植物生长发育和响应环境胁迫的激素。然而，我们对这种类固醇激素如何控制数千个基因来调节这些过程的理解是不完整的。该项目将生成并使用多个大规模数据集来模拟基因如何被控制以控制br调控的生长和干旱反应。BR通路在拟南芥和玉米、水稻等作物中具有良好的保守性，因此从本研究中获得的知识可用于设计策略，以优化干旱条件下的植物生长和作物产量。此外，该项目还为现代植物生物学的研究生和博士后提供了良好的培训机会。研究人员还将通过乔治·华盛顿·卡弗实习计划为代表性不足的本科生提供培训机会，并通过暑期实习吸引高中和社区大学教师，从而实现与社会相关的结果。通过与教师的合作，将为高中和社区大学的学生开发一个关于植物生长br调节的学习模块。此外，未发表的研究数据将被纳入功能基因组学、系统和网络生物学的高级本科课程，让学生在小组项目中自由地产生自己的假设，而不是简单地复制已发表的工作。最后，研究人员将通过组织一个关于植物表型组学、蛋白质组学和计算建模方法的研讨会，并通过出版物和首席研究员的实验室网站公开生成的数据，为研究界提供资源。拟南芥的分子遗传学研究极大地促进了我们对BR信号通路的理解。BRs信号调节BES1/BZR1家族转录因子（TFs）、数百个br相关转录因子（BR-TFs）和数千个靶基因。虽然已经鉴定了许多br - tf，但允许BES1/BZR1和这些br - tf调节大量br应答基因的转录复合物尚未被表征。此外，BR网络的建模已被证明是了解BES1如何指导控制数千个BR应答基因的网络的有力方法。然而，先前构建的BR网络只考虑转录，忽略了转录后和翻译后水平的重要调控。该项目将采用综合遗传学、基因组学和蛋白质组学方法，建立并实验测试一个全面的拟南芥基因调控网络（GRN），以控制br调控的生长和干旱响应。通过将尖端的蛋白质组学与先进的预测建模相结合，该项目将产生BR介导的转录调控的全面视图，并允许识别涉及BR反应的新因素。首先，研究人员将通过检测两种新型BR- tf的作用来揭示BR转录因子复合物的组成和功能。这两种BR- tf与BR通路的主调控因子BES1以及大量其他BR- tf相互作用，可能形成大的转录复合物来控制BR靶基因的表达。其次，研究人员将生成BR转录组、蛋白质组和磷蛋白质组数据集，这是联合首席研究员开创的基于这些组合组学数据构建grn的新方法的先决条件。与仅基于转录数据的网络相比，这些组合网络具有更高的预测能力，并将提供重要资源，允许更完整地了解br控制植物生长和胁迫反应的转录程序。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Plant steroid hormones called Brassinosteroids (BRs) signal to regulate plant growth, development and response environmental stresses. However, our understanding of how this steroid hormone controls thousands of genes to regulate these processes is incomplete. The project will generate and use multiple large-scale datasets to model how genes are controlled to govern BR-regulated growth and drought responses. BR pathways are well conserved among Arabidopsis and crop plants such as maize, rice and other crops, so the knowledge obtained from the proposed studies can be used to design strategies to optimize plant growth and crop production under drought conditions. Moreover, the project provides excellent training opportunities for graduate students and postdoctoral associates in modern plant biology. The investigators will also achieve societally relevant outcomes by providing training opportunities to underrepresented undergraduates through the George Washington Carver Internship program as well as engaging high school and community college teachers via summer internships. Through this partnership with teachers a learning module on BR-regulation of plant growth will be developed for high-school and community college students. Furthermore, unpublished data from the proposed studies will be incorporated into an upper level undergraduate course on functional genomics, systems, and network biology, freeing students to generate their own hypotheses during a group project rather than simply reproducing published work. Finally, the investigators will provide resources to the research community by organizing a workshop on plant phenomics, proteomics and computational modeling approaches and by making the data generated publicly accessible through publications and the Principal Investigator's laboratory website.Molecular genetic studies in Arabidopsis have greatly advanced our understanding of the BR signaling pathway. BRs signal to regulate BES1/BZR1 family transcription factors (TFs), hundreds of BR-Related Transcription Factors (BR-TFs) and thousands of target genes. Although numerous BR-TFs have been identified, the transcriptional complexes that allow BES1/BZR1 and these BR-TFs to regulate the large number of BR-responsive genes have not been characterized. In addition, modeling of BR networks has proven to be a powerful approach to understand how BES1 directs a network controlling thousands of BR responsive genes. However, previously constructed BR networks have only considered transcription, overlooking important regulation at the post-transcriptional and post-translational level. The project will use an integrated genetics, genomics, and proteomics approach to establish and experimentally test a comprehensive Arabidopsis Gene Regulatory Network (GRN) governing BR-regulated growth and drought responses. By combining cutting-edge proteomics with advanced predictive modeling the project will generate a comprehensive view of BR-mediated transcriptional regulation and allow for the identification of novel factors involved in BR responses. First, investigators will uncover the components and functions of BR transcription factor complexes by examining the role of two novel BR-TFs. These two BR-TFs interact with BES1, a master regulator of the BR pathway, as well as a large number of other BR-TFs, likely forming large transcriptional complexes to control the expression of BR target genes. Second, investigators will generate BR transcriptome, proteome, and phosphoproteome datasets that are a prerequisite for a novel approach pioneered by the Co-Principal Investigator to construct GRNs based on these combined omics data. These combined networks have increased predictive ability compared to networks based only on transcriptional data and will provide a vital resource, allowing for a more complete understanding of the transcriptional program through which BRs control plant growth and stress responses.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.