NSF Postdoctoral Fellowship in Biology FY 2019: The Contribution of the AUXIN RESPONSE FACTORS (ARF) Dimerization to ARF DNA-Binding

2019 财年 NSF 生物学博士后奖学金：生长素反应因子 (ARF) 二聚化对 ARF DNA 结合的贡献

• 批准号: 1907098
• 负责人: Nicholas Morffy
• 金额: $ 21.6万
• 依托单位: Morffy Nicholas J
• 依托单位国家: 美国
• 项目类别: Fellowship Award
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-07-01 至 2023-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1907098&HistoricalAwards=false
• 关键词: NSF; Postdoctoral; Fellowship; Biology; FY

This action funds an NSF National Plant Genome Initiative Postdoctoral Research Fellowship in Biology for FY 2019. The fellowship supports a research and training plan in a host laboratory for the Fellow who also presents a plan to broaden participation in biology. The title of the research and training plan for this fellowship to Dr. Nicholas Morffy is "The Contribution of the ARF Dimerization to ARF DNA-Binding." The host institution for the fellowship is the Washington University in St. Louis and the sponsoring scientist is Dr. Lucia C. Strader.Auxin is a small plant signaling molecule that is involved in altering growth and development and has a major impact on crop productivity. Auxin regulates these processes through AUXIN RESPONSE FACTORS (ARF), a large family of transcription factors found in many plant species. Transcription factors bind DNA and regulate gene transcription which alters how plants grow. Understanding how large transcription factor families, like the ARFs, mediate DNA-binding specificity across a plant genome is important for the study of plant development and is crucial for better directing crop development. The ARFs are known to work in pairs; however, scientists do not understand how different transcription factor pairs bind specific DNA, or how transcription factors might interact with different parts of the genome. This project will utilize the properties of the ARF transcription factor family to better understand how distinct transcription factor pairs alter DNA binding across a genome. This research will lead to a better understanding of how transcription factors regulate genes and may lay the ground work for more directed control of plant growth and development in important crop species such as maize. Broader impacts include broadening participation of underrepresented minority students in STEM fields through established programs at Washington University in St. Louis such as the Young Scientist Program (YSP; ysp.wustl.edu/) for K12 and the NIH-supported Research Education R25 and Maximizing Access to Research Careers (MARC) T34 programs for undergraduate students. Training objectives to prepare the Fellow for a successful career as a plant biologist include acquiring expertise in protein biochemistry, biophysics, genomics, plant evolution as well as in science communication and mentorship. The phytohormone auxin is a crucial regulator of all aspects of plant development. Many transcription factors work as homo- and heterodimers, but the relationship between transcription factor dimerization and DNA-binding specificity remains unstudied. The primary transcriptional regulators of auxin signaling, the AUXIN RESPONSE FACTORS (ARF) proteins present an appealing model to study transcription factor dimerization because the mechanisms of ARF function, including the molecular basis of ARF DNA binding and ARF dimerization, have recently been described. ARF proteins have a modular structure that includes a C- terminal type I/II Phox and Bem1 (PB1) domain. PB1 domains mediate protein interactions between ARFs in a directional manner, but how the PB1 domain contributes to ARF DNA-binding and dimerization specificity is currently unknown. This project will combine evolutionary, biophysical, and genetic/genomic techniques to study PB1-mediated interactions and their impact on DNA binding in two divergent land plant species, Marchantia polymorpha and Zea mays. There are three specific aims: 1) determine if ARF PB1 interactions contribute to ARF dimerization specificity by identifying amino acid residues participating in ARF-ARF PB1 interactions across the land plant lineage, informed by structural, biophysical, and comparative sequence data. Putative interactions will be tested using in vitro and in vivo protein interaction techniques to determine the interaction affinities of different ARF PB1 domains; 2) test if specific ARF dimers bind to distinct loci in Z. mays and M. polymorpha. Next generation sequencing approaches, including DAP-seq, will be used to test and compare DNA-binding patterns of different ARF homo- and heterodimers from both Z. mays and M. polymorpha; and, 3) determine if the M. polymorpha ARF1 PB1 domain contributes to chromatin interactions and ARF function. Reporter lines will be used to determine if ARF multimers can promote chromosomal interactions in M. polymorpha. All genomic data generated during the project will be made available in the NCBI Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/) for archiving. Sequence alignments and phylogenetic trees will be uploaded to Dryad (https://datadryad.org) and made publicly available. All experimental material and samples generated for these studies will be stored at Washington University and made available upon request. In addition to the genomic and phylogenetic data, experimental results generated from this project will be disseminated through the use of journal publications and presentations at scientific meetings (poster presentations and oral presentations) in a timely fashion. The data generated by this project will provide a framework for elucidating the relationship between protein interaction partners and DNA-binding specificity, as well increasing understanding of the ARFs and auxin signaling generally.Keywords: Maize, Marchantia polymorpha, DNA-binding, Auxin, Transcription Factors, ARFsThis 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.

该行动资助了 2019 财年 NSF 国家植物基因组计划生物学博士后研究奖学金。该奖学金支持该研究员在主办实验室的研究和培训计划，该研究员还提出了一项扩大生物学参与的计划。 Nicholas Morffy 博士的研究和培训计划的标题是“ARF 二聚化对 ARF DNA 结合的贡献”。该奖学金的主办机构是圣路易斯华盛顿大学，资助科学家是 Lucia C. Strader 博士。生长素是一种小型植物信号分子，参与改变生长和发育，并对作物生产力产生重大影响。生长素通过生长素反应因子 (ARF) 调节这些过程，ARF 是许多植物物种中发现的一大转录因子家族。转录因子结合 DNA 并调节基因转录，从而改变植物的生长方式。了解大型转录因子家族（如 ARF）如何介导植物基因组中的 DNA 结合特异性对于植物发育研究非常重要，对于更好地指导作物发育也至关重要。众所周知，ARF 是成对工作的。然而，科学家们并不了解不同的转录因子对如何结合特定的 DNA，也不了解转录因子如何与基因组的不同部分相互作用。该项目将利用 ARF 转录因子家族的特性来更好地了解不同的转录因子对如何改变基因组中的 DNA 结合。这项研究将有助于更好地理解转录因子如何调节基因，并可能为更直接地控制玉米等重要作物物种的植物生长和发育奠定基础。更广泛的影响包括通过圣路易斯华盛顿大学的既定项目扩大代表性不足的少数族裔学生对 STEM 领域的参与，例如针对 K12 的青年科学家项目 (YSP; ysp.wustl.edu/) 以及 NIH 支持的研究教育 R25 和针对本科生的研究职业最大化 (MARC) T34 项目。为使研究员成为一名成功的植物生物学家做好准备的培训目标包括获得蛋白质生物化学、生物物理学、基因组学、植物进化以及科学传播和指导方面的专业知识。植物激素生长素是植物发育各个方面的重要调节剂。许多转录因子以同二聚体和异二聚体的形式发挥作用，但转录因子二聚体和 DNA 结合特异性之间的关系仍未得到研究。生长素信号传导的主要转录调节因子，生长素响应因子 (ARF) 蛋白为研究转录因子二聚化提供了一个有吸引力的模型，因为最近已经描述了 ARF 功能的机制，包括 ARF DNA 结合和 ARF 二聚化的分子基础。 ARF 蛋白具有模块化结构，包括 C 端 I/II 型 Phox 和 Bem1 (PB1) 结构域。 PB1 结构域以定向方式介导 ARF 之间的蛋白质相互作用，但 PB1 结构域如何促进 ARF DNA 结合和二聚化特异性目前尚不清楚。该项目将结合进化、生物物理和遗传/基因组技术来研究 PB1 介导的相互作用及其对两种不同陆地植物物种（地钱和玉米）中 DNA 结合的影响。共有三个具体目标：1) 通过根据结构、生物物理和比较序列数据鉴定参与陆地植物谱系中 ARF-ARF PB1 相互作用的氨基酸残基，确定 ARF PB1 相互作用是否有助于 ARF 二聚化特异性。将使用体外和体内蛋白质相互作用技术来测试假定的相互作用，以确定不同 ARF PB1 结构域的相互作用亲和力； 2) 测试特定的 ARF 二聚体是否与玉米和地钱中的不同基因座结合。包括 DAP-seq 在内的下一代测序方法将用于测试和比较来自玉米和地钱的不同 ARF 同二聚体和异二聚体的 DNA 结合模式； 3) 确定地钱 ARF1 PB1 结构域是否有助于染色质相互作用和 ARF 功能。报告系将用于确定 ARF 多聚体是否可以促进地钱中的染色体相互作用。该项目期间生成的所有基因组数据将在 NCBI 基因表达综合库 (https://www.ncbi.nlm.nih.gov/geo/) 中提供以供存档。序列比对和系统发育树将上传至 Dryad (https://datadryad.org) 并公开发布。这些研究产生的所有实验材料和样本将存储在华盛顿大学，并可根据要求提供。除了基因组和系统发育数据外，该项目产生的实验结果将通过使用期刊出版物和科学会议上的演示（海报演示和口头演示）及时传播。该项目生成的数据将提供一个框架，用于阐明蛋白质相互作用伙伴与 DNA 结合特异性之间的关系，并增进对 ARF 和生长素信号传导的总体了解。 关键词：玉米、地钱、DNA 结合、生长素、转录因子、ARF 该奖项反映了 NSF 的法定使命，并通过使用基金会的智力评估进行评估，认为值得支持。 优点和更广泛的影响审查标准。

项目成果

Structural Aspects of Auxin Signaling

• DOI: 10.1101/cshperspect.a039883
• 发表时间: 2022-01-01
• 期刊: COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY
• 影响因子: 7.2
• 作者: Morffy, Nicholas;Strader, Lucia C.
• 通讯作者: Strader, Lucia C.

Direct photoresponsive inhibition of a p53-like transcription activation domain in PIF3 by Arabidopsis phytochrome B.

• DOI: 10.1038/s41467-021-25909-5
• 发表时间: 2021-09-23
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Yoo CY;He J;Sang Q;Qiu Y;Long L;Kim RJ;Chong EG;Hahm J;Morffy N;Zhou P;Strader LC;Nagatani A;Mo B;Chen X;Chen M
• 通讯作者: Chen M

Prediction and functional characterization of transcriptional activation domains

转录激活域的预测和功能表征

• DOI: 10.1109/ciss56502.2023.10089768
• 发表时间: 2023
• 期刊: 2023 57th Annual Conference on Information Sciences and Systems (CISS
• 作者: Mahatma, Saloni;Van den Broeck, Lisa;Morffy, Nicholas;Staller, Max V;Strader, Lucia C;Sozzani, Rosangela
• 通讯作者: Sozzani, Rosangela