Genome-wide Analysis of Small Signaling Peptides in Medicago truncatula with an Emphasis on Macro-nutrient Regulation of Root and Nodule Development

蒺藜苜蓿小信号肽的全基因组分析，重点是根和根瘤发育的宏观营养调控

• 批准号: 1444549
• 负责人: Joachim Wolf Scheible
• 金额: $ 331.97万
• 依托单位: Noble Research Institute, LLC
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-08-01 至 2021-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1444549&HistoricalAwards=false
• 关键词: Genome; wide; Analysis; Small; Signaling

PI: Wolf Scheible (The Samuel Roberts Noble Foundation) Co-PIs: Michael Udvardi and Patrick Xuechun Zhao (The Samuel Roberts Noble Foundation) and Hideki Takahashi (Michigan State University) Key Collaborators: Michael Sussman (University of Wisconsin-Madison), Hiroo Fukuda (University of Tokyo, Japan), and Fiona McAlister (Southern Oklahoma Technology Center, Ardmore, OK) Small signaling peptides (SSPs) emerge as an important class of regulatory molecules in plants, especially in the control of plant growth and development in response to environmental cues. Only a few of the many SSPs encoded in plant genomes have been characterized functionally in plants. In this respect, SSP-encoding genes represent some of the potentially most important "dark matter" of plant genomes. Medicago truncatula is a premier model legume species, which is closely related to the most important forage species in the USA, Medicago sativa (alfalfa), and to food legumes such as soybean and common bean. Legumes are key components of sustainable agricultural systems because they form symbioses with bacteria called rhizobia that reduce molecular nitrogen to ammonium in specialized root organs called nodules. Symbiotic nitrogen fixation provides legumes with a source of nitrogen, obviating the need for synthetic nitrogen fertilizers for these important crop species. Recently, it has become clear that SSPs can control both nodule and root development in legumes and the hunt is on for more SSPs that control important developmental traits in legumes of importance to agriculture. A priority objective of this project therefore is to identify novel SSPs that affect root and nodule development in M. truncatula, with a long-term view of using SSPs in non-transgenic approaches to improve plants for agriculture. Datasets and biological materials generated in this project will be made available through appropriate biological databases and stock centers. A database (MtSSPdb) will be developed and maintained for both project and public access to store, link and present the information on the comparative genomics of peptide-coding genes and to integrate and manage all experimental data emerging from this project. With regard to outreach and training, the project will leverage existing programs to provide research training for postdoctoral associates and graduate, undergraduate and high school students. A multidisciplinary strategy will be implemented, including bioinformatics, chemical genomics, genetics, biochemistry, molecular and developmental biology. Activities of this project comprise a genome-wide survey of SSP-encoding genes in Medicago truncatula and the identification of macronutrient (N, P, S, and K) -responsive SSP-encoding genes from transcriptome data. A library of genome-encoded, synthetic peptides will be established as a community resource for biochemical genetics and used to screen for developmental and molecular phenotypes in M. truncatula. Constitutive overexpression lines will be produced in Arabidopsis thaliana and M. truncatula for selected SSP-encoding genes that are prioritized because they have been shown to be either strongly responsive to macronutrients (N, P, S, K), produce strong visual/molecular phenotypes when chemically synthesized peptides are exogenously applied to M. truncatula, and/or have their mature peptides predicted to be produced through posttranslational modifications that make chemical synthesis and/or exogenous application impracticable. The synthetic peptides will be further tested for their effects on root nodule development and nitrogen fixation in M. truncatula. The Medicago HAPMAP genotypes will be employed to identify genetic loci associated with natural diversity in response to bioactive peptides, and specific SSPs will also be tested for their efficacy in improving alfalfa performance in the field. Identification of a peptide receptor through genetic or chemo-proteomic approaches is another activity included in this project.

Pi：Wolf Scheible(Samuel Roberts Noble Foundation)联合PIs：Michael Udvardi和Patrick Xecchun赵(Samuel Roberts Noble Foundation)和Hideki Takahashi(密歇根州立大学)的主要合作者：Michael Sussman(威斯康星大学麦迪逊分校)，Hiroo Fukuda(日本东京大学)和Fiona McAlister(南俄克拉荷马州技术中心，Ardmore，俄克拉荷马州)小信号肽(SSP)是植物中一类重要的调节分子，尤其是在控制植物生长和发育以响应环境胁迫方面。在植物基因组中编码的许多SSP中，只有一小部分在植物中进行了功能鉴定。在这方面，编码SSP的基因代表了植物基因组中一些潜在最重要的“暗物质”。元宝紫花苜蓿是一种重要的模式豆科牧草，与美国最重要的牧草紫花苜蓿以及大豆、菜豆等食用豆科牧草亲缘关系密切。豆类是可持续农业系统的关键组成部分，因为它们与被称为根瘤菌的细菌形成共生关系，这种细菌在被称为根瘤的特殊根器官中将分子氮还原为铵。共生固氮为豆科植物提供了氮源，消除了这些重要作物物种对合成氮肥的需求。近年来，SSP既能控制豆科植物的根瘤发育，又能控制根部发育，人们正在寻找更多的SSP来控制对农业具有重要意义的豆科植物的重要发育性状。因此，该项目的一个优先目标是确定影响元宝草根瘤发育的新型SSP，并着眼于在非转基因方法中使用SSP来改良农业植物。在该项目中产生的数据集和生物材料将通过适当的生物数据库和库存中心提供。将开发和维护一个数据库(MtSSPdb)，供项目和公众使用，以存储、链接和展示关于多肽编码基因的比较基因组学的信息，并整合和管理这一项目产生的所有实验数据。在外展和培训方面，该项目将利用现有的方案，为博士后助理和研究生、本科生和高中生提供研究培训。将实施多学科战略，包括生物信息学、化学基因组学、遗传学、生物化学、分子和发育生物学。该项目的活动包括对元胞紫花苜蓿SSP编码基因的全基因组调查，以及从转录组数据中鉴定对大量营养素(N、P、S和K)响应的SSP编码基因。将建立一个基因组编码的合成多肽文库，作为生化遗传学的社区资源，并用于筛选元胞杆菌的发育和分子表型。在拟南芥和拟南芥中，将产生一些SSP编码基因的结构性过表达系，这些基因被优先考虑，因为它们被证明要么对大量营养素(N，P，S，K)有强烈的响应，当化学合成肽被外源应用于元宝莲时产生强烈的视觉/分子表型，和/或其成熟的多肽被预测通过翻译后修饰而产生，使得化学合成和/或外源应用变得不可行。这些合成肽将进一步测试它们对元宝菇根瘤发育和固氮的影响。将使用Medicago HapMap基因型来识别与自然多样性相关的遗传基因座，以响应生物活性多肽，并将测试特定的SSP在改善紫花苜蓿田间表现方面的有效性。通过遗传或化学蛋白质组学方法鉴定多肽受体是该项目包括的另一项活动。