Collaborative Research: Elucidating the Role of Rhizobial tRNA-Derived Fragments in Soybean Nodule Development and Symbiotic Nitrogen Fixation

合作研究：阐明根瘤菌 tRNA 衍生片段在大豆根瘤发育和共生固氮中的作用

• 批准号: 2128023
• 负责人: Jianxin Ma
• 金额: $ 90万
• 依托单位: Purdue University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-06-01 至 2026-05-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2128023&HistoricalAwards=false
• 关键词: Collaborative; Research; Elucidating; Role; Rhizobial

Since the Green Revolution of the 1960s, nitrogen fertilizers have been widely deployed to boost crop yields to meet the demands of the growing world population. However, excessive reliance on fertilizers leads to water, soil and air pollution; therefore, environmentally friendly sources of nitrogen are needed for sustainable agriculture. Legume crops such as soybean, common bean, and peanuts have the capability to harness atmospheric nitrogen for their growth by establishing symbiotic relationships with a group of nitrogen-fixing soil bacteria known as rhizobia. The symbiotic interactions begin with a process called nodulation that forms root nodules, within which rhizobia convert atmospheric nitrogen into ammonia that can be utilized by host plants – a process called symbiotic nitrogen fixation. Approximately 50-60% of the nitrogen needed for soybean production is provided by symbiotic nitrogen fixation, thus positioning soybean as an important component of the biennial rotation with corn in the US agricultural system. Both nodulation and nitrogen fixation require coordinated exchanges of molecular signals between the symbiotic partners, and transfer RNA-derived small RNA fragments produced in rhizobia have recently been found to be one type of molecule mediating rhizobia-host plant communications. This project will address how and to what extent such RNA fragments mediate the nodulation and nitrogen fixation processes. Such knowledge will facilitate the development of new biotechnological tools for optimizing the legume-rhizobia symbioses for sustainable crop production. This project will provide hands-on experience to underrepresented minority undergraduate and high school students through an annual “Bioinformatics in Agricultural Science” summer workshop.Plant-microbe interactions require cross-kingdom small RNA (sRNA) interference. While the roles of eukaryotic sRNAs in plant-fungus interactions have been well characterized, sRNA-mediated prokaryote-eukaryote communications have just begun to garner attention. Transfer RNA-derived sRNA fragments (tRFs) are often viewed as degradation products and thus have been largely ignored in previous studies. Recently, the Ma laboratory demonstrated that three rhizobial tRFs were able to regulate the expression of five soybean genes affecting nodulation via soybean Argonaute 1-guided mRNA cleavage. This project will integrate genomic, molecular, and biochemical tools to elucidate the extent to which rhizobial tRFs hijack the host cellular machineries to regulate nodulation and symbiotic nitrogen fixation (SNF) and to further dissect mechanisms by which rhizobial tRFs regulate these processes using soybean-Bradyrhizobium diazoefficiens symbiotic partners as an experimental system. In Aim 1, the dynamics of rhizobial tRFs abundance and putative target gene expression in developing, mature, and senescing nodules will be investigated; in Aim 2, the mechanisms of rhizobial tRF-host gene interactions and relative magnitudes will be determined; in Aim 3, the functions of a subset of tRFs and their target genes underlying nodule development and SNF will be characterized; in Aim 4, experimental soybean lines with quantitative variation of nodule traits will be developed through gene-editing and evaluated for nodulation and SNF efficiencies and the plant productivity. This project may shed light on the potential roles of tRFs in diverse host-microbe interactions, towards translation of the discoveries into practice for control of bacterial pathogens or to promote beneficial interactions.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.

自20世纪60年代的绿色革命以来，氮肥被广泛应用于提高作物产量，以满足不断增长的世界人口的需求。然而，过度依赖化肥会导致水、土壤和空气污染；因此，可持续农业需要环境友好的氮源。豆类作物，如大豆、菜豆和花生，通过与一组被称为根瘤菌的固氮土壤细菌建立共生关系，有能力利用大气中的氮来促进它们的生长。共生相互作用始于一个名为结瘤的过程，它形成根瘤，在这个过程中，根瘤菌将大气中的氮转化为可被宿主植物利用的氨--这一过程被称为共生固氮。大豆生产所需氮素的大约50%-60%是由共生固氮提供的，因此大豆在美国农业系统中是两年一次的玉米轮作的重要组成部分。结瘤和固氮都需要共生伙伴之间的分子信号协调交换，而根瘤菌产生的转移RNA衍生的小RNA片段最近被发现是一种介导根瘤菌-寄主植物通讯的分子。该项目将探讨这些RNA片段如何以及在多大程度上调节结瘤和固氮过程。这些知识将有助于开发新的生物技术工具，以优化可持续作物生产的豆类-根瘤菌共生体。该项目将通过一年一度的“农业科学中的生物信息学”暑期工作坊，为未被充分代表的少数族裔本科生和高中生提供实践经验。植物与微生物的相互作用需要跨王国的小RNA(SRNA)干扰。虽然真核sRNA在植物-真菌相互作用中的作用已经被很好地描述，但sRNA介导的原核生物-真核生物的通讯才刚刚开始引起人们的注意。转移RNA衍生的SRNA片段(TRFs)通常被视为降解产物，因此在以前的研究中基本上被忽视。最近，Ma实验室证明了三个根瘤菌TRFs能够通过大豆Argavite 1引导的mRNA切割来调控五个影响结瘤的大豆基因的表达。该项目将结合基因组、分子和生化工具，阐明根瘤菌TRFs在多大程度上劫持宿主细胞机制来调节结瘤和共生固氮(SNF)，并以大豆-重氮慢生根瘤菌共生伙伴为实验系统，进一步剖析根瘤菌TRFs调节这些过程的机制。在目标1中，将研究根瘤菌TRFs丰度和可能的目标基因在根瘤发育、成熟和衰老过程中的动态；在目标2中，将确定根瘤菌TRFs与寄主基因相互作用的机制和相对大小；在目标3中，将表征TRFs的子集及其与根瘤发育和SNF相关的靶基因的功能；在目标4中，将通过基因编辑培育出具有根瘤性状数量变异的实验大豆品系，并对结瘤、SNF效率和植物生产力进行评估。该项目可能揭示TRF在不同宿主-微生物相互作用中的潜在作用，有助于将发现转化为实践，用于控制细菌病原体或促进有益的相互作用。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。