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Comparative Genomics Approach to Pathway Discovery and Engineering in Tomato Trichomes

番茄毛状体通路发现和工程的比较基因组学方法

基本信息

批准号：
1811055
负责人：
Craig Schenck
金额：
$ 21.6万
依托单位：
Schenck Craig A
依托单位国家：
美国
项目类别：
Fellowship Award
财政年份：
2018
资助国家：
美国
起止时间：
2018-10-01 至 2021-09-30
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1811055&HistoricalAwards=false
关键词：
Comparative Genomics Approach Pathway Discovery

项目摘要

This action funds an NSF National Plant Genome Initiative Postdoctoral Research Fellowship in Biology for FY 2018. 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. Craig Schenck is "Comparative Omics Approach to Pathway Discovery and Engineering in Tomato Trichomes" The host institution for the fellowship is Michigan State University and the sponsoring scientist is Dr. Robert Last.Metabolites produced in spatial and temporal manner, are the drivers to plant form and function. These metabolites are assembled from organic building blocks in a complex web of enzymatic reactions and allow plants to thrive in diverse environments. Many specialized metabolites are involved in ecological interactions, but also provide humans with diverse metabolites of nutritional and medicinal importance. The diversity and taxonomic restriction of plant specialized metabolism allows for discovery of novel biochemical reactions, and investigation of evolution on a macro and micro level. Fundamental understanding of the production of biologically active plant specialized metabolites will have broad impacts on improving nutrition and performance of crops. Specifically, increasing biologically active plant metabolites in agronomically important species provides a means to enhance crop defenses and productivity. This project will provide a fundamental understanding of how enzymes and metabolic pathways evolve, the principles of which can be applied to agriculture and extended to understand evolution in other biological systems. Training objectives include functional genomics, analytical chemistry, and bioinformatics. Broader impact activities include mentoring and training graduate and undergraduate students and organizing outreach events to raise public awareness of the plant sciences. Plants produce a myriad of lineage-specific specialized metabolites (e.g. alkaloids, terpenes, etc.), which are synthesized from essential primary metabolites like amino acids. Many specialized metabolites are involved in ecological interactions, but also provide humans with diverse metabolites of nutritional and medicinal importance. Evolution of specialized metabolism tends to occur more quickly than evolutionarily constrained primary metabolism. This recent evolution in plant specialized metabolism has given rise to hundreds of thousands of structurally diverse metabolites found in the green plant lineage. The diversity and taxonomic restriction of plant specialized metabolism allows for discovery of novel biochemical reactions, and investigation of evolution on a macro, metabolic pathway, and micro, enzyme, level. Sugar esters (acylsugars) are a group of specialized metabolites restricted to many species within the nightshade family (Solanaceae) that consist of a sugar core decorated with diverse acyl chains and have plant defense and commercial properties. The acyl chains attached to acylsugars vary in number, length, and branching pattern, which gives rise to natural variation in acylsugar types and abundance within Solanaceae. Branched-chain amino acids are the direct precursors of C4-C5 acyl chains, but synthesis of longer acyl chains requires elongation. However, the biochemical mechanisms responsible for chain elongation remain unknown. This project will leverage the wealth of data encompassing the Solanaceae to identify biochemical mechanisms and evolutionary processes leading to the diversity of acylsugars. Using comparative genomics, transcriptomics, metabolomics, biochemistry and traditional genetics, this project aims to identify and biochemically characterize the acyl chain elongation pathway in tomato and closely-related wild relatives, validate in vitro biochemistry by testing the in vivo function of the identified enzymes, and engineer the Solanum acyl chain elongation pathway in Nicotiana benthamiana to reconstitute the pathway and enhance production of biologically active acylsugars. All data obtained through this project will be submitted to publicly available websites and repositories and manuscripts will be published in open access journals.Keywords: biochemistry, specialized metabolism, defense compounds, acylsugar, chain elongationThis 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.

这项行动资助了2018财年的NSF国家植物基因组计划生物学博士后研究奖学金。该研究金支持研究员在东道实验室的研究和培训计划，研究员还提出了扩大生物学参与的计划。克雷格申克博士的研究和培训计划的标题是"比较组学方法在番茄毛状体中的途径发现和工程"。该奖学金的主办机构是密歇根州立大学，赞助科学家是罗伯特·拉斯特博士。这些代谢物是在复杂的酶促反应网络中由有机构件组装而成的，使植物能够在不同的环境中茁壮成长。许多专门的代谢物参与生态相互作用，但也为人类提供了具有营养和药用重要性的多种代谢物。植物特化代谢的多样性和分类学上的局限性，为发现新的生物化学反应，以及从宏观和微观水平上研究植物的进化提供了可能。对具有生物活性的植物特化代谢产物的生产的基本理解将对改善作物的营养和性能产生广泛的影响。具体而言，增加农学上重要物种的生物活性植物代谢物提供了增强作物防御和生产力的手段。该项目将提供酶和代谢途径如何进化的基本理解，其原理可应用于农业，并扩展到理解其他生物系统的进化。培训目标包括功能基因组学、分析化学和生物信息学。更广泛的影响活动包括指导和培训研究生和本科生，以及组织外联活动，以提高公众对植物科学的认识。植物产生无数谱系特异性的专门代谢物（例如生物碱、萜烯等），由必需的初级代谢产物如氨基酸合成。许多专门的代谢物参与生态相互作用，但也为人类提供了具有营养和药用重要性的多种代谢物。特化代谢的进化往往比受进化限制的初级代谢更快。这种植物特化代谢的最新进化产生了数十万种在绿色植物谱系中发现的结构多样的代谢物。植物特化代谢的多样性和分类学上的局限性使得人们可以在宏观代谢途径和微观酶水平上发现新的生化反应和研究进化。糖酯（酰基糖）是一组仅限于茄科（茄科）内许多物种的特化代谢产物，由不同酰基链修饰的糖核心组成，具有植物防御和商业性质。连接到酰基糖的酰基链在数量、长度和分支模式上变化，这引起了茄科中酰基糖类型和丰度的自然变化。支链氨基酸是C4-C5酰基链的直接前体，但较长酰基链的合成需要延长。然而，负责链延长的生化机制仍然未知。该项目将利用茄科丰富的数据来确定导致酰基糖多样性的生化机制和进化过程。该项目利用比较基因组学、转录组学、代谢组学、生物化学和传统遗传学，旨在鉴定和生化表征番茄及其近缘野生亲缘植物中的酰基链延伸途径，通过测试所鉴定酶的体内功能来验证体外生物化学，并对本氏烟草中的茄酰基链延长途径进行工程改造，以重建该途径并提高生物活性物质的产量。酰基糖通过该项目获得的所有数据将提交到公开网站和存储库，手稿将在开放获取期刊上发表。关键词：生物化学，专门代谢，防御化合物，酰基糖，链延长该奖项反映了NSF的法定使命，并已被认为是值得通过使用基金会的智力价值和更广泛的影响审查标准进行评估的支持。

项目成果

期刊论文数量（4）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Robust predictions of specialized metabolism genes through machine learning

DOI：
10.1073/pnas.1817074116
发表时间：
2019-02-05
期刊：
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
影响因子：
11.1
作者：
Moore, Bethany M.;Wang, Peipei;Shiu, Shin-Han
通讯作者：
Shiu, Shin-Han

Evolution of a plant gene cluster in Solanaceae and emergence of metabolic diversity