Discovery, Revision and Validation of Maize Genes by Proteogenomics

通过蛋白质组学发现、修正和验证玉米基因

• 批准号: 0924023
• 负责人: Steven Briggs
• 金额: $ 380.12万
• 依托单位: University of California-San Diego
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-15 至 2013-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0924023&HistoricalAwards=false
• 关键词: Discovery; Revision; Validation; Maize; Genes

PI: Steven P. Briggs (University of California - San Diego)CoPI: Vineet Bafna and Laurie G. Smith (University of California - San Diego)Collaborators: W. Joan Chen (San Diego State University), Laura J. Olsen (University of Michigan - Ann Arbor), Steven Rodermel and Patrick Schnable (Iowa State University), and Frank Hochholdinger (Universität Tübingen, Tübingen, Germany)The most fundamental goal of genome science is to discover all of the protein-coding genes, and then to discern the abundance, location, and exact chemical composition of every protein made during the life cycle of an organism; this is called the proteome. A complete and accurately annotated proteome provides the foundation for studies of systems biology and molecular evolution, as well as for hypothesis-driven research. Recent progress in proteogenomics (using proteomic information to annotate the genome) has established it as a data-driven method that complements nucleotide (DNA and RNA)-based annotation strategies. Genome-wide, quantitative proteomics also makes possible the creation of a protein atlas that reveals the anatomical distribution of the proteome and protein sub-cellular locations. This project has two research aims. Aim 1 is to create an Atlas of Maize Proteins. The atlas includes the identity and relative amount of 40,000-50,000 proteins in each of 37 different tissues and stages of maize development. The atlas also includes the protein composition of the plasma membrane, chloroplast, mitochondrion, and peroxisome along with information about the protein changes caused by abiotic and biotic stress. Aim 2 provides proteogenomic discovery, revision, and confirmation of 40,000-50,000 maize gene models, including the identification of exons, the definition of translation start sites and exon borders, and the determination of the correct exon reading frames. This project enhances genome-enabled maize research and breeding by increasing the completeness and accuracy of maize genome annotation. Furthermore, investigations of maize physiology, development, cell functions, and breeding benefit from knowledge of the anatomical and sub-cellular distribution of maize proteins provided by the Atlas of Maize Proteins. Interdisciplinary educational and outreach opportunities are provided to post-docs, graduate students, undergraduates, high school students and Cal State researchers, with an emphasis on involvement of under-represented minorities.This project will provide interdisciplinary educational and outreach opportunities for post-docs, graduate students, undergraduates, high school students and San Diego State University researchers, with an emphasis on involvement of under-represented minorities. All project participants in San Diego including post-docs, graduate students and undergraduates are receiving unique, interdisciplinary training made possible by the collaboration this project involves between investigators with expertise in mass spectrometry, bioinformatics, maize developmental and cell biology, and plant responses to stress. High school students are participating in the research via a module developed for BioBridge, a UC San Diego outreach program that brings hands-on learning activities into San Diego public schools. Researchers at San Diego State University will receive training and education in proteomics and bioinformatics through workshops. Access to the biological materials used in the project is provided by the Germplasm Resources Information Network (GRIN, http://www.ars-grin.gov/). Access to the project results, including data and software, is provided by websites and publications by the investigators (http://briggs.ucsd.edu/; http://www-cse.ucsd.edu/~vbafna/). The long-term repository for project data is Tranche (https://proteomecommons.org/index.jsp) and Gramene (http://www.gramene.org).

PI：Steven P. Briggs（加州大学圣地亚哥分校）CoPI：Vineet Bafna 和 Laurie G. Smith（加州大学圣地亚哥分校）合作者：W. Joan Chen（圣地亚哥州立大学）、Laura J. Olsen（大学）密歇根州安娜堡分校）、史蒂文·罗德梅尔（Steven Rodermel）和帕特里克·施纳布尔（Patrick Schnable）（爱荷华州立大学）以及弗兰克·霍赫霍尔丁格（Frank Hochholdinger）（德国图宾根大学）基因组的最基本目标科学是发现所有的蛋白质编码基因，然后辨别生物体生命周期中产生的每种蛋白质的丰度、位置和确切的化学成分；这被称为蛋白质组。蛋白质基因组学（使用蛋白质组信息注释基因组）的最新进展已使其成为一种补充核苷酸（DNA 和 DNA）的数据驱动方法，为系统生物学和分子进化研究以及假设驱动研究奠定了基础。基于全基因组的定量蛋白质组学还可以创建揭示蛋白质组和蛋白质亚细胞位置的解剖分布的蛋白质图谱。该项目有两个研究目标。玉米蛋白质图谱。该图谱包括 37 个不同组织和玉米发育阶段中 40,000-50,000 种蛋白质的身份和相对数量。该图谱还包括蛋白质组成。 Aim 2 提供质膜、叶绿体、线粒体和过氧化物酶体的信息，以及有关非生物和生物胁迫引起的蛋白质变化的信息，提供 40,000-50,000 个玉米基因模型的蛋白质组学发现、修订和确认，包括外显子、翻译起始位点和外显子边界的定义，以及正确外显子阅读框架的确定，该项目通过增加基因组玉米研究和育种。此外，玉米生理学、发育、细胞功能和育种的研究受益于玉米蛋白质图谱提供的关于玉米蛋白质的解剖和亚细胞分布的知识。提供给博士后、研究生、本科生、高中生和加州州立大学研究人员，重点关注代表性不足的少数群体的参与。该项目将为博士后、研究生、本科生、高中生和圣地亚哥州立大学研究人员，重点是少数族裔的参与，圣地亚哥的所有项目参与者，包括博士后、研究生和本科生，都在接受该项目所涉及的独特的跨学科培训。具有质谱、生物信息学、玉米发育和细胞生物学以及植物对压力反应方面专业知识的研究人员之间的合作 高中生正在通过为 BioBridge 开发的模块参与这项研究，BioBridge 是加州大学圣地亚哥分校的一个外展项目，提供实践学习活动。进入圣地亚哥公众圣地亚哥州立大学的研究人员将通过研讨会接受蛋白质组学和生物信息学方面的培训和教育，获得该项目中使用的生物材料由种质资源信息网络（GRIN，http://www.ars-grin.研究人员通过网站和出版物提供对项目结果（包括数据和软件）的访问（http://briggs.ucsd.edu/；http://www-cse.ucsd.edu/~vbafna）。 /）。项目数据的长期存储库是 Tranche (https://proteomecommons.org/index.jsp) 和 Gramene (http://www.gramene.org)。