Discovery, Revision and Validation of Maize Genes by Proteogenomics

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（密歇根大学安娜堡分校），Steven Rodermel和Patrick Schnable（爱荷华州立大学），以及Frank Hochholdinger （Universität t<s:1>宾根，t<s:1>宾根，德国）基因组科学最基本的目标是发现所有的蛋白质编码基因，然后识别在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。完整而准确的蛋白质组为系统生物学和分子进化的研究以及假设驱动的研究提供了基础。蛋白质基因组学（利用蛋白质组学信息对基因组进行注释）的最新进展使其成为一种数据驱动的方法，补充了基于核苷酸（DNA和RNA）的注释策略。全基因组的定量蛋白质组学也使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的创建成为可能。这个项目有两个研究目的。目标1是创建玉米蛋白质图谱。该图谱包括37个不同组织和玉米发育阶段的40,000-50,000个蛋白质的身份和相对数量。该图谱还包括质膜、叶绿体、线粒体和过氧化物酶体的蛋白质组成，以及由非生物和生物胁迫引起的蛋白质变化的信息。Aim 2提供40,000-50,000个玉米基因模型的蛋白质基因组学发现、修订和确认，包括外显子的鉴定、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的确定。该项目通过提高玉米基因组注释的完整性和准确性来促进玉米基因组化研究和育种。此外，对玉米生理、发育、细胞功能和育种的研究也受益于玉米蛋白图谱提供的玉米蛋白的解剖和亚细胞分布知识。跨学科的教育和推广机会提供给博士后，研究生，本科生，高中生和加州州立大学的研究人员，重点是参与代表性不足的少数民族。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的研究人员提供跨学科的教育和推广机会，重点是少数民族的参与。圣地亚哥的所有项目参与者，包括博士后、研究生和本科生，都在接受独特的跨学科培训，这是由于该项目涉及的研究人员在质谱、生物信息学、玉米发育和细胞生物学以及植物对胁迫的反应方面的专业知识的合作。高中生们通过为生物桥开发的一个模块参与了这项研究。生物桥是加州大学圣地亚哥分校的一个推广项目，将实践学习活动引入圣地亚哥公立学校。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。项目中使用的生物材料由种质资源信息网（GRIN, http://www.ars-grin.gov/）提供。研究人员可通过网站和出版物（http://briggs.ucsd.edu/; http://www-cse.ucsd.edu/~vbafna/）获取项目成果，包括数据和软件。项目数据的长期存储库是Tranche （https://proteomecommons.org/index.jsp）和Gramene （http://www.gramene.org）。

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).