Systems Analysis of Protein Interactome in Cytosol and Nuclei of Developing Soybean and Rapeseed Embryos

发育中的大豆和油菜籽胚胎细胞质和细胞核中蛋白质相互作用组的系统分析

• 批准号: 1126992
• 负责人: Jay Thelen
• 金额: $ 50万
• 依托单位: University of Missouri-Columbia
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-02-15 至 2016-01-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1126992&HistoricalAwards=false
• 关键词: Systems; Analysis; Protein; Interactome; Cytosol

PI: Jay Thelen (University of Missouri-Columbia)CoPIs: Dong Xu, Dmitry Korkin (University of Missouri-Columbia)Seeds are carbon- and nitrogen-dense structures that serve as the (plant) propagule and the (human) socioeconomic foundation for modern agriculture. Genetics and environmental conditions dictate the developmental program that ultimately determines both seed yield and composition, although the underlying regulatory proteins and mechanisms are only now beginning to be understood. Regulation of seed development has recently focused on transcriptional and epigenetic control of both embryogenesis and maturation. From a biochemical perspective, few regulatory processes take place within a cell without direct or indirect involvement of proteins, and protein-protein interactions. The nucleus and cytosol are the major locations for transcriptional, translational, and post-translational regulation. A quantitative inventory of the proteins involved in these processes and their interactome network, would be a valuable resource to develop testable models for regulatory control of embryo maturation. The main focus of this project is the parallel characterization of nuclear and cytosolic protein interactomes from developing embryos of soybean and rapeseed using a combination of biochemical, proteomic, and bioinformatic approaches. The major objectives of this project are to: 1) systematically and quantitatively analyze protein-protein interactions from cytosolic and nuclear fractions of developing embryos from soybean and rapeseed using a multi-dimensional biochemical strategy that includes protein crosslinking, co-sedimentation, and quantitative mass spectrometry; 2) perform bioinformatic and statistical analyses of potential interacting proteins using data from aim 1 for comparison between soybean and rapeseed, and develop generic protein complex identification tools for such data; and 3) disseminate software, proteomic and protein interaction data by deposition into extant databases (PRIDE, http://www.ebi.ac.uk/pride/; Database of Interacting Proteins, DIP, http://dip.doe-mbi.ucla.edu/; Soybean Knowledge Base, http://soykb.org) and develop a new web database.While the research project targets the protein interactome in developing soybean and rapeseed embryos, it has broader significance for studying plants (especially crops) in general. This study will greatly enrich the data describing plant protein interactions, which is currently limited. These data can be used as a template for studying protein interactomes of other plants. Besides the data and their analyses, the techniques and bioinformatic tools that will be developed can also be applied to study interactomes of other species; in particular, experimental protocols and bioinformatic tools (including source code) will be made freely available to the public. The project will provide critical interdisciplinary training in plant biology, proteomics, and bioinformatics for undergraduates, graduate students, and postdoctoral scholars. Current discipline-based education provides very limited training on integrating biology, biotechnology, and bioinformatics, which is often needed in large-scale biological projects. This project provides a problem-based, interdisciplinary environment to provide training in this regard. Students and postdocs will be mentored in scientific writing, scientific presentations, publishing, grant applications, constructive peer review, project management, time management, and personnel management in an effort to direct the next generation of scientists towards the realistic and professional expectations of modern academic or commercial research. Efforts will be made to recruit people with diverse backgrounds to work on this project. Undergraduate researchers in life sciences and journalism will have opportunities to gain unique experience in computational biology and scientific communication through support from a recently awarded Howard Hughes Medical Institute grant.

主要研究者：Jay Thelen（密苏里-哥伦比亚大学）CoPI：Dong Xu，Dmitry Korkin（密苏里-哥伦比亚大学）种子是碳和氮密集的结构，作为（植物）繁殖体和（人类）现代农业的社会经济基础。 遗传和环境条件决定了最终决定种子产量和组成的发育程序，尽管基本的调控蛋白和机制现在才开始被理解。 种子发育的调控最近集中在胚胎发生和成熟的转录和表观遗传控制。 从生物化学的角度来看，很少有调控过程在没有蛋白质直接或间接参与以及蛋白质-蛋白质相互作用的情况下在细胞内发生。 细胞核和胞质溶胶是转录、翻译和翻译后调节的主要场所。 参与这些过程的蛋白质及其相互作用网络的定量清单，将是一个宝贵的资源，以开发可测试的模型，调控胚胎成熟。 该项目的主要重点是使用生物化学，蛋白质组学和生物信息学方法的组合，从大豆和油菜籽的胚胎发育的核和胞质蛋白质相互作用组的平行表征。 本项目的主要目标是：1）利用蛋白质交联、共沉淀和定量质谱等多维生化技术，系统地定量分析大豆和油菜胚发育过程中胞质和核组分中蛋白质间的相互作用; 2）使用来自aim 1的数据对潜在的相互作用蛋白进行生物信息学和统计学分析，以在大豆和油菜籽之间进行比较，并为这些数据开发通用蛋白质复合物鉴定工具; 3）通过将软件、蛋白质组学和蛋白质相互作用数据存入现有数据库（PRIDE，http：//www.ebi.ac.uk/pride/; Database of Interacting Proteins，DIP，http：//dip.doe-mbi.ucla.edu/; Soybean Knowledge Base，http://soykb.org）来传播，并开发新的网络数据库。该项目针对大豆和油菜胚发育中的蛋白质相互作用组，它对研究植物（特别是作物）具有更广泛的意义。 该研究将极大地丰富描述植物蛋白质相互作用的数据，这是目前有限的。 这些数据可作为研究其他植物蛋白质相互作用组的模板。 除了数据及其分析之外，将开发的技术和生物信息学工具也可用于研究其他物种的相互作用组;特别是，实验方案和生物信息学工具（包括源代码）将免费向公众提供。 该项目将为本科生、研究生和博士后学者提供植物生物学、蛋白质组学和生物信息学方面的关键跨学科培训。 目前基于学科的教育提供了非常有限的培训整合生物学，生物技术和生物信息学，这往往是需要在大型生物项目。 该项目提供了一个以问题为基础的跨学科环境，以提供这方面的培训。 学生和博士后将在科学写作，科学演讲，出版，资助申请，建设性同行评审，项目管理，时间管理和人事管理方面得到指导，以指导下一代科学家实现现代学术或商业研究的现实和专业期望。 将努力招募具有不同背景的人来参与该项目。 生命科学和新闻学的本科研究人员将有机会通过最近获得的霍华德休斯医学研究所赠款的支持，获得计算生物学和科学交流方面的独特经验。