Building a Highly Automated Metabolic Pathway Reconstruction Infrastructure for Plants

构建高度自动化的植物代谢途径重建基础设施

• 批准号: 1026003
• 负责人: Seung Rhee
• 金额: $ 182.16万
• 依托单位: Carnegie Institution of Washington
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-09-01 至 2016-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1026003&HistoricalAwards=false
• 关键词: Building; Highly; Automated; Metabolic; Pathway

PI: Seung Yon (Sue) Rhee (Carnegie Institution for Science)Key Collaborator: Peter Karp (SRI International)Innovations in the basic understanding of plants and effective application of that knowledge in the field are essential to meet energy and food security challenges in the 21st century. Rapid advances in sequencing technologies will increase the number of sequenced plant genomes exponentially. There is a growing need to place the sequenced genomes in a biochemical context in order to facilitate enzyme discovery, metabolic-trait based breeding and metabolic engineering. Meeting the ever-expanding demand for food, biofuel and phytopharmaceutical production will require a comprehensive and accurate understanding of the enzymes, pathways and regulatory networks that control metabolism in plants. This project will develop an automated pipeline to reconstruct high-quality plant metabolic pathways from genome-scale sequence and functional genomics data. This pipeline will be used to create freely accessible metabolic pathway databases for 18 agriculturally and industrially important plants. Further value will be added to these species-specific databases and the multi-species PlantCyc reference database through literature-based curation of enzymes and pathways. In addition, new experimentally supported pathway regulation and metabolic flux data will be added to these databases to guide rational metabolic engineering. The computational pipelines, reference and species-specific databases and plant-specific "gold-standard" sets of rate-limiting enzymatic reactions and transcriptional regulatory relationships will facilitate systematic characterization of plant metabolism and metabolic engineering. The visibility, utility and potential impact of the resources generated by this project will be increased by engaging expert scientists working on both commercially valuable and socially valuable "orphan crops" in the pathway validation and curation process. Over 7 researchers world-wide have committed to participating in reconstructing pathway databases for their species of interest. The project will also train several undergraduate interns from a local community college to create a valuable species-tagged plant compound data resource. The interns will increase their biological knowledge and familiarity with a large number of valuable on-line resources. Furthermore, their exposure to scientists at the Carnegie Institution may prompt them to pursue a career in biological research. The project also plans to stimulate enthusiasm for plant metabolism, especially among under-represented groups of high school students. The project will collaborate with a high school teacher at a public charter school to produce a teaching module on plant metabolism that connects to state and national biology education standards. It will be presented at several schools serving under-represented minority and low-income students. It will also be made freely available at the project website and actively disseminated to high school biology teachers. All the data, tools and teaching materials produced from this project will be publicly and freely accessible from the project website (http://plantcyc.org), through complete database downloads under a Creative Commons "share-alike" license (http://creativecommons.org/licenses/bysa/3.0/), and as bulk data sets as downloadable text files.

PI：Seung Yon（Sue）Rhee（卡内基科学机构）主要合作者：Peter Karp（SRI International）在对植物的基本理解中的创新以及该领域的有效应用对应对21世纪能源和粮食安全挑战至关重要。测序技术的快速进步将指数增加测序的植物基因组的数量。为了促进酶发现，基于代谢性状的育种和代谢工程，越来越需要将测序基因组置于生化环境中。满足对食物，生物燃料和植物药物生产的不断扩展的需求，将需要对控制植物中代谢的酶，途径和调节网络有全面而准确的了解。该项目将开发自动化管道，以从基因组规模序列和功能基因组数据中重建高质量的植物代谢途径。该管道将​​用于为18种农业和工业重要的植物创建可自由访问的代谢途径数据库。通过基于文献的酶和途径的策展，将添加进一步的价值，以及这些物种特定的数据库和多物种PlantCyC参考数据库。此外，将添加新数据库中的新的经过实验支持的途径调节和代谢通量数据，以指导理性的代谢工程。计算管道，参考和物种特异性数据库以及植物特异性的“金标准”集限制速率酶促反应以及转录调节关系将促进植物代谢和代谢工程的系统表征。通过参与从事商业有价值和社会有价值的“孤儿作物”的专家科学家，在途径验证和策展过程中吸引专家科学家，可以增加该项目产生的资源的可见性，效用和潜在影响。全世界有7多名研究人员致力于为他们感兴趣的物种参与重建途径数据库。该项目还将培训当地社区学院的几位本科实习生，以创建有价值的物种植物化合物数据资源。实习生将通过大量有价值的在线资源来提高他们的生物学知识和熟悉程度。此外，他们接触卡内基机构的科学家可能会促使他们从事生物学研究职业。该项目还计划刺激对植物代谢的热情，尤其是在代表不足的高中生中。该项目将与一所公立特许学校的一位高中老师合作，​​以建立一个与州和国家生物学教育标准相关的植物代谢的教学模块。它将在为代表性不足的少数民族和低收入学生提供服务的几所学校中介绍。它也将在项目网站上免费提供，并积极传播给高中生物学老师。通过项目网站（http://plantcyc.org），该项目生产的所有数据，工具和教学材料都可以通过创意共享“共享 - 类似”许可（http://creativecommons.ormons.org/licenses/licenses/blicenses/bylicenses/bysa/bysa/3.0/），以及下载fields sets field fire textsss s in Procece Commons“ share-like”许可（http://creativecommons.orplake''license of the Project网站（http://plantcyc.org）公开访问。