A Web-Enabled Database for Rapid Metagenomic Biocatalyst Discovery and Validation

用于快速发现和验证宏基因组生物催化剂的网络数据库

• 批准号: 9048941
• 负责人: Jeffrey Kim
• 金额: $ 74.9万
• 依托单位: RADIANT GENOMICS, INC.
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-12-01 至 2018-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9048941
• 关键词: Acoustics; Address; Advanced Development; Apache; Automation; Basic Science; Biochemical; Biodiversity; Bioinformatics; Biological Assay; Biomanufacturing; Characteristics; Cloud Computing; Cluster Analysis; Collection; Communities; Complement; Complex; Computer Simulation; DNA; DNA biosynthesis; Data; Data Set; Databases; Development; Economics; Environment; Enzymes; Feedback; Gene Delivery; Genes; Genetic Engineering; Genetic Variation; Genomics; Goals; Guanine + Cytosine Composition; Imagery; Laboratories; Length; Libraries; Liquid substance; Metadata; Metagenomics; Methods; Microfluidics; Mining; Molecular Biology; Natural Products; Nucleotides; Nutrient; Organism; Outcome; Performance; Phase; Preparation; Principal Component Analysis; Process; Property; Proteins; Protocols documentation; Recovery; Reporting; Research; Research Infrastructure; Research Personnel; Sampling; Services; Site; Source; Structure; System; Technology; Time; Traction; Validation; Variant; base; combinatorial; computer infrastructure; cost; distributed data; e-commerce; gene synthesis; improved; interest; meetings; metabolic engineering; metagenome; metagenomic sequencing; nanolitre; novel; prediction algorithm; programs; public health relevance; research and development; sample fixation; search engine; success; thermostability; tool; web-enabled

 DESCRIPTION (provided by applicant): Radiant Genomics proposes to develop an integrated enzyme discovery service, the Enzyme Variant Engine (EVE), built upon the largest cloned metagenomic sequence collection reported to date. The goal is to combine a publicly­accessible search engine, richly­annotated sequence database, arrayed sample library, and LIMS automation platform to deliver novel enzyme variants to end­users for lower cost, in less time, and from a greater pool of biodiversity than alternative options, such as DNA synthesis. Importantly, this service overcomes a major bottleneck in enzyme discovery that has traditionally focused on easily­cultivated organisms which are now known to represent less than 1% of biodiversity. Phase I research and development milestones were met or exceeded. In particular, we successfully demonstrated a high­efficiency sequencing workflow that will allow us to sequence and assemble our clone library, which is predicted to encode ~600M genes, >99% of which are derived from uncultivated and essentially unstudied organisms. We next demonstrated a combinatorial barcoding strategy that yields assemblies with an average length of >30 kilobases, a dramatic improvement in metagenomic contiguity. This feature enables the discovery of clusters of functionally related genes, such as those that encode complex natural products and nutrient fixation. These services were successfully integrated into an online search engine and e­commerce platform available at www.eve.bio. Finally, we developed and demonstrated infrastructure for an automated LIMS gene recovery system that can recover thousands of genes of interest from our arrayed library per week. The success of Phase I research was complemented by general improvements in sequencing cost­efficiency and cloud­computing. The EVE service has gained commercial traction and we believe further development will benefit basic research while positively impacting a broad range of biomanufacturing processes. Based on customer feedback, the aims of this proposal are 1) continued sequencing of the library using contiguity­preserving strategies 2) scaling of computational infrastructure 3) development of advanced enzyme selectors and 4) third­party database integration. The overall outcome of this program will be a centralized search engine which allows end­users to rapidly select and receive genes identified in bioinformatic analyses. These genes will be accessible for lower cost, in less time, and from a greater pool of genetic diversity than existing services. Overall, we believe that our platform will improve our understanding of sequence­to­function relationships and annotation for metagenomic environments, helping to bridge the gap between in silico and biochemical characterization from unexplored pools of genetic diversity.

 描述（由适用提供）：辐射基因组学提案，以开发集成酶发现服务，酶变体引擎（EVE），建立在迄今报告的最大克隆的元基因组序列收集基础上。目的是将可公开访问的搜索引擎，丰富的序列数据库，阵列样本库和LIMS自动化平台相结合，以将新颖的酶变体传递到Ednusers，以较低的时间，更少的时间，而不是与其他选择相比，从更低的时间和更大的生物反应池（例如DNA合成）。重要的是，这项服务克服了酶发现中的主要瓶颈，传统上一直集中在易于文化的生物上，这些生物现在占生物多样性的不到1％。第一阶段的研发里程碑得出或超过了。特别是，我们成功地展示了一个高度测序的工作流程，这将使我们能够对克隆库进行测序和组装，该文库预计将编码约600m的基因，其中> 99％来自未经文化的且本质上未研究的生物体。接下来，我们展示了一种组合条形码策略，该策略的平均长度> 30千碱基的平均长度产生了巨大的核能连续性改善。此功能可以发现与功能相关的基因的簇，例如编码复杂天然产物和营养固定的基因。这些服务已成功地集成到www.eve.bio可用的在线搜索引擎和电子商务平台中。最后，我们为自动化的LIMS基因恢复系统开发并展示了基础架构，该系统可以从我们的阵列库中恢复数千个感兴趣的基因。第一阶段研究的成功是通过顺序的成本和云计算的一般改进来完成的。夏娃服务已经获得了商业吸引力，我们认为进一步的发展将使基础研究受益，同时积极影响广泛的生物制造过程。基于客户反馈，该提案的目的是1）使用CONTIGUITY推广策略对库进行测序2）计算基础架构的缩放3）开发高级酶选择器和4）第三部分数据库集成。该程序的总体结果将是一种集中式搜索引擎，该引擎允许终结者在生物信息学分析中迅速选择和接收基因。与现有服务相比，这些基因将以较低的时间，更少的时间和更大的遗传多样性库来访问。总体而言，我们认为我们的平台将提高我们对元基因组环境的测序功能关系和注释的理解，从而有助于从遗传多样性的意外池中弥合硅和生化表征之间的差距。