Genome Mining for Enediyne Natural Products from Actinomycetals

放线菌烯二炔天然产物的基因组挖掘

• 批准号: 9233171
• 负责人: Ben Shen
• 金额: $ 48万
• 依托单位: SCRIPPS FLORIDA
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-03-01 至 2019-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9233171
• 关键词: Actinomycetales; Anabolism; Architecture; Bacterial Genome; Biochemical; Bioinformatics; Biological; Biological Assay; Biology; Characteristics; Chemicals; Chemistry; Collection; Complex; DNA cassette; DNA sequencing; Data; Databases; Engineering; Enzymatic Biochemistry; Equipment and supply inventories; Event; Family; Fermentation; Gene Cluster; Genes; Genome; Genomics; Goals; Grant; Knowledge; Libraries; Medicine; Metabolic Pathway; Methods; Mining; Molecular; Natural Products; Natural Products Chemistry; Neighborhoods; Outcome; Pathway interactions; Pharmaceutical Preparations; Phylogenetic Analysis; Production; Rare Earth Metals; Reporting; Research; Research Institute; Soil; Source; Structure; Surveys; Time; analog; chromophore; clinical investigation; cytotoxicity; drug discovery; fascinate; follow-up; genetic manipulation; genome sequencing; innovation; insight; member; microbial; microorganism; novel; polyketide synthase; public health relevance; small molecule; virtual

 DESCRIPTION (provided by applicant): Natural products continue to inspire novel chemistry and biology. The enediynes represent one of the most fascinating families of natural products for their unprecedented molecular architecture and extraordinary biological activities. A great challenge is to develop innovative methods to discover new enediynes and produce them in sufficient quantities for chemical, biological, and clinical investigations. In this application, w propose to mine the genomes of the Actinomycetale collection at The Scripps Research Institute for new enediynes. Our hypotheses are: (i) genome survey of our strain collection for the enediyne polyketide synthase (PKS) gene cassettes will allow us to identify potential enediyne producers, (ii) genome sequencing of the potential producers for enediyne biosynthetic gene clusters will allow us to predict the structural novelty of the new enediynes, and (iii) genetic manipulation and fermentation optimization of the most promising strains will allow us to produce and isolate the new enediynes. We have completed a genome survey of 3,500 strains from our Actinomycetale collection and identified 92 strains (hits) that can be phylogenetically grouped into 48 clades according to the enediyne PKS cassettes. Genome sequencing of representative hits from 28 clades confirmed that each clade encodes distinct enediyne biosynthetic gene clusters. The specific aims for this grant are: (i) genome sequencing of representative hits from all 48 clades to identify a total of 48 distinct enediyne gene clusters and prioritize the hits for enediyne discovery and (ii) genetic manipulation and fermentation optimization of the most promising hits to produce and isolate the new enediynes for structural characterization. Discovery of an enediyne is a significant event in natural products chemistry, biology, and drug discovery. We aim at discovering 6-12 new enediynes from the 92 hits, nearly doubling the inventory of enediyne natural products known to date. The outcomes of this application include (i) fundamental contributions to genome mining and metabolic pathway engineering for natural product discovery and production, (ii) discovery of new enediyne natural products to inspire chemistry, biology, and medicine, and (iii) new insights into enediyne chemistry and biosynthetic machineries. The long-term goal of our research is to understand at a molecular level how microorganisms synthesize complex natural products and to exploit this knowledge to discover novel natural products and engineer their analogues for drug discovery.

 描述（由申请人提供）：天然产物因其前所未有的分子结构和非凡的生物活性而不断激发新的化学和生物学灵感，是最令人着迷的天然产物家族之一。烯二炔并生产足够的数量用于化学、生物和临床研究。在本申请中，我们建议挖掘斯克里普斯研究所的放线菌基因组来寻找新的烯二炔。 (i) 对我们收集的烯二炔聚酮合酶 (PKS) 基因盒菌株进行基因组调查将使我们能够识别潜在的烯二炔生产者，(ii) 对烯二炔生物合成基因簇的潜在生产者进行基因组测序将使我们能够预测结构新颖性新的烯二炔，以及（iii）最有希望的感染的基因操作和发酵优化将使我们能够生产和分离新的烯二炔。我们已经完成了基因组调查。我们对来自我们的放线菌收藏的 3,500 个菌株进行了鉴定，并根据来自 28 个分支的代表性命中的烯二炔 PKS 基因组测序，鉴定了 92 个菌株（命中），这些菌株可以在系统发育上分为 48 个分支，证实每个分支都编码不同的烯二炔生物合成基因簇。这笔赠款的目标是：(i) 对所有 48 个进化枝的代表性命中进行基因组测序，以确定总共 48 个不同的烯二炔基因簇 并优先考虑烯二炔发现的命中，以及 (ii) 最有希望产生和分离新烯二炔的基因操作和发酵优化，以进行结构表征。 烯二炔的发现是天然产物化学、生物学和药物发现中的重大事件。我们的目标是从 92 个命中中发现 6-12 个新烯二炔，使迄今为止已知的烯二炔天然产物的库存增加近一倍。该应用的成果包括 (i) 对基因组挖掘的基本贡献。用于天然产物发现和生产的代谢途径工程，（ii）发现新的烯二炔天然产物以激发化学、生物学和医学的灵感，以及（iii）对烯二炔化学和生物合成机械的新见解我们研究的长期目标。是在分子水平上了解微生物如何合成复杂的天然产物，并利用这些知识来发现新的天然产物并设计其类似物以进行药物发现。