Discovery and characterization of new natural products from uncultured bacteria

来自未培养细菌的新天然产物的发现和表征

• 批准号: 8292003
• 负责人: SEAN F BRADY
• 金额: $ 34.75万
• 依托单位: ROCKEFELLER UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-09-01 至 2015-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8292003
• 关键词: Actinobacteria class; Address; American; Anabolism; Anti-Bacterial Agents; Antibiotics; Antifungal Agents; Antineoplastic Agents; Area; Bacteria; Bacterial Genome; Base Pairing; Biological Assay; Biological Factors; Cells; Clinical; Collection; Complementary DNA; Conserved Sequence; Cosmids; DNA; DNA Library; Daptomycin; Development; Dimerization; Ecteinascidin 743; Environment; FDA approved; Family; Gene Cluster; Genes; Genetic; Genomics; Health; Human; Laboratories; Lead; Libraries; Metagenomics; Modeling; Peptides; Pharmaceutical Preparations; Population; Production; Proteobacteria; Recording of previous events; Recovery; Relative (related person); Research Design; Rewards; Sampling; Screening procedure; Soil; Source; Structure; System; Testing; Tetrahydroisoquinolines; Therapeutic; Time; Tryptophan; Variant; Work; anticancer activity; antimicrobial; base; clinically relevant; design; interest; metagenome; microbial; microorganism; novel; programs; small molecule; success

DESCRIPTION (provided by applicant): Natural products are the source of the majority of FDA approved drugs and, in particular, metabolites produced by microorganisms are the source of many of the antibiotics and anticancer agents used today. Over the past two decades large screening programs have largely deemphasized microbial extracts in spite of the historical success of microbial natural products as lead structures for the development of small molecule therapeutics and the continuing clinical need for new antimicrobials and chemotherapeutics. It is estimated that less than one percent of the bacteria present in the environment is readily cultured in the laboratory and therefore accessible to use in traditional small molecule discovery strategies. Uncultured bacteria are likely the largest remaining pool of biosynthetic diversity that has not yet been examined for the production of bioactive natural products. While it is still not possible to easily culture most bacteria in the environment, it is possible to extract microbial DNA directly from environmental samples (environmental DNA, eDNA) and clone this DNA into easily cultured bacteria where, for the first time, it can be functionally characterized. In this study a collection of eDNA mega-libraries constructed from soils collected in the four major deserts of the American Southwest (Sonoran Desert, Chihuahuan Desert, Mojave Desert and the Great Basin Desert) will be constructed and arrayed to permit screening for novel natural product biosynthetic gene clusters. Two related but complementary DNA-based screening approaches will then be used to recover novel small molecule biosynthetic gene clusters from these eDNA mega-libraries. In the first approach we will focus on the identification and recovery of clones containing biosynthetic systems with a history of producing structurally diverse bioactive natural products. In the second strategy we will focus on the identification and recovery of clones containing new variants of specific classes of pharmacologically important natural products. Molecules encoded by new environmental DNA-derived gene clusters will then be functionally accessed using heterologous expression in phylogenetically diverse cultured bacteria, and these metabolites will be tested in whole cell antibacterial, antifungal and anticancer assays. The historical success of natural products as starting points for the discovery of therapeutics provides support for our hypothesis that the metabolites found in these studies will have a high potential of being beneficial to human health.

描述（由申请人提供）：天然产物是大多数FDA批准药物的来源，特别是微生物产生的代谢产物是当今使用的许多抗生素和抗癌剂的来源。在过去的二十年中，尽管微生物天然产物作为开发小分子治疗剂的主要结构取得了历史性的成功，并且临床上持续需要新的抗菌剂和化疗剂，但大型筛选程序在很大程度上淡化了微生物提取物。据估计，在环境中存在的细菌中，只有不到1%的细菌容易在实验室中培养，因此可以用于传统的小分子发现策略。未培养的细菌可能是最大的生物合成多样性的剩余池，尚未被检查的生物活性天然产品的生产。虽然在环境中培养大多数细菌仍然是不可能的，但可以直接从环境样品中提取微生物DNA（环境DNA，eDNA），并将此DNA克隆到易于培养的细菌中，在那里它可以首次进行功能表征。在这项研究中，从收集在美国西南部的四个主要沙漠（索诺兰沙漠，奇瓦瓦沙漠，莫哈韦沙漠和大盆地沙漠）的土壤构建的eDNA巨型库的集合将被构建和排列，以允许筛选新的天然产物生物合成基因簇。两种相关但互补的基于DNA的筛选方法将用于从这些eDNA巨型文库中恢复新的小分子生物合成基因簇。在第一种方法中，我们将专注于含有生物合成系统的克隆的识别和恢复，该系统具有生产结构多样的生物活性天然产物的历史。在第二个战略中，我们将集中在识别和恢复的克隆含有新的变种的特定类别的非重要的天然产物。然后，将在遗传多样性培养的细菌中使用异源表达在功能上访问由新的环境DNA衍生的基因簇编码的分子，并且将在全细胞抗细菌、抗真菌和抗癌测定中测试这些代谢物。天然产物作为发现治疗方法的起点的历史性成功为我们的假设提供了支持，即在这些研究中发现的代谢物将具有有益于人类健康的高潜力。