Antibiotics Around Us: Improving metagenome mining for the discovery of novel natural products from microbial communities.

我们周围的抗生素：改善宏基因组挖掘，从微生物群落中发现新型天然产物。

• 批准号: 9120628
• 负责人: Bradley Morgan Hover
• 金额: $ 3.34万
• 依托单位: ROCKEFELLER UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-02-16 至 2016-09-01
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9120628
• 关键词: Address; Anabolism; Anti-Bacterial Agents; Anti-Infective Agents; Antibiosis; Antibiotics; Archives; Bacteria; Base Sequence; Biological Assay; Breathing; Bypass; Chemistry; Cloning; Collection; Computer Simulation; Cosmids; DNA; DNA Sequence; Development; Ensure; Environment; Enzymes; FDA approved; Family; Gene Cluster; Gene Targeting; Genes; Genetic Materials; Genome; Genomics; Geographic state; Growth; Immunosuppressive Agents; Laboratories; Lead; Libraries; Link; Marketing; Metagenomics; Methods; Microbe; Molecular Weight; Natural Products; Outcome; Pharmaceutical Preparations; Production; Property; Recombinants; Recording of previous events; Recovery; Regulatory Element; Sampling; Shipping; Ships; Soil; Source; Techniques; United States; Variant; aminoacid biosynthesis; analog; base; citizen science; density; improved; innovation; interest; metagenome; microbial; microbial community; novel; novel strategies; overexpression; promoter; public health relevance; screening; small molecule; soil sampling; success; text searching; tool; unnatural amino acids

 DESCRIPTION (provided by applicant): Historically, small molecule metabolites produced by bacteria have been a major source of lead compounds in the development of clinically used antibiotics - representing more than 60% of the FDA approved anti-infective agents currently on the market. Many of these clinically useful antibiotics are the metabolites of cultured bacteria bu the majority of environmental bacteria cannot be explored for antibiotic production using traditional laboratory techniques. It is possible to access the untapped biosynthetic potential of this uncultured majority of environmental bacteria by isolating and directly cloning their high molecular weight DNA from the environment (eDNA) and expressing the DNA in heterologous bacterial hosts. Cosmid libraries constructed from eDNA typically contain tens of millions of clones, a number that ensures the capture of the genomes of the majority of previously inaccessible bacteria but which presents a financial and logistical challenge to those wishing to screen these libraries for the production of metabolites. This proposal will address these aforementioned issues by developing and improving sequence-targeting tools to allow for the rapid exploration of environmental DNA for novel antibiotic production. As a proof of concept, these new approaches will be evaluated for their ability to identify new derivatives with potentially improved antibiosis activity for the recently discovered antibiotic, teixobactin. New methods will also be developed and employed in the discovery of structurally novel antibiotics linked only to teixobactin by the biosynthesis of its rare non-proteinogenic amino acid, enduracididine. For Aim 1 of this proposal, the trainee will first sequence and clone a diverse set eDNA samples identified to be rich in the target gene clusters. In Aim 2, the trainee will screen and annotate the metagenomic libraries for teixobactin-like NRPS genes and enduracididine biosynthesis genes and the recovery of gene clusters containing these genes. In Aim 3, the trainee will heterologous express the recovered and reassembled gene clusters and complete the functional analysis of antibiotics encoded by these clusters. All together, these endeavors will not only result in innovative tools to fully explore the environment for novel and otherwise inaccessible antibiotics, but will also tangibly generate new natural teixobactin derivatives and medically significant enduracididine-containing molecules.

 描述（由申请人提供）：从历史上看，细菌产生的小分子代谢物一直是临床使用抗生素开发中先导化合物的主要来源——占目前市场上 FDA 批准的抗感染药物的 60% 以上。这些临床上有用的抗生素中的一些是培养细菌的代谢产物，但大多数环境细菌无法使用传统的实验室技术来探索抗生素生产，但可以利用这种未开发的生物合成潜力。通过从环境中分离并直接克隆其高分子量 DNA (eDNA) 并在由 eDNA 构建的粘粒文库中表达 DNA，可以捕获大多数未培养的环境细菌，该数量可确保捕获该提案将通过开发和改进序列靶向工具来解决上述问题。作为概念验证，将评估这些新方法为最近发现的抗生素 teixobactin 鉴定具有潜在改善抗菌活性的新衍生物的能力，并开发新方法。用于通过生物合成稀有非蛋白氨基酸 enduracididine 来发现仅与 teixobactin 相关的结构新颖的抗生素。 对于本提案的目标 1，学员将首先对多种抗生素进行测序和克隆。放 在目标 2 中，学员将筛选和注释宏基因组文库中的 teixobactin 样 NRPS 基因和 enduracididine 生物合成基因，并恢复包含这些基因的基因簇。学员将异源表达恢复和重新组装的基因簇，并完成这些簇编码的抗生素的功能分析总之，这些努力不仅会产生结果。使用创新工具来充分探索新型和其他难以获得的抗生素的环境，但也将有形地产生新的天然泰克巴汀衍生物和具有医学意义的含有恩尿酸丁的分子。