Genomic approaches of discovery broad-spectrum antimicrobial agents

发现广谱抗菌药物的基因组方法

• 批准号: 7669772
• 负责人: Jon Clardy
• 金额: $ 34.21万
• 依托单位: HARVARD MEDICAL SCHOOL
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-03-25 至 2014-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7669772
• 关键词: Actinobacteria class; Actinomyces; Actinomycetales; Antibiotics; Bacteria; Bioinformatics; Biological Factors; Chemistry; Culture Media; Ecology; Elements; Environment; Funding; Gene Cluster; Genetic; Genome; Genomics; Goals; Grant; Institutes; Methodology; Microbe; National Institute of Allergy and Infectious Disease; New England; Nutrient; Pilot Projects; Production; Resistance; Screening procedure; Simulate; antimicrobial; antimicrobial drug; base; biodefense; combat; microbial; novel; pathogen; programs; promoter; scaffold; small molecule; tool

Most clinically-used antibiotics are bacterially-produced small molecules known as natural products, or their derivatives. However, natural products are not being featured in antibiotic discovery programs due to high rates of rediscovery and low rates of new molecule discovery. This proposal describes a new genomicsbased approach to natural product discovery that employs a combination of bioinformatics, microbial ecology, genetics, and chemistry to identify cryptic biosynthetic loci and stimulate them to produce their encoded natural products. All molecules identified will be characterized for antimicrobial activity. Specific Aim 1. Use bioinformatics to identify biosynthetic gene clusters and predict their products. New bioinformatic tools will be developed to identify biosynthetic gene clusters in the genomes of actinomycetes and other microbes, and to predict structural elements of their small molecule products. These predictions will be leveraged toward antibiotic discovery by using them as the basis for efforts to stimulate the production of cryptic natural products, as described in Specific Aims 2 and 3: Specific Aim 2. Stimulate the production of cryptic metabolites by simulating a multispecies environment. Most screens for new natural products have been performed with strains grown as pure cultures in nutrientrich growth media. A new screening format has recently been developed in which strains are grown as microcolonies on nutrient-poor growth media. This microcolony screening methodology will be used to identify cryptic natural products with antimicrobial activity. Specific Aim 3. Stimulate the production of cryptic metabolites by genetically manipulating producers. Most natural product-encoding gene clusters are thought to be repressed under standard culture conditions. Using actinomycete strains whose biosynthetic gene clusters have been identified by the efforts described in Specific Aim 1, endogenous gene cluster promoters will be systematically replaced with a strong, inducible promoter, enabling the controlled synthesis and isolation of their small molecule products and the subsequent characterization of their antimicrobial activity. .

大多数临床中使用的抗生素是细菌生产的小分子，称为天然产物，或其 衍生物。但是，由于高的抗生素发现计划，天然产品尚未出现 新分子发现的重新发现率和低率。该建议描述了一个新的基因组学 使用生物信息学，微生物的组合的自然产品发现方法 生态学，遗传学和化学，以鉴定神秘的生物合成基因座并刺激它们产生其 编码天然产品。鉴定出的所有分子将用于抗菌活性。 特定目的1。使用生物信息学来识别生物合成基因簇并预测其产品。新的 将开发生物信息学工具来鉴定放线菌基因组中的生物合成基因簇 和其他微生物，并预测其小分子产物的结构元素。这些预测 通过使用将其作为刺激生产的努力的基础，将利用抗生素发现 特定目的2和3中所述，神秘的天然产物的含义： 特定的目标2。通过模拟多物种环境来刺激神秘代谢产物的产生。 大多数新天然产品的屏幕都是用纯种作为Nutrientrich的纯培养的菌株进行的 增长媒体。最近已经开发了一种新的筛选格式，其中菌株会成长为 营养贫困生长培养基的微卵石。这种微菌株筛选方法将用于 鉴定具有抗菌活性的神秘天然产物。 特定目的3。通过遗传操纵生产者刺激神秘代谢产物的产生。最多 自然产物编码的基因簇被认为在标准培养条件下被抑制。 使用放线菌的菌株，其生物合成基因簇已通过所描述的努力确定 特定的目标1，内源基因簇启动子将被系统地替换为强，可诱导的 启动子，使其小分子产物的受控合成和分离 随后表征其抗菌活性。 。