Genome Mining the Full Diversity of the Actinomycete Biosynthetic Universe for Neomorph Antibiotic Discovery

基因组挖掘放线菌生物合成宇宙的全部多样性，以发现 Neomorph 抗生素

• 批准号: 9253641
• 负责人: Daniel Gray
• 金额: $ 22.5万
• 依托单位: WARP DRIVE BIO, INC
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-01-15 至 2017-10-14
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9253641
• 关键词: Address; Anti-Bacterial Agents; Antibiotic Resistance; Antibiotics; Bacteria; Bacterial Artificial Chromosomes; Bacterial Infections; Bioinformatics; Biological Assay; Candida albicans; Cells; Chemicals; Clinical; Cloning; Collection; Comb animal structure; Cytology; Databases; Development; Drug resistance; Engineering; Escherichia coli; Family; Fermentation; Future; Gene Cluster; Genes; Genetic; Genetic Transcription; Genome; Genomics; Growth; Housekeeping Gene; Hybrids; Length; Libraries; Link; Literature; Measures; Methodology; Methods; Mining; Modification; Multi-Drug Resistance; Natural Products; Pathogenicity; Pharmaceutical Preparations; Phenotype; Process; Production; Promoter Regions; Property; Pseudomonas aeruginosa; Reporting; Research Infrastructure; Resources; Source; Streptomyces; System; Techniques; Testing; bacterial resistance; base; combat; drug discovery; genetic signature; innovation; methicillin resistant Staphylococcus aureus; microbial; novel; overexpression; pathogen; polyketide synthase; promoter; resistance gene; resistance mechanism; screening; synthetic biology; tool; transcription factor

ABSTRACT To combat multidrug-resistant bacterial infections, novel classes of antibiotics with new mechanisms of action are desperately required. Genome mining for novel natural products is quickly replacing traditional approaches to antibiotic discovery. Warp Drive Bio has sequenced over 135,000 actinomycete strain genomes from diverse sources worldwide, and our proprietary genomic database contains approximately ~3,500,000 secondary metabolite gene clusters. Importantly ~75% of cluster families identified in our database have yet to be reported in the literature. Our vast microbial genomics-based approach is innovative because it provides an unprecedented opportunity to discover entirely novel antibiotics with new mechanisms of action (MOAs). The focus of this project will be to identify, express, and test biosynthetic gene clusters encoding new classes of antibiotics with novel MOAs to combat current and future drug-resistant pathogens, by combing our vast genomics resources and innovative bioinformatics search with our validated genomes-to-drugs platform for natural products discovery. First, we will harness our extensive, complementary genomic resources to identify and clone 10 candidate neomorph antibiotic clusters. We term biosynthetic clusters that are novel as “neomorphs,” and we have constructed a bioinformatic analysis pipeline of phylogenomic and chemoinformatic tools to assess novelty at the genetic and biosynthetic levels. We then will utilize our microbial genomic database to predict which neomorph clusters possess antibiotic activity, by searching for self-resistance genes within the neomorph cluster. Bacteria utilize a variety of self-resistance mechanisms to protect against the antibiotics they are actively producing, and this property can be exploited using genomic information. Our integrated bioinformatic analysis we will advance 10 candidate neomorph antibiotic clusters for expression and testing. A validated portfolio of synthetic biology techniques will be deployed for refactoring biosynthetic clusters to enhance the expression of clusters that are not expressed, or which are expressed at very low levels, to increase compound production. Finally we have developed a high throughput fermentation process, bioassay, and mass spectrometric infrastructure to analyze and identify neomorphs. Thus, by combing an innovative genomic search of novel biosynthetic clusters with embedded resistance genes, with our integrated genes-to-compound platform, we will identify, engineer, and screen candidate neomorph antibiotics to address the growing clinical need for new antibacterial agents with novel MOAs.

抽象的 为了打击多药耐药细菌感染，具有新的作用机理的新型抗生素类 迫切需要。新型天然产品的基因组采矿正在迅速取代传统方法 抗生素发现。 Warp Drive Bio已测序来自潜水员 全球来源，我们的专有基因组数据库包含大约3,500,000个次要 代谢产物基因簇。重要的是，在我们的数据库中确定的群集家庭中约有75％尚未 在文献中报道。我们庞大的基于微生物基因组学的方法具有创新性，因为它提供了 以新的作用机理（MOAS）发现完全新颖的抗生素的前所未有的机会。 该项目的重点是识别，表达和测试编码新类的生物合成基因簇 与新型MOA的抗生素通过结合我们的新生活来打击当前和未来的耐药病原体 基因组学资源和创新的生物信息学搜索我们经过验证的基因组到药物平台 天然产品发现。首先，我们将利用大量，完整的基因组资源来识别 和克隆10候选抗生素簇。我们将新颖的生物合成簇称为 “新畸形”，我们已经构建了系统基因和化学的生物信息学分析管道 在遗传和生物合成水平上评估新颖性的工具。然后，我们将利用我们的微生物基因组 通过寻找自我抗性基因来预测哪些Neomorph簇具有抗生素活性的数据库 在Neomorph群集中。细菌利用各种自我抗性机制来防止 它们正在积极生产抗生素，并且可以使用基因组信息来利用该特性。我们的 综合生物信息学分析我们将推进10个候选新抗生素抗生素簇进行表达和 测试。合成生物学技术的经过验证的投资组合将用于重构生物合成 簇以增强未表达或以非常低表达的簇的表达 水平，增加复合生产。最后，我们发展了高吞吐发酵过程， 生物测定和质谱基础架构，以分析和识别新塑料。通过结合一个 具有嵌入式抗药性基因的新型生物合成簇的创新基因组搜索，我们的综合 基因到混合平台，我们将确定，工程师和筛选候选候选抗生素来解决 新型MOA对新的抗菌剂的临床需求日益增长。