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 为了对抗多重耐药细菌感染，具有新作用机制的新型抗生素 是迫切需要的。新型天然产物的基因组挖掘正在迅速取代传统方法 到抗生素的发现。 Warp Drive Bio 已对来自不同国家的 135,000 多个放线菌菌株基因组进行了测序 全球来源，我们专有的基因组数据库包含大约 3,500,000 个二级 代谢基因簇。重要的是，我们数据库中确定的约 75% 的簇族尚未被确定 文献中报道。我们庞大的基于微生物基因组学的方法是创新的，因为它提供了 这是发现具有新作用机制（MOA）的全新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别的生物合成基因簇 结合我们广泛的研究成果，开发具有新型 MOA 的抗生素来对抗当前和未来的耐药病原体 使用我们经过验证的基因组到药物平台进行基因组学资源和创新生物信息学搜索 天然产物的发现。首先，我们将利用我们广泛的、互补的基因组资源来识别 并克隆 10 个候选 Neomorph 抗生素簇。我们将新颖的生物合成簇称为 “neomorphs”，我们构建了系统发育和化学信息学的生物信息学分析流程 评估遗传和生物合成水平新颖性的工具。然后我们将利用我们的微生物基因组 通过搜索自身抗性基因来预测哪些新形态簇具有抗生素活性的数据库 在neomorph集群内。细菌利用多种自我抵抗机制来防御 他们正在积极生产抗生素，并且可以使用基因组信息来利用这一特性。我们的 综合生物信息分析，我们将推进 10 个候选 Neomorph 抗生素簇的表达和 测试。将部署经过验证的合成生物学技术组合来重构生物合成 簇以增强未表达或表达量非常低的簇的表达 水平，以提高复合产量。最后我们开发了一种高通量发酵工艺， 用于分析和识别新变体的生物测定和质谱基础设施。因此，通过结合 具有嵌入式抗性基因的新型生物合成簇的创新基因组搜索，以及我们的集成 基因到化合物平台，我们将识别、设计和筛选候选新形态抗生素，以解决 临床对具有新型 MOAs 的新型抗菌剂的需求不断增长。