Methylotrophs: underexplored bacteria for discovering novel natural products and biochemistry

甲基营养菌：用于发现新型天然产物和生物化学的尚未开发的细菌

• 批准号: 10650386
• 负责人: Aaron Webster Puri
• 金额: $ 38.5万
• 依托单位: UNIVERSITY OF UTAH
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-07-01 至 2027-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10650386
• 关键词: Address; Anabolism; Antibiotic Resistance; Antibiotics; Bacteria; Biochemical; Biochemistry; Biological; Carbon; Collection; Environment; Gases; Gene Cluster; Genetic; Genome; Genomics; Growth; Health; Human; In Vitro; Knowledge; Libraries; Methane; Methods; Natural Products; Natural Source; Organism; Peptides; Pharmaceutical Chemistry; Pharmaceutical Preparations; Postdoctoral Fellow; Production; Reporting; Research; Ribosomes; Source; Stable Isotope Labeling; Testing; Therapeutic; Time; Work; anti-cancer; carbon compound; drug discovery; in vivo; metabolomics; novel; novel therapeutics; programs; scaffold; tool

PROJECT SUMMARY Natural products (NPs) and their derivatives are one of our main sources of therapeutics, due to the millennia these compounds have had to evolve interactions with their biological targets. However, the discovery of novel NPs from traditional sources has waned in recent decades, while at the same time we are facing mounting threats to human health such as increased antibiotic resistance. We therefore need new sources of NPs. One underexplored source of NPs is methylotrophs; bacteria that grow on reduced carbon compounds lacking carbon-carbon bonds such as methane gas. These organisms were overlooked during past NP discovery efforts due to their growth requirements, but genomic analysis demonstrates that they have significant potential to make novel NP scaffolds. I have been working with methylotrophs for close to a decade during my postdoctoral and independent research, and during that time I have developed genetic and metabolomic tools for these organisms. We are now ready to apply these tools to discover new methylotroph NPs with therapeutic value, as well as new enzymatic transformations that are involved in NP biosynthesis. Our research program is divided into two main directions. First, we will use our collection of ~100 unique bacterial strains isolated from methane enrichments to discover new therapeutically relevant leads. We are constructing a fraction library from this strain collection for use in bioactivity-based screens for antibiotic and anticancer compounds. Based on our findings, we will prioritize hits and perform advanced testing on these compounds with the help of our collaborators and supporting core centers. Because these strains almost all have sequenced genomes, we are also using similarity networking approaches and our genetic tools to identify and activate biosynthetic gene clusters that are likely to produce novel NPs. In our second research direction, we are capitalizing on our lab’s recently reported inverse stable isotopic labeling approach to identify methylotroph NPs that incorporate a known precursor. With this approach we will discover new NP scaffolds and associated novel biochemical transformations, and characterize these transformations both in vitro as well as in vivo in the native NP producing organisms. For both research directions, we have significant preliminary results that serve as examples of the types of projects that are developing within our research program. This work will identify new therapeutic leads with antibiotic and anticancer potential, and will also vet methods for prioritizing and activating the production of NPs from these underexplored bacteria. It will also address knowledge gaps in the biosynthesis of important NP classes (ribosomally synthesized and post-translationally modified peptides as well as enediynes), and characterize new enzymatic transformations that can be used as biocatalysts in medicinal chemistry efforts.

项目总结 由于数千年的历史，天然产物(NPs)及其衍生物是我们治疗的主要来源之一 这些化合物必须进化出与其生物目标的相互作用。然而，小说的发现 近几十年来，来自传统来源的核动力源已经减少，同时我们面临着越来越多的核动力源 对人类健康的威胁，如抗生素耐药性的增加。因此，我们需要新的NPs来源。一 未被开发的NPs来源是甲基营养细菌；以还原碳化合物为基础生长的细菌缺乏 碳-碳键，如甲烷气体。在过去的NP发现工作中，这些生物被忽视了 由于它们的生长需求，但基因组分析表明它们有很大的潜力 新型NP支架材料。在我的博士后期间，我已经在甲基营养物方面工作了近十年 独立研究，在此期间，我为这些有机体开发了遗传和新陈代谢工具。 我们现在准备好应用这些工具来发现具有治疗价值的新的甲基营养盐纳米粒，以及新的 参与NP生物合成的酶转化。我们的研究计划主要分为两个部分 方向。首先，我们将使用我们收集的从甲烷浓缩中分离出的~100个独特的细菌菌株 寻找与治疗相关的新线索。我们正在从这个菌株集合中构建一个片段文库 用于抗生素和抗癌化合物的生物活性筛选。根据我们的发现，我们将 在我们的合作者的帮助下，确定命中的优先级并对这些化合物进行高级测试 支持核心中心。由于这些菌株几乎都已经对基因组进行了测序，我们也使用了相似性 网络方法和我们的遗传工具来识别和激活生物合成基因簇，这些基因簇可能 制造新奇的NPs。在我们的第二个研究方向，我们正在利用我们实验室最近报道的反向 稳定同位素标记法鉴定含有已知前体的甲基硝化细菌NPs。有了这个 我们将发现新的NP支架和相关的新的生化转化，并表征 这些转化在体外和体内都发生在天然NP产生的有机体中。对于这两项研究 方向，我们有重要的初步结果，作为以下项目类型的范例 在我们的研究项目中发展。这项工作将确定新的抗生素和治疗线索 抗癌潜力，并将审查优先处理和激活从这些核物质生产核素的方法 未被开发的细菌。它还将解决重要NP类生物合成方面的知识差距 (核糖体合成和翻译后修饰的多肽以及烯二炔)，并表征了新的 可在药物化学工作中用作生物催化剂的酶转化。