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.

项目摘要 天然产物（NPs）及其衍生物是我们治疗的主要来源之一，由于数千年来 这些化合物不得不与它们的生物靶标发生相互作用。然而，小说的发现 近几十年来，传统来源的NP已经减少，而与此同时，我们正面临着越来越多的NP。 对人类健康的威胁，如增加抗生素耐药性。因此，我们需要新的NP来源。一 未充分开发的NP来源是甲基营养菌;在缺乏还原碳化合物的情况下生长的细菌 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 由于它们的生长需要，但基因组分析表明，它们具有巨大的潜力， 新型NP支架。在我的博士后期间，我一直在研究甲基营养菌近十年， 在此期间，我为这些生物开发了遗传和代谢组学工具。 我们现在准备应用这些工具来发现新的具有治疗价值的甲基营养型纳米颗粒，以及新的 参与NP生物合成的酶促转化。我们的研究计划分为两个主要部分 方向首先，我们将使用我们收集的约100种从甲烷富集中分离出来的独特细菌菌株， 去发现新的治疗相关线索我们正在从这个菌株集合中构建一个组分文库 用于基于生物活性筛选抗生素和抗癌化合物。根据我们的调查结果，我们将 在我们的合作者的帮助下，对这些化合物进行优先排序和高级测试， 支持核心中心。因为这些菌株几乎都有测序的基因组，我们也在使用相似性 网络方法和我们的遗传工具，以确定和激活生物合成基因簇， 产生新的NP。在我们的第二个研究方向，我们正在利用我们的实验室最近报告的反向 稳定同位素标记方法来鉴定并入已知前体的甲基营养型NP。与此 方法，我们将发现新的NP支架和相关的新的生化转化，并表征 这些转化在体外以及在天然NP生产生物体中的体内进行。用于研究 方向，我们有重要的初步结果，作为项目类型的例子， 在我们的研究计划中。这项工作将确定新的抗生素治疗线索， 抗癌潜力，并将审查优先考虑和激活从这些生产纳米粒子的方法。 未被探索的细菌它还将解决知识差距的生物合成的重要NP类 （核糖体合成和后修饰的肽以及烯二炔），并表征新的 酶促转化可用作药物化学工作中的生物催化剂。