Methane-oxidizing bacterial communities: A novel source of bioactive chemical diversity

甲烷氧化细菌群落：生物活性化学多样性的新来源

• 批准号: 9905580
• 负责人: Aaron Webster Puri
• 金额: $ 24.9万
• 依托单位: UNIVERSITY OF UTAH
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-07-18 至 2022-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9905580
• 关键词: Advisory Committees; Agar; Anti-Bacterial Agents; Antibiotics; Award; Bacteria; Bacterial Physiology; Biological; Biological Assay; Biological Models; Biological Process; California; Carbon; Cell Death; Chemical Structure; Chemicals; Chemistry; Clinic; Clostridium difficile; Coculture Techniques; Communication; Communities; Complex; Core Facility; Data; Diffuse; Drug resistance; Educational workshop; Ensure; Environment; Faculty; Follow-Up Studies; Fractionation; Future; Gene Cluster; Genetic; Genome; Genomics; Goals; Growth; Hospitals; Image; Laboratories; Learning; Link; Mass Spectrum Analysis; Mediating; Mentors; Metabolic; Methane; Methylococcaceae; Mining; Modeling; Modernization; Molecular; Molecular Mechanisms of Action; Mutagenesis; Natural Products; Nuclear Magnetic Resonance; Organism; Oxides; Pharmaceutical Preparations; Phase; Phenotype; Physiological; Pigmentation physiologic function; Pilot Projects; Positioning Attribute; Regulation; Reporter; Research; Resistance; Salmonella infections; Sampling; Schools; Signal Transduction; Site; Source; Structure; Surface; System; Techniques; Therapeutic; Therapeutic Uses; Time; Training; Universities; Washington; Work; alpha Toxin; antimicrobial; bacterial community; bacterial genetics; carbon compound; career; career development; experience; genome sequencing; medical schools; member; metabolic engineering; microbial; microbiome; mutant; novel; pathogen; post-doctoral training; programs; public health relevance; quorum sensing; resistant strain; scaffold; screening; small molecule; small molecule therapeutics; tool; transcriptome sequencing

 DESCRIPTION (provided by applicant): Candidate and Environment During graduate school in Dr. Matthew Bogyo's lab at Stanford University, I synthesized and applied chemical probes to both examine the activation mechanism of a toxin secreted by Clostridium difficile, a major hospital-acquired pathogen, and to understand how host cell death is triggered by Salmonella infection. I subsequently joined Dr. Mary Lidstrom's lab at the University of Washington for postdoctoral training in bacterial genetics and physiology, where I recently developed genetic tools for methane-oxidizing bacteria that have enabled both metabolic engineering and new physiological studies in these organisms. My long-term career goal is to establish a successful research program focused on leveraging biological context to understand the regulation and function of bacterially-produced secondary metabolites. My objective using this approach is to discover novel bioactive compounds with therapeutic potential, such as antibiotics, that will be used in the clinic. My scientific background at the interface of chemistry and bacterial genetics places me in a good position to accomplish this goal. However, I have not yet specifically worked on determining the function and structure of microbial secondary metabolites. Therefore, my immediate career goal is to obtain training enabled by the K99/R00 award in secondary metabolite discovery and characterization using a model methane-oxidizing bacterial community as a novel source of bioactive chemical diversity in order to transition to an independent faculty position. I have an excellent mentoring team to help me achieve these goals. At the UW I will be co-mentored by Dr. Mary Lidstrom, a distinguished bacterial physiologist and geneticist with expertise in bacteria that grow on one-carbon compounds, and Dr. Peter Greenberg, an expert and pioneer in the fields of quorum sensing and related forms of bacterial chemical communication. I will also receive guidance on secondary metabolite isolation and structural elucidation from renowned natural product chemist Dr. Jon Clardy of Harvard Medical School, and will learn to detect these compounds directly on agar surfaces using microbial imaging mass spectrometry at the University of California, San Diego in the lab of Pieter Dorrestein, the pioneer of the technique. I will also supplement this training by attending a course on microbial secondary metabolites. Furthermore, I will take advantage of the excellent academic environment at the UW to help me achieve my research and career goals. This will include using state-of-the-art core facilities for mass spectrometry and genomics, as well attending seminars, workshops, and courses on professional and career development offered by various organizations on campus. I will also receive one-on-one guidance on academic careers from mentors on my advisory committee. Together, these experiences will ensure that I will obtain the scientific experience and professional training necessary to successfully establish an independent research group studying the regulation and biological function of bacterially-produced secondary metabolites. Research Most therapeutics used today are derived from natural products, including microbially-produced secondary metabolites. However, the pipeline of these compounds has been diminishing over time, particularly in the case of novel antibiotic scaffolds. New sources of biosynthetic chemical diversity are therefore needed. Modern sequencing efforts have revealed large numbers of biosynthetic gene clusters (BGCs) in the genomes of bacteria not traditionally used for secondary metabolite discovery. However, in many cases these BGCs are not expressed at high levels in the laboratory, and the function of their products is unknown. Many diffusible secondary metabolites have evolved to mediate interactions between co-evolved species in the environment. Therefore, in order to activate and characterize the biological function of novel BGCs it is important to add biological context. The research proposed here will use a model methane-oxidizing bacterial community as a novel source of bioactive secondary metabolites. In this community methane-oxidizing bacteria support bacteria that cannot oxidize methane themselves, and the genome sequences of community isolates contain hundreds of predicted novel BGCs. Preliminary screening of community isolates alone and in pairwise interaction assays has already revealed multiple sources of antibacterial activity. The results of this work will: (1) use intra- and interspecies interactions in a metabolically-linked bacterial community to activate and characterize novel bioactive secondary metabolites, (2) determine the structure and function of a novel class of antibiotic, and (3) provide chemical probes for future studies examining how natural product-mediated interactions influence bacterial community composition, structure, and metabolic function.

 描述（由申请人提供）：候选人和环境在斯坦福大学 Matthew Bogyo 博士的实验室读研究生期间，我合成并应用了化学探针来检查艰难梭菌（一种主要的医院获得性病原体）分泌的毒素的激活机制，并了解沙门氏菌感染如何触发宿主细胞死亡。随后，我加入了华盛顿大学 Mary Lidstrom 博士的实验室，接受细菌遗传学和生理学方面的博士后培训，在那里我最近开发了用于甲烷氧化细菌的遗传工具，使这些生物体的代谢工程和新的生理学研究成为可能。我的长期职业目标是建立一个成功的研究计划，重点是利用生物背景来了解细菌产生的次级代谢产物的调节和功能。我使用这种方法的目的是发现具有治疗潜力的新型生物活性化合物，例如将在临床中使用的抗生素。我在化学和细菌遗传学领域的科学背景使我能够很好地实现这一目标。不过，我还没有具体研究过微生物次生代谢产物的功能和结构。因此，我近期的职业目标是获得 K99/R00 奖提供的二次代谢物发现和表征培训，使用模型甲烷氧化细菌群落作为生物活性化学多样性的新来源，以便过渡到独立的教职职位。我有一个优秀的指导团队来帮助我实现这些目标。在威斯康星大学，我将得到玛丽·利德斯特罗姆博士和彼得·格林伯格博士的共同指导。玛丽·利德斯特罗姆博士是一位杰出的细菌生理学家和遗传学家，在单碳化合物上生长的细菌方面具有专业知识，彼得·格林伯格博士是群体感应和相关形式的细菌化学通讯领域的专家和先驱。我还将接受哈佛医学院著名天然产物化学家 Jon Clardy 博士关于次级代谢物分离和结构阐明的指导，并将在加州大学圣地亚哥分校的技术先驱 Pieter Dorrestein 实验室中学习使用微生物成像质谱法直接在琼脂表面检测这些化合物。我还将通过参加微生物次生代谢物课程来补充本次培训。此外，我将利用华盛顿大学优良的学术环境来帮助我实现我的研究和职业目标。这将包括使用最先进的质谱和基因组学核心设施，以及参加校园内各个组织提供的研讨会、讲习班以及专业和职业发展课程。我还将获得咨询委员会导师对学术职业的一对一指导。总之，这些经验将确保我获得成功建立独立研究小组所需的科学经验和专业培训，研究细菌产生的次生代谢物的调节和生物功能。研究当今使用的大多数疗法都源自天然产物，包括微生物产生的次级代谢产物。然而，随着时间的推移，这些化合物的研发管线一直在减少，特别是在新型抗生素支架方面。因此，需要生物合成化学多样性的新来源。现代测序工作揭示了细菌基因组中存在大量生物合成基因簇（BGC），这些基因簇传统上不用于发现次级代谢物。然而，在许多情况下，这些 BGC 在实验室中并没有高水平表达，其产物的功能也是未知的。许多可扩散的次生代谢物已经进化到介导环境中共同进化物种之间的相互作用。因此，为了激活和表征新型 BGC 的生物学功能，添加生物学背景非常重要。这里提出的研究将使用模型甲烷氧化细菌群落作为生物活性次生代谢物的新来源。在这个群落中，甲烷氧化细菌支持本身不能氧化甲烷的细菌，并且群落分离株的基因组序列包含数百个预测的新型 BGC。单独对群落分离株和成对相互作用测定进行的初步筛选已经揭示了抗菌活性的多种来源。这项工作的结果将：（1）利用代谢相关的细菌群落中的种内和种间相互作用来激活和表征新型生物活性次生代谢物，（2）确定新型抗生素的结构和功能，（3）为未来研究提供化学探针，以检验天然产物介导的相互作用如何影响细菌群落的组成、结构和代谢功能。