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(申请人提供)：候选人和环境在斯坦福大学马修·博乔博士的实验室读研究生期间，我合成并应用化学探针来检测艰难梭菌(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引发宿主细胞死亡。随后，我加入了玛丽·利德斯特罗姆博士在华盛顿大学的实验室，接受细菌遗传学和生理学方面的博士后培训。在那里，我最近开发了甲烷氧化细菌的基因工具，使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项目，专注于利用生物学背景来了解细菌产生的次生代谢物的调节和功能。我使用这种方法的目的是发现新的具有治疗潜力的生物活性化合物，如抗生素，将用于临床。我在化学和细菌遗传学方面的科学背景使我处于实现这一目标的有利地位。然而，我还没有专门研究确定微生物次生代谢物的功能和结构。因此，我的直接职业目标是通过K99/R00奖获得次级代谢物发现和表征方面的培训，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员工职位。我有一个优秀的指导团队来帮助我实现这些目标。在威斯康星州大学，我将由Mary Lidstrom博士和Peter Greenberg博士共同指导，Mary Lidstrom博士是一位杰出的细菌生理学家和遗传学家，拥有在一碳化合物上生长的细菌的专业知识；Peter Greenberg博士是群体感应和相关形式细菌化学通信领域的专家和先驱。我还将接受哈佛医学院著名天然产品化学家乔恩·克拉迪博士关于次生代谢物分离和结构阐明的指导，并将学习如何在加州大学圣地亚哥分校的Pieter Dorrestein实验室使用微生物成像质谱仪直接在琼脂表面检测这些化合物，Pieter Dorrestein是该技术的先驱。我还将通过参加关于微生物次生代谢物的课程来补充这一培训。此外，我将利用威斯康星大学优越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核心设施进行质谱分析和基因组学，以及参加由不同组织在校园内提供的关于专业和职业发展的研讨会、研讨会和课程。我还将从我的顾问委员会的导师那里得到关于学术生涯的一对一指导。总而言之，这些经验将确保我将获得必要的科学经验和专业培训，以成功建立一个独立的研究小组，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治疗药物都来自天然产品，包括微生物产生的次生代谢物。然而，随着时间的推移，这些化合物的流水线一直在减少，特别是在新型抗生素支架的情况下。因此，需要新的生物合成化学多样性来源。现代测序工作发现，细菌基因组中存在大量生物合成基因簇(BGC)，传统上不用于次生代谢物的发现。然而，在许多情况下，这些BGC在实验室中不能高水平表达，其产物的功能尚不清楚。许多可扩散的次生代谢物已经进化，以调节环境中共同进化的物种之间的相互作用。因此，为了激活和表征新的BGC的生物学功能，添加生物背景是重要的。这里提出的研究将使用甲烷氧化细菌群落作为生物活性次生代谢物的新来源。在这个社区中，甲烷氧化菌支持本身不能氧化甲烷的细菌，社区分离株的基因组序列包含数百个预测的新型BGC。对单独和成对相互作用的社区分离株的初步筛选已经揭示了抗菌活性的多个来源。这项工作的结果将：(1)利用与代谢相关的细菌群落的种内和种间相互作用来激活和表征新的生物活性次生代谢物；(2)确定一类新的抗生素的结构和功能；(3)为未来研究天然产物介导的相互作用如何影响细菌群落的组成、结构和代谢功能提供化学探针。