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引发宿主细胞死亡。随后，我加入了华盛顿大学玛丽·利德斯特伦博士的实验室，进行细菌遗传学和生理学的博士后培训，在那里，我最近开发了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，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能够很好地实现这一目标。然而，我还没有专门研究微生物次级代谢产物的功能和结构。因此，我的近期职业目标是获得K99/R 00奖在次级代谢产物发现和表征中的培训，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师职位。我有一个优秀的指导团队来帮助我实现这些目标。在华盛顿大学，我将由玛丽里德斯特罗姆博士和彼得格林伯格博士共同指导，玛丽是一位杰出的细菌生理学家和遗传学家，擅长研究在一碳化合物上生长的细菌，彼得格林伯格博士是群体感应和细菌化学通讯相关形式领域的专家和先驱。我还将从哈佛医学院的著名天然产物化学家Jon Clardy博士那里获得次级代谢物分离和结构解析的指导，并将学习在加州大学圣地亚哥分校的Pieter Dorrestein实验室中使用微生物成像质谱法直接在琼脂表面上检测这些化合物，该技术是该技术的先驱。我还将参加一个关于微生物次级代谢物的课程，以补充这一培训。此外，我将利用UW优秀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，以及参加研讨会，讲习班和由校园内各种组织提供的专业和职业发展课程。我还将从我的顾问委员会的导师那里获得一对一的学术生涯指导。总之，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，研究细菌产生的次级代谢产物的调节和生物学功能。研究当今使用的大多数治疗药物都来自天然产物，包括微生物产生的次级代谢产物。然而，随着时间的推移，这些化合物的管道一直在减少，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。现代测序工作已经揭示了细菌基因组中大量的生物合成基因簇（BGC），这些基因簇传统上不用于次级代谢产物的发现。然而，在许多情况下，这些BGC在实验室中的表达水平并不高，其产物的功能尚不清楚。许多可扩散的次级代谢产物已经进化成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，重要的是添加生物学背景。本文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级代谢产物的新来源。在这个社区中，甲烷氧化细菌支持不能氧化甲烷的细菌，社区分离物的基因组序列包含数百个预测的新型BGC。社区分离株单独和成对相互作用试验的初步筛选已经揭示了多种来源的抗菌活性。这项工作的结果将：（1）在代谢相关的细菌群落中使用种内和种间相互作用来激活和表征新的生物活性次级代谢产物，（2）确定一类新型抗生素的结构和功能，以及（3）为未来研究提供化学探针，研究天然产物介导的相互作用如何影响细菌群落组成，结构和代谢功能。