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

基本信息

批准号：
10171589
负责人：
Aaron Webster Puri
金额：
$ 24.65万
依托单位：
UNIVERSITY OF UTAH
依托单位国家：
美国
项目类别：
财政年份：
2016
资助国家：
美国
起止时间：
2016-07-18 至 2023-05-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10171589
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

项目摘要

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（由适用提供）：我在斯坦福大学的Matthew Bogyo实验室研究生院期间的候选人和环境，我将化学问题合成并应用化学问题，以检查艰难梭菌（梭状芽胞杆菌（Clostridium）艰难梭菌（Clostridium Clostridium closium colledium）的激活机制，艰难梭菌（梭状芽胞杆菌（Clostridium coldridium cluck），一种主要的医院获得的病原体，以及了解鲑鱼菌感染的宿主细胞死亡是如何触发的。随后，我加入了华盛顿大学的玛丽·利德斯特罗姆（Mary Lidstrom）博士的实验室，从事细菌遗传学和生理学的博士后培训，最近我开发了用于甲烷氧化细菌的遗传工具，用于使这些生物体中的代谢工程和新生理学研究。我的长期职业目标是建立一项成功的研究计划，旨在利用生物学环境，以了解细菌生产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，例如抗生素，这些化合物将用于诊所。我在化学和细菌遗传学界面上的科学背景使我处于实现这一目标的良好位置。但是，我尚未专门研究微生物二级代谢产物的功能和结构。因此，我的直接职业目标是通过使用模型的甲烷氧化细菌群落作为二级代谢物发现和表征的K99/R00奖获得的培训，作为生物活性化学多样性的新来源，以过渡到独立的教师职位。我有一支出色的心理团队来帮助我实现这些目标。在UW上，我将由一位杰出的细菌生理学家兼遗传学家Mary Lidstrom博士授予细菌的专业知识，并在单碳化合物上生长，而彼得·格林伯格（Peter Greenberg）博士是彼得·格林伯格（Peter Greenberg）博士，他是国家敏感性和相关形式的生物化学化学交流的专家和先驱。我还将获得有关哈佛医学院的著名天然产品化学家乔恩·克拉迪（Jon Clardy）博士的二级代谢产物隔离和结构阐明的指导，并将学会使用加利福尼亚大学圣地亚哥大学Pieter Dorrestein，Pieter Dorrestein，Pioter Dorrestein，Pioter of Pioneer of Pioneer的San Dogo的San Diego，PIETER Dorresteer，Pieter of Pionique of Pionique of Pieter Dorresteique of Pieter Dorresteique。我还将通过参加微生物二级代谢的课程来补充这种培训。此外，我将利用UW上出色的学术环境来帮助我实现自己的研究和职业目标。这将包括使用最先进的核心设施用于质谱和基因组学，以及参加校园各种组织提供的专业和职业发展课程，参加的精灵，讲习班以及课程。我还将在我的咨询委员会的导师中获得有关学术职业的一对一指导。这些经验将共同确保我将获得成功建立一个独立研究小组所必需的科学经验和专业培训，该研究小组研究细菌生产的二级代谢产物的调节和生物学功能。当今使用的大多数疗法研究源自天然产物，包括微生物产生的二级代谢产物。但是，随着时间的流逝，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。现代的测序工作揭示了大量的生物合成基因簇（BGC），传统上不用于次生代谢物发现的细菌基因组中。但是，在许多情况下，这些BGC在实验室中并未在高水平上表达，并且其产品的功能尚不清楚。许多可扩散的二级代谢产物已经演变为介导环境中共同进化的物种之间的相互作用。因此，为了激活和表征新型BGC的生物学功能，添加生物学环境很重要。这里提出的研究将使用模型的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，甲烷氧化细菌支持无法氧化甲烷本身的细菌，社区分离株的基因组序列含有数百种预测的新型BGC。单独对社区隔离株和成对相互作用测定的初步筛查已经揭示了多种抗菌活性来源。这项工作的结果将：（1）在代谢链接的细菌群落中使用内部和间隔的相互作用来激活和表征新型的生物活性二级代谢物，（2）确定新型抗生素类别的结构和功能，（3）为将来研究的化学问题提供了对自然产品相互作用的化学问题的影响，从而对自然产物介导的相互作用的影响如何影响细菌群体组成，并具有结构的结构，并构成了结构，并具有综合的功能。

项目成果

期刊论文数量（8）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Methylotroph Quorum Sensing Signal Identification by Inverse Stable Isotopic Labeling.

DOI：
10.1021/acschembio.1c00329
发表时间：
2021-08-20
期刊：
ACS chemical biology
影响因子：
4
作者：
Cummings DA Jr;Snelling AI;Puri AW
通讯作者：
Puri AW

Tundrenone: An Atypical Secondary Metabolite from Bacteria with Highly Restricted Primary Metabolism.

DOI：
10.1021/jacs.7b12240
发表时间：
2018-02-14
期刊：
Journal of the American Chemical Society
影响因子：
15
作者：
Puri AW;Mevers E;Ramadhar TR;Petras D;Liu D;Piel J;Dorrestein PC;Greenberg EP;Lidstrom ME;Clardy J
通讯作者：
Clardy J

A widespread methylotroph acyl-homoserine lactone synthase produces a new quorum sensing signal that regulates swarming in Methylobacterium fujisawaense.

DOI：
10.1128/mbio.01999-23
发表时间：
2024-01-16
期刊：
MBIO
影响因子：
6.4
作者：
Wallace, Mike;Cummings, Dale A., Jr.;Roberts, Andrew G.;Puri, Aaron W.
通讯作者：
Puri, Aaron W.

A Conserved Biosynthetic Gene Cluster Is Regulated by Quorum Sensing in a Shipworm Symbiont.

船虫共生体中保守的生物合成基因簇由群体感应调节。

DOI：
10.1128/aem.00270-22
发表时间：
2022
期刊：
Applied and environmental microbiology
影响因子：
4.4
作者：
Robes,JoseMiguelD;Altamia,MarvinA;Murdock,EthanG;Concepcion,GiselaP;Haygood,MargoG;Puri,AaronW
通讯作者：
Puri,AaronW

Interspecies Chemical Signaling in a Methane-Oxidizing Bacterial Community.

甲烷氧化细菌群落中的种间化学信号。

DOI：
10.1128/aem.02702-18
发表时间：
2019
期刊：
Applied and environmental microbiology
影响因子：
4.4
作者：
Puri,AaronW;Liu,Darren;Schaefer,AmyL;Yu,Zheng;Pesesky,MitchellW;Greenberg,EPeter;Lidstrom,MaryE
通讯作者：
Lidstrom,MaryE