Bacterial Corrinoid Metabolism Across Scales: From Molecular Specificity to Community Dynamics

细菌跨尺度的类咕啉代谢：从分子特异性到群落动态

• 批准号: 10792408
• 负责人: Michiko E. Taga
• 金额: $ 36.41万
• 依托单位: UNIVERSITY OF CALIFORNIA BERKELEY
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-03-01 至 2026-02-28
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10792408
• 关键词: Address; Amino Acids; Anabolism; Archaea; Archaeal Genes; Area; Automobile Driving; Award; Bacillus subtilis; Bacteria; Biochemical Pathway; Biochemistry; Bioinformatics; Biological; Biosensor; Cobalt; Coenzymes; Communities; Complex; Corrinoids; Detection; Development; Environment; Enzymes; Family; Foundations; Funding; Future; Genes; Genetic; Genome; Goals; Health; Human; Human body; Mentorship; Metabolic; Metabolism; Methods; Microbiology; Modeling; Molecular; National Institute of General Medical Sciences; Outcome; Parents; Planet Earth; Reaction; Reporter; Research; Research Activity; Research Project Grants; Sampling; Scientist; Specificity; Structure; Students; Surveys; System; Testing; Training; Vitamin B 12; Work; bioinformatics pipeline; cofactor; comparative genomics; design; doctoral student; genetic approach; human model; microbial; microbial community; microorganism interaction; next generation; nucleobase; predictive signature; preference; programs; rapid detection; undergraduate student

PROPOSED ACTIVITIES RESEARCH STRATEGY Project Summary/Abstract Microbial communities inhabit nearly all environments on earth, including the human body, where they can influence health in myriad ways. These communities are often composed of hundreds or more species that form networks of metabolic interactions. Because metabolic interactions are complex and difficult to study at a molecular level, my research program focuses on interactions involving one family of metabolites – corrinoid cofactors – as a model to understand metabolic interactions among bacteria. Corrinoids are the vitamin B12 family of cobalt-containing metabolites that are used as enzyme cofactors for a variety of reactions. Corrinoids, like many amino acids, nucleobases, and other cofactors, are synthesized by only a fraction of bacteria that use them, and therefore are considered to be shared metabolites. Corrinoids are unique in their structural diversity, with over a dozen different forms discovered and up to eight of these forms found in microbial community samples, including the human gut. This structural diversity is a significant factor in microbial interactions because most bacteria are selective in the corrinoids they can use. The hypothesis driving this work is that structurally distinct corrinoids can be used as handles to manipulate microbial communities. Our previous NIGMS-funded research has laid the groundwork for the proposed research by establishing experimental methods; discovering and characterizing new genes; investigating corrinoid selectivity in enzymes, riboswitches, and bacteria; and creating a bioinformatic pipeline to predict corrinoid metabolism in bacteria. Our long-term vision is to build on this foundation to generate a newly detailed understanding of microbial community interactions through the study of corrinoids across scales, from molecular mechanisms to whole community perturbations. We will achieve this goal by (1) identifying genome sequence signatures predictive of bacterial corrinoid preferences in corrinoid- dependent enzymes and riboswitches, with an emphasis on evolutionary approaches and (2) investigating the molecular basis of corrinoid-dependent community dynamics by applying sequencing, culture-dependent, and genetic approaches to a model human gut-derived enrichment culture. As a test of our ability to understand and predict corrinoid-based metabolism and community dynamics, we will design and build bacterial strains with corrinoid-dependent metabolic networks, as well as consortia of bacteria with predictable dynamics. This research will be accomplished by using a combination of genetics, biochemistry, microbiology, and bioinformatics, building upon the past research of my group. Our work on corrinoids will not only serve as a model for microbial community interactions across systems, but may also lead to the development of new methods to alter microbial communities for beneficial outcomes. Specific Aims This proposal describes research projects to be conducted by two PhD students and one undergraduate. This support will provide tailored mentorship to each student while expanding our research into new areas within the scope of the parent award, which aims to apply the corrinoid model to the study of microbial community interactions. Each specific aim describes a project to be conducted by one student. Aim 1. Test the hypothesis that the Great Plate Count Anomaly can be influenced by corrinoids. PhD student Zoila Alvarez-Aponte will isolate bacteria from a human gut-derived bacterial enrichment culture in media containing different corrinoids to determine whether non-commercially available corrinoids can influence culturability. Aim 2. Use comparative genomics to define and survey corrinoid metabolism in the domain Archaea. PhD student Eleanor Wang will identify archaeal genes for corrinoid biosynthesis and corrinoid-dependent functions and survey their abundances throughout the domain Archaea. This will enable us to include archaea – understudied yet critical components of microbial communities – in future studies of microbial metabolic interactions. Aim 3. Construct and test riboswitch-based biosensors for rapid corrinoid detection. Undergraduate student Lesley Rodriguez will construct a panel of synthetic riboswitch-GFP reporters in Bacillus subtilis and test each strain for the ability to sense corrinoids. She will then use these strains as biosensors to rapidly detect corrinoids from diverse biological samples with high sensitivity. These projects will contribute to the training of the next generation of scientists, while providing the Taga lab with opportunities to pursue exciting new research directions.

拟议的活动 研究策略 项目摘要/摘要 微生物群落居住在地球上几乎所有的环境中，包括人体，在那里它们 会以多种方式影响健康。这些群落通常由数百种或更多物种组成，这些物种 形成代谢相互作用的网络。因为代谢相互作用是复杂的，很难在 在分子水平上，我的研究项目专注于涉及一种代谢物家族-皮质醇的相互作用 辅因子--作为了解细菌间代谢相互作用的模型。类胡萝卜素是维生素B12 一类含钴的代谢物，用作各种反应的酶辅助因子。科里诺斯， 像许多氨基酸一样，碱基和其他辅因子只由一小部分使用 因此被认为是共有的代谢物。科里诺类在结构多样性上是独一无二的， 在微生物群落中发现了十几种不同的形式和多达八种不同的形式 样本，包括人类的内脏。这种结构多样性是微生物相互作用的一个重要因素，因为 大多数细菌对它们可以使用的Corrinoid具有选择性。推动这项工作的假设是，在结构上 不同的Corrinoid可以用作操控微生物群落的把手。我们之前由NIGMS资助的 研究通过建立实验方法为拟议的研究奠定了基础；发现 鉴定新基因；研究酶、核糖开关和细菌中皮质醇的选择性；以及 创建一条生物信息学管道来预测细菌中的皮质醇代谢。我们的长期愿景是在 这一基础通过研究产生了对微生物群落相互作用的新的详细了解 从分子机制到整个群落的扰动。我们将实现这一目标 目标通过(1)识别预测皮质类菌偏爱的基因组序列特征- 依赖的酶和核糖开关，重点是进化方法和(2)研究 应用测序、培养依赖和 人类肠源性浓缩培养模型的遗传学方法。作为对我们理解和理解能力的测试 预测基于皮质激素的新陈代谢和群落动态，我们将设计和构建细菌菌株 依赖皮质激素的代谢网络，以及具有可预测动态的细菌联合体。这 研究将通过结合遗传学、生物化学、微生物学和 生物信息学，建立在我的团队过去的研究基础上。我们在Corrinoid方面的工作不仅将作为 微生物群落跨系统相互作用的模型，但也可能导致新的 改变微生物群落以获得有益结果的方法。 具体目标 这份提案描述了将由两名博士生和一名本科生进行的研究项目。 这种支持将为每个学生提供量身定做的指导，同时将我们的研究扩展到 家长奖的范围，旨在将皮质模型应用于微生物群落的研究 互动。每个具体目标都描述了一个学生要完成的项目。 目的1.验证大板块计数异常受科罗尼诺影响的假说。博士 学生Zoila Alvarez-Aponte将从人类肠道细菌培养物中分离细菌 含有不同的Corrinoid，以确定非商用Corrinoid是否会影响 可培育性。 目的2.利用比较基因组学对古生界皮质激素代谢进行定义和研究。 博士生埃莉诺·王将鉴定皮质醇生物合成和皮质醇依赖的古生菌基因 功能，并调查它们在整个古生界的丰度。这将使我们能够包括古生菌 -在未来的微生物代谢研究中，对微生物群落的关键组成部分研究不足 互动。 目的3.构建和测试用于皮质醇快速检测的核糖开关生物传感器。本科生 学生Lesley Rodriguez将在枯草杆菌中构建一个合成核糖开关-GFP记者小组，并测试 每一种菌株都有感知Corrinoid的能力。然后，她将使用这些菌株作为生物传感器来快速检测 从不同的生物样品中提取的Corrinoid具有很高的灵敏度。 这些项目将有助于培训下一代科学家，同时为TAGA实验室提供 追求激动人心的新研究方向的机会。