MTM2:CollaborativeResearch:Microbially-mediated epigenetic modifications alter host phenotypes

MTM2：协作研究：微生物介导的表观遗传修饰改变宿主表型

• 批准号: 2025389
• 负责人: Irene Newton
• 金额: $ 130.72万
• 依托单位: Indiana University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-01-01 至 2025-12-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2025389&HistoricalAwards=false
• 关键词: MTM2; CollaborativeResearch; Microbially; mediated; epigenetic

Symbiotic microbes can have enormous impacts on their hosts’ health and evolution. Indeed, our own cells contain remnants of an ancient microbial symbiosis – the mitochondrion – which continues to provide us with metabolic capabilities essential to our physiology. Understanding the causes, mechanisms, and consequences of host-microbe interactions has emerged as a critical research objective at the interface of evolutionary biology, microbiology, ecology, and development. This project is based on the discovery that a bacterial symbiont changes the host cell in a particular way to protect it from viruses. In this proposed project, the researchers will investigate these changes in the host cell and identify how they alter host, bacterial symbiont, and invading virus. The investigators will use the fruit fly, Drosophila, the bacterium, Wolbachia that is a prominent member of the Drosophila microbiome, and the Sindbis virus which infects Drosophila, as a model system to study this phenomenon. The investigators will focus on RNA modifications to the fruit fly caused by the bacterium, which affect virus infection. Novel computational tools and wet lab protocols will be generated for dissemination to the broader community. Understanding the molecular underpinnings of symbiosis will help to (a) leverage that mechanism in the manipulation of agricultural and medically important microbiomes (e.g. probiotics and paratransgenesis), (b) reveal basic biology of broad relevance to life on the planet, and (c) better model the evolution of these interactions. Broader impacts include the generation of a project-based course at Indiana University focused on mosquito vectored viruses and outreach to the broader public through Indiana’s Environmental Resilience Institute. Successful host-associated microbes sculpt host cell biology in ways that are useful to them. Often, these changes in host biology alter the ability of other microbes to colonize, protecting the host niche for the first microbe. For example, colonization of insects with Wolbachia endosymbionts can preclude infection by viruses. This fact has led to the deployment of Wolbachia-infected mosquitos across the globe to limit the transmission of vectored diseases. This project is based on RNA modifications induced by Wolbachia that directly alter Drosophila cell biology and affect the ability of viruses to colonize. Wolbachia upregulates a host methyltransferase to limit virus replication and preliminary data suggest that the virus genome itself is modified in a Wolbachia infected cell, altering mRNA stability. These data lead to the following question:“How does a microbial symbiont alter the epitranscriptomic landscape of host cells?” This proposed project will identify modifications in both host DNA and RNA induced by Wolbachia and virus using direct sequencing approaches (PacBio and ONT), benchmarked by more established methods (bisulfite sequencing and mass spectrometry). In the process, wet lab protocols for generation of appropriate controls for Nanopore sequencing and bioinformatic pipelines for the analyses of epitranscriptomic datasets from Nanopore sequencing will be developed. All resources will be made broadly available and open access. Finally, the importance of these changes will be identified using molecular virology and Drosophila genetics. In sum, this work will identify how epitranscriptomic modifications link genotype to phenotype in this important symbiotic system.This project is funded by the Understanding the Rules of Life: Microbiome Theory and Mechanisms Program, administered as part of NSF's Ten Big Ideas through the Division of Emerging Frontiers in the Directorate for Biological Sciences.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

事实上，共生微生物可以对其宿主的健康和进化产生巨大影响，我们自己的细胞中含有一种古老的微生物共生的残余物——线粒体——它继续为我们提供对我们的生理学至关重要的代谢能力。宿主与微生物相互作用的后果已成为进化生物学、微生物学、生态学和发育领域的一个关键研究目标，该项目基于细菌共生体以特定方式改变宿主细胞的发现。在这个拟议的项目中，研究人员将研究宿主细胞中的这些变化，并确定它们如何改变宿主、细菌共生体和入侵病毒。研究人员将使用果蝇、果蝇、沃尔巴克氏体细菌。果蝇微生物组的重要成员，以及感染果蝇的辛德比斯病毒，作为研究这一现象的模型系统，研究人员将重点关注由果蝇引起的 RNA 修饰。将产生影响病毒感染的新型计算工具和湿实验室协议，以传播到更广泛的社区。了解共生的分子基础将有助于（a）利用该机制来操纵农业和医学上重要的微生物组。益生菌和副转基因），（b）揭示与地球生命广泛相关的基础生物学，以及（c）更好地模拟这些相互作用的演变，包括在印第安纳大学创建基于项目的课程。专注于蚊子传播的病毒，并通过印第安纳州环境复原力研究所向更广泛的公众推广，成功的宿主相关微生物以对其有用的方式塑造宿主细胞生物学，通常，宿主生物学的这些变化会改变其他微生物的定殖能力，保护第一种微生物的宿主生态位，例如，带有沃尔巴克氏体内共生体的昆虫的定植可以阻止病毒的感染，这一事实导致了感染沃尔巴克氏体的蚊子的分布。该项目基于沃尔巴克氏菌诱导的 RNA 修饰，该修饰直接改变果蝇细胞生物学并影响病毒定殖的能力，上调宿主甲基转移酶以限制病毒复制。病毒基因组本身在沃尔巴克氏体感染的细胞中被修改，改变了 mRNA 的稳定性，这些数据引出了以下问题：“微生物共生体如何改变宿主细胞的表观转录组景观？”拟议的项目将使用直接测序方法（PacBio 和 ONT）识别由 Wolbachia 和病毒引起的宿主 DNA 和 RNA 的修饰，并以更成熟的方法（亚硫酸氢盐测序和质谱）为基准，在此过程中，湿实验室协议用于生成适当的方法。将开发用于纳米孔测序的控制和用于分析纳米孔测序的表观转录组数据集的生物信息学管道。最后，将使用分子来确定这些变化的重要性。总之，这项工作将确定表观转录组修饰如何在这个重要的共生系统中将基因型与表型联系起来。该项目由理解生命规则：微生物组理论和机制计划资助，该计划是 NSF 十大计划的一部分。通过生物科学理事会新兴前沿部门提出的想法。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力价值和更广泛的影响审查进行评估，被认为值得支持标准。