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: 2025384
• 负责人: Julie Hotopp
• 金额: $ 106.13万
• 依托单位: University of Maryland at Baltimore
• 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=2025384&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.

共生微生物可以增强对宿主健康和进化的影响。的确，我们自己的细胞包含一个古老的微生物共生（线粒体）的残余物，该细胞继续为我们提供对生理学必不可少的代谢能力。了解宿主 - 微生物相互作用的原因，机制和后果已成为进化生物学，微生物学，生态学和发展的界面的关键研究目标。该项目基于这样的发现，即细菌的象征能以一种保护宿主细胞来保护其免受病毒的影响。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，细菌符号和入侵病毒。研究人员将使用果蝇果蝇，细菌，Wolbachia，它是果蝇微生物组的杰出成员，以及感染果蝇的辛德比斯病毒作为研究这种现象的模型系统。研究人员将专注于对细菌引起的果蝇的修饰，这会影响病毒感染。将生成新颖的计算工具和湿实验室协议，以传播向更广泛的社区。了解共生的分子基础将有助于（a）利用这种机制在操纵农业和医学上重要的微生物组（例如益生菌和副发生）方面的机制，（b）揭示了对星球上生命的广泛相关性的基本生物学，以及（c）更好地模拟这些相互作用的效果。更广泛的影响包括在印第安纳大学的一项基于项目的课程的产生，该课程专注于蚊子媒介的病毒，并通过印第安纳州的环境弹性研究所向更广泛的公众推广。成功与宿主相关的微生物以对它们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定居的能力，从而保护第一个微生物的宿主利基市场。例如，用沃尔巴氏菌内共生体的昆虫定植可以阻止病毒感染。这一事实导致了沃尔巴契亚感染的蚊子在全球范围内部署，以限制矢量疾病的传播。该项目基于Wolbachia诱导的RNA修饰，该RNA直接改变了果蝇生物学，并影响病毒定居的能力。 Wolbachia上调宿主甲基转移酶以限制病毒复制，初步数据表明，病毒基因组本身在受沃尔巴氏菌感染细胞中修饰，从而改变了mRNA稳定性。这些数据导致了以下问题：“微生物象征能如何改变宿主细胞的同性转录景观？”该提出的项目将使用直接测序方法（PACBIO和ONT）诱导的宿主DNA和RNA中的修饰，并通过更既定的方法（Bisulfite测序和质谱法）进行了基准测试。在此过程中，将开发用于生成用于纳米孔测序和生物信息学管道的适当控制的湿实验方案，用于从纳米孔测序中分析表面转录数据集的分析。所有资源将被广泛提供并开放访问。最后，将使用分子病毒学和果蝇遗传学来确定这些变化的重要性。总而言之，这项工作将确定在这个重要的共生系统中如何将基因型与表型联系起来。该项目由理解生活规则的理解资助：微生物组理论和机制计划，作为NSF的一部分，作为NSF的十个大思想的一部分，是通过对生物学奖励的促进统治的分配。使用基金会的智力优点和更广泛的影响评估标准进行评估。