MTM 1: Does replicon biochemistry define the infection dynamics of viruses within ecosystems?

MTM 1：复制子生物化学是否定义了生态系统内病毒的感染动态？

• 批准号: 2025567
• 负责人: K. Wommack
• 金额: $ 42.5万
• 依托单位: University of Delaware
• 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 2024-12-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2025567&HistoricalAwards=false
• 关键词: MTM; Does; replicon; biochemistry; define

Microbial communities, consisting of single celled organisms such as bacteria and protists as well as virus particles, are ubiquitous throughout the biosphere. These communities are the engines of nutrient cycles, processing complex molecules into the simpler compounds essential for the growth of higher organisms such as plants and algae. While we appreciate the biosphere-sustaining role of microbes, our understanding of the ecological mechanisms supporting nutrient cycles is rudimentary. In particular, little is known of how the interactions between viruses and their microbial host cells influences nutrient cycles. This project is exploring whether the biochemical characteristics of an enzyme, DNA polymerase, which is responsible for a key step in viral replication, can provide detailed insights on the nature of interactions between viruses and their host cells. Connections between DNA polymerase biochemistry and viral biology, will provide a framework for predicting the outcomes of viral host interactions within microbial communities based on DNA sequence data gathered from entire microbial communities (known as metagenomic sequence data). Over the longer term, improved understanding of viral-host interactions within ecosystems will provide one component of the foundational information needed for future green technologies that will help in sustaining both natural and engineered agri-ecosystems. This multidisciplinary project supports the education of two PhD students in the fields of microbiology, biochemistry, and bioinformatics. The investigators and students are mentoring undergraduate students in laboratory research and provide educational outreach to K-12 students. Students are recruited from populations under-represented in the scientific workforce when possible. Creating a theoretical framework for predicting the infection phenotypes of unknown viruses based on genes within the replication module (i.e., the replicon) is the overarching objective of this interdisciplinary project. Using experimental and computational approaches, the project is seeking to uncover hypothesized genome to phenome linkages between the replicon and infection phenotypes of unknown viruses. Experimental objectives include: 1) synthesis of Family A DNA polymerase (PolA) enzymes representing a broad cross-section of PolA diversity within viruses; 2) in vitro biochemical characterization of viral PolA replicases (quantitative data on polymerase speed, strand displacement, processivity, exonuclease activity, and fidelity); 3) in vivo assessment of how changes in PolA impact phage infection dynamics; 4) development of a classification scheme for viruses based on the phylogeny of PolA and the genetic composition of the replicon; 5) development of genome to phenome rules that predict the infection phenotypes of unknown viruses based on PolA replicon classification groups; and 6) a comprehensive biogeographic study of phage infection phenotypes within the global ocean based on existing virome data and the application of predictive genome to phenome rules based on the PolA replicon. The success of the research will rely on an existing collaborative interdisciplinary team with expertise in enzyme biochemistry, phage biology, bioinformatics, microbial oceanography and molecular genetics.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.

微生物群落由细菌和原生生物等单细胞生物以及病毒颗粒组成，在整个生物圈中无处不在。 这些群落是营养循环的引擎，将复杂的分子加工成植物和藻类等高等生物生长所必需的简单化合物。 虽然我们认识到微生物在维持生物圈中的作用，但我们对支持营养循环的生态机制的理解还很初级。 特别是，人们对病毒与其微生物宿主细胞之间的相互作用如何影响营养循环知之甚少。 该项目正在探索负责病毒复制关键步骤的 DNA 聚合酶的生化特征是否可以提供有关病毒与其宿主细胞之间相互作用的性质的详细见解。 DNA聚合酶生物化学和病毒生物学之间的联系将提供一个框架，用于根据从整个微生物群落收集的DNA序列数据（称为宏基因组序列数据）来预测微生物群落内病毒宿主相互作用的结果。 从长远来看，加深对生态系统内病毒与宿主相互作用的了解将为未来绿色技术所需的基础信息提供一个组成部分，从而有助于维持自然和工程农业生态系统。 这个多学科项目支持微生物学、生物化学和生物信息学领域的两名博士生的教育。 研究人员和学生正在指导本科生进行实验室研究，并为 K-12 学生提供教育服务。 如果可能的话，学生是从科学队伍中代表性不足的人群中招募的。创建一个基于复制模块（即复制子）内的基因来预测未知病毒感染表型的理论框架是这个跨学科项目的首要目标。该项目试图利用实验和计算方法来揭示未知病毒的复制子和感染表型之间假设的基因组与表型组的联系。实验目标包括：1) 合成 A 族 DNA 聚合酶 (PolA)，代表病毒内 PolA 多样性的广泛横截面； 2) 病毒PolA复制酶的体外生化特征（聚合酶速度、链置换、持续合成能力、核酸外切酶活性和保真度的定量数据）； 3) 体内评估 PolA 的变化如何影响噬菌体感染动态； 4）根据PolA的系统发育和复制子的遗传组成制定病毒分类方案； 5）开发基因组到表型的规则，基于PolA复制子分类组预测未知病毒的感染表型； 6) 基于现有病毒组数据以及基于 PolA 复制子的预测基因组在表型组规则中的应用，对全球海洋内噬菌体感染表型进行全面的生物地理学研究。 该研究的成功将依赖于现有的跨学科协作团队，该团队拥有酶生物化学、噬菌体生物学、生物信息学、微生物海洋学和分子遗传学方面的专业知识。该奖项反映了 NSF 的法定使命，并通过利用基金会的智力优势进行评估，认为值得支持以及更广泛的影响审查标准。

项目成果

Novel Viral DNA Polymerases From Metagenomes Suggest Genomic Sources of Strand-Displacing Biochemical Phenotypes

来自宏基因组的新型病毒 DNA 聚合酶提示链置换生化表型的基因组来源

• DOI: 10.3389/fmicb.2022.858366
• 发表时间: 2022-04
• 期刊: Frontiers in Microbiology
• 影响因子: 5.2
• 作者: Keown, Rachel A.;Dums, Jacob T.;Brumm, Phillip J.;MacDonald, Joyanne;Mead, David A.;Ferrell, Barbra D.;Moore, Ryan M.;Harrison, Amelia O.;Polson, Shawn W.;Wommack, K. Eric
• 通讯作者: Wommack, K. Eric