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.

在整个生物圈中，由细菌和生物等单细胞生物（如细菌和生物颗粒）组成的微生物群落在整个生物圈中无处不在。 这些群落是营养循环的引擎，将复杂分子加工成对较高生物（例如植物和藻类）生长至关重要的更简单化合物。 尽管我们欣赏微生物的生物圈维持作用，但我们对支持营养周期的生态机制的理解是基本的。 特别是，知之甚少，关于病毒及其微生物宿主细胞之间的相互作用如何影响营养周期。 该项目正在探索酶，DNA聚合酶的生化特征是否负责病毒复制的关键步骤，它可以提供有关病毒与宿主细胞之间相互作用的性质的详细见解。 DNA聚合酶生物化学与病毒生物学之间的连接将提供一个框架，以根据从整个微生物群落（称为宏基因组序列数据）收集的DNA序列数据来预测微生物群落中病毒宿主相互作用的结果。 从长远来看，对生态系统内病毒宿主相互作用的改进理解将为未来绿色技术所需的基础信息提供一个组成部分，这将有助于维持自然和工程的农业生态系统。 这个多学科项目支持了微生物学，生物化学和生物信息学领域的两名博士学位学生的教育。 研究人员和学生正在指导本科生在实验室研究中，并向K-12学生提供教育宣传。 如果可能的话，学生是从科学劳动力中人口不足的人群中招募的。创建一个理论框架来预测基于复制模块中基因（即复制子）内基因的未知病毒的感染表型是该跨学科项目的总体目标。使用实验和计算方法，该项目正在寻求发现假设的基因组与未知病毒的复制子和感染表型之间的现象联系。实验目标包括：1）代表病毒中波拉多样性的广泛横截面的家族A DNA聚合酶（POLA）酶的合成； 2）病毒pola复制酶的体外生化表征（有关聚合酶速度，链位移，加工性，核酸酶活性和忠诚度的定量数据）； 3）体内评估波拉的变化如何影响噬菌体感染动态； 4）开发基于Pola的系统发育和复制子的遗传组成的病毒分类方案； 5）基因组开发基于Pola复制子分类组的未知病毒的感染表型的基因组发展； 6）基于现有的病毒蛋白数据以及基于Pola Replicon的现有基因组的应用，对全球海洋中噬菌体感染表型的全面生物地理研究。 这项研究的成功将依靠一个现有的合作跨学科团队，该团队在酶生物化学，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具有专业知识。该奖项反映了NSF的法定任务，并通过该基金会的知识优点和广泛的影响来评估NSF的法定任务。