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

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。虽然我们欣赏微生物维持生物圈的作用，但我们对支持营养循环的生态机制的理解是基本的。特别是，人们对病毒及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。这个项目正在探索一种酶的生化特征，DNA聚合酶，它是病毒复制的关键步骤，是否可以提供关于病毒和宿主细胞之间相互作用本质的详细见解。DNA聚合酶生物化学和病毒生物学之间的联系，将为基于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）预测微生物群落内病毒宿主相互作用的结果提供一个框架。从长远来看，提高对生态系统内病毒-宿主相互作用的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农业生态系统。该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。调查人员和学生正在指导本科生进行实验室研究，并为K-12学生提供教育推广。尽可能从科学队伍中代表性不足的人群中招募学生。创建一个基于复制模块（即复制子）内基因预测未知病毒感染表型的理论框架是本跨学科项目的首要目标。利用实验和计算方法，该项目正在寻求揭示未知病毒复制子和感染表型之间的假设基因组与表型之间的联系。实验目的包括：1)合成A族DNA聚合酶（PolA）酶，代表病毒内PolA多样性的广泛横截面；2)病毒PolA复制酶的体外生化表征（聚合酶速度、链位移、加工速度、外切酶活性和保真度的定量数据）；3)体内评估PolA变化对噬菌体感染动力学的影响；4)基于PolA的系统发育和复制子的遗传组成建立病毒分类方案；5)基于PolA复制子分类群预测未知病毒感染表型的基因组到表型规则的发展；6)基于现有病毒组数据的全球海洋噬菌体感染表型的综合生物地理研究以及基于PolA复制子的预测基因组对表型规则的应用。这项研究的成功将依赖于一个现有的跨学科合作团队，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。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

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.