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

微生物群落，包括单细胞生物，如细菌和原生生物以及病毒颗粒，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生物圈维持中的作用，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，很少有人知道病毒和它们的微生物宿主细胞之间的相互作用如何影响营养循环。 该项目正在探索负责病毒复制关键步骤的酶DNA聚合酶的生物化学特征是否可以提供病毒与其宿主细胞之间相互作用性质的详细见解。 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。 从长远来看，对生态系统内病毒-宿主相互作用的进一步了解将为未来的绿色技术提供所需的基础信息，这些技术将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实验室研究的本科生，并为K-12学生提供教育推广。 在可能的情况下，从科学劳动力中代表性不足的人群中招募学生。创建一个理论框架，用于基于复制模块内的基因预测未知病毒的感染表型（即，复制子）是这个跨学科项目的首要目标。利用实验和计算的方法，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表型联系。实验目标包括：1）代表病毒内PolA多样性广泛横截面的A家族DNA聚合酶（PolA）酶的合成; 2）病毒PolA复制酶的体外生化表征（关于聚合酶速度、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力学; 4）基于PolA的遗传发生和复制子的遗传组成开发病毒的分类方案; 5）基于PolA复制子分类组开发预测未知病毒的感染表型的基因组到表型组规则;和6）基于现有病毒组数据的全球海洋内噬菌体感染表型的综合性病毒学研究和基于PolA复制子的预测基因组对表型规则的应用。 该研究的成功将依赖于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NSF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.