EAGER: Identifying the genetic determinants of plasmid-dependent phage host range

在细菌的质粒上发现了许多功能基因，包括与抗生素耐药性有关的基因。这些质粒能够通过水平基因转移从一个细菌转移到另一个细菌。某些病毒，噬菌体，利用这些质粒感染细菌。最近的一项发现表明，这些依赖质粒的噬菌体很常见，很容易从环境中发现。该项目旨在利用一种独特的新型依赖质粒的噬菌体来回答与这一不寻常病毒群的生物学和进化有关的悬而未决的问题。特别地，本项目涉及确定质粒依赖噬菌体宿主范围的遗传因素的鉴定。该项目的更广泛影响包括用于噬菌体高通量表征的工具集，以及将更广泛地帮助社区的协议和软件。学生将接受生物信息学分析方面的培训，并将参与研究项目的噬菌体发现部分。加强对这些噬菌体和宿主范围的分子生物学的理解可能最终为抗生素耐药性问题提供新的解决方案。许多功能基因，包括抗生素耐药性的决定因素，很容易在结合质粒上转移。依赖质粒的噬菌体似乎以这些基因转移载体为目标，可能对诸如抗生素耐药性等性状施加负频率依赖的选择压力。研究人员的目标是利用他们独特的新型依赖质粒噬菌体的收集来回答与这一不寻常病毒群的生物学和进化有关的悬而未决的问题。利用受体引导的发现平台，利用工程靶菌进行高通量发现，研究人员已经鉴定出51种新的依赖于IncP结合质粒的噬菌体，它们的核苷酸平均同源性在82.5% - 99%之间，不含辅助基因。然而，尽管它们具有密切的遗传特性，噬菌体在宿主范围内表现出很大的差异，这与质粒的存在无关。该研究项目的一个目的是利用生物信息学和工程学以及测试导致宿主范围变化的突变来询问小的遗传差异如何表现为宿主特异性的大变化。另一个目的是确定宿主范围内变异的遗传机制，并阐明IncP结合质粒噬菌体如何能够适应多种生物学和生理学，并可能逃避各种细菌宿主的防御。更广泛地说，这些实验将阐明噬菌体通过等位基因变异适应新宿主的遗传机制，以及宿主反过来如何逃避和防御噬菌体。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。

Many functional genes, including genes involved in antibiotic resistance, are found on plasmids in bacteria. These plasmids are able to move from one bacterium to another, through horizontal gene transfer. Certain viruses, bacteriophages, exploit these plasmids to infect bacteria. A recent discovery suggests that these plasmid-dependent phages are common and readily discoverable from the environment. This project aims to leverage a unique collection of novel plasmid-dependent phages to answer outstanding questions related to the biology and evolution of this unusual group of viruses. In particular, this project concerns the identification of genetic factors that determine host range of plasmid-dependent phages. Broader impacts of the project include toolsets for high-throughput characterization of phages, as well as protocols and software that will aid the community more broadly. Students will be trained in bioinformatic analysis and will be involved in the phage discovery part of the research project. The enhanced understanding of the molecular biology of these phages and host range may eventually provide novel solutions to the problem of antibiotic resistance.Many functional genes, including determinants of antibiotic resistance, are readily transferred on conjugative plasmids. Plasmid-dependent phages appear to target these vectors of gene transfer, possibly exerting a negative frequency dependent selective pressure on traits such as antibiotic resistance. The investigators aim to leverage their unique collection of novel plasmid-dependent phages to answer outstanding questions related to the biology and evolution of this unusual group of viruses. Employing a receptor-guided discovery platform using engineered target bacteria for high-throughput discovery, the investigators have identified 51 new plasmid-dependent phages that are dependent on IncP conjugative plasmids, share between 82.5% - 99% average nucleotide identity, and contain no accessory genes. However, despite their close genetic identity, the phages demonstrate large differences in host range that is independent of plasmid presence. One aim of the research project is to interrogate how small genetic differences can manifest as large changes in host specificity using bioinformatics and engineering and testing mutations that result in changes in host range. Another aim is to determine the genetic mechanisms of the variation within host range and shed light on how the IncP conjugative plasmid phages are able to adapt to the diverse biology and physiology, and perhaps evade the defenses, of a wide range of bacterial hosts. More broadly, these experiments will illuminate the genetic mechanisms by which phages adapt to new hosts via allelic variation, and how the hosts, in turn, evade and defend against phages.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.