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

许多功能基因，包括与抗生素耐药性有关的基因，都存在于细菌的质粒上。这些质粒能够通过水平基因转移从一种细菌转移到另一种细菌。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，这些依赖质粒的细菌很常见，而且很容易从环境中分离出来。该项目旨在利用一系列独特的新型质粒依赖性病毒来回答与这组不寻常病毒的生物学和进化相关的悬而未决的问题。特别是，这个项目涉及到确定的遗传因素，决定宿主范围的质粒依赖性的寄生虫。该项目的更广泛影响包括用于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的培训，并将参与研究项目的噬菌体发现部分。随着对这些病原菌的分子生物学和宿主范围的深入了解，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，很容易转移到接合质粒上。质粒依赖性突变似乎靶向这些基因转移载体，可能对诸如抗生素抗性的性状施加负频率依赖性选择压力。研究人员的目标是利用他们独特的新型质粒依赖性病毒来回答与这组不寻常病毒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，使用工程化的靶细菌进行高通量发现，研究人员已经确定了51个新的依赖于IncP接合质粒的质粒依赖性突变体，平均核苷酸同一性在82.5% - 99%之间，并且不含辅助基因。然而，尽管它们的遗传特性很接近，但它们在宿主范围上表现出很大的差异，这与质粒的存在无关。该研究项目的一个目的是询问如何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表现出微小的遗传差异作为宿主特异性的巨大变化。另一个目的是确定宿主范围内变异的遗传机制，并阐明IncP接合性质粒p53如何能够适应多种多样的生物学和生理学，并可能逃避广泛的细菌宿主的防御。更广泛地说，这些实验将照亮的遗传机制，通过等位基因的变化，适应新的主机，以及主机，反过来，如何逃避和防御natural.This奖项反映了NSF的法定使命，并已被认为是值得通过使用基金会的智力价值和更广泛的影响审查标准进行评估的支持。

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.