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

EAGER：识别质粒依赖性噬菌体宿主范围的遗传决定因素

• 批准号: 2331228
• 负责人: Michael Baym
• 金额: $ 30万
• 依托单位: Harvard University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-08-15 至 2025-07-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2331228&HistoricalAwards=false
• 关键词: EAGER; Identifying; genetic; determinants; plasmid

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.

许多功能基因，包括涉及抗生素耐药性的基因，都在细菌的质粒上发现。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，噬菌噬细胞利用这些质粒感染细菌。最近的发现表明，这些与质粒相关的噬菌体很常见，并且可以从环境中很容易发现。该项目旨在利用独特的新型质粒依赖噬菌体集合来回答与这种不寻常病毒群体的生物学和进化有关的杰出问题。特别是，该项目涉及确定决定质粒依赖噬菌体宿主范围的遗传因素。该项目的更广泛的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的培训，并将参与研究项目的噬菌体发现部分。对这些噬菌体和宿主范围的分子生物学的增强理解最终可能为抗生素耐药性问题提供新的解决方案。在偶联质粒上很容易转移许多功能基因，包括抗生素耐药性的决定因素。质粒依赖性噬菌体似乎靶向基因转移的这些向量，可能对诸如抗生素耐药性等性状的负频率依赖性选择压力施加负频率。研究人员旨在利用其独特的新型质粒依赖性噬菌体收集，以回答与这种不寻常病毒群体的生物学和进化有关的杰出问题。研究人员使用工程目标细菌采用受体引导的发现平台进行高通量发现，已经确定了51个依赖于Incp偶联质粒的新质粒依赖性噬菌体，共享82.5％-99％-99％的平均核苷酸标识，并且不包含附属基因。然而，尽管具有紧密的遗传身份，但噬菌体在宿主范围内表现出很大的差异，而宿主范围与质粒的存在无关。研究项目的目的之一是审问小遗传差异如何使用生物信息学，工程和测试突变，从而导致宿主范围的变化，这是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，并可能逃避多种细菌宿主的防御能力。更广泛地说，这些实验将阐明噬菌体通过等位基因变化适应新宿主的遗传机制，以及宿主如何反过来避免噬菌体。该奖项反映了NSF的法定任务，并被认为是通过基金会的知识分子和宽广的影响来评估的，并被视为值得通过评估的支持。