CAREER: Mapping the functional landscape of bacteriophage-host interactions at molecular resolution

虽然许多细菌对人类无害，甚至对人类有益，但有些细菌是有害的病原体。找到一种在不损害有益微生物的情况下杀死病原体的方法可能会被证明是一个有用的工具。噬菌体研究已经成为微生物学中一个令人兴奋的新前沿，因为它在塑造微生物群方面发挥了作用，并作为一种潜在的治疗耐药细菌感染的方法。噬菌体通过一种称为受体结合蛋白的结构识别并与其特定的细菌目标相互作用。虽然已有数以千计的天然噬菌体被鉴定，但有限的研究探索了通过受体结合蛋白控制噬菌体与宿主相互作用的分子机制。这项研究将应用基因组工程、高通量DNA测序和病毒元基因组学方法来阐明蛋白质序列如何编码功能。这项研究将成为许多以病毒为重点的教育推广活动的基础，包括在中学课堂上，让不同的受众接触到病毒和细菌生物学中相关的、真实的问题。受体结合蛋白介导噬菌体与其细菌受体(S)的相互作用，从而构成噬菌体寄主范围和活性(毒力)的关键决定因素。噬菌体通过改变这些蛋白的基因来适应新的寄主环境，从而表现出高度的功能可塑性。尽管有广泛的研究来解决与这种相互作用相关的机制，但受体结合蛋白突变如何影响噬菌体活性和宿主范围仍不清楚。这项工作将检测大肠杆菌噬菌体受体结合蛋白的分子规则，并将寻求利用这些规则来设计对食源性病原体具有特异性的合成大肠杆菌噬菌体。此外，该项目还将研究另一组噬菌体的受体结合蛋白，这些噬菌体具有更复杂的受体结合结构，使噬菌体既能酶促降解保护某些细菌的囊膜，又能与宿主受体结合。为了从机制上理解这一过程，将使用突变和元基因组扫描来定位和鉴定具有双重功能的噬菌体受体结合蛋白中每个序列的功能。这些突变研究将为机器学习指导的蛋白质设计策略提供信息，以设计新的噬菌体-宿主相互作用。该项目有可能创建可被研究界广泛采用的工具，以研究各种噬菌体-宿主系统中的序列-功能关系。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

While many bacteria are inoffensive or even beneficial to humans, some are harmful pathogens. Finding a way to kill the pathogenic bacteria without harming the beneficial microbes could prove a useful tool. Phage research has emerged as an exciting new frontier in microbiology due to its role in shaping microbiomes and as a potential therapy against drug-resistant bacterial infections. Phages identify and interact with their specific bacterial target through a structure known as the receptor-binding protein. While characterization of thousands of natural phages have occurred, limited studies have explored the molecular mechanisms that govern phage-host interactions through the receptor-binding protein. This research will apply genome engineering, high-throughput DNA sequencing, and viral metagenomics approaches to elucidate how protein sequences encode function. The research will be the basis for numerous viral-focused educational outreach activities, including for middle school classrooms, to expose a diverse audience to relevant, real-word issues in viral and bacterial biology. Receptor binding proteins mediate the interaction of a phage with its bacterial receptor(s) and thus constitute key determinants of a phage’s host range and activity (virulence). Phages exhibit high functional plasticity through genetic alterations of these proteins to adapt to new host environments. Despite extensive research to address the mechanisms associated with this interaction, it remains unclear how receptor binding protein mutations influence phage activity and host range. This work will examine the molecular rules of receptor binding proteins of coliphages, viruses that infect coliform bacteria, and will seek to exploit those rules to engineer synthetic coliphages with specificity for foodborne pathogens. In addition, the project will study receptor binding proteins from another group of phages that have a more complex receptor binding architecture that permits the phage to both enzymatically degrade the capsule that protects certain bacteria and also to bind to host receptors. To understand this process mechanistically, mutational and metagenomic scanning will be used to map and identify the function of every sequence in the receptor binding protein of a phage with the dual capability. These mutational studies will inform protein design strategies guided by machine learning to engineer new phage-host interactions. The project has the potential to create tools that could be broadly adopted by the research community to study sequence-function relationships in a variety of phage-host systems.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.