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有益，但有些细菌是有害的病原体。找到一种杀死致病菌而不伤害有益微生物的方法可能是一种有用的工具。 噬菌体研究已成为微生物学中令人兴奋的新前沿，因为它在塑造微生物组中的作用，并作为对抗耐药细菌感染的潜在疗法。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靶标相互作用。虽然已经对数千种天然噬菌体进行了表征，但有限的研究探索了通过受体结合蛋白控制噬菌体-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测序和病毒宏基因组学方法来阐明蛋白质序列如何编码功能。 这项研究将成为众多以病毒为重点的教育推广活动的基础，包括中学课堂，以使不同的受众了解病毒和细菌生物学中的相关真实问题。 受体结合蛋白介导噬菌体与其细菌受体的相互作用，因此构成噬菌体宿主范围和活性（毒力）的关键决定因素。噬菌体通过这些蛋白质的遗传改变来适应新的宿主环境，从而表现出高度的功能可塑性。 尽管广泛的研究来解决与这种相互作用相关的机制，但仍不清楚受体结合蛋白突变如何影响噬菌体活性和宿主范围。这项工作将研究大肠杆菌受体结合蛋白的分子规则，感染大肠杆菌的病毒，并将寻求利用这些规则来设计具有食源性病原体特异性的合成大肠杆菌。此外，该项目还将研究来自另一组噬菌体的受体结合蛋白，这些蛋白具有更复杂的受体结合结构，允许噬菌体酶促降解保护某些细菌的胶囊，并与宿主受体结合。为了从机制上理解这一过程，将使用突变和宏基因组扫描来定位和鉴定具有双重能力的噬菌体的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。该项目有潜力创造的工具，可以广泛采用的研究社区，以研究在各种噬菌体宿主system.This奖项的序列功能关系反映了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。

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.