Mechanisms of interaction between bacteriophage and their hosts throughout the infection cycle

细菌病毒，称为噬菌体或噬菌体，是地球上最丰富的生物实体之一。 星球这些病毒在基因组内容、感染机制、复制周期和 结构随着使用噬菌体对抗抗生素抗性细菌的兴趣越来越大， 了解这些病毒如何感染宿主的机制是必要的;复制和调节它们的 基因及其宿主的基因;以及它们如何在各种环境中持续存在，包括人体和/或 储存条件然而，我们目前的模型系统本质上只代表了噬菌体的一小部分， 多样性这项工作的长期目标是开发另一种噬菌体系统--Moogleviruses-- 在环境中普遍存在并具有临床应用价值的细菌。然而，直到最近， 因为它们通常不感染细菌大肠杆菌的模式种， 肠道沙门氏菌相反，这些病毒通常是针对致病菌福氏志贺菌分离的 或机会致病菌如弗氏柠檬酸杆菌。因为这些病毒是专性裂解和特异性的 腹泻最常见的病原体之一，S.它们可以用来控制 食品或水中的细菌种类，或用于治疗抗药性感染。然而，目前我们缺乏 充分了解其生物学过程。Moogle病毒与其他病毒相比具有独特的特征， 噬菌体，包括半特异性宿主范围，在其基因组中编码的大量tRNA，以及 不常见的衣壳和基因组大小。这项工作的中心假设是，这些病毒使用替代的 策略感染和持续相比，更彻底的特点模型系统。的目标 因此，这项具体的建议是确定感染志贺氏菌的Moogleviruses用于识别 它们的宿主，在翻译水平上调节病毒和宿主基因的表达，并组装成新的 可以在环境中持久存在的粒子。该建议的预期成果是：1）确定 噬菌体受体结合蛋白与初级和次级之间的关键相互作用区域 S. flexneri宿主，沿着确定附着和进入的动力学; 2）完全Ribo- seq和RNA-seq数据集从各种环境和感染条件，导致一个机制， 理解噬菌体感染如何改变噬菌体和宿主基因的翻译效率;和3）广泛的 解析了穆格尔病毒衣壳的组装途径，并指示蛋白质或蛋白质结构域 负责影响衣壳稳定性。这项工作将对基础生物学产生影响， 已知的噬菌体感染和持久性策略和机制的库;和医疗 应用，告知如何这些武器本身可以应用于打击S。福氏杆菌感染 临床，或如何使用它们的特性来设计用于医疗或工业应用的新型纳米材料。

Bacterial viruses, known as bacteriophages or phages, are among the most abundant biological entities on the planet. These viruses vary broadly in terms of genome content, infection mechanisms, replication cycles, and structure. With an increasing interest in using bacteriophages to combat antibiotic resistant bacteria, it is necessary to understand mechanisms of how these viruses infect their hosts; replicate and regulate both their genes and their hosts’ genes; and how they persist in various environments, including the human body and/or storage conditions. However, our current model systems inherently only represent a fraction of bacteriophage diversity. The long-term goal of this work is to develop an additional bacteriophage system—the Moogleviruses— that appear to be ubiquitous in the environment and clinically useful qualities. They have, however, only recently been isolated because they do not commonly infect the model species of bacteria Escherichia coli and Salmonella enterica. Instead, these viruses are often isolated against the pathogenic bacteria Shigella flexneri or opportunistic pathogens such as Citrobacter freundii. Because these viruses are obligately lytic and specific to one of the most common etiological agents of diarrhea, S. flexneri, they could be used for controlling this species of bacteria in food or water, or for treating antibiotic-resistant infections. At this time, however, we lack sufficient understanding of their biological processes. Moogleviruses have distinct characteristics versus other bacteriophages, including a semi-specific host range, a large number of tRNAs encoded in their genomes, and uncommon capsid and genome sizes. The central hypothesis of this work is that these viruses use alternative strategies to infect and persist compared to more thoroughly characterized model systems. The objectives of this specific proposal are therefore to determine the mechanisms Shigella-infecting Moogleviruses use to identify their hosts, modulate the expression of viral and host genes on a translational level, and assemble into new particles that can persist in the environment. The expected outcomes of this proposal are: 1) the identification of critical interacting regions between the phage receptor-binding proteins and both primary and secondary receptors on the S. flexneri host, along with determining the kinetics of attachment and entry; 2) complete Ribo- seq and RNA-seq datasets from a variety of environments and infection conditions, leading to a mechanistic understanding of how phage infection alters translational efficiency of phage and host genes; and 3) a broadly resolved assembly pathway of the Mooglevirus capsid, with an indication of proteins or protein domains responsible for affecting capsid stability. This work will have impacts for both basic biology, expanding our repertoire of known bacteriophage strategies and mechanisms for infection and persistence; and medical application, informing how these phages themselves could be applied to combat S. flexneri infections in the clinic, or how their properties could be used to engineer novel phages for medical or industrial applications.