Viral jumping of genus and species barriers: engineering phage host range promiscuity for diverse bacteria

摘要（最多4000字）所有生物体都可以被病毒感染，包括植物、动物和人类。世纪以来，人们已经知道细菌也容易受到病毒（称为噬菌体或噬菌体）的攻击。噬菌体往往是非常特定的宿主，因为它们只感染它们的细菌宿主。噬菌体被认为是地球上最丰富的生物实体;地球上的细菌病毒比细菌多10倍。然而，这些病毒是专性细胞内寄生虫（完全依赖于易感细菌宿主进行繁殖）。细菌和它们的病毒寄生虫已经存在了数百万年，它们之间的关系是一场永久的“军备竞赛”-细菌进化出抗噬菌体的策略，但寄生虫也可以通过突变来绕过细菌细胞的防御。然后，细菌进化以抵抗进化的细菌，等等-永远如此。这种无休止的生物过程被称为共同进化。噬菌体在感染之前必须吸附到它们的细菌宿主上。吸附取决于两件事：1）细菌暴露出可以被噬菌体“识别”的特定细胞表面结构，以及2）病毒具有尾部结构，允许它们以特定的“锁和钥匙”机制“锁定”细菌表面受体。只有这样，病毒才能将其DNA注入细菌猎物。在注射时，病毒DNA重新编程细菌，迫使它们在细菌细胞内产生许多新的病毒颗粒，这些病毒颗粒破裂释放出新的病毒，然后感染更多的细菌。病毒尾部组分与细菌表面受体之间相互作用的特异性是噬菌体-宿主关系中的第一个关键要求，将在本项目中进行开发。噬菌体与细菌的相互作用与人类冠状病毒与人类细胞表面受体之间的作用有一些有趣的生物学相似之处。在冠状病毒的情况下，病毒“刺突”蛋白与人类细胞的表面受体成分结合-这种相互作用对于病毒在人类细胞中的吸附，渗透和最终复制至关重要。在这项研究中，我们将利用一种称为“类病毒”的噬菌体。类病毒是它们感染的细菌的杀手，但我们已经证明它们也有能力在细菌之间转移基因（“水平基因转移”），这一过程称为广义转导。病毒样病毒对它们自己特定的细菌宿主物种非常特异。然而，我们相信这些特定的病毒具有在广泛的细菌中复制的遗传能力，但仅仅因为病毒尾部-细菌宿主受体相互作用的紧密特异性而被阻止这样做。这个项目的一个目的是有力地检验这一假设。在这个合成生物学项目中，我们将把编码类病毒表面受体的基因转移到一系列细菌宿主中。病毒感染基因工程细菌的能力将得到证实，然后这些工程细菌将作为供体和受体进行测试，以确定噬菌体驱动的遗传转移能力。本研究中研究的生物体将包括与原始病毒样病毒宿主相关的非致病性细菌，但也包括可感染植物、动物和昆虫的其他细菌。此外，我们将扩大我们的方法，以测试分类无关的细菌，包括细菌的医疗，农业，环境和生物技术的重要性。我们的目标是利用这一策略，提供一个简单的，创新的通用途径，以病毒介导的操纵不同的细菌-从而提供特殊的一般效用，利用细菌遗传学和工程。

Summary (up to 4000 characters)All living organisms can be infected by viruses, including plants, animals and humans. It has been known for just over a century that bacteria are also susceptible to attack by viruses (called bacteriophages or phages). Phages tend to be very host-specific because they only infect their bacterial hosts. Phages are thought to be the most abundant biological entities on Earth; there are 10 times more bacterial viruses than bacteria on the planet. However, these viruses are obligate intracellular parasites (being utterly dependent on susceptible bacterial hosts for their propagation). Bacteria and their viral parasites have existed for millions of years and their relationship is a perpetual "arms race" - the bacteria evolve strategies to become phage-resistant but the phages can also evolve by mutation to get around the defences of the bacterial cells. The bacteria then evolve to resist the evolved phages, and so on - in perpetuity. This endless biological process is called co-evolution.Phages have to adsorb to their bacterial hosts before they can infect. Adsorption depends on two things: 1) the bacteria expose a specific cell surface structure that can be "recognised" by the phage, and 2) the viruses have tail structures that allow them to "lock on" to the bacterial surface receptors in a specific "lock and key" mechanism. Only then, the virus can inject its DNA into the bacterial prey. On injection, the viral DNA re-programmes the bacteria, forcing them to make many new virus particles inside the bacterial cells, which burst to release new viruses that then infect more bacteria. The specificity of the interaction between the virus tail components and the bacterial surface receptor is the first key requirement in the phage-host relationship and that will be exploited in this project. There are some interesting biological similarities between the phage-bacterium interaction and the situation operating between the human coronavirus and the surface receptor of human cells. In the coronavirus case, viral "spike" proteins bind to surface receptor components of human cells - and that interaction is essential for viral adsorption, penetration and eventual replication in human cells. In this study we will exploit a phage called a "viunalikevirus". The viunalikeviruses are killers of the bacteria that they infect, but we have shown that they also have the capacity to transfer genes between bacteria ("horizontal gene transfer") in a process called generalised transduction. The viunalikeviruses are very specific for their own particular bacterial host species. However, we believe that these particular viruses have the genetic capacity to replicate in a wide range of bacteria but are prevented from doing so simply because of the tight specificity of the virus tail-bacterial host receptor interaction. One aim of this project is to test that hypothesis robustly. We will transfer genes coding for the surface receptor of a viunalikevirus to a spectrum of bacterial hosts in this synthetic biology project. The ability of the virus to infect genetically engineered bacteria will be confirmed and then these engineered bacteria will be tested as donors and recipients for genetic transfer capacity driven by the phage. The organisms to be investigated in this study will include non-pathogenic bacteria related to the original viunalikevirus host but will also include other bacteria that can infect plants, animals and insects. Furthermore, we will expand our approach into testing of taxonomically unrelated bacteria, including bacteria of medical, agricultural, environmental and biotechnological significance. Our aim is to exploit this strategy to provide a facile, innovative generic route to virus-mediated manipulation of diverse bacteria - thereby providing exceptional general utility for exploitation in bacterial genetics and engineering.