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

摘要(最多4000个字符)所有活着的有机体都可能被病毒感染，包括植物、动物和人类。一个多世纪以来，人们就知道细菌也容易受到病毒(称为噬菌体或噬菌体)的攻击。噬菌体往往非常针对宿主，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；地球上细菌病毒的数量是细菌的10倍。然而，这些病毒是专性细胞内寄生虫(它们的繁殖完全依赖于敏感的细菌宿主)。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恒的“军备竞赛”--细菌进化出对噬菌体具有抵抗力的策略，但噬菌体也可以通过突变来进化，以绕过细菌细胞的防御。然后细菌进化以抵抗进化的噬菌体，以此类推--永无止境。这种没完没了的生物过程被称为协同进化。噬菌体必须先吸附到细菌宿主上，才能感染。吸附取决于两件事：1)细菌暴露出一种特定的细胞表面结构，可以被噬菌体“识别”；2)病毒的尾部结构允许它们以一种特定的“锁和钥匙”机制“锁定”细菌表面的受体。只有到那时，病毒才能将其DNA注入细菌猎物。在注射时，病毒DNA对细菌进行重新编程，迫使它们在细菌细胞内制造许多新的病毒颗粒，细菌细胞爆发释放新的病毒，然后感染更多的细菌。病毒尾部成分和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，这一点将在本项目中加以利用。噬菌体-细菌的相互作用和人类冠状病毒与人类细胞表面受体之间的运作情况之间有一些有趣的生物学相似之处。在冠状病毒的案例中，病毒“尖峰”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，我们将利用一种名为“ViunalikeVirus”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”)，这一过程被称为广义转导。类病毒对于它们自己特定的细菌宿主种类是非常特异的。然而，我们认为这些特定的病毒具有在广泛的细菌中复制的遗传能力，但由于病毒尾部与细菌宿主受体相互作用的紧密特异性而被阻止这样做。该项目的一个目标是强有力地检验这一假设。在这个合成生物学项目中，我们将把编码病毒表面受体的基因转移到一系列细菌宿主上。病毒感染基因工程菌的能力将得到确认，然后将测试这些工程菌作为供体和受体的由噬菌体驱动的基因转移能力。这项研究中要研究的生物将包括与原始病毒宿主相关的非致病细菌，但也将包括其他可以感染植物、动物和昆虫的细菌。此外，我们将把我们的方法扩展到分类上无关的细菌的测试，包括具有医学、农业、环境和生物技术意义的细菌。我们的目标是利用这一策略为病毒介导的对不同细菌的操纵提供一种简便、创新的通用方法-从而为细菌遗传学和工程中的开发提供特殊的通用工具。

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.