Harnessing the potential of atypical gDNA processing by domesticated viruses

水平基因转移(HGT)是细菌间基因交换的一种基本而强大的过程。HGT推动细菌进化、适应并扩散到新的生态位，是快速传播抗生素耐药性和致病性等特征的主要手段。感染细菌的病毒被称为噬菌体，或简称噬菌体，通常被认为是HGT最有影响力的机制。基因转移剂(GTA)是与噬菌体相关的小病毒颗粒，能够在细菌细胞之间不分青红皂白地转移几乎任何基因。对GTA在环境中的活性的研究表明，抗生素耐药基因可以以极高的频率传播，因此GTA介导的抗生素耐药性和毒力基因在病原菌中的传播具有巨大的潜在临床和经济后果。本研究的总体目标是表征GTA DNA识别机制的结构和功能。病毒通常是自私的成分，其主要目标是利用宿主的资源复制自己，然后再继续感染新的宿主。尽管GTA在许多方面与传统病毒相似，但它们不会复制自己的基因组，也不会以牺牲宿主为代价促进自己的生存。相反，GTA将其细菌宿主的整个基因组打包成一块大小的片段，并将这些片段分发给接受细菌。当产生GTA的物种含有增强致病机制或抗生素耐药性的基因时，这种不分青红皂白的基因转移变得非常令人担忧。在噬菌体中，负责特定识别噬菌体基因组的蛋白质称为小末端酶。小末端酶还调节大末端酶蛋白的酶活性，大末端酶蛋白切割目标DNA并快速将其送入预先形成的空病毒头部，直到整个基因组被打包。尽管由于经典的三磷酸腺苷水解序列基序，GTA大末端很容易通过生物信息学识别，但GTA小末端酶还没有被识别出来。我们的初步数据提供了第一个证据，证明GTA具有小末端酶，并允许在其他不同的GTA中预测类似的小末端。我们将研究GTA小末端的生物化学和结构，这将使我们能够定义这些非典型末端的基本性质，以期提高检测新的GTA的效率，并对病毒DNA识别和包装的一般机制提供宝贵的见解。我们的结果可能对科学界有广泛的吸引力，并可能回答病毒学和细菌进化中长期存在的问题。现代医学的几乎所有方面都依赖于有效的抗生素，但这一点正受到抗生素耐药性令人担忧的蔓延的破坏。如果我们要开发新的治疗方法，甚至保护目前的抗菌库，了解微生物快速获得毒力基因的方法是至关重要的。

Horizontal Gene Transfer (HGT) is a fundamental and powerful process for the exchange of genes between bacteria. HGT drives bacterial evolution, adaptation and spread into new ecological niches and is the primary means for rapid distribution of characteristics such as antibiotic resistance and pathogenicity. Viruses that infect bacteria are known as bacteriophages, or simply phages, and are generally accepted to be the most influential mechanism of HGT. Gene Transfer Agents (GTAs) are small viral particles that are related to bacteriophages and are able to indiscriminately transfer almost any gene between bacterial cells. Research into the activity of GTAs in the environment revealed that antibiotic resistance genes could be spread at extremely high frequencies and thus GTA-mediated spread of antibiotic resistance and virulence genes in pathogens has huge potential clinical and economic consequences.The overarching goal of this research project is to characterize the structure and function of the GTA DNA recognition machinery. Viruses are usually selfish elements whose main goal is to use the resources of their host to make copies of themselves that can then move on to infect new hosts. Despite being similar to traditional viruses in many ways, GTAs do not copy their own genome and do not promote their own survival at the expense of their host. Instead GTAs package the entire genome of their bacterial host in bitesize pieces and distribute these to recipient bacteria. When the species that produces GTAs contains genes for enhanced pathogenesis or antibiotic resistance, this indiscriminate gene transfer becomes of great concern. In bacteriophages, the protein that is responsible for specific recognition of the phage genome is called the small terminase. The small terminase also regulates the enzymatic activities of the large terminase protein, which cuts the target DNA and rapidly feeds it into a pre-formed empty viral head until the whole genome is packaged. Although GTA large terminases are easily identified through bioinformatics owing to classical ATP hydrolysis sequence motifs, no GTA small terminase has ever been identified.Our preliminary data provide the first evidence that a GTA possesses a small terminase and allows prediction of similar small terminases in other diverse GTAs. We will examine the biochemistry and structure of GTA small terminases, which will allow the fundamental properties of these atypical terminases to be defined with a view to increasing the efficiency of detection of novel GTAs and to provide invaluable insights into the mechanism of viral DNA recognition and packaging in general. Our results are likely to have a broad appeal to the scientific community and could answer long standing questions in Virology and Bacterial Evolution. Almost all aspects of modern medicine rely on effective antibiotics but this is being undermined by the alarming spread of antibiotic resistance. Understanding the methods used by microbes to rapidly acquire virulence genes is crucial if we are to develop new treatments or even to preserve the current antimicrobial armoury.