Exploring transcription of a large DNA virus of importance for global food security

最近的新冠肺炎大流行将病毒带到了公众关注的风口浪尖。然而，令人震惊的是，我们对病毒的工作方式知之甚少，包括它们的基因组在一个称为转录的过程中是如何控制的。充当“基因组守门人”的酶被称为RNA聚合酶，简称RNAP。RNAP是一种分子机器，可以比作我们日常生活中的其他机器，比如汽车。在规模较小的情况下，汽车由由小部件组成的发动机提供动力，要使汽车的移动方式合理化，需要了解汽车的形状和功能。虽然这对了解汽车的机械原理和驾驶过程很重要，但它不提供有关交通的信息。在更大的范围内，在交通规则指引下的繁忙城市中，许多不同类型的车辆共享道路，协调移动。在最大的范围内，城市通过一个复杂的网络相互连接，使旅行成为可能。同样，RNAP是生命的分子机器，由许多亚基组成，这些亚基被结合到更高级别的转录复合体中。为了了解它们是如何工作的，我们需要确定它们的结构和架构，并在严格控制的条件下，在体外试管中表征它们的功能。但在体内，在细胞中，RNAP并不是孤立的，而是相互作用的，并与不同的机器(包括复制我们基因组的机器)相互作用，这将影响转录的动态，RNAP在基因组中的分布和功能。这项提议旨在发现一种病毒RNAP的地图、机制和“交通规则”。对RNAP转录的变革性、详细但全面的理解要求我们在一系列生物尺度上研究这一过程，从原子到基因组再到细胞水平，这需要专门的多学科和多标度的研究策略。在我的职业生涯中，我指导了基础研究，利用我的综合多学科研究哲学，这改变了古迹转录领域。最近，我的团队首次表征了古生菌RNAP转录在病毒与宿主的军备竞赛中的抑制。我们在皮尔布赖特研究所的合作者Linda Dixon和Chris Netherton是ASFV病毒学领域的全球领导者，我们是开展这项突破性研究的完美团队。

The recent covid-19 pandemic has brought viruses to the forefront of public attention. Yet it is shocking how little we know about how viruses work, including the way by which their genomes are controlled in a process called transcription. The enzymes that serve as the 'gatekeepers of the genome' are called RNA polymerases, RNAP. RNAPs are molecular machines which can be likened to other machines in our daily lives such as cars. At smaller scales, cars are powered by engines that are made of small parts, and to rationalise how cars move requires knowledge about their shape and function. While this is important to understand the mechanics of the car and the process of driving, it does not provide information about traffic. Towards larger scales, many different types of vehicles share the roads and move in a coordinated fashion in a busy city guided by traffic rules. At the largest scale, cities are interconnected by a complex network that enables travel. Likewise, RNAPs are molecular machines of life that consist of many subunits that are incorporated into higher-order transcription complexes. To understand how they work, we need to determine their structure and architecture, and characterise their function under rigorously controlled conditions in vitro, in the test tube. But in vivo, in the cell, RNAPs are not alone but interact with each other and with different machines (including the ones that replicate our genomes) and this will affect the dynamics of transcription, how RNAPs are distributed and function in the context of the genome. This proposal aims to discover the maps, the mechanics, and the 'traffic rules' of a virus RNAP. A transformative, detailed yet comprehensive, understanding of RNAP transcription requires that we study the process over a range of biological scales from the atomic- via the genomic- to the cellular level, which requires a dedicated multidisciplinary and multiscalar research strategy. I have during my career directed fundamental research which has transformed the field of transcription in the Archaea using my brand of integrative multidisciplinary research philosophy. Recently my team characterised, for the first time, the inhibition of archaeal RNAP transcription in the virus-host arms race. Our collaborators Linda Dixon and Chris Netherton at the Pirbright Institute are global leaders in ASFV virology, together we are the perfect team to carry out this ground-breaking study.