A world of virus structures: understanding how non-icosahedral capsids are built

病毒结构的世界：了解非二十面体衣壳是如何构建的

• 批准号: BB/T004525/1
• 负责人: Neil Ranson
• 金额: $ 78.56万
• 依托单位: University of Leeds
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2020
• 资助国家: 英国
• 起止时间: 2020 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FT004525%2F1
• 关键词: world; virus; structures; understanding; how

Viruses are probably the most successful pathogens on earth. They are everywhere, and they infect every other type of organism, including plants, animals (including humans), fungi, bacteria of all types, and even other viruses. Wherever we have looked for them, they have been found. As a result, they are of huge societal importance, impacting directly on our lives because of their effects on human and animal health, agriculture, and thus on food security on a truly global scale. All viruses face a common challenge, in that they must package their genomic information (either DNA or RNA) within a protective container called a capsid, that shields the genome from the external environment, and delivers it intact to a new cell to start a new round of infection. One way in which these capsids are made is to build a highly symmetric container from a single type of protein. However, to do this the single type of protein has to adopt multiple shapes to build a container of the right size - much like the hexagons and pentagons that are needed to make a football. Building the right capsid, and building it perfectly, is a fundamental part of the viral replication cycle, but our understanding of how this 'conformational switching' happens is very poor. One way that it could occur is for the protein to bind to defined sequences within the genomic DNA or RNA; this binding would drive the conformational change. However, this process is poorly understood. In part, this is because for the vast majority of viruses the capsids have the very high symmetry described above, which means that when we solve their structures, symmetry averaging washes out details of any specific interactions between the protein (which is the same in each position) and the DNA or RNA (which is not, because it has to have a unique sequence that encodes the virus' genes). The high symmetry many viruses rely on is therefore tremendously unhelpful when we try to study the molecular mechanisms involved in assembly. In this proposal we want to exploit two hugely exciting recent discoveries in our laboratories, that will allow us to overcome this barrier and discover, for the first time, the cryptic rules that allow these viruses to efficiently self-assemble. We have been working on two different families of virus that are each important pathogens of food and textile crops globally, and thus are major threats to food security and agricultural economies across the developed and developing world; Geminiviruses and Umbraviruses. In each, the virus has evolved a (different) novel innovation that means the capsid has a "non-standard" structure which is no longer quite as symmetric as is normally the case. Remarkably, in the preliminary structure of each which we have solved with 5-fold symmetry (rather than the 60-fold symmetry for an icosahedral virus), we can now see details of DNA (for Geminiviruses) and RNA (for Umbraviruses) bound to the viral coat proteins. This grant application will allow us to solve high resolution structures of these non-standard virus capsids without any symmetry averaging at all. Together with biochemical and bioinformatics experiments, we will uncover the details of genome binding, how this changes protein conformation, and where these features lie within the viral genome. This will (a) provide fascinating new fundamental biological insights that are important in understanding how viruses work, (b) provide a mechanistic understanding that could lead to new ways to prevent them working, and (c) make clear the rules for virus assembly that could allow us to change the way viruses assemble, to make capsids of, for example, different sizes for biotechnology applications.

病毒可能是地球上最成功的病原体。它们无处不在，它们感染其他每种类型的生物，包括植物，动物（包括人），真菌，各种细菌，甚至其他病毒。无论我们在哪里寻找它们，都可以找到它们。结果，它们具有巨大的社会重要性，由于它们对人类和动物健康，农业的影响以及在全球范围内对粮食安全的影响，直接影响了我们的生活。所有病毒都面临着一个普遍的挑战，因为它们必须在称为CAPSID的保护容器中包装其基因组信息（DNA或RNA），从而使基因组免受外部环境的影响，并将其完整地提供给新细胞以开始新的感染。制作这些衣壳的一种方法是从单一类型的蛋白质中构建一个高度对称的容器。但是，要做到这一点，单一类型的蛋白质必须采用多种形状来构建一个适合的容器，就像六角形和五角大车一样，需要制作足球。构建右皮环并完美地构建它是病毒复制周期的基本组成部分，但是我们对这种“构象切换”如何发生的理解非常差。它可能发生的一种方法是蛋白质与基因组DNA或RNA中定义的序列结合。这种结合将驱动构象变化。但是，这个过程对此很了解。在某种程度上，这是因为对于绝大多数病毒，capsids具有上面描述的很高的对称性，这意味着，当我们解决它们的结构时，对称平均会消除蛋白质之间的任何特定相互作用的详细信息（每个位置在每个位置）与DNA或RNA之间（不是相同的）（不是，这不是一个独特的序列，因为它必须具有代码属于Virus'genes的独特序列）。因此，当我们尝试研究组装中涉及的分子机制时，许多病毒依赖的高对称性是无益的。在这项建议中，我们希望利用实验室中的两个令人兴奋的最近发现，这将使我们能够克服这一障碍，并首次发现这些病毒可以有效自我组装的隐秘规则。我们一直在为全球粮食和纺织品作物的各种病原体而努力，因此是对发达国家和发展中国家的粮食安全和农业经济体的主要威胁。双子病毒和伞病病毒。在每种情况下，病毒都进化出一种（不同的）新颖创新，这意味着Capsid具有“非标准”结构，这种结构不再像通常情况一样对称。值得注意的是，在我们已经使用5倍对称性（而不是二十体病毒的60倍对称性）求解的每个初步结构中，我们现在可以看到与病毒蛋白蛋白结合的DNA（用于双子座病毒）和RNA（用于伞状病毒）的细节。该赠款应用将使我们能够解决这些非标准病毒衣壳的高分辨率结构，而无需平均任何对称性。与生化和生物信息学实验一起，我们将发现基因组结合的细节，如何改变蛋白质构象以及这些特征位于病毒基因组中的位置。这将（a）提供引人入胜的新基本生物学见解，这些洞察力对于理解病毒的工作方式很重要，（b）提供了一种机械理解，可以导致新的方法来防止它们工作，并且（c）明确说明病毒组装的规则，这些规则可以使我们可以改变病毒的方式，以使生物技术应用程序不同，以不同的范围。

项目成果

In vitro functional analysis of gRNA sites regulating assembly of hepatitis B virus.

• DOI: 10.1038/s42003-021-02897-2
• 发表时间: 2021-12-16
• 期刊: Communications biology
• 影响因子: 5.9
• 作者: Patel N;Clark S;Weiß EU;Mata CP;Bohon J;Farquhar ER;Maskell DP;Ranson NA;Twarock R;Stockley PG
• 通讯作者: Stockley PG

Plant-expressed virus-like particles reveal the intricate maturation process of a eukaryotic virus.

• DOI: 10.1038/s42003-021-02134-w
• 发表时间: 2021-05-24
• 期刊: Communications biology
• 影响因子: 5.9
• 作者: Castells-Graells R;Ribeiro JRS;Domitrovic T;Hesketh EL;Scarff CA;Johnson JE;Ranson NA;Lawson DM;Lomonossoff GP
• 通讯作者: Lomonossoff GP

The structure of a plant-specific partitivirus capsid reveals a unique coat protein domain architecture with an intrinsically disordered protrusion.

• DOI: 10.1038/s42003-021-02687-w
• 发表时间: 2021-10-06
• 期刊: Communications biology
• 影响因子: 5.9
• 作者: Byrne M;Kashyap A;Esquirol L;Ranson N;Sainsbury F
• 通讯作者: Sainsbury F

A Replicating Viral Vector Greatly Enhances Accumulation of Helical Virus-Like Particles in Plants.

• DOI: 10.3390/v13050885
• 发表时间: 2021-05-11
• 期刊: Viruses
• 作者: Thuenemann EC;Byrne MJ;Peyret H;Saunders K;Castells-Graells R;Ferriol I;Santoni M;Steele JFC;Ranson NA;Avesani L;Lopez-Moya JJ;Lomonossoff GP
• 通讯作者: Lomonossoff GP

CryoEM and stability analysis of virus-like particles of potyvirus and ipomovirus infecting a common host.

• DOI: 10.1038/s42003-023-04799-x
• 发表时间: 2023-04-19
• 期刊: COMMUNICATIONS BIOLOGY
• 影响因子: 5.9
• 作者: Chase, Ornela;Javed, Abid;Byrne, Matthew J.;Thuenemann, Eva C.;Lomonossoff, George P.;Ranson, Neil A.;Lopez-Moya, Juan Jose
• 通讯作者: Lopez-Moya, Juan Jose