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，它们感染所有其他类型的生物，包括植物、动物（包括人类）、真菌、所有类型的细菌，甚至其他病毒。无论我们在哪里找他们，他们都被找到了。因此，它们具有巨大的社会重要性，直接影响到我们的生活，因为它们影响到人类和动物的健康、农业，从而影响到真正全球范围的粮食安全。所有病毒都面临着一个共同的挑战，它们必须将基因组信息（DNA或RNA）包装在一个叫做衣壳的保护性容器中，衣壳保护基因组免受外部环境的影响，并将其完整地传递给新细胞，开始新一轮的感染。制造衣壳的一种方法是用一种蛋白质构建一个高度对称的容器。然而，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合适大小的容器——就像制造足球所需的六边形和五边形一样。构建正确的衣壳，并完美地构建它，是病毒复制周期的基本组成部分，但我们对这种“构象转换”是如何发生的了解甚少。一种可能发生的方式是蛋白质与基因组DNA或RNA中的特定序列结合；这种结合会导致构象的变化。然而，人们对这一过程知之甚少。在某种程度上，这是因为对绝大多数病毒来说，衣壳具有上面描述的非常高的对称性，这意味着当我们解决它们的结构时，对称平均会掩盖蛋白质（在每个位置都是相同的）与DNA或RNA（不是，因为它必须有一个编码病毒基因的独特序列）之间任何特定相互作用的细节。因此，当我们试图研究与组装有关的分子机制时，许多病毒所依赖的高度对称性是非常无用的。在这个提案中，我们想利用我们实验室最近的两个非常令人兴奋的发现，这将使我们能够克服这一障碍，并首次发现允许这些病毒有效自组装的神秘规则。我们一直在研究两个不同的病毒科，它们都是全球粮食和纺织作物的重要病原体，因此对发达国家和发展中国家的粮食安全和农业经济构成重大威胁；双子星病毒和伞形病毒。在每一种病毒中，病毒都进化出了一种（不同的）新颖的创新，这意味着衣壳具有“非标准”结构，不再像通常情况下那样对称。值得注意的是，在我们用5倍对称（而不是二十面体病毒的60倍对称）解决的每个病毒的初步结构中，我们现在可以看到结合在病毒外壳蛋白上的DNA（对于双子星病毒）和RNA（对于umbrbravirus）的细节。这项拨款申请将使我们能够在没有任何对称平均的情况下解决这些非标准病毒衣壳的高分辨率结构。结合生化和生物信息学实验，我们将揭示基因组结合的细节，这是如何改变蛋白质构象的，以及这些特征在病毒基因组中的位置。这将(a)提供对理解病毒如何工作很重要的迷人的新的基本生物学见解，(b)提供可能导致防止病毒工作的新方法的机制理解，以及(c)明确病毒组装的规则，使我们能够改变病毒组装的方式，例如，为生物技术应用制造不同大小的衣壳。

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

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

植物特异性partitivirus capsid的结构揭示了具有本质上无序突出的独特外套蛋白结构域结构。

• 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

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

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

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