遗传多样性是RNA病毒的标志,也是其进化成功的基础。利用SARS-CoV-2独特的大型基因组数据库,我们研究了跨可行氨基酸序列谱的突变对高表达和多功能核衣壳蛋白的生物物理表型的影响。我们发现其扩展的固有无序区域(IDR)的物理化学参数变化足以允许局部可塑性,但也观察到在相关冠状病毒中类似发生的功能约束。在一些携带与主要变异相关的突变的N蛋白种类的生物物理实验中,我们发现IDR中的点突变可以产生非局部影响并调节热力学稳定性,二级结构,蛋白质寡聚状态,颗粒形成,液-液相分离。在Omicron变体中,不同IDR中的远处突变在改变控制蛋白质组装特性的相互作用的微妙平衡方面具有代偿作用,并且包括通过定义的P13L突变在N端IDR中创建新的蛋白质-蛋白质相互作用界面。出现了一幅图片,其中遗传多样性伴随着功能性N蛋白物种的生物物理特征的显着变化,特别是在IDR中。
像其他类型的RNA病毒一样,SARS-CoV-2(负责COVID-19的病原体)的遗传物质由易于积累突变的RNA分子形成。这使SARS-CoV-2具有快速进化的能力,通常比治疗领先一步。因此,了解这些突变如何影响RNA病毒的行为对于控制COVID-19等疾病至关重要。编码“包装”SARS-CoV-2内部遗传信息的蛋白质的基因特别容易发生突变。这种核衣壳(N)蛋白参与病毒生命周期中的许多关键过程,包括可能干扰免疫反应。目前尚不清楚N蛋白的物理特性到底是如何受到其遗传序列突变的影响的。为了调查这个问题,Nguyen等人。基于对SARS-CoV-2遗传数据库的计算机分析,预测了N蛋白不同区域的各种生物物理特性。这使他们能够确定特定蛋白质区域在不同突变体中是否带正电荷或负电荷。分析表明,一些结构域在蛋白质变体之间的电荷表现出很大的变异性-反映出相应的遗传序列显示出高水平的可塑性。其他地区仍然保持保守,然而,包括相关的冠状病毒。Nguyen等人。还对从临床相关的SARS-CoV-2变体中获得的一系列N蛋白进行了生化实验。他们的结果强调了没有固定三维结构的蛋白质片段的重要性。相关序列的突变在这些“内在无序”区域的物理特性中产生了高水平的变化,这产生了广泛的后果。这些遗传变化中的一些甚至使单个N蛋白能够以全新的方式相互作用。这些结果为基因突变与RNA病毒蛋白的可变物理特性之间的关系提供了新的思路。Nguyen等人。希望这些知识最终将有助于开发更有效的治疗病毒感染。
Genetic diversity is a hallmark of RNA viruses and the basis for their evolutionary success. Taking advantage of the uniquely large genomic database of SARS-CoV-2, we examine the impact of mutations across the spectrum of viable amino acid sequences on the biophysical phenotypes of the highly expressed and multifunctional nucleocapsid protein. We find variation in the physicochemical parameters of its extended intrinsically disordered regions (IDRs) sufficient to allow local plasticity, but also observe functional constraints that similarly occur in related coronaviruses. In biophysical experiments with several N-protein species carrying mutations associated with major variants, we find that point mutations in the IDRs can have nonlocal impact and modulate thermodynamic stability, secondary structure, protein oligomeric state, particle formation, and liquid-liquid phase separation. In the Omicron variant, distant mutations in different IDRs have compensatory effects in shifting a delicate balance of interactions controlling protein assembly properties, and include the creation of a new protein-protein interaction interface in the N-terminal IDR through the defining P13L mutation. A picture emerges where genetic diversity is accompanied by significant variation in biophysical characteristics of functional N-protein species, in particular in the IDRs.
Like other types of RNA viruses, the genetic material of SARS-CoV-2 (the agent responsible for COVID-19) is formed of an RNA molecule which is prone to accumulating mutations. This gives SARS-CoV-2 the ability to evolve quickly, and often to remain one step ahead of treatments. Understanding how these mutations shape the behavior of RNA viruses is therefore crucial to keep diseases such as COVID-19 under control. The gene that codes for the protein that ‘packages’ the genetic information inside SARS-CoV-2 is particularly prone to mutations. This nucleocapsid (N) protein participates in many key processes during the life cycle of the virus, including potentially interfering with the immune response. Exactly how the physical properties of the N-Protein are impacted by the mutations in its genetic sequence remains unclear. To investigate this question, Nguyen et al. predicted the various biophysical properties of different regions of the N-protein based on a computer-based analysis of SARS-CoV-2 genetic databases. This allowed them to determine if specific protein regions were positively or negatively charged in different mutants. The analyses showed that some domains exhibited great variability in their charge between protein variants – reflecting the fact that the corresponding genetic sequences showed high levels of plasticity. Other regions remained conserved, however, including across related coronaviruses. Nguyen et al. also conducted biochemical experiments on a range of N-proteins obtained from clinically relevant SARS-CoV-2 variants. Their results highlighted the importance of protein segments with no fixed three-dimensional structure. Mutations in the related sequences created high levels of variation in the physical properties of these ‘intrinsically disordered’ regions, which had wide-ranging consequences. Some of these genetic changes even gave individual N-proteins the ability to interact with each other in a completely new way. These results shed new light on the relationship between genetic mutations and the variable physical properties of RNA virus proteins. Nguyen et al. hope that this knowledge will eventually help to develop more effective treatments for viral infections.