Comparative Multiplexed Interactomics of SARS-CoV-2 and Homologous Coronavirus Nonstructural Proteins Identifies Unique and Shared Host-Cell Dependencies
Comparative Multiplexed Interactomics of SARS-CoV-2 and Homologous Coronavirus Nonstructural Proteins Identifies Unique and Shared Host-Cell Dependencies
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DOI：
10.1021/acsinfecdis.0c00500
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发表时间：
2020-12-11
影响因子：
5.3
通讯作者：
Plate, Lars
中科院分区：
文献类型：
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作者：
Davies, Jonathan P.;Almasy, Katherine M.;Plate, Lars
人类冠状病毒（human coronaviruses，hCoV）已经成为全球健康和社会的威胁，这从2002年由SARS-CoV-1引起的SARS爆发和最近由SARS-CoV-2引起的COVID-19大流行中可以看出。尽管SARS-CoV-1和SARS-CoV-2之间具有很高的序列相似性，但每种毒株都具有独特的毒力。需要更好地了解介导毒力变化的基本分子机制。在这里，我们的档案的病毒宿主蛋白质蛋白质的相互作用的两个hCoV非结构蛋白（nsps）的病毒复制是至关重要的。我们使用串联质量标签多重定量蛋白质组学敏感地比较和对比nsp 2和nsp 4的相互作用组从三个β冠状病毒株：SARS-CoV-1，SARS-CoV-2和hCoV-OC 43-与普通感冒相关的地方性菌株。这种方法能够鉴定独特的和共享的宿主细胞蛋白结合配偶体，并能够进一步比较来自相关菌株的同源物之间的共同相互作用的富集。我们确定共同的nsp 2相互作用参与内质网（ER）的Ca 2+信号和线粒体生物合成。我们还确定了每种毒株特有的nsp 4相互作用因子，如SARS-CoV-1的E3泛素连接酶复合物和SARS-CoV-2的ER稳态因子。常见的nsp 4相互作用物包括N-连接的糖基化机制、未折叠蛋白反应相关蛋白和抗病毒先天免疫信号传导因子。两个nsp 2和nsp 4相互作用强烈富集蛋白定位在ESTA相关的ER膜表明一个新的功能作用，调节宿主过程，如钙稳态，在这些细胞器接触网站。我们的研究结果揭示了这些hCoV蛋白在感染周期中的作用，以及可能介导OC 43与SARS菌株不同发病机制的宿主因素。我们的质谱工作流程能够快速、稳健地比较多种诱饵蛋白，并可应用于其他病毒蛋白。此外，确定的共同相互作用可能会提出新的目标，探索宿主导向的抗病毒治疗。
Human coronaviruses (hCoVs) have become a threat to global health and society, as evident from the SARS outbreak in 2002 caused by SARS-CoV-1 and the most recent COVID-19 pandemic caused by SARS-CoV-2. Despite a high sequence similarity between SARS-CoV-1 and -2, each strain has a distinctive virulence. A better understanding of the basic molecular mechanisms mediating changes in virulence is needed. Here, we profile the virus-host protein-protein interactions of two hCoV nonstructural proteins (nsps) that are critical for virus replication. We use tandem mass tag-multiplexed quantitative proteomics to sensitively compare and contrast the interactomes of nsp2 and nsp4 from three betacoronavirus strains: SARS-CoV-1, SARS-CoV-2, and hCoV-OC43-an endemic strain associated with the common cold. This approach enables the identification of both unique and shared host cell protein binding partners and the ability to further compare the enrichment of common interactions across homologues from related strains. We identify common nsp2 interactors involved in endoplasmic reticulum (ER) Ca2+ signaling and mitochondria biogenesis. We also identify nsp4 interactors unique to each strain, such as E3 ubiquitin ligase complexes for SARS-CoV-1 and ER homeostasis factors for SARS-CoV-2. Common nsp4 interactors include N-linked glycosylation machinery, unfolded protein response associated proteins, and antiviral innate immune signaling factors. Both nsp2 and nsp4 interactors are strongly enriched in proteins localized at mitochondria-associated ER membranes suggesting a new functional role for modulating host processes, such as calcium homeostasis, at these organelle contact sites. Our results shed light on the role these hCoV proteins play in the infection cycle, as well as host factors that may mediate the divergent pathogenesis of OC43 from SARS strains. Our mass spectrometry workflow enables rapid and robust comparisons of multiple bait proteins, which can be applied to additional viral proteins. Furthermore, the identified common interactions may present new targets for exploration by host-directed antiviral therapeutics.