Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Würzburg, Germany.
School of Medicine, Stanford University, Palo Alto, CA, USA.
Nat Microbiol. 2021 Mar;6(3):339-353. doi: 10.1038/s41564-020-00846-z. Epub 2020 Dec 21.
Characterizing the interactions that SARS-CoV-2 viral RNAs make with host cell proteins during infection can improve our understanding of viral RNA functions and the host innate immune response. Using RNA antisense purification and mass spectrometry, we identified up to 104 human proteins that directly and specifically bind to SARS-CoV-2 RNAs in infected human cells. We integrated the SARS-CoV-2 RNA interactome with changes in proteome abundance induced by viral infection and linked interactome proteins to cellular pathways relevant to SARS-CoV-2 infections. We demonstrated by genetic perturbation that cellular nucleic acid-binding protein (CNBP) and La-related protein 1 (LARP1), two of the most strongly enriched viral RNA binders, restrict SARS-CoV-2 replication in infected cells and provide a global map of their direct RNA contact sites. Pharmacological inhibition of three other RNA interactome members, PPIA, ATP1A1, and the ARP2/3 complex, reduced viral replication in two human cell lines. The identification of host dependency factors and defence strategies as presented in this work will improve the design of targeted therapeutics against SARS-CoV-2.
鉴定 SARS-CoV-2 病毒 RNA 在感染过程中与宿主细胞蛋白的相互作用，可以增进我们对病毒 RNA 功能和宿主固有免疫反应的理解。利用 RNA 反义纯化和质谱分析，我们鉴定出多达 104 种在感染的人类细胞中可直接且特异性结合 SARS-CoV-2 RNA 的人类蛋白质。我们将 SARS-CoV-2 RNA 互作组与病毒感染诱导的蛋白质组丰度变化进行整合，并将互作组蛋白与与 SARS-CoV-2 感染相关的细胞途径相联系。我们通过遗传干扰证明，细胞核酸结合蛋白 (CNBP) 和 LARP1 是两种丰度最高的病毒 RNA 结合蛋白，它们可限制感染细胞中的 SARS-CoV-2 复制，并提供其直接 RNA 结合位点的全局图谱。三种其他 RNA 互作组成员（PPIA、ATP1A1 和 ARP2/3 复合物）的药理学抑制，可降低两种人类细胞系中的病毒复制。本研究中提出的宿主依赖性因子和防御策略的鉴定，将有助于设计针对 SARS-CoV-2 的靶向治疗方法。
