A direct RNA-protein interaction atlas of the SARS-CoV-2 RNA in infected human cells

ABSTRACT: Schmidt N, Lareau CA, Keshishian H, Melanson R, Zimmer M, Kirschner L, Ade J, Simone Werner S, Caliskan N, Lander ES, Vogel J, Carr SA, Bodem J, and Munschauer M. 2020. SARS-CoV-2 infections pose a global threat to human health and an unprecedented research challenge. Among the most urgent tasks is obtaining a detailed understanding of the molecular interactions that facilitate viral replication or contribute to host defense mechanisms in infected cells. While SARS-CoV-2 co-opts cellular factors for viral translation and genome replication, a comprehensive map of the host cell proteome in direct contact with viral RNA has not been elucidated. Here, we use RNA antisense purification and mass spectrometry (RAP-MS) to obtain an unbiased and fully quantitative picture of the human proteome that directly binds the SARS-CoV-2 RNA in virally infected human cells. We discover known host factors required for coronavirus replication, regulators of RNA metabolism and host defense pathways, along with dozens of potential drug targets among direct SARS-CoV-2 binders. We further integrate the SARS-CoV-2 RNA interactome with proteome dynamics induced by viral infection, linking interactome proteins to emerging SARS-CoV-2 biology. Validating RAP-MS, we show that CNBP, a transcriptional regulator linked to a specific cytokine response, directly engages the SARS-CoV-2 RNA. Finally, we show that the interferon-induced protein RYDEN suppresses ribosomal frameshifting during SARS-CoV-2 RNA translation, and further demonstrate that inhibition of SARS-CoV-2-bound proteins or their interactors is sufficient to manipulate viral replication. The SARS-CoV-2 RNA interactome provides an unprecedented RNA-centric perspective on SARS-CoV-2 infections and enables the dissection of host dependency factors and host defense strategies, a crucial prerequisite for designing novel therapeutic strategies.

INSTRUMENT(S): Q Exactive Plus, Orbitrap Exploris 480

ORGANISM(S): Sars-cov-2 Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Steven A. Carr  

PROVIDER: MSV000085734 | MassIVE | Mon Jul 13 19:51:00 BST 2020

REPOSITORIES: MassIVE