SARS-CoV-2 Nsp1 binds ribosomal mRNA channel to inhibit translation

Abstract

<jats:title>Abstract</jats:title><jats:p>The non-structural protein 1 (Nsp1), also referred to as the host shutoff factor, is the first viral protein that is synthesized in SARS-CoV-2 infected human cells to suppress host innate immune functions<jats:sup>1,2</jats:sup>. By combining cryo-electron microscopy and biochemical experiments, we show that SARS-CoV-2 Nsp1 binds to the human 40S subunit in ribosomal complexes including the 43S pre-initiation complex. The protein inserts its C-terminal domain at the entrance to the mRNA channel where it interferes with mRNA binding. We observe potent translation inhibition in the presence of Nsp1 in lysates from human cells. Based on the high-resolution structure of the 40S-Nsp1 complex, we identify residues of Nsp1 crucial for mediating translation inhibition. We further show that the full-length 5’ untranslated region of the genomic viral mRNA stimulates translation <jats:italic>in vitro</jats:italic>, suggesting that SARS-CoV-2 combines inhibition of translation by Nsp1 with efficient translation of the viral mRNA to achieve expression of viral genes<jats:sup>3</jats:sup>.</jats:p>

SARS-CoV-2 Nsp1 suppresses host but not viral translation through a bipartite mechanism

“…Quantification of mScarlet reporter intensities showed that MBP-Nsp1 decreased mScarlet expression by over 4-fold (p < 0.001) ( Figure 1B). These data demonstrate that SARS-CoV-2 Nsp1 potently inhibits protein translation in cells, recapitulating previous reports (Narayanan et al, 2008;Schubert et al, 2020;Thoms et al, 2020;Tohya et al, 2009).…”

“…It has been shown that Nsp1 effectively suppresses the translation of host mRNAs by directly binding to the 40S small ribosomal subunit (Narayanan et al, 2008;Tohya et al, 2009). The recent cryo-electron microscopy (cryo-EM) structures indeed revealed the binding of the C-terminal domain (CT) of Nsp1 to the mRNA entry channel of the 40S (Schubert et al, 2020;Thoms et al, 2020), blocking translation. However, how SARS-CoV-2 overcomes the Nsp1-mediated translation suppression for its own replication remains an open question.…”

Dynamic competition between SARS-CoV-2 NSP1 and mRNA on the human ribosome inhibits translation initiation

“…The first protein encoded in the viral genomic RNA, NSP1, directly targets the small subunit of the human ribosome to inhibit protein synthesis. Based on our findings and recent structural studies 31,32 , we suggest that NSP1 preferentially associates with the open conformation of the 40S subunit to prevent proper accommodation of mRNA during translation initiation (Fig. 6).…”

“…The high affinity of NSP1 for the 40S subunit likely demands buildup of NSP1 protein levels before translation is inhibited broadly, which may enable viral protein synthesis to proceed unimpeded during early stages of infection. Once NSP1 has accumulated, the increased translation efficiency of the viral mRNAs relative to human mRNAs we and others 32 have observed may enable the virus to synthesize sufficient amounts of viral proteins, even when translation is largely shutdown. However, it is possible that another viral protein, a different segment of the viral genome, or another mechanism (e.g., sequestration) allows the virus to evade translation inhibition.…”

“…While this work was in progress, multiple groups reported structures of NSP1 bound to the human ribosome 31,32 . Despite its apparent flexibility, the N-terminal globular domain of NSP1 was localized to the solvent-exposed surface of the 40S subunit, near the entrance to the mRNA entry channel (Supp.…”