The viral protein NSP1 acts as a ribosome gatekeeper for shutting down host translation and fostering SARS-CoV-2 translation

Abstract

SARS-CoV-2 coronavirus is responsible for Covid-19 pandemic. In the early phase of infection, the single-strand positive RNA genome is translated into non-structural proteins (NSP). One of the first proteins produced during viral infection, NSP1, binds to the host ribosome and blocks the mRNA entry channel. This triggers translation inhibition of cellular translation. In spite of the presence of NSP1 on the ribosome, viral translation proceeds however. The molecular mechanism of the so-called viral evasion to NSP1 inhibition remains elusive. Here, we confirm that viral translation is maintained in the presence of NSP1. The evasion to NSP1-inhibition is mediated by the cis-acting RNA hairpin SL1 in the 5′UTR of SARS-CoV-2. NSP1-evasion can be transferred on a reporter transcript by SL1 transplantation. The apical part of SL1 is only required for viral translation. We show that NSP1 remains bound on the ribosome during viral translation. We suggest that the interaction between NSP1 and SL1 frees the mRNA accommodation channel while maintaining NSP1 bound to the ribosome. Thus, NSP1 acts as a ribosome gatekeeper, shutting down host translation or fostering SARS-CoV-2 translation depending on the presence of the SL1 5′UTR hairpin. SL1 is also present and necessary for translation of sub-genomic RNAs in the late phase of the infectious program. Consequently, therapeutic strategies targeting SL1 should affect viral translation at early and late stages of infection. Therefore, SL1 might be seen as a genuine 'Achille heel' of the virus.

Mechanisms of Coronavirus Nsp1-Mediated Control of Host and Viral Gene Expression

“…For SARS-CoV-2, it has been reported that the presence of a viral leader sequence at the 5′ end of expressed non-viral transcripts facilitates escape of the transcripts from nsp1-mediated suppression of gene expression [ 70 , 71 ]. The cis-acting RNA hairpin SL1 in the leader sequence of SARS-CoV-2 facilitates evasion of viral RNAs from the nsp1-induced translational suppression [ 71 , 72 ]. Banerjee et al proposed a model where the viral leader sequence allosterically modulates nsp1 structure, leading to potential dissociation of the nsp1 from the 40S subunits and allowing viral translation [ 71 ], while Tidu et al showed that nsp1 remains bound on the ribosome during viral translation and proposed that the interaction between nsp1 and SL1 frees the mRNA accommodation channel while maintaining nsp1 bound to the ribosome [ 72 ].…”

“…The cis-acting RNA hairpin SL1 in the leader sequence of SARS-CoV-2 facilitates evasion of viral RNAs from the nsp1-induced translational suppression [ 71 , 72 ]. Banerjee et al proposed a model where the viral leader sequence allosterically modulates nsp1 structure, leading to potential dissociation of the nsp1 from the 40S subunits and allowing viral translation [ 71 ], while Tidu et al showed that nsp1 remains bound on the ribosome during viral translation and proposed that the interaction between nsp1 and SL1 frees the mRNA accommodation channel while maintaining nsp1 bound to the ribosome [ 72 ]. It should be noted that data shown by Tidu et al revealed that nsp1 suppressed translation of viral mRNAs in RRL, the extent of which was less efficient than IRES-mediated translation [ 72 ]; hence, like SARS-CoV nsp1 [ 57 ], SARS-CoV-2 nsp1 suppresses gene expression of viral mRNAs in RRL.…”

Nsp1 of SARS-CoV-2 Stimulates Host Translation Termination

“…Nsp1 stimulates expression of host genes via increasing translation termination rate, but at the same time, Nsp1 suppresses cell translation at the initiation stage via binding to the 40S ribosome subunit to transfer components of protein biosynthesis into the translation of virus proteins (Banerjee et al, 2020; Lapointe et al, 2020; Schubert et al, 2020; Shi et al, 2020; Thoms et al, 2020; Tidu et al, 2020; Yuan et al, 2020). That’s why this work could not be done using cell-based experiments, since the effect of Nsp1 on translation termination could not be detected on the background of suppression of translation initiation by this protein.…”

“…In this case, the 40S subunit associated with Nsp1 binds to mRNA much worse and is unable to form a native translation initiation complex. Thus, Nsp1 inhibits the initiation of host mRNA translation (Banerjee et al, 2020; Lapointe et al, 2020; Schubert et al, 2020; Shi et al, 2020; Thoms et al, 2020; Tidu et al, 2020; Yuan et al, 2020). In addition to free 40S subunits, Nsp1 SARS-CoV-2 is also found in aberrant 48S initiator complexes and 80S ribosomes (Lapointe et al, 2020; Schubert et al, 2020; Thoms et al, 2020; Yuan et al, 2020).…”

Type I and III IFN-mediated antiviral actions counteracted by SARS-CoV-2 proteins and host inherited factors

“…A virus-cell protein interaction map identified several innate immune signaling proteins as partners of viral proteins in cells [ 77 ]. One of the first proteins produced during viral infection, nsp1, binds to the host ribosome and blocks the mRNA entry channel, thus inhibiting cellular translation but not the viral translation; such viral escape is mediated by the cis-acting RNA hairpin SL1 in the 5'UTR of SARS-CoV-2 [ 78 ]. Other viral proteins such as nsp8, nsp9, and nsp16 are produced early during viral replication, before the generation of double-stranded RNA (dsRNA).…”