Cap-independent translation and a precisely located RNA sequence enable SARS-CoV-2 to control host translation and escape anti-viral response

Abstract

Translation of SARS-CoV-2-encoded mRNAs by the host ribosomes is essential for its propagation. Following infection, the early expressed viral protein NSP1 binds the ribosome, represses translation, and induces mRNA degradation, while the host elicits an anti-viral response. The mechanisms enabling viral mRNAs to escape this multifaceted repression remain obscure. Here we show that expression of NSP1 leads to destabilization of multi-exon cellular mRNAs, while intron-less transcripts, such as viral mRNAs and anti-viral interferon genes, remain relatively stable. We identified a conserved and precisely located cap-proximal RNA element devoid of guanosines that confers resistance to NSP1-mediated translation inhibition. Importantly, the primary sequence rather than the secondary structure is critical for protection. We further show that the genomic 5′UTR of SARS-CoV-2 drives cap-independent translation and promotes expression of NSP1 in an eIF4E-independent and Torin1-resistant manner. Upon expression, NSP1 further enhances cap-independent translation. However, the sub-genomic 5′UTRs are highly sensitive to eIF4E availability, rendering viral propagation partially sensitive to Torin1. We conclude that the combined NSP1-mediated degradation of spliced mRNAs and translation inhibition of single-exon genes, along with the unique features present in the viral 5′UTRs, ensure robust expression of viral mRNAs. These features can be exploited as potential therapeutic targets.

Optimization of 5′UTR to evade SARS-CoV-2 Nonstructural protein 1-directed inhibition of protein synthesis in cells

“…It was suggested that SL1 specifically interact to Nsp1 via its unique structure and discharge the blockage of mRNA entry tunnel (Simeoni et al 2021 ). However, we showed that the integrity of secondary structure may not be absolutely needed for SL1 to mediate an escape from translational inhibition, in agreement with some recent studies that report poor structural relevance of SL1 to protein expression (Bujanic et al 2022 ; Slobodin et al 2022 ). Also, in these studies, they have found that the presence of specific C residues and the absence of G residues in SL1 are critical for sufficient protein expression, respectively, in spite of that the SL-like structure of the SL1 was mainly preserved in their mutagenesis experiments.…”

Buffy Coat Transcriptomic Analysis Reveals Alterations in Host Cell Protein Synthesis and Cell Cycle in Severe COVID-19 Patients

“…RNA post-transcriptional modifications stand out as a basic mechanism of transcript and protein regulation [ 90 ]. SARS-CoV-2 interferes with this process in various ways; for example, NSP1 destabilizes a certain type of mRNA to evade antiviral proteins [ 91 ]. FBL is a protein responsible for RNA modification, with multiple possible important targets being down-regulated in critically ill individuals.…”

SARS-CoV-2 Protein Nsp2 Stimulates Translation Under Normal and Hypoxic Conditions

“…The presence of 5’-cap on genomic and sub-genomic SARS-CoV-2 mRNAs indicates the requirement of eIF4F for initiation of translation. Indeed, it was demonstrated that translation of sub-genomic SARS-CoV-2 mRNAs is cap-dependent and was shown to be highly sensitive to the eIF4E level (Slobodin et al, 2022). However, translation of genomic SARS-CoV-2 RNA does not require eIF4E and occurs in a cap-independent manner.…”