Viral and cellular translation during SARS-CoV-2 infection

Abstract

SARS-CoV-2 is a betacoronavirus that emerged in China in December 2019 and which is the causative agent of the Covid-19 pandemic. This enveloped virus contains a large positive-sense single-stranded RNA genome. In this review, we summarize the current knowledge on the molecular mechanisms for the translation of both viral transcripts and cellular messenger RNAs. Non-structural proteins are encoded by the genomic RNA and are produced in the early steps of infection. In contrast, the structural proteins are produced from subgenomic RNAs that are translated in the late phase of the infectious program. Non-structural protein 1 (NSP1) is a key molecule that regulates both viral and cellular translation. In addition, NSP1 interferes with multiple steps of the interferon I pathway and thereby blocks host antiviral responses. Therefore, NSP1 is a drug target of choice for the development of antiviral therapies.

Keywords: NSP1-SL1; SARS-CoV-2; immune response; interferon; ribosome; translation.

Fig. 1

Cis‐acting elements on viral SARS‐CoV‐2 transcripts. (A) Genomic and subgenomic RNA transcripts. The secondary structures of the 5’UTRs of the genomic RNA and the subgenomic RNAs and the Programmed −1 Frameshift Stimulation Element (PFSE) are shown in boxes. The nucleotides of TRS‐L and TRS are shown in green in the 5’UTRs. In the PFSE, the pseudoknot consists of stems S1 (green), S2 (blue), and S3 (orange). The slippery site is shown in red and underlined. The −1 frameshifting site is indicated by a black arrow. The codons of NSP11 (frame 0) and NSP12 (frame −1) are shown under the nucleotide sequence. The NSP11 stop codon in S1 is indicated by a black arrow. In the subgenomic transcripts, proteins encoded by leaky scanning are indicated in brackets (B) Structure of a translating ribosome that pauses at the PFSE (PDB:7o7z) [24]. The 80S ribosome is shown gray. The PFSE and the slippery sequence are shown in red: It interacts with ribosomal proteins eS10 (orange) and uS3 (dark blue) and the 18S rRNA helix h16 (yellow). The E‐site tRNA is shown in pink and the P‐site tRNA is shown in green. (C) The cryo‐EM structure of the free PFSE is shown in red (EMD‐22296) [25]. The positions of stems S1, S2, and S3 are indicated. The slippery site is circled by a dashed line. The presence of a central ring is shown in yellow. (D) Crystallographic structures of the free PFSE (PDB:7mlx) [26] (left) and (PDB:7mky) [27] (right). The stems S1 (green), S2 (blue) and S3 (orange) are shown.

Fig. 2

Non‐Structural Protein 1 or NSP1. (A) Linear representation of the three domains of SARS‐CoV‐2 NSP1: the Nt‐domain in blue, the linker domain and the Ct‐domain in red. The mutations of the residues that have been shown to be important for the functions of NSP1 are shown according to the color code indicated on the right. (B) Protein sequence alignment of SARS‐CoV‐2 and SARS‐CoV‐1 NSP1 proteins. For SARS‐CoV‐1, only the divergent amino acids are shown. The NSP1 proteins are subdivided into three domains: the N‐terminal domain, the central linker domain, and a C‐terminal domain. The amino acids are shown according to the following color code: negatively charged amino acids in pink, hydrophobic amino acids in blue, positively charged amino acids in green, aromatic amino acids in cyan, glycines and prolines in orange. Residues involved in interactions with ribosomal components are shaded in gray in SARS‐CoV‐2 [41, 42, 53]. Negative charge variations from SARS‐CoV‐2 to SARS‐CoV‐1 are indicated by blue squares, and positive charge variations are indicated by red squares. Residues that are divergent on the front side of NSP1 are boxed in black. Critical residues implicated in various functions of NSP1 are boxed in red. Deletions that have been found in SARS‐CoV‐2 variants are boxed in orange. (C) Surface representation of crystal structure of SARS‐CoV‐2 NSP1 from residues E10 to L123 (PDB: 7K7P) [50]. The upper panels are two views from the front (left) and back sides (right) of NSP1. The N‐terminal end is shown in in blue and the C‐terminal end in red. The position of residue R99 in SARS‐CoV‐2 NSP1 is indicated in red. Divergent residues from SARS‐CoV‐1 are circled in black. The lower panels represent the electrostatic surfaces of the protein with negative and positive charges colored in red and blue, respectively. (D) Secondary structures of SL1 from SARS‐CoV‐1 (left) and SARS‐CoV‐2 (right). (E) Cryo‐EM structure of the SARS‐CoV‐2 NSP1‐ribosomal 40S complex (PDB: 6ZLW) [41]. The C‐terminal domain of NSP1 is shown in red at the mRNA entry channel. The interactions between NSP1 (red) and the ribosomal proteins uS3 (green), uS5 (dark blue) and helix h18 of the 18S rRNA (orange) are shown.

Fig. 3

SARS‐CoV‐2 NSP1 interferes with the host antiviral responses. (Left) The entry of SARS‐CoV‐2 in the cytoplasm of the infected cell introduces double‐stranded RNA (dsRNA) that triggers the activation of innate immune pathways that lead to the production of type I interferon IFN‐α and ‐β which are secreted by the infected cell. (Right) The produced type I interferons will then activate, through a cascade of phosphorylations, the antiviral response by stimulating the expression of IFN‐Stimulated Genes (ISGs). The SARS‐CoV‐2 viral protein NSP1 shuts down the antiviral response by interfering with multiple steps of this pathway (the steps inhibited by NSP1 are shown in red).

Fig. 4

Classification of CoV genera and role of animals in transmission. The four genera Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus are shown. Some examples from each genus are given. The analysis includes the four main subgenera of Betacoronavirus: Sarbecovirus, Embecovirus, Merbecovirus, and Nobecovirus. The Hibecovirus subgenus containing only Bat Hp‐betacoronavirus Zhejiang 2013 is not shown. The diagram shows the possible role of animals in the transmission of the different coronaviruses, intermediate hosts, and potential ancestor origins.

Fig. 5

Genome organization of members in Beta‐, Alpha‐ and Deltacoronavirus genera. The genomic viral genomes are single‐stranded, positive‐sense RNA with a 5′ m⁷G‐cap (black circle) and a poly‐A tail (A_30‐60) at the 3′ end. The genome encodes 16 non‐structural proteins (ORF1a: nsp1‐11 and ORF1b: nsp12‐16), 4 structural proteins (S, spike; E, envelope; M, membrane; N, nucleocapsid) and a varying number of accessory proteins (numbered boxes or ns). The upper 6 genomes are infectious for humans and are responsible for severe pathologies (SARS‐CoV‐2 and MERS‐CoV) or common pathologies (colds) (HCoV‐OC43, ‐HKU1, ‐229E, ‐NL63). HCoV‐OC43 and ‐HKU1 are characterized by a fifth structural protein: HE (hemagglutinin‐esterase). Infectious bronchitis virus (IBV) and Porcine CoV HKU15 are Gammacoronaviruses and Deltacoronavirus, respectively. They lack NSP1 protein and are among the smallest viruses in coronaviridae.