Correlated sequence signatures are present within the genomic 5′UTR RNA and NSP1 protein in coronaviruses

Abstract

The 5’UTR part of coronavirus genomes plays key roles in the viral replication cycle and the translation of the viral mRNAs. The first 75-80 nucleotides, also called the leader sequence, are identical for the genomic mRNA and for the subgenomic mRNAs. Recently, it was shown that cooperative actions of a 5’UTR segment and the non-structural protein NSP1 are essential for both the inhibition of host mRNAs and for specific translation of viral mRNAs. Here, sequence analyses of both the 5’UTR RNA segment and the NSP1 protein have been done for several coronaviruses with special attention to the betacoronaviruses. The conclusions are (i) precise specific molecular signatures can be found in both the RNA and the NSP1 protein; (ii) both types of signatures strongly correlate between each other. Indeed, definite sequence motifs in the RNA correlate with sequence motifs in the protein indicating a co-evolution of 5’UTR with NSP1 in betacoronaviruses. Experimental mutational data on 5’UTR and NSP1 from SARS-CoV-2 using cell-free translation extracts support those conclusions and show that the N-terminal half of the NSP1 protein contains conserved key residues that are essential for evasion to the inhibitory effect of NSP1 on translation.

Viral and cellular translation during SARS‐CoV‐2 infection

“…2D). Swapping experiments of key residues in both NSP1 and SL1 from SARS‐CoV‐1 and ‐2 have demonstrated that these two elements have actually co‐evolved thereby confirming the tight functional link between the NSP1 protein and SL1 hairpin [34]. In these structures of NSP1, the sole N‐terminal domain is visible because the remaining parts of NSP1 are intrinsically disordered [52].…”

“…2A ). NSP1 proteins are conserved in alpha‐ and betacoronaviruses, and therefore were being studied prior to the appearance of SARS‐CoV‐2 [ 34 ]. Early studies in SARS‐CoV‐1 have shown that NSP1 is responsible for efficient shut down of host cell translation [ 35 , 36 , 37 ].…”

“…As NSP1 evasion is mediated by the hairpin SL1 located in the 5′ leader of the genomic and subgenomic RNAs, the positively charged front side of NSP1 is more susceptible to interact with negatively charged nucleic acids. Concerning SL1 hairpins, slight but significant differences between the two viruses are found; indeed, SARS‐CoV‐1 contains type I SL1 in its 5′ leader, while SARS‐CoV‐2 has a type III SL1 [ 34 ] (Fig. 2D ).…”

“…This main difference in the 5′ end of polyprotein 1a is often considered to be a genus‐specific marker. In the alpha and betacoronavirus genera, NSP1 proteins differ in size between ~110 and 245 amino acids [ 34 , 95 ]. However, despite highly divergent sequences, NSP1 always exhibits similar functions to induce translational suppression and to evade host responses [ 35 , 43 , 96 , 97 ].…”

Translation of SARS-CoV-2 gRNA Is Extremely Efficient and Competitive despite a High Degree of Secondary Structures and the Presence of an uORF

“…of all the viral mRNAs and contains five stem-loop structures (SL1 to SL5) that have recently been modelized by chemical probing analyses ( Figure 2 ) [ 73 , 74 ]. These SL are critical for replication, RNA synthesis and escape from nsp1-mediated translation inhibition [ 75 , 76 , 77 , 78 , 79 , 80 , 81 ]; however, they could potentially represent hurdles for translation, notably at the level of ribosome recruitment and scanning. Although the viral genome of SARS-CoV-2 is capped and polyadenylated, the translation initiation mechanism used to locate the AUG start codon inside the SL5 remains undetermined.…”