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. 2020 Sep 23;18(4):447–456. doi: 10.1080/15476286.2020.1814556

Secondary structure of the SARS-CoV-2 5’-UTR

Zhichao Miao a,b,c, Antonin Tidu d, Gilbert Eriani d, Franck Martin d,*
PMCID: PMC7544965  PMID: 32965173

ABSTRACT

The SARS-CoV-2, a positive-sense single-stranded RNA Coronavirus, is a global threat to human health. Thus, understanding its life cycle mechanistically would be important to facilitate the design of antiviral drugs. A key aspect of viral progression is the synthesis of viral proteins by the ribosome of the human host. In Coronaviruses, this process is regulated by the viral 5ʹ and 3ʹ untranslated regions (UTRs), but the precise regulatory mechanism has not yet been well understood. In particular, the 5ʹ-UTR of the viral genome is most likely involved in translation initiation of viral proteins. Here, we performed inline probing and RNase V1 probing to establish a model of the secondary structure of SARS-CoV-2 5ʹ-UTR. We found that the 5ʹ-UTR contains stable structures including a very stable four-way junction close to the AUG start codon. Sequence alignment analysis of SARS-CoV-2 variants 5ʹ-UTRs revealed a highly conserved structure with few co-variations that confirmed our secondary structure model based on probing experiments.

KEYWORDS: SARS-CoV-2, 5ʹ-UTR, secondary structure, probing

Introduction

Coronaviruses are found to infect a large variety of animals and humans. Besides enteric diseases, they mainly cause severe respiratory defects sometimes leading to death [1]. The recently emerged SARS-CoV-2 belongs to the betacoronavirus genome, subgenus Sarbecovirus [2]. Its genome is a positive single-stranded RNA molecule (+)ssRNA (Coronaviridae Study Group of the International Committee on Taxonomy of Viruses, 2020). The genomic sequence of SARS-CoV-2 was determined at the end of 2019 [3]. The RNA genome is capped at the 5ʹ end and polyadenylated at the 3ʹ end. The genome encodes two long open reading frames (ORF1a and ORF1b) at the 5ʹ end and several ORFs that are expressed in the late phase of infection from subgenomic RNAs (sgRNAs) [4]. After cell entry, the translation of ORF1a and ORF1b from the whole ss(+)RNA are the first events of the infectious process. The translation of ORF1b requires a − 1 frameshifting event [5,6]. The polyprotein synthesized from ORF1a is processed into eleven non-structural proteins (NSP1-NSP11). The first one, NSP1 binds to the host small ribosomal subunit 40S and recruits a yet unidentified cellular nuclease that triggers the degradation of the host mRNAs, while viral RNA is being translated [7,8]. Thus, the virus specifically degrades the cellular mRNAs that are translated by the canonical cap-dependent translation mechanism. Other studies have shown that NSP1 is also able to prevent 48S ribosomal complex formation by another so far uncharacterized mechanism [8,9]. Interestingly, it has been shown that IRES (Internal Ribosome Entry Site)-mediated translation initiation of class III- and IV–IRES (e.g., in Hepatitis C Virus (HCV) and Cricket paralysis virus (CrPV)) respectively, is immune to the NSP1 inhibition. Instead, the translation initiation driven by the encephalomyocarditis virus (EMCV) class II–IRES is efficiently inhibited by NSP1 [8]. The NSP1 binding site to the ribosomal 40S subunit has not yet been determined.

Since the SARS-CoV-2 genomic RNA is capped at the 5ʹ end, it is generally believed that its translation initiation is canonical and cap-dependent. However, two major observations provide hints that the translation mechanism of SARS-CoV-2 RNA is in fact mediated by an unconventional translation initiation mechanism rather than a canonical one. First, the secondary structure of the SARS-CoV-2 5ʹ-UTR is likely to be complex in the proximity of the 5ʹ cap, based on the experimental SHAPE structure of the 5ʹ-UTR of Mouse Hepatitis Virus (MHV), a Coronavirus belonging to the Embecovirus subgroup, and on related structural predictions of the 5ʹ-UTR of the SARS-CoV Sarbecovirus [10]. RNA structures proximal to the cap are known to inhibit the recruitment of cap-binding translation factors (eIF4E and consequently eIF4F), thus indicating canonical cap-dependent translation improbable [11,12]. Second, after the translation of ORF1a, the rapidly produced NSP1 protein would shut down the canonical cap-dependent translation of cellular mRNAs. Yet, the translation of SARS-CoV-2 proteins is not inhibited by NSP1. Indeed, class III- and class IV–IRES are immune to this NSP1-mediated inhibitory mechanism [8,13]. This suggests that translation initiation of SARS-CoV-2 may be less dependent on eIF4F. Previous structural studies from other coronavirus 5ʹ-UTRs have shown that stable hairpin structures are found in the proximity of the cap structure. When these structures are present in the vicinity of the cap, translation initiation efficiency is significantly modulated by these secondary structures [11]. In both cap-dependent and cap-independent mechanisms, the secondary structure of the 5ʹ-UTR is critical for translation initiation efficiency.

In order to better understand the translation initiation mechanism of viral translation during SARS-CoV-2 infection, the first step is to determine the secondary structure of the 5ʹ-UTR. Here, we report the first experimental determination of SARS-CoV-2 5ʹ-UTR structure using inline probing and RNAse V1 enzymatic probing.

Material and methods

Coronavirus complete genome sequence

The complete genome sequence of SARS-CoV-2 was downloaded from NCBI nucleotide database Genbank [14] MN908947.3.

Secondary structure probing

The RNA transcripts have been synthesized by in vitro transcription. The RNA transcripts were then separated on PAGE containing 8 M urea and purified by electro-elution using Bio Trap apparatus and Schleicher & Schuell membranes. The purified transcript was then 32P-labelled by 5ʹ capping using the ScriptCap m7G Capping System kit from CELLSCRIPT™. The RNA transcripts were probed directly after purification without any denaturation-renaturation step. Briefly, for inline probing, 50 000 cpm of radiolabelled RNA was incubated in 50 mM Tris-HCl pH 8.8, 100 mM KCl without MgCl2 or with 1 or 10 mM MgCl2 for 72 h at room temperature. The cuts in the RNA backbone were analysed on denaturating PAGE containing 8 M urea. For V1 probing, the RNA was incubated with serial dilutions of RNase V1 in order to have statistically one digestion cut per molecule for 10 min at room temperature as previously described [15]. The cuts were mapped by an RNase T1 ladder performed in a denaturing buffer according to previously established protocol [16]. Each segment of the 5ʹ-UTR has been probed at least twice and representative gels for all the parts of the 5ʹ-UTR are shown in the figures and supplemental figures. The inline reactivities have been classified as ‘accessible’ or ‘not accessible’ for inline probing. For V1 probing, the reactivities are shown as ‘weak’ or ‘strong’ according to the band intensities.

Sequence alignments

Homologous sequences, most of which were from SARS-CoV-2, were retrieved by BLAST [17] search. Sequences were aligned with ClustalW [18] before the alignment-based prediction of RNAalifold [19]. Forna [20] and R2R [21] were used to visualize the secondary structures.

Results and discussion

SARS-CoV-2 5ʹ-UTR inline probing

Using in vitro transcription, we synthesized a transcript encompassing nucleotides 1 to 301 from the SARS-CoV-2 variant (GenBank: MN908947.3). It contains the whole 5ʹ-UTR and the sequence coding for the 12 N-terminal codons of NSP1 Fig. 1. Since the viral genomic RNA is capped at the 5ʹ end, we labelled the transcript at the 5ʹ end with a radioactive m7G cap. In order to determine the secondary structure of this transcript, we first performed inline probing in the absence and presence of 1 or 10 mM Mg2+. We then analysed the cuts in the RNA backbone by migration on denaturing polyacrylamide gel electrophoresis. The cuts were mapped using an RNase T1 ladder performed in denaturing conditions. We analysed regions from nt 1 to 128 and 94 to 295 Figs. 2 and 3, respectively. Interestingly, RNase T1 digestion of G residues from 188 to 219 was inefficient even though digestion was performed in denaturing conditions (Fig. 3, right panel). This indicates that these residues are embedded in a highly stable structural region that is still efficiently folded in denaturing conditions thereby preventing the access of RNase T1. Inline probing with and without Mg2+ allowed us to map the structurally accessible regions of the RNA that generally correspond to single-stranded regions. Using this method, we could also detect inaccessible areas that are potentially forming base pairs.

Figure 3.

Figure 3.

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Inline probing of the SARS-CoV-2 5ʹ-UTR from nucleotides 94 to 295

(A) Inline probing of the SARS-CoV-2 without Mg2+, with 1 and 10 mM Mg2+. The cuts are mapped using an RNase T1 denaturing ladder that cuts after G residues. The left panel shows the reactivity of nucleotides 94–227 and the right panel shows the same gel with a longer exposure. (B) Inline probing of the SARS-CoV-2 without Mg 2+, with 1 and 10 mM Mg2+. The upper panel shows the reactivity of nucleotides 165–262, and the lower panels show the reactivity of nucleotides 220–295 (short exposure on the left and long exposure on the right).

Figure 1.

Figure 1.

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SARS-CoV-2 5ʹ-UTR

An RNA transcript containing the 301 5ʹ proximal nucleotides from SARS-CoV-2 is represented. The positions of the uORF and the N-terminal coding sequence of NSP1 are shown in green.

Figure 2.

Figure 2.

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Inline probing of the SARS-CoV-2 5ʹ-UTR from nucleotides 1 to 128

Inline probing of the SARS-CoV-2 without Mg2+, with 1 and 10 mM Mg2+. The cuts are mapped using an RNase T1 denaturing ladder that cuts after G residues. The left panel shows the reactivity of nucleotides 1–56 and the right panel shows the reactivity of nucleotides 30–128.

Figure 3.

Figure 3.

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(continued)

In order to confirm these putative stems, we performed RNase V1 probing. The V1 enzyme specifically cuts in stem regions Figs. 4 and 5. We confirmed that most of the inaccessible regions by inline probing do actually correspond to areas containing base pairs. Altogether, these data allowed us to establish a solid model of the 2D structure of the whole SARS-CoV-2 5ʹ-UTR Fig. 6. The 5ʹ-UTR is highly structured with a few accessible bulges and loops. It contains five simple hairpin structures that were named SL1, SL2, SL3, SL4 and SL5 in good agreement with bioinformatic secondary structure predictions for the SARS-CoV-2 [22] and also from other coronaviruses [23]. Our model is also highly similar to the models obtained by probing of the whole SARS-CoV-2 genome in vitro [24] and in vivo [25,26]. However, we found an additional hairpin located between SL4 and SL5 that we named SL4.5. As predicted, SL1 is located close to the 5ʹ extremity. It has been proposed that the low overall stability of SL1, due to a high proportion of A-U and U-A base pairs, is important for replication in Mouse Hepatitis Virus MHV [27]. The loop of SL1 is not conserved in SARS-CoV-2 variants and the two bulged nucleotides in the middle of SL1 can be involved in base pairs as observed in some variants suggesting that the loop and the bulge of SL1 are not required for efficient viral propagation Fig. 7. The SL2 hairpin domain is comparable to the SL3 domain in Bovine coronavirus (BCoV), which is known to form a hairpin structure according to NMR spectroscopy [28] as well as enzymatic probing [29,30]. This domain is expected to be involved in the replication complex formation Fig. 8. The loop (CUUGY) of SL2 is important for Mouse Hepatitis Virus replication [28]. It contains a U-turn like motif. In contrast, the SARS-CoV SL2 rather adopts a typical tetraloop structure [31]. This is in good agreement with our inline reactivity profile of the SL2 loop since C50 and G53 are not accessible in the loop but the U54 is highly accessible, a well-characterized feature of a tetraloop structure [31]. Hairpin SL3 is known to encompass the leader TRS (TRS-L) sequence as previously observed for group IIb coronavirus [23] Fig. 8. The SL4 structure is a relatively stable and long hairpin and three base pairs in the stem region have been described to contain covariations (R90-Y121, R97-U115 and G101-Y111), indicating structural conservation. SL4 contains the start codon of a uORF that is present in all coronaviruses although there is no evidence of translation of this uORF so far [23]. The integrity of the upper part of SL4 is important for replication of BCoV [29] Fig. 9. It has also been proposed that SL4 is involved in the synthesis of subgenomic RNA fragments [23]. In the 3ʹ part, the 5ʹ-UTR contains a more complex structure named SL5 that comprises a four-way junction formed by SL5a, SL5b and SL5c. This four-way junction is found in all the coronavirus 5ʹ-UTRs that have been probed so far [23,32–35] Fig. 9. Importantly, in the SARS-CoV-2, the NSP1 AUG start codon is part of the SL5. We observed the same reactivity pattern in the identical loops from SL5a and SL5b, the inline reactivities are in good agreement with classical U-turns [36]. In contrast, SL5c contains a typical GNRA loop as previously observed in group IIb coronaviruses [23]. The loops of SL5 are most likely involved in RNA packaging as previously suggested [37]. These stems are separated by short single-stranded regions that are generally accessible except for two short regions (A34-C40) and (C75-A80) that are accessible in our inline experiments but also contain V1 cuts indicating the potential forming of base pairs. These apparently contradictory results can be explained as follows: these regions are dynamic and can be considered as single-stranded regions in a so-called ‘open’ state or double-stranded in a ‘closed’ state. Interestingly, the sequences can fold into putative pseudo-knots structures with loop of SL2 and SL3 that we named, respectively, PK1 and PK2. The position of SL1 close to the m7G cap might interfere with the binding of eIF4F complex thereby preventing canonical cap-dependent translation [12]. This observation is important for some SARS-CoV-2 variants that are shorter in which the 5ʹ extremity is located just one nucleotide upstream of SL1 Fig. 7. We also probed a truncated version lacking the 5ʹ proximal half of the 5-UTR (∆105). Interestingly, the folding of SL4 and SL5 in this shorter version is identical to the folding found in the full-length 5ʹ-UTR (Supplemental Figure 1). This also allowed us to confirm the highly stable structure of SL5abc three-way junction. Moreover, these experiments demonstrate that SL5 can fold without nt 1–105 which suggests the existence of independent motifs in the 5ʹ-UTR that do not interact with each other. Importantly, sequence alignments of recently sequenced SARS-CoV-2 variants also enabled the discovery of co-variations in SL1, SL4 SL5 and SL5a thereby validating our secondary structure model for these structural regions Fig. 7. SL5a is a structurally stable region that is not cut by RNase T1 in denaturing conditions. This hairpin contains 10 G-C base pairs and its minimal free energy is predicted to be −17.30 kcal.mol−1, probably explaining its resistance to RNase T1 digestion even in denaturing conditions. The 5ʹ-UTR also contains an upstream opened reading frame (uORF) that is overlapping with SL4 and SL4.5. The location and the sequence of uAUG are absolutely conserved. On the contrary, the UAA stop codon is mutated in a few variants but another in-frame UAA stop is present immediately downstream, implying that the uORF is present and conserved in all variants Fig. 7. The NSP1 AUG start codon is embedded in the four-way junction structure. For an efficient translation initiation, the sequences surrounding the AUG start codon have to be unfolded. The mechanism used by the virus is still unknown and an important issue to investigate is the role and the putative function of the stable SL5 structure (SL5a, SL5b, SL5c) in the translation of the SARS-CoV-2 polyprotein. Although the viral genome is capped at its 5ʹ end, the translation initiation mechanism used to locate the AUG start codon in SL5 remains elusive. The presence of the 5ʹ m7G cap and hairpins SL1, SL2, SL3, SL4 and SL5 suggest that a canonical cap-dependent scanning mechanism would require the eIF4A helicase [38,39]. On the other hand, the fact that the AUG start codon is located in the vicinity and downstream of a four-way junction structure is reminiscent of similar structures found in the HCV IRES [40] (and references therein). Indeed, IRES elements are typically highly structured RNA motifs [40]. In addition, the 5ʹ-UTR contains a uORF that is conserved in SARS-CoV-2 variants, which indicates that it can be translated by the host ribosome. The use of uORF is another way of translation regulation [41,42]. It is possible that the viral translation may use all these mechanisms at distinct stages of the infectious process. We hope that our investigations of the 5ʹ-UTR structure in SARS-CoV-2 translation will pave the way to further studies in understanding its functions in the viral infection life cycle.

Figure 4.

Figure 4.

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Enzymatic probing by RNase V1 of the SARS-CoV-2 5ʹ-UTR from nucleotides 1 to 56

Enzymatic probing of the SARS-CoV-2 which are performed by decreasing amount of RNase V1. The cuts are mapped using an RNase T1 denaturing ladder that cuts after G residues.

Figure 5.

Figure 5.

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Enzymatic probing by RNase V1 of the SARS-CoV-2 5ʹ-UTR from nucleotides 105 to 295

Enzymatic probing of the SARS-CoV-2 which are performed by decreasing amount of RNase V1. The cuts are mapped using an RNase T1 denaturing ladder that cuts after G residues. The panel shows the reactivity of nucleotides 53–295. The right panel shows a long run of the same samples to improve the resolution of the T1 ladder 127 to 236.

Figure 6.

Figure 6.

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Secondary structural model of SARS-CoV-2 5ʹ-UTR

The model of the 5ʹ-UTR is represented based on Inline probing and enzymatic probing by RNase V1. Reactivity determined by inline probing experiments is shown in grey and V1 cuts are shown by red triangles. A dashed line boxes the area that is resistant to RNase T1 digestion in denaturing conditions. The positions of the uAUG and the AUG codons are highlighted in yellow.

Figure 7.

Figure 7.

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Sequence alignments of 5ʹ-UTRs from SARS-CoV-2 variants

The sequence alignments of 5ʹ-UTRs from 28 SARS-CoV-2 variants are presented in two panels from nt #1 to 151 (top) and from nt 1#50 to 300 (bottom). The stems of SL1 to SL5 are underlined by distinct colours. The positions of uORF and the beginning of NSP1 ORF are indicated in light green on top of the sequences. In several variants, the stop codon of the uORF is shifted from one codon (also shown in green). Covariations in stems are indicated by red arrows and the corresponding nucleotides are shown in yellow on the consensus sequence.

Figure 8.

Figure 8.

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Functional motifs in the 5ʹ-UTR of SARS-CoV-2

The previously described functional motifs for replication, transcription, viral packaging and translation are shown on our secondary structural model. These motifs have been characterized in the coronavirus family.

Figure 9.

Figure 9.

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Comparison of the 2D structure of SARS-CoV-2 5ʹUTR with other probed coronavirus 5ʹ-UTRs

Our model for the SARS-CoV-2 5ʹ-UTR is compared with other coronavirus 5ʹ-UTR that have been determined by experimental probing. The 5ʹ-UTR secondary structures from Mouse Hepatitis Virus (MHV) [34], Human coronavirus (HCoV) [35] and Bovine coronavirus (B-CoV) [23,32,33] are shown. The position of the NSP1 AUG start codon is highlighted in green.

Supplementary Material

Supplemental Material
Click here for additional data file. (1.2MB, docx)

Acknowledgments

ZM is supported by Single Cell Gene Expression Atlas grant from the Wellcome Trust (108437/Z/15/Z). FM, GE and AT are funded by ‘Agence Nationale pour la Recherche’ (ANR-17-CE12-0025-01, ANR-17-CE11-0024, ANR-20-COVI-0078), by ‘Fondation pour la Recherche Médicale’ (project CoronaIRES), by University of Strasbourg and by the ‘Centre National de la Recherche Scientifique’. We gratefully thank Eric Westhof for helpful discussion.

Funding Statement

This work was supported by the Agence Nationale de la Recherche (FR) [ANR-17-CE12-0025-01]; Agence Nationale de la Recherche (FR) [ANR-17-CE11-0024]; Welcome Trust [108437/Z/15/Z]; Fondation pour la Recherche Médicale [CoronaIRES]; Agence Nationale de la Recherche (FR) [ANR-20-COVI-0078].

Disclosure statement

No potential conflict of interest was reported by the authors.

Supplementary material

Supplemental data for this article can be accessed here.

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