Structural and functional conservation of the programmed −1 ribosomal frameshift signal of SARS-CoV-2
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Abstract
17 years after the SARS-CoV epidemic, the world is facing the COVID-19 pandemic. COVID-19 is caused by a coronavirus named SARS-CoV-2. Given the most optimistic projections estimating that it will take over a year to develop a vaccine, the best short-term strategy may lie in identifying virus-specific targets for small molecule interventions. All coronaviruses utilize a molecular mechanism called −1 PRF to control the relative expression of their proteins. Prior analyses of SARS-CoV revealed that it employs a structurally unique three-stemmed mRNA pseudoknot to stimulate high rates of −1 PRF, and that it also harbors a −1 PRF attenuation element. Altering −1 PRF activity negatively impacts virus replication, suggesting that this molecular mechanism may be therapeutically targeted. Here we present a comparative analysis of the original SARS-CoV and SARS-CoV-2 frameshift signals. Structural and functional analyses revealed that both elements promote similar rates of −1 PRF and that silent coding mutations in the slippery sites and in all three stems of the pseudoknot strongly ablated −1 PRF activity. The upstream attenuator hairpin activity has also been functionally retained. Small-angle x-ray scattering indicated that the pseudoknots in SARS-CoV and SARS-CoV-2 had the same conformation. Finally, a small molecule previously shown to bind the SARS-CoV pseudoknot and inhibit −1 PRF was similarly effective against −1 PRF in SARS-CoV-2, suggesting that such frameshift inhibitors may provide promising lead compounds to counter the current pandemic.
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SciScore for 10.1101/2020.03.13.991083: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Cell culture and plasmid transfection: Human embryonic kidney (HEK293T/17) (CRL-11268) and HeLa (CCL-2) cells were purchased from the American Type Culture Collection (Manassas, VA) HeLasuggested: CLS Cat# 300194/p772_HeLa, RRID:CVCL_0030)HEK293T and HeLa cells were seeded at 4 × 104 cells per well into 24-well plates. HEK293Tsuggested: NoneSoftware and Algorithms Sentences Resources The EMBOSS Water pairwise alignment tool was used to … SciScore for 10.1101/2020.03.13.991083: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Cell culture and plasmid transfection: Human embryonic kidney (HEK293T/17) (CRL-11268) and HeLa (CCL-2) cells were purchased from the American Type Culture Collection (Manassas, VA) HeLasuggested: CLS Cat# 300194/p772_HeLa, RRID:CVCL_0030)HEK293T and HeLa cells were seeded at 4 × 104 cells per well into 24-well plates. HEK293Tsuggested: NoneSoftware and Algorithms Sentences Resources The EMBOSS Water pairwise alignment tool was used to identify sequences in the SARS-CoV-2 genome most similar to the SARS-CoV −1 PRF sequence. EMBOSSsuggested: (EMBOSS, RRID:SCR_008493)Statistical analyses were conducted using Student’s t test or one-way analysis of variance as appropriate using Prism 8 software (GraphPad). Prismsuggested: (PRISM, RRID:SCR_005375)GraphPadsuggested: (GraphPad Prism, RRID:SCR_002798)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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