Abolished frameshifting for predicted structure-stabilizing SARS-CoV-2 mutants: implications to alternative conformations and their statistical structural analyses
- 1Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER-R)-Raebareli, Lucknow 226002, India
- 2Department of Chemistry, New York University, New York, New York 10003, USA
- 3Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, USA
- 4NYU-ECNU Center for Computational Chemistry, NYU Shanghai, Shanghai 200062, P.R. China
- 5NYU Simons Center for Computational Physical Chemistry, New York University, New York, New York 10003, USA
- 6Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Corresponding author: rf.abhishek.dey{at}niperrbl.ac.in
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Handling editor: Peter Stadler
Abstract
The SARS-CoV-2 frameshifting element (FSE) has been intensely studied and explored as a therapeutic target for coronavirus diseases, including COVID-19. Besides the intriguing virology, this small RNA is known to adopt many length-dependent conformations, as verified by multiple experimental and computational approaches. However, the role these alternative conformations play in the frameshifting mechanism and how to quantify this structural abundance has been an ongoing challenge. Here, we show by DMS and dual-luciferase functional assays that previously predicted FSE mutants (using the RAG graph theory approach) suppress structural transitions and abolish frameshifting. Furthermore, correlated mutation analysis of DMS data by three programs (DREEM, DRACO, and DANCE-MaP) reveals important differences in their estimation of specific RNA conformations, suggesting caution in the interpretation of such complex conformational landscapes. Overall, the abolished frameshifting in three different mutants confirms that all alternative conformations play a role in the pathways of ribosomal transition.
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Footnotes
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Article is online at http://www.rnajournal.org/cgi/doi/10.1261/rna.080035.124.
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Freely available online through the RNA Open Access option.
- Received March 27, 2024.
- Accepted July 21, 2024.
This article, published in RNA, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
