Effect of the SARS-CoV-2 Delta-associated G15U mutation on the s2m element dimerization and its interactions with miR-1307-3p

DOI

10.1261/rna.079627.123

Authors

Caylee L. Cunningham, Duquesne University
Caleb J. Frye, Duquesne University
Joseph A. Makowski, Duquesne University
Adam H. Kensinger, Duquesne University
Morgan Shine, Westminster College, New Wilmington
Ella J. Milback, Duquesne University
Patrick E. Lackey, Westminster College, New Wilmington
Jeffrey D. Evanseck, Duquesne University
Mihaela Rita Mihailescu, Duquesne University

Document Type

Journal Article

Publication Date

11-1-2023

Publication Title

RNA (New York, N.Y.)

Volume

29

Issue

11

First Page

1754

Last Page

1771

Keywords

dimerization, kissing complex, miR-1307-3p, s2m, SARS-CoV-2 Delta

Abstract

The s2m, a highly conserved 41-nt hairpin structure in the SARS-CoV-2 genome, serves as an attractive therapeutic target that may have important roles in the virus life cycle or interactions with the host. However, the conserved s2m in Delta SARS-CoV-2, a previously dominant variant characterized by high infectivity and disease severity, has received relatively less attention than that of the original SARS-CoV-2 virus. The focus of this work is to identify and define the s2m changes between Delta and SARS-CoV-2 and the subsequent impact of those changes upon the s2m dimerization and interactions with the host microRNA miR-1307-3p. Bioinformatics analysis of the GISAID database targeting the s2m element reveals a >99% correlation of a single nucleotide mutation at the 15th position (G15U) in Delta SARS-CoV-2. Based on 1H NMR spectroscopy assignments comparing the imino proton resonance region of s2m and the s2m G15U at 19°C, we show that the U15-A29 base pair closes, resulting in a stabilization of the upper stem without overall secondary structure deviation. Increased stability of the upper stem did not affect the chaperone activity of the viral N protein, as it was still able to convert the kissing dimers formed by s2m G15U into a stable duplex conformation, consistent with the s2m reference. However, we show that the s2m G15U mutation drastically impacts the binding of host miR-1307-3p. These findings demonstrate that the observed G15U mutation alters the secondary structure of s2m with subsequent impact on viral binding of host miR-1307-3p, with potential consequences on immune responses.

Open Access

Green Accepted

Preprint

Link to Free Full Text

Repository Citation

Cunningham, C., Frye, C., Makowski, J., Kensinger, A., Shine, M., Milback, E., Lackey, P., Evanseck, J., & Mihailescu, M. (2023). Effect of the SARS-CoV-2 Delta-associated G15U mutation on the s2m element dimerization and its interactions with miR-1307-3p. RNA (New York, N.Y.), 29 (11), 1754-1771. https://doi.org/10.1261/rna.079627.123