Poster abstracts
Poster number 34 submitted by Caylee Cunningham
Characterization of the s2m G15U mutation associated with the SARS-CoV-2 Delta variant
Caylee L. Cunningham (Chemistry and Biochemistry, Duquesne University), Caleb J. Frye, Adam H. Kensinger, Joseph A. Makowski (Chemistry and Biochemistry, Duquesne University), Morgan J. Shine (Chemistry and Biochemistry, Westminster College), Ella J. Milback (Chemistry and Biochemistry, Duquesne University), Patrick Lackey (Chemistry and Biochemistry, Westminster College), Jeffrey D. Evanseck, Mihaela-Rita Mihailescu (Chemistry and Biochemistry, Duquesne University)
Abstract:
The s2m, a highly conserved 41-nucleotide structure in the 3' UTR of the SARS-CoV-2 genome, may have important roles in the life cycle of the virus as well as participate in interactions with the host upon infection. 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 characterize changes between the s2m elements of Delta and the original strain of SARS-CoV-2 and investigating 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 reveals a greater than 99% correlation of a single nucleotide mutation at the 15th position of the s2m in Delta SARS-CoV-2. Based on 1H NMR spectroscopy assignments comparing the imino proton resonance region of s2m and the s2m G15U, we show that the U15-A29 base pair closes, resulting in better stability of the upper stem without overall secondary structure deviation. Increased stabilization of the upper stem did not affect the chaperone activity of the viral N protein, as it was still able to convert the s2m G15U into a stable duplex conformation, consistent with the original s2m SARS-CoV-2. However, we find that the s2m G15U mutation drastically impacts the binding of the host miR-1307-3p. Specifically, miR-1307-3p binding is greatly reduced, likely due to the inability of the miR to invade the paired bases of the s2m. These findings demonstrate that the G15U mutation alters the secondary structure of s2m with subsequent impact on viral binding of host miR-1307-3p, with potential consequences on the immune response.
Keywords: s2m, SARS-CoV-2, miR-1307-3p