tetano
Editor, Senior Moderator
RNA
. 2023 Aug 21;rna.079627.123.
doi: 10.1261/rna.079627.123. Online ahead of print. Effect of the SARS-CoV-2 Delta-associated G15U mutation on the s2m element dimerization and its interactions with miR-1307-3p
Caylee L Cunningham[SUP] 1 [/SUP], Caleb J Frye[SUP] 1 [/SUP], Joseph A Makowski[SUP] 1 [/SUP], Adam H Kensinger[SUP] 1 [/SUP], Morgan Shine[SUP] 2 [/SUP], Ella J Milback[SUP] 1 [/SUP], Patrick E Lackey[SUP] 2 [/SUP], Jeffrey D Evanseck[SUP] 1 [/SUP], Mihaela Rita Mihailescu[SUP] 3 [/SUP]
Affiliations
The stem loop 2 motif (s2m), a highly conserved 41-nucleotide hairpin structure in the severe acute respiratory syndrome coronavirus 2 (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 subsequent impact of those changes upon the s2m dimerization and interactions with the host microRNA miR-1307-3p. Bioinformatics analysis of the Global Initiative on Sharing All Influenza Data (GISAID) database targeting the s2m element reveals a greater than 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 find that the s2m G15U mutation drastically impacts the binding of the 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 the immune response.
Keywords: SARS-CoV-2 Delta; dimerization; kissing complex; miR-1307-3p; s2m.
. 2023 Aug 21;rna.079627.123.
doi: 10.1261/rna.079627.123. Online ahead of print. Effect of the SARS-CoV-2 Delta-associated G15U mutation on the s2m element dimerization and its interactions with miR-1307-3p
Caylee L Cunningham[SUP] 1 [/SUP], Caleb J Frye[SUP] 1 [/SUP], Joseph A Makowski[SUP] 1 [/SUP], Adam H Kensinger[SUP] 1 [/SUP], Morgan Shine[SUP] 2 [/SUP], Ella J Milback[SUP] 1 [/SUP], Patrick E Lackey[SUP] 2 [/SUP], Jeffrey D Evanseck[SUP] 1 [/SUP], Mihaela Rita Mihailescu[SUP] 3 [/SUP]
Affiliations
- PMID: 37604684
- DOI: 10.1261/rna.079627.123
The stem loop 2 motif (s2m), a highly conserved 41-nucleotide hairpin structure in the severe acute respiratory syndrome coronavirus 2 (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 subsequent impact of those changes upon the s2m dimerization and interactions with the host microRNA miR-1307-3p. Bioinformatics analysis of the Global Initiative on Sharing All Influenza Data (GISAID) database targeting the s2m element reveals a greater than 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 find that the s2m G15U mutation drastically impacts the binding of the 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 the immune response.
Keywords: SARS-CoV-2 Delta; dimerization; kissing complex; miR-1307-3p; s2m.