Two mutations P/L and Y/C in SARS-CoV-2 helicase domain exist together and influence helicase RNA binding

Abstract

RNA helicases play pivotal role in RNA replication by catalysing the unwinding of complex RNA duplex structures into single strands in ATP/NTP dependent manner. SARS coronavirus 2 (SARS-CoV-2) is a single stranded positive sense RNA virus belonging to the family Coronaviridae. The viral RNA encodes non structural protein Nsp13 or the viral helicase protein that helps the viral RNA dependent RNA polymerase (RdRp) to execute RNA replication by unwinding the RNA duplexes. In this study we identified a novel mutation at position 541of the helicase where the tyrosine (Y) got substituted with cytosine (C). We found that Y541C is a destabilizing mutation increasing the molecular flexibility and leading to decreased affinity of helicase binding with RNA. Earlier we had reported a mutation P504L in the helicase protein for which had not performed RNA binding study. Here we report that P504L mutation leads to increased affinity of helicase RNA interaction. So, both these mutations have opposite effects on RNA binding. Moreover, we found a significant fraction of isolate population where both P504L and Y541C mutations were coexisting.

Functional and druggability analysis of the SARS-CoV-2 proteome

“…In structural proteins, the most notorious case is the D614G mutation in the RBD domain of the S protein, which became predominant during the first months of the outbreak ( Plante et al, 2020 ), along with other changes such as the D936Y in the FP domain ( Cavallo and Oliva, 2020 ). In non-structural proteins, the P504L and Y541C are the predominant mutations in the helicase nsp13 ( Table S6 ), and they were reported to affect the RNA binding ( Begum et al, 2020 ). Among accessory proteins, the mutation Q57H in orf3a is becoming dominant and appears to be associated with disease severity; orf3a also possesses other relevant polymorphism such as S171L, G196V and G251V ( Issa et al, 2020 ) ( Table S6 ).…”

Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2

“…Dual mutations in Nsp13 were reported with profound effect on its activity specifically in the Pacific Northwest of the United States ( 23 ). The P409L mutation leads to increased affinity of helicase RNA interaction, whereas Y446C is a destabilizing mutation increasing the molecular flexibility and leading to decreased affinity of helicase binding with RNA ( 24 ). Therefore, both the mutations were antagonistic in nature.…”

Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hotspots, Functional Crosstalk and Regulatory Interactions in SARS-CoV-2

“…Dual mutations in Nsp13 were reported with profound effect on its activity specifically in Pacific northwest of USA (49). P409L, mutation leads to increased affinity of helicase RNA interaction, whereas Y446C is a destabilizing mutation increasing the molecular flexibility and leading to decreased affinity of helicase binding with RNA (50). Therefore, both the mutations were antagonistic in nature.…”