Computational Analysis of Silent Mutation Effects on SARS-CoV-2 RNA-Host RNA-Binding Protein Interactome

RNA-binding proteins (RBPs) play critical roles in host-virus interaction. They facilitate the regulation of viral RNA (vRNA) turnover by recognizing and forming complexes with the vRNA structure via specific RNA motifs-RNA binding domain interaction. However, due to consistent evolving nature of viruses, silent mutations in the viral genome can impact RBP-vRNA binding thereby altering the RNA processing. While efforts have been made in characterizing other forms of mutations leading to changes in amino acid sequences in SARS-CoV-2 variants, details on how silent mutations impact RBP-vRNA interaction remain limited. Here, we use extensive in silico mutagenesis to introduce silent mutations in the SARS-CoV-2 genome to generate four different synthetic variants and map the interaction of the variants and the wild-type with a catalogue of human RBPs. Our result shows variation in accumulation and reduction of the RBPs binding motifs in the variants compared to the virus reference sequence on a global scale and at the UTRs. The majority of the RBPs with AU-rich binding motifs are reduced in the variants, while RBPs with mostly GC-rich motifs accumulate more binding positions, suggesting that a single change from U/A to G/C and vice versa can impact RBP-viral interactions. Furthermore, we use structural analysis to show the interaction of the vRNA with PUF60 and KHDRBS3 proteins, two RBPs that have not been previously implicated in SARS-CoV-2 interactome. Our findings show that loss to the conserved poly(U) in PUF60 binding motifs in some of the variants affects its interaction with the protein at the 5′ end, which may disrupt the function of the protein as an anti-viral RNA regulator. We also predicted the key residues in KHDRBS3 interacting with its binding motif in the wild-type at the 3′ end, while noting that the vRNA structural changes in the variants may contribute to the loss of this interaction. Overall, our predictions contribute to the insights into virus evolution and pathogenicity of potential new variants due to the impact of synonymous changes in the nucleotide sequences on protein-RNA interaction.