Abolished frameshifting for predicted structure-stabilizing SARS-CoV-2 mutants: Implications to alternative...

Area of Science:

• Molecular Biology
• Virology
• RNA Structure and Dynamics

Background:

• The SARS-CoV-2 frameshifting element (FSE) is a key therapeutic target for COVID-19, known to adopt diverse length-dependent conformations.
• Understanding the role and abundance of these alternative RNA structures in the frameshifting mechanism remains a significant challenge.

Approach:

• Utilized dimethyl sulfate (DMS) and dual-luciferase functional assays to investigate FSE mutants predicted by RAG graph theory.
• Employed correlated mutation analysis with DREEM, DRACO, and DANCE-MaP programs to assess RNA conformational landscapes.

Key Points:

• Predicted FSE mutants were shown to suppress structural transitions and abolish frameshifting.
• Correlated mutation analysis revealed discrepancies among different programs in estimating specific RNA conformations.
• Abolished frameshifting in three distinct mutants underscores the functional importance of all alternative conformations.

Conclusions:

• Alternative RNA conformations are integral to the ribosomal frameshifting pathway in SARS-CoV-2.
• The study highlights the need for caution when interpreting complex RNA conformational data from computational analyses.
• Findings contribute to a deeper understanding of coronavirus RNA biology and potential therapeutic interventions.