Multivalent Interactions Between the Picornavirus 3C(D) Main Protease and RNA Oligonucleotides Induce Liquid-Liquid...

Area of Science:

• Virology
• Molecular Biology
• Biochemistry

Background:

• Picornavirus 3CD protein is essential for viral replication, acting as a precursor to protease and RNA polymerase.
• The 3C protease domain interacts with viral RNA elements (CREs) to regulate viral processes.
• Understanding 3C-RNA interactions is crucial for deciphering viral replication mechanisms.

Purpose of the Study:

• To investigate the molecular basis of RNA binding by the picornavirus 3C protein.
• To determine the sequence and structure dependence of 3C-RNA interactions.
• To explore the potential for 3C-RNA interactions to induce liquid-liquid phase separation (LLPS).

Main Methods:

• Biophysical techniques (e.g., spectroscopy, binding assays) were employed.
• Computational methods were utilized to analyze protein-RNA interactions.
• RNA binding affinities and specificity were assessed using various oligonucleotide sequences and structures.

Main Results:

• The 3C protein binds a wide range of RNA oligonucleotides.
• RNA binding by 3C shows minimal sequence and structure dependence for short RNAs.
• Both 3C-RNA and 3CD-RNA interactions were found to induce liquid-liquid phase separation (LLPS).

Conclusions:

• Picornavirus 3C protein exhibits non-specific RNA binding capabilities.
• 3C-RNA interactions can drive LLPS, suggesting a novel regulatory mechanism.
• These findings may offer insights into viral pathogenesis, apoptosis, and stress granule dynamics.