A folded viral noncoding RNA blocks host cell exoribonucleases through a conformationally dynamic RNA structure

Area of Science:

• Molecular Biology
• Virology
• Structural Biology

Background:

• Folded RNA elements, exoribonuclease-resistant RNAs (xrRNAs), block 5′ → 3′ cellular exoribonucleases to produce biologically active viral noncoding RNAs in flaviviruses.
• It was unclear if this RNA structure-dependent mechanism exists in other viruses and if a singular RNA fold is required.

Purpose of the Study:

• To investigate the existence and mechanism of xrRNAs in dianthoviruses, plant-infecting viruses.
• To determine if the RNA fold is conserved across different xrRNA types.

Main Methods:

• Biochemistry and virology techniques were used to characterize sequence requirements and the mechanism of exoribonuclease inhibition.
• X-ray crystallography was employed to solve the structure of a dianthovirus xrRNA.
• Single-molecule Förster Resonance Energy Transfer (FRET) experiments were conducted to study RNA conformational changes.

Main Results:

• Authentic RNA structure-dependent xrRNAs were identified in dianthoviruses, which are unrelated to flaviviruses and lack sequence similarity to known xrRNAs.
• A complex, distinct RNA fold was revealed for dianthovirus xrRNAs, differing from flavivirus xrRNAs.
• Both viral xrRNA types share a pseudoknot feature forming a protective ring around the RNA 5′ end.
• Dianthovirus xrRNAs utilize "codegradational remodeling," employing exoribonuclease-linked helicase activity for structure formation.

Conclusions:

• RNA structure-dependent exoribonuclease resistance is a general RNA maturation mechanism, established through convergent evolution in different viral contexts.
• Exoribonuclease-resistant RNAs (xrRNAs) represent an authentic functional class of RNAs.
• A conserved topological feature, the pseudoknot ring, may define xrRNAs across different viral families.