Xrn1-resistant RNA structures are well-conserved within the genus flavivirus.

Area of Science:

• Virology
• Molecular Biology
• RNA Biology

Background:

• Subgenomic RNAs (sgRNAs) are vital for RNA virus replication and pathogenicity.
• Flaviviruses utilize exoribonuclease Xrn1-resistant RNA motifs for sgRNA production.
• Distinct sgRNA motif classes were previously proposed for mosquito-borne versus tick-borne/no-known-vector flaviviruses.

Purpose of the Study:

• To investigate the structural conservation of Xrn1-resistant RNA motifs in tick-borne and no-known-vector flaviviruses.
• To determine if these motifs share similar structural configurations.
• To assess the functional impact of these motifs on viral RNA generation in vivo.

Main Methods:

• Systematic in vitro mutational analysis of tick-borne and no-known-vector flavivirus RNA motifs.
• Structural characterization of RNA motifs, including pseudoknots and base-triples.
• In vivo studies using Modoc virus to assess the impact of mutations on sgRNA generation.

Main Results:

• Tick-borne and no-known-vector flavivirus Xrn1-resistant RNA motifs exhibit highly similar structural configurations.
• Identical, conserved locations for key structural elements like double pseudoknots and base-triples were identified.
• Mutations targeting these conserved structural features in Modoc virus significantly affected in vivo sgRNA generation.

Conclusions:

• Xrn1-resistant RNA motifs in flaviviruses share a conserved topological structure across different vector classes.
• This conserved structure is essential for the generation of subgenomic flaviviral RNA.
• The findings suggest a unified mechanism for sgRNA production throughout the Flavivirus genus.