Long non-coding subgenomic flavivirus RNAs have extended 3D structures and are flexible in solution

Area of Science:

• Virology
• Molecular Biology
• Structural Biology

Background:

• Mosquito-borne flaviviruses like Zika, Dengue, and West Nile viruses produce long non-coding subgenomic RNAs (sfRNAs).
• These sfRNAs are implicated in viral pathogenicity and immune evasion.
• Limited structural characterization of these crucial viral RNAs exists.

Purpose of the Study:

• To determine the 3D structures of individual subdomains and complete sfRNAs from Dengue virus serotype 2 (DENV2), Zika virus (ZIKV), and West Nile virus (WNV).
• To visualize the accessible 3D conformational spaces of these sfRNAs in solution.
• To provide structural insights into the function of flavivirus sfRNAs and demonstrate visualization strategies for other long non-coding RNAs (lncRNAs).

Main Methods:

• Small-angle X-ray scattering (SAXS) was employed to study sfRNA structures in solution.
• Computational modeling was used in conjunction with SAXS data.
• Structural analysis of individual and combined subdomains (xrRNA1, xrRNA2, DB12, 3'SLs) was performed.

Main Results:

• Individual xrRNA1 and xrRNA2 domains adopt compact structures in solution, consistent with known ZIKV xrRNA1 crystal structures.
• DENV2 DB12 is extended, whereas ZIKV and WNV DB12 domains are compact due to intertwined double pseudoknots.
• All 3' stem-loops (3'SLs) exhibit similar rod-like structures.
• Complete sfRNAs are extended and occupy a broad conformational space in solution.

Conclusions:

• The study provides the first visualization of complete flavivirus sfRNAs in solution, revealing their extended and conformationally dynamic nature.
• Distinct structural features of sfRNA subdomains contribute to overall RNA conformation and likely influence viral function.
• The combined SAXS and computational approach offers a powerful strategy for studying the structure and dynamics of other lncRNAs in solution.