Abstract
Most mosquito‐borne flaviviruses, including Zika virus (ZIKV), Dengue virus (DENV), and West Nile virus (WNV), produce long non‐coding subgenomic RNAs (sfRNAs) in infected cells that link to pathogenicity and immune evasion. Until now, the structural characterization of these lncRNAs remains limited. Here, we studied the 3D structures of individual and combined subdomains of sfRNAs, and visualized the accessible 3D conformational spaces of complete sfRNAs from DENV2, ZIKV, and WNV by small angle X‐ray scattering (SAXS) and computational modeling. The individual xrRNA1s and xrRNA2s adopt similar structures in solution as the crystal structure of ZIKV xrRNA1, and all xrRNA1‐2s form compact structures with reduced flexibility. While the DB12 of DENV2 is extended, the DB12s of ZIKV and WNV are compact due to the formation of intertwined double pseudoknots. All 3′ stem‐loops (3′SLs) share similar rod‐like structures. Complete sfRNAs are extended and sample a large conformational space in solution. Our work not only provides structural insight into the function of flavivirus sfRNAs, but also highlights strategies of visualizing other lncRNAs in solution by SAXS and computational methods.
Highlights
Long non-coding RNAs are an expanding group of cellular transcripts that range from 200 nt to over 100 kb in length and possess no protein-coding potential [1]
Complete subgenomic flavivirus RNAs (sfRNA) from DENV2, Zika virus (ZIKV), and West Nile virus (WNV) were prepared by following the native purification protocols which have been successfully used to obtain other Long non-coding RNAs (lncRNAs) in large amount (> 10 mg) [37]
The overall structural parameters, including the radius of gyration Rg calculated from Guinier slops, Rg, and the maximum diameter Dmax from pair distance distribution functions (PDDFs) functions, as well as molecular weights derived from volume of correlation (Vc) [38], are summarized in Appendix Table S1, among which the molecular weights calculated from small angle X-ray scattering (SAXS) data are consistent with those predicted from sequences, indicating that the complete sfRNAs are all monomeric in our solution conditions
Summary
Long non-coding RNAs (lncRNAs) are an expanding group of cellular transcripts that range from 200 nt to over 100 kb in length and possess no protein-coding potential [1]. Like their host cells, many if not all viruses can make their own lncRNAs with multiple biological functions, including the regulation of viral replication, viral persistence, host immune evasion, and pathogenesis [2,3]. The 50 UTR, 30 UTR, and capsid coding sequences are highly structured and contain many cis-acting elements which are involved in gRNA replication, translation, and perhaps encapsidation [9,10,11]
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