Nanoscale Structure Determination of Murray Valley Encephalitis and Powassan Virus Non-Coding RNAs

Abstract

Viral infections are responsible for numerous deaths worldwide. Flaviviruses, which contain RNA as their genetic material, are one of the most pathogenic families of viruses. There is an increasing amount of evidence suggesting that their 5' and 3' non-coding terminal regions are critical for their survival. Information on their structural features is essential to gain detailed insights into their functions and interactions with host proteins. In this study, the 5' and 3' terminal regions of Murray Valley encephalitis virus and Powassan virus were examined using biophysical and computational modeling methods. First, we used size exclusion chromatography and analytical ultracentrifuge methods to investigate the purity of in-vitro transcribed RNAs. Next, we employed small-angle X-ray scattering techniques to study solution conformation and low-resolution structures of these RNAs, which suggest that the 3' terminal regions are highly extended as compared to the 5' terminal regions for both viruses. Using computational modeling tools, we reconstructed 3-dimensional structures of each RNA fragment and compared them with derived small-angle X-ray scattering low-resolution structures. This approach allowed us to reinforce that the 5' terminal regions adopt more dynamic structures compared to the mainly double-stranded structures of the 3' terminal regions.

Molecular characterization of the RNA-protein complex directing −2/−1 programmed ribosomal frameshifting during arterivirus replicase expression

“…We utilized the DAMMIN program ( 50 ) to calculate 20 models for the nsp1β:PCBP2:nucleic acid complex, as described earlier ( 51 , 52 ). The χ 2 values in each case were ∼1.3, representing a good agreement between the experimentally collected and low-resolution structure–derived data ( Table 1 ), as presented in Fig.…”

An African tick flavivirus forming an independent clade exhibits unique exoribonuclease-resistant RNA structures in the genomic 3′-untranslated region

“…5 a). The overall composition of the 5′-UTR resembles that of other flaviviruses 43 , 44 with an extended SLA side-stem loop characteristic of TBFVs (unpublished data). Similarly, the MPFV 3′-UTR consists of a set of functional elements that are organized into three domains and exhibit structural homology to known elements within other flaviviruses.…”

An African Tick Flavivirus Forming an Independent Clade Exhibits Unique Exoribonuclease-Resistant RNA Structures in the Genomic 3′-Untranslated Region

“…5a). The overall composition of the 5′-UTR resembles that of other aviviruses 43,44 with an extended SLA side-stem loop characteristic of TBFVs (unpublished data). Similarly, the MPFV 3′-UTR consists of a set of functional elements that are organized into three domains and exhibit structural homology to known elements within other aviviruses.…”