Abstract
To understand how RNA dynamics is regulated and connected to its function, we investigate the folding, conformational dynamics and robustness of Xrn1 resistance of a set of flaviviral xrRNAs using SAXS, smFRET and in vitro enzymatic assays. Flaviviral xrRNAs form discrete ring-like 3D structures, in which the length of a conserved long-range pseudoknot (PK2) ranges from 2 bp to 7 bp. We find that xrRNAs’ folding, conformational dynamics and Xrn1 resistance are strongly correlated and highly Mg2+-dependent, furthermore, the Mg2+-dependence is modulated by PK2 length variations. xrRNAs with long PK2 require less Mg2+ to stabilize their folding, exhibit reduced conformational dynamics and strong Xrn1 resistance even at low Mg2+, and tolerate mutations at key tertiary motifs at high Mg2+, which generally are destructive to xrRNAs with short PK2. These results demonstrate an unusual regulatory mechanism of RNA dynamics providing insights into the functions and future biomedical applications of xrRNAs.
Highlights
To understand how RNA dynamics is regulated and connected to its function, we investigate the folding, conformational dynamics and robustness of Xrn[1] resistance of a set of flaviviral xrRNAs using small-angle X-ray scattering (SAXS), single-molecule Fluorescence Resonance Energy Transfer (smFRET) and in vitro enzymatic assays
Elements that block the processive exoribonucleolytic degradation of RNA9. xrRNAs were originally identified at the beginning of the 3′ untranslated region (UTR) of genomic RNAs of several mosquito-borne flaviviruses (MBFVs), including Dengue virus (DENV), Zika virus (ZIKV), and West Nile virus (WNV), which enable the generation of noncoding subgenomic flaviviral RNAs in infected cells linking to pathogenicity and immune evasion[10,11,12,13,14]
To test how PK2 length variation affects the folding of flaviviral xrRNAs, SAXS measurements were performed for a set of 11 flaviviral xrRNAs in the presence of 5 mM Mg2+ or 5 mM EDTA, respectively
Summary
To understand how RNA dynamics is regulated and connected to its function, we investigate the folding, conformational dynamics and robustness of Xrn[1] resistance of a set of flaviviral xrRNAs using SAXS, smFRET and in vitro enzymatic assays. XrRNAs with long PK2 require less Mg2+ to stabilize their folding, exhibit reduced conformational dynamics and strong Xrn[1] resistance even at low Mg2+, and tolerate mutations at key tertiary motifs at high Mg2+, which generally are destructive to xrRNAs with short PK2. These results demonstrate an unusual regulatory mechanism of RNA dynamics providing insights into the functions and future biomedical applications of xrRNAs. Many RNAs, including the noncoding RNAs, the untranslated and/or coding regions of viral genomic RNAs, fold into complex and unique 3D structures[1,2,3]. As PK1, PK2, and J2/3 in xrRNAs are critical for maintaining the ring-like 3D architecture and/or mechanical anisotropy[18,22], how PK2 length variation and these tertiary motifs modulate xrRNAs’s folding, conformational dynamics and the robustness of Xrn[1] resistance is intriguing
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
