Identification and characterization of host proteins bound to dengue virus 3′ UTR reveal an antiviral role for quaking proteins

Abstract

The four dengue viruses (DENV1-4) are rapidly reemerging infectious RNA viruses. These positive-strand viral genomes contain structured 3′ untranslated regions (UTRs) that interact with various host RNA binding proteins (RBPs). These RBPs are functionally important in viral replication, pathogenesis, and defense against host immune mechanisms. Here, we combined RNA chromatography and quantitative mass spectrometry to identify proteins interacting with DENV1-4 3′ UTRs. As expected, RBPs displayed distinct binding specificity. Among them, we focused on quaking (QKI) because of its preference for the DENV4 3′ UTR (DENV-4/SG/06K2270DK1/2005). RNA immunoprecipitation experiments demonstrated that QKI interacted with DENV4 genomes in infected cells. Moreover, QKI depletion enhanced infectious particle production of DENV4. On the contrary, QKI did not interact with DENV2 3′ UTR, and DENV2 replication was not affected consistently by QKI depletion. Next, we mapped the QKI interaction site and identified a QKI response element (QRE) in DENV4 3′ UTR. Interestingly, removal of QRE from DENV4 3′ UTR abolished this interaction and increased DENV4 viral particle production. Introduction of the QRE to DENV2 3′ UTR led to QKI binding and reduced DENV2 infectious particle production. Finally, reporter assays suggest that QKI reduced translation efficiency of viral RNA. Our work describes a novel function of QKI in restricting viral replication.

Fragile X mental retardation protein is a Zika virus restriction factor that is antagonized by subgenomic flaviviral RNA

“…Besides interferon responses, there are intrinsic restriction factors that recognize viral components and block replication ( Yan and Chen, 2012 ). For flaviviruses, a few intrinsic anti-viral factors have been described: YTHDF1-3 proteins that bind methylated RNA and regulate stability, were reported to interact with ZIKV RNA and inhibit infection ( Lichinchi et al, 2016 ); YB-1 and QKI bind to the DENV 3′ UTR and repress DENV RNA translation ( Liao et al, 2018 ; Paranjape and Harris, 2007 ); similarly, FBP1 blocks translation of JEV through interacting with untranslated regions of JEV RNA ( Chien et al, 2011 ). The association of these antiviral factors with the viral genome and their functional consequences have only been observed in cell culture and it remains to be seen whether or not these will be validated in vivo.…”

“…Synthetic DNA fragments corresponding to the complete 3′ UTRs of African (strain MR766, accession number KX377335.1) and pandemic Asian-lineage ZIKV (PRVABC59 strain, KX377337.1) were obtained from IDT (Integrated DNA Technologies) and cloned into pcDNA3.1(+) plasmid containing tobramycin aptamer ( Liao et al, 2018 ). As a control RNA we used a sequence corresponding to the DENV NS2A sequence as previously reported ( Manokaran et al, 2015 ).…”

Zika Virus Subverts Stress Granules to Promote and Restrict Viral Gene Expression

“…Interestingly, the role of G3BP1 varies in viral infections from limiting alphavirus replication (66)(67)(68) to interacting with the HCV RdRp NS5B and enhancing HCV infectious virus production (42,69,70). In DENV-infected cells, G3BP1 interacts with the small flaviviral RNA (37,71), and sequestration of G3BP1 by the sfRNA was shown to inhibit ISG translation (38). Hou et al, showed that siRNA depletion of G3BP1 decreased ZIKV titers and that G3BP1 also bound ZIKV RNA (39).…”

Universal RNA Secondary Structure Insight Into Mosquito-Borne Flavivirus (MBFV) cis-Acting RNA Biology

“…The length of the AUrich region varies among MBFVGs, with the WNV and MVEV having the longest AU-rich regions (Gritsun and Gould, 2006b). Importantly, the 3 VR contains a succession of hypervariable exonuclease-resistant structures (xRNAs) structures and plays critical roles in virus-host interactions ( Table 3; Pijlman et al, 2008;Roby et al, 2014;Gokhale and Horner, 2017;Chiu et al, 2018;Liao et al, 2018;Soto-Acosta et al, 2018).…”