Identification of antiviral roles for the exon–junction complex and nonsense-mediated decay in flaviviral infection

Abstract

West Nile virus (WNV) is an emerging mosquito-borne flavivirus, related to dengue virus and Zika virus. To gain insight into host pathways involved in WNV infection, we performed a systematic affinity-tag purification mass spectrometry (AP-MS) study to identify 259 WNV-interacting human proteins. RNAi screening revealed 26 genes that both interact with WNV proteins and influence WNV infection. We found that WNV, dengue and Zika virus capsids interact with a conserved subset of proteins that impact infection. These include the exon-junction complex (EJC) recycling factor, PYM1, which is antiviral against all three viruses. The EJC has roles in nonsense-mediated decay (NMD), and we found that both the EJC and NMD are antiviral and the EJC protein RBM8A directly binds WNV RNA. To counteract this, flavivirus infection inhibits NMD and the capsid-PYM1 interaction interferes with EJC protein function and localization. Depletion of PYM1 attenuates RBM8A binding to viral RNA, suggesting that WNV sequesters PYM1 to protect viral RNA from decay. Together, these data suggest a complex interplay between the virus and host in regulating NMD and the EJC.

A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing

“…Along with SARS-CoV-2, we have previously utilized global affinity purification-mass spectrometry (AP-MS) analysis to map the host-pathogen interfaces of a number of human pathogens including Ebola 22 23 . Excitingly, we have uncovered both shared and unique mechanisms in which these pathogens co-opt the host machinery during the course of infection.…”

“…3). We studied the interacting human proteins in regards to their cell biology, anatomical expression patterns, expression changes during SARS-CoV-2 infection 21 and in relation to other maps of pathogen interacting proteins 19,[22][23][24][25][26][27][28][29][30] (Fig. 2a).…”

“…We compared our SARS-CoV-2 interaction map with those derived for 10 other pathogens ( Fig. 2e), identifying West Nile Virus (WNV) 23 and Mycobacterium tuberculosis (Mtb) 27 as having the most similar host protein interaction partners. Like SARS, these distinct pathogens are known to be associated with pulmonary conditions, indicating that they may have converged on similar mechanisms of hijacking of the cell.…”

The Multifunctional Long-Distance Movement Protein of Pea Enation Mosaic Virus 2 Protects Viral and Host Transcripts from Nonsense-Mediated Decay

“…Viral proteins from HTLV-1, MHV, ZIKV, HCV, and CaMV confer NMD resistance by directly targeting NMD or RNA decay factors (e.g., UPF1 or the EJC) (15,16,25,29,30). However, evidence of viral proteins directly binding to viral (or nonviral) transcripts and conferring NMD resistance is limited.…”

“…The genomic organization of many RNA viruses results in extensive 3= UTRs, since translation of the genomic RNA (gRNA) 5=-proximal open reading frame (ORF) often terminates upstream of ORFs that are expressed from subgenomic RNAs (sgRNAs). UPF1 overexpression is detrimental to RNA viruses (13), and diverse viruses benefit from UPF1 knockdown (14)(15)(16). Although unspliced RNA virus transcripts are targeted by NMD in an EJC-independent manner (17), EJC components (MAGOH, PYM1, and RBM8A) were recently found to have antiviral activity against flaviviruses West Nile virus and Zika virus (ZIKV) (15).…”