Dengue and Zika Virus 5′ Untranslated Regions Harbor Internal Ribosomal Entry Site Functions

Abstract

The Flavivirus genus of the Flaviviridae family encompasses numerous enveloped plus-strand RNA viruses. Dengue virus (DENV), a flavivirus, is the leading cause of serious arthropod-borne disease globally. The genomes of DENV, like the genomes of yellow fever virus (YFV), West Nile fever virus (WNV), or Zika virus (ZIKV), control their translation by a 5′-terminal capping group. Three other genera of Flaviviridae are remarkable because their viruses use internal ribosomal entry sites (IRESs) to control translation, and they are not arthropod transmitted. In 2006, E. Harris’ group published work suggesting that DENV RNA does not stringently need a cap for translation. They proposed that instead DENV translation is controlled by an interplay between 5′ and 3′ termini. Here we present evidence that the DENV or ZIKV 5′ untranslated regions (5′-UTRs) alone have IRES competence. This conclusion is based, first, on the observation that uncapped monocistronic mRNAs 5′ terminated with the DENV or ZIKV 5′-UTRs can efficiently direct translation of a reporter gene in BHK and C6/36 cells and second, that either 5′-UTR placed between two reporter genes can efficiently induce expression of the downstream gene in BHK cells but not in C6/36 cells. These experiments followed observations that uncapped DENV/ZIKV genomic transcripts, 5′ terminated with pppAN… or GpppAN…, can initiate infections of mammalian (BHK) or mosquito (C6/36) cells. IRES competence of the 5′-UTRs of DENV/ZIKV raises many open questions regarding the biology and control, as well as the evolution, of insect-borne flaviviruses. IMPORTANCE Members of the genus Flavivirus of Flaviviridae are important human pathogens of great concern because they cause serious diseases, sometimes death, in human populations living in tropical, subtropical (dengue virus [DENV], Zika virus [ZIKV], and yellow fever virus), or moderate climates (West Nile virus). Flaviviruses are known to control their translation by a cap-dependent mechanism. We have observed, however, that the uncapped genomes of DENV or ZIKV can initiate infection of mammalian and insect cells. We provide evidence that the short 5′ untranslated region (5′-UTR) of DENV or ZIKV genomes can fulfill the function of an internal ribosomal entry site (IRES). This strategy frees these organisms from the cap-dependent mechanism of gene expression at an as yet unknown stage of proliferation. The data raise new questions about the biology and evolution of flaviviruses, possibly leading to new controls of flavivirus disease.

Discordant Activity of Kaempferol Towards Dengue Virus and Japanese Encephalitis Virus

“…IRES sequences allow cap-independent translation under certain conditions, including cellular stress (reviewed in [28]). IRES sequences were originally identified in viruses [29,30], and since then a number of viruses including DENV and ZIKV have been shown to have functional IRES sequences [31]. However, to date we have been unable to find reports of a functional IRES sequence in JEV.…”

Norovirus infection results in eIF2α independent host translation shut-off and remodels the G3BP1 interactome evading stress granule formation

“…This is reminiscent of the uncoupling of translational suppression from cellular stress responses observed during flavivirus infection, with the difference that DENV and ZIKV infection antagonize eIF2α phosphorylation [79]. Since flavivirus and MNV infection results in the activation of the p38-Mnk1 signaling cascade to regulate eIF4E activity, and PABP activity for MNV, and given that both flavivirus and calicivirus translation are driven by cap-independent translation mechanisms, we propose that the suppression of the host translation by targeting the cap-binding complex, rather than through eIF2α activity, could confer a selective advantages to maintain viral translation in conditions where global translation is impaired [37,40,45,79,80]. Noticeably, it has also been reported that some forms of stress lead to a phosphorylation of eIF2α correlating with only moderate translation shut-off and without any SG formation [53,54].…”

A memory of RPS25 loss drives resistance phenotypes

“…Given the prior connection of RPS25 to IRES-mediated translation events, one interpretation from the potent DENV resistance phenotype of RPS25-deficient cells is that DENV utilizes a specialized translation mechanism despite the presence of a cap on its gRNA (Hafirassou et al, 2017). Such an interpretation may be supported by the observation that DENV translation can operate under cellular conditions where cap-dependent translation is inhibited (Edgil et al, 2006), and the recent suggestion that the DENV and ZIKV 5' untranslated regions harbor certain IRES properties (Song et al, 2019).…”