The 5' and 3' Untranslated Regions of the Japanese Encephalitis Virus (JEV): Molecular Genetics and Higher Order Structures.

Hong Liu,Guodong Liang,Jun Zhang,Yuzhen Niu

doi:10.3389/fmicb.2021.730045

Abstract

The untranslated region (UTRs) of viral genome are important for viral replication and immune modulation. Japanese encephalitis virus (JEV) is the most significant cause of epidemic encephalitis worldwide. However, little is known regarding the characterization of the JEV UTRs. Here, systematic analyses of the UTRs of JEVs isolated from a variety of hosts worldwide spanning about 80 years were made. All the important cis-acting elements and structures were compared with other mosquito-borne Flaviviruses [West Nile virus (WNV), Yellow fever virus (YFV), Zika virus (ZIKV), Dengue virus (DENV)] and annotated in detail in the UTRs of different JEV genotypes. Our findings identified the JEV-specific structure and the sequence motif with unique JEV feature. (i) The 3’ dbsHP was identified as a small hairpin located in the DB region in the 3′ UTR of JEV, with the structure highly conserved among the JEV genotypes. (ii) The spacer sequence UARs of JEV consist of four discrete spacer sequences, whereas the UARs of other mosquito-borne Flaviviruses are continuous sequences. In addition, repetitive elements have been discovered in the UTRs of mosquito-borne Flaviviruses. The lengths, locations, and numbers of the repetitive elements of JEV also differed from other Flaviviruses (WNV, YFV, ZIKV, DENV). A 300 nt-length region located at the beginning of the 3′ UTR exhibited significant genotypic specificity. This study lays the basis for future research on the relationships between the JEV specific structures and elements in the UTRs, and their important biological function.

Highlights

Flaviviruses are enveloped viruses with 11 kb, positive-sense single-stranded RNA genome containing highly structured 5 and 3 untranslated region (UTRs) between which lies a single open reading frame (ORF) encoding three structural proteins (C-prM-E) and seven non-structural (NS) proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B, NS5) (Sumiyoshi et al, 1987; Liu and Qin, 2020)
This study provides comprehensive and detailed information of the sequence features and the exact sequence composition, position and distribution of the Flavivirus-conserved cis-acting elements in the Japanese encephalitis virus (JEV) UTRs
The 5 and 3 terminal structures of JEV share the general characteristics of Flaviviruses, the reported structures and cis-acting elements of other Flaviviruses are all existed in the UTRs of JEV

Summary

Introduction

Flaviviruses are enveloped viruses with 11 kb, positive-sense single-stranded RNA genome containing highly structured 5 and 3 untranslated region (UTRs) between which lies a single open reading frame (ORF) encoding three structural proteins (C-prM-E) and seven non-structural (NS) proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B, NS5) (Sumiyoshi et al, 1987; Liu and Qin, 2020). Within the 5 UTR, there are several conserved stem-loop (SL) structures These include (i) SLA, which serves as a viral polymerase binding site (Filomatori et al, 2006); and (ii) Stem-loop B (SLB), which contains the upstream of AUG region (5 UAR) (Alvarez et al, 2005) and 5 -UAR-flanking stem (UFS) (Liu et al, 2016) are involved in long-range RNA-RNA interactions and genome replication. Besides the viral genome cyclization-related sequences, 3 UTR has a panel of stem-loop structures that halt XRN1 exoribonuclease digestion This results in the synthesis of sets of subgenomic flaviviral RNA (sfRNA) (Pijlman et al, 2008) which are associated with viral pathogenicity, host adaption, and immune evasion and immune evasion (Moon et al, 2012; Chapman et al, 2014; Filomatori et al, 2017)

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