The conserved stem-loop II structure at the 3' untranslated region of Japanese encephalitis virus genome is required for the formation of subgenomic flaviviral RNA

Flaviviruses accumulate abundant subgenomic RNA (sfRNA) in infected cells. It has been reported that sfRNA results from stalling of host 5'-to-3' exoribonuclease XRN1 at the highly structured RNA of the 3' untranslated region (UTR). Although XRN1 digestion of a 3'-terminal 800-nt...

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Published in:PloS one 2018-07, Vol.13 (7), p.e0201250
Main Authors: Chen, Yi-Shiuan, Fan, Yi-Hsin, Tien, Chih-Feng, Yueh, Andrew, Chang, Ruey-Yi
Format: Article
Language:English
Subjects:
3' Untranslated regions
Accumulation
Biology and life sciences
Cloning
Dengue fever
Diagnosis
DNA-directed RNA polymerase
Encephalitis
Genetic aspects
Genomes
Infections
Japanese encephalitis
Life sciences
Medicine and health sciences
Mosquitoes
Mutagenesis
Pathogenesis
Plasmids
Proteins
Research and analysis methods
Ribonuclease
Ribonucleic acid
RNA
RNA-directed RNA polymerase
Stalling
Transcription
Transcription (Genetics)
Vector-borne diseases
Virology
Viruses
West Nile virus
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Summary:Flaviviruses accumulate abundant subgenomic RNA (sfRNA) in infected cells. It has been reported that sfRNA results from stalling of host 5'-to-3' exoribonuclease XRN1 at the highly structured RNA of the 3' untranslated region (UTR). Although XRN1 digestion of a 3'-terminal 800-nt RNA could stall at a position to generate the sfRNA in vitro, we found that knocking out XRN1 had no effect on the accumulation of sfRNA in Japanese encephalitis virus (JEV) infected cells. Mutagenesis studies revealed that the stemloop II (SLII) at the 3' UTR is required for the accumulation of sfRNA. According to the results of an in vitro RNA-dependent RNA polymerase (RdRp) assay, the (-)10431-10566 RNA fragment, containing the putative promoter on the antigenome for the sfRNA transcription, binds to RdRp protein and exhibits a strong promoter activity. Taken together, our results indicate that the JEV sfRNA could be transcribed initially and then be trimmed by XRN1 or other unidentified exoribonucleases.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0201250