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...
Saved in:
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2018-01-01
|
| Series: | PLoS ONE |
| Online Access: | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0201250&type=printable |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850045119983517696 |
|---|---|
| author | Yi-Shiuan Chen Yi-Hsin Fan Chih-Feng Tien Andrew Yueh Ruey-Yi Chang |
| author_facet | Yi-Shiuan Chen Yi-Hsin Fan Chih-Feng Tien Andrew Yueh Ruey-Yi Chang |
| author_sort | Yi-Shiuan Chen |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-661c236b08ae44b1b3e24a6e2bd01aec |
| institution | DOAJ |
| issn | 1932-6203 |
| language | English |
| publishDate | 2018-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-661c236b08ae44b1b3e24a6e2bd01aec2025-08-20T02:54:47ZengPublic Library of Science (PLoS)PLoS ONE1932-62032018-01-01137e020125010.1371/journal.pone.0201250The conserved stem-loop II structure at the 3' untranslated region of Japanese encephalitis virus genome is required for the formation of subgenomic flaviviral RNA.Yi-Shiuan ChenYi-Hsin FanChih-Feng TienAndrew YuehRuey-Yi ChangFlaviviruses 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.https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0201250&type=printable |
| spellingShingle | Yi-Shiuan Chen Yi-Hsin Fan Chih-Feng Tien Andrew Yueh Ruey-Yi Chang 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. PLoS ONE |
| title | 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. |
| title_full | 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. |
| title_fullStr | 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. |
| title_full_unstemmed | 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. |
| title_short | 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. |
| title_sort | conserved stem loop ii structure at the 3 untranslated region of japanese encephalitis virus genome is required for the formation of subgenomic flaviviral rna |
| url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0201250&type=printable |
| work_keys_str_mv | AT yishiuanchen theconservedstemloopiistructureatthe3untranslatedregionofjapaneseencephalitisvirusgenomeisrequiredfortheformationofsubgenomicflaviviralrna AT yihsinfan theconservedstemloopiistructureatthe3untranslatedregionofjapaneseencephalitisvirusgenomeisrequiredfortheformationofsubgenomicflaviviralrna AT chihfengtien theconservedstemloopiistructureatthe3untranslatedregionofjapaneseencephalitisvirusgenomeisrequiredfortheformationofsubgenomicflaviviralrna AT andrewyueh theconservedstemloopiistructureatthe3untranslatedregionofjapaneseencephalitisvirusgenomeisrequiredfortheformationofsubgenomicflaviviralrna AT rueyyichang theconservedstemloopiistructureatthe3untranslatedregionofjapaneseencephalitisvirusgenomeisrequiredfortheformationofsubgenomicflaviviralrna AT yishiuanchen conservedstemloopiistructureatthe3untranslatedregionofjapaneseencephalitisvirusgenomeisrequiredfortheformationofsubgenomicflaviviralrna AT yihsinfan conservedstemloopiistructureatthe3untranslatedregionofjapaneseencephalitisvirusgenomeisrequiredfortheformationofsubgenomicflaviviralrna AT chihfengtien conservedstemloopiistructureatthe3untranslatedregionofjapaneseencephalitisvirusgenomeisrequiredfortheformationofsubgenomicflaviviralrna AT andrewyueh conservedstemloopiistructureatthe3untranslatedregionofjapaneseencephalitisvirusgenomeisrequiredfortheformationofsubgenomicflaviviralrna AT rueyyichang conservedstemloopiistructureatthe3untranslatedregionofjapaneseencephalitisvirusgenomeisrequiredfortheformationofsubgenomicflaviviralrna |