Identification and Characterization of Two Novel Noda-like Viruses from Rice Plants Showing the Dwarfing Symptom
Nodaviruses are small bipartite RNA viruses and are considered animal viruses. Here, we identified two novel noda-like viruses (referred to as rice-associated noda-like virus 1 (RNLV1) and rice-associated noda-like virus 2 (RNLV2)) in field-collected rice plants showing a dwarfing phenotype through...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-05-01
|
| Series: | Viruses |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1999-4915/14/6/1159 |
| _version_ | 1797481517146963968 |
|---|---|
| author | Yi Xie Shuai Fu Li Xie Yaqin Wang Mengji Cao Xueping Zhou Jianxiang Wu |
| author_facet | Yi Xie Shuai Fu Li Xie Yaqin Wang Mengji Cao Xueping Zhou Jianxiang Wu |
| author_sort | Yi Xie |
| collection | DOAJ |
| description | Nodaviruses are small bipartite RNA viruses and are considered animal viruses. Here, we identified two novel noda-like viruses (referred to as rice-associated noda-like virus 1 (RNLV1) and rice-associated noda-like virus 2 (RNLV2)) in field-collected rice plants showing a dwarfing phenotype through RNA-seq. RNLV1 genome consists of 3335 nt RNA1 and 1769 nt RNA2, and RNLV2 genome consists of 3279 nt RNA1 and 1525 nt RNA2. Three conserved ORFs were identified in each genome of the two novel viruses, encoding an RNA-dependent RNA polymerase, an RNA silencing suppressor, and a capsid protein, respectively. The results of sequence alignment, protein domain prediction, and evolutionary analysis indicate that these two novel viruses are clearly different from the known nodaviruses, especially the CPs. We have also determined that the B2 protein encoded by the two new noda-like viruses can suppress RNA silencing in plants. Two reverse genetic systems were constructed and used to show that RNLV1 RNA1 can replicate in plant cells and RNLV1 can replicate in insect Sf9 cells. We have also found two unusual peptidase family A21 domains in the RNLV1 CP, and RNLV1 CP can self-cleave in acidic environments. These findings provide new knowledge of novel nodaviruses. |
| first_indexed | 2024-03-09T22:15:44Z |
| format | Article |
| id | doaj.art-ddd9ead5638446ca937c5e9294c8e3b7 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-09T22:15:44Z |
| publishDate | 2022-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-ddd9ead5638446ca937c5e9294c8e3b72023-11-23T19:24:36ZengMDPI AGViruses1999-49152022-05-01146115910.3390/v14061159Identification and Characterization of Two Novel Noda-like Viruses from Rice Plants Showing the Dwarfing SymptomYi Xie0Shuai Fu1Li Xie2Yaqin Wang3Mengji Cao4Xueping Zhou5Jianxiang Wu6State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, ChinaState Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, ChinaAnalysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou 310058, ChinaState Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, ChinaNational Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, ChinaState Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, ChinaState Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, ChinaNodaviruses are small bipartite RNA viruses and are considered animal viruses. Here, we identified two novel noda-like viruses (referred to as rice-associated noda-like virus 1 (RNLV1) and rice-associated noda-like virus 2 (RNLV2)) in field-collected rice plants showing a dwarfing phenotype through RNA-seq. RNLV1 genome consists of 3335 nt RNA1 and 1769 nt RNA2, and RNLV2 genome consists of 3279 nt RNA1 and 1525 nt RNA2. Three conserved ORFs were identified in each genome of the two novel viruses, encoding an RNA-dependent RNA polymerase, an RNA silencing suppressor, and a capsid protein, respectively. The results of sequence alignment, protein domain prediction, and evolutionary analysis indicate that these two novel viruses are clearly different from the known nodaviruses, especially the CPs. We have also determined that the B2 protein encoded by the two new noda-like viruses can suppress RNA silencing in plants. Two reverse genetic systems were constructed and used to show that RNLV1 RNA1 can replicate in plant cells and RNLV1 can replicate in insect Sf9 cells. We have also found two unusual peptidase family A21 domains in the RNLV1 CP, and RNLV1 CP can self-cleave in acidic environments. These findings provide new knowledge of novel nodaviruses.https://www.mdpi.com/1999-4915/14/6/1159ricenodavirusnoda-like virusreverse genetic systemRNA silencing suppressor |
| spellingShingle | Yi Xie Shuai Fu Li Xie Yaqin Wang Mengji Cao Xueping Zhou Jianxiang Wu Identification and Characterization of Two Novel Noda-like Viruses from Rice Plants Showing the Dwarfing Symptom Viruses rice nodavirus noda-like virus reverse genetic system RNA silencing suppressor |
| title | Identification and Characterization of Two Novel Noda-like Viruses from Rice Plants Showing the Dwarfing Symptom |
| title_full | Identification and Characterization of Two Novel Noda-like Viruses from Rice Plants Showing the Dwarfing Symptom |
| title_fullStr | Identification and Characterization of Two Novel Noda-like Viruses from Rice Plants Showing the Dwarfing Symptom |
| title_full_unstemmed | Identification and Characterization of Two Novel Noda-like Viruses from Rice Plants Showing the Dwarfing Symptom |
| title_short | Identification and Characterization of Two Novel Noda-like Viruses from Rice Plants Showing the Dwarfing Symptom |
| title_sort | identification and characterization of two novel noda like viruses from rice plants showing the dwarfing symptom |
| topic | rice nodavirus noda-like virus reverse genetic system RNA silencing suppressor |
| url | https://www.mdpi.com/1999-4915/14/6/1159 |
| work_keys_str_mv | AT yixie identificationandcharacterizationoftwonovelnodalikevirusesfromriceplantsshowingthedwarfingsymptom AT shuaifu identificationandcharacterizationoftwonovelnodalikevirusesfromriceplantsshowingthedwarfingsymptom AT lixie identificationandcharacterizationoftwonovelnodalikevirusesfromriceplantsshowingthedwarfingsymptom AT yaqinwang identificationandcharacterizationoftwonovelnodalikevirusesfromriceplantsshowingthedwarfingsymptom AT mengjicao identificationandcharacterizationoftwonovelnodalikevirusesfromriceplantsshowingthedwarfingsymptom AT xuepingzhou identificationandcharacterizationoftwonovelnodalikevirusesfromriceplantsshowingthedwarfingsymptom AT jianxiangwu identificationandcharacterizationoftwonovelnodalikevirusesfromriceplantsshowingthedwarfingsymptom |