Molecular characterization and In Vitro synthesis of infectious RNA of a Turnip vein-clearing virus isolated from Alliaria petiolata in Hungary

Autoři: Tamás Tóth aff001;  Péter Gyula aff001;  Pál Salamon aff002;  Szilvia Kis aff001;  Anita Sós-Hegedűs aff001;  György Szittya aff001
Působiště autorů: Department of Plant Biotechnology, Agricultural Biotechnology Institute, National Agricultural Research and Innovation Center, Gödöllő, Hungary aff001;  Department of Genetics, Agricultural Biotechnology Institute, National Agricultural Research and Innovation Center, Gödöllő, Hungary aff002
Vyšlo v časopise: PLoS ONE 14(10)
Kategorie: Research Article
doi: 10.1371/journal.pone.0224398


A tobamovirus was isolated from leaves of Alliaria petiolata plants, showing vein-clearing, interveinal chlorosis, and moderate deformation. Host range experiments revealed a high similarity of isolate ApH both to ribgrass mosaic viruses and turnip vein-clearing viruses. The complete nucleotide sequence of the viral genome was determined. The genomic RNA is composed of 6312 nucleotides and contains four open reading frames (ORF). ORF1 is 3324 nt-long and encodes a polypeptide of about 125.3 kDa. The ORF1 encoded putative replication protein contains an Alphavirus-like methyltransferase domain. ORF2 is 4806 nt-long and encodes a polypeptide of about 182 kDa. The ORF2 encoded putative replication protein contains an RNA-dependent RNA polymerase, catalytic domain. ORF3 encodes the putative cell-to-cell movement protein with a molecular weight of 30.1 kDa. ORF4 overlaps with ORF3 and encodes the coat protein with a size of 17.5 kDa. Sequence comparisons revealed that the ApH isolate has the highest similarity to turnip vein-clearing viruses and should be considered an isolate of Turnip vein-clearing virus (TVCV). This is the first report on the occurrence of TVCV in Hungary. In vitro transcripts prepared from the full-length cDNA clone of TVCV-ApH were highly infectious and induced typical symptoms characteristic to the original isolate of the virus. Since infectious clones of TVCV-ApH and crTMV (another isolate of TVCV) markedly differed in respect to recovery phenotype in Arabidopsis thaliana, it is feasible to carry out gene exchange or mutational studies to determine viral factors responsible for the symptom recovery phenotype.

Klíčová slova:

Arabidopsis thaliana – Phylogenetic analysis – Plant genomics – RNA viruses – Viral genomics – Viral replication – Nicotiana – Plant viral pathogens


1. Lefkowitz EJ, Dempsey DM, Hendrickson RC, Orton RJ, Siddell SG, Smith DB. Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV). Nucleic Acids Res. 2018;46: D708–D717. doi: 10.1093/nar/gkx932 29040670

2. Ishibashi K, Ishikawa M. Replication of Tobamovirus RNA. Annu Rev Phytopathol. 2016;54: 55–78. doi: 10.1146/annurev-phyto-080615-100217 27296148

3. Csorba T, Bovi A, Dalmay T, Burgyán J. The p122 subunit of Tobacco mosaic virus replicase is a potent silencing suppressor and compromises both small interfering RNA- and microRNA-mediated pathways. J Virol. 2007;81: 11768–11780. doi: 10.1128/JVI.01230-07 17715232

4. Vogler H, Akbergenov R, Shivaprasad PV, Dang V, Fasler M, Kwon M-O, et al. Modification of small RNAs associated with suppression of RNA silencing by tobamovirus replicase protein. J Virol. 2007;81: 10379–10388. doi: 10.1128/JVI.00727-07 17634237

5. Ding XS, Liu J, Cheng N-H, Folimonov A, Hou Y-M, Bao Y, et al. The Tobacco mosaic virus 126-kDa protein associated with virus replication and movement suppresses RNA silencing. Mol Plant-Microbe Interact MPMI. 2004;17: 583–592. doi: 10.1094/MPMI.2004.17.6.583 15195941

6. Chavan RR, Pearson MN. Molecular characterisation of a novel recombinant Ribgrass mosaic virus strain FSHS. Virol J. 2016;13: 29. doi: 10.1186/s12985-016-0487-5 26891841

7. Gibbs AJ, Wood J, Garcia-Arenal F, Ohshima K, Armstrong JS. Tobamoviruses have probably co-diverged with their eudicotyledonous hosts for at least 110 million years. Virus Evol. 2015;1: vev019. doi: 10.1093/ve/vev019 27774289

8. Heinze C, Lesemann D-E, Ilmberger N, Willingmann P, Adam G. The phylogenetic structure of the cluster of tobamovirus species serologically related to ribgrass mosaic virus (RMV) and the sequence of streptocarpus flower break virus (SFBV). Arch Virol. 2006;151: 763–774. doi: 10.1007/s00705-005-0640-8 16328151

9. Lartey RT. Occurrence of a vein-clearing tobamovirus in turnip. Plant Dis. 1993;77: 21. doi: 10.1094/PD-77-0021

10. Lartey RT, Lane LC, Melcher U. Electron microscopic and molecular characterization of turnip vein-clearing virus. Arch Virol. 1994;138: 287–298. doi: 10.1007/bf01379132 7998835

11. Dorokhov IL, Ivanov PA, Novikov VK, Yefimov VA, Atabekov IG. [Tobamovirus of cruciferous plants: nucleotide sequence of genes of the transport protein, capsid protein, and 3’-terminal untranslated region]. Dokl Akad Nauk. 1993;332: 518–522. 8260923

12. Dorokhov YL, Ivanov PA, Novikov VK, Agranovsky AA, Morozov SY, Efimov VA, et al. Complete nucleotide sequence and genome organization of a tobamovirus infecting cruciferae plants. FEBS Lett. 1994;350: 5–8. doi: 10.1016/0014-5793(94)00721-7 7545946

13. Dorokhov IL, Ivanov PA, Novikov VK, Efimov VA, Atabekov IG. [Tobamovirus of the Cruciferae family: nucleotide sequence of the 5’-untranslated region and nonstructural protein genes controlling replication viral genome]. Dokl Akad Nauk. 1994;335: 792–798. 8025551

14. Lartey RT, Voss TC, Melcher U. Completion of a cDNA sequence from a tobamovirus pathogenic to crucifers. Gene. 1995;166: 331–332. doi: 10.1016/0378-1119(95)00674-5 8543186

15. Melcher U. Turnip vein-clearing virus, from pathogen to host expression profile. Mol Plant Pathol. 2003;4: 133–140. doi: 10.1046/j.1364-3703.2003.00159.x 20569373

16. Chapman SN. Tobamovirus isolation and RNA extraction. In: Foster GD, Taylor SC, editors. Plant Virology Protocols: From Virus Isolation to Transgenic Resistance. Totowa, NJ: Humana Press; 1998. pp. 123–129. doi: 10.1385/0-89603-385-6:123

17. Huang X, Madan A. CAP3: A DNA sequence assembly program. Genome Res. 1999;9: 868–877. doi: 10.1101/gr.9.9.868 10508846

18. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215: 403–410. doi: 10.1016/S0022-2836(05)80360-2 2231712

19. Szittya G, Molnár A, Silhavy D, Hornyik C, Burgyán J. Short defective interfering RNAs of tombusviruses are not targeted but trigger post-transcriptional gene silencing against their helper virus. Plant Cell. 2002;14: 359–372. doi: 10.1105/tpc.010366 11884680

20. Szittya G, Salamon P, Burgyán J. The complete nucleotide sequence and synthesis of infectious RNA of genomic and defective interfering RNAs of TBSV-P. Virus Res. 2000;69: 131–136. doi: 10.1016/s0168-1702(00)00178-7 11018282

21. Baksa I, Nagy T, Barta E, Havelda Z, Várallyay É, Silhavy D, et al. Identification of Nicotiana benthamiana microRNAs and their targets using high throughput sequencing and degradome analysis. BMC Genomics. 2015;16: 1025. doi: 10.1186/s12864-015-2209-6 26626050

22. Kis S, Salamon P, Kis V, Szittya G. Molecular characterization of a beet ringspot nepovirus isolated from Begonia ricinifolia in Hungary. Arch Virol. 2017;162: 3559–3562. doi: 10.1007/s00705-017-3521-z 28812162

23. Brister JR, Ako-Adjei D, Bao Y, Blinkova O. NCBI viral genomes resource. Nucleic Acids Res. 2015;43: D571–577. doi: 10.1093/nar/gku1207 25428358

24. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32: 1792–1797. doi: 10.1093/nar/gkh340 15034147

25. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4: 406–425. doi: 10.1093/oxfordjournals.molbev.a040454 3447015

26. Kumar S, Stecher G, Li M, Knyaz C, Tamura K, Battistuzzi FU. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol. 2018;35: 1547–1549. doi: 10.1093/molbev/msy096 29722887

27. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evol Int J Org Evol. 1985;39: 783–791. doi: 10.1111/j.1558-5646.1985.tb00420.x 28561359

28. Tamura K, Kumar S. Evolutionary distance estimation under heterogeneous substitution pattern among lineages. Mol Biol Evol. 2002;19: 1727–1736. doi: 10.1093/oxfordjournals.molbev.a003995 12270899

29. Mitchell AL, Attwood TK, Babbitt PC, Blum M, Bork P, Bridge A, et al. InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Res. 2019;47: D351–D360. doi: 10.1093/nar/gky1100 30398656

30. Lartey RT, Voss TC, Melcher U. Tobamovirus evolution: gene overlaps, recombination, and taxonomic implications. Mol Biol Evol. 1996;13: 1327–1338. doi: 10.1093/oxfordjournals.molbev.a025579 8952077

31. Kørner CJ, Pitzalis N, Peña EJ, Erhardt M, Vazquez F, Heinlein M. Crosstalk between PTGS and TGS pathways in natural antiviral immunity and disease recovery. Nat Plants. 2018;4: 157–164. doi: 10.1038/s41477-018-0117-x 29497161

Článek vyšel v časopise


2019 Číslo 10