Molecular and in silico analysis of the coat protein of hibiscus chlorotic ringspot virus isolates

Mosharaf, Nadia; Tabein, Saeid; Mehrabi-Koushki, Mehdi; Hemmati, Seyed Ali; Ghorbani, Abozar

doi:10.48311/jcp.2023.1617

Molecular and in silico analysis of the coat protein of hibiscus chlorotic ringspot virus isolates

https://doi.org/10.48311/jcp.2023.1617

Volume 12, Issue 1
March 2023

Pages 1-13

Document Type : Original Research

Authors

N. Mosharaf ¹

S. Tabein ¹

M. Mehrabi-Koushki ¹

S. A. Hemmati ¹

A. Ghorbani ²

¹ Department of Plant Protection, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran.

² Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI), Karaj, Iran.

Abstract

Hibiscus chlorotic ringspot virus (HCRSV), genus Betacarmovirus, family Tombusviridae, is a common pathogen of hibiscus plants in tropical and subtropical regions. During 2020-2021, leaf samples of Chinese hibiscus Hibiscus rosa-sinensis L. with mottling and chlorotic ring spot symptoms were collected from Ahvaz and Molasani Khuzestan province, southwestern Iran. Total RNA extracted from symptomatic samples was subjected to RT-PCR analysis to amplify the sequence of the coat protein gene (CP) (p38) of HCRSV. Complete (1038 bp) and partial (932 bp) p38 sequences were determined and deposited in the GenBank database. The consensus sequences obtained from CP were compared with those of known isolates using the nBLAST program and phylogenetic analysis. The phylogenetic tree constructed based on the p38 sequences showed different ancestors for Iranian isolates of HCRSV. Additionally, the isolates studied were grouped into clades regardless of their geographic distribution, suggesting that there is no differentiation of population based on location and that populations are interconnected. Recombination analysis based on p38 sequences predicted at least two acceptable recombinant isolates, Ahvaz (Iran) and Israel. In silico prediction of CP structures of isolates involved in recombination events showed low sequence to structure identity between HCRSV isolates. In addition to reporting two new HCRSV isolates from Iran, our work demonstrated that HCRSV exhibits a high genetic variation through recombination and that the classification criterion could be changed from low nucleotide sequence identity to a higher value, along with the structural analysis of betacarmovirus proteins.

Keywords

HCRSV

Coat Protein

Recombination

Tertiary structure

20.1001.1.22519041.2023.12.1.1.9

Subjects

Plant Virology

Adams, M. J., Lefkowitz, E. J., King, A. M. Q., Harrach, B., Harrison, R. L., Knowles, N. J., Kropinski, A. M., Krupovic, M., Kuhn, J. H., Mushegian, A. R., Nibert, M., Sabanadzovic, S., Sanfaçon, H., Siddell, S. G., Simmonds, P., Varsani, A., Zerbini, F. M., Gorbalenya, A. E., and Davison, A. J. 2016. Ratification vote on taxonomic proposals to the international committee on taxonomy of viruses. Archives of Virology, 161: 2921-2949.
Adhab, M., Angel, C., Rodriguez, A., Fereidouni, M., Király, L., Scheets, K., and Schoelz, J. E. 2019. Tracing the lineage of two traits associated with the coat protein of the Tombusviridae: silencing suppression and HR elicitation in Nicotiana species. Viruses, 11(7): 588.
Al-Khayyat, M. Z., and Al-Dabbagh, A. G. 2016. In silico prediction and docking of tertiary structure of LuxI, an inducer synthase of Vibrio fischeri. Reports of Biochemistry and Molecular Biology, 4(2): 66-75.
Ayadi, R., Hanana, M., Mzid, R., Hamrouni, L., Khouja, M. L., and Salhi-Hanachi, A. 2016. Hibiscus Cannabinus L. «Kenaf»: a review paper. Journal of Natural Fibers, 14(4): 1-19.
Brugidou, C., Holt, C., Yassi, M. N., Zhang, S., Beachy, R., and Fauquet, C. 1995. Synthesis of an infectious full-length cDNA clone of rice yellow mottle virus and mutagenesis of the coat protein. Virology, 206(1): 108-115.
Brunt, A. A., and Spence, N. J. 2000. The natural occurrence of Hibiscus chlorotic ringspot virus (Carmovirus; Tombusviridae) in aibika or bele (Abelmoschus manihot) in some South Pacific Island countries. Plant Pathology, 49(6): 798-798.
Cheng, C. P., and Nagy, P. D. 2003. Mechanism of RNA recombination in carmo-and tombusviruses: evidence for template switching by the RNA-dependent RNA polymerase in vitro. Journal of Virology, 77(22): 12033-12047.
Colovos, C., and Yeates, T. O. 1993. Verification of protein structures: patterns of nonbonded atomic interactions. Protein Science, 2(9): 1511-1519.
Darriba, D., Taboada, G. L., Doallo, R., and Posada, D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods, 9: 772.
da Silva, A. B., Wiest, J. M., Paim, M. P., and Girolometto, G. 2014. Caracterização antibacteriana e fitoquímica de flores de Hibiscus rosa-sinensis L. (mimo-de-vênus) e Hibiscus syriacus L. (hibisco-da-síria). Revista do Instituto Adolfo Lutz ,73: 264-271.
Edler, D., Klein, J., Antonelli, A., and Silvestro, D. 2020. raxmlGUI 2.0 beta: A graphical interface and toolkit for phylogenetic analyses using RAxML. Methods in Ecology and Evolution, 12(2): 1-5.
Fuentes, A. L., and Hamilton, R. I. 1993. Failure of long-distance movement of southern bean mosaic virus in a resistant host is correlated with lack of normal virion formation. Journal of General Virology, 74(9): 1903-1910.
Hall, T. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium, 41: 95-98.
Huang, M., Koh, D. C, Weng, L. J., Chang, M. L., Yap, Y. K., Zhang, L., and Wong, S. M. 2000. Complete nucleotide sequence and genome organization of hibiscus chlorotic ringspot virus, a new member of the genus Carmovirus: evidence for the presence and expression of two novel open reading frames. Journal of Virology, 74(7): 3149-3155.
Iki, T., Tschopp, M. A., and Voinnet, O. 2017. Biochemical and genetic functional dissection of the P38 viral suppressor of RNA silencing. RNA, 23(5): 639-654.
Jain, R. K., Smith, K. M., and Culligan, P. J., and Taylor, J. E. 2014. Forecasting energy consumption of multi-family residential buildings using support vector regression: Investigating the impact of temporal and spatial monitoring granularity on performance accuracy. Applied Energy, 123: 168-178.
Jones, D. R., and Behncken, G. M. 1980. Hibiscus chlorotic ringspot, a widespread virus disease in the ornamental Hibiscus rosa-sinensis. Australasian Plant Pathology, 9: 4-5.
Karanfil, A., and Korkmaz, S. 2017. First report of Hibiscus chlorotic ringspot virus in Turkey. New Disease Reports 35: 22.
Lian, S., Lee, J. S., Cho, W. K., Yu, J., Kim, M. K., Choi, H. S., and Kim, K. H. 2013. Phylogenetic and recombination analysis of tomato spotted wilt virus. PloS one, 8: 63380.
Liang, C., Pan, H., Li, H., Zhao, Y., and Feng, Y. 2017. In vitro anticancer activity and cytotoxicity screening of phytochemical extracts from selected traditional Chinese medicinal plants. Journal of the Balkan :union: of Oncology, 22(2): 543-551.
Liu, C., and Huang, Y. 2016. Chinese herbal medicine on cardiovascular diseases and the mechanisms of action. Frontiers in Pharmacology, 7: 469.
Luria, N., Reingold, V., Lachman, O., and Dombrovsky, A. 2013. Full-genome sequence of hibiscus chlorotic ringspot virus from Israel. Genome Announcements, 1(6): e01050-13.
Martin, D., and Rybicki, E. 2000. RDP: detection of recombination amongst aligned sequences. Bioinformatics, 16(6): 562-563.
Meng, C., Chen, J., Peng, J., and Wong, S. M. 2006. Host-induced avirulence of hibiscus chlorotic ringspot virus mutants correlates with reduced gene-silencing suppression activity. Journal of General Virology, 87(2): 451-459.
Meng, C., Chen, J., Ding, S. W., Peng, J., and Wong, S. M. 2008. Hibiscus chlorotic ringspot virus coat protein inhibits trans-acting small interfering RNA biogenesis in Arabidopsis. Journal of General Virology, 89(9): 2349-58.
Navarro, J. A., and Pallás, V. 2017. An update on the intracellular and intercellular trafficking of carmoviruses. Frontiers in Plant Science, 8: 1801.
Niu, S., Gil-Salas, F. M., Tewary, S. K., Samales, A. K., Johnson, J., Swaminathan, K., and Wong, S. M. 2014. Hibiscus chlorotic ringspot virus coat protein is essential for cell-to-cell and long-distance movement but not for viral RNA replication. PloS one, 9(11): 113347.
Olmedo-Velarde, A., Hu, J., and Melzer, M. J. 2021. A virus infecting Hibiscus rosa-sinensis represents an evolutionary link between cileviruses and higreviruses. Frontiers in Microbiology, 12: 660237.
Pérez-Losada, M., Arenas, M., Galán, J. C., Palero, F., and González-Candelas, F. 2015. Recombination in viruses: mechanisms, methods of study, and evolutionary consequences. Infection, Genetics and Evolution, 30: 296-307.
Pourrahim, R., Ghobakhlo, A., and Farzadfar, S. 2013. Biological and molecular detection of Hibiscus chlorotic ringspot virus infecting Hibiscus rosa-sinensis in Iran. Phytopathologia Mediterranea, 52(3): 528-531.
Ramos-González, P. L., Santos, G. F., Chabi-Jesus, C., Harakava, R., Kitajima, E. W., and Freitas-Astúa, J. 2020. Passion fruit green spot virus genome harbors a new orphan orf and highlights the flexibility of the 5′-end of the RNA2 segment across cileviruses. Frontiers in Microbiology, 11: 206.
Ronquist, F., Teslenko, M., Van Der Mark, P., Ayres, D. L., Darling, A., Höhna, S., Larget, B., Liu, L., Suchard, M. A., and Huelsenbeck, J. P. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systemic Biology, 61(3): 539-542.
Spitsin, S., Steplewski, K., Fleysh, N., Belanger, H., Mikheeva, T., Shivprasad, S., Dawson, W., Koprowski, H., and Yusibov, V. 1999. Expression of alfalfa mosaic virus coat protein in tobacco mosaic virus (TMV) deficient in the production of its native coat protein supports long-distance movement of a chimeric TMV. Proceedings of the National Academy of Sciences of the United States of America, 96(5): 2549-2553.
Suzuki, M., Kuwata, S., Kataoka, J., Masuta, C., Nitta, N., and Takanami, Y. 1991. Functional analysis of deletion mutants of cucumber mosaic virus RNA3 using an in vitro transcription system. Virology, 183(1): 106-113.
Sztuba-Solińska, J., Urbanowicz, A., Figlerowicz, M., and Bujarski, J. J. 2011. RNA-RNA recombination in plant virus replication and evolution. Annual Review of Phytopathology, 49: 415-443.
Tang, J., Elliott, D. R., Quinn, B. D., Clover, G. R. G., and Alexander, B. J. R. 2008. Occurrence of Hibiscus chlorotic ringspot virus in Hibiscus spp. in New Zealand. Plant Disease, 92(9): 1367-1367.
Vaewhongs, A. A., and Lommel, S. A. 1995. Virion formation is required for the long-distance movement of red clover necrotic mosaic virus in movement protein transgenic plants. Virology, 212(2): 607-613.
Waterworth, H. E., Lawson, R. H., and Monroe, R. L. 1976. Purification and properties of Hibiscus chlorotic ringspot virus. Phytopathology, 66(5): 570-575.
Yang, J., and Zhang, Y. 2015. Protein structure and function prediction using I‐TASSER. Current Protocols in Bioinformatics, 52: 5-8.
Zhang, X., and Wong, S. M. 2009. Hibiscus chlorotic ringspot virus upregulates plant sulfite oxidase transcripts and increases sulfate levels in kenaf (Hibiscus cannabinus L.). Journal of General Virology, 90(12): 3042-3050.
Zhou, T., Fan, Z., F, Li, H. F., and Wong, S. M. 2006. Hibiscus chlorotic ringspot virus p27 and its isoforms affect symptom expression and potentiate virus movement in kenaf (Hibiscus cannabinus L.). Molecular Plant Microbe Interaction, 19(9): 948-957.

XML

PDF 992.03 K