Molecular Characterization of Cylindrical Inclusion Protein Gene Regions of Turkish Zucchini yellow mosaic virus (ZYMV) Isolates

Year 2022, , 25 - 34, 30.04.2022

Şerife Topkaya , Filiz Ertunç

https://doi.org/10.55507/gopzfd.1116025

Abstract

Zucchini yellow mosaic virus (ZYMV) is an economically important viral pathogen that causes intense mosaic symptoms and disfigurement in cucurbits. The aim of this study is to characterize ZYMV isolates obtained from Ankara, Antalya, Burdur, Konya, Karaman, Aksaray provinces of Turkey according to cylindrical inclusion (CI) protein sequences and to determine conserved areas on protein in Potyviruses. For this purpose, molecular studies and sequence analyzes were performed with primers specific to the CI protein region of collected cucurbit samples during 2019-2014 years. At the end of the study, the N terminus of Turkish ZYMV's CI protein 888 nucleotides long and 296 amino acids (aa) was amplified. Phylogenetic analysis of the nucleotide sequences of the CI region showed that the majority of isolates (40) belonged to a large molecular subgroup (A1) most common in Europe and the world, and three isolates (Y4, Y21, Y23) belonged to subgroup A5. Moreover, according to the coat protein nucleotide analysis, these three isolates (Y4, Y21, Y23) were grouped with the molecular subgroup A4, the group that emerged recently in Europe. The CI ZYMV nucleotide binding motif (NTBM) and RNA helicase activity site (five motifs) were conserved among isolates according to amino acid analysis.

Keywords

Cucurbites, cylindrical inclusion, helicase activity, Phylogenetic analysis, Sequence analyzes, ZYMV

Türkiye ZYMV İzolatlarının CI Protein Gen Bölgelerinin Moleküler Karakterizasyonu

Abstract

Kabak sarı mozaik virüsü (ZYMV), kabakgillerde yoğun mozaik semptomlarına ve şekil bozukluğuna neden olan ekonomik açıdan önemli bir viral etmendir. Bu çalışmanın amacı, Türkiye’de farklı illerden (Ankara, Antalya, Burdur, Konya, Karaman, Aksaray) elde edilen ZYMV izolatlarının silindirik inklüzyon (CI) protein dizilerine göre karakterize edilmesi ve Potyvirüslerde protein üzerinde korunan alanların belirlenmesidir. Bu amaçla CI protein bölgesine spesifik primerler ile moleküler çalışmalar ve dizi analizleri yapılmıştır. Çalışma sonunda, Türk ZYMV'nin CI proteini 888 nükleotid uzunluğunda ve 296 amino asit (aa) olan N uç kısmı çoğaltılmıştır. CI bölgesinin nükleotid dizilerinin filogenetik analizi, izolatların (40) çoğunluğunun Avrupa ve dünyada en yaygın olan büyük bir moleküler alt grubuna (A1) ve üç izolatın (Y4, Y21, Y23) A5 alt grubuna ait olduğunu göstermiştir. Ayrıca, kılıf proteini nükleotid analizine göre, bu üç izolat (Y4, Y21, Y23), Avrupa'da son zamanlarda ortaya çıkan grup olan A4 moleküler alt grubu ile gruplanmıştır. CI ZYMV nükleotid bağlama motifi (NTBM) ve RNA helikaz aktivite bölgesinin (beş motif) aa analizine göre izolatlar arasında korunduğu görülmüştür.

Keywords

Filogenetik analiz, Sekans analizi, Kabakgiller

References

• Adams, M. J., Antoniw, J. F., & Beaudoin, F. (2005). Overview and analysis of the polyprotein cleavage sites in the family Potyviridae. Molecular Plant Pathology, 6(4), 471–487. https://doi.org/10.1111/j.1364-3703.2005.00296.x
• Astruc, N., Marcos, J. F., Macquaire, G., Candresse, T., & Pallas, V. (1996). Studies on the diagnosis of hop stunt viroid in fruit trees: identification of new hosts and application of nucleic acid extraction procedure based on non-organic solvents. European Journal of Plant Pathology, 102 (9), 837-846. https://doi.org/10.1007/BF01877053
• Choi, S. K., Yoon, J. Y., & Sohn, S. H. (2007). Analysis of the complete genome sequence of ZYMV strain A isolated from Hollyhock. The Plant Pathology Journal. Korean Society of Plant Pathology, 23 (4), 245-250. https://doi.org/10.5423/PPJ.2007.23.4.245
• Coutts, B. A., Kehoe, M. A., Webster, C. G., Wylie, S. J., & Jones, A. L. (2011). Zucchini yellow mosaic virus: Biological properties, detection procedures and comparison of coat protein gene sequences. Archives of Virology, 156(12), 2119–2131. https://doi.org/10.1007/s00705-011-1102-0
• Desbiez, C., & Lecoq, H. (1997). Zucchini yellow mosaic virus. Plant Pathology, 46 (6), 809–829. https://doi.org/10.1046/j.1365-3059.1997.d01-87.x
• Desbiez, C., Wipf-Scheibel, C., & Lecoq, H. (2002). Biological and serological variability, evolution and molecular epidemiology of Zucchini yellow mosaic virus (ZYMV, Potyvirus) with special reference to Caribbean islands. Virus Research, 85(1), 5-16. https://doi.org/10.1016/S0168-1702(02)00013-8
• Gal-On, A. (2007). Zucchini yellow mosaic virus: insect transmission and pathogenicity – the tails of two proteins. Molecular Plant Pathology, 8(2), 139–150. https://doi.org/10.1111/j.1364-3703.2007.00381.x
• Glasa, M., & Pittnerova, S. (2006). Complete Genome Sequence of a Slovak Isolate of Zucchini Yellow Mosaic Virus (ZYMV) Provides Further Evidence of a Close Molecular Relationship Among Central European ZYMV Isolates. Journal of Phytopathology, 154(7-8), 436–440. https://doi.org/10.1111/j.1439-0434.2006.01124.x
• Glasa, M., Svoboda, J., & Novakova, S. (2007). Analysis of the molecular and biological variability of Zucchini yellow mosaic virus isolates from Slovakia and Czech Republic. Virus Genes, 35(2), 415-421. https://doi.org/10.1007/s11262-007-0101-4
• Ha, C., Coombs, S., Revill, P. A., Harding, R. M., Vu, M., & Dale, J. L. (2008). Design and application of two novel degenerate primer pairs for the detection and complete genomic characterization of potyviruses. Archives of Virology, 153(1), 25-36. https://doi.org/10.1007/s00705-007-1053-7
• Helvacı, M., Yilmaz, N., & Fidan, H. (2019). Evaluatıon of Some Cucurbit Accessıons Collected from Northern Cyprus for Resıstance to Zucchini Yellow Mosaic Virus (ZYMV). Fresenius Environmental Bulletin, 28(7), Article 54025404.
• Hull, R. (2002). Matthews’Plant Virology, (4th. Ed) San Diego; Academic Press.
• Kamberoglu, M. A., Caliskan, A. F., & Desbiez, C. (2016). Current status of some cucurbit viruses in Cukurova region (Adana and Mersin Provinces) of Turkey and molecular characterization of zucchini yellow mosaic virus isolates. Romanian Biotechnological Letters, 21(4),11709–11719.
• Kaya, A., & Erkan, S. (2011). İzmir, Aydın, Manisa ve Balıkesir illerinde üretilen kabakgillerdeki viral etmenlerin tanılanması ve yaygınlıklarının belirlenmesi. Bitki Koruma Bülteni, 51 (4), 387-405.
• Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Molecular Biology and Evolution, 35(6), 1547–1549. https://doi.org/10.1093/molbev/msy096
• Lee, K. C., Wong, S. M., Mahtani, P. H., Chng, C. G., (1997). Sequence and phylogenetic analysis of the cytoplasmic inclusion protein gene of zucchini yellow mosaic potyvirus: its role in classification of the potyviridae. Virus Genes, 14(1), 41-53. https://doi.org/10.1023/A:1007935423180
• Lisa, V., & Lecoq, H. (1984). Zucchini Yellow Mosaic Virus. CMI/AAB Description of plant viruses, no 282.
• Nacar, C., Aras, V., Tekin, S., & Fidan, H. (2021). Determination of Specific Combining Ability of ZYMV Tolerant Lines in Summer Squash. Alatarım, 20 (2), 60- 69.
• Nováková, S., Svoboda, J., & Glasa, M. (2014). Analysis of the complete sequences of two biologically distinct Zucchini yellow mosaic virus isolates further evidences the involvement of a single amino acid in the virus pathogenicity. Acta Virology, 58(4), 364-7. doi:10.4149/av_2014_04_364
• Özer, M., Sipahioğlu, H. M., Usta, M., Fidan, H. (2012). Cloning and sequencing of coat protein gene of Zucchini yellow mosaic virus isolated from squash and muskmelon in Turkey. Turkish Journal of Biology, 36(4), 423–429.
• Pfosser, M. F., & Bauman, H. (2002). Phylogeny and geographical differentiation of ZYMV isolates based on molecular analysis of the coat protein and part of the cytoplasmic inclusion protein genes. Archives of Virology, 147, 1599–1609. https://doi.org/10.1007/s00705-002-0839-x
• Revers, F., Le Gall, O., Candresse, T., & Maule, A. J. (1999). New advances in understanding the molecular biology of plant/potyvirus interactions. Molecular Plant-Microbe Interactions, 12(5), 367-376. https://doi.org/10.1094/MPMI.1999.12.5.367
• Sertkaya, G., Sertkaya, E., Yetişir, E., & Kaya, K. (2004). Investigations on incidence and transmission of ZYMV in Cucurbits in Hatay Province. In: Proceedings of the first plant protection congress of Samsun in Turkey, 217.
• Sorel, M., Garcia, J. A., & German-Retana, S. (2014). The Potyviridae cylindrical inclusion helicase: a key multi-partner and multifunctional protein. Molecular plant-microbe interactions : MPMI, 27(3), 215–226. https://doi.org/10.1094/MPMI-11-13-0333-CR
• Sevik, M. A., & Arli-Sokmen, M. (2003). Viruses infecting cucurbits in Samsun, Turkey. Plant Disease, 87(4), 341–344. https://doi.org/10.1094/PDIS.2003.87.4.341
• Topkaya, Ş. (2020). Kastamonu İli ve Çevresinde Kabakgil Yetiştirilen Alanlarda Enfeksiyon Oluşturan Viral Etmenlerin Saptanması. Gaziosmanpaşa Bilimsel Araştırma Dergisi, 9 (1), 65-72.
• Topkaya, S., Desbiez, C., & Ertunc, F. (2019). Presence of cucurbit viruses in Ankara and Antalya province and molecular characterization of coat protein gene of zucchini yellow mosaic virus Turkish isolates. Fresenius Environmental Bulletin, 28(4), 2442- 2449.
• Urcuqui-Inchima, S., Walter, J., Drugeon, G., German-Retana, S., Haenni, A. L., Candresse, T., Bernardi, F., Le Gall, O. (1999). Potyvirus helper component–proteinase self interaction in the yeast two-hybrid system and delineation of the interaction domain involved. Virology, 258, 95–99. https://doi.org/10.1006/viro.1999.9725
• Yakoubi, S., Desbiez, C,. Fakhfakh, H., Wipf-Scheibel, C., Fabre, F., Pitrat, M., Marrakchi, M., & Lecoq, H. (2008). Molecular, biological, and serological variability of Zucchini yellow mosaic virus in Tunisia. Plant Pathology, 57, 1146–1154. https://doi.org/10.1111/j.1365-3059.2008.01934.x
• Yesil, S. (2014). Virus Diseases of Edible Seed Squash (Cucurbita pepo L.) in Konya Province. In: Book of Proceedings Fifth International Scientific Agricultural Symposium (AGROSYM-2014), October, 23-26th, 2014, Jahorina, Sarajevo, Bosnia-Herzegovina, 576-581
• Yesil, S., & Ertunc, F. (2012). Virus Diseases of Cucurbits in Konya Province. In: Proceedings of the Xth EUCARPIA meeting on genetics and breeding of Cucurbitaceae (eds. Sari, Solmaz and Aras), October, 15-18th, 2012, Antalya, Turkey, 791-796.
• Yeşil, S. (2019a). Some virus diseases of edible seed squash (Cucurbita pepo L.) in Aksaray Province, Turkey. Yüzüncü Yıl Üniversitesi Tarım Bilimleri Dergisi, 29,63–71. https://doi.org/10.29133/ yyutbd.476052.
• Yeşil, S. (2019b). Detection of viruses on edible seed squash (Cucurbita pepo L.) in Yozgat Province, Turkey. Iğdır Üniversitesi Fen Bilimleri Enstitüsü Dergisi, 9(3), 1202–1219. https://doi.org/10. 21597/jist.509235.
• Yeşil, S. (2020). Detection of some virus diseases of edible seed squash (Cucurbita pepo L.) in Nevşehir Province, Turkey. Selcuk Journal of Agriculture and Food Sciences, 34(1),49–56. https://doi.org/10.15316/SJAFS.2020.194
• Zhao, M. F., Chen, J., Zheng, H. Y., Adams, M. J., & Chen, J. P. (2003). Molecular analysis of Zucchini yellow mosaic virus isolates from Hangzhou, China. Journal of Phytopathology, 151(6), 307–311. https://doi.org/10.1046/j.1439-0434.2003.00724.x