Potato virus S (PVS)-Bitlis izolatının Kılıf Proteinin in silico Karakterizasyonu ve Konak Proteini ile Docking Analizi

Yıl 2022, Cilt: 5 Sayı: 1, 57 - 67, 30.06.2022

Gülüstan Korkmaz , Mustafa Usta , Serap Demirel

https://doi.org/10.46876/ja.1048589

Cited By: 1

Öz

Patates virus S (PVS) dünya çapında yaygın olan virüslerden biridir ve patates bitkilerinde genellikle orta düzeyde simptomlar oluşturur. Viral proteinlerin konakçılarıyla etkileşimleri başarılı bir enfeksiyon oluşturmada ve sistemik yayılmayı sağlamada oldukça önemlidir. Bu çalışmada PVS’nün kılıf proteini (CP) ve patates bitkisi tarafından kodlanan savunma sisteminde yer alan PSH-RGH6 proteini arasındaki interaksiyon homoloji modelleme ve protein-protein docking yaklaşımı kullanılarak araştırılmıştır. PVS-Bitlis izolatının CP geni gen spesifik primerler kullanılarak RT-PCR ile çoğaltıldı. İlgili gen pGEM-T Easy vektöre klonlandı ve PVS-Bitlis CP genini taşıyan plazmid sekanslandı. Elde edilen sekansa ait amino ait dizisi kullanılarak I-TASSER programı ile homolojiye ait protein modeli oluşturuldu. PSH-RGH6 proteini için Swiss-model programı kullanılarak proteine ait model oluşturuldu. Her iki proteine ait modeller arasında interaksiyon Chimera 1.15 programında AutoDock yaklaşımı ile araştırıldı. Docking sonucuna göre PVS-Bitlis CP ve PSH-RGH6 proteinleri arasında interaksiyon varlığı belirlenmiş olup bu interaksiyonun ayrıntılı analizler ile doğrulanması gerekmektedir.

Anahtar Kelimeler

PVS, Patates, Protein-protein interaksiyonu, Docking

In Silico Characterization of Coat Protein of PVS-Bitlis Isolate and Docking Analysis with Host Protein

Öz

Potato virus S (PVS) is one of the common viruses worldwide and usually produces moderate symptoms in potato plants. The interactions of viral proteins with their hosts are very important in establishing a successful infection and ensuring systemic spread. In this study, the interaction between the PVS coat protein (CP) and the PSH-RGH6 protein in the defense system encoded by the potato plant was investigated using homology modeling and protein-protein docking approach. The CP gene of the PVS-Bitlis isolate was amplified by RT-PCR using gene-specific primers. The gene of interest was cloned into the pGEM-T Easy vector and the plasmid carrying the PVS-Bitlis CP gene was sequenced. By using the amino subsequence of the obtained sequence, I-TASSER program created a protein model based on homology. For the PSH-RGH6 protein, a model of the protein was created using the Swiss-model program. The interaction among both proteins was investigated with the AutoDock approach in Chimera 1.15 program. According to the docking results, the existence of interaction between PVS-Bitlis CP and PSH-RGH6 proteins has been determined and this interaction needs to be confirmed with further analysis.

Anahtar Kelimeler

PVS, Potato, Protein-protein interaction, Docking

Kaynakça

• Abouhaidar, M. G., & Lai, R. (1989). Nucleotide sequence of the 3′-terminal region of clover yellow mosaic virus RNA. Journal of general virology, 70(7), 1871-1875.
• Akhter, M., Nakahara, K. S., & Masuta, C. (2021). Resistance induction based on the understanding of molecular interactions between plant viruses and host plants. Virology journal, 18(1), 1-12.
• Amirnia, F., Eini, O., & Koolivand, D. (2016). In silico analysis of microRNA binding to the genome of Beet curly top Iran virus in tomato. Archives of Phytopathology and Plant Protection, 49(17-18), 434-444.
• Bostan, H., & Haliloglu, K. (2004). Distribution of PLRV, PVS, PVX and PVY (PVYN, PVYO and PVYC) in the seed potato tubers in Turkey. Pakistan Journal of Biological Sciences, 7(7), 1140-1143.
• Cox, B. A., & Jones, R. A. (2010). Genetic variability in the coat protein gene of Potato virus S isolates and distinguishing its biologically distinct strains. Archives of virology, 155(7), 1163-1169.
• Demirel, F (2021). Soyada Protein Disülfitİzomeraz’ların İn Silico Analizi. Journal of Agriculture, 4(1), 48-56.
• DeYoung, B. J., & Innes, R. W. (2006). Plant NBS-LRR proteins in pathogen sensing and host defense. Nature immunology, 7(12), 1243–1249.
• Dodds, P. N., &Rathjen, J. P. (2010). Plant immunity: towards an integrated view of plant–pathogen interactions. Nature Reviews Genetics, 11(8), 539-548.
• Foissac X., Savalle-Dumas L., Gentit P., Dulucq M.J. and Candresse T. 2001. Polyvalent detection of fruit tree Tricho, Capillo, and Foveaviruses by nested RTPCR using degenerated and inosine-containing primers (PDO RT-PCR). ActaHorticulturae, 550: 37–44.
• Foster, G. D. (1992). The structure and expression of the genome of carlaviruses. Research in Virology, 143, 103-112. Foster, G. D., & Mills, P. R. (1992). The 3′-nucleotide sequence of an ordinary strain of potato virus S. Virus genes, 6(3), 213-220.
• Gutiérrez, P. A., Alzate, J. F., &Marín-Montoya, M. A. (2013). Complete genome sequence of a novel Potato virus S strain infecting Solanum phureja in Colombia. Archives of virology, 158(10), 2205-2208.
• Jones, R. A. C. (1980). The ecology of viruses infecting wild and cultivated potatoes in the Andean region of South America. Proceedings... Pest, pathogens, and vegetations.
• Koeda, S., Onouchi, M., Mori, N., Pohan, N. S., Nagano, A. J., &Kesumawati, E. (2021). A recessive gene pepy-1 encoding Pelota confers resistance to begomovirus isolates of PepYLCIV and PepYLCAV in Capsicum annuum. Theoretical and Applied Genetics, 1-18.
• Lin, Y. H., Abad, J. A., Maroon-Lango, C. J., Perry, K. L., &Pappu, H. R. (2014). Molecular characterization of domestic and exotic potato virus S isolates and a global analysis of genomic sequences. Archives of virology, 159(8), 2115-2122.
• Loebenstein, G., Berger, P. H., & Brunt, A. A. (Eds.). (2001). Virus and virus-like diseases of potatoes and production of seed-potatoes. Springer Science & Business Media.
• Mackenzie, D. J., Tremaine, J. H., &Stace-Smith, R. (1989). Organization and interviral homologies of the 3′-terminal portion of potato virus S RNA. Journal of general Virology, 70(5), 1053-1063.
• Maiti, S., Paul, S., & Pal, A. (2012). Isolation, characterization, and structure analysis of a non-TIR-NBS-LRR encoding candidate gene from MYMIV-resistant Vigna mungo. Molecular biotechnology, 52(3), 217-233.
• Mandadi, K. K., &Scholthof, K. B. G. (2013). Plant immune responses against viruses: how does a virus cause disease?. The plant cell, 25(5), 1489-1505.
• Matoušek, J., Schubert, J., Ptáček, J., Kozlová, P., &Dědič, P. (2005). Complete nucleotide sequence and molecular probing of potato virus S genome. ActaVirol, 49, 195-205.
• Monis, J., Daniels, S., Dezoeten, G., & Slack, S. A. (1987). Characterızatıon of Potato VIRUS-S (PVS) Genomic RNA. In Phytopathology (Vol. 77, No. 12, pp. 1742-1742).
• Nova, B., &Jamsari, J. (2020, April). In silico analysis of PepYLCV-βC1 protein interaction with pepper-SnRK1 for pathogenicity prediction. In IOP Conference Series: Earth and Environmental Science (Vol. 497, No. 1, p. 012027). IOP Publishing.
• Rashid, M., Mittal, S., & Venkataraman, S. (2020). Analysis of host protein interactions in plant viruses: an in silico study using Sesbania mosaic virus. Virus genes, 56(6), 756-766.
• Rizvi, I., Choudhury, N. R., & Tuteja, N. (2015). Insights into the functional characteristics of geminivirus rolling-circle replication initiator protein and its interaction with host factors affecting viral DNA replication. Archives of virology, 160(2), 375-387.
• Rose, D. G. (1983). Some properties of an unusual isolate of potato virus S. Potato research, 26(1), 49-62.
• Rupazov V. V., Morozov S. Yu., Kanyuka K. V., Zavriev S. K. (1989). Partial nucleotide sequence of potato virus M RNA shows similarities to potexviruses in gene arrangement and the encoded amino acid sequences. Journal of General Virology 70:1861–1869
• Salari, K., Massumi, H., Heydarnejad, J., Pour, A. H., &Varsani, A. (2011). Analysis of Iranian Potato virus S isolates. Virus Genes, 43(2), 281-288.
• Sertkaya, G., Çarpar, H., & Sertkaya, E. (2017). Hatay ili patates üretim alanlarında yonca mozaik virüsü (Alfalfa Mosaic Virus: AMV)’nün araştırılması. Journal of the Institute of Science and Technology, 7(1), 23-29.
• Slootweg, E., Koropacka, K., Roosien, J., Dees, R., Overmars, H., Lankhorst, R. K., ...&Goverse, A. (2017). Sequence exchange between homologous NB-LRR genes converts virus resistance into nematode resistance, and vice versa. Plant physiology, 175(1), 498-510.
• Stevenson, W. R., Loria, R., Franc, G. D., and Weingartner, D. P., eds. 2001. Compendium of Potato Diseases, 2nd ed. American Phytopathological Society, St. Paul, MN.
• Topkaya, Ş. (2020). Determination of some viruses by serological and molecular techniques in potato production areas in Tokat Province. Gaziosmanpaşa Üniversitesi Ziraat Fakültesi Dergisi, 37(1), 53-59.
• Uchiyama, A., Shimada-Beltran, H., Levy, A., Zheng, J. Y., Javia, P. A., &Lazarowitz, S. G. (2014). The Arabidopsis synaptotagmin SYTA regulates the cell-to-cell movement of diverse plant viruses. Frontiers in plant science, 5, 584.
• Valkonen, J. P. (2007). Viruses: economical losses and biotechnological potential. In Potato biology and biotechnology (pp. 619-641). Elsevier Science BV.
• Van Der Vossen, E. A., Van Der Voort, J. N. R., Kanyuka, K., Bendahmane, A., Sandbrink, H., Baulcombe, D. C., ... & Klein‐Lankhorst, R. M. (2000). Homologues of a single resistance‐gene cluster in potato confer resistance to distinct pathogens: a virus and a nematode. The Plant Journal,23(5), 567-576.
• Yılmaz, M. A., Baloğlu, S., & Nas, Z. (1990). Çukurova Bölgesi’nde Yetiştirilen Turfanda Patateslerde Patates Yaprak Kıvırcıklığı Virüsünün (PLRV) ELISA Testiyle Surveyi. J. Faculty Agri. Çukurova Univ, 5(3), 95-106.