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Evolutionary features of 8K (KDa) silencing suppressor protein of Potato mop-top virus | ||
| Molecular Biology Research Communications | ||
| مقاله 6، دوره 7، شماره 1، 2018، صفحه 43-50 اصل مقاله (682.85 K) | ||
| نوع مقاله: Original article | ||
| شناسه دیجیتال (DOI): 10.22099/mbrc.2018.28458.1304 | ||
| نویسندگان | ||
| Aminalah Tahmasebi* 1؛ Alireza Afsharifar1؛ Ahmad Heydari2؛ Mohammad Mehrabadi3 | ||
| 1Plant Virology Research Center, College of Agriculture, Shiraz University, Shiraz, Iran | ||
| 2Firoozabad Center for Higher Education, Iran | ||
| 3Department of Entomology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran. | ||
| چکیده | ||
| The cysteine-rich 8K protein of Potato mop-top virus (PMTV) suppresses host RNA silencing. In this study, evolutionary analysisof 8K sequences of PMTV isolates was studied on the basis of nucleotide and amino acid sequences. Twenty-one positively selected sites were identified in 8K codingregions. Recombination events were found in the 8K of PMTV isolates with a rate of 1.8. Totally 30 haplotypes were detected with haplotype diversity ranging from 0.8 to 1.0 and nucleotide diversity from 7.58 to 13.62. The positions 33 and 30 indicated the highly positive and negative selection (with the highest and the lowest dN-dS values), respectively. Tajima’s D test suggested that 8K is evolving with a strong positive selection for worldwide isolates. High frequency of segregating sites was identified along 204 positions of 8K. Moreover, in this study, we used Shannon entropy-based approach to evaluate the variability of each site of nucleotide and corresponding amino acid. Based on Shannon entropy method, 139 and 97 nucleotide sites had the highest entropy value, while 47 and 33 amino acid sites showed the most diversity along 8K sequences. Our findings suggest that 8K as an RNA silencing suppressor evolves rapidly. Taken together, its variability might play a big threat to infect other plants or overcome resistant cultivars. | ||
| کلیدواژهها | ||
| Genetic Variation؛ 8K؛ Potato mop-top virus؛ RNA silencing suppressor | ||
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1. Adams MJ, Antoniw JF, Kreuze J. Virgaviridae: a new family of rod-shaped plant viruses. Arch Virol 2009;154:1967-1972. 2. Hu X, Dickison V, Lei Y, He C, Singh M, Yang Y, Xiong X, Nie X. Molecular characterization of Potato mop-top virus isolates from China and Canada and development of RT-PCR differentiation of two sequence variant groups. CanJ Plant Pathol 2016;38:231-242. 3. Ramesh SV, Raikhy G, Brown CR, Whitworth JL, Pappu HR. Complete genomic characterization of a Potato mop-top virus isolate from the United States. Arch Virol 2014; 159:3427-3433. 4. Santala J, Samuilova O, Hannukkala A, Latvala S, Kortemaa H, Beuch U, Kvarnheden A, Persson P, Topp K, Ørstad K, Spetz C. Detection, distribution and control of potato mop‐top virus, a soil‐borne virus, in northern Europe. Ann Appl Biol 2010;157:163-178. 5. Scott KP, Kashiwazaki S, Reavy B, Harrison BD. The nucleotide sequence of potato mop-top virus RNA 2: a novel type of genome organization for a furovirus. J Gen Virol 1994;75: 3561- 3568. 6. Savenkov EI, Sandgren M, Valkonen JP. Complete sequence of RNA 1 and the presence of tRNA-like structures in all RNAs of Potato mop-top virus, genus Pomovirus. J Gen Virol 1999;80:2779-2784. 7. Sandgren M, Savenkov EI, Valkonen JP. The readthrough region of Potato mop-top virus (PMTV) coat protein encoding RNA, the second largest RNA of PMTV genome, undergoes structural changes in naturally infected and experimentally inoculated plants. Arch Virol 2001;146:467-477. 8. Morozov SY, Solovyev AG. Triple gene block: modular design of a multifunctional machine for plant virus movement. JGen Virol 2003;84:1351-1366. 9. Zamyatnin Jr AA, Solovyev AG, Savenkov EI, Germundsson A, Sandgren M, Valkonen JP, Morozov SY. Transient coexpression of individual genes encoded by the triple gene block of Potato mop-top virus reveals requirements for TGBp1 trafficking. Mol Plant Microbe Interact 2004;17:921-930. 10. Lukhovitskaya NI, Thaduri S, Garushyants SK, Torrance L, Savenkov EI. Deciphering the mechanism of defective interfering RNA (DI RNA) biogenesis reveals that a viral protein and the DI RNA act antagonistically in virus infection. JGen Virol 2013;87:6091-6103. 11. Nielsen SL, Nicolaisen M. Identification of two nucleotide sequence sub-groups within Potato mop-top virus. Arch Virol 2003;148:381-388. 12. Xu H, DeHaan TL, De Boer SH. Detection and confirmation of Potato mop-top virus in potatoes produced in the United States and Canada. Plant Dis 2004;88:363-367. 13. Cerovska N, Pecenkova T, Filigarova M, Dedic P. Sequence analysis of the Czech potato mop-top virus (PMTV) isolate Korneta-Nemilkov. Folia Microbiol 2007;52:61-64. 14. Latvala-Kilby S, Aura JM, Pupola N, Hannukkala A, Valkonen JP. Detection of Potato mop-top virus in potato tubers and sprouts: combinations of RNA2 and RNA3 variants and incidence of symptomless infections. Phytopathology 2009;99:519-531. 15. David N, Mallik I, Crosslin JM, Gudmestad NC. First report of Potato mop-top virus in North Dakota. Plant Dis 2010;94:1506. 16. Whitworth JL, Crosslin JM. Detection of Potato mop top virus (Furovirus) on potato in southeast Idaho. Plant Dis 2013;97:149. 17. Brigneti G, Voinnet O, Li WX, Ji LH, Ding SW, Baulcombe DC. Viral pathogenicity determinants are suppressors of transgene silencing in Nicotiana benthamiana. EMBO J 1998;17:6739-6746. 18. Voinnet O, Pinto VM, Baulcombe DC. Suppression of gene silencing: a general strategy used by diverse DNA and RNA viruses of plants. Proc Natl Acad Sci USA 1999;96:14147-14152. 19. Pumplin N, Voinnet O. RNA silencing suppression by plant pathogens: defence, counter-defence and counter-counter-defence. Nat Rev Microbiol 2013;11:745. 20. Murray GGR, Kosakovsky Pond SL, Obbard DJ. Suppressors of RNAi from plant viruses are subject to episodic positive selection. Proc Royal Soc 2013;280:20130965. 21. Kalyandurg P, Gil JF, Lukhovitskaya NI, Flores B, Müller G, Chuquillanqui C, Palomino L, Monjane A, Barker I, Kreuze J, Savenkov EI. Molecular and pathobiological characterrization of 61 Potato mop‐top virus full‐length cDNAs reveals great variability of the virus in the center of potato domestication, novel genotypes and evidence for recombination. Mol Plant Pathol 2017;18:864-877. 22. Kosman E, Leonard KJ. Conceptual analysis of methods applied to assessment of diversity within and distance between populations with asexual or mixed mode of reproduction. New Phytol 2007;174:683-696. 23. Sherwin WB. Entropy and information approaches to genetic diversity and its expression: genomic geography. Entropy 2010;12:1765-1798. 24. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33:1870-1874. 25. Rozas J, Sánchez-DelBarrio JC, Messeguer X, Rozas R. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 2003;19:2496-2497. 26. Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci: CABIOS 1992;8:275-282. 27. Sereme D, Lacombe S, Konate M, Bangratz M, Pinel-Galzi A, Fargette D, Traoré AS, Konaté G, Brugidou C. Sites under positive selection modulate the RNA silencing suppressor activity of rice yellow mottle virus movement protein P1. JGen Virol 2014;95: 213-218. 28. Touriol C, Bornes S, Bonnal S, Audigier S, Prats H, Prats AC, Vagner S. Generation of protein isoform diversity by alternative initiation of translation at non‐AUG codons. Biol Cell 2003;95:169-178. 29. Shirako Y. Non-AUG translation initiation in a plant RNA virus: a forty-amino-acid extension is added to the N terminus of the soil-borne wheat mosaic virus capsid protein. J Virol 1998;72:1677-1682. 30. González-Jara P, Atencio FA, Martínez-García B, Barajas D, Tenllado F, Díaz-Ruíz JR. A single amino acid mutation in the Plum pox virus helper component-proteinase gene abolishes both synergistic and RNA silencing suppression activities. Phytopathology 2005; 95:894-901. 31. Yambao MLM, Yagihashi H, Sekiguchi H, Sekiguchi T, Sasaki T, Sato M, Atsumi G, Tacahashi Y, Nakahara KS, Uyeda I. Point mutations in helper component protease of clover yellow vein virus are associated with the attenuation of RNA-silencing suppression activity and symptom expression in broad bean. Arch Virol 2008;153:105-115. 32. Torres-Barceló C, Martín S, Daròs JA, Elena SF. From hypo-to hypersuppression: effect of amino acid substitutions on the RNA-silencing suppressor activity of the Tobacco etch potyvirus HC-Pro. Genetics 2008;180:1039-1049. 33. Fraile A, Alonso-Prados JL, Aranda MA, Bernal JJ, Malpica JM, Garcia-Arenal F. Genetic exchange by recombination or reassortment is infrequent in natural populations of a tripartite RNA plant virus. J Virol 1997;71:934-940. 34. Obbard DJ, Jiggins FM, Halligan DL, Little TJ. Natural selection drives extremely rapid evolution in antiviral RNAi genes. Curr Biol 2006;16:580-585. | ||
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