Advertisement

Biochemical Genetics

, Volume 46, Issue 11–12, pp 835–846 | Cite as

Role of Genetic Recombination in the Molecular Architecture of Papaya ringspot virus

  • Satendra K. Mangrauthia
  • B. Parameswari
  • R. K. Jain
  • Shelly Praveen
Article

Abstract

Papaya ringspot virus (PRSV) has a single-stranded RNA genome and causes severe economic losses both in cucurbits and papaya worldwide. The extent to which the genome of PRSV is shaped by recombination provides an understanding of the molecular evolution of PRSV and helps in studying features such as host specificity, geographic distribution, and its emergence as new epidemics. The PRSV-P-Indian isolate was completely sequenced and compared with 14 other isolates reported from the rest of the world for their phylogenetic survey of recombination events. Cistron-by-cistron sequence comparison and phylogenetic analysis based on full-genome polyprotein showed two distinct groupings of Asian and American isolates, although PRSV-P and W-India clustered along with the American isolates. Recombination sites were found throughout the genomes, except in the small 6K1 protein gene. A significant proportion of recombination hotspots was found in the P1 gene, followed by P3, cylindrical inclusion (CI), and helper component proteinase (HcPro). Correlations between the presence of recombination sites, geographic distribution, and phylogenetic relationship provide an opportunity to establish the molecular evolution and geographic route of PRSV.

Keywords

Potyvirus Genome diversity P1 PRSV-P-India 

Notes

Acknowledgment

Satendra K. Mangrauthia was supported by a fellowship from the Council of Scientific and Industrial Research, New Delhi.

References

  1. Bag S, Agarwal S, Jain RK (2007) Sequence diversity in the coat proteins of Papaya ringspot virus isolates originating from different locations in India. Indian Phytopath 60(2):244–250Google Scholar
  2. Bateson MF, Henderson J, Chaleeprom W, Gibbs AG, Dale JL (1994) Papaya ringspot potyvirus: isolate variability and the origin of PRSV type (Australia). J Gen Virol 75:3547–3553PubMedCrossRefGoogle Scholar
  3. Bateson MF, Lines RE, Revill P, Chaleepron W, Ha VC, Gibbs AJ, Dale JL (2002) On the evolution and molecular epidemiology of potyvirus Papaya ringspot virus. J Gen Virol 83:2575–2585PubMedGoogle Scholar
  4. Bujarski JJ, Kaesberg P (1986) Genetic recombination between RNA components of a multipartite plant virus. Nature 321:528–531PubMedCrossRefGoogle Scholar
  5. Chare ER, Holmes EC (2006) A phylogenetic survey of recombination frequency in plant RNA viruses. Arch Virol 151:933–946PubMedCrossRefGoogle Scholar
  6. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefGoogle Scholar
  7. Fernandez-Rodriguez T, Rubio L, Carballo O, Marys E (2008) Genetic variation of papaya ringspot virus in Venezuela. Arch Virol 153:343–349PubMedCrossRefGoogle Scholar
  8. Gonsalves D (1998) Control of papaya ringspot virus in papaya: a case study. Annu Rev Phytopathol 36:415–437PubMedCrossRefGoogle Scholar
  9. Hall TA (1999) BioEdit: a user friendly biological sequence alignment editor and analysis programs for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98Google Scholar
  10. Hon C-C, Lam T-Y, Shi Z-L, Drummond AJ, Yip C-W, Zeng F, Lam P-Y, Leung FC-C (2008) Evidence of the recombinant origin of a bat severe acute respiratory syndrome (SARS)-like coronavirus and its implications on the direct ancestor of SARS coronavirus. J Virol 82(4):1819–1826PubMedCrossRefGoogle Scholar
  11. Inoue-Nagata AK, Franco CM, Martin DP, Rezende JA, Ferreira GB, Dutra LS, Nagata T (2007) Genome analysis of a severe and a mild isolate of Papaya ringspot virus-type W found in Brazil. Virus Genes 35:881–882CrossRefGoogle Scholar
  12. Jain RK, Pappu HR, Pappu SS, Varma A, Ram RD (1998) Molecular characterization of Papaya ringspot potyvirus isolates from India. Ann Appl Biol 132:413–425CrossRefGoogle Scholar
  13. Jain RK, Sharma J, Sivakumar AS, Sharma PK, Byadgi AS, Verma AK, Varma A (2004) Variability in the coat protein gene of Papaya ringspot virus isolates from multiple locations in India. Arch Virol 149:2435–2442PubMedCrossRefGoogle Scholar
  14. Klein PG, Klein RR, Rodriguez-Cerezo E, Hunt AG, Shaw JG (1994) Mutational analysis of the Tobacco vein mottling virus genome. Virology 204:759–769PubMedCrossRefGoogle Scholar
  15. Lai MMC (1992) RNA recombination in animal and plant viruses. Microbiol Rev 56:61–79PubMedGoogle Scholar
  16. Noa-Carrazana JC, Gonzalez-De-Leon D, Silva-Rosales L (2007) Molecular characterization of a severe isolate of Papaya ringspot virus in Mexico and its relationship with other isolates. Virus Genes 35:109–117PubMedCrossRefGoogle Scholar
  17. Ohshima K, Yamaguchi Y, Hirota R, Hamamoto T, Tomimura K, Tan Z, Sano T, Azuhata F, Walsh JA et al (2002) Molecular evolution of Turnip mosaic virus: evidence of host adaptation, genetic recombination and geographical spread. J Gen Virol 83:1511–1521PubMedGoogle Scholar
  18. Ohshima K, Tomitaka Y, Wood JT, Minematsu Y, Kajiyama H, Tomimura K, Gibbs AJ (2007) Pattern of recombination in Turnip mosaic virus genomic sequences indicates hotspots of recombination. J Gen Virol 88:298–315PubMedCrossRefGoogle Scholar
  19. Parameswari B, Mangrauthia SK, Praveen S, Jain RK (2007) Complete genome sequence of an isolate of Papaya ringspot virus from India. Arch Virol 152(4):843–845PubMedCrossRefGoogle Scholar
  20. Posada D, Crandall KA, Holmes EC (2002) Recombination in evolutionary genomics. Annu Rev Genet 36:75–97PubMedCrossRefGoogle Scholar
  21. Praveen S, Kushwaha CM, Mishra AK, Singh V, Jain RK, Varma A (2005) Engineering tomato for resistance to tomato leaf curl disease using viral rep gene sequences. Plant Cell Tissue Organ Cult 83:311–318CrossRefGoogle Scholar
  22. Purcifull DE, Edwardson JR, Hiebert E, Gonsalves D (1984) Papaya ringspot virus. CMI/AAB description of plant viruses. No. 292. CAB International, Wallingford, UKGoogle Scholar
  23. Ramesh SV, Mishra AK, Praveen S (2007) Hairpin RNA mediated strategies for silencing of Tomato leaf curl virus AC1 and AC4 genes for effective resistance in plants. Oligonucleotide 17:251–257CrossRefGoogle Scholar
  24. Reichmann JL, Lain S, Garcia JA (1992) Highlights and prospects of potyvirus molecular biology. J Gen Virol 73:1–16CrossRefGoogle Scholar
  25. Roossinck MJ (1997) Mechanisms of plant virus evolution. Annu Rev Phytopathol 35:191–209PubMedCrossRefGoogle Scholar
  26. Roy G, Jain RK, Bhat AI, Varma A (1999) Comparative host range and serological studies of Papaya ringspot potyvirus isolates. Indian Phytopath 62:14–17Google Scholar
  27. Salvador B, Saénz P, Yangüez E, Quiot JB, Quiot L, Delgadillo MO, García JA, Simón-Mateo C (2008) Host-specific effect of P1 exchange between two potyviruses. Mol Plant Path 9(2):147–155CrossRefGoogle Scholar
  28. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876–4882CrossRefGoogle Scholar
  29. Urcuqui-Inchima S, Haenni AL, Bernardi F (2001) Potyvirus proteins: a wealth of functions. Virus Res 74:157–175PubMedCrossRefGoogle Scholar
  30. Valli A, Lopez-Moya JJ, Garcia JA (2007) Recombination and gene duplication in the evolutionary diversification of P1 proteins in the family potyviridae. J Gen Virol 88:1016–1028PubMedCrossRefGoogle Scholar
  31. Varma A (1988) The economic impact of filamentous plant virus—the Indian subcontinent. In: Milne RG (ed) The plant viruses, vol 4. Plenum Press, New York, pp 371–376Google Scholar
  32. Verchot J, Carrington JC (1995a) Debilitation of plant potyvirus infectivity by P1 proteinase-inactivating mutations and restoration by second-site modifications. J Virol 69:1582–1590PubMedGoogle Scholar
  33. Verchot J, Carrington JC (1995b) Evidences that the potyvirus P1 proteinase functions in trans as an accessory factor for genome amplification. J Virol 69:3668–3674PubMedGoogle Scholar
  34. Worobey M, Holmes EC (1999) Evolutionary aspects of recombination in RNA viruses. J Gen Virol 80:2535–2543PubMedGoogle Scholar
  35. Yang LJ, Hidaka M, Masaki H, Uozumi T (1998) Detection of Potato virus Y P1 protein in infected cells and analysis of its cleavage sites. Biosci Biotechnol Biochem 62:380–382PubMedCrossRefGoogle Scholar
  36. Yeh SD, Jan FJ, Chiang CH, Doong TJ, Chen MC, Chung PH, Bau HJ (1992) Complete nucleotide sequence and genetic organization of Papaya ringspot virus RNA. J Gen Virol 73:2531–2541PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Satendra K. Mangrauthia
    • 1
  • B. Parameswari
    • 2
  • R. K. Jain
    • 2
  • Shelly Praveen
    • 2
  1. 1.Division of BiochemistryIndian Agricultural Research InstituteNew DelhiIndia
  2. 2.Division of Plant PathologyIndian Agricultural Research InstituteNew DelhiIndia

Personalised recommendations