About this Journal Submit a Manuscript Table of Contents
International Journal of Plant Genomics
Volume 2012 (2012), Article ID 417935, 12 pages
http://dx.doi.org/10.1155/2012/417935
Research Article

Evolutionary and Molecular Aspects of Indian Tomato Leaf Curl Virus Coat Protein

1Department of Bioinformatics, Applied Botany Center, University School of Sciences, Gujarat University, Ahmedabad 380 009, India
2Department of Botany, University School of Sciences, Gujarat University, Ahmedabad 380 009, India

Received 24 August 2012; Revised 7 November 2012; Accepted 8 November 2012

Academic Editor: Akhilesh Kumar Tyagi

Copyright © 2012 Sivakumar Prasanth Kumar et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. B. Gronenbor, “The Tomato yellow leaf curl virus genome,” in Tomato Yellow Leaf Curl Virus Disease: Management, Molecular Biology, Breeding For Resistance, H. Czosnek, Ed., vol. 8, pp. 67–84, Springer, Netherlands, 2007.
  2. M. J. Melzer, D. Y. Ogata, S. K. Fukuda et al., “First report of Tomato yellow leaf curl virus in Hawaii,” Plant Disease, vol. 94, no. 5, pp. 641–643, 2010.
  3. A. A. Sanderfoot, D. J. Ingham, and S. G. Lazarowitz, “A viral movement protein as a nuclear shuttle: the geminivirus BR1 movement protein contains domains essential for interaction with BL1 and nuclear localization,” Plant Physiology, vol. 110, no. 1, pp. 23–33, 1996. View at Scopus
  4. H. Liu, M. I. Boulton, C. L. Thomas, D. A. M. Prior, K. J. Oparka, and J. W. Davies, “Maize streak virus coat protein is karyophyllic and facilitates nuclear transport of viral DNA,” Molecular Plant-Microbe Interactions, vol. 12, no. 10, pp. 894–900, 1999. View at Scopus
  5. T. Kunik, K. Palanichelvam, H. Czosnek, V. Citovsky, and Y. Gafni, “Nuclear import of the capsid protein of Tomato yellow leaf curl virus (TYLCV) in plant and insect cells,” Plant Journal, vol. 13, no. 3, pp. 393–399, 1998. View at Publisher · View at Google Scholar · View at Scopus
  6. S. Chakraborty, P. K. Pandey, M. K. Banerjee, G. Kalloo, and C. M. Fauquet, “Tomato leaf curl Gujarat virus, a New begomovirus species causing a severe leaf curl disease of tomato in Varanasi, India,” Phytopathology, vol. 93, no. 12, pp. 1485–1495, 2003. View at Scopus
  7. R. W. Briddon, J. K. Brown, E. Moriones et al., “Recommendations for the classification and nomenclature of the DNA-β satellites of Begomoviruses,” Archives of Virology, vol. 153, no. 4, pp. 763–781, 2008. View at Publisher · View at Google Scholar · View at Scopus
  8. A. Kheyr-Pour, M. Bendahmane, V. Matzeit, G. P. Accotto, S. Crespi, and B. Gronenborn, “Tomato yellow leaf curl virus from Sardinia is a whitefly-transmitted monopartite geminivirus,” Nucleic Acids Research, vol. 19, no. 24, pp. 6763–6769, 1991. View at Scopus
  9. P. Jyothsna, R. Rawat, and V. G. Malathi, “Predominance of Tomato leaf curl Gujarat virus as a monopartite Begomovirus: association with Tomato yellow leaf curl Thailand betasatellite,” Archives of Virology. In press. View at Publisher · View at Google Scholar
  10. P. Pandey, S. Mukhopadhya, A. R. Naqvi, S. K. Mukherjee, G. S. Shekhawat, and N. R. Choudhury, “Molecular characterization of two distinct monopartite Begomoviruses infecting tomato in india,” Virology Journal, vol. 7, article no. 337, 2010. View at Publisher · View at Google Scholar · View at Scopus
  11. T. Kunik, R. Salomon, D. Zamir et al., “Transgenic tomato plants expressing the Tomato yellow leaf curl virus capsid protein are resistant to the virus,” Nature Biotechnology, vol. 12, no. 5, pp. 500–504, 1994. View at Scopus
  12. S. K. Raj, R. Singh, S. K. Pandey, and B. P. Singh, “Agrobacterium-mediated tomato transformation and regeneration of transgenic lines expressing Tomato leaf curl virus coat protein gene for resistance against TLCV infection,” Current Science, vol. 88, no. 10, pp. 1674–1679, 2005. View at Scopus
  13. D. Pratap, S. K. Raj, S. Kumar, S. K. Snehi, K. K. Gautam, and A. K. Sharma, “Coat protein-mediated transgenic resistance in tomato against a IB subgroup Cucumber mosaic virus strain,” Phytoparasitica, vol. 40, no. 4, pp. 375–382, 2012.
  14. S. Chakraborty, R. Vanitharani, B. Chattopadhyay, and C. M. Fauquet, “Supervirulent pseudorecombination and asymmetric synergism between genomic components of two distinct species of Begomovirus associated with severe tomato leaf curl disease in India,” Journal of General Virology, vol. 89, no. 3, pp. 818–828, 2008. View at Publisher · View at Google Scholar · View at Scopus
  15. N. Kirthi, S. P. Maiya, M. R. N. Murthy, and H. S. Savithri, “Evidence for recombination among the Tomato leaf curl virus strains/species from Bangalore, India,” Archives of Virology, vol. 147, no. 2, pp. 255–272, 2002. View at Publisher · View at Google Scholar · View at Scopus
  16. D. A. Benson, I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, and D. L. Wheeler, “GenBank,” Nucleic Acids Research, vol. 34, pp. D16–D20, 2006. View at Scopus
  17. A. Marchler-Bauer and S. H. Bryant, “CD-Search: protein domain annotations on the fly,” Nucleic Acids Research, vol. 32, pp. W327–W331, 2004. View at Publisher · View at Google Scholar · View at Scopus
  18. S. F. Altschul, T. L. Madden, A. A. Schäffer et al., “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs,” Nucleic Acids Research, vol. 25, no. 17, pp. 3389–3402, 1997. View at Publisher · View at Google Scholar · View at Scopus
  19. A. Bateman, E. Birney, L. Cerruti et al., “The pfam protein families database,” Nucleic Acids Research, vol. 30, no. 1, pp. 276–280, 2002. View at Scopus
  20. S. Kosugi, M. Hasebe, T. Entani, S. Takayama, M. Tomita, and H. Yanagawa, “Design of peptide inhibitors for the importin α/β nuclear import pathway by activity-based profiling,” Chemistry and Biology, vol. 15, no. 9, pp. 940–949, 2008. View at Publisher · View at Google Scholar · View at Scopus
  21. H. Liu, M. I. Boulton, and J. W. Davies, “Maize streak virus coat protein binds single- and double-stranded DNA in vitro,” Journal of General Virology, vol. 78, no. 6, pp. 1265–1270, 1997. View at Scopus
  22. P. Rice, L. Longden, and A. Bleasby, “EMBOSS: the European molecular biology open software suite,” Trends in Genetics, vol. 16, no. 6, pp. 276–277, 2000. View at Scopus
  23. M. A. Larkin, G. Blackshields, N. P. Brown et al., “Clustal W and Clustal X version 2.0,” Bioinformatics, vol. 23, no. 21, pp. 2947–2948, 2007. View at Publisher · View at Google Scholar · View at Scopus
  24. J. Felsenstein, “PHYLIP- phylogeny inference package (version 3. 2),” Cladistics, vol. 5, no. 2, pp. 164–166, 1989.
  25. M. Johnson, I. Zaretskaya, Y. Raytselis, Y. Merezhuk, S. McGinnis, and T. L. Madden, “NCBI BLAST: a better web interface,” Nucleic acids research, vol. 36, pp. W5–9W, 2008. View at Publisher · View at Google Scholar · View at Scopus
  26. F. C. Bernstein, T. F. Koetzle, and G. J. B. Williams, “The protein data bank: a computer based archival file for macromolecular structures,” Journal of Molecular Biology, vol. 112, no. 3, pp. 535–542, 1977. View at Scopus
  27. J. J. Ward, L. J. McGuffin, K. Bryson, B. F. Buxton, and D. T. Jones, “The DISOPRED server for the prediction of protein disorder,” Bioinformatics, vol. 20, no. 13, pp. 2138–2139, 2004. View at Publisher · View at Google Scholar · View at Scopus
  28. D. E. Kim, D. Chivian, and D. Baker, “Protein structure prediction and analysis using the Robetta server,” Nucleic Acids Research, vol. 32, pp. W526–W531, 2004. View at Publisher · View at Google Scholar · View at Scopus
  29. L. A. Kelley and M. J. Sternberg, “Protein structure prediction on the web: a case study using the Phyre server,” Nature protocols, vol. 4, no. 3, pp. 363–371, 2009. View at Publisher · View at Google Scholar · View at Scopus
  30. Tripos, A Certara Company, “Tripos benchware 3D explorer for interactive molecular visualizations and structure manipulations,” St. Louis, Miss, USA, http://www.tripos.com/.
  31. G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, “Stereochemistry of polypeptide chain configurations,” Journal of Molecular Biology, vol. 7, pp. 95–99, 1963. View at Scopus
  32. S. C. Lovell, I. W. Davis, W. B. Arendall et al., “Structure validation by Cα geometry: φ,ψ and Cβ deviation,” Proteins, vol. 50, no. 3, pp. 437–450, 2003. View at Publisher · View at Google Scholar · View at Scopus
  33. E. Pascal, A. A. Sanderfoot, B. M. Ward, R. Medville, R. Turgeon, and S. G. Lazarowitz, “The geminivirus BR1 movement protein binds single-stranded DNA and localizes the cell nucleus,” Plant Cell, vol. 6, no. 7, pp. 995–1006, 1994. View at Publisher · View at Google Scholar · View at Scopus
  34. M. R. Rojas, A. O. Noueiry, W. J. Lucas, and R. L. Gilbertson, “Bean dwarf mosaic Geminivirus movement proteins recognize DNA in a form- and size-specific manner,” Cell, vol. 95, no. 1, pp. 105–113, 1998. View at Publisher · View at Google Scholar · View at Scopus
  35. L. Wang and S. J. Brown, “BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences,” Nucleic Acids Research, vol. 34, pp. W243–W248, 2006. View at Publisher · View at Google Scholar · View at Scopus
  36. Y. Tsuchiya, K. Kinoshita, and H. Nakamura, “PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces,” Bioinformatics, vol. 21, no. 8, pp. 1721–1723, 2005. View at Publisher · View at Google Scholar · View at Scopus
  37. M. van Dijk and A. M. Bonvin, “3D-DART: a DNA structure modelling server,” Nucleic Acids Research, vol. 37, no. 2, pp. W235–W239, 2009. View at Publisher · View at Google Scholar · View at Scopus
  38. S. J. de Vries, M. van Dijk, and A. M. Bonvin, “The HADDOCK web server for data-driven biomolecular docking,” Nature protocols, vol. 5, no. 5, pp. 883–897, 2010. View at Publisher · View at Google Scholar · View at Scopus
  39. S. Jo, M. Vargyas, J. Vasko-Szedlar, B. Roux, and W. Im, “PBEQ-Solver for online visualization of electrostatic potential of biomolecules,” Nucleic acids research, vol. 36, pp. W270–W275, 2008. View at Publisher · View at Google Scholar · View at Scopus
  40. T. J. Dolinsky, J. E. Nielsen, J. A. McCammon, and N. A. Baker, “PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations,” Nucleic Acids Research, vol. 32, pp. W665–W667, 2004. View at Publisher · View at Google Scholar · View at Scopus
  41. M. A. Lill and M. L. Danielson, “Computer-aided drug design platform using PyMOL,” Journal of Computer-Aided Molecular Design, vol. 25, no. 1, pp. 13–19, 2011. View at Publisher · View at Google Scholar · View at Scopus
  42. A. O. Noueiry, W. J. Lucas, and R. L. Gilbertson, “Two proteins of a plant DNA virus coordinate nuclear and plasmodesmal transport,” Cell, vol. 76, no. 5, pp. 925–932, 1994. View at Publisher · View at Google Scholar · View at Scopus
  43. K. Palanichelvam, T. Kunik, V. Citovsky, and Y. Gafni, “The capsid protein of Tomato yellow leaf curl virus binds cooperatively to single-stranded DNA,” Journal of General Virology, vol. 79, no. 11, pp. 2829–2833, 1998. View at Scopus
  44. S. Qin, B. M. Ward, and S. G. Lazarowitz, “The bipartite geminivirus coat protein aids BR1 function in viral movement by affecting the accumulation of viral single-stranded DNA,” Journal of Virology, vol. 72, no. 11, pp. 9247–9256, 1998. View at Scopus
  45. M. Hussain, S. Mansoor, S. Iram, A. N. Fatima, and Y. Zafar, “The nuclear shuttle protein of Tomato leaf curl New Delhi virus is a pathogenicity determinant,” Journal of Virology, vol. 79, no. 7, pp. 4434–4439, 2005. View at Publisher · View at Google Scholar · View at Scopus
  46. M. R. Rojas, H. Jiang, R. Salati et al., “Functional analysis of proteins involved in movement of the monopartite Begomovirus, Tomato yellow leaf curl virus,” Virology, vol. 291, no. 1, pp. 110–125, 2001. View at Publisher · View at Google Scholar · View at Scopus
  47. E. Noris, A. M. Vaira, P. Caciagli, V. Masenga, B. Gronenborn, and G. P. Accotto, “Amino acids in the capsid protein of Tomato yellow leaf curl virus that are crucial for systemic infection, particle formation, and insect transmission,” Journal of Virology, vol. 72, no. 12, pp. 10050–10057, 1998. View at Scopus
  48. T. A. Jones and L. Liljas, “Structure of satellite tobacco necrosis virus after crystallographic refinement at 2.5 Å resolution,” Journal of Molecular Biology, vol. 177, no. 4, pp. 735–767, 1984. View at Scopus
  49. W. Zhang, N. H. Olson, T. S. Baker et al., “Structure of the maize streak virus geminate particle,” Virology, vol. 279, no. 2, pp. 471–477, 2001. View at Publisher · View at Google Scholar · View at Scopus
  50. M. S. Pinner, V. Medina, K. A. Plaskitt, and P. G. Markham, “Viral inclusions in monocotyledons infected by Maize streak and related viruses,” Plant Pathology, vol. 42, no. 1, pp. 75–87, 1993.
  51. A. Zrachya, P. P. Kumar, U. Ramakrishnan et al., “Production of siRNA targeted against TYLCV coat protein transcripts leads to silencing of its expression and resistance to the virus,” Transgenic Research, vol. 16, no. 3, pp. 385–398, 2007. View at Publisher · View at Google Scholar · View at Scopus
  52. S. V. Ramesh, A. K. Mishra, and S. Praveen, “Hairpin RNA-mediated strategies for silencing of tomato leaf curl virus AC1 and AC4 genes for effective resistance in plants,” Oligonucleotides, vol. 17, no. 2, pp. 251–257, 2007. View at Publisher · View at Google Scholar · View at Scopus
  53. R. . Gorovitsa, A. Moshea, M. Kolotb, I. Sobola, and H. Czosneka, “Progressive aggregation of Tomato yellow leaf curl virus coat protein in systemically infected tomato plants, susceptible and resistant to the virus,” Virus Research. In press. View at Publisher · View at Google Scholar