Advertisement

Biochemistry (Moscow)

, Volume 76, Issue 12, pp 1347–1359 | Cite as

Classification and characterization of putative cytochrome P450 genes from Panax ginseng C. A. Meyer

  • Balusamy Sri Renuka Devi
  • Yu-Jin Kim
  • Subramaniyum Sathiyamoorthy
  • Altanzul Khorolragchaa
  • Sathiyaraj Gayathri
  • Shohana Parvin
  • Dong-Uk Yang
  • Senthil Kalai Selvi
  • Ok Ran Lee
  • Sungyoung Lee
  • Deok-Chun YangEmail author
Article

Abstract

In plants heme containing cytochrome P450 (P450) is a superfamily of monooxygenases that catalyze the addition of one oxygen atom from O2 into a substrate, with a substantial reduction of the other atom to water. The function of P450 families is attributed to chemical defense mechanism under terrestrial environmental conditions; several are involved in secondary and hormone metabolism. However, the evolutionary relationships of P450 genes in Panax ginseng remain largely unknown. In the present study, data mining methods were implemented and 116 novel putative P450 genes were identified from Expressed Sequence Tags (ESTs) of a ginseng database. These genes were classified into four clans and 22 families by sequence similarity conducted at amino acid level. The representative putative P450 sequences of P. ginseng and known P450 family from other plants were used to construct a phylogenetic tree. By comparing with other genomes, we found that most of the P450 genes from P. ginseng can be found in other dicot species. Depending on P450 family functions, seven P450 genes were selected, and for that organ specific expression, abiotic, and biotic studies were performed by quantitative reverse transcriptase-polymerase chain reaction. Different genes were found to be expressed differently in different organs. Biotic stress and abiotic stress transcript level was regulated diversely, and upregulation of P450 genes indicated the involvement of certain genes under stress conditions. The upregulation of the P450 genes under methyl jasmonate and fungal stress justifies the involvement of specific genes in secondary metabolite biosynthesis. Our results provide a foundation for further elucidating the actual function and role of P450 involved in various biochemical pathways in P. ginseng.

Key words

abiotic biotic ESTs gene expression in silico Panax ginseng secondary metabolites 

Abbreviations

CDART

conserved domain architecture retrieval tool

EST

Expressed Sequence Tags

MeJA

methyl jasmonate

P450

cytochrome P450

qRT-PCR

quantitative real time reverse transcriptase-polymerase chain reaction

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Klingenberg, M. (1958) Arch. Biochem. Biophys., 75, 376–386.PubMedCrossRefGoogle Scholar
  2. 2.
    Werck-Reichhart, D., and Feyereisen, R. (2000) Genome Biol., 1, REVIEWS, 3003.Google Scholar
  3. 3.
    Chapple, C. (1998) Annu. Rev. Plant Physiol. Plant Mol. Biol., 49, 311–343.PubMedCrossRefGoogle Scholar
  4. 4.
    Nelson, D. R., Koymans, L., Kamataki, T., Stegeman, J. J., Feyereisen, R., Waxman, D. J., Waterman, M. R., Gotoh, O., Coon, M. J., Estabrook, R. W., Gunsalus, I. C., and Nebert, D. W. (1996) Pharmacogenetics, 6, 1–42.PubMedCrossRefGoogle Scholar
  5. 5.
    Nelson, D. R. (1999) Arch. Biochem. Biophys., 369, 1–10.PubMedCrossRefGoogle Scholar
  6. 6.
    Nelson, D. R., Schuler, M. A., Paquette, S. M., Werck-Reichert, D., and Bak, S. (2004) Plant Physiol., 135, 756–772.PubMedCrossRefGoogle Scholar
  7. 7.
    Durst, F., and Nelson, D. R. (1995) Drug Metab. Drug Interact., 12, 189–206.CrossRefGoogle Scholar
  8. 8.
    Paquette, S. M., Bak, S., and Feyereisen, R. (2000) DNA Cell Biol., 19, 307–317.PubMedCrossRefGoogle Scholar
  9. 9.
    Christoffersen, R. E., Percival, F. W., and Bozak, K. (1995) in Drug Metabolism and Drug Interactions (Durst, F., and O’Keefe, D. P., eds.) Freund, UK, pp. 207–219.Google Scholar
  10. 10.
    Woo, S. S., Song, J. S., Lee, J. Y., In, D. S., Chung, H. J., Liu, J. R., and Choi, D. W. (2004) Phytochemistry, 65, 2751–2761.PubMedCrossRefGoogle Scholar
  11. 11.
    Jung, J. D., Park, H. W., Hur, C. G., In, D. S., Chung, H. J., Liu, J. R., and Choi, D. W. (2003) Plant Cell Rep., 22, 224–230.PubMedCrossRefGoogle Scholar
  12. 12.
    Parvin, S., Pulla, R. K., Kim, Y. J., Sathiyaraj, G., Jung, S. K., Khorolragchaa, A., In, J. G., and Yang, D. C. (2009) J. Ginseng Res., 33, 249–255.CrossRefGoogle Scholar
  13. 13.
    Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990) J. Mol. Biol., 215, 403–410.PubMedGoogle Scholar
  14. 14.
    Masoudi-Nejad, A., Tonomura, K., Kawashima, S., Moriya, Y., Suzuki, M., Itoh, M., Kanehisa, M., Endo, T., and Goto, S. (2006) Nucleic Acids Res., 34, W459–W462.PubMedCrossRefGoogle Scholar
  15. 15.
    Huang, X., and Madan, A. (1999) Genome Res., 9, 868–877.PubMedCrossRefGoogle Scholar
  16. 16.
    Emanuelson, O., Nielsen, H., Brunak, S., and Heijne (2000) J. Mol. Biol., 300, 1005–1016.CrossRefGoogle Scholar
  17. 17.
    Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., and Higgins, D. G. (1997) Nucleic Acids Res., 25, 4876–4882.PubMedCrossRefGoogle Scholar
  18. 18.
    Tamura, K., Dudley, J., Nei, M., and Kumar, S. (2007) Mol. Biol. Evol., 24, 1596–1599.PubMedCrossRefGoogle Scholar
  19. 19.
    Murashige, T., and Skoog, F. (1962) Physiol. Plant, 15, 473–497.CrossRefGoogle Scholar
  20. 20.
    Sathiyamoorthy, S., In, J. G., Sathiyaraj, G., Kim, Y. J., and Yang, D. C. (2009) Mol. Biol. Rep., 46, 932–939.Google Scholar
  21. 21.
    Kim, J. H., Kim, S. G., Kim, M. S., Jeon, Y. H., Cho, D. H., and Kim, Y. H. (2009) Plant Pathol. J., 25, 1–5.CrossRefGoogle Scholar
  22. 22.
    Sathiyaraj, G., Srinivasan, S., Sathiyamoorthy, S., Kim, Y. J., Kim, Y. J., Kwon, S. W., and Yang, D. C. (2010) Mol. Biol. Rep., 37, 3445–3454.PubMedCrossRefGoogle Scholar
  23. 23.
    Tanabe, S., Ashikari, M., Fujioka, S., Takatsuto, S., Youshida, S., Yano, M., Yoshimura, A., Kitano, H., Matsuoka, M., Fujisawa, Y., Kato, H., and Iwasaki, Y. (2005) Plant Cell, 17, 776–790.PubMedCrossRefGoogle Scholar
  24. 24.
    Mizutani, M., and Ohta, D. (2010) Annu. Rev. Plant Biol., 61, 291–315.PubMedCrossRefGoogle Scholar
  25. 25.
    Gill, N., Findley, S., Walling, J. G., Hans, C., Ma, J., Doyle, J., Stacey, G., and Jackson, S. A. (2009) Plant Physiol., 151, 1167–1174.PubMedCrossRefGoogle Scholar
  26. 26.
    Sun, C., Li, Y., Wu, Q., Luo, H., Sun, H., Song, J., Lui, E. M. K., and Chen, S. (2010) BMC Genomics, 11, 262.PubMedCrossRefGoogle Scholar
  27. 27.
    Williams, P. A., Cosme, J., Sridhar, V., Johnson, E. F., and Mc Ree, D. E. (2000) Mol. Cell, 5, 121–131.PubMedCrossRefGoogle Scholar
  28. 28.
    Guttikonda, S. K., Trupti, J., Bisht, N. C., Chen, H., An, Y. Q. C., Pandey, S., Xu, D., and Yu, O. (2010) BMC Plant Biol., 10, 243–261.PubMedCrossRefGoogle Scholar
  29. 29.
    Dobritsa, A. A., Shrestha, J., Morant, M., Pinot, F., Matsuno, M., Swanson, R., Moller, B. L., and Preuss, D. (2009) Plant Physiol., 151, 574–589.PubMedCrossRefGoogle Scholar
  30. 30.
    Kandel, S., Sauveplane, V., Olry, A., Diss, L., Benveniste, I., and Pinot, F. (2006) Phytochem. Rev., 5, 359–372.CrossRefGoogle Scholar
  31. 31.
    Mizutani, M., Ward, E., DiMaio, J., Ohta, D., Ryals, J., and Sata, R. (1993) Biochem. Biophys. Res. Commun., 190, 875–880.PubMedCrossRefGoogle Scholar
  32. 32.
    Frank, M. R., Deyneka, J. M., and Schuler, M. A. (1996) Plant Physiol., 110, 1035–1046.PubMedCrossRefGoogle Scholar
  33. 33.
    Anastasiou, E., Kenz, S., Gerstung, M., MacLean, D., Timmer, J., Fleck, C., and Lenhard, M. (2007) Dev. Cell, 13, 843–856.PubMedCrossRefGoogle Scholar
  34. 34.
    Wellesen, K., Durst, F., Pinot, F., Benveniste, I., Nettesheism, K., Wisman, E., Steiner-Lange, S., Saedler, H., and Yephremov, A. (2001) Proc. Natl. Acad. Sci. USA, 98, 94–99.CrossRefGoogle Scholar
  35. 35.
    Helliwell, C. A., Chandler, P. M., Poole, A., Dennis, E. S., and Peacock, W. J. (2001) Proc. Natl. Acad. Sci. USA, 98, 2065–2070.PubMedCrossRefGoogle Scholar
  36. 36.
    Hallahan, D. L., Lau, S. M., Harder, P. A., Smiley, D. W., Dawson, G. W., Pickett, J. A., Christoffersen, R. E., and O’Keefe, D. P. (1994) Drug Metab. Interact., 12, 285–297.Google Scholar
  37. 37.
    Irmler, S., Schroder, G., St-Pierre, B., Crouch, N. P., Hotze, M., Schmidt, J., Strack, D., Matern, U., and Schroder, J. (2000) Plant J., 24, 797–804.PubMedCrossRefGoogle Scholar
  38. 38.
    Noguchi, T., Fujioka, S., Choe, S., Takatsuto, S., Tax, F. E., Yoshida, S., and Feldmann, K. A. (2000) Plant Physiol., 124, 201–209.PubMedCrossRefGoogle Scholar
  39. 39.
    Kim, B. G., Ko, J. H., Hur, H. G., and Ahn, J. H. (2004) Agric. Chem. Biotechnol., 47, 173–177.Google Scholar
  40. 40.
    Nagaraj, S. H., Gasser, R. B., and Ranganathan, S. (2007) Brief Bioinform., 8, 6–21.PubMedCrossRefGoogle Scholar
  41. 41.
    Pal, D. (2006) Bioinformation, 1, 97–98.PubMedGoogle Scholar
  42. 42.
    Yendo, A. C., de Costa, F., Gosmann, G., and Fett-Neto, A. G. (2010) Mol. Biotechnol., 46, 94–104.PubMedCrossRefGoogle Scholar
  43. 43.
    Osbourn, E. A. (1996) The Plant Cell, 8, 1821–1831.PubMedCrossRefGoogle Scholar
  44. 44.
    Ralston, L., Kwon, S. T., Schoenbeck, M., Ralston, J., Schenk, D. J., Coates, R. M., and Chappell, J. (2001) Arch. Biochem. Biophys., 393, 222–235.PubMedCrossRefGoogle Scholar
  45. 45.
    Harrison, T. L., Zangerl, A. R., Schuler, M. A., and Berenbaum, M. R. (2001) Arch. Insect Biochem. Physiol., 48, 179–189.PubMedCrossRefGoogle Scholar
  46. 46.
    Werck-Reichhart, D., Bak, S., and Paquette, S. (2002) in Cytochrome P450 (Somerville, C. R., and Meyerowitz, E. M., eds.) American Society of Plant Biologists, Rockville, MD, doi/10.1199/tab.0028, http://www.aspb.org/oublications/arabidopsis.Google Scholar
  47. 47.
    Kolattukudy, P. E., Rogers, L. M., Li, D., Hwang, C. S., Beilen, H. S., and Qrtiz de Montellano, P. R. (1993) J. Biol. Chem., 258, 4202–4207.Google Scholar
  48. 48.
    Whitbred, J. M. (1998) MS dissertation, University of Illinois Urbana-Champaign.Google Scholar
  49. 49.
    Oh, B. J., Ko, M. K., Kim, Y. S., Kim, K. S., Kostenyuk, I., and Kee, K. H. (1999) MPMI, 12, 1044–1052.PubMedCrossRefGoogle Scholar
  50. 50.
    Keeling, C. I., and Bohlmann, J. (2006) Phytochemistry, 67, 2415–2423.PubMedCrossRefGoogle Scholar
  51. 51.
    Leveau, J. H. J. (2006) in Microbial Communities in the Phyllosphere (Riederer, M., and Muller, C., eds.) Blackwell, Oxford, pp. 334–367.Google Scholar
  52. 52.
    Creelman, R. A., and Mullet, J. E. (1992) Proc. Natl. Acad. Sci. USA, 89, 4938–4941.PubMedCrossRefGoogle Scholar
  53. 53.
    Felton, G. W., Korth, K. L., Bi, J. L., Wesley, S. V., Huhman, D. V., Mathews, M. C., Murphy, J. B., Lamb, C., and Dixon, R. A. (1999) Curr. Biol., 9, 317–320.PubMedCrossRefGoogle Scholar
  54. 54.
    Preston, C. A., Lewendowski, C., Enyedi, A. J., and Balswin, I. T. (1999) Planta, 209, 87–95.PubMedCrossRefGoogle Scholar
  55. 55.
    Shim, J. S., Kim, Y. J., Jung, S. K., Kwon, W. S., Kim, S. Y., and Yang, D. C. (2009) J. Ginseng Res., 33, 212–218.CrossRefGoogle Scholar
  56. 56.
    Kessmann, H., Choudhary, A. D., and Dixon, R. A. (1990) Plant Cell Rep., 9, 38–41.CrossRefGoogle Scholar

Copyright information

© Pleiades Publishing, Ltd. 2011

Authors and Affiliations

  • Balusamy Sri Renuka Devi
    • 1
  • Yu-Jin Kim
    • 1
  • Subramaniyum Sathiyamoorthy
    • 1
  • Altanzul Khorolragchaa
    • 1
  • Sathiyaraj Gayathri
    • 1
  • Shohana Parvin
    • 1
  • Dong-Uk Yang
    • 1
  • Senthil Kalai Selvi
    • 2
  • Ok Ran Lee
    • 1
  • Sungyoung Lee
    • 3
  • Deok-Chun Yang
    • 1
    Email author
  1. 1.Korean Ginseng Center and Ginseng Genetic Resource BankKyung Hee UniversityGyeonggi-doSouth Korea
  2. 2.Avinashilingam University for WomenCoimbatoreIndia
  3. 3.Department of Computer EngineeringKyung Hee UniversitySeocheonSouth Korea

Personalised recommendations