Applied Biochemistry and Biotechnology

, Volume 174, Issue 4, pp 1272–1285 | Cite as

In Silico Analysis of DREB Transcription Factor Genes and Proteins in Grasses

  • Ertugrul FilizEmail author
  • Huseyin Tombuloğlu


Plants are exposed to various environmental stresses, including drought, salinity, low temperature, etc. Dehydration responsive element binding (DREB) genes, the members of AP2/ERF transcription factor family, regulate the biological processes against cold and dehydration stresses. In this study, we analyzed a total of 19 DREB transcription factor genes and proteins from 14 grass species by using bioinformatic approaches, including their physiochemical properties, conserved motif structures, homology models, and phylogenetic relationships. The domain analysis showed that all grass species contained an AP2 domain whereas some residual substitutions and/or insertions were observed in the AP2 domains of some grasses. The physiochemical analysis revealed that many DREB proteins (89.5 %) were of acidic character while the number of amino acids ranged from 213 (Aegilops speltoides subsp. speltoides) to 394 (Triticum aestivum). Based on the subcellular prediction, 16 of 19 DREB proteins were predicted to be localized in the nuclear region. According to the sequence analysis of grass DREBs, the average value of pairwise distance was found to be 0.588, while nucleotide diversity (π) was found to be 0.435. Thus, among all DREB proteins, two most divergent ones (Oryza sativa and Avena sativa) were selected for 3D structure and protein cavity comparison. In addition, 19 DREB proteins were analyzed according to their phylogenetic relationships, and as a consequence, two main groups were observed. In this study, our analyses could be a scientific base to understand DREB genes and proteins to further wet lab studies in plants, particularly in grass species.


DREB AP2/ERF Grass Protein modeling In silico analysis 



Dehydration responsive element binding




Low-temperature-responsive element


C-repeat binding factor


Conflict of Interest

The authors confirm that the contents of this article have no conflicts of interest.

Supplementary material

12010_2014_1093_Fig9_ESM.jpg (201 kb)

(JPEG 201 kb)

12010_2014_1093_MOESM1_ESM.tif (956 kb)
High Resolution Image (TIFF 956 kb)


  1. 1.
    Yamaguchi-Shinozaki, K., & Shinozaki, K. (2006). Annual Review of Plant Biology, 57, 781–803.CrossRefGoogle Scholar
  2. 2.
    Knight, H., & Knight, M. R. (2001). Trends in Plant Science, 6, 262–267.CrossRefGoogle Scholar
  3. 3.
    Lata, C., & Prasad, M. (2011). Journal of Experimental Botany, 14, 4731–4748.CrossRefGoogle Scholar
  4. 4.
    Shinozaki, K., Yamaguchi-Shinozaki, K., & Seki, M. (2003). Current Opinion in Plant Biology, 5, 410–417.CrossRefGoogle Scholar
  5. 5.
    Agarwal, P. K., Agarwal, P., Reddy, M. K., & Sopory, S. K. (2006). Plant Cell Reports, 25, 1263–1274.CrossRefGoogle Scholar
  6. 6.
    Sakuma, Y., Maruyama, K., Osakabe, Y., Qin, F., Seki, M., Shinozaki, K., & Yamaguchi-Shinozaki, K. (2006). The Plant Cell, 18, 1292–1309.CrossRefGoogle Scholar
  7. 7.
    Stockinger, E. J., Gilmour, S. J., & Thomashow, M. F. (1997). Proceedings of the National Academy of Sciences of the United States of America, 94, 1035–1040.CrossRefGoogle Scholar
  8. 8.
    Liu, Q., Kasuga, M., Sakuma, Y., Abe, H., Miura, S., Yamaguchi-Shinozaki, K., & Shinozaki, K. (1998). Plant Cell, 10, 1391–1406.CrossRefGoogle Scholar
  9. 9.
    Furihata, T., Maruyama, K., Fujita, Y., Umezawa, T., Yoshida, R., Shinozaki, K., & Yamaguchi-Shinozaki, K. (2006). Proceedings of the National Academy of Sciences of the United States of America, 103, 1988–1993.CrossRefGoogle Scholar
  10. 10.
    Nakashima, K., Ito, Y., & Yamaguchi-Shinozaki, K. (2009). Plant Physiology, 149, 88–95.CrossRefGoogle Scholar
  11. 11.
    Sakuma, Y., Liu, Q., Dubouzet, J. G., Abe, H., Shinozaki, K., & Yamaguchi–Shinozaki, K. (2002). Biochemical and Biophysical Research Communications, 290, 998–1009.CrossRefGoogle Scholar
  12. 12.
    Timothy, L., Mikael Bodén, B., Buske, F. A., Frith, M., Grant, C. E., Clementi, L., Ren, J., Li, W. W., & Noble, W. S. (2009). Nucleic Acids Research, 37, 202–208.CrossRefGoogle Scholar
  13. 13.
    Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M. R., Appel, R. D., et al. (2005). Protein identification and analysis tools on the ExPASy server, In: John M. Walker (ed): The Proteomics Protocols Handbook Humana, 571–607.Google Scholar
  14. 14.
    Yu, C. S., Chen, Y. C., Lu, C. H., & Hwang, K. (2006). Proteins: Structure Function and Bioinformatics, 64, 643–651.CrossRefGoogle Scholar
  15. 15.
    Horton, P., Park, K., Obayashi, T., Fujita, N., Harada, H., Adams-Collier, C. J., & Nakai, K. (2007). Nucleic Acids Research. doi: 10.1093/nar/gkm259.Google Scholar
  16. 16.
    Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994). Nucleic Acids Research, 22, 4673–4680.CrossRefGoogle Scholar
  17. 17.
    Schneider, T. D., & Stephens, R. M. (1990). Nucleic Acids Research, 18, 6097–6100.CrossRefGoogle Scholar
  18. 18.
    Crooks, G. E., Hon, G., Chandonia, J. M., & Brenner, S. E. (2004). Genome Research, 14, 1188–1190.CrossRefGoogle Scholar
  19. 19.
    Saitou, N., & Nei, M. (1987). Molecular Biology and Evolution, 4, 406–425.Google Scholar
  20. 20.
    Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011). Molecular Biology and Evolution, 28, 2731–2739.CrossRefGoogle Scholar
  21. 21.
    Felsenstein, J. (1985). Evolution, 39, 783–791.CrossRefGoogle Scholar
  22. 22.
    Tajima, F. (1989). Genetics, 123, 585–595.Google Scholar
  23. 23.
    Tamura, K., Nei, M., & Kumar, S. (2004). Proceedings of the National Academy of Sciences of the United States of America, 101, 11030–11035.CrossRefGoogle Scholar
  24. 24.
    Tamura, K., & Nei, M. (1993). Molecular Biology and Evolution, 10, 512–526.Google Scholar
  25. 25.
    Buchan, D. W. A., Minneci, F., Nugent, T. C. O., Bryson, K., & Jones, D. T. (2013). Nucleic Acids Research, 41, 340–348.CrossRefGoogle Scholar
  26. 26.
    Lovell, S. C., Davis, I. W., Arendall, W. B., Bakker, P. I. W., Word, J. M., Prisant, M. G., Richardson, J. S., & Richardson, D. C. (2003). Proteins: Structure Function and Genetics, 50, 437–450.CrossRefGoogle Scholar
  27. 27.
    Guex, N., & Peitsch, M. C. (1997). Electrophoresis, 18, 2714–2723.CrossRefGoogle Scholar
  28. 28.
    Reineke, A. R., Bornberg-Bauer, E., & Gu, J. (2011). Nucleic Acids Research, 39, 6029–6043.CrossRefGoogle Scholar
  29. 29.
    Rosenberg, M. S., Subramanian, S., & Kumar, S. (2003). Patterns of transitional mutation biases within and among mammalian genomes. Molecular Biology and Evolution, 20, 988–993.CrossRefGoogle Scholar
  30. 30.
    Nei, M., & Li, W. H. (1979). PNAS, 76, 5269–5273.CrossRefGoogle Scholar
  31. 31.
    Hao, D., Ohme-Takagi, M., & Sarai, A. (1998). The Journal of Biological Chemistry, 273, 26857–26861.CrossRefGoogle Scholar
  32. 32.
    Shigyo, M., Hasebe, M., & Ito, M. (2006). Gene, 366, 256–265.CrossRefGoogle Scholar
  33. 33.
    Falcon, C. M., & Matthews, K. S. (1999). Journal of Biological Chemistry, 274, 30849–30857.CrossRefGoogle Scholar
  34. 34.
    Watanabe, T. M., Imada, K., Yoshizawa, K., Nishiyama, M., Kato, C., Abe, F., & Yanagida, T. (2013). PLoS ONE, 8, e73212.CrossRefGoogle Scholar
  35. 35.
    Wang, S. X., Wang, Z. Y., & Peng, Y. K. (2004). Plant Physiology Communication, 40, 7–13.Google Scholar
  36. 36.
    Rayon, C., Lerouge, P., & Faye, L. (1998). Journal of Experimental Botany, 49, 1463–1472.CrossRefGoogle Scholar
  37. 37.
    Doebley, J., & Lukens, L. (1998). Plant Cell, 10, 1075–1082.CrossRefGoogle Scholar
  38. 38.
    Saleh, A., & Pagés, M. (2003). Genetika, 35, 37–50.CrossRefGoogle Scholar
  39. 39.
    Saito, H., Kashida, S., Inoue, T., & Inoue, K. (2007). Nucleic Acids Research, 35, 6357–6366.CrossRefGoogle Scholar
  40. 40.
    Bjorklund, A. K., Ekman, D., Light, S., Frey-Skott, J., & Elofsson, A. (2005). Journal of Molecular Biology, 353, 911–923.CrossRefGoogle Scholar
  41. 41.
    Hubbard, S. J., Gross, K. H., & Argos, P. (1994). Protein Engineering, 7, 613–626.CrossRefGoogle Scholar
  42. 42.
    Liang, J., Edelsbrunner, H., Fu, P., Sudhakar, P. V., & Subramaniam, S. (1998). Proteins: Structure Function and Genetics, 33, 18–29.CrossRefGoogle Scholar
  43. 43.
    Chen, J. Q., Meng, X. P., Zhang, Y., Xia, M., & Wang, X. P. (2008). Biotechnology Letters, 30, 2191–2198.CrossRefGoogle Scholar
  44. 44.
    Zhang, J. (2003). Trends in Ecology & Evolution, 18, 292–298.CrossRefGoogle Scholar
  45. 45.
    Cannon, S. B., Mitra, A., Baumgarten, A., Young, N. D., & May, G. (2004). BMC Plant Biology, 4, 53–62.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  1. 1.Department of Crop and Animal Production, Cilimli Vocational SchoolDüzce UniversityÇilimliTurkey
  2. 2.Department of Biology, Faculty of Science and ArtsFatih UniversityBüyükçekmeceTurkey

Personalised recommendations