Skip to main content
SpringerLink
Log in

Comparative Analysis and Modeling of Superoxide Dismutases (SODs) in Brachypodium distachyon L.

  • Published:
Applied Biochemistry and Biotechnology Aims and scope Submit manuscript

Abstract

Superoxide dismutase (SOD, EC 1.15.1.1) is an enzyme catalyzing the dismutation of superoxide radical to hydrogen peroxide and dioxygen. To date, four types of SODs — Cu/ZnSOD, MnSOD, FeSOD, and NiSOD — have been identified. In this study, SOD proteins of Brachypodium distachyon (L.) Beauv. were screened by utilization of bioinformatics approaches. According to our results, Mn/FeSODs and Cu/ZnSODs of B. distachyon were found to be in basic and acidic character, respectively. Domain analyzes of SOD proteins revealed that iron/manganese SOD and copper/zinc SOD were within studied SOD proteins. Based on the seconder structure analyzes, Mn/FeSODs and Cu/ZnSODs of B. distachyon were found as having similar sheets, turns and coils. Although helical structures were noticed in the types of Mn/FeSODs, no the type of Cu/ZnSODs were identified having helical structures. The predicted binding sites of Fe/MnSODs and Cu/ZnSODs were confirmed for having His-His-Asp-His and His-His-His-Asp-Ser residues with different positions, respectively. The 3D structure analyzes of SODs revealed that some structural divergences were observed in patterns of SODs domains. Based on phylogenetic analysis, Mn/FeSODs were found to have similarities whereas Cu/ZnSODs were clustered independently in phylogenetic tree.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

Abbreviations

SOD:

Superoxide dismutase

FeSOD:

Iron superoxide dismutase

MnSOD:

Manganese superoxide dismutase

Cu/ZnSOD:

Copper/zinc superoxide dismutase

ROS:

Reactive oxygen species

References

  1. Uzilday, B., Turkan, I., Ozgur, R., & Sekmen, A. H. (2014). Journal of Plant Physiology, 171, 65–75.

    Article  CAS  Google Scholar 

  2. Sharma, P., Jha, A. B., Dubey, R. S., & Pessarakli, M. (2012). Journal of Botany. doi:10.1155/2012/217037.

    Google Scholar 

  3. Smirnoff, N. (1993). New Phytologist, 125, 27–58.

    Article  CAS  Google Scholar 

  4. Sainz, M., Diaz, P., Monza, J., & Borsani, O. (2010). Physiologia Plantarum, 140, 46–56.

    Article  CAS  Google Scholar 

  5. Liochev, S., & Fridovich, I. (1994). Free Radical Biology and Medicine, 16, 29–33.

    Article  CAS  Google Scholar 

  6. Abreu, I. A., & Cabelli, D. E. (2010). Biochimica et Biophysica Acta, 1804, 263–274.

    Article  CAS  Google Scholar 

  7. Youn, H. D., Kim, E. J., Roe, J. H., Hah, Y. C., & Kang, S. O. (1996). Biochemical Journal, 318, 889–896.

    CAS  Google Scholar 

  8. Miller, A. F. (2012). FEBS Letters, 586, 585–595.

    Article  CAS  Google Scholar 

  9. Carlioz, A., & Touati, D. (1986). EMBO Journal, 5, 623–630.

    CAS  Google Scholar 

  10. Møller, I. M. (2001). Annual Review of Plant Physiology and Plant Molecular Biology, 52, 561–591.

    Article  Google Scholar 

  11. del Río, L. A., Sandalio, L. M., Altomare, D. A., & Zilinskas, B. A. (2003). Journal of Experimental Botany, 54, 923–933.

    Article  Google Scholar 

  12. Fink, R. C., & Scandalios, J. G. (2002). Archives of Biochemistry and Biophysics, 399, 19–36.

    Article  CAS  Google Scholar 

  13. Pilon, M., Ravet, K., & Tapken, W. (2011). Biochimica et Biophysica Acta, 1807, 989–998.

    Article  CAS  Google Scholar 

  14. Whittaker, J. W. (2003). Biochemical Society Transactions, 31, 1318–1321.

    Article  CAS  Google Scholar 

  15. Kliebenstein, D. J., Monde, R. A., & Last, R. L. (1998). Plant Physiology, 118, 637–650.

    Article  CAS  Google Scholar 

  16. Kernodle, S. P., & Scandalios, J. G. (2001). Archives of Biochemistry and Biophysics, 391, 137–147.

    Article  CAS  Google Scholar 

  17. Fernández-Ocána, A., Chaki, M., Luque, F., Gómez-Rodríguez, M. V., Carreras, A., Valderrama, R., et al. (2011). Journal of Plant Physiology, 168, 1303–1308.

    Article  Google Scholar 

  18. Muñoz, I. G., Moran, J. F., Becana, M., & Montoya, G. (2005). Protein Science, 14, 387–394.

    Article  Google Scholar 

  19. Draper, J., Mur, L. A. J., Jenkins, G., Ghosh-Biswas, G. C., Bablak, P., Hasterok, R., et al. (2001). Plant Physiology, 127, 1539–1555.

    Article  CAS  Google Scholar 

  20. Ozdemir, B. S., Hernandez, P., Filiz, E., & Budak, H. (2008). International Journal of Plant Genomics. doi:10.1155/2008/536104. Article ID 536104.

    Google Scholar 

  21. Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M. R., Appel, R. D., et al. (2005). In J. M. Walker (Ed.), The proteomics protocols handbook (pp. 571–607). Totowa, NJ, USA: Humana Press.

    Chapter  Google Scholar 

  22. Geourjon, C., & Deléage, G. (1995). Computer Applications in the Biosciences, 11, 681–684.

    CAS  Google Scholar 

  23. Timothy, L., Mikael Bodén, B., Buske, F. A., Frith, M., Grant, C. E., Clementi, L., et al. (2009). Nucleic Acids Research, 37, 202–208.

    Article  Google Scholar 

  24. Yu, C. S., Chen, Y. C., Lu, C. H., & Hwang, K. (2006). Proteins: Structure, Function, and Bioinformatics, 64, 643–651.

    Article  CAS  Google Scholar 

  25. Horton, P., Park, K., Obayashi, T., Fujita, N., Harada, H., Adams-Collier, C. J., et al. (2007). Nucleic Acids Research. doi:10.1093/nar/gkm259.

    Google Scholar 

  26. Guo, A. Y., Zhu, Q. H., Chen, X., & Luo, J. C. (2007). Yi Chuan, 29, 1023–1026.

    Article  CAS  Google Scholar 

  27. Wass, M. N., Kelley, L. A., & Sternberg, M. J. (2010). Nucleic Acids Research, 38(Suppl), 469–473.

    Article  Google Scholar 

  28. Guex, N., Peitsch, M. C., & Schwede, T. (2009). Electrophoresis, 1(Suppl), S162–S173.

    Article  Google Scholar 

  29. Lovell, S. C., Davis, I. W., Arendall, W., Bakker, P. I. W., Word, J. M., Prisant, M. G., et al. (2003). Proteins: Structure, Function, and Genetics, 50, 437–450.

    Article  CAS  Google Scholar 

  30. Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., et al. (2007). Bioinformatics, 23, 2947–2948.

    Article  CAS  Google Scholar 

  31. Felsenstein, J. (1985). Evolution, 39, 783–791.

    Article  Google Scholar 

  32. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011). Molecular Biology and Evolution, 28, 2731–2739.

    Article  CAS  Google Scholar 

  33. Jones, D. T., Taylor, W. R., & Thornton, J. M. (1992). Computer Applications in the Biosciences, 8, 275–282.

    CAS  Google Scholar 

  34. Zuckerkandl, E., & Pauling, L. (1965). Edited in Evolving Genes and Proteins by Bryson V. Vogel HJ: Academic Press New York.

    Google Scholar 

  35. Perry, J. J. P., Shin, D. S., Getzoff, E. D., & Tainer, J. A. (2010). Biochimica et Biophysica Acta, 1804, 245–262.

    Article  CAS  Google Scholar 

  36. Dehury, B., Sarma, K., Sarmah, R., Sahu, J., Sahoo, S., Sahu, M., et al. (2012). Journal of Plant Biochemistry and Biotechnology, DOI 10.1007/s13562-012-0121-6. Long M 2002.

  37. Gopavajhula, V. R., Chaitanya, K. V., Khan, P. A. A., Shaik, J. P., Reddy, P. N., & Alanazi, M. (2013). Genetics and Molecular Biology, 36, 225–236.

    Article  CAS  Google Scholar 

  38. Buxbaum, E. (2007). Fundamentals of protein structure and function. New York: Springer Science Business Media.

    Google Scholar 

  39. Miller, A. F. (2004). Current Opinion in Chemical Biology, 8, 162–168.

    Article  CAS  Google Scholar 

  40. Grishin, N. V. (2001). Journal of Structural Biology, 134, 167–185.

    Article  CAS  Google Scholar 

  41. Kinch, L. N., & Grishin, N. V. (2002). Current Opinion in Structural Biology, 12, 400–408.

    Article  CAS  Google Scholar 

  42. Richardson, J. S. (1977). Nature, 268, 495–500.

    Article  CAS  Google Scholar 

  43. Lah, M. S., Dixon, M. M., Pattridge, K. A., Stallings, W. C., Fee, J. A., & Ludwig, M. L. (1995). Biochemistry, 34, 1646–1660.

    Article  CAS  Google Scholar 

  44. Gupta, R. S. (1998). Microbiology and Molecular Biology Reviews, 62, 1435–1491.

    CAS  Google Scholar 

  45. Balasubramanian, A., Das, S., Bora, A., Sarangi, S., & Mandal, A. B. (2012). American Journal of Plant Sciences, 3, 1311–1321.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Crop and Animal Production, Cilimli Vocational School, Duzce University, 81750, Cilimli, Duzce, Turkey

    Ertugrul Filiz

  2. Faculty of Science, Department of Molecular Biology and Genetics, Gebze Institute of Technology, Gebze, Kocaeli, 41400, Turkey

    Ibrahim Koc

  3. Faculty of Science and Arts, Department of Biology, Marmara University, 34722, Goztepe, Istanbul, Turkey

    Ibrahim Ilker Ozyigit

Authors
  1. Ertugrul Filiz
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ibrahim Koc
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ibrahim Ilker Ozyigit
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ertugrul Filiz.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Filiz, E., Koc, I. & Ozyigit, I.I. Comparative Analysis and Modeling of Superoxide Dismutases (SODs) in Brachypodium distachyon L.. Appl Biochem Biotechnol 173, 1183–1196 (2014). https://doi.org/10.1007/s12010-014-0922-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12010-014-0922-2

Keywords

Search

Navigation