Skip to main content
SpringerLink
Log in

Cloning, Sequence Analysis and Three-dimensional Structure Prediction of DNA Pol I from Thermophilic Geobacillus sp. MKK Isolated from an Iranian Hot Spring

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

Abstract

Molecular phylogenetic analysis of a novel thermophilic eubacterium isolated from an Iranian hot spring using 16S rDNA sequence showed that the new isolate belongs to genera Geobacillus. DNA pol I gene from this isolate was amplified, cloned, sequenced, and the three-dimensional (3D) structure of deduced amino acid sequence was predicted. Sequence analysis revealed the gene is 2,631 bp long, encodes a protein of 876 amino acids with a calculated molecular mass of 99 kDa, and belongs to family A DNA polymerases. Comparison of 3′–5′exonuclease domain of Klenow fragment (KF) with corresponding region of newly identified DNA pol I (MF), the large fragment of Bacillus stearothermophilus DNA pol I (BF) and Klentaq1, revealed not only deletions in three regions compared to KF, but that three of the four critical metal-binding residues in KF (Asp355, Glu357, Asp424, and Asp501) are altered in MF as well. Predicted 3D structure and sequence alignments between MF and BF showed that all critical residues in the polymerase active site are conserved.

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

Similar content being viewed by others

Abbreviations

KF:

Klenow fragment of E. coli DNA pol I

BF:

large fragment of Bacillus stearothermophilus DNA pol I

Klentaq1:

Klenow-like fragment of Taq DNA polymerase

MF:

Klenow-like region of Geobacillus sp. MKK DNA pol I

Gsm pol I :

DNA pol I of Geobacillus sp. MKK

References

  1. Fileé, J., Forterre, P., Sen-Lin, T., & Laurent, J. (2002). Journal of Molecular Evolution, 54, 763–773.

    Article  Google Scholar 

  2. Choi, J. J., Jung, S. E., Kim, H., & Kwon1, S. (1999). Biotechnology and Applied Biochemistry, 30, 19–25.

    CAS  Google Scholar 

  3. Chien, A., Edgar, D. B., Trela, J. M. (1976). Journal of Bacteriology, 127(3), 1550–1557.

    CAS  Google Scholar 

  4. Kaledin, A. S., Slyusarenko, A. G., & Gorodetskii, S. I. (1980). Biokhimiia, 45(4), 644–651.

    CAS  Google Scholar 

  5. Shandilya, H., Griffiths, K., Flynn, E. K., Astatke, M., Shih, P., Lee, J. E., et al. (2004). Extremophiles, 8, 243–251.

    Article  CAS  Google Scholar 

  6. Tafreshi, N. K., Sadeghizadeh, M., Olyaee, S., Ahadi, A. M., Jahanzad, I., & Roostaee, M. H. (2005). Journal of Clinical Virology, 32, 318–324.

    Article  CAS  Google Scholar 

  7. Sleigh, J., Cursons, R., & Pine, M. L. (2001). Intensive Care Medicine, 27, 1269–1273.

    Article  CAS  Google Scholar 

  8. Paas, Y., Devillers-Thiéry, A., Teichberg, V. I., Changeux, J., & Eisenstein, M. (2000). Trends in Pharmacological Sciences, 21(3), 87–92.

    Article  CAS  Google Scholar 

  9. Kiefer, J. R., Mao, C., Hansen, C. J., Basehore, S. L., Hogrefe, H. H., Braman, J. C., et al. (1997). Structure, 5, 95–108.

    Article  CAS  Google Scholar 

  10. Kornberg, A. (1960). Science, 131, 1503–1508.

    Article  CAS  Google Scholar 

  11. Delarue, M., Poch, O., Tordo, N., Moras, D., & Argos, P. (1990). Protein Engineering, 3, 461–467.

    Article  CAS  Google Scholar 

  12. Kohlstaedt, L. A., Wang, J., Friedman, J. M., Rice, P. A., & Steitz, T. A. (1992). Science, 256, 1783–1790.

    Article  CAS  Google Scholar 

  13. Molina, A. J., & Arnold, E. (1993). Proceedings of the National Academy of Sciences of the United States of America, 90, 6320–6324.

    Article  Google Scholar 

  14. Georgiadis, M. M., Jessen, S. M., Ogata, C. M., Telesnitsky, A., Goff, S. P., & Hendrickson, W. A. (1995). Structure, 3, 879–892.

    Article  CAS  Google Scholar 

  15. Rose, T. M., Schultz, E. R., Heniko, J. G., Pietrokovski, S., McCallum, C. M., & Heniko, S. (1998). Nucleic Acids Research, 26, 1637–1644.

    Article  Google Scholar 

  16. Sajedi, R. H., Naderi-Manesh, H., Khajeh, K., Ranjbar, B., Ghaemi, N., & Naderi-Manesh, M. (2004). Applied Biochemistry and Biotechnology, 119(1), 41–50.

    Article  CAS  Google Scholar 

  17. Combet, C., Jambon, M., Deleage, G., & Geourjon, C. (2002). Bioinformatics, 18, 213–214.

    Article  CAS  Google Scholar 

  18. Nazina, T. N., Tourova, T. P., Poltaraus, A. B., Novikova, E. V., Grigoryan, A. A., Ivanova, A., et al. (2001). International Journal of Systematic and Evolutionary Microbiology, 51, 433–446.

    CAS  Google Scholar 

  19. Blackwood, K. S., Turenne, C. Y., Harmsen, D., & Kabani, A. M. (2004). Journal of Clinical Microbiology, 42, 1626–1630.

    Article  CAS  Google Scholar 

  20. Rueckert, A., Ronimus, R. S., & Morgan, H. W. (2005). Journal of Microbiological Methods, 60, 155–167.

    Article  CAS  Google Scholar 

  21. Ollis, D. L., Brick, P., Hamlin, R., Xuong, N. G., & Steitz, T. A. (1985). Nature, 313, 762–766.

    Article  CAS  Google Scholar 

  22. Sousa, R., Chung, Y. J., Rose, J. P., & Wang, B. C. (1993). Nature, 364, 593–599.

    Article  CAS  Google Scholar 

  23. Beese, L. S., Derbyshire, V., & Steitz, T. A. (1993). Science, 260, 352–355.

    Article  CAS  Google Scholar 

  24. Polesky, A. H., Steitz, T. A., Grindley, N. D. F., & Joyce, C. M. (1990). Journal of Biological Chemistry, 265, 14579–14591.

    CAS  Google Scholar 

  25. Polesky, A. H., Dahlberg, M. E., Benkovic, S. J., Grindley, N. D. F., & Joyce, C. M. (1992). Journal of Biological Chemistry, 267, 8417–8428.

    CAS  Google Scholar 

  26. Beese, L. S., & Steitz, T. A. (1991). European Molecular Biology Organization Journal, 10, 25–33.

    CAS  Google Scholar 

  27. Korolev, S., Nayal, M., Barnes, W., Di Cera, E., & Waksman, G. (1995). Proceedings of the National Academy of Sciences of United States of America, 92, 9264–9268.

    Article  CAS  Google Scholar 

  28. Rodgers, D. W., & Harrison, S. C. (1995). Proceedings of the National Academy of Sciences of United States of America, 92, 1222–1226.

    Article  CAS  Google Scholar 

  29. Derbyshire, V., Grindley, N. D. F., & Joyce, C. M. (1991). European Molecular Biology Organization Journal, 10, 17–24.

    CAS  Google Scholar 

  30. Derbyshire, V., Freemont, P. S., Sanderson, M. R., Beese, L., Friedman, J. M., Joyce, C. M., et al. (1988). Science, 240, 199–201.

    Article  CAS  Google Scholar 

  31. Kim, Y., Eom, S. H., Wang, J., Lee, D.-S., Suh, S. W., & Steitz, T. A. (1995). Nature, 376, 612–616.

    Article  CAS  Google Scholar 

  32. Dabrowski, S., & Kur, J. (1998). Protein Expression and Purification, 14(1), 131–138.

    Article  CAS  Google Scholar 

  33. McPherson, M. J., & Moller, S. G. (2000). PCR, first edition, BIOS Scientific Publication.

Download references

Acknowledgments

This work was supported by Ministry of Mines and Industries, High Tech. Department (Iran) grant 84/8/337 to M. S. We thank Dr. S. Gharavi and Dr. M. Naderi-Manesh for reading the manuscript.

Author information

Authors and Affiliations

  1. Department of Biology, Faculty of Basic Sciences, Tarbiat Modares University, 14115-175, Tehran, Iran

    Mohammad Khalaj-Kondori, Majid Sadeghizadeh, Khosro Khajeh, Hossein Naderi-Manesh, Ali Mohammad Ahadi & Abdorahman Emamzadeh

Authors
  1. Mohammad Khalaj-Kondori
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Majid Sadeghizadeh
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Khosro Khajeh
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Hossein Naderi-Manesh
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Ali Mohammad Ahadi
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Abdorahman Emamzadeh
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Majid Sadeghizadeh.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Khalaj-Kondori, M., Sadeghizadeh, M., Khajeh, K. et al. Cloning, Sequence Analysis and Three-dimensional Structure Prediction of DNA Pol I from Thermophilic Geobacillus sp. MKK Isolated from an Iranian Hot Spring. Appl Biochem Biotechnol 142, 200–208 (2007). https://doi.org/10.1007/s12010-007-0010-y

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12010-007-0010-y

Keywords

Search

Navigation