Skip to main content
SpringerLink
Log in

Application of gyrB and parE sequence similarity analyses for differentiation of species within the genus Geobacillus

  • Experimental Articles
  • Published:
Microbiology Aims and scope Submit manuscript

Abstract

The primary structures of the genes encoding the β-subunits of a type II topoisomerase (gyrase, gyrB) and a type IV topoisomerase (parE) were determined for 15 strains of thermophilic bacteria of the genus Geobacillus. The obtained sequences were used for analysis of the phylogenetic similarity between members of this genus. Comparison of the phylogenetic trees of geobacilli constructed on the basis of the 16S rRNA, gyrB, and parE gene sequences demonstrated that the level of genetic distance between the sequences of the genes encoding the β-subunits of type II topoisomerases significantly exceeded the values obtained by comparative analysis of the 16S rRNA gene sequences of Geobacillus strains. It was shown that, unlike the 16S rRNA gene analysis, comparative analysis of the gyrB and parE gene sequences provided a more precise determination of the phylogenetic position of bacteria at the species level. The data obtained suggest the possibility of using the genes encoding the β-subunits of type II topoisomerases as phylogenetic markers for determination of the species structure of geobacilli.

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

Similar content being viewed by others

References

  1. Wayne, L.G., Brenner, D.J., Colwell, R.R., Grimont, P.A.D., Kandler, O., Krichevsky, M.O., Moore, L.H., Moore, W.E.C., Murray, R.G.E., Stackebrandt, E., Starr, M.P., and Trüper, H.G., International Committee on Systematic Bacteriology. Report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematic, Int. J. Syst. Bacteriol., 1987, vol. 37, no. 4, pp. 463–464.

    Article  Google Scholar 

  2. Woese, C.R., Bacterial Evolution, Microbiol. Rev., 1987, vol. 51, pp. 221–271.

    CAS  PubMed  Google Scholar 

  3. Stackebrandt, E., Frederiksen, W., Garrity, G.M., Grimont, P.A., Kämpfer, P., Maiden, M.C., Nesme, X., Rossello-Mora, R., Swings, G., Trüper, H.G., Vauterin, L., Ward, A.C., and Whitman, W.B., Report of the ad hoc Committee for the Re-Evaluation of the Species Definition in Bacteriology, Int. J. Syst. Evol. Microbiol., 2002, vol. 52, pp. 1043–1047.

    Article  CAS  PubMed  Google Scholar 

  4. Ludwig, W., Nucleic Acid Techniques in Bacterial Systematics and Identification, Int. J. Food. Microbiol., 2007, vol. 120, pp. 225–236.

    Article  CAS  PubMed  Google Scholar 

  5. Tourova, T.P., Copy Number of Ribosomal Operons in Prokaryotes and Its Effect on Phylogenetic Analyses, Mikrobiologiya, 2003, vol. 72, no. 4, pp. 437–452 [Microbiology (Engl. Transl.), vol. 72, no. 4, pp. 389–402].

    Google Scholar 

  6. Santos, S.R. and Ochman, H., Identification and Phylogenetic Sorting of Bacterial Lineages with Universally Conserved Genes and Proteins, Environ. Microbiol., 2004, vol. 6, pp. 754–759.

    Article  CAS  PubMed  Google Scholar 

  7. Zeigler, D.R., Application of a recN Sequence Similarity Analysis to the Identification of Species within the Bacterial Genus Geobacillus, Int. J. Syst. Evol. Microbiol., 2005, vol. 55, pp. 1171–1179.

    Article  CAS  PubMed  Google Scholar 

  8. Zeigler, D.R., Gene Sequences Useful for Predicting Relatedness of Whole Genomes in Bacteria, Int. J. Syst. Evol. Microbiol., 2003, vol. 53, pp. 1893–1900.

    Article  CAS  PubMed  Google Scholar 

  9. Yamamoto, S. and Harayama, S., Phylogenetic Relationships of Pseudomonas putida Strains Deduced from the Nucleotide Sequences of gyrB, rpoD and 16S rRNA Genes, Int. J. Syst Bacteriol., 1998, vol. 48, pp. 813–819.

    Article  CAS  PubMed  Google Scholar 

  10. Weng, F.Y., Chiou, C.S., Lin, P.H.P., and Yang, S.S., Application of recA and rpoB Sequence Analysis on Phylogeny and Molecular Identification of Geobacillus Species, J. Appl. Microbiol., 2009, vol. 107, pp. 452–464.

    Article  CAS  PubMed  Google Scholar 

  11. Meintanis C., Chalkou K.I., Kormas K.Ar., Lymperopoulou D.S., Katsifas E.A., Hatzinikolaou D.G., Karagouni A.D. Application of rpoB Sequence Similarity Analysis, REP-PCR and BOX-PCR for the Differentiation of Species within the Genus Geobacillus, Lett. Appl. Microbiol., 2008, vol. 46, pp. 395–401.

    Article  CAS  PubMed  Google Scholar 

  12. Huang, W.M., Bacterial Diversity Based on Type II DNA Topoisomerase Genes, Ann. Rev. Genetics, 1996, vol. 30, pp. 79–107.

    Article  CAS  Google Scholar 

  13. Suzuki, M., Narayama, S., and Yamamoto, S., Phylogenetic Analysis and Taxonomic Study of Marine Cytophaga-Like Bacteria: Proposal for Tenacibaculum gen. nov. with Tenacibaculum maritimum comb. nov. and Tenacibaculum ovolyticum comb. nov., and Description of Tenacibaculum mesophilum sp. nov. and Tenacibaculum amylolyticum sp. nov., Int. J. Syst. Evol. Microbiol., 2001, vol. 51, pp. 1639–1652.

    CAS  PubMed  Google Scholar 

  14. Wang, L.T., Lee, F.L., Tai, C.J., and Kasai, H., Comparison of gyrB Gene Sequences, 16S rRNA Gene Sequences and DNA-DNA Hybridization in the Bacillus subtilis Group, Int. J. Syst. Evol. Microbiol., 2007, vol. 57, pp. 1846–1850.

    Article  CAS  PubMed  Google Scholar 

  15. Kasai, H., Watanabe, K., Gasteiger, E., Bairoch, A., Isono, K., Yamamoto, S., and Harayama, S., Construction of the gyrB Database for the Identification and classification of Bacteria, in Genome Informatics, Miyano, S. and Takagi, T., Eds., Tokyo: Universal Academic Press, 1998, pp. 13–21.

    Google Scholar 

  16. Yamamoto, S. and Harayama, S., PCR Amplification and Direct Sequencing of gyrB Genes with Universal Primers and Their Application to the Detection and Taxonomic Analysis of Pseudomonas putida Strains, Appl. Environ. Microbiol., 1995, vol. 61, pp. 1104–1109.

    CAS  PubMed  Google Scholar 

  17. Yamada, S., Ohashi, E., Agata, N., and Venkateswaran, K., Cloning and Nucleotide Sequence Analysis of gyrB of Bacillus cereus, B. thuringiensis, B. mycoides, and B. anthracis and Their Application to the Detection of B. cereus in Rice, Appl. Environ. Microbiol., 1999, vol. 65, pp. 1483–1490.

    CAS  PubMed  Google Scholar 

  18. Yamamoto, S. and Harayama, S., Phylogenetic Analysis of Acinetobacter Strains Based on the Nucleotide Sequences of gyrB Genes and on the Amino Acid Sequences of Their Products, Int. J. Syst. Bacteriol., 1996, vol. 46, pp. 506–511.

    Article  CAS  PubMed  Google Scholar 

  19. Kang, Y., Takeda, K., Yazawa, K., and Mikami, Y., Phylogenetic Studies of Gordonia Species Based on gyrB and secA1 Gene Analyses, Mycopathologia, 2008, vol. 167, pp. 95–105.

    Article  PubMed  Google Scholar 

  20. Nazina, T.N., Tourova, T.P., Poltaraus, A.B., Novikova, E.V., Grigoryan, A.A., Ivanova, A.E., Lysenko, A.M., Petrunyaka, V.V., Osipov, G.A., Belyaev, S.S., and Ivanov, M.B., Taxonomic Study of Aerobic Thermophilic Bacilli: Descriptions of Geobacillus subterraneus gen. nov., sp. nov. and Geobacillus uzenensis sp. nov. from Petroleum Reservoirs and Transfer of Bacillus stearothermophilus, Bacillus thermocatenulatus, Bacillus thermoleovorans, Bacillus kaustophilus, Bacillus thermoglucosidasius and Bacillus thermodenitrificans to Geobacillus as the New Combinations G. stearothermophilus, G. thermocatenulatus, G. thermoleovorans, G. kaustophilus, G. thermoglucosidasius and G. thermodenitrificans, Int. J. Syst. Evol. Microbiol., 2001, vol. 51, pp. 433–446.

    CAS  PubMed  Google Scholar 

  21. Nazina, T.N., Sokolova, D.Sh., Grigoryan, A.A., Shestakova, N.M., Mikhailova, E.M., Poltaraus, A.B., Tourova, T.P., Lysenko, A.M., Osipov, G.A., and Belyaev, S.S., Geobacillus jurassicus sp. nov., a New Thermophilic Bacterium Isolated from a High-Temperature Petroleum Reservoir, and the Validation of the Geobacillus Species, Syst. Appl. Microbiol., 2005, vol. 28, pp. 43–53.

    Article  CAS  PubMed  Google Scholar 

  22. Lane, D.J, 16S/23S RNA Sequencing, in Nucleic Acid Techniques in Bacterial Systematics, Stackebrandt, E. and Goodfellow, M., Eds., New York: Wiley, 1991, pp. 115–175.

    Google Scholar 

  23. Watanabe, K., Nelson, N., Harayama, S., and Kasai, H., ICB Database: the gyrB Database for Identification and Classification of Bacteria, Nucleic Acids Res., 2001, vol. 29, pp. 344–345.

    Article  CAS  PubMed  Google Scholar 

  24. Nazina, T.N., Lebedeva, E.V., Poltaraus, A.B., Tourova, T.P., Grigoryan, A.A., Sokolova, D.Sh., Lysenko, A.M., and Osipov, G.A., Geobacillus gargensis sp. nov., a Novel Thermophile from a Hot Spring, and the Reclassification of Bacillus vulcani as Geobacillus vulcani comb. nov., Int. J. Syst. Evol. Microbiol., 2004, vol. 54, pp. 2019–2024.

    Article  CAS  PubMed  Google Scholar 

  25. Kuisiene, N., Raugalas, J., and Chitavichius, D., Geobacillus lituanicus sp. nov., Int. J. Syst. Evol. Microbiol., 2004, vol. 54, pp. 1991–1995.

    Article  CAS  PubMed  Google Scholar 

  26. Caccamo, D., Gugliandolo, C., Stackebrandt, E., and Maugeri, T.L., Bacillus vulcani sp. nov., a Novel Thermophilic Species Isolated from a Shallow Marine Hydrothermal Vent, Int. J. Syst. Evol. Microbiol., 2000, vol. 50, pp. 2009–2012.

    PubMed  Google Scholar 

  27. Schäffer, C., Franck, W.L., Scheberl, A., Kosma, P., McDermott, T.R., and Messner, P., Classification of Isolates from Locations in Austria and Yellowstone National Park as Geobacillus tepidamans sp. nov., Int. J. Syst. Evol. Microbiol., 2004, vol. 54, pp. 2361–2368.

    Article  PubMed  Google Scholar 

  28. Banat, I.B., Marchant, R., and Rahman, T.J., Geobacillus debilis sp. nov., a Novel Obligately Thermophilic Bacterium Isolated from a Cool Soil Environment, and Reassignment of Bacillus pallidus to Geobacillus pallidus comb. nov., Int. J. Syst. Evol. Microbiol., 2004, vol. 54, pp. 2197–2201.

    Article  CAS  PubMed  Google Scholar 

  29. Sung, M.H., Kim, H., Bae, J.W., Rhee, S.K., Jeon, C.O., Kim, K., Kim, J.J., Hong, S.P., Lee, S.G., Yoon, J.H., Park, Y.H., and Baek, D.H., Geobacillus toebii sp. nov., a Novel Thermophilic Bacterium Isolated from Hay Compost, Int. J. Syst. Evol. Microbiol., 2002, vol. 52, pp. 2251–2255.

    Article  CAS  PubMed  Google Scholar 

  30. Sunna, A., Tokajian, S., Burghardt, J., Rainey, F., Antranikian, G., and Hashwa, F., Identification of Bacillus kaustophilus, Bacillus thermocatenulatus and Bacillus Strain HSR as Members of Bacillus thermoleovorans, Syst. Appl. Microbiol., 1997, vol. 20, pp. 232–237.

    CAS  Google Scholar 

  31. Minana-Galbis, D., Pinzón, D.L., Loren, J.G., Manresa, A., and Oliart-Ros, R.M., Reclassification of Geobacillus pallidus (Scholz et al. 1988) Banat et al. 2004 as Aeribacillus pallidus gen nov., comb. nov., Int. J. Syst. Evol. Microbiol., 2009. doi: 10.1099/ijs.0.003699-0.

  32. Felsenstein, J., PHYLIP, Phylogenetic Inference Package (Version 3.2), Cladistics, 1989, vol. 5, pp. 164–166.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Winogradsky Institute of Microbiology, Russian Academy of Sciences, pr. 60-letiya Oktyabrya 7, k. 2, Moscow, 117312, Russia

    T. P. Tourova, E. M. Mikhailova, D. Sh. Sokolova & T. N. Nazina

  2. Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, 119991, Russia

    A. V. Korshunova

  3. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow, 119991, Russia

    A. B. Poltaraus

Authors
  1. T. P. Tourova
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. A. V. Korshunova
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. E. M. Mikhailova
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. D. Sh. Sokolova
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. A. B. Poltaraus
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. T. N. Nazina
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to T. N. Nazina.

Additional information

Original Russian Text © T.P. Tourova, A.V. Korshunova, E.M. Mikhailova, D.Sh. Sokolova, A.B. Poltaraus, T.N. Nazina, 2010, published in Mikrobiologiya, 2010, Vol. 79, No. 3, pp. 376–389.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Tourova, T.P., Korshunova, A.V., Mikhailova, E.M. et al. Application of gyrB and parE sequence similarity analyses for differentiation of species within the genus Geobacillus . Microbiology 79, 356–369 (2010). https://doi.org/10.1134/S0026261710030124

Download citation

  • Received:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S0026261710030124

Key words

Search

Navigation