Analysis of RNA Polymerase Beta Subunit (rpoB) Gene Sequences for the Discrimination of Cyanobacteria Anabaena Species

남조세균 Anabaena 종 구분을 위한 RNA Polymerase Beta Subunit (rpoB) 유전자 염기서열 분석

  • Cheon, Ju-Yong (Department of Green Life Science, Sangmyung University) ;
  • Lee, Min-Ah (Department of Green Life Science, Sangmyung University) ;
  • Ki, Jang-Seu (Department of Green Life Science, Sangmyung University)
  • 천주용 (상명대학교 그린생명과학과) ;
  • 이민아 (상명대학교 그린생명과학과) ;
  • 기장서 (상명대학교 그린생명과학과)
  • Received : 2011.08.29
  • Accepted : 2011.09.28
  • Published : 2011.09.30

Abstract

Anabaena (Cyanobacteria, Nostocales) are important for water quality controls, because they are often responsible for freshwater green tides; moreover, some species are reported to produce hepatotoxin. In this study, we sequenced RNA polymerase beta subunit (rpoB) gene of Anabaena, and evaluated their sequences for the potential use of a molecular taxonomic marker in this taxon. Anabaena rpoB showed low DNA similarity and high genetic divergences when compared those of 16S rRNA, and the molecular differences were statistically significant (Student t-test, p<0.01). Parsimony analyses showed the rpoB gene evolves 4.8-fold faster than 16S rRNA. In addition, phylogeny of the rpoB gene separated each Anabaena strain more clearly compared with a 16S rRNA tree. These results suggest that the rpoB gene is a useful marker for the molecular phylogenetics and the species discrimination of Anabaena.

Keywords

Anabaena;cyanobacteria;DNA similarity;genetic distance;rpoB gene

Acknowledgement

Supported by : 상명대학교

References

  1. Al-Thukair, A.A., R.M. Abed, and L. Mohamed. 2007. Microbial community of cyanobacteria mats in the intertidal zone of oil-polluted coast of Saudi Arabia. Mar. Pollut. Bull. 54, 173-179. https://doi.org/10.1016/j.marpolbul.2006.08.043
  2. Allen, M.B. and I.A Daniel. 1955. Studies on nitrogen-fixing blue-green algae I. Growth and nitrogen fixation by Anabaena cylindrical. Lemm. Plant Physiol. 30, 366-372. https://doi.org/10.1104/pp.30.4.366
  3. Castiglioni, B., E. Rizzi, A. Frosini, K. Sivonen, P. Rajaniemi, A. Rantala, M.A. Mugnai, S. Ventura, A. Wilmotte, C. Boutte, and et al. 2004. Development of a universal microarray based on the ligation detection reaction and 16S rRNA gene polymorphism to target diversity of cyanobacteria. Appl. Environ. Microbiol. 70, 7161-7172. https://doi.org/10.1128/AEM.70.12.7161-7172.2004
  4. Choi, A.R., J.H. Park, and J.A. Lee. 2002. Population dynamics and the toxin of Anabaena in the Lower Naktong River. Algae 17, 95-104. https://doi.org/10.4490/ALGAE.2002.17.2.095
  5. Dahllof, I., H. Baillie, and S. Kjelleberg. 2000. rpoB-based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity. Appl. Environ. Microbiol. 66, 3376-3380. https://doi.org/10.1128/AEM.66.8.3376-3380.2000
  6. Doers, M.P.and D.L. Parker.1988. Properties of Microcystis aeruginosa and M.flos-aquae (Cyanophyta) in culture: taxonomic implications. J. Phycol. 24, 502-508.
  7. Fegatella, F., J. Lim, S. Kjelleberg, and R. Cavicchioli. 1998. Implications of rRNA operon copy number and ribosome content in the marine oligotrophic ultramicrobacterium Sphingomonas sp. strain RB2256. Appl. Environ. Microbiol. 64, 4433-4438.
  8. Gilroy, D.J., K.W. Kauffman, R.A. Hall, X. Huang, and F. S. Chu. 2000. Assessing potential health risks from microcystin toxins in blue-green algae dietary supplements. Environ. Health Perspect. 108, 435-439. https://doi.org/10.1289/ehp.00108435
  9. Gorham, P.R., J. McLachlan, U.T. Hammer, and W.K. Kim. 1964. Isolation and culture of toxic strains of Anabaena flos-aquae (Lyngb.) de Breb. Int. Assoc. Theor. Appl. Limnol. 15, 796-804.
  10. Gugger, M., C. Lyra, P. Henriksen, A. Coute, J.F. Humbert, and K. Sivonen. 2002. Phylogenetic comparison of the cyanobacterial genera Anabaena and Aphanizomenon. Int. J. Syst. Evol. Microbiol. 52, 1867-1880 https://doi.org/10.1099/ijs.0.02270-0
  11. Ha, J.H., T. Hidaka, and H. Tsunos. 2009. Quantification of toxic Anabaena and evaluation of its dominance ratio in blooms using real-time PCR. Environ. Sci. Technol. 43, 812-818. https://doi.org/10.1021/es801265f
  12. Harmsen, D. and H. Karch. 2004. 16S rDNA for diagnosing pathogens: a living tree. ASM News 70, 19-24.
  13. Huelsenbeck, J.P. and F. Ronquist. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755. https://doi.org/10.1093/bioinformatics/17.8.754
  14. Kaneko, T., Y. Nakamura, C.P. Wolk, T. Kuritz, S. Sasamoto, A. Watanabe, M. Iriguchi, A. Ishikawa, K. Kawashima, T. Kimura, and et al. 2001. Complete genomic sequence of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120. DNA Res. 8, 205-213. https://doi.org/10.1093/dnares/8.5.205
  15. Ki, J.S. 2009. Heterogeneity analysis of the 16S rRNA gene sequences of the genus Vibrio. Korean J. Microbiol. 45, 430- 434.
  16. Ki, J.S. 2010. Divergence analysis of 16S rRNA and rpoB gene sequences revealed from the harmful cyanobacterium Microcystis aeruginosa. Korean J. Microbiol. 46, 296-302.
  17. Ki, J.S., R. Zhang, W. Zhang, Y.L. Huang, and P.-Y. Qian. 2009a. Analysis of RNA polymerase beta subunit (rpoB) gene sequences for the discriminative power of marine Vibrio species. Microb. Ecol. 58, 679-691. https://doi.org/10.1007/s00248-009-9519-7
  18. Kim, Y.J. and J.H. Lee. 1996. Comparison of phytoplankton communities of six dam lakes in the Naktong river system. Korean J. Limnol. 29, 347-362.
  19. Komarek, J. and K. Anagnostidis. 1989. Modern approach to the classification system of Cyanophytes 4 - Nostocales. Arch Hydrobiol. 82, 247-345.
  20. Lee, E.J., B.C. Kim, and K.S. Cho. 1998. Patterns of phytoplankton community structure at inlet site (Sanggul-Ri) in Lake Soyang from 1984 to 1997. Korean J. Limnol. 31, 119- 128.
  21. Nubel, U., F. Garcia-Pichel, and G. Muyzer. 1997. PCR primers to amplify 16S rRNA genes from cyanobacteria. Appl. Environ. Microbiol. 63, 3327:3332.
  22. Rajaniemi, P., P. Hrouzek, K. Kastovská, R. Willame, A. Rantala, L. Hoffmann, J. Komárek, and K. Sivonen. 2005. Phylogenetic and morphological evaluation of the genera Anabaena, Aphanizomenon, Trichormus and Nostoc (Nostocales, Cyanobacteria). Int. J. Syst. Evol. Microbiol. 55, 11-26. https://doi.org/10.1099/ijs.0.63276-0
  23. Rice, D., B.J. Mazur, and R. Haselkorn. 1982. Isolation and physical mapping of nitrogen fixation genes from the cyanobacterium Anabaena 7120. J. Biol. Chem. 257, 13157-13163.
  24. Richert, K., E. Brambilla, and Stackebrandt. 2007. The phylogenetic significance of peptidoglycan types: molecular analysis of the genera Microbacterium and Aureobacterium based upon sequence comparison of gyrB, rpoB, recA and ppk and 16S rRNA genes. Syst. Appl. Microbiol. 30, 102-108. https://doi.org/10.1016/j.syapm.2006.04.001
  25. Stanier, R.Y., R. Kunisawa, M. Mandel, and G. Cohen-Bazire. 1971. Purification and properties of unicellular blue-green algae (order Chroococcales). Bacteriol. Rev. 35, 171-205.
  26. Tamas, I., Z. Svircev, and S.G. Andersson. 2000. Determinative value of a portion of the nifH sequence for the genera Nostoc and Anabaena (cyanobacteria). Curr. Microbiol. 41, 197-200.
  27. Tamura, K., J. Dudley, M. Nei, and S. Kumar. 2007. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24, 1596-1599. https://doi.org/10.1093/molbev/msm092
  28. Thompson, J.D., D.G. Higgins, and T.J. Gibbson. 1997. Clustal X: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673.
  29. Tomioka, N. and Sugiura, M. 1984, Nucleotide sequence of the 16S-23S spacer region in the rrnA operon from a blue-green alga, Anacystis nidulans. Mol. Gen. Gen. 193, 427-430. https://doi.org/10.1007/BF00382079