Cloning and Phylogenetic Analysis of Two Different bphC Genes and bphD Gene From PCB-Degrading Bacterium, Pseudomonas sp. Strain SY5

  • Na, Kyung-Su (Department of Environmental Engineering, Chonnam National University) ;
  • Kim, Seong-Jun (Department of Environmental Engineering, Chonnam National University) ;
  • Kubo, Motoki (Department of Bio Science & Technology, Faculty of Science and Engineering, Retsumeikan University) ;
  • Chung, Seon-Yong (Department of Environmental Engineering, Chonnam National University)
  • Published : 2001.08.01

Abstract

Pseudomonas sp. strain SY5 is a PCB-degrading bacterium [24] that includes two different enzymes (BphC1 and BphC2) encoding 2,3-dihdroxybiphenyl 1,2-dioxygenase and BphD encoding 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase. The bphC1 and bphC2 genes were found to consist of 897 based encoding 299 amino acids and 882 bases encoding 294 amino acids, respectively, whereas the bphD gene consisted of 861 bases encoding 287 amino acids. According to a homology search, a 50% and 39% similarity between the bphC1 and bphC2 genes at the nucleotide and amino acid level was shown, respectively. The bphC1 gene showed a 38% and 45% similarity at the amino acid level to Alcaligenes eutrophus A5 and Rhodococcus rhodochrous, respectively, whereas, bphC2 showed a 95% and 43% similarity, respectively. A comparison of the deduced amino acid sequence of the bphD product of Pseudomonas sp. SY5 with that of A. eutrophus A5, Pseudomons sp. KKS102, and LB400 showed a sequence identity of 92, 92, and 79%, respectively. Strain SY5 was originally isolated from municipal sewage containing recalcitrant organic compounds an found to have a high degradability of various aromatic compounds [23]. The current study found that strain SY5 had two extradiol-type dioxygenases, which did not hybridize with each other as they had a low similarity, yet a similar structure of evolutionarily conserved amino acids residues for catalytic activity between BphC1 and BphC2 was observed.

Keywords

References

  1. J. Bacteriol. v.175 Three different 2,3-dihydrxybiphenyl 1,2-dioxygenase genes in the Grampositive polychlorobiphenyl-degrading bacterium Rhodococcus globerulus P6 Asturias, J.A.;K.N. Timmis
  2. J. Biol. Chem v.269 Analysis of three 2,3-dihydroxybiphenyl 1,2-dioxygenase found in Rhodococcus globerulus P6. Asturias, J.A.;L.D. Eltis;M. Prucha;K.N. Timmis
  3. Analytical Chemistry of PCBs Erchson, M.D.
  4. J. Bacteriol v.166 Cloning of a gene cluster encoding biphenyl and chlorobiphenl degradation in Pseudomonas pseudoalcaligenes Furukawa, K.;T. Miyazaki
  5. J. Microbiol. Biotechnol. v.10 Reaction characteristics of 4-mcthylcatcchol 2,3-dioxygenase from pseudomonas putida SU10 Ha, Y.M.;Y.H. Jung;D.Y. Kwon;Y.S. Kim;C.K. Kim;K.H. Min
  6. Science v.270 Crystal structure of the biphenl-cleaving extradiol dioxygenase from a PCB-degrading Pseudomonad Han, S.G.;L.D. Eltis;K.N. Timmis;S.W. Muchmore;J.T. Bolin
  7. J. Mol. Biol. v.166 Studies on transformation of Escherichia coli with plasmids Hanahan, D.
  8. Appl. Environ. Microbiol. v.62 Identification of an alternative 2,3-dihydroxybiphenyl 1,2-dioxygenase in Rhodococcus sp. strain RHA1 and cloning of the gene Hauschild, J. E.;E. Masai;K. Sugiyama;T. Hatta;K. Kimbara;M. Fukuda;K. Yano
  9. J. Bacteriol. v.172 Pseudomonas putida KF715 bphABCD operon encoding bipheny1 and polychlorinated bipheny1 degradation:Cloning, analysis, and expression in soil bacteria Hayase, H.;K. Taira;K. Furukawa
  10. Gene v.28 Unidirectional digestion with exonuclease Ⅲ creates targeted breakpoints for DNA sequencing Henikoff, S.
  11. Gene v.130 Genetic analysis of a Pseudomonas locus encoding a pathway for biphen1/polychlorinated bipheny1 degradation Hofer, B.;L.D. Eltis;D.N. Dowling;K.N. Timis
  12. Appl. Environ. Microbiol. v.62 Purification of 2,3-dihydroxybipheny1 1,2-dioxyenase from Pseudimonas putida OU83 and characterization of the gene (bphC) Khan. A. A.;R.F. Wang;M.S. Nawaz;W.W. Cao;C.E. Cerniglia
  13. Appl. Environ. Microbiol. v.62 Genetic structures of the genes encoding 2,3-dihydroxybipheny1 1,2-dioxygenase and 2-hydroxy-6-oxo-phenylhexa-2,4-dienoic acid hydrolase from biphenyl and 4-chlorobiphenyl-degrading Pseudomonas sp. strain DJ-12 Kim, F. H.;Y.S. Kim;C. K. Kim
  14. J. Bacteriol. v.171 Cloning and sequencing of two tandem genes involved in degradation of 2,3-dihydroxybiphenyl to benzoic acid in the polychlorinated biphenyl-degrading soil bacterium pseudomonas sp. strain KKS102 Kimbara, K.;T. Hashimoto;M. Fukuda;T. Koana;M. Takagi;M. Oishi;K. Yano
  15. Appl. Environ. Microbiol. v.63 Three of the seven bphC genes of Rhodococcus erythropolis TA421, isolated from a termite ecosystem, are locatch on an indigenous plasmid associated with biphenyl degradatin Kosono, S.;M. Maeda;F. Fusi;H. Arai;T. Kudo
  16. Cloning of New Rhodococcus Extradiol Dioxygenase Genes and Study of Distribution in Different Rhodococcus Strains. Questor Centre Kulakov, L.S.;V.A. Delcrox;M.J. Larkin;V.N. Ksenzenki;A. N. Kulakova
  17. J. Microbiol. Biotechnol. v.10 Characterization of the pcbD gene conoding 2-hydroxy-6-ox0-6-phenylhexa-2,4-dienoate hydrolase from Pseudomonas sp. P20 Lim, J.C.;J.R. Lee;J.Y. Lim;K.R. Min;C.K.Kim;Y.S. Kim
  18. Appl. Environ. Microbiol. v.60 Recombination of the bph(Biphenyl) catabolic genes from plasmid pWW100 and their deletion during growth on benzoate Lloyd-Jones, G.;C. Jong;R.C. Ogden;W.A. Duetz;P.A.. Williams
  19. App. Environ. Microbiol. v.61 Multiple genes encoding 2,3-dihydroxybiphenyl 1,2-dioxygenase in the Gram-positive polychlorinated biphenyl-degrading bacterium Rhodococcus erythropolis TA421, isolated from a termite ecosystem Maeda, M.;S.Y. Chung;E. Song;T. Kudo
  20. App. Environ. Microbiol. v.61 Characterization of biphenyl catabolic genes of Gram-positive polychlorinated biphenyl degrader Rhodococcus sp. strain RhA1 Masai, E.;A. Yamada;J.M.Healy;T. Hatta;K. Kimbara;M. Fukuda;K. Yano
  21. Mol. Gen. Genet v.253 Genetic organization of the bph gene cluster of transposon Tn4371, encoding enzymes for the degradation of biphenyl and 4-chlorobiphenyl compoinds Merlin,C.;D. Springael;M. M. Mergeay;A. Toussaint
  22. Archives of Biochemisty Biophysics v.332 Characterization of the gene encoding catechol 2,3-dioxygenase of Alcaligenes sp. KF711: Overexpression enzyme purification, and nucleotide sequencing Moon, J.H.;K.R. Min;C.K. Kim;K.H. Min;Y.S. Kim
  23. Environ. Eng. Res. v.3 Isolation and characterization of polychlorinated biphenyls (PCBs) degrading bacteria from a municipal sewage treatment plant Na, K.S.;T.W. Lee;J.S. Lee;J.S. Lee;M. Kubo;S.Y. Chung
  24. J. Biosci. Bioeng v.90 Characterization of PCB-degrading bacteria immobilized in polyurethane foam Na, K.S.;Y.W. Lee;W.J. Lee;Y. I. Huh;J.S. Lee;J.S. Lee;M. Kubo;S. Y. Chung
  25. J. Microbiol. Biotechnol. v.8 Extradiol cleavage of two-ring structures of bipheny and indole oxidation by biphenyl dioxygenase in Commamonas acidovorans On, H.Y.;L.R. Lee;Y.C. Kim;C.K. Kim;Y.S. Kim;Y.K. Park;J.O. Ka;K.S. Lee;K.H. Min
  26. Computer Applications in the Biosciences v.12 TREEVIEW: An application to displaly phylogenetic trees on personal computers Page, R. D. M.
  27. Kor. J. Appl. Microbiol. Biotechnol. v.24 Purification and characterization of 2,3-dihydroxybiphenyl dioxygenase form recombinant E. coli CK1092 Park, H. N.;Y.S. Kim;Y.C. Kim;C.K. Kim;J.Y. Lim
  28. J. Microbiol. Biotechnol. v.9 Induction by carvone of the polychlorinate biphenyl (PCB)- degradative pathway in Alcaligenes eutrophus H850 and its molecular monitoring Park, Y.I.;S. So;S. C. Koh
  29. J. Bacteriol. v.181 Catalytic properties of the 3-chlorocatechol-oxidizing 2,3-dihydroxybiphenyl 1,2-dioxygenase from Sphingomonas sp. Strain BN6. Riegert, U.;G. Heiss;A.E. Kuhm;C. Muller;M. Contzen;H.-J. Knackmuss;A. Stolz
  30. Molecular Clining: A Laboratory Manual (second FD.) Sambrook, J.;E.F. Fritsch;T. Maniatis
  31. Proc. Natl. Acad. Sci. USA v.74 DNA sequencing with chain-terminatiing inhibitors Sanger, F.;S. Nichlen;A. R. Coulsen
  32. J. Bacteriol. v.175 Cloning of genes involved in carbazole degradation of Pseudomonas sp. strain CA10: Nucleotide sequences of genes and characteriaztion of Meta-cleavage enzymes and hydrolase Sato, S.I.;N. Ouchiyama;T. Kimura;H. Nojiri;H. Yamane;T. Omori
  33. J. Mol. Biol. v.255 Three-dimensional structures of free form and two substrate complexes of an extradiol ring-cleavage type dioxygenase, the BphC enzyme from Pseudomonas sp. strain KKS102 Senda, T.;K. Sugiyama;H. Narita;T. Yamamoto;K. Kimbara;M. Fukuda;M. Sato;K. Yano;Y. Mitsui
  34. J. Bacteriol. v.175 Identification of a catabolic transposon, Tn4371, carrying biphenyl and 4-chlorobiphenyl degradation genes in Alcaligenes eutrophus A5 Springael, D.;S. Kreps;M. Mergeay
  35. J. Biol. Chem v.267 Analysis of bph operon from polychlorinated biphenyl-degrading strain of Pseudomonas pseudoalcaligenes KF707 Taira, K.;J. Hirose; S. Hayashida;K. Furukawa
  36. Nucleic Acids Res. v.22 CLOSTAL W: Improving the sensitivity of progressive multiple sequence alignment the sensitivity of progressive multiple sequence alignment through sequence weighting positive-specific gap penalties and weigh matrix choice Thompson, J.D.;D. G. Higgins;T. J. Gibson
  37. Microniol. Rev. v.56 Molecular mechanisms of genetic adaptation to xenobiotic compounds Van Der Meer, J.R.;W.M. De Vos;S. Harayama;A.J.B. Zhender
  38. Appl. Environ. Microbiol. v.64 Two nearly identical aromatic compound hydrolase genes in al strong polychlorinated biphenyl degrader, Phodococcus sp. strain RHA1 Yamada, A.;H. Kishi;K. Sugiyama;T. Hatta;K. Nakamura;E. Masai;M. Fukuda
  39. Gene v.33 Improved M13 phage cloning vectors and host strains: Nucleotide sequences of the M13 mp18 and pUC19 vectors Yanisch-Perron, C.;J. Vieira;J. Messing