Skip to main content
Applied and Environmental Microbiology logoLink to Applied and Environmental Microbiology
. 1997 Dec;63(12):4899–4906. doi: 10.1128/aem.63.12.4899-4906.1997

Acquisition of a deliberately introduced phenol degradation operon, pheBA, by different indigenous Pseudomonas species.

M Peters 1, E Heinaru 1, E Talpsep 1, H Wand 1, U Stottmeister 1, A Heinaru 1, A Nurk 1
PMCID: PMC168818  PMID: 9406411

Abstract

Horizontal transfer of genes of selective value in an environment 6 years after their introduction into a watershed has been observed. Expression of the gene pheA, which encodes phenol monooxygenase and is linked to the pheBA operon (A. Nurk, L. Kasak, and M. Kivisaar, Gene 102:13-18, 1991), allows pseudomonads to use phenol as a growth substrate. Pseudomonas putida strains carrying this operon on a plasmid were used for bioremediation after an accidental fire in the Estonia oil shale mine in Estonia in 1988. The water samples used for studying the fate of the genes introduced were collected in 1994. The same gene cluster was also detected in Pseudomonas strains isolated from water samples of a nearby watershed which has been continuously polluted with phenols due to oil shale industry leachate. Together with the more frequently existing counterparts of the dmp genes (V. Shingler, J. Powlowski, and U. Marklund, J. Bacteriol. 174:711-724, 1992), the pheA gene was also represented in the phenol-degrading strains. The area where the strains containing the pheA gene were found was restricted to the regular route of phenolic leachate to the Baltic Sea. Nine Pseudomonas strains belonging to four different species (P. corrugata, P. fragi, P. stutzeri, and P. fluorescens biotypes B, C, and F) and harboring horizontally transferred pheBA operons were investigated. The phe genes were clustered in the same manner in these nine phe operons and were connected to the same promoter as in the case of the original pheBA operon. One 10.6-kb plasmid carrying a pheBA gene cluster was sequenced, and the structure of the rearranged pheBA operon was described. This data indicates that introduced genetic material could, if it encodes a beneficial capability, enrich the natural genetic variety for biodegradation.

Full Text

The Full Text of this article is available as a PDF (1.8 MB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. BAUCHOP T., ELSDEN S. R. The growth of micro-organisms in relation to their energy supply. J Gen Microbiol. 1960 Dec;23:457–469. doi: 10.1099/00221287-23-3-457. [DOI] [PubMed] [Google Scholar]
  2. Beadle C. A., Smith A. R. The purification and properties of 2,4-dichlorophenol hydroxylase from a strain of Acinetobacter species. Eur J Biochem. 1982 Apr 1;123(2):323–332. doi: 10.1111/j.1432-1033.1982.tb19771.x. [DOI] [PubMed] [Google Scholar]
  3. Bi X., Liu L. F. DNA rearrangement mediated by inverted repeats. Proc Natl Acad Sci U S A. 1996 Jan 23;93(2):819–823. doi: 10.1073/pnas.93.2.819. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bradford M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 1976 May 7;72:248–254. doi: 10.1006/abio.1976.9999. [DOI] [PubMed] [Google Scholar]
  5. Connors M. A., Barnsley E. A. Naphthalene plasmids in pseudomonads. J Bacteriol. 1982 Mar;149(3):1096–1101. doi: 10.1128/jb.149.3.1096-1101.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. DiGiovanni G. D., Neilson J. W., Pepper I. L., Sinclair N. A. Gene transfer of Alcaligenes eutrophus JMP134 plasmid pJP4 to indigenous soil recipients. Appl Environ Microbiol. 1996 Jul;62(7):2521–2526. doi: 10.1128/aem.62.7.2521-2526.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Ehrt S., Schirmer F., Hillen W. Genetic organization, nucleotide sequence and regulation of expression of genes encoding phenol hydroxylase and catechol 1,2-dioxygenase in Acinetobacter calcoaceticus NCIB8250. Mol Microbiol. 1995 Oct;18(1):13–20. doi: 10.1111/j.1365-2958.1995.mmi_18010013.x. [DOI] [PubMed] [Google Scholar]
  8. Heinaru A. L., Duggleby C. J., Broda P. Molecular relationships of degradative plasmids determined by in situ hybridisation of their endonuclease-generated fragments. Mol Gen Genet. 1978 Apr 17;160(3):347–351. doi: 10.1007/BF00332979. [DOI] [PubMed] [Google Scholar]
  9. KING E. O., WARD M. K., RANEY D. E. Two simple media for the demonstration of pyocyanin and fluorescin. J Lab Clin Med. 1954 Aug;44(2):301–307. [PubMed] [Google Scholar]
  10. Kasak L., Hôrak R., Nurk A., Talvik K., Kivisaar M. Regulation of the catechol 1,2-dioxygenase- and phenol monooxygenase-encoding pheBA operon in Pseudomonas putida PaW85. J Bacteriol. 1993 Dec;175(24):8038–8042. doi: 10.1128/jb.175.24.8038-8042.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Kim I. C., Oriel P. J. Characterization of the Bacillus stearothermophilus BR219 phenol hydroxylase gene. Appl Environ Microbiol. 1995 Apr;61(4):1252–1256. doi: 10.1128/aem.61.4.1252-1256.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Kivisaar M. A., Habicht J. K., Heinaru A. L. Degradation of phenol and m-toluate in Pseudomonas sp. strain EST1001 and its Pseudomonas putida transconjugants is determined by a multiplasmid system. J Bacteriol. 1989 Sep;171(9):5111–5116. doi: 10.1128/jb.171.9.5111-5116.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Kivisaar M., Hõrak R., Kasak L., Heinaru A., Habicht J. Selection of independent plasmids determining phenol degradation in Pseudomonas putida and the cloning and expression of genes encoding phenol monooxygenase and catechol 1,2-dioxygenase. Plasmid. 1990 Jul;24(1):25–36. doi: 10.1016/0147-619x(90)90022-5. [DOI] [PubMed] [Google Scholar]
  14. Kivisaar M., Kasak L., Nurk A. Sequence of the plasmid-encoded catechol 1,2-dioxygenase-expressing gene, pheB, of phenol-degrading Pseudomonas sp. strain EST1001. Gene. 1991 Feb 1;98(1):15–20. doi: 10.1016/0378-1119(91)90098-v. [DOI] [PubMed] [Google Scholar]
  15. Kukor J. J., Olsen R. H. Complete nucleotide sequence of tbuD, the gene encoding phenol/cresol hydroxylase from Pseudomonas pickettii PKO1, and functional analysis of the encoded enzyme. J Bacteriol. 1992 Oct;174(20):6518–6526. doi: 10.1128/jb.174.20.6518-6526.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Kukor J. J., Olsen R. H. Molecular cloning, characterization, and regulation of a Pseudomonas pickettii PKO1 gene encoding phenol hydroxylase and expression of the gene in Pseudomonas aeruginosa PAO1c. J Bacteriol. 1990 Aug;172(8):4624–4630. doi: 10.1128/jb.172.8.4624-4630.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Louws F. J., Fulbright D. W., Stephens C. T., de Bruijn F. J. Specific genomic fingerprints of phytopathogenic Xanthomonas and Pseudomonas pathovars and strains generated with repetitive sequences and PCR. Appl Environ Microbiol. 1994 Jul;60(7):2286–2295. doi: 10.1128/aem.60.7.2286-2295.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Matheson V. G., Forney L. J., Suwa Y., Nakatsu C. H., Sexstone A. J., Holben W. E. Evidence for Acquisition in Nature of a Chromosomal 2,4-Dichlorophenoxyacetic Acid/(alpha)-Ketoglutarate Dioxygenase Gene by Different Burkholderia spp. Appl Environ Microbiol. 1996 Jul;62(7):2457–2463. doi: 10.1128/aem.62.7.2457-2463.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Morgan J. A., Rhodes G., Pickup R. W., Winstanley C., Saunders J. R. The effect of microcosm design on the survival of recombinant Pseudomonas putida in lake water. Microb Releases. 1992 Dec;1(3):155–159. [PubMed] [Google Scholar]
  20. Nakatsu C. H., Fulthorpe R. R., Holland B. A., Peel M. C., Wyndham R. C. The phylogenetic distribution of a transposable dioxygenase from the Niagara River watershed. Mol Ecol. 1995 Oct;4(5):593–603. doi: 10.1111/j.1365-294x.1995.tb00259.x. [DOI] [PubMed] [Google Scholar]
  21. Nakatsu C. H., Wyndham R. C. Cloning and expression of the transposable chlorobenzoate-3,4-dioxygenase genes of Alcaligenes sp. strain BR60. Appl Environ Microbiol. 1993 Nov;59(11):3625–3633. doi: 10.1128/aem.59.11.3625-3633.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Ng L. C., Shingler V., Sze C. C., Poh C. L. Cloning and sequences of the first eight genes of the chromosomally encoded (methyl) phenol degradation pathway from Pseudomonas putida P35X. Gene. 1994 Dec 30;151(1-2):29–36. doi: 10.1016/0378-1119(94)90629-7. [DOI] [PubMed] [Google Scholar]
  23. Nordlund I., Powlowski J., Hagström A., Shingler V. Conservation of regulatory and structural genes for a multi-component phenol hydroxylase within phenol-catabolizing bacteria that utilize a meta-cleavage pathway. J Gen Microbiol. 1993 Nov;139(11):2695–2703. doi: 10.1099/00221287-139-11-2695. [DOI] [PubMed] [Google Scholar]
  24. Nordlund I., Powlowski J., Shingler V. Complete nucleotide sequence and polypeptide analysis of multicomponent phenol hydroxylase from Pseudomonas sp. strain CF600. J Bacteriol. 1990 Dec;172(12):6826–6833. doi: 10.1128/jb.172.12.6826-6833.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Nurk A., Kasak L., Kivisaar M. Sequence of the gene (pheA) encoding phenol monooxygenase from Pseudomonas sp. EST1001: expression in Escherichia coli and Pseudomonas putida. Gene. 1991 Jun 15;102(1):13–18. doi: 10.1016/0378-1119(91)90531-f. [DOI] [PubMed] [Google Scholar]
  26. Parsek M. R., Kivisaar M., Chakrabarty A. M. Differential DNA bending introduced by the Pseudomonas putida LysR-type regulator, CatR, at the plasmid-borne pheBA and chromosomal catBC promoters. Mol Microbiol. 1995 Mar;15(5):819–828. doi: 10.1111/j.1365-2958.1995.tb02352.x. [DOI] [PubMed] [Google Scholar]
  27. Perkins E. J., Gordon M. P., Caceres O., Lurquin P. F. Organization and sequence analysis of the 2,4-dichlorophenol hydroxylase and dichlorocatechol oxidative operons of plasmid pJP4. J Bacteriol. 1990 May;172(5):2351–2359. doi: 10.1128/jb.172.5.2351-2359.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Sala-Trepat J. M., Murray K., Williams P. A. The metabolic divergence in the meta cleavage of catechols by Pseudomonas putida NCIB 10015. Physiological significance and evolutionary implications. Eur J Biochem. 1972 Jul 24;28(3):347–356. doi: 10.1111/j.1432-1033.1972.tb01920.x. [DOI] [PubMed] [Google Scholar]
  29. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Shingler V., Powlowski J., Marklund U. Nucleotide sequence and functional analysis of the complete phenol/3,4-dimethylphenol catabolic pathway of Pseudomonas sp. strain CF600. J Bacteriol. 1992 Feb;174(3):711–724. doi: 10.1128/jb.174.3.711-724.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Sobecky P. A., Schell M. A., Moran M. A., Hodson R. E. Adaptation of model genetically engineered microorganisms to lake water: growth rate enhancements and plasmid loss. Appl Environ Microbiol. 1992 Nov;58(11):3630–3637. doi: 10.1128/aem.58.11.3630-3637.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Swannell R. P., Lee K., McDonagh M. Field evaluations of marine oil spill bioremediation. Microbiol Rev. 1996 Jun;60(2):342–365. doi: 10.1128/mr.60.2.342-365.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Tsuda M., Minegishi K., Iino T. Toluene transposons Tn4651 and Tn4653 are class II transposons. J Bacteriol. 1989 Mar;171(3):1386–1393. doi: 10.1128/jb.171.3.1386-1393.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Williams P. A., Murray K. Metabolism of benzoate and the methylbenzoates by Pseudomonas putida (arvilla) mt-2: evidence for the existence of a TOL plasmid. J Bacteriol. 1974 Oct;120(1):416–423. doi: 10.1128/jb.120.1.416-423.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Zhou J. Z., Tiedje J. M. Gene transfer from a bacterium injected into an aquifer to an indigenous bacterium. Mol Ecol. 1995 Oct;4(5):613–618. doi: 10.1111/j.1365-294x.1995.tb00261.x. [DOI] [PubMed] [Google Scholar]

Articles from Applied and Environmental Microbiology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES