1887

Abstract

sp. strain IC is able to grow on biphenyl, 3-methylbiphenyl and 4-methylbiphenyl. These are converted to benzoate and the corresponding methylbenzoates. The lower pathway genes for the catabolism of the benzoates were cloned on a 22 kb dIII fragment. Hybridization with gene-specific probes from the pathways of other catabolic plasmids showed that the gene order was identical to that of the operons carrying the same function from TOL plasmids. The nucleotide sequence of a 1241 bp region carrying the whole of the gene (for a catechol 2,3-dioxygenase) and the 5′ end of the downstream gene (for 2-hydroxy semialdehyde dehydrogenase) was determined. Both genes showed a high degree of homology with genes encoding isofunctional proteins from other strains. The upper pathway genes for the conversion of biphenyl to benzoate have also been cloned but no linkage with the lower pathway operon has been detected. strain IC contains a large plasmid pWW110 (> 200 kb) and there are indications that this plasmid carries the genes.

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1994-03-01
2024-04-26
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References

  1. Assinder S.J., Williams P.A. Comparison of the metapathway operon on NAH plasmid pWW60-22 and the TOL plasmid pWW53-4 and its evolutionary significance. J Gen Microbiol (1988); 134:2769–2778
    [Google Scholar]
  2. Assinder S.J., Williams P.A. The TOL plasmids: determinants of the catabolism of toluene and the xylenes. Adv Microb Physiol (1990); 31:1–69
    [Google Scholar]
  3. Ausubel F.M., Brent M., Kingston R.E., Moore D.D., Seidman J.G., Smith J.A., Struhl K. Current Protocols in Molecular Biology (1989) New York: John Wiley & Sons;
    [Google Scholar]
  4. Bagdasarian M., Lurz R., Ruckert B., Franklin F.C.H., Bag-dasarian M.M., Frey J., SiTimmis K.N. Specific-purpose cloning vectors. II. Broad host range, high copy number RSF1010-derived vectors and a host: vector system for gene cloning. Gene (1981); 16:237–247
    [Google Scholar]
  5. Bartilson M., Shingler V. Nucleotide sequence and expression of the catechol 2,3-dioxygenase encoding gene of the phenol catabolising Pseudomonas CF600. Gene (1989); 85:233–238
    [Google Scholar]
  6. Benjamin R.C., Voss J.A., Kunz D.A. Nucleotide sequence of xylE from TOL pDK1 plasmid and structural comparison with isofunctional catechol 2,3-dioxygenase genes from TOL pWWO and NAH7. J Bacteriol (1991); 173:2724–2728
    [Google Scholar]
  7. Cane P.A., Williams P.A. The plasmid-coded metabolism of naphthalene and 2-methylnaphthalene in Pseudomonas strains: phenotype changes correlated with structural modification of the plasmid pWW60-1. J Gen Microbiol (1982); 128:2281–2290
    [Google Scholar]
  8. Catelani D., Sorlini C., Treccani V. The metabolism of biphenyl by Pseudomonas putida. Experientia (1971); 27:1173–1174
    [Google Scholar]
  9. Chang H., Lee J., Roh S., Kim S.R., Min K.R., Kim C.-K., Kim E.-G., Kim Y. Characterisation of catechol 2,3-dioxygenases. Biochem Biophys Res Commun (1992); 187:609–614
    [Google Scholar]
  10. Chatfield L.K., Williams P.A. Naturally occuring TOL plasmids in Pseudomonas strains carrying either two homologous or two non-homologous catechol 2,3-dioxygenase genes. J Bacteriol (1986); 168:878–885
    [Google Scholar]
  11. Cohen S.N., Chang A.C.Y., Hsu C.L. Nonchromosomal antibiotic resistance in bacteria: genetic transformation of Escherichia coli by R factor DNA. Proc Natl Acad Sci USA (1972); 69:2110–2114
    [Google Scholar]
  12. Duggleby C.J., Williams P.A. Purification and some properties of the 2-hydroxy-6-oxohepta-2,4-dienoate hydrolase (2-hydroxymuconic semialdehyde hydrolase) encoded by the TOL plasmid pWWO from Pseudomonas putida mt-2. J Gen Microbiol (1986); 132:717–726
    [Google Scholar]
  13. Erickson B.D., Mondelo F.J. Nucleotide sequencing and transcriptional mapping of the genes encoding biphenyl dioxygenase, a multi-component polychlorinated-biphenyl-degrading enzyme in Pseudomonas strain LB400. J Bacteriol (1992); 174:2903–2912
    [Google Scholar]
  14. Felsenstein J. 1993 phylip (Phylogeny Inference Package) version 3.5. Department of Genetics, University of Washington, Seattle, WA, USA.
  15. Franklin F.C.H., Bagdasarian M., Bagdasarian M.M., Timmis K.N. Molecular and functional analysis of TOL plasmid pWWO from Pseudomonas putida and cloning of genes for the entire regulated aromatic ring meta cleavage pathway. Proc Natl Acad Sri USA (1983); 78:7458–7462
    [Google Scholar]
  16. Furukawa K., Hayashe N., Taira K., Tomizuka N. Molecular relationship of chromosomal genes encoding biphenyl/polychlorinated biphenyl catabolism: some bacteria possess a highly conserved bph operon. J Bacteriol (1989); 171:5467–5472
    [Google Scholar]
  17. Ghosal D., You I.-S., Gunsulas I.G. Nucleotide sequence and expression of gene nahH of plasmid NAH7 and homology with gene xylE of TOL (pWWO). Gene (1987); 55:19–28
    [Google Scholar]
  18. Girvitz S.G., Bacchetti S., Rainbow A.J., Graham F.W. A rapid and efficient procedure for the purification of DNA from agarose gels. Anal Biochem (1980); 106:492–496
    [Google Scholar]
  19. Grinter N.J. A broad host range cloning vector trans-posable to various replicons. Gene (1983); 21:133–143
    [Google Scholar]
  20. Guerry P., Leblanc D.J., Falkow S. General method for isolation of plasmid deoxyribonucleic acid. J Bacteriol (1973); 116:1064–1066
    [Google Scholar]
  21. Harayama S., Rekik M. The meta cleavage operon of TOL degradative plasmid pWWO comprises 13 genes. Mol & Gen Genet (1990); 221:113–120
    [Google Scholar]
  22. Harayama S., Rekik M. Comparison of the nucleotide sequences of the meta-cleavage pathway genes of TOL plasmid pWWO from Pseudomonas putida with other meta-cleavage genes suggests that both single and multiple nucleotide substitutions contribute to enzyme evolution. Mol & Gen Genet (1993); 239:81–89
    [Google Scholar]
  23. Harayama S., Rekik M., Wubbolts M., Rose K., Leppik R.A., Timmis K.N. Characterisation of the five genes in the upper-pathway operon of the TOL plasmid pWWO from Pseudomonas putida and identification of the gene products. J Bacteriol (1989); 171:5048–5055
    [Google Scholar]
  24. Harayama S., Polissi A., Rekik M. Divergent evolution of chloroplast-type ferredoxins. FEBS Letters (1991a); 28:85–88
    [Google Scholar]
  25. Harayama S., Rekik M., Bairoch A., Neidle E.L., Ornston L.N. Potential DNA slippage structures acquired during evolutionary divergence of Acinetobacter calcoaceticus chromosomal benABC and Pseudomonas putida TOL pWWO plasmid xylXYZ, genes encoding benzoate dioxygenases. J Bacteriol (1991b); 173:7540–7548
    [Google Scholar]
  26. Hayase N., Taira K., Furukawa K. Pseudomonas putida KF715 bphABCD operon encoding biphenyl and polychlorinated biphenyl degradation: cloning, analysis and expression in soil bacteria. J Bacteriol (1990); 172:1160–1164
    [Google Scholar]
  27. Henikoff S. Unidirectional digestion with exonuclease III creates targeted breakpoints for DNA sequencing. Gene (1984); 28:351–359
    [Google Scholar]
  28. Higgins D.G., Bleasby A.J., Fuchs R. clustal V -improved software for multiple sequence alignment. Comput Appl Biosci (1992); 8:189–191
    [Google Scholar]
  29. Higson F.K. Microbial degradation of biphenyl and its derivatives. Adv Appl Microbiol (1992); 37:135–164
    [Google Scholar]
  30. Holmes D.S., Quigley M. A rapid boiling method for the preparation of bacterial plasmids. Anal Biochem (1981); 114:193–197
    [Google Scholar]
  31. Horn J.M., Harayama S., Timmis K.N. DNA sequence determination of the TOL plasmid (pWWO) xylGFJ genes of Pseudomonas putida: implications for the evolution of aromatic catabolism. Mol Microbiol (1991); 5:2459–2474
    [Google Scholar]
  32. Jeenes D.J., Williams P.A. Excision and integration of degradative pathway genes from TOL plasmid pWWO. J Bacteriol (1982); 150:188–194
    [Google Scholar]
  33. Keil H., Williams P.A. A new class of TOL plasmid deletion mutants in Pseudomonas putida MT15 and their reversion by random gene amplification. J Gen Microbiol (1985); 131:1023–1033
    [Google Scholar]
  34. Keil H., Keil S., Pickup R.W., Williams P.A. The complete meta pathway operon of the toluene/xylene catabolic pathway cloned from TOL plasmid pWW53. J Bacteriol (1985); 164:887–895
    [Google Scholar]
  35. Keil H., Keil S., Williams P.A. Molecular analysis of regulatory and structural xyl genes of the TOL plasmid pWW53-4. J Gen Microbiol (1987); 133:1149–1158
    [Google Scholar]
  36. Kim Y., Choi B., Lee J., Chang H., Min K.R. Molecular cloning and characterisation of catechol 2,3-dioxygenases from biphenyl, polychlorinated biphenyl-degrading bacteria. Biochem Biophys Res Commun (1992); 183:77–82
    [Google Scholar]
  37. King E.D., Ward M.K., Raney D.C. Simple method for the demonstration of pyrocyanin and fluorescin. J Lab Clin Med (1954); 44:301–307
    [Google Scholar]
  38. Kukor J.J., Olsen R.H. Genetic organisation and regulation of a meta-cleavage pathway for catechols produced from catabolism of toluene, benzene, phenol and cresols by Pseudomonas pickettii PK01. J Bacteriol (1991); 173:4587–4594
    [Google Scholar]
  39. Maniatis J., Fritsch E.F., Sambrook J. Molecular Cloning: a Laboratory Manual (1982) Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  40. Murray N.E., Brammar W.J., Murray K. Lambdoid phages that simplify the recovery of in vitro recombinants. Mol & Gen Genet (1977); 150:53–61
    [Google Scholar]
  41. Nakai C., Kagiyama H., Nozaki M., Nakazawa T., Inouye S., Ebina Y., Nakazawa A. Complete nucleotide sequence of the metapyrocatechase gene on the TOL plasmid of Pseudomonas putida mt-2. J Biol Chem (1983); 258:2923–2928
    [Google Scholar]
  42. Neidle E.L., Hartnett C., Ornston L.N., Bairoch A., Rekik M., Harayama S. Nucleotide sequence of the Acinetobacter calcoaceticus benABC genes for benzoate 1,2-dioxygenase reveal evolutionary relationships among multicomponent oxygenases. J Bacteriol (1991); 173:5385–5395
    [Google Scholar]
  43. Neidle E.L., Hartnett C., Ornston L.N., Bairoch A., Rekik M., Harayama S. CA-diol dehydrogenases encoded by the TOL pWWO plasmid xylL gene and the Acinetobacter calcoaceticus chromosome benD gene are members of the short chain alcohol dehydrogenase family. Eur J Biochem (1992); 204:113–120
    [Google Scholar]
  44. Nordlund I., Shingler V. Nucleotide sequences of the meta-cleavage pathway enzymes 2-hydroxymuconic semialdehyde dehydrogenase and 2-hydroxymuconic semialdehyde hydrolase from Pseudomonas putida CF600. Biochim Biophys Acta (1990); 1049:227–230
    [Google Scholar]
  45. Palleroni N.J. Present situation of the taxonomy of aerobic pseudomonads. In Pseudomonas : Molecular Biology and Biotechnology (1992) Edited by Galli E., Silver S., Witholt B. Washington, DC : American Society for Microbiology; pp 105–115
    [Google Scholar]
  46. Rigby P.W., Dieckmann M., Rhodes G., Berg P. Labelling deoxyribonucleic acid to high specific activity in vitro by nick-translation with DNA polymerase I. J Mol Biol (1977); 113:237–245
    [Google Scholar]
  47. Saint C.P., McClure N.C., Venables W.A. Physical map of the aromatic amine and w-toluate catabolic plasmid pTDN1 in Pseudomonas putida: location of a unique meta-cleavage pathway. J Gen Microbiol (1990); 136:615–625
    [Google Scholar]
  48. Sala-Trepat J.-M., Evans W.C. The metabolism of 2-hydroxymuconic semialdehyde by Azotobacter species. Biochem Biophys Res Commun (1971); 43:456–462
    [Google Scholar]
  49. Sala-Trepat J.-M., Murray K., Williams P.A. The metabolic divergence in the meta cleavage of catechols by Pseudomonas putida NCIB10015: Physiological significance and evolutionary implications. Eur J Biochem (1972); 28:347–356
    [Google Scholar]
  50. Sanger F., Nicklen S., Coulson A.R. DNA sequencing with chain terminating inhibitors. Proc Natl Acad Sci USA (1977); 74:5463–5467
    [Google Scholar]
  51. 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); 174:711–724
    [Google Scholar]
  52. Southern E.M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol (1975); 98:503–517
    [Google Scholar]
  53. Taira K., Hirose J., Hayashida S., Furukawa K. Analysis of the bph operon from the polychlorinated-biphenyl-degrading strain of Pseudomonas pseudoalcaligenes KF707. J Biol Chem (1992); 267:4844–4853
    [Google Scholar]
  54. Vieira J., Messing J. The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene (1982); 19:259–268
    [Google Scholar]
  55. Wheatcroft R., Williams P.A. Rapid methods for the study of both stable and unstable plasmids in Pseudomonas. J Gen Microbiol (1981); 124:433–437
    [Google Scholar]
  56. Williams P.A., Assinder S.J., Shaw L.E. Construction of hybrid xylE genes between two duplicate homologous genes from TOL plasmid pWW53: comparison of the kinetic properties of the gene product. J Gen Microbiol (1990); 136:1583–1589
    [Google Scholar]
  57. Williams P.A., Sayers J. The evolution of pathways for aromatic hydrocarbon oxidation in Pseudomonas. Biodegradation (1994) (in press)
    [Google Scholar]
  58. Yen L.-M., Gunsalus I.G. Plasmid gene organization: naphthalene/salicylate oxidation. Proc Natl Acad Sci USA (1982); 79:874–878
    [Google Scholar]
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