1887

Abstract

strain OC is able to grow on toluene, -xylene and -xylene through benzoate and the corresponding methylbenzoates (toluates). The catabolic genes are encoded on a large TOL plasmid, pWW102, of >220 kb. The complete catabolic genes were cloned on four large overlapping restriction fragments covering a total of 28 kb of the plasmid, which was carefully mapped by restriction enzyme analysis. The presence of the genes on the cloned DNA was confirmed by assay of representative enzymes of both operons. Virtually all the genes were located on the cloned DNA by hybridization of Southern blots with gene-specific probes from related pathways of other catabolic plasmids. Within the limitations of available restriction sites, the analysis showed that the genes are in two blocks. The major block carries the pathway operon with the two regulatory genes immediately downstream. The upper pathway operon is about 2-3 kb downstream of the regulatory genes and transcribed in the same direction as the pathway operon. Within each operon the gene order appears to be identical to that found in other TOL plasmids, but the relative location of the operons most closely resembles that found on plasmid pWW53, although there is no evidence of any duplications on pWW102. The nucleotide sequence of the gene for the acetaldehyde dehydrogenase (acylating; ADA), together with the 3-end of the upstream (for 2-oxopent-4-enoate hydratase) and the 5-end of the downstream (for 4-hydroxy-2-oxovalerate aldolase), was determined. The gene was ligated into expression vector pTrc99a and high levels of XylQ protein were detected by enzyme assay and by SDS-PAGE. All three genes showed a high degree of homology with genes encoding isofunctional proteins from other pathways, the highest being with the naphthalene catabolic genes from the plasmid of sp. NCIB 9816. The implications of the sequence homologies to the evolution of these pathways are discussed.

Loading

Article metrics loading...

/content/journal/micro/10.1099/00221287-144-5-1387
1998-05-01
2021-10-17
Loading full text...

Full text loading...

/deliver/fulltext/micro/144/5/mic-144-5-1387.html?itemId=/content/journal/micro/10.1099/00221287-144-5-1387&mimeType=html&fmt=ahah

References

  1. Altschul, S. F., Gish, W., Miller, W.„ Myers, E., W., Lipman, D. J. (1990); Basic local alignment search tool.. J 215:(3)403–410 [View Article]
    [Google Scholar]
  2. Assinder, S. J., Williams, P. A. (1988); Comparison of the meta pathway operons on NAH plasmid pWW60-22 and TOL plasmid pWW53-4 and its evolutionary significance.. Journal of General Microbiology 134:2769–2778
    [Google Scholar]
  3. Assinder, S. J., Williams, P. A. (1990); The TOL plasmids: determinants of the catabolism of toluene and the xylenes.. Recent Advances in Microbial Oxygen-binding Proteins 31:1–69
    [Google Scholar]
  4. Assinder, S. J., De Marco, P., Osborne, D. J., Poh, C. L., Shaw, L. E. et al. (1993); A comparison of the multiple alleles of xylS carried by TOL plasmids pWW53 and pDKl and its implications for their evolutionary relationship.. Journal of General Microbiology 139:(3)557–568 [View Article]
    [Google Scholar]
  5. Bartilson, M., Shingler, V. (1989); Nucleotide sequence and expression of the catechol 2,3-dioxygenase-encoding gene of phenol-catabolizing Pseudomonas CF600.. Gene 85:(1)233–238 [View Article]
    [Google Scholar]
  6. Benjamin, R. C., Voss, J. A., Kunz, D. A. (1991); Nucleotide sequence of xylE from the TOL pDKl plasmid and structural comparison with isofunctional catechol 2,3-dioxygenase genes from TOL pWWO and NAH7.. Journal of Bacteriology 173:(8)2724–2728 [View Article]
    [Google Scholar]
  7. Cane, P. A., Williams, P. A. (1982); The plasmid-encoded metabolism of naphthalene and 2-methylnaphthalene in Pseudomonas: phenotypic changes correlated with structural modification of the plasmid pWW60-l.. Journal of General Microbiology 128:2281–2290
    [Google Scholar]
  8. Cane, P. A., Williams, P. A. (1986); A restriction map of naphthalene catabolic plasmid pWW60-l and the location of some of its catabolic genes.. Journal of General Microbiology 132:2919–2929
    [Google Scholar]
  9. Carrington, B., Lowe, A., Shaw, L. E., Williams, P. A. (1994); The lower pathway operon for benzoate catabolism in biphenylutilizing Pseudomonas sp. strain IC and the nucleotide sequence of the bpbE gene for catechol 2,3-dioxygenase.. Microbiology 140:(3)499–508 [View Article]
    [Google Scholar]
  10. Chatfield, L. K., Williams, P. A. (1986); Naturally-occuring TOL plasmids isolated from soil carry either two homologous or two nonhomologous catechol 2,3-oxygenase genes.. Journal of Bacteriology 168:(2)878–885 [View Article]
    [Google Scholar]
  11. Duggleby, C. J., Williams, P. A. (1986); 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.. Journal of General Microbiology 132:717–726
    [Google Scholar]
  12. Eaton, R. W. (1996); p-Cumate catabolic pathway in Pseudomonas putida FI. Cloning and characterization of DNA carrying the CMT operon.. / Bacteriol 178:(5)1351–1362 [View Article]
    [Google Scholar]
  13. Girvitz, S. C., Bacchetti, S., Rainbow, A. J., Graham F. W. (1980); A rapid and efficient procedure for the purification of DNA from agarose gels.. Analytical Biochemistry 106:(2)492–496 [View Article]
    [Google Scholar]
  14. Guerry, P., Leblanc, D. J., Falkow, S. (1973); General method for isolation of plasmid deoxyribonucleic acid.. Journal of Bacteriology 116:(2)1064–1066 [View Article]
    [Google Scholar]
  15. Habe, H., Kimura, T., Nojiri, H., Yamana, H., Omori, T. (1996); Cloning and nucleotide sequences of the genes involved in the meta cleavage pathway of cumene degradation in Pseudomonas fluorescens IP01.. Journal of Fermentation and Bioengineering 81:(3)187–196 [View Article]
    [Google Scholar]
  16. Harayama, S., Rekik, M. (1990); The weta-cleavage operon of TOL degradative plasmid pWWO comprises 13 genes.. Molecular & General Genetics 222:(1)113–120 [View Article]
    [Google Scholar]
  17. Harayama, S., Rekik, M. (1993); Comparison of the nucleotide sequences of the weta-cleavage pathway of TOL plasmid pWWO from Pseudomonas putida with other meta-cleavage genes suggests that both single and multiple nucleotide substitutions contribute to enzyme evolution.. Molecular & General Genetics 239:(1–2)81–89 [View Article]
    [Google Scholar]
  18. Harayama, S., Rekik, M., Wasserfallen, A., Bairoch, A. (1987); Evolutionary relationship between catabolic pathways for aromatics : conservation of gene order and nucleotide sequences for catechol oxidation genes of pWWO and NAH7 plasmids.. Molecular & General Genetics 210:(2)241–247 [View Article]
    [Google Scholar]
  19. Harayama, S., Rekik, M., Wubbolts, M., Rose, K., Leppik, R. A. et al. (1989); Characterization of 5 genes in the upper pathway operon of TOL plasmid pWWO from Pseudomonas putida and identification of the gene products,. 1 Bacteriol 1715048–5055
  20. Hofer, B., Backhaus, S., Timmis, K. N. (1994); The biphenyl/ polychlorinated biphenyl-degradation locus (bph) of Pseudomonas sp. LB400 encodes four additional metabolic enzymes.. Gene 144:(1)9–16 [View Article]
    [Google Scholar]
  21. Holmes, D. S., Quigley, M. (1981); A rapid boiling method for the preparation of bacterial plasmids.. Analytical Biochemistry 114:(1)193–197 [View Article]
    [Google Scholar]
  22. Keil, H., Williams, P. A. (1985); A new class of TOL plasmid deletion mutants in Pseudomonas putida MT15 and their reversion by tandem gene amplification.. Journal of General Microbiology 131:1023–1033
    [Google Scholar]
  23. Keil, H., Keil, S., Pickup, R. W., Williams, P. A. (1985); Evolutionary conservation of genes coding for meta pathway enzymes within TOL plasmids pWWO and pWW53.. Journal of Bacteriology 164:(2)887–895 [View Article]
    [Google Scholar]
  24. Keil, H., Saint, C. M., Williams, P. A. (1987); Gene organization of the first catabolic operon of TOL plasmid pWW53: production of indigo by the xylA gene product.. Journal of Bacteriology 169:(2)764–770 [View Article]
    [Google Scholar]
  25. Kikuchi, Y., Yasukochi, Y., Nagata, Y., Fukuda M, Takagi, M. (1994); Nucleotide sequence and functional analysis of the metacleavage pathway involved in biphenyl and polychlorinated biphenyl degradation in Pseudomonas sp. strain KKS102.. Journal of Bacteriology 176:(14)4269–4276 [View Article]
    [Google Scholar]
  26. Kimura, N., Nishi, A., Goto, M., Furukawa, K. (1997); Functional analyses of a variety of chimeric dioxygenases constructed from two biphenyl dioxygenases that are structurally similar but different functionally.. Journal of Bacteriology 179:(12)3936–3943 [View Article]
    [Google Scholar]
  27. King, E. D., Ward, M. K., Raney, D. C. (1954); Simple method for the demonstration of pyocyanin and fluorescein.. J Lab Clin Methods 44:301–307
    [Google Scholar]
  28. Lau, P. C. K., Bergeron, H., Labbé, D., Wang, Y., Brousseau, R., Gibson, D. T. (1994); Sequence and expression of the todGIH genes involved in the last three steps of toluene degradation by Pseudomonas putida FI.. Gene 146:(1)7–13 [View Article]
    [Google Scholar]
  29. van der Meer, J. R., De Vos, W. M., Harayama, S., Zehnder, A. B. (1992); Molecular mechanisms of genetic adaptation to xenobiotic compounds.. Microbiological Reviews 56:(4)677–694 [View Article]
    [Google Scholar]
  30. Mermod, N., Harayama, S., Timmis, K. N. (1986); New route for the bacterial production of indigo.. Biotechnology 4:321–324
    [Google Scholar]
  31. Neidle, E. L., Hartnett, C., Ornston, L. N., Bairoch, A., Rekik, M. et al. (1991); Nucleotide sequences of the Acinetobacter calcoaceticus benABC genes for benzoate dioxygenase reveal evolutionary relationships among multicomponent oxygenases.. Journal of Bacteriology 173:(17)5385–5395 [View Article]
    [Google Scholar]
  32. Neidle, E. L., Hartnett, G., Ornston, L. N., Bairoch, A., Rekik, M., Harayama, S. (1992); Cis-diol dehydrogenases encoded by the TOL (pWWO) plasmid and the Acinetobacter calcoaceticus chromosomal benD gene are members of the short-chain alcohol dehydrogenase superfamily.. European Journal of Biochemistry 204:(1)113–120 [View Article]
    [Google Scholar]
  33. O\\'Donnell, K., Williams P. A. (1991); Duplication of both xyl operons on TOL plasmid pWW15.. Journal of General Microbiology 137:(12)2831–2838 [View Article]
    [Google Scholar]
  34. Osborne, D. J., Pickup, R. W., Williams P. A. (1988); The presence of two complete homologous meta pathway operons on TOL plasmid pWW53.. Journal of Bacteriology 134:2965–2975
    [Google Scholar]
  35. Pickup, R. W., Williams P. A. (1982); Spontaneous deletions in the TOL plasmid pWW20 which give rise to the B3 mutants of Pseudomonas putida MT20.. Journal of General Microbiology 128:1385–1390
    [Google Scholar]
  36. Platt, A., Shingler, V., Taylor, S. C., Williams P. A. (1995); The 4-hydroxy-2-oxovalerate aldolase and acetaldehyde dehydrogenase (acylating) encoded by the nahM and nahO genes of the naphthalene catabolic plasmid pWW60-22 provide further evidence of conservation of meta-cleavage pathway gene sequences.. Microbiology 141:(9)2223–2233 [View Article]
    [Google Scholar]
  37. Polissi, A., Harayama S. (1993); In vivo reactivation of catechol 2,3-dioxygenase mediated by a chloroplast-type ferredoxin - a bacterial strategy to expand the substrate specificity of aromatic degradative pathways.. Embo Journal 12:(8)3339–3347 [View Article]
    [Google Scholar]
  38. Saitou, N., Nei M. (1987); The neighbour-joining method - a new method for reconstructing phylogenetic trees.. Molecular Biology and Evolution 4:426–444
    [Google Scholar]
  39. Sala-Trepat, J. M., Evans W. C. (1971); The meta cleavage of catechols by Azotobacter species.. European Journal of Biochemistry 20:(3)400–413 [View Article]
    [Google Scholar]
  40. Sambrook, J., Fritsch, E. F., Maniatis T. (1989) Molecular Cloning: a Laboratory Manual., 2nd edn.. Cold Spring Harbor, NY:: Cold Spring Harbor Laboratory;
    [Google Scholar]
  41. Shingler, V., Powlowski, J., Marklund, U. (1992); Nucleotide sequence and functional analysis of the complete phenol/3,4- dimethylphenol catabolic pathway of Pseudomonas sp. strain CF600.. Journal of Bacteriology 174:(3)711–724 [View Article]
    [Google Scholar]
  42. Southern, E. M. (1975); Detection of specific sequences among DNA fragments separated by gel electrophoresis.. J Mol Microbiol 98:503–517
    [Google Scholar]
  43. Thompson, J. D., Higgins, D. G., Gibson, T. J. (1994); clustal w - improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.. Nucleic Acids Research 22:(22)4673–4680 [View Article]
    [Google Scholar]
  44. Vieira, J., Messing, J. (1982); The pUC plasmids, an M13mp7- derived system for insertion mutagenesis and sequencing with synthetic universal primers.. Gene 19:(3)259–268 [View Article]
    [Google Scholar]
  45. Wheatcroft, R., Williams, P. A. (1981); Rapid methods for the study of both stable and unstable plasmids in Pseudomonas.. Journal of General Microbiology 124:433–437
    [Google Scholar]
  46. Williams, P. A., Murray, K. (1974); Metabolism of benzoate and the methylbenzoates by Pseudomonas putida (arvilla) mt-2: evidence for the existence of a TOL plasmid.. Journal of Bacteriology 120:(1)416–423 [View Article]
    [Google Scholar]
  47. Williams, P. A., Sayers, J. R. (1994); The evolution of pathways for aromatic hydrocarbon oxidation in Pseudomonas.. Biodegradation 5:(3–4)195–217 [View Article]
    [Google Scholar]
  48. Williams, P. A., Worsey, M. J. (1976); Ubiquity of plasmids in coding for toluene and xylene metabolism in soil bacteria: evidence for the existence of new TOL plasmids.. ] Bacteriol 125:(3)818–828 [View Article]
    [Google Scholar]
  49. Williams, P. A., Shaw, L. E., Pitt, C. W., Vred, M. (1997); xylUW, two genes at the start of the upper pathway operon of TOL plasmid pWWO, appear to play no essential part in determining its catabolic phenotype.. Microbiology 143:(1)101–107 [View Article]
    [Google Scholar]
  50. Worsey, M. J., Williams P. A. (1975); Metabolism of toluene and xylenes by Pseudomonas putida (arvilla) mt-2: evidence for a new function of the toluene plasmid.. Journal of Bacteriology 124:(1)7–13 [View Article]
    [Google Scholar]
  51. Worsey, M. J., Franklin, F. C. H., Williams, P. A. (1978); Regulation of the degradative pathway enzymes coded for by the TOL plasmid (pWWO) from Pseudomonas putida mt-2.. Journal of Bacteriology 134:(3)757–764 [View Article]
    [Google Scholar]
  52. Yanisch-Perron, C., Vieira, J., Messing, J. (1985); Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mpl8 and pUC19 vectors.. Gene 33:(1)103–119 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/00221287-144-5-1387
Loading
/content/journal/micro/10.1099/00221287-144-5-1387
Loading

Data & Media loading...

Most cited this month Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error