1887

Abstract

In strain G7, a LysR-type positive transcriptional activator protein encoded by is necessary for activation of two operons involved in naphthalene catabolism [Schell, M. A. & Poser, E. F. (1989) . 171, 837–846]. The role of an homologue, NCIB-, in another naphthalene-metabolizing bacterium, NCIB 9816-4 was verified. Targeted disruption of NCIB- by homologous recombination resulted in a growth defect in the presence of naphthalene or salicylate as sole carbon and energy source. The homologues and intergenic regions between -like and -like genes from NCIB 9816-4 and seven bacteria native to a naphthalene-rich coal tar contaminated site were amplified by PCR using degenerate primers. The amplified homologues and the intergenic regions were cloned and sequenced. Alignment of the deduced amino acid sequences from NahR homologues revealed that NahR-like proteins showed only minor variations in all investigated naphthalene-degrading isolates. The intergenic regions, together with known NahR-binding sites showed the consensus NahR-protein-binding sites (5′-ATTCACGCTNTGAT-3′). Surprisingly, amplified intergenic regions from naphthalene-degrading micro-organisms native to this study site were 100% identical to that of the pDTG1 plasmid (an archetypal naphthalene-catabolic plasmid from NCIB 9816-4), but the coding regions were not. DNA representing the uncultured microbial community was extracted from six sediment samples with varying coal tar exposure histories. PCR amplification of from sediment DNA was observed in contaminated samples, but in uncontaminated samples only following laboratory incubation with naphthalene. The sediment-derived PCR products were sequenced and also found to be almost identical to known genes. Thus, the structure and function of - regulatory genes appear to be highly conserved.

Loading

Article metrics loading...

/content/journal/micro/10.1099/00221287-148-8-2319
2002-08-01
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/micro/148/8/1482319a.html?itemId=/content/journal/micro/10.1099/00221287-148-8-2319&mimeType=html&fmt=ahah

References

  1. Ausubel F. M., Brent R., Kingston R. E., Moore D. D., Seidman J. G., Smith J. A., Struhl K. 1994 Current Protocols in Molecular Biology. New York: Wiley;
    [Google Scholar]
  2. Beaulieu M., Becaert V., Deschenes L., Villemur R. 2000; Evolution of bacterial diversity during enrichment of PCP-degrading activated soils. Microb Ecol 40:345–355
    [Google Scholar]
  3. Bosch R., Garcia-Valdes E., Moore E. R. 1999; Genetic characterization and evolutionary implications of a chromosomally encoded naphthalene-degradation upper pathway from Pseudomonas stutzeri AN10. Gene 236:149–157 [CrossRef]
    [Google Scholar]
  4. Bosch R., Garcia-Valdes E., Moore E. R. 2000; Complete nucleotide sequence and evolutionary significance of a chromosomally encoded naphthalene-degradation lower pathway from Pseudomonas stutzeri AN10. Gene 245:65–74 [CrossRef]
    [Google Scholar]
  5. Cane P. A., Williams P. A. 1986; A restriction map of the catabolic plasmid pWW60-1 and location of some of its catabolic genes. J Gen Microbiol 132:2919–2929
    [Google Scholar]
  6. Cases I., de Lorenzo V. 2001; The black cat/white cat principle of signal integration in bacterial promoter. EMBO J 20:1–11 [CrossRef]
    [Google Scholar]
  7. Cebolla A., Sousa C., de Lorenzo V. 1997; Effector specificity mutants of the transcriptional activator NahR of naphthalene degrading Pseudomonas define protein sites involved in binding of aromatic inducers. J Biol Chem 272:3986–3992 [CrossRef]
    [Google Scholar]
  8. Connors M. A., Barnsley E. A. 1980; Metabolism of naphthalene by pseudomonads: salicylaldehyde as the first possible inducer in the metabolic pathway. J Bacteriol 141:1052–1054
    [Google Scholar]
  9. de Lorenzo V., Perez-Martin J. 1996; Regulatory noise in prokaryotic promoters: how bacteria learn to respond to novel environmental signals. Mol Microbiol 19:1177–1184 [CrossRef]
    [Google Scholar]
  10. Dunbar J., White S., Forney L. 1997; Genetic diversity through the looking glass: effect of enrichment bias. Appl Environ Microbiol 63:1326–1331
    [Google Scholar]
  11. Eaton R. W. 1994; Organization and evolution of naphthalene catabolic pathways: sequence of the DNA encoding 2-hydroxychromene-2-carboxylate isomerase and trans-o-hydroxybenzylidenepyruvate hydratase-aldolase from the NAH7 plasmid. J Bacteriol 176:7757–7762
    [Google Scholar]
  12. Fuenmayor S. L., Wild M., Boyes A. L., Williams P. A. 1998; A gene cluster encoding steps in conversion of naphthalene to gentisate in Pseudomonas sp. strain U2. J Bacteriol 180:2522–2530
    [Google Scholar]
  13. Goyal A. K., Zylstra G. J. 1996; Molecular cloning of novel genes for polycyclic aromatic hydrocarbon degradation from Comamonas testosteroni GZ39. Appl Environ Microbiol 62:230–236
    [Google Scholar]
  14. Goyal A. K., Zylstra G. J. 1997; Genetics of naphthalene and phenanthrene degradation by Comamonas testosteroni . J Ind Microbiol Biotechnol 19:401–407 [CrossRef]
    [Google Scholar]
  15. Herrick J. B. 1995 Detection, divergence, and phylogeny of a naphthalene dioxygenase and naphthalene degrading bacteria native to a coal tar-contaminated site PhD thesis Cornell University; Ithaca, NY, USA:
    [Google Scholar]
  16. Herrick J. B., Stuart-Keil K. G., Ghiorse W. C., Madsen E. L. 1997; Natural horizontal transfer of a naphthalene dioxygenase gene between bacteria native to a coal tar-contaminated field site. Appl Environ Microbiol 63:2330–2337
    [Google Scholar]
  17. Hohnstock A. M., Stuart-Keil K. G., Kull E. E., Madsen E. L. 2000; Naphthalene and donor cell density influence field conjugation of naphthalene catabolism plasmids. Appl Environ Microbiol 66:3088–3092 [CrossRef]
    [Google Scholar]
  18. Huang J. Z., Schell M. A. 1991; In vivo interactions of the NahR transcriptional activator with its target sequences. Inducer-mediated changes resulting in transcription activation. J Biol Chem 266:10830–10838
    [Google Scholar]
  19. Kalogeraki V. S., Winans S. C. 1997; Suicide plasmids containing promoterless reporter genes can simultaneously disrupt and create fusions to target genes of diverse bacteria. Gene 188:69–75 [CrossRef]
    [Google Scholar]
  20. Kurkela S., Lehvaslaiho H., Palva E. T., Teeri T. H. 1988; Cloning, nucleotide sequence and characterization of genes encoding naphthalene dioxygenase of Pseudomonas putida strain NCIB 9816. Gene 73:355–362 [CrossRef]
    [Google Scholar]
  21. Larkin M. J., Allen C. C., Kulakov L. A., Lipscomb D. A. 1999; Purification and characterization of a novel naphthalene dioxygenase from Rhodococcus sp. strain NCIMB12038. J Bacteriol 181:6200–6204
    [Google Scholar]
  22. Laurie A. D., Lloyd-Jones G. 1999; The phn genes of Burkholderia sp. strain RP007 constitute a divergent gene cluster for polycyclic aromatic hydrocarbon catabolism. J Bacteriol 181:531–540
    [Google Scholar]
  23. Laurie A. D., Lloyd-Jones G. 2000; Quantification of phnAc and nahAc in contaminated New Zealand soils by competitive PCR. Appl Environ Microbiol 66:1814–1817 [CrossRef]
    [Google Scholar]
  24. Madsen E. L., Sinclair J. L., Ghiorse W. C. 1991; In situ biodegradation: microbiological patterns in a contaminated aquifer. Science 252:830–833 [CrossRef]
    [Google Scholar]
  25. Miller J. H. 1972 Experiments in Molecular Genetics Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  26. Pieper D. H., Reineke W. 2000; Engineering bacteria for bioremediation. Curr Opin Biotechnol 11:262–270 [CrossRef]
    [Google Scholar]
  27. Ramirez-Saad H. C., Sessitsch A., de Vos W., Akkermans A. D. 2000; Bacterial community change and enrichment of Burkholderia -like bacteria induced by chlorinated benzoates in a peat-forest soil-microcosm. Syst Appl Microbiol 23:591–598 [CrossRef]
    [Google Scholar]
  28. Saito A., Iwabuchi T., Harayama S. 2000; A novel phenanthrene dioxygenase from Nocardioides sp.Strain KP7: expression in Escherichia coli . J Bacteriol 182:2134–2141 [CrossRef]
    [Google Scholar]
  29. 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]
  30. Schell M. A. 1985; Transcriptional control of the nah and sal hydrocarbon-degradation operons by the nahR gene product. Gene 36:301–309 [CrossRef]
    [Google Scholar]
  31. Schell M. A. 1986; Homology between nucleotide sequences of promoter regions of nah and sal operons of NAH7 plasmid of Pseudomonas putida . Proc Natl Acad Sci USA 83:369–373 [CrossRef]
    [Google Scholar]
  32. Schell M. A. 1993; Molecular biology of the LysR family of transcriptional regulators. Annu Rev Microbiol 47:597–626 [CrossRef]
    [Google Scholar]
  33. Schell M. A., Poser E. F. 1989; Demonstration, characterization, and mutational analysis of NahR protein binding to nah and sal promoters. J Bacteriol 171:837–846
    [Google Scholar]
  34. Schell M. A., Wender P. E. 1986; Identification of the nahR gene product and nucleotide sequences required for its activation of the sal operon. J Bacteriol 166:9–14
    [Google Scholar]
  35. Schell M. A., Brown P. H., Raju S. 1990; Use of saturation mutagenesis to localize probable functional domains in the NahR protein, a LysR-type transcription activator. J Biol Chem 265:3844–3850
    [Google Scholar]
  36. Serdar C. M., Gibson D. T. 1989; Studies of nucleotide sequence homology between naphthalene-utilizing strains of bacteria. Biochem Biophys Res Commun 164:772–779 [CrossRef]
    [Google Scholar]
  37. Shuttleworth K. L., Cerniglia C. E. 1995; Environmental aspects of PAH biodegradation. Appl Biochem Biotechnol 54:291–302 [CrossRef]
    [Google Scholar]
  38. Silva M. C., More M. I., Batt C. A. 1995; Development of a molecular detection method for naphthalene degrading pseudomonads. FEMS Microbiol Lett 18:225–235 [CrossRef]
    [Google Scholar]
  39. Simon M. J., Osslund T. D., Saunders R. 7 other authors 1993; Sequences of genes encoding naphthalene dioxygenase in Pseudomonas putida strains G7 and NCIB 9816-4. Gene 127:31–37 [CrossRef]
    [Google Scholar]
  40. Simon R., Priefer U., Pühler A. 1983; A broad host-range mobilization system for in vivo genetic engineering: transposon mutagenesis in gram-negative bacteria. Bio/Technology 1:784–791 [CrossRef]
    [Google Scholar]
  41. Stanier R. Y., Palleroni N. J., Doudorhoff M. 1966; The aerobic pseudomonads: a taxonomic study. J Gen Microbiol 43:159–271 [CrossRef]
    [Google Scholar]
  42. Stuart-Keil K. G., Hohnstock A. M., Drees K. P., Herrick J. B., Madsen E. L. 1998; Plasmids responsible for horizontal transfer of naphthalene catabolism genes between bacteria at a coal tar-contaminated site are homologous to pDTG1 from Pseudomonas putida NCIB 9816-4. Appl Environ Microbiol 64:3633–3640
    [Google Scholar]
  43. Sutherland J. B., Rafii F., Khan A. A., Cerniglia C. E. 1995; Mechanisms of polycyclic aromatic hydrocarbon degradation. In Microbial Transformation and Degradation of Toxic Organic Chemicals pp 269–306 Edited by Young L. Y., Cerniglia C. E. New York: Wiley;
    [Google Scholar]
  44. Timmis K. N., Pieper D. H. 1999; Bacteria designed for bioremediation. Trends Biotechnol 17:200–204
    [Google Scholar]
  45. van der Meer J. R., de Vos W. M., Harayama S., Zehnder A. J. B. 1992; Molecular mechanism of genetics adaptation to xenobiotics compounds. Microbiol Rev 56:677–694
    [Google Scholar]
  46. Williams P. A., Sayers J. R. 1994; The evolution of pathways for aromatic hydrocarbon oxidation in Pseudomonas . Biodegradation 5:195–217 [CrossRef]
    [Google Scholar]
  47. Yen K. M., Gunsalus I. C. 1982; Plasmid gene organization: naphthalene/salicylate oxidation. Proc Natl Acad Sci USA 79:874–878 [CrossRef]
    [Google Scholar]
  48. Yen K. M., Serdar C. M. 1988; Genetics of naphthalene catabolism in pseudomonads. Crit Rev Microbiol 15:247–268 [CrossRef]
    [Google Scholar]
  49. Zhou N. Y., Fuenmayor S. L., Williams P. A. 2001; nag genes of Ralstonia (formerly Pseudomonas ) sp. strain U2 encoding enzymes for gentisate catabolism. J Bacteriol 183:700–708 [CrossRef]
    [Google Scholar]
  50. Zhou N. Y., Al-Dulayymi J., Baird M. S., Williams P. A. 2002; Salicylate 5-hydroxylase from Ralstonia sp. strain U2: a monooxygenase with close relationships to and shared electron transport proteins with naphthalene dioxygenase. J Bacteriol 184:1547–1555 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/00221287-148-8-2319
Loading
/content/journal/micro/10.1099/00221287-148-8-2319
Loading

Data & Media loading...

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