Genes for Mn(II)-dependent NahC and Fe(II)-dependent NahH located in close proximity in the thermophilic naphthalene and PCB degrader, sp. JF8: cloning and characterization Free

Abstract

A 10 kb DNA fragment was isolated using a DNA probe derived from the N-terminal amino acid sequence of the extradiol dioxygenase purified from naphthalene-grown sp. JF8, a thermophilic naphthalene and polychlorinated biphenyl degrader. The cloned DNA fragment had six open reading frames, designated based on sequence homology, of which the products NahH_JF8 and NahC_JF8 were extradiol dioxygenases. Although NahC_JF8 and NahH_JF8 exhibit low homology to known extradiol dioxygenases, the active-site residues and metal ion ligands are conserved. The presence of Mn(II) in culture medium was found to be essential for production of active recombinant NahC_JF8, while Fe(II) was necessary for active recombinant NahH_JF8. Inductively coupled plasma mass spectrometry analysis of active NahC_JF8 identified the cofactor to be manganese, indicating a Mn(II)-dependent extradiol dioxygenase. NahC_JF8 exhibited values of 32±5 μM for 1,2-dihydroxynaphthalene and 510±90 μM for 2,3-dihydroxybiphenyl at 60 °C. In cell-free extracts, NahH_JF8 exhibited a broad substrate range for 2,3-dihydroxybiphenyl, catechol, and 3- and 4-methylcatechol at 25 °C. Stability studies on the Mn(II)-dependent NahC_JF8 indicated that it was thermostable, retaining 50 % activity after incubation at 80 °C for 20 min, and it exhibited resistance to EDTA and HO. Northern hybridization studies clarified that both NahC_JF8 and NahH_JF8 were induced by naphthalene; RT-PCR showed that is expressed as a single transcript.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.26858-0
2004-04-01
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/micro/150/4/mic1500993.html?itemId=/content/journal/micro/10.1099/mic.0.26858-0&mimeType=html&fmt=ahah

References

  1. Asturias J. A., Timmis K. N. 1993; Three different 2,3-dihydroxybiphenyl-1,2-dioxygenase genes in the gram-positive polychlorobiphenyl-degrading bacterium Rhodococcus globerulus P6. J Bacteriol 175:4631–4640
    [Google Scholar]
  2. Asturias J. A., Eltis L. D., Prucha M., Timmis K. N. 1994; Analysis of three 2,3-dihydroxybiphenyl 1,2-dioxygenases found in Rhodococcus globerulus P6. Identification of a new family of extradiol dioxygenases. J Biol Chem 269:7807–7815
    [Google Scholar]
  3. Axcell B. C., Geary P. J. 1975; Purification and some properties of a soluble benzene-oxidizing system from a strain of Pseudomonas. Biochem J 146:173–183
    [Google Scholar]
  4. Bayly R. C., Dagley S., Gibson D. T. 1966; The metabolism of cresols by species of Pseudomonas. Biochem J 101:293–301
    [Google Scholar]
  5. Boldt Y. R., Sadowsky M. J., Ellis L. B., Wackett L. P., Que L., Jr. 1995; A manganese-dependent dioxygenase from Arthrobacter globiformis CM-2 belongs to the major extradiol dioxygenase family. J Bacteriol 177:1225–1232
    [Google Scholar]
  6. Boldt Y. R., Whiting A. K., Wagner M. I., Sadowsky M. J., Wackett L. P., Que L. Jr 1997; Manganese(II) active site mutants of 3,4-dihydroxyphenylacetate 2,3-dioxygenase from Arthrobacter globiformis strain CM-2. Biochemistry 36:2147–2153 [CrossRef]
    [Google Scholar]
  7. 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]
  8. Buswell J. A. 1974; The meta-cleavage of catechol by a thermophilic Bacillus species. Biochem Biophys Res Commun 60:934–941 [CrossRef]
    [Google Scholar]
  9. Buswell J. A. 1975; Metabolism of phenol and cresols by Bacillus stearothermophilus. J Bacteriol 124:1077–1083
    [Google Scholar]
  10. Chen C., Taylor R. 1995; Thermophilic biodegradation of BTEX by two Thermus species. Biotechnol Bioeng 48:614–624 [CrossRef]
    [Google Scholar]
  11. Dong F. M., Wang L. L., Wang C. M., Cheng J. P., He Z. Q., Sheng Z. J., Shen R. Q. 1992; Molecular cloning and mapping of phenol degradation genes from Bacillus stearothermophilus FDTP-3 and their expression in Escherichia coli. Appl Environ Microbiol 58:2531–2535
    [Google Scholar]
  12. Duffner F. M., Muller R. 1998; A novel phenol hydroxylase and catechol 2,3-dioxygenase from the thermophilic Bacillus thermoleovorans strain A2: nucleotide sequence and analysis of the genes. FEMS Microbiol Lett 161:37–45 [CrossRef]
    [Google Scholar]
  13. Duffner F. M., Kirchner U., Bauer M. P., Muller R. 2000; Phenol/cresol degradation by the thermophilic Bacillus thermoglucosidasius A7: cloning and sequence analysis of five genes involved in the pathway. Gene 256:215–221 [CrossRef]
    [Google Scholar]
  14. Eaton R. W., Chapman P. J. 1992; Bacterial metabolism of naphthalene: construction and use of recombinant bacteria to study ring cleavage of 1,2-dihydroxynaphthalene and subsequent reactions. J Bacteriol 174:7542–7554
    [Google Scholar]
  15. Eltis L. D., Bolin J. T. 1996; Evolutionary relationships among extradiol dioxygenases. J Bacteriol 178:5930–5937
    [Google Scholar]
  16. Eltis L. D., Hofmann B., Hecht H. J., Lunsdorf H., Timmis K. N. 1993; Purification and crystallization of 2,3-dihydroxybiphenyl 1,2-dioxygenase. J Biol Chem 268:2727–2732
    [Google Scholar]
  17. Ensley B. D., Gibson D. T., Laborde A. L. 1982; Oxidation of naphthalene by a multicomponent enzyme system from Pseudomonas sp. strain NCIB 9816. J Bacteriol 149:948–954
    [Google Scholar]
  18. 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]
  19. Haddock J. D., Nadim L. M., Gibson D. T. 1993; Oxidation of biphenyl by a multicomponent enzyme system from Pseudomonas sp. strain LB400. J Bacteriol 175:395–400
    [Google Scholar]
  20. Han S., Eltis L. D., Timmis K. N., Muchmore S. W., Bolin J. T. 1995; Crystal structure of the biphenyl-cleaving extradiol dioxygenase from a PCB-degrading pseudomonad. Science 270:976–980 [CrossRef]
    [Google Scholar]
  21. Hatta T., Mukerjee-Dhar G., Damborsky J., Kiyohara H., Kimbara K. 2003; Characterization a novel thermostable Mn(II)-dependent 2,3-dihydroxybiphenyl 1,2-dioxygenase from a PCB and naphthalene-degrading Bacillus sp. JF8. J Biol Chem 278:21483–21492 [CrossRef]
    [Google Scholar]
  22. 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]
  23. Hirose J., Kimura N., Suyama A., Kobayashi A., Hayashida S., Furukawa K. 1994; Functional and structural relationship of various extradiol aromatic ring-cleavage dioxygenases of Pseudomonas origin. FEMS Microbiol Lett 118:273–277 [CrossRef]
    [Google Scholar]
  24. Innis M. A., Gelfand D. H., Sninsky J. J., White T. J. 1990 PCR Protocols: a Guide to Methods and Applications San Diego, California: Academic Press;
  25. Khan A. A., Wang R. F., Nawaz M. S., Cao W. W., Cerniglia C. E. 1996; Purification of 2,3-dihydroxybiphenyl 1,2-dioxygenase from Pseudomonas putida OU83 and characterization of the gene (bphC. Appl Environ Microbiol 62:1825–1830
    [Google Scholar]
  26. Kita A., Kita S., Fujisawa I., Inaka K., Ishida T., Horiike K., Nozaki M., Miki K. 1999; An archetypical extradiol-cleaving catecholic dioxygenase: the crystal structure of catechol 2,3-dioxygenase (metapyrocatechase) from Pseudomonas putida mt-2. Structure Fold Des 7:25–34 [CrossRef]
    [Google Scholar]
  27. Kiyohara H., Torigoe S., Kaida N., Asaki T., Iida T., Hayashi H., Takizawa N. 1994; Cloning and characterization of a chromosomal gene cluster, pah, that encodes the upper pathway for phenanthrene and naphthalene utilization by Pseudomonas putida OUS82. J Bacteriol 176:2439–2443
    [Google Scholar]
  28. Kuhm A. E., Stolz A., Knackmuss H. J. 1991a; Metabolism of naphthalene by the biphenyl-degrading bacterium Pseudomonas paucimobilis Q1. Biodegradation 2:115–120 [CrossRef]
    [Google Scholar]
  29. Kuhm A. E., Stolz A., Ngai K. L., Knackmuss H. J. 1991b; Purification and characterization of a 1,2-dihydroxynaphthalene dioxygenase from a bacterium that degrades naphthalenesulfonic acids. J Bacteriol 173:3795–3802
    [Google Scholar]
  30. Laemmli U. K. 1970; Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680–685 [CrossRef]
    [Google Scholar]
  31. Lu J., Nogi Y., Takami H. 2001; Oceanobacillus iheyensis gen. nov., sp. nov., a deep-sea extremely halotolerant and alkaliphilic species isolated from a depth of 1050 m on the Iheya Ridge. FEMS Microbiol Lett 205:291–297 [CrossRef]
    [Google Scholar]
  32. Miller M. A., Lipscomb J. D. 1996; Homoprotocatechuate 2,3-dioxygenase from Brevibacterium fuscum. A dioxygenase with catalase activity. J Biol Chem 271:5524–5535 [CrossRef]
    [Google Scholar]
  33. Milo R. E., Duffner F. M., Muller R. 1999; Catechol 2,3-dioxygenase from the thermophilic, phenol-degrading Bacillus thermoleovorans strain A2 has unexpected low thermal stability. Extremophiles 3:185–190 [CrossRef]
    [Google Scholar]
  34. Nozaki M., Ono K., Nakazawa T., Kotani S., Hayaishi O. 1968; Metapyrocatechase. II. The role of iron and sulfhydryl groups. J Biol Chem 243:2682–2690
    [Google Scholar]
  35. Page R. D. 1996; TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357–358
    [Google Scholar]
  36. Patel T. R., Barnsley E. A. 1980; Naphthalene metabolism by pseudomonads: purification and properties of 1,2-dihydroxynaphthalene oxygenase. J Bacteriol 143:668–673
    [Google Scholar]
  37. Sambrook J., Fritsch E. F., Maniatis T. 1989 Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
  38. Senda T., Sugiyama K., Narita H., Yamamoto T., Kimbara K., Fukuda M., Sato M., Yano K., Mitsui Y. 1996; 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. J Mol Biol 255:735–752 [CrossRef]
    [Google Scholar]
  39. She Q., Singh R. K., Confalonieri F. & 28 other authors; 2001; The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc Natl Acad Sci U S A 98:7835–7840 [CrossRef]
    [Google Scholar]
  40. Shimura M., Mukerjee-Dhar G., Kimbara K., Nagato H., Kiyohara H., Hatta T. 1999; Isolation and characterization of a thermophilic Bacillus sp. JF8 capable of degrading polychlorinated biphenyls and naphthalene. FEMS Microbiol Lett 178:87–93 [CrossRef]
    [Google Scholar]
  41. 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]
  42. Sterner R., Liebl W. 2001; Thermophilic adaptation of proteins. Crit Rev Biochem Mol Biol 36:39–106 [CrossRef]
    [Google Scholar]
  43. Taira K., Hayase N., Arimura N., Yamashita S., Miyazaki T., Furukawa K. 1988; Cloning and nucleotide sequence of the 2,3-dihydroxybiphenyl dioxygenase gene from the PCB-degrading strain of Pseudomonas paucimobilis Q1. Biochemistry 27:3990–3996 [CrossRef]
    [Google Scholar]
  44. Thompson J. D., Higgins D. G., Gibson T. J. 1994; CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680 [CrossRef]
    [Google Scholar]
  45. Treadway S. L., Yanagimachi K. S., Lankenau E., Lessard P. A., Stephanopoulos G., Sinskey A. J. 1999; Isolation and characterization of indene bioconversion genes from Rhodococcus strain I24. Appl Microbiol Biotechnol 51:786–793 [CrossRef]
    [Google Scholar]
  46. Tsuda M., Genka H. 2001; Identification and characterization of Tn4656, a novel class II transposon carrying a set of toluene-degrading genes from TOL plasmid pWW53. J Bacteriol 183:6215–6224 [CrossRef]
    [Google Scholar]
  47. Vieille C., Hess J. M., Kelly R. M., Zeikus J. G. 1995; xylA cloning and sequencing and biochemical characterization of xylose isomerase from Thermotoga neapolitana. Appl Environ Microbiol 61:1867–1875
    [Google Scholar]
  48. Vieille C., Burdette D. S., Zeikus J. G. 1996; Thermozymes. Biotechnol Annu Rev 2:1–83
    [Google Scholar]
  49. White O., Eisen J. A., Heidelberg J. F.23 other authors 1999; Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science 286:1571–1577 [CrossRef]
    [Google Scholar]
  50. Whiting A. K., Boldt Y. R., Hendrich M. P., Wackett L. P., Que L. Jr 1996; Manganese(II)-dependent extradiol-cleaving catechol dioxygenase from Arthrobacter globiformis CM-2. Biochemistry 35:160–170 [CrossRef]
    [Google Scholar]
  51. Wyndham R. C., Cashore A. E., Nakatsu C. H., Peel M. C. 1994a; Catabolic transposons. Biodegradation 5:323–342 [CrossRef]
    [Google Scholar]
  52. Wyndham R. C., Nakatsu C., Peel M., Cashore A., Ng J., Szilagyi F. 1994b; Distribution of the catabolic transposon Tn5271 in a groundwater bioremediation system. Appl Environ Microbiol 60:86–93
    [Google Scholar]
  53. Yeh W. K., Gibson D. T., Liu T. N. 1977; Toluene dioxygenase: a multicomponent enzyme system. Biochem Biophys Res Commun 78:401–410 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.26858-0
Loading
/content/journal/micro/10.1099/mic.0.26858-0
Loading

Data & Media loading...

Most cited Most Cited RSS feed