Gene cloning and in vivo characterization of a dibenzothiophene dioxygenase from Xanthobacter polyaromaticivorans

Applied Microbiology and Biotechnology

Volumn 69, Issue 6, 2006, Pages 672-681

  Hirano, Shin Ichi ^a   Haruki, Mitsuru ^a,b   Takano, Kazufumi ^a,c   Imanaka, Tadayuki ^d   Morikawa, Masaaki ^a,e   Kanaya, Shigenori ^a  

^a OSAKA UNIVERSITY   (Japan)

^b NIHON UNIVERSITY   (Japan)

^c JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^d KYOTO UNIVERSITY   (Japan)

^e HOKKAIDO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; AROMATIC HYDROCARBONS; BACTERIA; CLONING; DEGRADATION; GENES; NAPHTHALENE; YEAST;

GENE CLONING; GENE DISRUPTION; XANTHOBACTER POLYAROMATICIVORANS;

ENZYMES;

ANTHRACENE; AROMATIC HYDROCARBON; BIPHENYL; DIBENZOTHIOPHENE DERIVATIVE; DIBENZOTHIOPHENE DIOXYGENASE; DIOXYGENASE; NAPHTHALENE; OXYGEN; PHENANTHRENE; UNCLASSIFIED DRUG;

BIODEGRADATION; BIOTECHNOLOGY; CHEMICAL POLLUTANT; ENZYME ACTIVITY; MICROBIAL ACTIVITY;

ALPHA CHAIN; AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; CONTROLLED STUDY; GENE DISRUPTION; IN VIVO STUDY; MICROBIAL ACTIVITY; MICROBIAL DEGRADATION; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; OXYGEN CONCENTRATION; PHYLOGENY; XANTHOBACTER; XANTHOBACTER POLYAROMATICIVORANS;

AMINO ACID SEQUENCE; ANTHRACENES; CLONING, MOLECULAR; CLONING, ORGANISM; DIOXYGENASES; GENE DELETION; GENE ORDER; HYDROCARBONS, AROMATIC; MOLECULAR SEQUENCE DATA; MUTAGENESIS, INSERTIONAL; PHYLOGENY; PROTEIN SUBUNITS; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID; THIOPHENES; XANTHOBACTER;

BACTERIA (MICROORGANISMS); XANTHOBACTER; XANTHOBACTER POLYAROMATICIVORANS;

EID: 31144439476     PISSN: 01757598     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00253-005-0007-9     Document Type: Article

References (33)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410
2. Calvin NM, Hanawalt PC (1988) High-efficiency transformation of bacterial cells by electroporation. J Bacteriol 170:2796-2801
3. Crawford RL (1976) Pathways of 4-hydroxybenzoate degradation among species of Bacillus. J Bacteriol 127:204-210
4. Denome SA, Stanley DC, Olson ES, Young KD (1993) Metabolism of debenzothiophene and naphthalene in Pseudomonas strains: complete DNA sequence of an upper naphthalene catabolic pathway. J Bacteriol 175:6890-6901
5. Gibson JS, Harwood C (2002) Metabolic diversity in aromatic compound utilization by anaerobic microbes. Annu Rev Microbiol 56:345-369
6. Habe H, Omori T (2003) Genetics of polycyclic aromatic hydrocarbon metabolism in diverse aerobic bacteria. Biosci Biotechnol Biochem 67:225-243
7. Haddock JD, Gibson DT (1995) Purification and characterization of the oxygenase component of biphenyl 2,3-dioxygenase from Pseudomonas sp. strain LB400. J Bacteriol 177:5834-5839
8. Herrick JB, Stuart-Keil KG, Ghiorse WC, Madsen EL (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
9. Hirano S, Kitauchi F, Haruki M, Imanaka T, Morikawa M, Kanaya S (2004) Isolation and characterization of Xanthobacter polyaromaticivorans sp. nov. 127W that degrades polycyclic and heterocyclic aromatic compounds under extremely low oxygen conditions. Biosci Biotechnol Biochem 68:557-564
10. Jiang H, Parales RE, Lynch NA, Gibson DT (1996) Site-directed mutagenesis of conserved amino acids in the alpha subunit of toluene dioxygenase: potential mononuclear non-heme iron coordination sites. J Bacteriol 171:3133-3139
11. Kanaly RA, Harayama S (2000) Biodegradation of high-molecular mass polycyclic aromatic hydrocarbons by bacteria. J Bacteriol 182:2059-2067
12. Kauppi B, Lee K, Carredano E, Parales RE, Gibson DT, Eklund H, Ramaswamy S (1998) Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2-dioxygenase. Structure 6:571-586
13. Kawasaki H, Suzuki K (1990) Separation of peptides dissolved in a sodium dodecyl sulfate solution by reversed-phase liquid chromatography: removal of sodium dodecyl sulfate from peptides using an ion-exchange precolumn. Anal Biochem 186:264-268
14. Kesseler M, Dabbs ER, Averhoff B, Gottschalk G (1996) Studies on the isopropylbenzene 2,3-dioxygenase and the 3-isopropylcatechol 2,3-dioxygenase genes encoded by the linear plasmid of Rhodococcus erythropolis BD2. Microbiology 142:3241-3251
15. Kimura N, Nishi A, Goto M, Furukawa K (1997) Functional analyses of a variety of chimeric dioxygenases constructed from two biphenyl dioxygenases that are similar structurally but different functionally. J Bacteriol 179:3936-3943
16. Kitauchi F, Hirano S, Haruki M, Imanaka T, Morikawa M, Kanaya S (2005) A comparative study of dibenzothiophene degrading bacteria under a low oxygen condition. J Environ Biotechnol 4:117-120
17. Kok M, Oldenhuis R, van der Linden MP, Raatjes P, Kingma J, van Lelyveld PH, Witholt B (1989) The Pseudomonas oleovorans alkane hydroxylase gene. Sequence and expression. J Biol Chem 264:5435-5441
18. Kukor JJ, Olsen RH (1996) Catechol 2,3-dioxygenases functional in oxygen-limited (hypoxic) environments. Appl Environ Microbiol 62:1728-1740
19. Maeda K, Nojiri H, Shintani M, Yoshida T, Habe H, Omori T (2003) Complete nucleotide sequence of carbazole/dioxin-degrading plasmid pCAR1 in Pseudomonas resinovorans strain CA10 indicates its mosaicity and the presence of large catabolic transposon Tn4676. J Mol Biol 326:21-33
20. McKay DB, Prucha M, Reineke W, Timmis KN, Pieper DH (2003) Substrate specificity and expression of three 2,3-dihydroxybiphenyl 1,2-dioxygenases from Rhodococcus globerulus strain P6. J Bacteriol 185:2944-2951
21. Menzie CA, Potocki BB, Santodonato J (1992) Exposure to carcinogenic PAHs in the environment. Environ Sci Technol 26:1278-1284
22. Merlin C, Springael D, Mergeay M, Toussaint A (1997) Organisation of the bph gene cluster of transposon Tn4371 encoding enzymes for the degradation of biphenyl and 4-chlorobiphenyl compounds. Mol Gen Genet 253:499-506
23. Nam JW, Nojiri H, Yoshida T, Habe H, Yamane H, Omori T (2001) New classification system for oxygenase components involved in ring-hydroxylating oxygenations. Biosci Biotechnol Biochem 65:254-263
24. Page RDM (1996) Tree view: an application to display phylogenetic trees on personal computers. Comp Appl Biosci 12:357-358
25. Parales RE (2003) The role of active-site residues in naphthalene dioxygenase. J Ind Microbiol Biotechnol 30:271-278
26. Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbor Laboratory, Cold Spring Harbor, pp 1.31-1.122
27. Tan HM, Tang HY, Joannou CL, Abdel-Wahab NH, Mason JR (1993) The Pseudomonas putida ML2 plasmid-encoded genes for benzene dioxygenase are unusual in codon usage and low in G+C content. Gene 130:33-39
28. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680
29. Tovey ER, Baldo BA (1989) Protein binding to nitrocellulose, nylon and PVDF membranes in immunoassays and electroblotting. J Biochem Biophys Methods 19:169-183
30. Werlen C, Kohler HP, van der Meer JR (1996) The broad substrate chlorobenzene dioxygenase and cis-chlorobenzene dihydrodiol dehydrogenase of Pseudomonas sp. strain P51 are linked evolutionarily to the enzymes for benzene and toluene degradation. J Biol Chem 271:4009-4016
31. Wyndham RC, Cashore AE, Nakatsu CH, Peel MC (1994) Catabolic transposons. Biodegradation 5:323-342
32. Zhou NY, Al-Dulayymi J, Baird MS, Williams PA (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
33. Zielinski M, Backhaus S, Hofer B (2002) The principal determinants for the structure of the substrate-binding pocket are located within central core of a biphenyl dioxygenase alpha subunit. Microbiology 148:2439-2448