Xanthobacter polyaromaticivorans sp. nov. 127W is a bacterial strain that is capable of degrading a wide range of cyclic aromatic compounds such as dibenzothiophene, biphenyl, naphthalene, anthracene, and phenanthrene even under extremely low oxygen [dissolved oxygen (DO)≤0.2 ppm] conditions (Hirano et al., Biosci Biotechnol Biochem 68:557–564, 2004). A major protein fraction carrying dibenzothiophene degradation activity was purified. Based on its partial amino acid sequences, dbdCa gene encoding alpha subunit terminal oxygenase (DbdCa) and its flanking region were cloned and sequenced. A phylogenetic analysis based on the amino acid sequence demonstrates that DbdCa is a member of a terminal oxygenase component of group IV ring-hydroxylating dioxygenases for biphenyls and monocyclic aromatic hydrocarbons, rather than group III dioxygenases for polycyclic aromatic hydrocarbons. Gene disruption in dbdCa abolished almost of the degradation activity against biphenyl, dibenzothiophene, and anthracene. The gene disruption also impaired degradation activity of the strain under extremely low oxygen conditions (DO≤0.2 ppm). These results indicate that Dbd from 127W represents a group IV dioxygenase that is functional even under extremely low oxygen conditions.
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Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Calvin NM, Hanawalt PC (1988) High-efficiency transformation of bacterial cells by electroporation. J Bacteriol 170:2796–2801
Crawford RL (1976) Pathways of 4-hydroxybenzoate degradation among species of Bacillus. J Bacteriol 127:204–210
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
Gibson JS, Harwood C (2002) Metabolic diversity in aromatic compound utilization by anaerobic microbes. Annu Rev Microbiol 56:345–369
Habe H, Omori T (2003) Genetics of polycyclic aromatic hydrocarbon metabolism in diverse aerobic bacteria. Biosci Biotechnol Biochem 67:225–243
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
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
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
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
Kanaly RA, Harayama S (2000) Biodegradation of high-molecular mass polycyclic aromatic hydrocarbons by bacteria. J Bacteriol 182:2059–2067
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
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
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
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
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
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
Kukor JJ, Olsen RH (1996) Catechol 2,3-dioxygenases functional in oxygen-limited (hypoxic) environments. Appl Environ Microbiol 62:1728–1740
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
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
Menzie CA, Potocki BB, Santodonato J (1992) Exposure to carcinogenic PAHs in the environment. Environ Sci Technol 26:1278–1284
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
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
Page RDM (1996) Tree view: an application to display phylogenetic trees on personal computers. Comp Appl Biosci 12:357–358
Parales RE (2003) The role of active-site residues in naphthalene dioxygenase. J Ind Microbiol Biotechnol 30:271–278
Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbor Laboratory, Cold Spring Harbor, pp 1.31–1.122
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
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
Tovey ER, Baldo BA (1989) Protein binding to nitrocellulose, nylon and PVDF membranes in immunoassays and electroblotting. J Biochem Biophys Methods 19:169–183
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
Wyndham RC, Cashore AE, Nakatsu CH, Peel MC (1994) Catabolic transposons. Biodegradation 5:323–342
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
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
This work was supported by a grant from the Program for Promotion of Basic Research Activities for Innovative Biosciences (PROBRAIN).
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Hirano, S., Haruki, M., Takano, K. et al. Gene cloning and in vivo characterization of a dibenzothiophene dioxygenase from Xanthobacter polyaromaticivorans . Appl Microbiol Biotechnol 69, 672–681 (2006). https://doi.org/10.1007/s00253-005-0007-9
- Degradation Activity