Abstract
A novel genotype for the initial steps of the oxidative degradation of dibenzothiophene(DBT) is described in a Burkholderia sp. strain isolated from a drain receiving oil refinery wastewater. The strain is capable of transforming DBT with significant efficiency when compared to other microorganisms. Its genotype was discovered by investigating insertional mutants of genes involved in DBT degradation by the Kodama pathway. The cloned dbt genes show a novel genomic organization when compared to previously described genes capable of DBT catabolism in that they constitute two distinct operons and are not clustered in a single transcript. Sequence analysis suggests the presence of a σ54-dependent positive transcriptional regulator that may be involved in the control of the transcription of the two operons, both activated by DBT. The achieved results suggest the possibility of novel features of DBT biotransformation in nature.
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References
Armengaud J, Happe B & Timmis KN (1998) Genetic analysis of dioxyn dioxygenase of Sphingomonas sp. strain RW1: catabolic genes dispersed on the genome. J. Bacteriol. 180: 3954–3966
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W & Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 17: 3389–3340
Bence AE, Kvenvolden KA & Kennicutt II MC (1996) Organic geochemistry applied to environmental assessments of PriceWilliam Sound, Alaska, after the Exxon Valdez oil spill – a review. Org. Geochem. 24: 7–42
Bressler DC & Fedorak PM (2001) Purification, stability, and mineralisation of 3-hydroxy-2-formylbenzothiophene, a metabolite of dibenzothiophene. Appl. Environ. Micribiol. 67: 821–826
Buikema WJ, Szeto WW, Lemley PV, Orme-Johnson WH & Ausubel FM (1995) Nitrogen fixation specific regulatory genes of Klebsiella pneumoniae and Rhizobium meliloti share homology with the general nitrogen regulatory gene ntrC of K. pneumoniae. Nucleic Acids Res. 13: 4539–4555
Crawford DL & Gupta R (1990) Oxidation of dibenzothiophene by Cunninghamella elegans. Curr. Microbiol. 21: 229–231
Dennis JJ & Sokol PA (1995) Elettrotransformation of Pseudomonas. In: Nickoloff JA (Ed) Elettroporation and Elettrofusion of Microorganism (pp 125–133). Humana press, Clifton, N.J.
Denome SA, Stanley DC, Olson ES & Young KD (1993) Metabolism of dibenzothiophene and naphthalene in Pseudomonas strains: complete DNA sequence of an upper naphthalene catabolic pathway. J. Bacteriol. 175: 6890–6901
Ditta G (1986) Tn5 mapping of Rhizobium nitrogen fixation genes. In: Methods in Enzimology, Vol 118 (pp 529–536). Academic Press, New York
Frassinetti S, Setti L, Corti A, Farinelli P, Montevecchi P & Vallini G (1998) Biodegradation of dibenzothiophene by a nodulating isolate of Rhizobium meliloti. Can. J. Microbiol. 44: 289–297
Gage JD, Bobo T & Long SR (1996) Use of green fluorescent protein to visualize the early events of symbiosis between Rhizobium meliloti and Alfalfa (Medicago sativa). J. Bacteriol. 178: 7159–7166
Geiselbrecht AD, Hedlund BP, Tichi MA & Staley JT (1998) Isolation of marine polycyclic aromatic hydrocarbon (PAH)-degrading Cycloclasticus strains from the Gulf of Mexico and comparison of their PAH degradation ability with that of Puget Sound Cycloclasticus strains. Appl. Environ. Microbiol. 64: 4703–4710
Inouye S, Nakazawa A & Nakazawa T (1988) Nucleotide sequence of the regulatory gene xylR of the TOL plasmid from Pseudomonas putida. Gene 66: 301–306
Jefferson R (1987) Assaying chimeric genes in plants: the GUS gene fusion system. Plant Mol. Biol. Rep. 5: 387–405
Kiyohara H, Nagao K & Yana K (1982) Rapid screen for bacteria degrading water insoluble, solid hydrocarbons on agar plates. Appl. Environ. Microbial. 43: 454–457
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
Kodama K, Nakatami S, Umehara K, Shimizu K, Minoda Y & Yamada K (1970) Microbial conversion of petro-sulfur compounds Part III. Isolation and identification of products from dibenzothiophene. Agr. Biol. Chem. 34: 1320-1324
Kodama K, Umehara K, Shimizu K, Nakatami S, Minoda Y & Yamada K (1973) Identification of microbial products from dibenzothiophene and its proposed oxidation pathway. Agric. Biol. Chem. 37: 45–50
Kropp KG & Fedorak PM (1998) A review of occurrence, toxicity, and biodegradation of condensed thiophenes found in petroleum. Can. J. Microbiol. 44: 605–622
Laurie AD & Lloyd-Jones G (1999) The phn genes of Burkholderia sp. strain RP007 constitute a divergent gene cluster of polycyclic aromatic hydrocarbon catabolism. J. Bacteriol. 181: 531–540
Laurie AD & Lloyd-Jones G (2000) Quantification of phnAc and nahAc in contaminated New Zealand Soil by competitive PCR. Appl. Environ. Microbiol. 66: 1814–1817
Menn FM, Applegate BM & Sayler GS (1993) NAH plasmidmediated catabolism of anthracene and phenanthrene to naphthoic acids. Appl. Environ. Microbiol. 59: 1938–1942
Ng LC, Poh CL & Shingler V (1995) Aromatic effector activation of NtrC-like transcriptional regulator PnhR limits the catabolic potential of the (methyl)phenol degradative pathway it controls. J. Bacteriol. 177: 1485–1490
Romine MF, Stillwell LC, Wong KK, Thurston SJ, Sisk EC, Sensen C, Gaasterland T, Fredrickson JK & Saffer JD (1999) Complete sequence of a 184-kilobase catabolic plasmid from Sphingomonas aromaticivorans strain F199. J. Bacteriol. 18: 1585–1602
Sambrook J, Fritsch EF & Maniatis T (1989) Molecular Cloning: A Laboratory Manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
Sanseverino J, Applegate BM, King JM & Sayler GS (1993) Plasmid-mediated mineralization of naphthalene, phenanthrene, and anthracene. Appl. Environ. Microbiol. 59: 1931–1937
Setti L, Lanzarini G & Pifferi PG (1995) Dibenzothiophene biodegradation by a Pseudomonas sp. in model solutions. Process. Biochem. 30: 721–728
Shingler V, Bartilson M & Moore T (1993) Cloning and nucleotide sequence of the gene encoding the positive regulator (DmpR) of the phenol catabolic pathway encoded by pVI150 and identification of DmpR as a member of NtrC family of transcriptional activators. J. Bacteriol. 175: 1596–1604
Simon MJ, Osslund TD, Saunders R, Ensley BD, Suggs S, Harcourt A, Suen WC, Cruden DL, Gibson DT & Zylstra GJ (1993) Sequences of genes encoding naphthalene dioxygenase in Pseudomonas putida strains G7 and NCIB 9816-4. Gene 127: 31–37
Speight JG (1980) The Chemistry and Technology of Petroleum. Marcel Dekker Inc., New York, N.Y.
Thompson JD, Higgins DG & Gibson TJ (1994) CLUSTALW: 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
Weisburg WG, Barns SM, Pelletier DA & Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173: 697–703
Wilson KJ, Sessitch A, Corbo JC, Giller K, Akkermans ADL & Jefferson RA (1995) β-glucoronidase (GUS) transposons for ecological and genetic studies of Rhizobia and Gram-negative bacteria. Microbiology 141: 1691–1705
Zylstra GJ & Kim E (1997) Aromatic hydrocarbon degradation by Sphingomonas yanoikuyae B1. J. Ind. Miocrobiol. Biotechnol. 19: 408–414
Zylstra GJ, Kim E & Goyal AK (1997) Comparative molecular analysis of genes for polycyclic aromatic hydrocarbons degradation. Gen. Eng. 19: 257–269
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Di Gregorio, S., Zocca, C., Sidler, S. et al. Identification of Two New Sets of Genes for Dibenzothiophene Transformation in Burkholderia sp. DBT1. Biodegradation 15, 111–123 (2004). https://doi.org/10.1023/B:BIOD.0000015624.52954.b6
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DOI: https://doi.org/10.1023/B:BIOD.0000015624.52954.b6