Genetic and biochemical characterization of the dioxygenase involved in lateral dioxygenation of dibenzofuran from Rhodococcus opacus strain SAO101

Applied Microbiology and Biotechnology

Volumn 73, Issue 2, 2006, Pages 474-484

  Kimura, Nobutada ^a   Kitagawa, Wataru ^b   Mori, Toshio ^a   Nakashima, Nobutaka ^b   Tamura, Tomohiro ^b,c   Kamagata, Yoichi ^b  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^c HOKKAIDO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; BIODEGRADATION; GENE EXPRESSION; NAPHTHALENE; OXYGENATION; POLYCYCLIC AROMATIC HYDROCARBONS;

BIOCHEMICAL CHARACTERIZATION; COSMID CLONE; GENOMIC DNA; RHODOCOCCUS OPACUS STRAIN;

BACTERIA;

AROMATIC HYDROCARBON; DIBENZOFURAN; DIHYDRODIOL DEHYDROGENASE; DIOXYGENASE; NAPHTHALENE DIOXYGENASE; POLYCYCLIC AROMATIC HYDROCARBON; UNCLASSIFIED DRUG; BENZOFURAN DERIVATIVE; DNA; HYDROCARBON; OXYGEN;

AROMATIC HYDROCARBON; BACTERIUM; BIOCHEMISTRY; DETECTION METHOD; ENZYME ACTIVITY; GENE EXPRESSION; GENETIC ANALYSIS; IDENTIFICATION METHOD; METABOLITE; OXYGENATION; PLASMID; POLYMERASE CHAIN REACTION;

ARTICLE; BACTERIAL CELL; BACTERIAL STRAIN; CHEMICAL ANALYSIS; DNA SEQUENCE; GENETIC TRAIT; NONHUMAN; NUCLEOTIDE SEQUENCE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RHODOCOCCUS; RHODOCOCCUS OPACUS; SAO101 STRAIN; CHEMICAL MODEL; CHEMISTRY; COSMID; ENZYME SPECIFICITY; GENE LIBRARY; METABOLISM; PH; PHYSIOLOGY; PLASMID;

RHODOCOCCUS; RHODOCOCCUS OPACUS;

BENZOFURANS; COSMIDS; DIOXYGENASES; DNA; GENE LIBRARY; HYDROCARBONS; HYDROGEN-ION CONCENTRATION; METABOLIC NETWORKS AND PATHWAYS; MODELS, CHEMICAL; OXYGEN; PLASMIDS; RHODOCOCCUS; SUBSTRATE SPECIFICITY;

EID: 36549009124     PISSN: 01757598     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00253-006-0481-8     Document Type: Article

References (37)

1. Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K (eds) (1990) Current protocols in molecular biology, Suppl. 11. unit 16.2. Wiley, New York
2. Becher D, Specht M, Hammer E, Francke W, Schauer F (2000) Cometabolic degradation of dibenzofuran by biphenyl-cultivated Ralstonia sp. strain SBUG 290. Appl Environ Microbiol 66:4528-4531
3. Beil S, Happe B, Timmis KN, Pieper DH (1997) Genetic and biochemical characterization of the broad spectrum chlorobenzene dioxygenase from Burkholderia sp. strain PS12 - dechlorination of 1, 2, 4, 5-tetracjlorobenzene. Eur J Biochem 247:190-199
4. Bressler DC, Fedorak PM (2000) Bacterial metabolism of fluorene, dibenzofuran, dibenzothiophene, and carbazole. Can J Microbiol 46:397-409
5. Cerniglia CE, Morgan JC, Gibson DT (1979) Bacterial and fungal oxidation of dibenzofuran. Biochem J 180:175-185
6. Eaton RW, Chapman PJ (1995) Formation of indigo and related compounds from indole carboxylic acids by aromatic acid-degrading bacteria: chromogenic reactions for cloning genes encoding dioxygenases that act on aromatic acids. J Bacteriol 177:6983-6988
7. Eaton RW, Selifonova OV, Gedney RM (1998) Isopropylbenzene catabolic pathway in Pseudomonas putida RE204: nucleotide sequence analysis of the ipb operon and neighboring DNA from pRE4. Biodegradation 9:119-132
8. Ensley BD, Ratzkin BJ, Osslund TD, Simon MJ, Wackett LP, Gibson DT (1983) Expression of naphthalene oxidation genes in Escherichia coli results in the biosynthesis of indigo. Science 222:167-169
9. Evans GA, Lewis K, Rothenberg BE (1989) High efficiency vectors for cosmid microcloning and genomic analysis. Gene 79:9-20
10. Fortnagel P, Harms H, Wittich RM, Krohn S, Meyer H, Sinnwell V, Wilkes H, Francke W (1990) Metabolism of dibenzofuran by Pseudomonas sp. strain HH69 and the mixed culture HH27. Appl Environ Microbiol 56:1148-1156
11. Fukuda K, Nagata S, Taniguchi H (2002) Isolation and characterization of dibenzofuran-degrading bacteria. FEMS Microbiol Lett 208:179-185
12. Harms H, Wittich RM, Sinnwell V, Meyer H, Fortnagel P, Francke W (1990) Transformation of dibenzo-p-dioxin by Pseudomonas sp. strain HH69. Appl Environ Microbiol 56:1157-1159
13. Hart S, Koch KR, Woods DR (1992) Identification of indigo-related pigments produced by Escherichia coli containing a cloned Rhodococcus gene. J Gen Microbiol 138(Pt 1):211-216
14. Hiraishi A, Yonemitsu Y, Matsushita M, Shin K, Kuraishi H, Kawahara K (2002) Characterization of Porphyrobacter sanguineus sp. nov., an aerobic bacteriochlorophyll-containing bacterium capable of degrading biphenyl and dibenzofuran. Arch Microbiol 178:45-52
15. Iida T, Mukouzaka Y, Nakamura K, Kudo T (2002) Plasmid-borne genes code for an angular dioxygenase involved in dibenzofuran degradation by Terrabacter sp. strain YK3. Appl Environ Microbiol 68:3716-3723
16. Jornvall H, Persson B, Krook M, Atrian S, Gonzalez-Duarte R, Jeffery J, Ghosh D (1995) Short-chain dehydrogenases/reductases (SDR). Biochemistry 34:6003-6013
17. Kasuga K, Habe H, Chung JS, Yoshida T, Nojiri H, Yamane H, Omori T (2001) Isolation and characterization of the genes encoding a novel oxygenase component of an angular dioxygenase from the gram-positive dibenzofuran-degrader Terrabacter sp. strain DBF63. Biochem Biophys Res Commun 283:195-204
18. Kimura N, Urushigawa Y (2000) Metabolism of dibenzo-p-dioxin and chlorinated dibenzo-p-dioxin by a gram-positive bacterium, Rhodococcus opacus SAO101. J Biosci Bioeng 92:138-143
19. Kitagawa W, Kimura N, Kamagata Y (2004) A novel p-nitrophenol degradation gene cluster from a gram-positive bacterium, Rhodococcus opacus SAO101. J Bacteriol 186:4894-4902
20. Klecka GM, Gibson DT (1979) Metabolism of dibenzo[1,4]dioxan by a Pseudomonas species. Biochem J 180:639-645
21. Klecka GM, Gibson DT (1980) Metabolism of dibenzo-p-dioxin and chlorinated dibenzo-p-dioxin by a Beijerinckia species. Appl Environ Microbiol 39:288-296
22. Kulakov LA, Allen CC, Lipscomb DA, Larkin MJ (2000) Cloning and characterization of a novel cis-naphthalene dihydrodiol dehydrogenase gene (narB) from Rhodococcus sp. NCIMB12038. FEMS Microbiol Lett 182:327-331
23. Kulakov LA, Chen S, Allen CC, Larkin MJ (2005) Web-type evolution of rhodococcus gene clusters associated with utilization of naphthalene. Appl Environ Microbiol 71:1754-1764
24. Kurkela S, Lehvaslaiho H, Palva ET, Teeri TH (1988) Cloning, nucleotide sequence and characterization of genes encoding naphthalene dioxygenase of Pseudomonas putida strain NCIB9816. Gene 73:355-362
25. Larkin MJ, Allen CC, Kulakov LA, Lipscomb DA (1999) Purification and characterization of a novel naphthalene dioxygenase from Rhodococcus sp. strain NCIMB12038. J Bacteriol 181:6200-6204
26. Laurie AD, 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
27. Maruyama T, Ishikura M, Taki H, Shindo K, Kasai H, Haga M, Inomata Y, Misawa N (2005) Isolation and characterization of o-xylene oxygenase genes from Rhodococcus opacus TKN14. Appl Environ Microbiol 71:7705-7715
28. Monna L, Omori T, Kodama T (1993) Microbial degradation of dibenzofuran, fluorene, and dibenzo-p-dioxin by Staphylococcus auriculans DBF63. Appl Environ Microbiol 59:285-289
29. Nakashima N, Tamura T (2004) A novel system for expressing recombinant proteins over a wide temperature range from 4 to 35°C. Biotechnol Bioeng 86(2):136-148, 20
30. Raschke H, Meier M, Burken JG, Hany R, Muller MD, Van Der Meer JR, Kohler HP (2001) Biotransformation of various substituted aromatic compounds to chiral dihydrodihydroxy derivatives. Appl Environ Microbiol 67:3333-3339
31. Sambrook J, Fritsch E, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor, New York
32. Sato SI, Nam JW, Kasuga K, Nojiri H, Yamane H, Omori T (1997) Identification and characterization of genes encoding carbazole 1,9a-dioxygenase in Pseudomonas sp. strain CA10. J Bacteriol 179:4850-4858
33. Steinmetz M, Winoto A, Minard K, Hood L (1982) Clusters of genes encoding mouse transplantation antigens. Cell 28:489-498
34. Strubel V, Rast HG, Fietz W, Knackmuss HJ, Engesser KH (1989) Enrichment of dibenzofuran utilizing bacteria with high co-metabolic potential towards dibenzodioxin and other anellated aromatics. FEMS Microbiol Lett 49:233-238
35. Treadway SL, Yanagimachi KS, Lankenau E, Lessard PA, Stephanopoulos G, Sinskey AJ (1999) Isolation and characterization of indene bioconversion genes from Rhodococcus strain I24. Appl Microbiol Biotechnol 51:786-793
36. Wittich RM (1998) Degradation of dioxin-like compounds by microorganisms. Appl Microbiol Biotechnol 49:489-499
37. Yen KM, Karl MR (1992) Identification of a new gene, tmoF, in the Pseudomonas mendocina KR1 gene cluster encoding toluene-4-monooxygenase. J Bacteriol 174:7253-7261