Molecular characterization of dioxygenases from polycyclic aromatic hydrocarbon-degrading Mycobacterium spp.

FEMS Microbiology Letters

Volumn 223, Issue 2, 2003, Pages 177-183

  Brezna, Barbara ^a,b   Khan, Ashraf A ^a   Cerniglia, Carl E ^a  

^a NATIONAL CENTER FOR TOXICOLOGICAL RESEARCH   (United States)

^b INSTITUTE OF CHEMISTRY   (Slovakia)

Author keywords

Dioxygenase; Diversity; DNA sequence; Mycobacterium; Polycyclic aromatic hydrocarbon degradation

Indexed keywords

BACTERIAL DNA; BACTERIAL ENZYME; BACTERIAL PROTEIN; DIOXYGENASE; POLYCYCLIC AROMATIC HYDROCARBON; PROTEIN NIDA; PROTEIN NIDB; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; CONTROLLED STUDY; ENZYME ANALYSIS; GENE AMPLIFICATION; GENE SEQUENCE; GENETIC SCREENING; MICROBIAL DEGRADATION; MOLECULAR BIOLOGY; MOLECULAR CLONING; MYCOBACTERIUM; MYCOBACTERIUM FLAVESCENS; MYCOBACTERIUM FREDERIKSBERGENSE; MYCOBACTERIUM GILVUM; MYCOBACTERIUM VANBAALENII; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RHODOCOCCUS; SEQUENCE ANALYSIS; SOUTHERN BLOTTING; UNINDEXED SEQUENCE;

MYCOBACTERIUM; MYCOBACTERIUM FLAVESCENS; MYCOBACTERIUM FREDERIKSBERGENSE; MYCOBACTERIUM GILVUM; MYCOBACTERIUM SP.; MYCOBACTERIUM SP. PAH2.135; MYCOBACTERIUM VANBAALENII; RHODOCOCCUS;

EID: 0038771927     PISSN: 03781097     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1097(03)00328-8     Document Type: Article

References (46)

1. Mumtaz M.M., George J.D., Gold K.W., Cibulas W., DeRosa C.T. ATSDR evaluation of health effects of chemicals. IV. Polycyclic aromatic hydrocarbons (PAHs): understanding a complex problem. Toxicol. Ind. Health. 12:1996;742-971.
2. Kalf D.F., Crommentuijn T., van de Plassche E.J. Environmental quality objectives for 10 polycyclic aromatic hydrocarbons (PAHs). Ecotoxicol. Environ. Saf. 36:1997;89-97.
3. Mueller, J.G., Cerniglia, C.E. and Pritchard, P.H. (1996) In: Bioremediation: Principles and Applications (Crawford, R.L. and Crawford, D.L., Eds.), pp. 125-194. Cambridge University Press, Cambridge.
4. Mason J.R., Cammack R. The electron-transport proteins of hydroxylating bacterial dioxygenases. Annu. Rev. Microbiol. 46:1992;277-305.
5. Kauppi B., Lee K., Carredano E., Parales R.E., Gibson D.T., Eklund H., Ramaswamy S. Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2-dioxygenase. Structure. 6:1998;571-586.
6. Parales R.E., Parales J.V., Gibson D.T. Aspartate 205 in the catalytic domain of naphthalene dioxygenase is essential for activity. J. Bacteriol. 181:1999;1831-1837.
7. Hurtubise Y., Barriault D., Sylvestre M. Involvement of the terminal oxygenase beta subunit in the biphenyl dioxygenase reactivity pattern toward chlorobiphenyls. J. Bacteriol. 180:1998;5828-5835.
8. Khan A.A., Walia S.K. Expression, localization, and functional analysis of polychlorinated biphenyl degradation genes cbpABCD of Pseudomonas putida. Appl. Environ. Microbiol. 57:1991;1325-1332.
9. Kim E., Aversano P.J., Romine M.F., Schneider R.P., Zylstra G.J. Homology between genes for aromatic hydrocarbon degradation in surface and deep-subsurface Sphingomonas strains. Appl. Environ. Microbiol. 62:1996;1467-1470.
10. Treadway S.L., Yanagimachi K.S., Lankenau E., Lessard P.A., Stephanopoulos G., Sinskey A.J. Isolation and characterization of indene bioconversion genes from Rhodococcus strain I24. Appl. Microbiol. Biotechnol. 51:1999;786-793.
11. Khan A.A., Wang R.F., Cao W.W., Doerge D.R., Wennerstrom D., Cerniglia C.E. Molecular cloning, nucleotide sequence, and expression of genes encoding a polycyclic aromatic ring dioxygenase from Mycobacterium sp. strain PYR-1. Appl. Environ. Microbiol. 67:2001;3577-3585.
12. Wang R.F., Wennerstrom D., Cao W.W., Khan A.A., Cerniglia C.E. Cloning, expression, and characterization of the katG gene, encoding catalase-peroxidase, from the polycyclic aromatic hydrocarbon-degrading bacterium Mycobacterium sp. strain PYR-1. Appl. Environ. Microbiol. 66:2000;4300-4304.
13. Saito A., Iwabuchi T., Harayama S. A novel phenanthrene dioxygenase from Nocardioides sp. strain KP7 expression in Escherichia coli. J. Bacteriol. 182:2000;2134-2141.
14. Kasuga K., Habe H., Chung J.S., Yoshida T., Nojiri H., Yamane H., Omori T. Isolation and characterization of the genes encoding a novel oxygenase component of angular dioxygenase from the gram-positive dibenzofuran-degrader Terrabacter sp. strain DBF63. Biochem. Biophys. Res. Commun. 283:2001;195-204.
15. Larkin M.J., Allen C.C., Kulakov L.A., Lipscomb D.A. Purification and characterization of a novel naphthalene dioxygenase from Rhodococcus sp. strain NCIMB12038. J. Bacteriol. 181:1999;6200-6204.
16. Andreoni V., Bernasconi S., Colombo M., van Beilen J.B., Cavalca L. Detection of genes for alkane and naphthalene catabolism in Rhodococcus sp. strain 1BN. Environ. Microbiol. 2:2000;572-577.
17. Heitkamp M.A., Franklin W., Cerniglia C.E. Microbial metabolism of polycyclic aromatic hydrocarbons: isolation and characterization of a pyrene-degrading bacterium. Appl. Environ. Microbiol. 54:1988;2549-2555.
18. Dean-Ross D., Cerniglia C.E. Degradation of pyrene by Mycobacterium flavescens. Appl. Microbiol. Biotechnol. 46:1996;307-312.
19. Boldrin B., Tiehm A., Fritzsche C. Degradation of phenanthrene, fluorene, fluoranthene, and pyrene by a Mycobacterium sp. Appl. Environ. Microbiol. 59:1993;1927-1930.
20. Grosser R.J., Warshawsky D., Vestal J.R. Indigenous and enhanced mineralization of pyrene, benzo[a]pyrene, and carbazole in soils. Appl. Environ. Microbiol. 57:1991;3462-3469.
21. Heitkamp M.A., Cerniglia C.E. Mineralization of polycyclic aromatic hydrocarbons by a bacterium isolated from sediment below an oil field. Appl. Environ. Microbiol. 54:1988;1612-1614.
22. Moody J.D., Doerge D.R., Freeman J.P., Cerniglia C.E. Degradation of biphenyl by Mycobacterium sp. strain PYR-1. Appl. Microbiol. Biotechnol. 58:2002;364-369.
23. Kiyohara H., Nagao K., Yana K. Rapid screen for bacteria degrading water-insoluble, solid hydrocarbons on agar plates. Appl. Environ. Microbiol. 43:1982;454-457.
24. Hamann C., Hegemann J., Hildebrandt A. Detection of polycyclic aromatic hydrocarbon degradation genes in different soil bacteria by polymerase chain reaction and DNA hybridization. FEMS Microbiol. Lett. 173:1999;255-263.
25. Fleming, M.A., Kukor, J.J. and Haggblom, M. (2002) In: Abstracts: American Society for Microbiology, 102nd General Meeting, p. 384, Salt Lake City, UT.
26. Khan A.A., Kim S.-J., Paine D.D., Cerniglia C.E. Classification of a polycyclic aromatic hydrocarbon-metabolizing bacterium, Mycobacterium sp. strain PYR-1, as Mycobacterium vanbaalenii sp. nov. Int. J. Syst. Evol. Microbiol. 52:2002;1997-2002.
27. Khan A.A., Cerniglia C.E. Detection of Pseudomonas aeruginosa from clinical and environmental samples by amplification of the exotoxin A gene using PCR. Appl. Environ. Microbiol. 60:1994;3739-3745.
28. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:1997;3389-3402.
29. Zylstra G.J., Kim E. Aromatic hydrocarbon degradation by Sphingomonas yanoikuiae B1. J. Ind. Microbiol. Biotechnol. 19:1997;408-414.
30. Kitagawa W., Suzuki A., Hoaki T., Masai E., Fukuda M. Multiplicity of aromatic ring hydroxylation dioxygenase genes in a strong PCB degrader, Rhodococcus sp. strain RHA1 demonstrated by denaturing gradient gel electrophoresis. Biosci. Biotechnol. Biochem. 65:2001;1907-1911.
31. Wang R.F., Cao W.W., Cerniglia C.E. Phylogenetic analysis of polycyclic aromatic hydrocarbon degrading mycobacteria by 16S rRNA sequencing. FEMS Microbiol. Lett. 130:1995;75-80.
32. Willumsen P., Karlson U., Stackebrandt E., Kroppenstedt R.M. Mycobacterium frederiksbergense sp. nov., a novel polycyclic aromatic hydrocarbon-degrading Mycobacterium species. Int. J. Syst. Evol. Microbiol. 51:2001;1715-1722.
33. Bastiaens L., Springael D., Wattiau P., Harms H., deWachter R., Verachtert H., Diels L. Isolation of adherent polycyclic aromatic hydrocarbon (PAH)-degrading bacteria using PAH-sorbing carriers. Appl. Environ. Microbiol. 66:2000;1834-1843.
34. Bottger E.C., Kirschner P., Springer B., Zumft W. Mycobacteria degrading polycyclic aromatic hydrocarbons. Int. J. Syst. Bacteriol. 47:1997;247.
35. Bogan B.W., Lahner L.M., Sullivan W.R., Paterek J.R. Degradation of straight-chain aliphatic and high-molecular-weight polycyclic aromatic hydrocarbons by a strain of Mycobacterium austroafricanum. J. Appl. Microbiol. 94:2003;230-239.
36. Heitkamp M.A., Cerniglia C.E. Polycyclic aromatic hydrocarbon degradation by a Mycobacterium sp. in microcosms containing sediment and water from a pristine ecosystem. Appl. Environ. Microbiol. 55:1989;1968-1973.
37. Moody J.D., Freeman J.P., Doerge D.R., Cerniglia C.E. Degradation of phenanthrene and anthracene by cell suspensions of Mycobacterium sp. strain PYR-1. Appl. Environ. Microbiol. 67:2001;1476-1483.
38. Schneider J., Grosser R., Jayasimhulu K., Xue W., Warshawsky D. Degradation of pyrene, benz[a]anthracene, and benzo[a]pyrene by Mycobacterium sp. strain RJGII-135, isolated from a former coal gasification site. Appl. Environ. Microbiol. 62:1996;13-19.
39. Cerniglia C.E., Blevins W.T., Perry J.J. Microbial oxidation and assimilation of propylene. Appl. Environ. Microbiol. 32:1976;764-768.
40. Beam H.W., Perry J.J. Microbial degradation of cycloparaffinic hydrocarbons via co-metabolism and commensalism. J. Gen. Microbiol. 82:1974;163-169.
41. Vestal J.R., Perry J.J. Divergent metabolic pathways for propane and propionate utilization by a soil isolate. J. Bacteriol. 99:1969;216-221.
42. King D.H., Perry J.J. The origin of fatty acids in the hydrocarbon-utilizing microorganism Mycobacterium vaccae. Can. J. Microbiol. 21:1975;85-89.
43. Burback B.L., Perry J.J. Biodegradation and biotransformation of groundwater pollutant mixtures by Mycobacterium vaccae. Appl. Environ. Microbiol. 59:1993;1025-1029.
44. Blevins W.T., Perry J.J. Metabolism of propane, n-propylamine, and propionate by hydrocarbon-utilizing bacteria. J. Bacteriol. 112:1972;513-518.
45. Iizuka, H. et al. (1975) Method of recovering microbial cells containing protein. US Patent No. 3888736.
46. Apajalahti J.H., Salkinoja-Salonen M.S. Dechlorination and para-hydroxylation of polychlorinated phenols by Rhodococcus chlorophenolicus. J. Bacteriol. 169:1987;675-681.