Isolation and characterization of a gene cluster involved in PAH degradation in Mycobacterium sp. strain SNP11: Expression in Mycobacterium smegmatis mc2155

Research in Microbiology

Volumn 158, Issue 2, 2007, Pages 175-186

  Pagnout, Christophe ^a   Frache, Gilles ^b   Poupin, Pascal ^a   Maunit, Benoît ^b   Muller, Jean François ^b   Férard, Jean François ^a  

^a Faculté des Sciences et Technologies   (France)

^b UNIVERSITÉ DE LORRAINE   (France)

Author keywords

Biodegradation; Mycobacterium gilvum; phd Gene cluster; Polycyclic aromatic hydrocarbon

Indexed keywords

AMINO ACID; CARBON; DIBENZOFURAN; DIOXYGENASE; DNA FRAGMENT; FLUORANTHENE; FLUORENE; FLUORINE; OXYGENASE; PHENANTHRENE; POLYCYCLIC AROMATIC HYDROCARBON; PYRENE;

ALPHA CHAIN; AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GROWTH; BACTERIAL STRAIN; DNA SEQUENCE; ENZYME SUBUNIT; GENE CLUSTER; GENE EXPRESSION; GENE ISOLATION; MYCOBACTERIUM SMEGMATIS; MYCOBACTERIUM SMEGMATIS MC2 155; MYCOBACTERIUM SNP11; NOCARDIOIDACEAE; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PDOA2 GENE; PHDA GENE; PRIORITY JOURNAL; PROMOTER REGION;

ANTHRACENES; CLONING, MOLECULAR; DIOXYGENASES; FLUORENES; FLUORINE; GENES, BACTERIAL; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; MYCOBACTERIUM; MYCOBACTERIUM SMEGMATIS; OPEN READING FRAMES; PHENANTHRENES; POLYCYCLIC HYDROCARBONS, AROMATIC; SUBSTRATE SPECIFICITY;

MYCOBACTERIUM GILVUM; MYCOBACTERIUM SMEGMATIS; MYCOBACTERIUM SP.; NOCARDIOIDES SP.;

EID: 33847400228     PISSN: 09232508     EISSN: 17697123     Source Type: Journal    
DOI: 10.1016/j.resmic.2006.11.002     Document Type: Article

References (48)

1. Altschul S.F., Gish W., Miller W., Myersand E.W., and Lipman D.J. Basic local alignement search tool. J. Mol. Biol. 215 (1990) 403-410
2. Bastiaens L., Springael D., Wattiau P., Harms H., deWachter R., Verachtert H., and Diels L. Isolation of adherent polycyclic aromatic hydrocarbon (PAH)-degrading bacteria using PAH-sorbing carriers. Appl. Environ. Microbiol. 66 (2000) 1834-1843
3. Boldrin B., Tiehm A., and Fritzsche C. Degradation of phenanthrene, fluorene, fluoranthene, and pyrene by a Mycobacterium sp. Appl. Environ. Microbiol. 59 (1993) 1927-1930
4. Bosch R., Garcia-Valdés E., and Moore E.R.B. Genetic characterization and evolutionary implications of a chromosomally encoded naphthalene-degradation upper pathway from Pseudomonas stutzeri AN10. Gene 236 (1999) 149-157
5. Böttger E.C., Kirschmer P., Springer B., and Zumft W. Mycobacteria degrading polycyclic aromatic hydrocarbons. Int. J. Syst. Bacteriol 47 (1997) 247
6. Brezna B., Khan A.A., and Cerniglia C.E. Molecular characterization of dioxygenases from polycyclic aromatic hydrocarbon-degrading Mycobacterium spp. FEMS Microbiol. Lett. 223 (2003) 177-183
7. Cerniglia C.E. Biodegradation of polycyclic aromatic hydrocarbons. Biodegradation 3 (1992) 351-368
8. Chang H.-K., and Zylstra G.J. Novel organization of the genes for phthalate degradation from Burkholderia cepacia DB01. J. Bacteriol 180 (1998) 6529-6537
9. Churchill S.A., Harper J.P., and Churchill P.F. Isolation and characterization of a Mycobacterium species capable of degrading three- and four-ring aromatic and aliphatic hydrocarbons. Appl. Environ. Microbiol. 65 (1999) 549-552
10. Dean-Ross D., and Cerniglia C.E. Degradation of pyrene by Mycobacterium flavescens. Appl. Microbiol. Biotechnol 46 (1996) 307-312
11. Denome S.A., Stanley D.C., Olson E.S., and Young K.D. Metabolism of dibenzothiophene and naphthalene in Pseudomonas strains: complete DNA sequence of an upper naphthalene catabolic pathway. J. Bacteriol 175 (1993) 6890-6901
12. Dower W.J., Miller J.F., and Ragsdale C.W. High efficiency transformation of E. coli by high voltage electroporation. Nucleic Acids Res. 16 (1998) 6127-6145
13. Eaton R.W., and Chapman P.J. Bacterial metabolism of naphthalene: construction and use of recombinant bacteria to study ring cleavage of 1,2-dihydroxynaphthalene and subsequent reaction. J. Bacteriol 174 (1992) 7542-7554
14. Eaton R.W. Plasmid-encoded phthalate catabolic pathway in Arthrobacter keyser 12B. J. Bacteriol 183 (2001) 3689-3703
15. Eltis L.D., and Bolin J.T. Evolutionary relationships among extradiol dioxygenases. J. Bacteriol 178 (1996) 5930-5937
16. Habe H., Miyakoshi M., Chung J.S., Kasuga K., Yoshida T., Nojiri H., and Omori T. Phthalate catabolic gene cluster is linked to the angular dioxygenase gene in Terrabacter sp. strain DBF63. Appl. Microbiol. Biotechnol 61 (2003) 44-54
17. Habe H., Chung J.S., Kato H., Ayabe Y., Kasuga K., Yoshida T., Nojiri H., Yamane H., and Omori T. Characterization of the upper pathway genes for fluorene metabolism in Terrabacter sp. strain DBF63. J. Bacteriol 186 (2004) 5938-5944
18. Hatfull G.F., and Jacobs Jr. W.R. Molecular genetics of mycobacteria (2000), ASM Press, Washington, DC
19. Heitkamp M.A., and 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
20. Houssaini-Iraqui M., Lazraq R., Clavel-Sérès S., Rastogi N., and David H.L. Cloning and expression of Mycobacterium aurum carotenogenesis genes in Mycobacterium smegmatis. FEMS Microbiol. Lett. 90 (1992) 239-244
21. Iida T., Mukouzaka Y., Nakamura K., Yamaguchi I., and Kudo T. Isolation and characterization of dibenzofuran-degrading actinomycetes: analysis of multiple extradiol dioxygenase genes in dibenzofuran-degrading Rhodococcus species. Biosci. Biotechnol. Biochem 66 (2002) 1462-1472
22. Kasuga K., Habe H., Chung J.-S., Yoshida T., Nojiri H., Yamane H., and 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
23. Kelley I., Freeman J.P., Evans F.E., and Cerniglia C.E. Identification of metabolites from the degradation of fluoranthene by Mycobacterium sp. strain PYR-1. Appl. Environ. Microbiol. 59 (1993) 800-806
24. Khan A.A., Wang R.F., Cao W.W., Doerge D.R., Wennerstrom D., and 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
25. Kim S.J., Jones R.C., Cha C.J., Kweon O., Edmondson R.D., and Cerniglia C.E. Identification of proteins induced by polycyclic aromatic hydrocarbon in Mycobacterium vanbaalenii PYR-1 using two-dimensional polyacrylamide gel electrophoresis and de novo sequencing methods. Proteomics 12 (2004) 3899-3908
26. Kim Y.H., Moody J.D., Freeman J.P., Brezna B., Engesser K.H., and Cerniglia C.E. Evidence for the existence of PAH-quinone reductase and catechol-O-methyltransferase in Mycobacterium vanbaalenii PYR-1. J. Ind. Microbiol. Biotechnol 31 (2004) 507-516
27. Kiyohara H., Nagao K., and Yana K. Rapid screen for bacteria degrading water-insoluble, solid hydrocarbons on agar plates. Appl. Environ. Microbiol. 43 (1982) 454-457
28. Krivobok S., Kuony S., Meyer C., Louwagie M., Willison J.C., and Jouanneau Y. Identification of pyrene-induced proteins in Mycobacterium sp. strain 6PY1: evidence for two ring-hydroxylating dioxygenases. J. Bacteriol 185 (2003) 3828-3841
29. Laurie A.D., and Lloyd-Jones G. The phn genes of Burkholderia sp. strain RP007 constitute a divergent gene cluster for polycyclic aromatic hydrocarbon catabolism. J. Bacteriol 181 (1999) 531-540
30. Miller J.H. Experiments in molecular genetics (1972), Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y
31. Nakatsu C.H., Providenti M., and Wyndham R.C. The cis-diol dehydrogenase cbaC gene of Tn5271 is required for growth on 3-chlorobenzoate but not 3,4-dichlorobenzoate. Gene 196 (1997) 209-218
32. Nomura Y., Nakagawa M., Ogawa N., Harashima S., and Oshima Y. Genes in PHT plasmid encoding the initial degradation pathway of phthalate in Pseudomonas putida. J. Ferment. Bioeng 74 (1992) 333-344
33. Pagnout C., Férard J.-F., and Poupin P. Characterization of IS1110-like sequences found in Mycobacterium species other than Mycobacterium avium. Res. Microbiol. 157 (2006) 650-658
34. Pearson W.R. Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol 183 (1990) 63-98
35. Pelicic V., Reyrat J.M., and Gicquel B. Expression of the Bacillus subtilis sacB gene confers sucrose sensitivity on mycobacteria. J. Bacteriol 178 (1996) 1197-1199
36. Rehmann K., Noll H.P., Steinberg C.E.W., and Kettrup A.A. Pyrene degradation by Mycobacterium sp. strain KR2. Chemosphere 36 (1998) 2977-2992
37. Saito A., Iwabuchi T., and Harayama S. Characterization of genes for enzymes involved in the phenanthrene degradation in Nocardioides sp. KP7. Chemosphere 38 (1999) 1331-1337
38. Saito A., Iwabuchi T., and Harayama S. A novel phenanthrene dioxygenase from Nocardioides sp. strain KP7: Expression in Escherichia coli. J. Bacteriol 182 (2000) 2134-2141
39. Sambrook J., Fritsch E.F., and Maniatis T. Molecular Cloning: a Laboratory Manual. 2nd Edn (1989), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
40. Sho M., Hamel C., and Greer C.W. Two distinct gene clusters encode pyrene degradation in Mycobacterium sp. strain S65. FEMS Microbiol. Ecol 48 (2004) 209-220
41. Snapper S.B., Melton R.E., Mustafa S., Kieser T., and Jacobs Jr. W.R. Isolation and characterization of efficient plasmid transformation mutants of Mycobacterium smegmatis. Mol. Microbiol. 4 (1990) 1911-1919
42. Spence E.L., Kawamukai M., Sanvoisin J., Braven H., and Bugg T.D. Catechol dioxygenases from Escherichia coli (MhpB) and Alcaligenes eutrophus (MpcI): sequence analysis and biochemical properties of a third family of extradiol dioxygenases. J. Bacteriol 178 (1996) 5249-5256
43. Stingley R.L., Brezna B., Khan A.A., and Cerniglia C.E. Novel organization of genes in a phthalate degradation operon of Mycobacterium vanbaalenii PYR-1. Microbiology 150 (2004) 3749-3761
44. Stingley R.L., Khan A.A., and Cerniglia C.E. Molecular characterization of a phenanthrene degradation pathway in Mycobacterium vanbaalenii PYR-1. Biochem. Biophys. Res. Commun 322 (2004) 133-146
45. Takizawa N., Iida T., Sawada T., Yamauchi K., Wang Y.-W., Fukuda M., and Kiyohara H. Nucleotide sequences and characterization of genes encoding naphthalene upper pathway of Pseudomonas aeruginosa PaK1 and Pseudomonas putida OUS82. J. Biosci. Bioeng 87 (1999) 723-731
46. Timm J., Lim E.M., and Gicquel B. Escherichia coli-mycobacteria shuttle vectors for operon and gene fusions to lacZ: the pJEM series. J. Bacteriol 176 (1994) 6749-6753
47. Wang R.F., Cao W.W., and Cerniglia C.E. Phylogenetic analysis of polycyclic aromatic hydrocarbon degrading mycobacteria by 16S rRNA sequencing. FEMS Microbiol. Lett. 130 (1995) 75-80
48. Willumsen P., Karlson U., Stackebrandt E., and Kroppenstedt R.M. Mycobacterium frederiksbergense sp. nov., a novel polycyclic aromatic hydrocarbon-degrading Mycobacterium species. Int. J. Syst. Evol. Microbiol. 51 (2001) 1715-1722