Functional and transcriptional analyses of the initial oxygenase genes for acenaphthene degradation from Sphingomonas sp. strain A4

Microbiology

Volumn 152, Issue 8, 2006, Pages 2455-2467

  Kouzuma, Atsushi ^a   Pinyakong, Onruthai ^b   Nojiri, Hideaki ^a   Omori, Toshio ^c   Yamane, Hisakazu ^a   Habe, Hiroshi ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b CHULALONGKORN UNIVERSITY   (Thailand)

^c SHIBAURA INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ACENAPHTHENE DERIVATIVE; DNA FRAGMENT; FERREDOXIN; FERREDOXIN NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE REDUCTASE; OXYGENASE;

ARTICLE; BACTERIAL GENETICS; BACTERIAL STRAIN; BACTERIUM MUTANT; BINDING SITE; BIODEGRADATION; CONTROLLED STUDY; GENE DISRUPTION; GENE EXPRESSION; GENE IDENTIFICATION; GENE INSERTION; GENE ISOLATION; GENE LOCUS; GENETIC TRANSCRIPTION; MUTAGENESIS; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; OPERON; PRIORITY JOURNAL; PROTEIN MOTIF; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SPHINGOMONAS; TRANSCRIPTION INITIATION SITE; TRANSPOSON;

ACENAPHTHENES; BASE SEQUENCE; DNA TRANSPOSABLE ELEMENTS; FERREDOXINS; GENES, REGULATOR; MOLECULAR SEQUENCE DATA; OPERON; OXYGENASES; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; SPHINGOMONAS; TRANSCRIPTION, GENETIC;

SPHINGOMONAS SP.;

EID: 33747142661     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/mic.0.28825-0     Document Type: Article

References (51)

1. Adkins, A. (1999). Degradation of the phenoxy acid herbicide diclofop-methyl by Sphingomonas paucimobilis isolated from a Canadian prairie soil. J Ind Microbiol Biotechnol 23, 332-335.
2. Alexeyev, M. F., Shokolenko, I. N. & Croughan, T. P. (1995). New mini-Tn5 derivatives for insertion mutagenesis and genetic engineering in gram-negative bacteria. Can J Microbiol 41, 1053-1055.
3. 450-type reductases. Eur J Biochem 253, 437-444.
4. Armengaud, J., Happe, B. & Timmis, K. N. (1998). Genetic analysis of dioxin dioxygenase of Sphingomonas sp. strain RW1: catabolic genes dispersed on the genome. J Bacteriol 180, 3954-3966.
5. Bastiaens, L., Springael, D., Wattiau, P., Harms, H., deWachter, R., Verachtert, H. & Diels, L. (2000). Isolation of adherent polycyclic aromatic hydrocarbon (PAH)-degrading bacteria using PAH-sorbing carriers. Appl Environ Microbiol 66, 1834-1843.
6. Brooks, C. J. W., Cole, W. J., Borthwick, J. H. & Brown, G. M. (1982). Characterization of dihydroarenediols and related compounds by gas chromatography-mass spectrometry: comparison of derivatives. J Chromatogr 239, 191-216.
7. Cai, M. & Xun, L. (2002). Organization and regulation of pentachlorophenol-degrading genes in Sphingobium chlorophenolicum ATCC 39723. J Bacteriol 184, 4672-4680.
8. de Lorenzo, V. & Timmis, K. N. (1994). Analysis and construction of stable phenotypes in gram-negative bacteria with Tn5- and Tn10-derived minitransposons. Methods Enzymol 235, 386-405.
9. Demanèche, S., Meyer, C., Micoud, J., Louwagie, M., Willison, J. C. & Jouanneau, Y. (2004). Identification and functional analysis of two aromatic-ring-hydroxylating dioxygenases from a Sphingomonas strain that degrades various polycyclic aromatic hydrocarbons. Appl Environ Microbiol 70, 6714-6725.
10. Dennis, J. J. & Zylstra, G. J. (2004). Complete sequence and genetic organization of pDTG1, the 83 kilobase naphthalene degradation plasmid from Pseudomonas putida strain NCIB 9816-4. J Mol Biol 341, 753-768.
11. Ferraro, D. J., Gakhar, L. & Ramaswamy, S. (2005). Rieske business: structure-function of Rieske non-heme oxygenases. Biochem Biophys Res Commun 338, 175-190.
12. Fredrickson, J. K., Balkwill, D. L., Drake, G. R., Romine, M. F., Ringelberg, D. B. & White, D. C. (1995). Aromatic-degrading Sphingomonas isolates from the deep subsurface. Appl Environ Microbiol 61, 1917-1922.
13. Gabriel, F. L., Giger, W., Guenther, K. & Kohler, H. P. (2005). Differential degradation of nonylphenol isomers by Sphingomonas xenophaga Bayram. Appl Environ Microbiol 71, 1123-1129.
14. Gruez, A., Roig-Zamboni, V., Grisel, S., Salomoni, A., Valencia, C., Campanacci, V., Tegoni, M. & Cambillau, C. (2004). Crystal structure and kinetics identify Escherichia coli YdcW gene product as a medium-chain aldehyde dehydrogenase. J Mol Biol 343, 29-41.
15. Habe, H., Ashikawa, Y., Saiki, Y., Yoshida, T., Nojiri, H. & Omori, T. (2002). Sphingomonas sp. strain KA1, carrying a carbazole dioxygenase gene homologue, degrades chlorinated dibenzo-p-dioxins in soil. FEMS Microbiol Lett 211, 43-49.
16. Hernáez, M. J., Reineke, W. & Santero, E. (1999). Genetic analysis of biodegradation of tetralin by a Sphingomonas strain. Appl Environ Microbiol 65, 1806-1810.
17. Imai, R., Nagata, Y., Senoo, K., Wada, H., Fukuda, M., Takagi, M. & Yano, K. (1989). Dehydrochlorination of γ-hexachlorocyclohexane (γ-BHC) by γ-BHC-assimilating Pseudomonas paucimobilis. Agric Biol Chem 53, 2015-2017.
18. Khan, A. A., Wang, R. F., Cao, W. W., Franklin, W. & Cerniglia, C. E. (1996). Reclassification of a polycyclic aromatic hydrocarbon-metabolizing bacterium, Beijerinckia sp. strain B1, as Sphingomonas yanoikuyae by fatty acid analysis, protein pattern analysis, DNA-DNA hybridization, and 16S ribosomal DNA sequencing. Int J Syst Bacteriol 46, 466-469.
19. Kiyohara, H., Nagao, K., Kouno, K. & Yano, K. (1982). Phenanthrene-degrading phenotype of Alcaligenes faecalis AFK2. Appl Environ Microbiol 43, 458-461.
20. Kohler, H. P. (1999). Sphingomonas herbicidovorans MH: a versatile phenoxyalkanoic acid herbicide degrader. J Ind Microbiol Biotechnol 23, 336-340.
21. Kohler, M., Künnifer, T., Schmid, P., Gujer, E., Crockett, R. & Wolfensberger, M. (2000). Inventory and emission factor of creosote, polycyclic aromatic hydrocabons (PAH), and phenols from railroad ties treated with creosote. Environ Sci Technol 34, 4766-4772.
22. Komatsu, T., Omori, T. & Kodama, T. (1993). Microbial degradation of the polycyclic aromatic hydrocarbons acenaphthene and acenaphthylene by a pure bacterial culture. Biosci Biotechnol Biochem 57, 864-865.
23. Lessner, D. J., Parales, R. E., Narayan, S. & Gibson, D. T. (2003). Expression of the nitroarene dioxygenase genes in Comamonas sp. strain JS765 and Acidovorax sp. strain JS42 is induced by multiple aromatic compounds. J Bacteriol 185, 3895-3904.
24. Martínez-Pérez, O., Moreno-Ruiz, E., Floriano, B. & Santero, E. (2004). Regulation of tetralin biodegradation and identification of genes essential for expression of thn operons. J Bacteriol 186, 6101-6109.
25. McFall, S. M., Klem, T. J., Fujita, N., Ishihama, A. & Chakrabarty, A. M. (1997). DNase I footprinting, DNA bending and in vitro transcription analyses of ClcR and CatR interactions with the clcABD promoter: evidence of a conserved transcriptional activation mechanism. Mol Microbiol 24, 965-976.
26. McFall, S. M., Chugani, S. A. & Chakrabarty, A. M. (1998). Transcriptional activation of the catechol and chlorocatechol operons: variations on a theme. Gene 223, 257-267.
27. Miyauchi, K., Lee, H. S., Fukuda, M., Takagi, M. & Nagata, Y. (2002). Cloning and characterization of linR, involved in regulation of the downstream pathway for γ-hexachlorocyclohexane degradation in Sphingomonas paucimobilis UT26. Appl Environ Microbiol 68, 1803-1807.
28. Moreno-Ruiz, E., Hernáez, M. J., Martínez-Pérez, O. & Santero, E. (2003). Identification and functional characterization of Sphingomonas macrogolitabida strain TFA genes involved in the first two steps of the tetralin catabolic pathway. J Bacteriol 185, 2026-2030.
29. Mueller, J. G., Chapman, P. J., Blattmann, B. O. & Pritchard, P. H. (1990). Isolation and characterization of a fluoranthene-utilizing strain of Pseudomonas paucimobilis. Appl Environ Microbiol 56, 1079-1086.
30. Pinyakong, O. (2003). Biochemical and genetic analyses of polycyclic aromatic hydrocarbons degradation in sphingomonads. PhD thesis, University of Tokyo, Tokyo.
31. Pinyakong, O., Habe, H., Supaka, N. & 7 other authors (2000). Identification of novel metabolites in the degradation of phenanthrene by Sphingomonas sp. strain P2. FEMS Microbiol Lett 191, 115-121.
32. Pinyakong, O., Habe, H. & Omori, T. (2003a). The unique aromatic catabolic genes in sphingomonads degrading polycyclic aromatic hydrocarbons (PAHs). J Gen Appl Microbiol 49, 1-19.
33. Pinyakong, O., Habe, H., Yoshida, T., Nojiri, H. & Omori, T. (2003b). Identification of three novel salicylate 1-hydroxylases involved in the phenanthrene degradation of Sphingobium sp. strain P2. Biochem Biophys Res Commun 301, 350-357.
34. Pinyakong, O., Habe, H., Kouzuma, A., Nojiri, H., Yamane, H. & Omori, T. (2004). Isolation and characterization of genes encoding polycyclic aromatic hydrocarbon dioxygenase from acenaphthene and acenaphthylene degrading Sphingomonas sp. strain A4. FEMS Microbiol Lett 238, 297-305.
35. 70), promoters, and the kinetics of the steps of transcription initiation. In Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd edn, pp. 792-820. Edited by F. C. Neidhardt & others. Washington, DC: American Society for Microbiology.
36. Saber, D. L. & Crawford, R. L. (1985). Isolation and characterization of Flavobacterium strains that degrade pentachlorophenol. Appl Environ Microbiol 50, 1512-1518.
37. Sambrook, J., Fritsch, E. F. & Maniatis, T. (1989). Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
38. Schäfer, A., Tauch, A., Jager, W., Kalinowski, J., Thierbach, G. & Pühler, A. (1994). Small mobilizable multi-purpose cloning vectors derived from the Escherichia coli plasmids pK18 and pK19: selection of defined deletions in the chromosome of Corynebacterium glutamicum. Gene 145, 69-73.
39. Schell, M. A. (1993). Molecular biology of the LysR family of transcriptional regulators. Annu Rev Microbiol 47, 597-626.
40. Selifonov, S. A., Slepen'kin, A. V., Adanin, V. M., Grechkina, G. M. & Starovoitov, I. I. (1993). Acenaphthene catabolism by strains of Alcaligenes eutrophus and Alcaligenes paradoxus. Microbiology [English translation of Mikrobiologiia] 62, 85-92.
41. Selifonov, S. A., Grifoll, M., Eaton, R. W. & Chapman, P. J. (1996). Oxidation of naphthenoaromatic and methyl-substituted aromatic compounds by naphthalene 1,2-dioxygenase. Appl Envir Microbiol 62, 507-514.
42. Shi, T., Fredrickson, J. K. & Balkwill, D. L. (2001). Biodegradation of polycyclic aromatic hydrocarbons by Sphingomonas strains isolated from the terrestrial subsurface. J Ind Microbiol Biotechnol 26, 283-289.
43. Sukchawalit, R., Vattanaviboon, P., Sallabhan, R. & Mongkolsuk, S. (1999). Construction and characterization of regulated L-arabinose-inducible broad host range expression vectors in Xanthomonas. FEMS Microbiol Lett 181, 217-223.
44. Takeuchi, M., Hamana, K. & Hiraishi, A. (2001). Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Int J Syst Evol Microbiol 51, 1405-1417.
45. Thompson, J. D., Higgins, D. G. & Gibson, T. J. (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.
46. Tropel, D. & van der Meer, J. R. (2004). Bacterial transcriptional regulators for degradation pathways of aromatic compounds. Microbiol Mol Biol Rev 68, 474-500.
47. White, D. C., Sutton, S. D. & Ringelberg, D. B. (1996). The genus Sphingomonas: physiology and ecology. Curr Opin Biotechnol 7, 301-306.
48. Wise, S. A., Benner, B. A., Burd, G. D., Chester, S. N., Rebbert, R. E. & Schantz, M. M. (1988). Determination of polycyclic aromatic hydrocarbons in a coal tar standard reference material. Anal Chem 60, 887-894.
49. Wittich, R. M., Wilkes, H., Sinnwell, V., Francke, W. & Fortnagel, P. (1992). Metabolism of dibenzo-p-dioxin by Sphingomonas sp. strain RW1. Appl Environ Microbiol 58, 1005-1010.
50. Yanisch-Perron, C., Vieira, J. & Messing, J. (1985). Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33, 103-119.
51. Yoshida, T., Ayabe, Y., Yasunaga, M., Usami, Y., Habe, H., Nojiri, H. & Omori, T. (2003). Genes involved in the synthesis of the exopolysaccharide methanolan by the obligate methylotroph Methylobacillus sp. strain 12S. Microbiology 149, 431-444.