Soluble methane monooxygenase gene clusters from trichloroethylene- degrading Methylomonas sp. strains and detection of methanotrophs during in situ bioremediation

Applied and Environmental Microbiology

Volumn 65, Issue 12, 1999, Pages 5198-5206

  Shigematsu, Toru ^a,c   Hanada, Satoshi ^a   Eguchi, Masahiro ^b   Kamagata, Yoichi ^a   Kanagawa, Takahiro ^a   Kurane, Ryuichiro ^a  

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

^b Japan Organo Co   (Japan)

^c KUMAMOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; GENE AMPLIFICATION; GENE CLUSTER; METHYLOCOCCACEAE; METHYLOTROPHIC BACTERIUM; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY;

EID: 0032751752     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.65.12.5198-5206.1999     Document Type: Article

References (54)

1. Altschul, S. F., T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
2. Bowman, J. P., L. I. Sly, P. D. Nichols, and A. C. Hayward. 1993. Revised taxonomy of the methanotrophs: description of Methylobacter gen. nov., emendation of Methylococcus, validation of Methylosinus and Methylocystis species, and a proposal that the family Methylococcaceae includes only the group I methanotrophs. Int. J. Syst. Bacteriol. 43:735-753.
3. Burrows, K. J., A. Cornish, D. Scott, and I. J. Higgins. 1984. Substrate specificities of the soluble and particulate methane monooxygenase of Methylosinus trichosporium OB3b. J. Gen. Microbiol. 130:3327-3333.
4. Byrne, A. M., J. J. Kukor, and R. H. Olsen. 1995. Sequence analysis of the gene cluster encoding toluene-3-monooxygenase from Pseudomonas pickettii PKO1. Gene 154:65-70.
5. Cardy, D. L. N., V. Laidler, G. P. C. Salmond, and J. C. Murrell. 1991. Molecular analysis of the methane monooxygenase (MMO) gene cluster of Methylosinus trichosporium OB3b. Mol. Microbiol. 5:335-342.
6. Cardy, D. L. N., V. Laidler, G. P. C. Salmond, and J. C. Murrell. 1991. The methane monooxygenase gene cluster of Methylosinus trichosporium: cloning and sequencing of the mmoC gene. Arch. Microbiol. 156:477-483.
7. Colby, J., and H. Dalton. 1978. Resolution of the methane monooxygenase from Methylococcus capsulatus (Bath) into three components: purification and properties of component C, a flavoprotein. Biochem. J. 171:461-468.
8. Colby, J., and H. Dalton. 1979. Characterization of the second prosthetic group of the flacoenzyme NADH-acceptor reductase (Component C) of the methane monooxygenase from Methylococcus capsulatus (Bath). Biochem. J. 177:903-908.
9. Collins, M. D., and P. N. Green. 1985. Isolation and characterization of a novel coenzyme Q from some methane-oxidizing bacteria. Biochem. Biophys. Res. Commun. 133:1125-1131.
10. Correll, C. C., C. J. Batie, D. P. Ballou, and M. L. Ludwig. 1992. Phthalate dioxygenase reductase: a modular structure for electron transfer from pyridine nucleotides to [2Fe-2S]. Science 258:1604-1610.
11. Correll, C. C., M. L. Ludwig, C. M. Bruns, and P. A. Karplus. 1993. Structural prototypes for an extended family of flavoprotein reductases: comparison of phthalate dioxygenase reductase with ferredoxin reductase and ferredoxin. Protein Sci. 2:2112-2133.
12. Dalton, H., D. D. S. Smith, and S. J. Pilkington. 1990. Towards a unified mechanism of biological methane oxidation. FEMS Microbiol. Rev. 87:201-207.
13. Dedysh, S. N., N. S. Panikov, and J. M. Tiedje. 1998. Acidophilic methanotrophic communities from Sphagnum peat bogs. Appl. Environ. Microbiol. 64:922-929.
14. Dedysh, S. N., N. S. Panikov, W. Liesack, R. Großkopf, J. Zhou, and J. M. Tiedje. 1998. Isolation of acidophilic methane-oxidizing bacteria from northern peat wetlands. Science 282:281-284.
15. DiSpirito, A. A., J. Gulledge, A. K. Shiemke, J. C. Murrell, M. E. Lidstrom, and C. L. Krema. 1992. Trichloroethylene oxidation by the membrane-associated methane monooxygenase in type I. type II and type X methanotrophs. Biodegradation 2:151-164.
16. Elango, N., R. Radhakrishnan, W. A. Froland, B. J. Wallar, C. A. Earhart, J. D. Lipscomb, and D. H. Ohlendorf. 1997. Crystal structure of the hydroxylase component of methane monooxygenase from Methylosinus trichosporium OB3b. Protein Sci. 6:556-568.
17. Fox, B. G., W. A. Froland, J. Dege, and J. D. Lipscumb. 1989. Methane monooxygenase from Methylosinus trichosporium OB3b: purification and properties of a three component system with high specific activity from a type II methanotroph. J. Biol. Chem. 264:10023-10033.
18. Fox, B. G., Y. Liu, J. E. Dege, and J. D. Lipscomb. 1991. Complex formation between the protein components of methane monooxygenase from Methylosinus trichosporium OB3b. J. Biol. Chem. 266:540-550.
19. Fuse, H., M. Ohta, O. Takimura, K. Murakami, H. Inoue, Y. Yamaoka, J. M. Oclarit, and T. Omori. 1998. Oxidation of trichloroethylene and dimethyl sulfide by a marine Methylomicrobium strain containing soluble methane monooxygenase. Biosci. Biotechnol. Biochem. 62:1925-1931.
20. Green, J., and H. Dalton. 1985. Protein B of soluble methane monooxygenase from Methylococcus capsulatus (Bath). J. Biol. Chem. 260:15795-15801.
21. Hanada, S., T. Shigematsu, K. Shibuya, M. Eguchi, T. Hasegawa, F. Suda, Y. Kamagata, T. Kanagawa, and R. Kurane. 1998. Phylogenetic analysis of trichroloethylene-degrading bacteria newly isolated from the polluted soil with the contaminant. J. Ferment. Bioeng. 86:539-544.
22. Hanson, R. S., and T. E. Hanson. 1996. Methanotrophic bacteria. Microbiol. Rev. 60:439-471.
23. Helmann, J. D., and M. J. Chamberlin. 1998. Structure and function of bacterial sigma factors. Annu. Rev. Biochem. 57:839-872.
24. Kamagata, Y., and E. Mikami. 1991. Isolation and characterization of a novel thermophilic Methanosaeta strain. Int. J. Syst. Bacteriol. 41:191-196.
25. Karplus, P. A., M. J. Daniels, and J. R. Herriott. 1991. Atomic structure of ferredoxin-NADP+ reductase: prototype for a structurally novel flavoenzyme family. Science 251:60-66.
26. Koh, S.-C., J. P. Bowman, and G. S. Sayler. 1993. Soluble methane monooxygenase production and trichloroethylene degradation by a type I methanotroph. Methylomonas methanica 68-1. Appl. Environ. Microbiol. 59:960-967.
27. Kumar, S., K. Tamura, and M. Nei. 1993. MEGA: molecular evolutionary genetics analysis, version 1.0. The Pennsylvania State University, University Park.
28. Kushida, H. 1980. An improved embedding method using ERL 4206 and Quetol 653. J. Electron. Microsc. 29:193-194.
29. Levin, J. M. 1997. Exploring the limits of nearest neighbour secondary structure prediction. Protein Eng. 10:771-776.
30. Lipscomb, J. D. 1994. Biochemistry of the soluble methane monooxygenase. Annu. Rev. Microbiol. 48:371-399.
31. Lloyd, J. S., A. Bhamhra, J. C. Murrell, and H. Dalton. 1997. Inactivation of the regulatory protein B of soluble methane monooxygenase from Methylococcus capsulatus (Bath) by proteolysis can be overcome by a Gly to Gln modification. Eur. J. Biochem. 248:72-79.
32. 2 redox centres of component C. the NADH:acceptor reductase of the soluble methane monooxygenase of Methylococcus capsulatus (Bath). Eur. J. Biochem. 147:291-296.
33. McDonald, I. R., E. M. Kenna, and J. C. Murrell. 1995. Detection of methanotrophic bacteria in environmental samples with the PCR. Appl. Environ. Microbiol. 61:116-121.
34. McDonald, I. R., H. Uchiyama, S. Kambe, O. Yagi, and J. C. Murrell. 1997. The soluble methane monooxygenase gene cluster of the trichloroethylenedegrading methanotroph Methylocystis sp. strain M. Appl. Environ. Microbiol. 63:1898-1904.
35. Miguez, C. B., D. Bourque, J. A. Sealy, C. W. Greer, and D. Groleau. 1997. Detection and isolation of methanotrophic bacteria possessing soluble methane monooxygenase (sMMO) genes using the polymerase chain reaction (PCR). Microb. Ecol. 33:21-31.
36. Murrell, J. C. 1994. Molecular genetics of methane oxidation. Biodegradation 5:145-159.
37. Nakajima, T., H. Uchiyama, O. Yagi, and T. Nakahara. 1992. Purification and properties of a soluble methane monooxygenase from Methylocystis sp. M. Biosci. Biotech. Biochem. 56:736-740.
38. Nordlund, I., J. Powlowski, and V. Shingler. 1990. Complete nucleotide sequence and polypeptide analysis of multicomponent phenol hydroxylase from Pseudomonus sp. strain CF600. J. Bacteriol. 172:6826-6833.
39. Nordlund, P., H. Dalton, and H. Eklund. 1992. The active site structure of methane monooxygenase is closely related to the binuclear iron center of ribonucleotide reductase. FEBS Lett. 307:257-262.
40. Rosenzweig, A. C., C. A. Frederick, S. J. Lippard, and P. Nordlund. 1993. Crystal structure of a bacterial non-haem iron hydroxylase that catalyses the biological oxidation of methane. Nature 366:537-543.
41. Saitou, N., and M. Nei. 1987. The neighbor joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425
42. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
43. Semrau, J. D., A. Chistoserdov, J. Lebron, A. Costello, J. Davagnino, E. Kenna, A. J. Holmes, R. Finch, J. C. Murrell, and M. E. Lidstrom. 1995. Particulate methane monooxygenase genes in methanotrophs. J. Bacteriol. 177:3071-3079.
44. Shen, R.-N., C.-L. Yu, Q.-Q. Ma, and S.-B. Li. 1997. Direct evidence for a soluble methane monooxygenase from type I methanotrophic bacteria: purification and properties of a soluble methane monooxygenase from Methylomonas sp. GYJ3. Arch. Biochem. Biophys. 345:223-229.
45. Stainthorpe, A. C., J. C. Murrell, G. P. C. Salmond, H. Dalton, and V. Lees. 1989. Molecular analysis of methane monooxygenase from Methylococcus capsulatus (Bath). Arch. Microbiol. 152:154-159.
46. Stainthorpe, A. C., V. Lees, G. P. C. Salmond, H. Dalton, and J. C. Murrell. 1990. The methane monooxygenase gene cluster of Methylococcus capsulatus (Bath). Gene 91:27-34.
47. Stainthorpe, A. C., G. P. C. Salmond, H. Dalton, and J. C. Murrell. 1990. Screening of obligate methanotrophs for soluble methane monooxygenase genes. FEMS Microbiol. Lett. 70:211-216.
48. Tamaoka, K., Y. Katayama-Fujimura, and H. Kuraishi. 1983. Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J. Appl. Bacteriol. 54:31-36.
49. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 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.
50. Tsien, H.-C., and R. S. Hanson. 1992. Soluble methane monooxygenase component B gene probe for identification of methanotrophs that rapidly degrade trichloroethylene. Appl. Environ. Microbiol. 58:953-960.
51. Whittenbury, R., K. Philips, and J. F. Willkinson. 1970. Enrichment, isolation and some properties of methane-utilizing bacteria. J. Gen. Microbiol. 61:205-218.
52. Whittenbury, R., and N. R. Krieg. 1989. Family IV. Methylococcaceae fam. nov., p. 256-261. In N. R. Krieg and J. G. Holt (ed.), Bergey's manual of systematic bacteriology, vol. 1. The Williams & Wilkins Co., Baltimore, Md.
53. Woodland, M. P., and H. Dalton. 1984. Purification and characterization of component A of the methane monooxygenase from Methylococcus capsulatus (Bath). J. Biol. Chem. 259:53-60.
54. Zahn, J. A., and A. A. DiSpirito. 1996. Membrane-associated methane monooxygenase from Methylococcus capsulatus (Bath). J. Bacteriol. 178:1018-1029.