Diversity of α-halocarboxylic acid dehalogenases in bacteria isolated from a pristine soil after enrichment and selection on the herbicide 2,2-dichloropropionic acid (Dalapon)

Environmental Microbiology

Volumn 5, Issue 1, 2003, Pages 48-54

  Marchesi, Julian R ^a,b   Weightman, Andrew J ^a  

^a CARDIFF UNIVERSITY   (United Kingdom)

^b UNIVERSITY COLLEGE CORK   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; BETAPROTEOBACTERIA; BRADYRHIZOBIUM; BRUCELLA; CULTURE MEDIA; DNA, RIBOSOMAL; HYDROLASES; MOLECULAR SEQUENCE DATA; PHYLOGENY; POACEAE; PROPIONIC ACIDS; PROTEOBACTERIA; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY; VARIATION (GENETICS);

BACTERIA (MICROORGANISMS); BETAPROTEOBACTERIA; BRADYRHIZOBIUM; BRUCELLA; PROKARYOTA; PROTEOBACTERIA;

EID: 0037226865     PISSN: 14622912     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1462-2920.2003.00384.x     Document Type: Article

References (46)

1. Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A., and Struhl, K. (1994) Current Protocols in Molecular Biology. New York: Greene Publishing Associates Wiley Interscience, p. 2.4.
2. Barth, P.T., Bolton, L., and Thomson, J.C. (1992) Cloning and partial sequencing of an operon encoding 2 Pseudomonas putida haloalkanoate dehalogenases of opposite stereospecificity. J Bacteriol 174: 2612-2619.
3. Breen, A., Jimenez, L., Sayler, G.S., and Federle, T.W. (1992) Plasmid incidence and linear alkylbenzene sulfonate biodegradation in waste-water and pristine pond ecosystems. J Ind Microbiol 9: 37-43.
4. Brokamp, A., and Schmidt, F.J. (1991) Survival of alcaligenes-xylosoxidans degrading 2,2-dichloropropionate and horizontal transfer of its halidohydrolase gene in a soil microcosm. Curr Microbiol 22: 299-306.
5. Brokamp, A., Happe, B., and Schmidt, F.J. (1997a) Cloning and nucleotide sequence of a D,L-haloalkanoic acid dehalogenase encoding gene from Alcaligenes xylosoxidans ssp. denitrificans ABIV. Biodegradation 7: 383-396.
6. Brokamp, A., Schwarze, R., and Schmidt, F.J. (1997b) Homologous plasmids from soil bacteria encoding D,L-halidohydrolases. Curr Microbiol 34: 97-102.
7. Brunner, W., Staub, D., and Leisinger, T. (1980) Bacterial degradation of dichloromethane. Appl Environ Microbiol 40: 950-958.
8. Cairns, S.S., Cornish, A., and Cooper, R.A. (1996) Cloning, sequencing and expression in Eschenchia coli of two Rhizobium sp. genes encoding haloalkanoate dehalogenases of opposite stereospecificity. Eur J Biochem 235: 744-749.
9. Copley, S.D. (1998) Microbial dehalogenases: enzymes recruited to convert xenobiotic substrates. Curr Opin Chem Biol 2: 613-617.
10. Davison, A.D., and Veal, D.A. (1997) Synergistic mineralization of biphenyl by Alcaligenes faecalis type II BPSI-2 and Sphingomonas paucimobilis BPSI-3. Lett Appl Microbiol 25: 58-62.
11. Federle, T.W., and Schwab, B.S. (1992) Mineralization of surfactants in anaerobic sediments of a laundromat wastewater pond. Water Res 26: 123-127.
12. Fetzner, S., and Lingens, F. (1994) Bacterial dehalogenases - biochemistry, genetics, and biotechnological applications. Microbiol Rev 58: 641-685.
13. Fulthorpe, R.R., and Schofield, L.N. (1999) A comparison of the ability of forest and agricultural soils to mineralize chlorinated aromatic compounds. Biodegradation 10: 235-244.
14. Fulthorpe, R.R., McGowan, C., Maltseva, O.V., Holben, W.E., and Tiedje, J.M. (1995) 2,4-Dichlorophenoxyacetic acid-degrading bacteria contain mosaics of catabolic genes. Appl Environ Microbiol 61: 3274-3281.
15. Fulthorpe, R.R., Rhodes, A.N., and Tiedje, J.M. (1996) Pristine soils mineralize 3-chlorobenzoate and 2,4- dichlorophenoxyacetate via different microbial populations. Appl Environ Microbiol 62: 1159-1166.
16. Fulthorpe, R.R., Rhodes, A.N., and Tiedje, J.M. (1998) High levels of endemicity of 3-chlorobenzoate-degrading soil bacteria. Appl Environ Microbiol 64: 1620-1627.
17. Gribble, G.W. (1996) Naturally occurring organohalogen compounds - a comprehensive survey. Fortschr Chem Org Naturst 68: 1-423.
18. Haggblom, M.M. (1992) Microbial breakdown of halogenated aromatic pesticides and related- compounds. FEMS Microbiol Rev 103: 29-72.
19. Hill, K.E., Marchesi, J.R., and Wefghtman, A.J. (1999) Investigation of two evolutionarily unrelated halocarboxylic acid dehalogenase gene families. J Bacteriol 81: 2535-2547.
20. Hisano, T., Hata, Y., Fujii, T., Liu, J.Q., Kurihara, T., Esaki, N., and Soda, K. (1996) Crystallization and preliminary X-ray crystallographic studies of L-2-haloacid dehalogenase from Pseudomonas sp. YL proteins. Struct Funct Genet 24: 520-522.
21. Jukes, T.H., and Cantor, C.R. (1969) Evolution of protein molecules. In Mammalian Protein Metabolism. Munro, H.N. (ed.). New York: Academic Press, pp. 21-132.
22. Kado, C.I., and Liu, S.T. (1981) Rapid procedure for detection and isolation of large and small plasmids. J Bacteriol 145: 1365-1373.
23. Kamagata, Y., Fulthorpe, R.R., Tamura, K., Takami, H., Forney, L.J., and Tiedje, J.M. (1997) Pristine environments harbor a new group of oligotrophic 2,4- dichlorophenoxyacetic acid-degrading bacteria. Appl Environ Microbiol 63: 2266-2272.
24. Kaufman, D.D. (1964) Microbial degradation of 2,2-Dichloropropionic acid in five soils. Can J Microbiol 10: 843-852.
25. Kawasaki, H., Tsuda, K., Matsushita, I., and Tonomura, K. (1992) Lack of homology between 2 haloacetate dehalogenase genes encoded on a plasmid from Moraxella sp. strain-b. J Gen Microbiol 138: 1317-1323.
26. Kawasaki, H., Toyama, T., Maeda, T., Nishino, H., and Tonomura, K. (1994) Cloning and sequence-analysis of a plasmid-encoded 2-haloacid dehalogenase gene from Pseudomonas putida no-109. Biosci Biotechnol Biochem 58: 160-163.
27. Kearney, P.C., Kaufman, D.D., and Beall, M.L. (1964) Enzymatic dehalogenation of 2,2-dichloropropionate. Biochem Biophys Res Commun 14: 29-33.
28. Köhler, R., Brokamp, A., Schwarze, R., Reiting, R.H., and Schmidt, F.J. (1998) Characteristics and DNA-sequence of a cryptic haloalkanoic acid dehalogenase from Agrobacterium tumefaciens RS5. Curr Microbiol 36: 96-101.
29. Kurihara, T., Liu, J.Q., NardiDei, V., Koshikawa, H., Esaki, N., and Soda, K. (1995) Comprehensive site-directed mutagenesis of L-2-halo acid dehalogenase to probe catalytic amino-acid-residues. J Biochem 117: 1317-1322.
30. Li, Y.F., Hata, Y., Fujii, T., Hisano, T., Nishihara, M., Kurihara, T., and Esaki, N. (1998) Crystal structures of reaction intermediates of L-2-haloacid dehalogenase and implications for the reaction mechanism. J Biol Chem 273: 15035-15044.
31. Marchesi, J.R., Sato, T., Weightman, A.J., Martin, T.A., Fry, J.C., Hiom, S.J., and Wade, W.G. (1998) Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microbiol 64: 795-799.
32. van der Meer, J.R., de Vos, W.M., Harayama, S., and Zehnder, A.J. (1992) Molecular mechanisms of genetic adaptation to xenobiotic compounds. Microbiol Rev 56: 677-694.
33. Murdiyatmo, U., Asmara, W., Tsang, J.H., Baines, A.J., Bull, A.T., and Hardman, D.J. (1992) Molecular-biology of the 2-haloacid halidohydrolase IVa from Pseudomonas cepacia MBA4. Biochem J 284: 87-93.
34. Nardi-Dei, V., Kurihara, T., Okamura, T., Liu, J.Q., Koshikawa, H., Ozaki, H., et al. (1994) Comparative-studies of genes encoding thermostable L-2-halo acid dehalogenase from Pseudomonas sp. strain YL, other dehalogenases, and two related hypothetical proteins from Escherichia coli. Appl Environ Microbiol 60: 3375-3380.
35. Nardi-Dei, V., Kurihara, T., Park, C., Esaki, N., and Soda, K. (1997) Bacterial DL-2-haloacid dehalogenase from Pseudomonas sp. strain 113: gene cloning and structural comparison with D- and L-2-haloacid dehalogenases. J Bacteriol 179: 4232-4238.
36. van der Ploeg, J.R., Willemsen, M., van Hall, G., and Janssen, D.B. (1995) Adaptation of Xanthobacter autotrophicus GJ10 to bromoacetate due to activation and mobilization of the haloacetate dehalogenase gene by insertion element IS1247. J Bacteriol 177: 1348-1356.
37. Poelarends, G.J., Kulakov, L.A., Larkin, M.J., van Hylckama Vlieg, J.E., and Janssen, D.B. (2000) Roles of horizontal gene transfer and gene integration in evolution of 1,3-dichloropropene- and 1,2-dibromoethane-deg radative pathways. J Bacteriol 182: 2191-2199.
38. Schwarze, R., Brokamp, A., and Schmidt, F.J. (1997) Isolation and characterization of dehalogenases from 2,2-dichloropropionate-degrading soil bacteria. Curr Microbiol 34: 103-109.
39. Seemuller, E., Schneider, B., Maurer, R., Ahrens, U., Daire, X., Kison, H., et al. (1994) Phylogenetic classification of phytopathogenic mollicutes by sequence-analysis of 16S ribosomal DNA. Int J Syst Bacterio144: 440-446.
40. Slater, J.H., Weightman, A.J., and Hall, B.G. (1985) Dehalogenase genes of Pseudomonas putida PP3 on chromosomally located transposable elements. Mol Biol Evol 2: 557-567.
41. Slater, J.H., Bull, A.T., and Hardman, D.J. (1997) Microbial dehalogenation of halogenated alkanoic acids, alcohols and alkanes. Adv Microb Physiol 38: 133-176.
42. Soda, K., Kurihara, T., Liu, J.Q., NardiDei, V., Park, C., Miyagi, M., et al. (1996) Bacterial 2-haloacid dehalogenases: structures and catalytic properties. Pure Appl Chem 68' 2097-2103.
43. Stringfellow, J.M., Cairns, S.S., Cornish, A., and Cooper, R.A. (1997) Haloalkanoate dehalogenase II (DehE) of a Rhizobium sp. - molecular analysis of the gene and formation of carbon monoxide from trihaloacetate by the enzyme. Eur J Biochem 250: 789-793.
44. Thomas, A.W., Slater, J.H., and Weightman, A.J. (1992) The dehalogenase gene dehl from Pseudomonas putida PP3 is carried on an unusual mobile genetic element designated deh. J Bacteriol 174: 1932-1940.
45. Tsang, J.S.H., Sallis, P.J., Bull, A.T., and Hardman, D.J. (1988) A monobromoacetate dehalogenase from Pseudomonas cepacia MBA4. Arch Microbiol 150: 441-446.
46. Weightman, A.J., and Slater, J.H. (1980) Selection of Pseudomonas putida strains with elevated dehalogenase activities by continuous culture-growth on chlorinated alkanoic acids. J Gen Microbiol 121: 187-193.