Investigation of two evolutionarily unrelated halocarboxylic acid dehalogenase gene families

Journal of Bacteriology

Volumn 181, Issue 8, 1999, Pages 2535-2547

  Hill, Katja E ^a   Marchesi, Julian R ^a   Weightman, Andrew J ^a  

^a CARDIFF UNIVERSITY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ENZYME; HALOCARBOXYLIC ACID DEHALOGENASE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENE; DEHALOGENATION; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; RHIZOBIUM;

BACTERIA (MICROORGANISMS); NEGIBACTERIA; PROKARYOTA; PROTEOBACTERIA; RHIZOBIUM; RHIZOBIUM SP.;

EID: 0032909021     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/jb.181.8.2535-2547.1999     Document Type: Article

References (67)

1. Aravind, L., M. Y. Galperin, and E. V. Koonin. 1998. The catalytic domain of the P-type ATPase has the haloacid dehalogenase fold. Trends Biochem. Sci. 23:127-129.
2. Ausubel, F. M., R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl (ed.). 1989. Current protocols in molecular biology. John Wiley & Sons, Inc., New York, N.Y.
3. Barth, P. T., L. Bolton, and J. C. Thomson. 1992. Cloning and partial sequencing of an operon encoding two Pseudomonas putida haloalkanoate dehalogenases of opposite sterospecificity. J. Bacteriol. 174:2612-2619.
4. Brokamp, A., B. Happe, and F. R. J. Schmidt. 1997. Cloning and nucleotide sequence of a D,L-haloalkanoic acid dehalogenase encoding gene from Alcaligenes xylosoxidans ssp. denitrificans ABIV. Biodegradation 7:383-396.
5. Brokamp, A., R. Schwarze, and F. R. J. Schmidt. 1997. Homologous plasmids from soil bacteria encoding D,L-halidohydrolases. Curr. Microbiol. 34: 97-102.
6. Brunner, W., D. Staub, and T. Leisinger. 1980. Bacterial degradation of dichloromethane. Appl. Environ. Microbiol. 40:950-958.
7. Cairns, S. S., A. Cornish, and R. A. Cooper. 1996. Cloning, sequencing and expression in Escherichia coli of two Rhizobium sp. genes encoding haloalkanoate dehalogenases of opposite stereospecificity. Eur. J. Biochem. 235: 744-749.
8. Environment Protection Act. 1990. c.43. Her Majesty's Stationery Office, London, United Kingdom.
9. European Bioinformatics Institute. 25 July 1997, revision date. [Online.] http://www.ebi.ac.uk. [8 March 1999, last date accessed.]
10. Felsenstein, J. 1985. Confidence limits on phytogenies: an approach using the bootstrap. Evolution 39:783-791.
11. Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package), version 3.5c. Distributed by the author Department of Genetics, University of Washington, Seattle.
12. Fetzner, S., and F. Lingens. 1994. Bacterial dehalogenases: biochemistry, genetics, and biotechnological applications. Microbiol. Rev. 58:641-685.
13. Goldman, P. 1965. The enzymatic cleavage of the C-F bond in fluoroacetate. J. Biol. Chem. 240:3434-3438.
14. Gribble, G. W. 1996. The diversity of natural organochlorines in living organisms. Pure Appl. Chem. 68:1699-1712.
15. Guenter, S., M. A. Moseley, J. Sleep, M. McGowran, M. Garcia-Pastor, and P. Sterk. 1998. The EMBL nucleotide sequence database. Nucleic Acids Res. 26:8-15.
16. Hall, B. G. 1998. Activation of the bgl operon by adaptive mutation. Mol. Biol. Evol. 15:1-5.
17. Hardman, D. J. 1991. Biotransformation of halogenated compounds. Crit. Rev. Biotechnol. 11:1-40.
18. Hill, K. E., L. O'Sullivan, J. R. Marchesi, and A. J. Weightman. Unpublished data.
19. Hisano, T., Y. Hata, T. Fujii, J-Q. Liu, T. Kurihara, N. Esaki, and K. Soda. 1996. Crystal structure of L-2-haloacid dehalogenase from Pseudomonas sp. YL. J. Biol. Chem. 271:20322-20330.
20. Honnens, E., R. Reiting, A. Brokamp, and F. J. R. Schmidt. GenBank accession no. X94147, unpublished data.
21. Janssen, D. B., F. Pries, J. R. van der Ploeg, B. Kazemler, P. Terpstra, and B. Witholt. 1985. Degradation of halogenated aliphatic compounds by Xanthobacter autotrophicus GJ10. Appl. Environ. Microbiol. 49:673-677.
22. Janssen, D. B., F. Pries, and J. R. van der Ploeg. 1994. Genetics and biochemistry of dehalogenating enzymes. Annu. Rev. Microbiol. 48:163-191.
23. Janssen, D. B., T. Bosma, and G. J. Poelarends. 1997. Diversity and mechanisms of bacterial dehalogenation reactions, p. 119-129. In D. B. Janssen, K. Soda, and R. Wever. (ed.). Proceedings of Colloquium on Mechanisms of Biodehalogenation and Dehalogenation, National Academy of Sciences, Amsterdam. Royal Netherlands Academy of Sciences, Amsterdam. Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands.
24. Jensen, H. L. 1960. Decomposition of chloroacetates and chloropropionates by bacteria. Acta Agric. Scand. 10:83-103.
25. Jones, D. H., P. T. Barth, D. Byrom, and C. M. Thomas. 1992. Nucleotide sequence of the structural gene encoding a 2-haloalkanoic acid dehalogenase of Pseudomonas putida strain AJ1 and purification of the encoded protein. J. Gen. Microbiol. 138:675-683.
26. Jukes, T. H., and C. R. Cantor. 1969. Evolution of protein molecules, p. 21-132. In H. N. Munro (ed.), Mammalian protein metabolism. Academic Press, New York, N.Y.
27. Kawasaki, H., H. Yahara, and K. Tonomura. 1981. Isolation and characterization of plasmid pUO1 mediating dehalogenation of haloacetate and mercury resistance in Moraxella sp. B. Agric. Biol. Chem. 45:1477-1481.
28. Kawasaki, H., K. Tsuda, I. Matsusita, and K, Tonomura. 1992. Lack of homology between two haloacetate dehalogenase genes encoded on a plasmid from Moraxella sp. strain B. J. Gen. Microbiol. 138:1317-1323.
29. Kawasaki, H., T. Toyama, T. Maeda, H. Nishino, and K. Tonomura. 1994. Cloning and sequence analysis of a plasmid-encoded 2-haloacid dehalogenase gene from Pseudomonas putida no. 109. Biosci. Biotechnol. Biochem. 58:160-163.
30. Kawasaki, H. 1997. The haloacetate dehalogenase gene dehH2 carried on a transposon residing in a plasmid of Moraxella sp. B, p. 175-184. In D. B. Janssen, K. Soda, and R. Wever. (eds). Proceedings of Colloquium on Mechanisms of Biodehalogenation and Dehalogenation, National Academy of Sciences, Amsterdam. Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands.
31. Köhler, R., A. Brokamp, R. Schwarze, R. H. Reiting, and F. R. J. Schmidt. 1998. Characteristics and DNA-sequence of a cryptic haloalkanoic acid dehalogenase from Agrobacterium tumefaciens RS5. Curr. Microbiol. 36:96-101.
32. Kohler-Staub, D., and H.-P. E. Kohler. 1989. Microbial degradation of β-chlorinated four-carbon aliphatic acids. J. Bacteriol. 171:1428-1434.
33. Koonin, E. V., and R. L. Tatusov. 1994. Computer analysis of bacterial haloacid dehalogenases defines a large superfamily of hydrolases with diverse specificity: application of an iterative approach to database search. J. Mol. Biol. 244:125-132.
34. Kurihara, T., J. Q. Liu, V. Nardi-Dei, H. Koshikawa, N. Esaki, and K. Soda. 1995. Comprehensive site-directed mutagenesis of L-2-halo acid dehalogenase to probe catalytic amino-acid-residues. J. Biochem. 117:1317-1322.
35. Leisinger, T., and R. Bader. 1993. Microbial dehalogenation of synthetic organohalogen compounds - hydrolytic dehalogenases. Chimia 47:116-121.
36. Li, Y.-F., Y. Hata, T. Fujii, T. Hisano, M. Nishihara, T. Kurihara, and N. Esaki. 1998. Crystal structures of reaction intermediates of L-2-haloacid dehalogenase and implications for the reaction mechanism. J. Biol. Chem. 273:15035-15044.
37. Maidak, B. L., G. J. Olsen, N. Larsen, R. Overbeek, M. J. McCaughey, and C. R. Woese. 1997. The RDP (Ribosomal Database Project). Nucleic Acids Res. 25:109-110.
38. Marchesi, J. R., T. Sato, A. J. Weightman, T. A. Martin, J. C. Fry, S. J. Hlom, D. Dymock, and W. G. Wade. 1998. Design and evaluation of useful bacterial specific PCR primers that amplify bacterial 16S rDNA genes. Appl. Environ. Microbiol. 64:795-799.
39. Marchesi, J. R., K. E. Hill, and A. J. Weightman. Unpublished results.
40. Messing, J. 1983. New M13 vectors for cloning. Methods Enzymol. 101:20-78.
41. Murdiyatmo, U., W. Asmara, J. S. Tsang, A. J. Baines, A. T. Bull, and D. J. Hardman. 1992. Molecular biology of the 2-haloacid halidohydrolase IVa from Pseudomonas cepacia MBA4. Biochem. J. 284:87-93.
42. Nardi-Dei, V., T. Kurihara, T. Okamura, J. Q. Liu, H. Koshikawa, H. Ozaki, Y. Terashima, N. Esaki, and K. Soda. 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.
43. Nardi-Dei, V., T. Kurihara, C. Park, N. Esaki, and K. Soda. 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.
44. Olsen, G. J., C. R. Woese, and R. Overbeek. 1994. The winds of (evolutionary) change - breathing new life into microbiology. J. Bacteriol. 176:1-6.
45. Parker, L. L., and B. G. Hall. 1990. Characterization and nucleotide sequence of the cryptic cel operon of Escherichia coli K12. Genetics 124:455-471.
46. Parker, L. L., and B. G. Hall. 1990. Mechanisms of activation of the cryptic ceel operon of Escherichia coli K12, Genetics 124:473-482.
47. Pearson, W. R., and D. J. Lipman. 1988. Improved tools for biological sequence analysis. Proc. Natl. Acad. Sci. USA 85:2444-2448.
48. Pearson, W. R. 1990. Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol. 183:63-98.
49. Ridder, I. S., H. J. Rozeboom, K. H. Kalk, D. B. Janssen, and B. W. Dykstra. 1997. Three-dimensional structure of L-2-haloacid dehalogenase from Xanthobacter autotrophicus GJ10 with the substrate analogue formate. J. Biol. Chem. 272:33015-33022.
50. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
51. 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.
52. Schäferjohann, J., J.-G. Yoo, B. Kusian, and B. Bowein. 1993. The cbb operons of the facultative chemoautotroph Alcaligenes eutrophus encode phosphoglycolate phosphatases. J. Bacteriol. 175:7329-7340.
53. Schneider, B., R. Muller, R. Frank, and F. Lingens. 1991. Complete nucleotide sequences and comparison of the structural genes of two 2-haloalkanoic acid dehalogenases from Pseudomonas sp. strain CBS3. J. Bacteriol. 173:1530-1535.
54. Slater, J. H., D. Lovatt, A. J. Weightman, E. Senior, and A. T. Bull. 1979. The growth of Pseudomonas putida on chlorinated aliphatic acids and its dehalogenase activity. J. Gen. Microbiol. 114:125-136.
55. Slater, J. H., A. J. Weightman, and B. G. Hall. 1985. Dehalogenase genes of Pseudomonas putida PP3 on chromosomally located transposable elements. Mol. Biol. Evol. 2:557-567.
56. Slater, J. H., A. T. Bull, and D. J. Hardman. 1995. Microbial dehalogenation. Biodegradation 6:181-189.
57. Slater, J. H., A. T. Bull, and D. J. Hardman. 1997. Microbial dehalogenation of halogenated alkanoic acids, alcohols and alkanes. Adv. Microb. Physiol. 38:133-176.
58. Smith, J. M., K. Harrison, and J. Colby. 1990. Purification and characterization of D-2-haloacid dehalogenase from Pseudomonas putida strain AJ1/ 23. J. Gen. Microbiol. 136:881-886.
59. Stringfellow, J. M., S. S. Cairns, A. Cornish, and R. A. Cooper. 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.
60. Thomas, A. W., J. H. Slater, and A. J. Weightman. 1992. The dehalogenase gene dehI from Pseudomonas putida PP3 is carried on an unusual mobile genetic element designated deh. J. Bacteriol. 174:1932-1940.
61. Thomas, A. W., J. Lewington, S. Hope, A. W. Topping, A. J. Weightman, and J. H. Slater. 1992. Environmentally directed mutations in the dehalogenase system of Pseudomonas pulida strain PP3. Arch. Microbiol. 158:176-182.
62. 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.
63. I) from Pseudomonas putida strain PP3 and its relationship with σ(54)-dependent activators. Biodegradation 6:247-255.
64. van de Peer, Y., and R. De Wachter. 1994. TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment Comput. Applic. Biosci. 10:569-570.
65. van der Ploeg, J., G. van Hall, and J. B. Janssen. 1991. Characterization of the haloacid dehalogenase from Xanthobacter autotrophicus GJ10 and sequencing of the dhlB gene. J. Bacteriol. 173:7925-7933.
66. van Hylckama Vlieg, J. E. T., and D. B. Janssen. Personal communication.
67. Weightman, A. J., A. L. Weightman, and J. H. Slater. 1982. Stereospecificity of 2-monochloropropionate dehalogenation by the two dehalogenases of Pseudomonas putida PP3: evidence for two different dehalogenation mechanisms. J. Gen. Microbiol. 128:1755-1762.