Evolution of a chlorobenzene degradative pathway among bacteria in a contaminated groundwater mediated by a genomic island in Ralstonia

Environmental Microbiology

Volumn 5, Issue 3, 2003, Pages 163-173

  Müller, Tina Andrea ^a   Werlen, Christoph ^a   Spain, Jim ^b   Van Der Meer, Jan Roelof ^a  

^a SWISS FEDERAL INSTITUTE OF AQUATIC SCIENCE AND TECHNOLOGY   (Switzerland)

^b AIR FORCE RESEARCH LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BASE SEQUENCE; BETAPROTEOBACTERIA; BIODEGRADATION, ENVIRONMENTAL; CHLOROBENZENES; CHROMOSOMES, BACTERIAL; CONJUGATION, GENETIC; DNA TRANSPOSABLE ELEMENTS; EVOLUTION, MOLECULAR; FRESH WATER; MOLECULAR SEQUENCE DATA; SEQUENCE ANALYSIS, DNA; WATER POLLUTION, CHEMICAL;

INSERTION SEQUENCES; PROKARYOTA; PSEUDOMONAS; PSEUDOMONAS PUTIDA; PSEUDOMONAS SP.; RALSTONIA;

EID: 0037345571     PISSN: 14622912     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1462-2920.2003.00400.x     Document Type: Article

References (43)

1. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
2. Arber, W. (2000) Genetic variation: molecular mechanisms and impact on microbial evolution. FEMS Microbiol Rev 24: 1-7.
3. Beil, S., Happe, B., Timmis, K.N., and Pieper, D.H. (1997) Genetic and biochemical characterization of the broad spectrum chlorobenzene dioxygenase from Burkholderia sp. strain PS12: dechlorination of 1,2,4,5-tetrachlorobenzene. Eur J Biochem 247: 190-199.
4. Beil, S., Timmis, K.N., and Pieper, D.H. (1999) Genetic and biochemical analyses of the tec operon suggest a route for evolution of chlorobenzene degradation genes. J Bacteriol 181: 341-346.
5. Benes, V., Hostomsky, Z., Arnold, L., and Paces, V. (1993) M13 and pUC vectors with new unique restriction sites for cloning. Gene 130: 151-152.
6. Coco, W.M., Rothmel, R.K., Henikoff, S., and Chakrabarty, A.M. (1993) Nucleotide sequence and initial functional characterization of the clcR gene encoding a LysR family activator of the clcABD chlorocatechol operon in Pseudomonas putida. J Bacteriol 175: 417-427.
7. Davis, J.K., Paoli, G.C., He, Z., Nadeau, L.J., Somerville, C.C., and Spain, J.C. (2000) Sequence analysis and initial characterization of two isozymes of hydroxylaminobenzene mutase from Pseudomonas pseudoalcaligenes JS45. Appl Environ Microbiol 66: 2965-2971.
8. Di Gioia, D., Peel, M., Fava, F., and Wyndham, R.C. (1998) Structures of homologous composite transposons carrying cbaABC genes from Europe and North America. Appl Environ Microbiol 64: 1940-1946.
9. Don, R.H., Weightman, A.J., Knackmuss, H.-J., and Timmis, K.N. (1985) Transposon mutagenesis and cloning analysis of the pathways for degradation of 2,4-dichlorophenoxyacetic acid and 3-chlorobenzoate in Alcaligenes eutrophus JMP134 (pJP4). J Bacteriol 161: 85-90.
10. Dorn, E., Hellwig, M., Reineke, W., and Knackmuss, H.-J. (1974) Isolation and characterization of a 3-chlorobenzoate degrading Pseudomonad. Arch Microbiol 99: 61-70.
11. Figurski, D.H., and Helinski, D.R. (1979) Replication of an origin-containing derivative of plasmid RK2 dependent on a plasmid function provided in trans. Proc Natl Acad Sci USA 76: 1648-1652.
12. Frantz, B., and Chakrabarty, A.M. (1987) Organization and nucleotide sequence determination of a gene cluster involved in 3-chlorocatechol degradation. Proc Natl Acad Sci USA 84: 4460-4464.
13. 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.
14. Herrick, J.B., Stuart-Keil, K.G., Ghiorse, W.C., and Madsen, E.L. (1997) Natural horizontal transfer of a naphthalene dioxygenase gene between bacteria native to a coal tarcontaminated field site. Appl Environ Microbiol 63: 2330-2337.
15. Hickey, W.J., Sabat, G., Yuroff, A.S., Arment, A.R., and Perez-Lesher, J. (2001) Cloning, nucleotide sequencing, and functional analysis of a novel, mobile cluster of biodegradation genes from Pseudomonas aeruginosa strain JB2. Appl Environ Microbiol 67: 4603-4609.
16. Leveau, J.H.J., and van der Meer, J.R. (1997) Genetic characterization of insertion sequence ISJP4 on plasmid pJP4 from Ralstonia eutropha JMP134. Gene 202: 103-114.
17. McGowan, C., Fulthorpe, R., Wright, A., and Tiedje, J.M. (1998) Evidence for interspecies gene transfer in the evolution of 2,4-dichlorophenoxyacetic acid degraders. Appl Environ Microbiol 64: 4089-4092.
18. Mars, A.E., Kasberg, T., Kaschabek, S.R., van Agteren, M.H., Janssen, D.B., and Reineke, W. (1997) Microbial degradation of chloroaromatics: use of the meta-cleavage pathway for mineralization of chlorobenzene. J Bacteriol 179: 4530-4537.
19. Mars, A.E., Kingma, J., Kaschabek, S.R., Reineke, W., and Janssen, D.B. (1999) Conversion of 3-chlorocatechol by various catechol 2,3-dioxygenases and sequence analysis of the chlorocatechol dioxygenase region of Pseudomonas putida GJ31. J Bacteriol 181: 1309-1318.
20. Martinez, B., Tomkins, J., Wackett, L.P., Wing, R., and Sadowsky, M.J. (2001) Complete nucleotide sequence and organization of the atrazine catabolic plasmid pADP-1 from Pseudomonas sp. strain ADP. J Bacteriol 183: 5684-5697.
21. van der Meer, J.R. (1997) Evolution of novel metabolic pathways for the degradation of aromatic compounds. Ant Leeuwenhoek Int J Microbiol 71: 159-178.
22. van der Meer, J.R., Zehnder, A.J.B., and de Vos, W.M. (1991) Identification of a novel composite transposable element, Tn5280, carrying chlorobenzene dioxygenase genes of Pseudomonas sp. strain P51. J Bacteriol 173: 7077-7083.
23. van der Meer, J.R., Werlen, C., Nishino, S., and Spain, J.C. (1998) Evolution of a pathway for chlorobenzene metabolism leads to natural atttenuation in a contaminated groundwater. Appl Environ Microbiol 64: 4185-4193.
24. van der Meer, J.R., Ravatn, R., and Sentchilo, V.S. (2001) The clc element of Pseudomonas sp. strain B13 and other mobile degradative elements employing phage-like integrases. Arch Microbiol 175: 79-85.
25. Menn, F.M., Zylstra, G.J., and Gibson, D.T. (1991) Location and sequence of the todF gene encoding 2-hydroxy-6-oxohepta-2,4-dienoate hydrolase. Gene 104: 91-94.
26. Mosqueda, G., Ramos-Gonzalez, M.I., and Ramos, J.L. (1999) Toluene metabolism by the solvent-tolerant Pseudomonas putida DOT-T1 strain, and its role in solvent impermeabilization. Gene 232: 69-76.
27. Nishino, S.F., Spain, J.C., Belcher, L.A., and Litchfield, C.D. (1992) Chlorobenzene degradation by bacteria isolated from contaminated groundwater. Appl Environ Microbiol 58: 1719-1726.
28. Nishino, S.F., Spain, J.C., and Pettigrew, C.A. (1994) Biodegradation of chlorobenzene by indigenous bacteria. Environ Toxic Chem 13: 871-877.
29. Ornston, L.N., Neidle, E.L., and Houghton, J.E. (1990) Gene rearrangements, a force for evolutionary change; DNA sequence arrangements, a source of genetic constancy. In The Bacterial Chromosome. Riley, M., and Drlica, K. (eds). Washington, DC: American Society for Microbiology Press, pp. 325-334.
30. Peters, M., Heinaru, E., Talpsep, E., Wand, H., Stottmeister, U., Heinaru, A., and Nurk, A. (1997) Acquisition of a deliberately introduced phenol degradation operon, pheBA, by different indigenous Pseudomonas species. Appl Environ Microbiol 63: 4899-4906.
31. Ravatn, R., Studer, S., Springael, D., Zehnder, A.J.B., and van der Meer, J.R. (1998a) Chromosomal integration, tandem amplification, and deamplification in Pseudomonas putida F1 of a 105-kilobase genetic element containing the chlorocatechol degradative genes from Pseudomonas sp. strain B13. J Bacteriol 180: 4360-4369.
32. Ravatn, R., Studer, S., Zehnder, A.J.B., and van der Meer, J.R. (1998b) Int-B13, an unusual site-specific recombinase of the bacteriophage P4 integrase family, is responsible for chromosomal insertion of the 105- kilobase clc element of Pseudomonas sp. strain B13. J Bacteriol 180: 5505-5514.
33. Ravatn, R., Zehnder, A.J.B., and van der Meer, J.R. (1998c) Low-frequency horizontal transfer of an element containing the chlorocatechol degradation genes from Pseudomonas sp. strain B13 to Pseudomonas putida F1 and to indigenous bacteria in laboratory-scale activated-sludge microcosms. Appl Environ Microbiol 64: 2126-2132.
34. Reineke, W., and Knackmuss, H.-J. (1979) Construction of haloaromatics utilizing bacteria. Nature (London) 277: 385-386.
35. Sambrook, J., Frisch, E.F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
36. Simon, R., O'Connell, M., Labes, M., and Pühler, A. (1986) Plasmid vectors for the genetic analysis and manipulation of rhizobia and other gram-negative bacteria. Methods Enzymol 186: 640-659.
37. de Souza, M.L., Seffernick, J., Martinez, B., Sadowsky, M.J., and Wackett, L.P. (1998) The atrazine catabolism genes atzABC are widespread and highly conserved. J Bacteriol 180: 1951-1954.
38. Spain, J.C., and Nishino, S.F. (1987) Degradation of 1,4-dichlorobenzene by a Pseudomonas sp. Appl Environ Microbiol 53: 1010-1019.
39. Springael, D., Peys, K., Ryngaert, A., Van Roy, S., Hooyberghs, L., Ravatn, R., et al. (2002) Community shifts in a seeded 3-chlorobenzoate degrading membrane biofilm reactor: indications for involvement of in situ horizontal transfer of the clc-element from inoculum to contaminant bacteria. Environ Microbiol 4: 70-80.
40. Werlen, C., Kohler, H.-P.E., and van der Meer, J.R. (1996) The broad substrate chlorobenzene dioxygenase and cis-chlorobenzene dihydrodiol dehydrogenase of Pseudomonas sp. strain P51 are linked evolutionarily to the enzymes for benzene and toluene degradation. J Biol Chem 271: 4009-4016.
41. Yanisch-Perron, C., Vieira, J., and Messing, J. (1985) Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33:103-119.
42. Zylstra, G.J., and Gibson, D.T. (1989) Toluene degradation by Pseudomonas putida F1. J Biol Chem 264: 14940-14946.
43. Zylstra, G.J., McCombie, W.R., Gibson, D.T., and Finette, B.A. (1988) Toluene degradation by Pseudomonas putida F1: genetic organization of the tod operon. Appl Environ Microbiol 54: 1498-1503.