Roles of horizontal gene transfer and gene integration in evolution of 1,3-dichloropropene- and 1,2-dibromoethane-degradative pathways

Journal of Bacteriology

Volumn 182, Issue 8, 2000, Pages 2191-2199

  Poelarends, Gerrit J ^a   Kulakov, Leonid A ^b   Larkin, Michael J ^b   Van Hylckama Vlieg, Johan E T ^a   Janssen, Dick B ^a  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

^b QUEEN'S UNIVERSITY BELFAST   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

1,2 DIBROMOETHANE; ALCOHOL DEHYDROGENASE; ALDEHYDE DEHYDROGENASE; BUTANOL; BUTYRIC ACID; PROPYLENE; REGULATOR PROTEIN;

ARTICLE; BACTERIAL GENE; BACTERIAL METABOLISM; CONTROLLED STUDY; GENE CLUSTER; GENE EXPRESSION; GENE SEQUENCE; GENE TRANSFER; MOLECULAR EVOLUTION; MYCOBACTERIUM; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PSEUDOMONAS; RHODOCOCCUS;

ALLYL COMPOUNDS; AMINO ACID SEQUENCE; BASE SEQUENCE; BIODEGRADATION, ENVIRONMENTAL; CONSERVED SEQUENCE; DNA TRANSPOSABLE ELEMENTS; DNA-BINDING PROTEINS; ENVIRONMENTAL POLLUTANTS; ESCHERICHIA COLI PROTEINS; ETHYLENE DIBROMIDE; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, BACTERIAL; GENE TRANSFER, HORIZONTAL; GENES, BACTERIAL; HYDROCARBONS, BROMINATED; HYDROCARBONS, HALOGENATED; HYDROLASES; INTEGRASES; MOLECULAR SEQUENCE DATA; MYCOBACTERIUM; PSEUDOMONAS; RECOMBINATION, GENETIC; RHODOCOCCUS; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, AMINO ACID; TRANS-ACTIVATORS;

ACTINOBACTERIA (CLASS); BACTERIA (MICROORGANISMS); MYCOBACTERIUM; MYCOBACTERIUM SP.; NEGIBACTERIA; PROKARYOTA; PSEUDOMONAS; PSEUDOMONAS PAVONACEAE; PSEUDOMONAS SP.; RHODOCOCCUS; RHODOCOCCUS RHODOCHROUS; UNCULTURED ACTINOMYCETE;

EID: 0034029582     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.182.8.2191-2199.2000     Document Type: Article

References (51)

1. Abremski, K. E., and R. H. Hoess. 1992. Evidence for a second conserved arginine residue in the integrase family of recombination proteins. Protein Eng. 5:87-91.
2. Albertini, A. M., M. Hofer, M. P. Calos, and J. H. Miller. 1982. On the formation of spontaneous deletions: the importance of short sequence homologies in the generation of large deletions. Cell 29:319-328.
3. 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.
4. Argos, P., A. Landy, K. Abremski, J. B. Egan, E. Haggard-Ljungquist, R. H. Hoess, et al. 1986. The integrase family of site-specific recombinases: regional similarities and global diversity. EMBO J. 5:433-440.
5. Belser, N. O., and C. E. Castro. 1971. Biodehalogenation - the metabolism of the nematocides cis-and trans-3-chloroallyl alcohol by a bacterium isolated from soil. J. Agric. Food Chem. 19:23-26.
6. Blatter, E. E., D. P. Abriola, and R. Pietruszko. 1992. Aldehyde dehydrogenase. Covalent intermediate in aldehyde dehydrogenation and ester hydrolysis. Biochem. J. 282:353-360.
7. Boyer, H. W., and D. Roulland-Dussoix. 1969. A complementation analysis of the restriction and modification of DNA in Escherichia coli. J. Mol. Biol. 41:459-472.
8. Cole, S. T., R. Brosch, J. Parkhill, T. Garnier, C. Churcher, D. Harris, et al. 1998. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393:537-544.
9. Curragh, H., O. Flynn, M. J. Larkin, T. M. Stafford, J. T. G. Hamilton, and D. B. Harper. 1994. Haloalkane degradation and assimilation by Rhodococcus rhodochrous NCIMB13064. Microbiology 140:1433-1442.
10. Dodd, I. B., and J. B. Egan. 1987. Systematic method for the detection of potential 8 Cro-like DNA-binding regions in proteins. J. Mol. Biol. 194:557-564.
11. Eaton, R. W. 1996. p-Cumate catabolic pathway in Pseudomonas putida F1: cloning and characterization of DNA carrying the cmt operon. J. Bacteriol. 178:1351-1362.
12. Farrés, J., T. T. Y. Wang, S. J. Cunningham, and H. Weiner. 1995. Investigation of the active site cysteine residue of rat liver mitochondrial aldehyde dehydrogenase by site-directed mutagenesis. Biochemistry 34:2592-2598.
13. Finan, T. M., B. Kunkel, G. F. De Vos, and E. R. Signer. 1986. Second symbiotic megaplasmid in Rhizobium meliloti carrying exopolysaccharide and thiamine synthesis genes. J. Bacteriol. 167:66-72.
14. Glasgow, A. C., K. T. Hughes, and M. I. Simon. 1989. Bacterial DNA inversion systems, p. 637-659. In D. E. Berg and M. M. Howe (ed.). Mobile DNA. American Society for Microbiology, Washington, D.C.
15. Hall, R. M., D. E. Brookes, and H. W. Stokes. 1991. Site-specific insertion of genes into integrons: role of the 59-base element and determination of the recombination cross-over point. Mol. Microbiol. 5:1941-1959.
16. Hall, R. M., and H. W. Stokes. 1993. Integrons: novel DNA elements which capture genes by site-specific recombination. Genetica (The Hague) 90:115-132.
17. Janssen, D. B., A. Scheper, and B. Witholt. 1984. Biodegradation of 2-chloroethanol and 1,2-dichloroethane by pure bacterial cultures. Prog. Ind. Microbiol. 20:169-178.
18. Janssen, D. B., F. Pries, J. Van der Ploeg, B. Kazemier, P. Terpstra, and B. Witholt. 1989. Cloning of 1,2-dichloroethane degradation genes of Xanthobacter autotrophicus GJ10 and expression and sequencing of the dhlA gene. J. Bacteriol. 171:6791-6799.
19. Keen, N. T., S. Tamaki, D. Kobayashi, and D. Trollinger. 1988. Improved broad-host-range plasmids for DNA cloning in Gram-negative bacteria. Gene 70:191-197.
20. Keuning, S., D. B. Janssen, and B. Witholt. 1985. Purification and characterization of hydrolytic haloalkane dehalogenase from Xanthobacter autotrophicus GJ10. J. Bacteriol. 163:635-639.
21. Kulakov, L. A., G. J. Poelarends, D. B. Janssen, and M. J. Larkin. 1999. Characterization of IS2112, a new insertion sequence from Rhodococcus, and its relationship with mobile elements belonging to the IS110 family. Microbiology 145:561-568.
22. Kulakova, A. N., T. M. Stafford, M. J. Larkin, and L. A. Kulakov. 1995. Plasmid pRTL1 controlling 1-chloroalkane degradation by Rhodococcus rhodochrous NCIMB13064. Plasmid 33:208-217.
23. Kulakova, A. N., M. J. Larkin, and L. A. Kulakov. 1997. The plasmid-located haloalkane dehalogenase gene from Rhodococcus rhodochrous NCIMB13064. Microbiology 143:109-115.
24. Larkin, M. J., R. De Mot, L. A. Kulakov, and I. Nagy. 1998. Applied aspects of Rhodococcus genetics. Antonie Leeuwenhoek 74:133-153.
25. Martinez, E., and F. De la Cruz. 1990. Genetic elements involved in Tn21 site-specific integration, a novel mechanism for the dissemination of antibiotic resistance genes. EMBO J. 9:1275-1281.
26. Nakatsu, C., J. Ng, R. Singh, N. Straus, and C. Wyndham. 1991. Chlorobenzoate catabolic transposon Tn5271 is a composite class I element with flanking class II insertion sequences. Proc. Natl. Acad. Sci. USA 88:8312-8316.
27. Nunes-Düby, S. E., H. J. Kwon, R. S. Tirumalai, T. Ellenberger, and A. Landy. 1998. Similarity and differences among 105 members of the Int family of site-specific recombinases. Nucleic Acids Res. 26:391-406.
28. Okamoto, S., K. Nakamura, T. Nihira, and Y. Yamada. 1995. Virginiae butanolide binding protein from Streptomyces virginiae: evidence that VbrA is not the virginiae butanolide binding protein and reidentification of the true binding protein. J. Biol. Chem, 270:12319-12326.
29. Onaka, H., N. Ando, T. Nihira, Y. Yamada, T. Beppu, and S. Horinouchi. 1995. Cloning and characterization of the A-factor receptor gene from Streptomyces griseus. J. Bacteriol. 177:6083-6092.
30. Pabo, C. O., and R. T. Sauer. 1984. Protein-DNA recognition. Annu. Rev. Biochem. 53:293-321.
31. Pargellis, C. A., S. E. Nunes-Düby, L. M. De Vargas, and A. Landy. 1988. Suicide recombination substrates yield covalent lambda integrase-DNA complexes and lead to identification of the active site tyrosine. J. Biol. Chem. 263:7678-7685.
32. Park, D. H., and B. V. Plapp. 1991. Isoenzymes of horseliver alcohol dehydrogenase active on ethanol and steroids. cDNA cloning, expression, and comparison of active sites. J. Biol. Chem. 266:13296-13302.
33. Persson, B., T. Bergman, W. M. Keung, U. Waldenstrom, B. Holmquist, B. L. Vallee, and H. Jornvall. 1993. Basic features of class-1 alcohol dehydrogenase: variable and constant segments coordinated by inter-class and intraclass variability. Conclusions from characterization of the alligator enzyme. Eur. J. Biochem. 216:49-56.
34. Plasterk, R. H., A. Brinkman, and P. Van de Putte. 1983. DNA inversions in the chromosome of Escherichia coli and in bacteriophage Mu: relationship to other site-specific recombination systems. Proc. Natl. Acad. Sci. USA 80: 5355-5358.
35. Poelarends, G. J., M. Wilkens, M. J. Larkin, J. D. Van Elsas, and D. B. Janssen. 1998. Degradation of 1,3-dichloropropene by Pseudomonas cichorii 170. Appl. Environ. Microbiol. 64:2931-2936.
36. Poelarends, G. J., J. E. T. van Hylckama Vlieg, J. R. Marchesi, L. M. Freitas dos Santos, and D. B. Janssen. 1999. Degradation of 1,2-dibromoethane by Mycobacterium sp. strain GP1. J. Bacteriol. 181:2050-2058.
37. Reid, M. F., and C. A. Fewson. 1994. Molecular characterization of microbial alcohol dehydrogenases. Crit. Rev. Microbiol. 20:13-56.
38. 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.
39. Staskawicz, B., D. Dahlbeck, N. Keen, and C. Napoli. 1987. Molecular characterization of cloned avirulence genes from race 0 and race 1 of Pseudomonas syringae pv. glycinea. J. Bacteriol. 169:5789-5794.
40. Stokes, H. W., and R. M. Hall. 1989. A novel family of potentially mobile DNA elements encoding site-specific gene-integration functions: integrons. Mol. Microbiol. 3:1669-1683.
41. Thompson, J. D., D. G. Higgens, 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.
42. Tschäpe, H. 1994. The spread of plasmids as a function of bacterial adaptability. FEMS Microbiol. Ecol. 15:23-32.
43. Van der Waarde, J. J, R. Kok, and D. B. Janssen. 1991. Degradation of 2-chloroallyl alcohol by a Pseudomonas sp. Appl. Environ. Microbiol. 59: 528-535.
44. Verhagen, C., E. Smit, D. B. Janssen, and J. D. Van Elsas. 1995. Bacterial dichloropropene degradation in soil; screening of soils and involvement of plasmids carrying the dhlA gene. Soil Biol. Biochem. 27:1547-1557.
45. Waki, M., T. Nihira, and Y. Yamada. 1997. Cloning and characterization of the gene (farA) encoding the receptor for an extracellular regulatory factor (IM-2) from Streptomyces sp. strain FRI-5. J. Bacteriol. 179:5131-5137.
46. Willuhn, J., H. P. Schmitt-Wrede, A. Otto, and F. Wunderlich. 1996. Cadmium-detoxification in the earthworm Enchytraeus: specific expression of a putative aldehyde dehydrogenase. Biochem. Biophys. Res. Commun. 226: 128-134.
47. Wyndham, R. C, A. E. Cashore, C. H. Nakatsu, and M. C. Peel. 1994. Cataholic transposons. Biodegradation 5:323-342.
48. Xia, X., A. R. W. Smith, and I. J. Brace. 1996. Identification and sequencing of a novel insertion sequence, IS1471, in Burkholderia cepacia strain 2a. FEMS Microbiol. Lett. 144:203-206.
49. Yanisch-Perron, C., J. Vieira, and J. Messing. 1985. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33:103-109.
50. Yu, F., T. Nakamura, W. Mizunashi, and I. Watanabe. 1994. Cloning of two halohydrin halogen-halide lyase genes from Corynebacterium sp. strain N-1074 and structural comparison of the genes and gene products. Biosci. Biotechnol. Biochem. 58:1451-1457.
51. Zieg, J., and M. Simon. 1980. Analysis of the nucleotide sequence of an invertable controlling element. Proc. Natl. Acad. Sci. USA 77:4196-4200.