Complete nucleotide sequence and evolutionary significance of a chromosomally encoded naphthalene-degradation lower pathway from Pseudomonas stutzeri AN10

Gene

Volumn 245, Issue 1, 2000, Pages 65-74

  Bosch, Rafael ^a,b   García Valdés, Elena ^a   Moore, Edward R B ^b  

^a UNIVERSITAT DE LES ILLES BALEARS   (Spain)

^b Bereich Mikrobiologie   (Germany)

Author keywords

Accelerated evolution; Catabolic pathway evolution; Recombination

Indexed keywords

NAPHTHALENE;

ARTICLE; BIODEGRADATION; CATABOLISM; CODON USAGE; DNA SEQUENCE; EVOLUTION; GENETIC RECOMBINATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; PRIORITY JOURNAL; PSEUDOMONAS STUTZERI; SEQUENCE ANALYSIS;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BASE SEQUENCE; CHROMOSOME MAPPING; CHROMOSOMES, BACTERIAL; CLONING, MOLECULAR; DNA, BACTERIAL; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, BACTERIAL; MOLECULAR SEQUENCE DATA; NAPHTHALENES; OPERON; PROMOTER REGIONS (GENETICS); PSEUDOMONAS; SALICYLATES; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION FACTORS;

PROKARYOTA; PSEUDOMONAS; PSEUDOMONAS PUTIDA; PSEUDOMONAS STUTZERI;

EID: 0343485080     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(00)00038-X     Document Type: Article

References (30)

1. Aemprapa S., Williams P.A. Implications of the xylQ gene of TOL plasmid pWW102 for the evolution of aromatic catabolic pathways. Microbiology. 144:1998;1387-1396.
2. Assinder S.J.de, Marco P., Osborne D.J., Poh C.L., Shaw E., Winson M.K., Williams P.A. A comparison of the multiple alleles of xylS carried by TOL plasmids pWW53 and pDK1 and its implications for their evolutionary relationship. J. Gen. Microbiol. 139:1993;557-568.
3. Benjamin R.C., Voss J.A., Kunz D.A. Nucleotide sequence of xylE from the TOL pDK1 plasmid and structural comparison with isofunctional catechol-2,3-dioxygenase genes from TOL pWW0 and NAH7. J. Bacteriol. 173:1991;2724-2728.
4. Bosch R., García-Valdés E. Tn3685, a novel composite transposable element carrying the nahW gene of Pseudomonas stutzeri AN10. Microbiology. 2000;. submitted.
5. Bosch R., García-Valdés E., Moore E.R.B. Genetic characterization and evolutionary implications of a chromosomally encoded naphthalene-degradation upper pathway from Pseudomonas stutzeri AN10. Gene. 236:1999;149-157.
6. Bosch R., Moore E.R.B., García-Valdés E., Pieper D.H. NahW, a novel, inducible salicylate hydroxylase involved in mineralization of naphthalene by Pseudomonas stutzeri AN10. J. Bacteriol. 181:1999;2315-2322.
7. Eaton R.W., Selifonova O.V., Gedney R.M. Isopropylbenzene catabolic pathway in Pseudomonas putida RE204: nucleotide sequence analysis of the ipb operon and neighboring DNA from pRE4. Biodegradation. 9:1998;119-132.
8. Favaro R., Bernasconi C., Passini N., Bertoni G., Bestetti G., Galli E., Dehò G. Organisation of the tmb catabolic operons of Pseudomonas putida TMB and evolutionary relationship with the xyl operons of the TOL plasmid pWW0. Gene. 182:1996;189-193.
9. García-Valdés E., Cozar E., Lalucat J., Rotger R. Molecular cloning of aromatic degradative genes from Pseudomonas stutzeri. FEMS Microbiol. Lett. 61:1989;301-306.
10. Goethals K.M., VanMontagu M., Holsters M. Conserved motifs in a divergent nod box of Azorhizobium caulinodans ORS571 reveal a common structure in promoters regulated by LysR- type proteins. Proc. Natl. Acad. Sci. USA. 89:1992;1646-1650.
11. Grimm A.C., Harwood C.S. NahY, a catabolic plasmid-encoded receptor required for chemotaxis of Pseudomonas putida to the aromatic hydrocarbon naphthalene. J. Bacteriol. 181:1999;3310-3316.
12. Hanahan D. Studies on transformation of Escherichia coli with plasmids. J. Mol. Biol. 166:1983;557-580.
13. Harayama S., Rekik M. The meta cleavage operon of TOL plasmid pWW0 comprises 13 genes. Mol. Gen. Genet. 221:1990;113-120.
14. Harayama S., Rekik M., Wubbolts M., Rose K., Leppik R.A., Timmis K.N. Characterization of five genes in the upper-pathway operon of TOL plasmid pWW0 from Pseudomonas putida and identification of the gene products. J. Bacteriol. 171:1989;5048-5055.
15. Harayama S., Rekik M., Bairoch A., Neidle E.L., Ornston L.N. Potential DNA slippage structures acquired during evolutionary divergence of Acinetobacter calcoaceticus chromosomal benABC and Pseudomonas putida TOL pWW0 plasmid xylXYZ, genes encoding benzoate dioxygenases. J. Bacteriol. 173:1991;7540-7548.
16. Harayama S. Codon usage patterns suggest independent evolution of two catabolic operons on toluene-degradative plasmid TOL pWW0 of Pseudomonas putida. J. Mol. Evol. 38:1994;328-335.
17. Inouye S., Nakazawa A., Nakazawa T. Nucleotide sequence of the regulatory gene xylR of the TOL plasmid from Pseudomonas putida. Gene. 66:1988;301-306.
18. Ramos-González M.I., Ramos-Díaz M.A., Ramos J.L. Chromosomal gene capture mediated by the Pseudomonas putida TOL catabolic plasmid. J. Bacteriol. 176:1994;4635-4641.
19. Reddy B.R., Shaw L.E., Sayers J.R., Williams P.A. Two identical copies of IS1246 a 1275-bp sequence related to other bacterial insertion sequences enclose the xyl genes on TOL plasmid pWW0. Microbiology. 140:1994;2305-2307.
20. Rossello R., García-Valdés E., Lalucat J., Ursing J. Genotypic and phenotypic diversity of Pseudomonas stutzeri. System. Appl. Microbiol. 14:1991;150-157.
21. Rosselló-Mora R.A., Lalucat J., García-Valdés E. Comparative biochemical and genetic analysis of naphthalene degradation among Pseudomonas stutzeri strains. Appl. Environ. Microbiol. 60:1994;966-972.
22. Sambrook J., Fritsch E.F., Maniatis T. Molecular Cloning: A Laboratory Manual. second ed. 1989;Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
23. Schell M.A. Transcriptional control of the nah and sal hydrocarbon-degradation operons by the nahR gene product. Gene. 36:1985;301-309.
24. Schell M.A. Homology between nucleotide sequences of promoter regions of nah and sal operons of NAH7 plasmid of Pseudomonas putida. Proc. Natl. Acad. Sci. USA. 83:1986;369-373.
25. Schell M.A., Wender P.E. Identification of the nahR gene product and nucleotide sequences required for its activation of the sal operon. J. Bacteriol. 166:1986;9-14.
26. Shingler V., Powlowski J., Marklund U. Nucleotide sequence and functional analysis of the complete phenol/3,4-dimethylphenol catabolic pathway of Pseudomonas sp. strain CF600. J. Bacteriol. 174:1992;711-724.
27. van der Meer J.R., de Vos W.M., Harayama S., Zehnder A.J.B. Molecular mechanisms of genetic adaptation to xenobiotic compounds. Microbiol. Rev. 56:1992;677-694.
28. Williams P.A., Assinder S.J.de, Marco P.O, Donell K.J., Poh C.L., Shaw L.E., Winson M.K. Catabolic gene duplications in TOL plasmids. Galli E., Silver S., Witholt B. Pseudomonas. Molecular Biology and Biotechnology. 1992;341-352 American Society for Microbiology, Washington, DC.
29. Williams P.A., Sayers J.R. The evolution of pathways for aromatic hydrocarbon oxidation in Pseudomonas. Biodegradation. 5:1994;195-217.
30. Wyndham R.C., Cashore A.E., Nakatsu C.H., Peel M.C. Catabolic transposons. Biodegradation. 5:1994;323-342.