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PMID: 8510667 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't

Comparison of the nucleotide sequences of the meta-cleavage pathway genes of TOL plasmid pWW0 from Pseudomonas putida with other meta-cleavage genes suggests that both single and multiple nucleotide substitutions contribute to enzyme evolution.

Molecular & general genetics : MGG ·Vol. 239 ·No. 1-2 ·1993-05-00 ·Pages 81-9

Harayama S, Rekik M

Abstract

TOL plasmid pWW0 from Pseudomonas putida mt-2 encodes catabolic enzymes required for the oxidation of toluene and xylenes. The structural genes for these catabolic enzymes are clustered into two operons, the xylCMABN operon, which encodes a set of enzymes required for the transformation of toluene/xylenes to benzoate/toluates, and the xylXYZLTEGFJQKIH operon, which encodes a set of enzymes required for the transformation of benzoate/toluates to Krebs cycle intermediates. The latter operon can be divided physically and functionally into two parts, the xylXYZL cluster, which is involved in the transformation of benzoate/toluates to (methyl)catechols, and the xylTEGFJQKIH cluster, which is involved in the transformation of (methyl)catechols to Krebs cycle intermediates. Genes isofunctional to xylXYZL are present in Acinetobacter calcoaceticus, and constitute a benzoate-degradative pathway, while xylTEGFJQKIH homologous encoding enzymes of a methylphenol-degradative pathway and a naphthalene-degradative pathway are present on plasmid pVI150 from P. putida CF600, and on plasmid NAH7 from P. putida PpG7, respectively. Comparison of the nucleotide sequences of the xylXYZLTEGFJQKIH genes with other isofunctional genes suggested that the xylTEGFJQKIH genes on the TOL plasmid diverged from these homologues 20 to 50 million years ago, while the xylXYZL genes diverged from the A. calcoaceticus homologues 100 to 200 million years ago. In codons where amino acids are not conserved, the substitutions rate in the third base was higher than that in synonymous codons. This result was interpreted as indicating that both single and multiple nucleotide substitutions contributed to the amino acid-substituting mutations, and hence to enzyme evolution. This observation seems to be general because mammalian globin genes exhibit the same tendency.

MeSH Terms
Amino Acid Sequence Base Sequence Biological Evolution DNA, Bacterial Genes, Bacterial Introns Molecular Sequence Data Operon Plasmids Pseudomonas putida/enzymology,genetics Toluene/metabolism Xylenes/metabolism
Chemicals
DNA, Bacterial Xylenes Toluene
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Harayama S
Department of Medical Biochemistry, University of Geneva, Switzerland.
Rekik M
References (39)
39 references, click to expand
  1. Molecular considerations in the evolution of bacterial genes.
    J Mol Evol. 1991 Sep;33(3):241-50 PMID: 1757995
  2. Theoretical foundations for a quantitative approach to paleogenetics. Part I: DNA.
    J Mol Evol. 1971;1(1):115-33 PMID: 5173651
  3. Plasmid gene organization: naphthalene/salicylate oxidation.
    Proc Natl Acad Sci U S A. 1982 Feb;79(3):874-8 PMID: 6278499
  4. The TOL plasmids: determinants of the catabolism of toluene and the xylenes.
    Adv Microb Physiol. 1990;31:1-69 PMID: 2264522
  5. Spontaneous mutation.
    Annu Rev Genet. 1991;25:125-46 PMID: 1812804
  6. Nucleotide sequences of the meta-cleavage pathway enzymes 2-hydroxymuconic semialdehyde dehydrogenase and 2-hydroxymuconic semialdehyde hydrolase from Pseudomonas CF600.
    Biochim Biophys Acta. 1990 Jun 21;1049(2):227-30 PMID: 2194577
  7. Molecular analysis of regulatory and structural xyl genes of the TOL plasmid pWW53-4.
    J Gen Microbiol. 1987 May;133(5):1149-58 PMID: 3309179
  8. The meta cleavage operon of TOL degradative plasmid pWW0 comprises 13 genes.
    Mol Gen Genet. 1990 Mar;221(1):113-20 PMID: 2183008
  9. DNA sequencing with chain-terminating inhibitors.
    Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463-7 PMID: 271968
  10. A constant rate of spontaneous mutation in DNA-based microbes.
    Proc Natl Acad Sci U S A. 1991 Aug 15;88(16):7160-4 PMID: 1831267
  11. Evolution in bacteria: evidence for a universal substitution rate in cellular genomes.
    J Mol Evol. 1987;26(1-2):74-86 PMID: 3125340
  12. The evolution of multigene families: human haptoglobin genes.
    Annu Rev Genet. 1986;20:81-108 PMID: 2880559
  13. Location and organization of the dimethylphenol catabolic genes of Pseudomonas CF600.
    Mol Gen Genet. 1990 Jan;220(2):294-300 PMID: 2325624
  14. 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. 1991 Apr;173(8):2724-8 PMID: 1672868
  15. DNA sequence determination of the TOL plasmid (pWWO) xylGFJ genes of Pseudomonas putida: implications for the evolution of aromatic catabolism.
    Mol Microbiol. 1991 Oct;5(10):2459-74 PMID: 1791759
  16. Metabolism of toluene and xylenes by Pseudomonas (putida (arvilla) mt-2: evidence for a new function of the TOL plasmid.
    J Bacteriol. 1975 Oct;124(1):7-13 PMID: 1176436
  17. The origin of mutants.
    Nature. 1988 Sep 8;335(6186):142-5 PMID: 3045565
  18. The presence of two complete homologous meta pathway operons on TOL plasmid pWW53.
    J Gen Microbiol. 1988 Nov;134(11):2965-75 PMID: 3076178
  19. 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. 1991 Dec;173(23):7540-8 PMID: 1938949
  20. Characterization of five genes in the upper-pathway operon of TOL plasmid pWW0 from Pseudomonas putida and identification of the gene products.
    J Bacteriol. 1989 Sep;171(9):5048-55 PMID: 2549010
  21. cis-diol dehydrogenases encoded by the TOL pWW0 plasmid xylL gene and the Acinetobacter calcoaceticus chromosomal benD gene are members of the short-chain alcohol dehydrogenase superfamily.
    Eur J Biochem. 1992 Feb 15;204(1):113-20 PMID: 1740120
  22. Construction of hybrid xylE genes between the two duplicate homologous genes from TOL plasmid pWW53: comparison of the kinetic properties of the gene products.
    J Gen Microbiol. 1990 Aug;136(8):1583-9 PMID: 2262792
  23. Complete nucleotide sequence and polypeptide analysis of multicomponent phenol hydroxylase from Pseudomonas sp. strain CF600.
    J Bacteriol. 1990 Dec;172(12):6826-33 PMID: 2254258
  24. Nucleotide sequence and expression of the catechol 2,3-dioxygenase-encoding gene of phenol-catabolizing Pseudomonas CF600.
    Gene. 1989 Dec 21;85(1):233-8 PMID: 2620833
  25. Nucleotide sequence and expression of gene nahH of plasmid NAH7 and homology with gene xylE of TOL pWWO.
    Gene. 1987;55(1):19-28 PMID: 3623105
  26. Complete nucleotide sequence of the metapyrocatechase gene on the TOI plasmid of Pseudomonas putida mt-2.
    J Biol Chem. 1983 Mar 10;258(5):2923-8 PMID: 6826546
  27. Nucleotide sequence analysis of the Pseudomonas putida PpG7 salicylate hydroxylase gene (nahG) and its 3'-flanking region.
    Biochemistry. 1991 Feb 12;30(6):1635-41 PMID: 1993181
  28. Evolutionary relationships between catabolic pathways for aromatics: conservation of gene order and nucleotide sequences of catechol oxidation genes of pWW0 and NAH7 plasmids.
    Mol Gen Genet. 1987 Dec;210(2):241-7 PMID: 3481421
  29. Directed evolution of a bacterial operon.
    Bioessays. 1990 Nov;12(11):551-8 PMID: 2085322
  30. Adaptive evolution that requires multiple spontaneous mutations: mutations involving base substitutions.
    Proc Natl Acad Sci U S A. 1991 Jul 1;88(13):5882-6 PMID: 2062865
  31. Nucleotide sequence divergence and functional constraint in mRNA evolution.
    Proc Natl Acad Sci U S A. 1980 Dec;77(12):7328-32 PMID: 6938980
  32. The use of fluorescein isothiocyanate in the determination of the bacterial biomass of grassland soil.
    Can J Microbiol. 1970 Feb;16(2):57-62 PMID: 4984775
  33. Physical and functional mapping of two cointegrate plasmids derived from RP4 and TOL plasmid pDK1.
    J Gen Microbiol. 1988 Sep;134(9):2463-74 PMID: 3076182
  34. Divergent evolution of chloroplast-type ferredoxins.
    FEBS Lett. 1991 Jul 8;285(1):85-8 PMID: 2065785
  35. Nucleotide sequence and functional analysis of the complete phenol/3,4-dimethylphenol catabolic pathway of Pseudomonas sp. strain CF600.
    J Bacteriol. 1992 Feb;174(3):711-24 PMID: 1732207
  36. Nucleotide sequences of the Acinetobacter calcoaceticus benABC genes for benzoate 1,2-dioxygenase reveal evolutionary relationships among multicomponent oxygenases.
    J Bacteriol. 1991 Sep;173(17):5385-95 PMID: 1885518
  37. Physically associated enzymes produce and metabolize 2-hydroxy-2,4-dienoate, a chemically unstable intermediate formed in catechol metabolism via meta cleavage in Pseudomonas putida.
    J Bacteriol. 1989 Nov;171(11):6251-8 PMID: 2681159
  38. Recent development of the neutral theory viewed from the Wrightian tradition of theoretical population genetics.
    Proc Natl Acad Sci U S A. 1991 Jul 15;88(14):5969-73 PMID: 2068072
  39. Fidelity mechanisms in DNA replication.
    Annu Rev Biochem. 1991;60:477-511 PMID: 1883202
Article Info
Journal
Molecular & general genetics : MGG
Abbr.
Mol Gen Genet
ISSN
0026-8925
DOI
10.1007/BF00281605
Published
1993-05-00
Pages
81-9
Language
English
Region
Germany
NLM ID
0125036
Subset
IM
Databases
GENBANK
M94186
External Links
PubMed source DOI: 10.1007/BF00281605
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