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. 1997 Jan;179(2):370–381. doi: 10.1128/jb.179.2.370-381.1997

Characterization of catechol catabolic genes from Rhodococcus erythropolis 1CP.

D Eulberg 1, L A Golovleva 1, M Schlömann 1
PMCID: PMC178706  PMID: 8990288

Abstract

The biochemical characterization of the muconate and the chloromuconate cycloisomerases of the chlorophenol-utilizing Rhodococcus erythropolis strain 1CP previously indicated that efficient chloromuconate conversion among the gram-positive bacteria might have evolved independently of that among gram-negative bacteria. Based on sequences of the N terminus and of tryptic peptides of the muconate cycloisomerase, a fragment of the corresponding gene has now been amplified and used as a probe for the cloning of catechol catabolic genes from R. erythropolis. The clone thus obtained expressed catechol 1,2-dioxygenase, muconate cycloisomerase, and muconolactone isomerase activities. Sequencing of the insert on the recombinant plasmid pRER1 revealed that the genes are transcribed in the order catA catB catC. Open reading frames downstream of catC may have a function in carbohydrate metabolism. The predicted protein sequence of the catechol 1,2-dioxygenase was identical to the one from Arthrobacter sp. strain mA3 in 59% of the positions. The chlorocatechol 1,2-dioxygenases and the chloromuconate cycloisomerases of gram-negative bacteria appear to be more closely related to the catechol 1,2-dioxygenases and muconate cycloisomerases of the gram-positive strains than to the corresponding enzymes of gram-negative bacteria.

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Selected References

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  1. Aldrich T. L., Chakrabarty A. M. Transcriptional regulation, nucleotide sequence, and localization of the promoter of the catBC operon in Pseudomonas putida. J Bacteriol. 1988 Mar;170(3):1297–1304. doi: 10.1128/jb.170.3.1297-1304.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Amy P. S., Schulke J. W., Frazier L. M., Seidler R. J. Characterization of aquatic bacteria and cloning of genes specifying partial degradation of 2,4-dichlorophenoxyacetic acid. Appl Environ Microbiol. 1985 May;49(5):1237–1245. doi: 10.1128/aem.49.5.1237-1245.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Babbitt P. C., Mrachko G. T., Hasson M. S., Huisman G. W., Kolter R., Ringe D., Petsko G. A., Kenyon G. L., Gerlt J. A. A functionally diverse enzyme superfamily that abstracts the alpha protons of carboxylic acids. Science. 1995 Feb 24;267(5201):1159–1161. doi: 10.1126/science.7855594. [DOI] [PubMed] [Google Scholar]
  4. Bradford M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 1976 May 7;72:248–254. doi: 10.1006/abio.1976.9999. [DOI] [PubMed] [Google Scholar]
  5. Chung C. T., Niemela S. L., Miller R. H. One-step preparation of competent Escherichia coli: transformation and storage of bacterial cells in the same solution. Proc Natl Acad Sci U S A. 1989 Apr;86(7):2172–2175. doi: 10.1073/pnas.86.7.2172. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Dorn E., Hellwig M., Reineke W., Knackmuss H. J. Isolation and characterization of a 3-chlorobenzoate degrading pseudomonad. Arch Microbiol. 1974;99(1):61–70. doi: 10.1007/BF00696222. [DOI] [PubMed] [Google Scholar]
  7. Dorn E., Knackmuss H. J. Chemical structure and biodegradability of halogenated aromatic compounds. Substituent effects on 1,2-dioxygenation of catechol. Biochem J. 1978 Jul 15;174(1):85–94. doi: 10.1042/bj1740085. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Eck R., Belter J. Cloning and characterization of a gene coding for the catechol 1,2-dioxygenase of Arthrobacter sp. mA3. Gene. 1993 Jan 15;123(1):87–92. doi: 10.1016/0378-1119(93)90544-d. [DOI] [PubMed] [Google Scholar]
  9. Ehrt S., Schirmer F., Hillen W. Genetic organization, nucleotide sequence and regulation of expression of genes encoding phenol hydroxylase and catechol 1,2-dioxygenase in Acinetobacter calcoaceticus NCIB8250. Mol Microbiol. 1995 Oct;18(1):13–20. doi: 10.1111/j.1365-2958.1995.mmi_18010013.x. [DOI] [PubMed] [Google Scholar]
  10. Frantz B., Chakrabarty A. M. Organization and nucleotide sequence determination of a gene cluster involved in 3-chlorocatechol degradation. Proc Natl Acad Sci U S A. 1987 Jul;84(13):4460–4464. doi: 10.1073/pnas.84.13.4460. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Fulthorpe R. R., McGowan C., Maltseva O. V., Holben W. E., Tiedje J. M. 2,4-Dichlorophenoxyacetic acid-degrading bacteria contain mosaics of catabolic genes. Appl Environ Microbiol. 1995 Sep;61(9):3274–3281. doi: 10.1128/aem.61.9.3274-3281.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Hammer A., Hildenbrand T., Hoier H., Ngai K. L., Schlömann M., Stezowski J. J. Crystallization and preliminary X-ray data of chloromuconate cycloisomerase from Alcaligenes eutrophus JMP134 (pJP4). J Mol Biol. 1993 Jul 5;232(1):305–307. doi: 10.1006/jmbi.1993.1385. [DOI] [PubMed] [Google Scholar]
  13. Hart S., Kirby R., Woods D. R. Structure of a Rhodococcus gene encoding pigment production in Escherichia coli. J Gen Microbiol. 1990 Jul;136(7):1357–1363. doi: 10.1099/00221287-136-7-1357. [DOI] [PubMed] [Google Scholar]
  14. Hartnett C., Neidle E. L., Ngai K. L., Ornston L. N. DNA sequences of genes encoding Acinetobacter calcoaceticus protocatechuate 3,4-dioxygenase: evidence indicating shuffling of genes and of DNA sequences within genes during their evolutionary divergence. J Bacteriol. 1990 Feb;172(2):956–966. doi: 10.1128/jb.172.2.956-966.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Helin S., Kahn P. C., Guha B. L., Mallows D. G., Goldman A. The refined X-ray structure of muconate lactonizing enzyme from Pseudomonas putida PRS2000 at 1.85 A resolution. J Mol Biol. 1995 Dec 15;254(5):918–941. doi: 10.1006/jmbi.1995.0666. [DOI] [PubMed] [Google Scholar]
  16. Higgins D. G., Sharp P. M. Fast and sensitive multiple sequence alignments on a microcomputer. Comput Appl Biosci. 1989 Apr;5(2):151–153. doi: 10.1093/bioinformatics/5.2.151. [DOI] [PubMed] [Google Scholar]
  17. Hoier H., Schlömann M., Hammer A., Glusker J. P., Carrell H. L., Goldman A., Stezowski J. J., Heinemann U. Crystal structure of chloromuconate cycloisomerase from Alcaligenes eutrophus JMP134 (pJP4) at 3 A resolution. Acta Crystallogr D Biol Crystallogr. 1994 Jan 1;50(Pt 1):75–84. doi: 10.1107/S090744499300900X. [DOI] [PubMed] [Google Scholar]
  18. Holben W. E., Schroeter B. M., Calabrese V. G., Olsen R. H., Kukor J. K., Biederbeck V. O., Smith A. E., Tiedje J. M. Gene probe analysis of soil microbial populations selected by amendment with 2,4-dichlorophenoxyacetic acid. Appl Environ Microbiol. 1992 Dec;58(12):3941–3948. doi: 10.1128/aem.58.12.3941-3948.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Houghton J. E., Brown T. M., Appel A. J., Hughes E. J., Ornston L. N. Discontinuities in the evolution of Pseudomonas putida cat genes. J Bacteriol. 1995 Jan;177(2):401–412. doi: 10.1128/jb.177.2.401-412.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Ikehata O., Nishiyama M., Horinouchi S., Beppu T. Primary structure of nitrile hydratase deduced from the nucleotide sequence of a Rhodococcus species and its expression in Escherichia coli. Eur J Biochem. 1989 May 15;181(3):563–570. doi: 10.1111/j.1432-1033.1989.tb14761.x. [DOI] [PubMed] [Google Scholar]
  21. Inoue H., Nojima H., Okayama H. High efficiency transformation of Escherichia coli with plasmids. Gene. 1990 Nov 30;96(1):23–28. doi: 10.1016/0378-1119(90)90336-p. [DOI] [PubMed] [Google Scholar]
  22. Ka J. O., Holben W. E., Tiedje J. M. Genetic and phenotypic diversity of 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacteria isolated from 2,4-D-treated field soils. Appl Environ Microbiol. 1994 Apr;60(4):1106–1115. doi: 10.1128/aem.60.4.1106-1115.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Kaschabek S. R., Reineke W. Maleylacetate reductase of Pseudomonas sp. strain B13: dechlorination of chloromaleylacetates, metabolites in the degradation of chloroaromatic compounds. Arch Microbiol. 1992;158(6):412–417. doi: 10.1007/BF00276301. [DOI] [PubMed] [Google Scholar]
  24. Katti S. K., Katz B. A., Wyckoff H. W. Crystal structure of muconolactone isomerase at 3.3 A resolution. J Mol Biol. 1989 Feb 5;205(3):557–571. doi: 10.1016/0022-2836(89)90226-x. [DOI] [PubMed] [Google Scholar]
  25. Kivisaar M., Kasak L., Nurk A. Sequence of the plasmid-encoded catechol 1,2-dioxygenase-expressing gene, pheB, of phenol-degrading Pseudomonas sp. strain EST1001. Gene. 1991 Feb 1;98(1):15–20. doi: 10.1016/0378-1119(91)90098-v. [DOI] [PubMed] [Google Scholar]
  26. Kukor J. J., Olsen R. H., Ballou D. P. Cloning and expression of the catA and catBC gene clusters from Pseudomonas aeruginosa PAO. J Bacteriol. 1988 Oct;170(10):4458–4465. doi: 10.1128/jb.170.10.4458-4465.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. doi: 10.1038/227680a0. [DOI] [PubMed] [Google Scholar]
  28. Lee S. Y., Rasheed S. A simple procedure for maximum yield of high-quality plasmid DNA. Biotechniques. 1990 Dec;9(6):676–679. [PubMed] [Google Scholar]
  29. Marchuk D., Drumm M., Saulino A., Collins F. S. Construction of T-vectors, a rapid and general system for direct cloning of unmodified PCR products. Nucleic Acids Res. 1991 Mar 11;19(5):1154–1154. doi: 10.1093/nar/19.5.1154. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Matsudaira P. Limited N-terminal sequence analysis. Methods Enzymol. 1990;182:602–613. doi: 10.1016/0076-6879(90)82047-6. [DOI] [PubMed] [Google Scholar]
  31. Merril C. R., Goldman D., Sedman S. A., Ebert M. H. Ultrasensitive stain for proteins in polyacrylamide gels shows regional variation in cerebrospinal fluid proteins. Science. 1981 Mar 27;211(4489):1437–1438. doi: 10.1126/science.6162199. [DOI] [PubMed] [Google Scholar]
  32. Nakai C., Horiike K., Kuramitsu S., Kagamiyama H., Nozaki M. Three isozymes of catechol 1,2-dioxygenase (pyrocatechase), alpha alpha, alpha beta, and beta beta, from Pseudomonas arvilla C-1. J Biol Chem. 1990 Jan 15;265(2):660–665. [PubMed] [Google Scholar]
  33. Nakai C., Uyeyama H., Kagamiyama H., Nakazawa T., Inouye S., Kishi F., Nakazawa A., Nozaki M. Cloning, DNA sequencing, and amino acid sequencing of catechol 1,2-dioxygenases (pyrocatechase) from Pseudomonas putida mt-2 and Pseudomonas arvilla C-1. Arch Biochem Biophys. 1995 Aug 20;321(2):353–362. doi: 10.1006/abbi.1995.1405. [DOI] [PubMed] [Google Scholar]
  34. Neidle E. L., Hartnett C., Bonitz S., Ornston L. N. DNA sequence of the Acinetobacter calcoaceticus catechol 1,2-dioxygenase I structural gene catA: evidence for evolutionary divergence of intradiol dioxygenases by acquisition of DNA sequence repetitions. J Bacteriol. 1988 Oct;170(10):4874–4880. doi: 10.1128/jb.170.10.4874-4880.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Ornston L. N. The conversion of catechol and protocatechuate to beta-ketoadipate by Pseudomonas putida. 3. Enzymes of the catechol pathway. J Biol Chem. 1966 Aug 25;241(16):3795–3799. [PubMed] [Google Scholar]
  36. Ornston L. N. The conversion of catechol and protocatechuate to beta-ketoadipate by Pseudomonas putida. II. Enzymes of the protocatechuate pathway. J Biol Chem. 1966 Aug 25;241(16):3787–3794. [PubMed] [Google Scholar]
  37. Pearson W. R., Lipman D. J. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444–2448. doi: 10.1073/pnas.85.8.2444. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Perkins E. J., Gordon M. P., Caceres O., Lurquin P. F. Organization and sequence analysis of the 2,4-dichlorophenol hydroxylase and dichlorocatechol oxidative operons of plasmid pJP4. J Bacteriol. 1990 May;172(5):2351–2359. doi: 10.1128/jb.172.5.2351-2359.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Romero-Arroyo C. E., Schell M. A., Gaines G. L., 3rd, Neidle E. L. catM encodes a LysR-type transcriptional activator regulating catechol degradation in Acinetobacter calcoaceticus. J Bacteriol. 1995 Oct;177(20):5891–5898. doi: 10.1128/jb.177.20.5891-5898.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Schlömann M. Evolution of chlorocatechol catabolic pathways. Conclusions to be drawn from comparisons of lactone hydrolases. Biodegradation. 1994 Dec;5(3-4):301–321. doi: 10.1007/BF00696467. [DOI] [PubMed] [Google Scholar]
  42. Schlömann M., Schmidt E., Knackmuss H. J. Different types of dienelactone hydrolase in 4-fluorobenzoate-utilizing bacteria. J Bacteriol. 1990 Sep;172(9):5112–5118. doi: 10.1128/jb.172.9.5112-5118.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Schmidt E., Knackmuss H. J. Chemical structure and biodegradability of halogenated aromatic compounds. Conversion of chlorinated muconic acids into maleoylacetic acid. Biochem J. 1980 Oct 15;192(1):339–347. doi: 10.1042/bj1920339. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Scopes R. K. Measurement of protein by spectrophotometry at 205 nm. Anal Biochem. 1974 May;59(1):277–282. doi: 10.1016/0003-2697(74)90034-7. [DOI] [PubMed] [Google Scholar]
  45. Shanley M. S., Harrison A., Parales R. E., Kowalchuk G., Mitchell D. J., Ornston L. N. Unusual G + C content and codon usage in catIJF, a segment of the ben-cat supra-operonic cluster in the Acinetobacter calcoaceticus chromosome. Gene. 1994 Jan 28;138(1-2):59–65. doi: 10.1016/0378-1119(94)90783-8. [DOI] [PubMed] [Google Scholar]
  46. Solyanikova I. P., Maltseva O. V., Vollmer M. D., Golovleva L. A., Schlömann M. Characterization of muconate and chloromuconate cycloisomerase from Rhodococcus erythropolis 1CP: indications for functionally convergent evolution among bacterial cycloisomerases. J Bacteriol. 1995 May;177(10):2821–2826. doi: 10.1128/jb.177.10.2821-2826.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Stanier R. Y., Ornston L. N. The beta-ketoadipate pathway. Adv Microb Physiol. 1973;9(0):89–151. [PubMed] [Google Scholar]
  48. Top E. M., Holben W. E., Forney L. J. Characterization of diverse 2,4-dichlorophenoxyacetic acid-degradative plasmids isolated from soil by complementation. Appl Environ Microbiol. 1995 May;61(5):1691–1698. doi: 10.1128/aem.61.5.1691-1698.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Tsou A. Y., Ransom S. C., Gerlt J. A., Buechter D. D., Babbitt P. C., Kenyon G. L. Mandelate pathway of Pseudomonas putida: sequence relationships involving mandelate racemase, (S)-mandelate dehydrogenase, and benzoylformate decarboxylase and expression of benzoylformate decarboxylase in Escherichia coli. Biochemistry. 1990 Oct 23;29(42):9856–9862. doi: 10.1021/bi00494a015. [DOI] [PubMed] [Google Scholar]
  50. Varadaraj K., Skinner D. M. Denaturants or cosolvents improve the specificity of PCR amplification of a G + C-rich DNA using genetically engineered DNA polymerases. Gene. 1994 Mar 11;140(1):1–5. doi: 10.1016/0378-1119(94)90723-4. [DOI] [PubMed] [Google Scholar]
  51. Vollmer M. D., Fischer P., Knackmuss H. J., Schlömann M. Inability of muconate cycloisomerases to cause dehalogenation during conversion of 2-chloro-cis,cis-muconate. J Bacteriol. 1994 Jul;176(14):4366–4375. doi: 10.1128/jb.176.14.4366-4375.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Vollmer M. D., Stadler-Fritzsche K., Schlömann M. Conversion of 2-chloromaleylacetate in Alcaligenes eutrophus JMP134. Arch Microbiol. 1993;159(2):182–188. doi: 10.1007/BF00250280. [DOI] [PubMed] [Google Scholar]
  53. van der Meer J. R., Eggen R. I., Zehnder A. J., de Vos W. M. Sequence analysis of the Pseudomonas sp. strain P51 tcb gene cluster, which encodes metabolism of chlorinated catechols: evidence for specialization of catechol 1,2-dioxygenases for chlorinated substrates. J Bacteriol. 1991 Apr;173(8):2425–2434. doi: 10.1128/jb.173.8.2425-2434.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]

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