Cloning and characterization of the genes encoding enzymes for the protocatechuate Meta-degradation pathway of Pseudomonas ochraceae NGJ1

Bioscience, Biotechnology and Biochemistry

Volumn 68, Issue 7, 2004, Pages 1434-1441

  Maruyama, Kiyofumi ^a   Shibayama, Tomohiko ^a   Ichikawa, Aki ^a   Sakou, Yukari ^a   Yamada, Satsue ^a   Sugisaki, Hiroyuki ^b  

^a GIFU UNIVERSITY   (Japan)

^b KYOTO UNIVERSITY   (Japan)

Author keywords

2 pyrone 4,6 dicarboxylate; Protocatechuate 4,5 dioxygenase; Protocatechuate meta degradation operon

Indexed keywords

CLONING; DEGRADATION; DNA; ENZYMES; ESCHERICHIA COLI; PURIFICATION;

META-DEGRADATION; PLASMIDS; TERMINATOR SEQUENCES; TRANSCRIPTION;

GENES;

2 HYDROXY 4 CARBOXYMUCCONATE 6 SEMIALDEHYDE DEHYDROGENASE; 2-HYDROXY-4-CARBOXYMUCCONATE-6-SEMIALDEHYDE DEHYDROGENASE; ALDEHYDE DEHYDROGENASE; BACTERIAL DNA; DIOXYGENASE; HYDROXYBENZOIC ACID DERIVATIVE; PROTOCATECHUATE 4,5 DIOXYGENASE; PROTOCATECHUATE 4,5-DIOXYGENASE; PROTOCATECHUIC ACID; RECOMBINANT PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CHEMISTRY; DNA SEQUENCE; ENZYMOLOGY; ESCHERICHIA COLI; GENETICS; METABOLISM; MOLECULAR CLONING; MOLECULAR GENETICS; MOLECULAR WEIGHT; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; OPERON; PSEUDOMONAS; SEQUENCE ANALYSIS; SITE DIRECTED MUTAGENESIS;

ALDEHYDE OXIDOREDUCTASES; AMINO ACID SEQUENCE; BASE SEQUENCE; CLONING, MOLECULAR; DIOXYGENASES; DNA, BACTERIAL; ESCHERICHIA COLI; HYDROXYBENZOIC ACIDS; MOLECULAR SEQUENCE DATA; MOLECULAR WEIGHT; MUTAGENESIS, SITE-DIRECTED; OPEN READING FRAMES; OPERON; PSEUDOMONAS; RECOMBINANT PROTEINS; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, PROTEIN;

ESCHERICHIA COLI; PROKARYOTA; PSEUDOMONAS; PSEUDOMONAS STRAMINEA;

EID: 11244352142     PISSN: 09168451     EISSN: None     Source Type: Journal    
DOI: 10.1271/bbb.68.1434     Document Type: Article

References (43)

1. Pujar, B. G., and Ribbons, D. W., Phthalate metabolism in Pseudomonas fluorescens PHK: purification and properties of 4,5-dihydroxyphthalate decarboxylase. Appl. Environ. Microbiol., 49, 374-376 (1985).
2. Schläfli, H. R., Weiss, M. A., Leisinger, T., and Cook, A. M., Terephthalate 1,2-dioxygenase system from Comamonas testosteroni T-2: purification and some properties of the oxygenase component. J. Bacteriol., 176, 6644-6652 (1994).
3. Wattiau, P., Bastiaens, L., van Herwijnen, R., Daal, L., Parsons, J. R., Renard, M.-E., Springael, D., and Cornelis, G. R., Fluorene degradation by Sphingomonas sp. LB126 proceeds through protocatechuic acid: a genetic analysis. Res. Microbiol., 152, 861-872 (2001).
4. Michalover, J. L., and Ribbons, D. W., 3-Hydroxybenzoate 4-hydroxylase from Pseudomonas testosteroni. Biochem. Biophys. Res. Commun., 55, 888-896 (1973).
5. Howell, L. G., Spector, T., and Massey, V., Purification and properties of p-hydroxybenzoate hydroxylase from Pseudomonas fluorescens. J. Biol. Chem., 247, 4340-4350 (1972).
6. Nadeau, L. J., and Spain, J. C., Bacterial degradation of m-nitrobenzoic acid. Appl. Environ. Microbiol., 61, 840-843 (1995).
7. Hughes, M. A., and Williams, P. A., Cloning and characterization of the pnb genes, encoding enzymes for 4-nitrobenzoate catabolism in Pseudomonas putida TW3. J. Bacteriol., 183, 1225-1232 (2001).
8. Providenti, M. A., and Wyndham, R. C., Identification and functional characterization of CbaR, a MarR-like modulator of the cbaABC-encoded chlorobenzoate catabolism pathway. Appl. Environ. Microbiol., 67, 3530-3541 (2001).
9. Locher, H. H., Leisinger, T., and Cook, A. M., 4-Sulphobenzoate 3,4-dioxygenase: purification and properties of a desulphonative two-component enzyme system from Comamonas testosteroni T-2. Biochem. J., 274, 833-842 (1991).
10. Sutherland, J. B., Crawford, D. L., and Pometto, A. L. 3rd., Metabolism of cinnamic, p-coumaric, and ferulic acids by Streptomyces setonii. Can. J. Microbiol., 29, 1253-1257 (1983).
11. Arciero, D. M., Orville, A. M., and Lipscomb, J. D., Protocatechuate 4,5-dioxygenase from Pseudomonas testosteroni. Methods Enzymol., 188, 89-95 (1990).
12. Maruyama, K., Ariga, N., Tsuda, M., and Deguchi, K., Purification and properties of α-hydroxy-γ-carboxymuconic ε-semialdehyde dehydrogenase. J. Biochem., 83, 1125-1134 (1978).
13. Maruyama, K., Isolation and identification of the reaction product of α-hydroxy-γ-carboxymuconic ε-semialdehyde dehydrogenase. J. Biochem., 86, 1671-1677 (1979).
14. Kersten, P. J., Dagley, S., Wittaker, J. W., Arciero, D. M., and Lipscomb, J. D., 2-Pyrone-4,6-dicarboxylic acid, a catabolite of gallic acids in Pseudomonas species. J. Bacteriol., 152, 1154-1162 (1982).
15. Maruyama, K., Purification and properties of 2-pyrone-4,6-dicarboxylate hydrolase. J. Biochem., 93, 557-565 (1983).
16. Maruyama, K., Purification and properties of γ-oxalomesaconate hydratase from Pseudomonas ochraceae grown with phthalate. Biochem. Biophys. Res. Commun., 128, 271-277 (1985).
17. Tack, B. F., Chapman, P. J., and Dagley, S., Purification and properties of 4-hydroxy-4-methyl-2-oxoglutarate aldolase. J. Biol. Chem., 247, 6444-6449 (1972).
18. Maruyama, K., Purification and properties of 4-hydroxy-4-methyl-2- oxoglutarate aldolase from Pseudomonas ochraceae grown on phthalate. J. Biochem., 108, 327-333 (1990).
19. Maruyama, K., Miwa, M., Tsujii, N., Nagai, T., Tomita, N., Harada, T., Sobajima, H., and Sugisaki, H., Cloning, sequencing and expression of the gene encoding 4-hydroxy-4-methy-2-oxoglutarate aldolase from Pseudomonas ochraceae NGJ1. Biosci. Biotechnol. Biochem., 65, 2701-2709 (2001).
20. Noda, Y., Nishikawa, S., Shiozuka, K., Kadokura, H., Nakajima, H., Yoda, K., Katayama, Y., Morohoshi, N., Haraguchi, T., and Yamasaki, M., Molecular cloning of the protocatechuate 4,5-dioxygenase genes of Pseudomonas paucimobilis. J. Bacteriol., 172, 2704-2709 (1990).
21. Nishikawa, S., Katayama, Y., Masai, E., Hanashiro, K., Yamasaki, M., and Morohoshi, N., Cloning of the gene cluster involved in protocatechuate meta-cleavage pathway. In "Proceedings of the 6th International Symposium on Wood and Pulping Chemistry" 2nd ed., pp. 311-313 (1991).
22. Masai, E., Shinohara, S., Hara, H., Nishikawa, S., Katayama, Y., and Fukuda, M., Genetic and biochemical characterization of a 2-pyrone-4,6- dicarboxylic acid hydrolase involved in the protocatechuate 4,5-cleavage pathway of Sphingomonas paucimobilis SYK-6. J. Bacteriol., 181, 55-62 (1999).
23. Masai, E., Momose, K., Hara, H., Nishikawa, S., Katayama, Y., and Fukuda, M., Genetic and biochemical characterization of 4-carboxy-2-hydroxymuconate-6- semialdehyde dehydrogenase and its role in the protocatechuate 4,5-cleavage pathway in Sphingomonas paucimobilis SYK-6. J. Bacteriol., 182, 6651-6658 (2000).
24. Hara, H., Masai, E., Katayama, Y., and Fukuda, M., The 4-oxalomesaconate hydratase gene, involved in the protocatechuate 4,5-cleavage pathway, is essential to vanillate and syringate degradation in Sphingomonas paucimobilis SYK-6. J. Bacteriol., 182, 6950-6957 (2000).
25. Hara, H., Masai, E., Miyauchi, K., Katayama, Y., and Fukuda, M., Characterization of the 4-carboxy-4-hydroxy-2-oxoadipate aldolase gene and operon structure of the protocatechuate 4,5-cleavage pathway genes in Sphingomonas paucimobilis SYK-6. J. Bacteriol., 183, 41-50 (2003).
26. Providenti, M. A., Mampel, J., MacSween, S., Cook, A. M., and Wyndham, R. C., Comamonas testosteroni BR6020 possesses a single genetic locus for extradiol cleavage of protocatechuate. Microbiol., 147, 2157-2167 (2001).
27. Eaton, R. W., Plasmid-encoded phthalate catabolic pathway in Arthrobacter keyseri 12B. J. Bacteriol., 183, 3689-3703 (2001).
28. Hashimoto-Gotoh, T., Mizuno, T., Ogasahara, Y., and Nakagawa, M., An oligodeoxyribonucleotide-directed dual amber method for site-directed mutagenesis. Gene, 152, 271-275 (1995).
29. Sambrook, J., Fritsch, E. F., and Maniatis, T., Molecular cloning: a laboratory manual, 2nd ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1989).
30. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acid Res., 25, 3389-3402 (1997).
31. Pearson, W. R., and Lipman, D. J., Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. U.S.A., 85, 2444-2448 (1988).
32. Andrews, P., Determination of molecular weight of proteins. Biochem. J., 91, 222-233 (1964).
33. Laemmli, U. K., Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature (London), 227, 680-685 (1970).
34. Lowry, O. H., Rosebrough, N. J., Farr, A. L., and Randall, R. J., Protein measurement with the Folin phenol reagent. J. Biol. Chem., 193, 265-275 (1951).
35. Bennett, T. P., Membrane filtration for determining protein in the presence of interfering substances. Nature, 18, 1131-1132 (1967).
36. Shine, J., and Dalgarno, L., The 3′-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc. Natl. Acad. Sci. U.S.A., 71, 1342-1346 (1974).
37. Ollis, D. L., Cheah, E., Cygler, M., Dijkstra, B., Frolow, F., Franken, S. M., Harel, M., Remington, S. J., Silman, I., Schrag, J., Sussman, J. L., Verschueren, K. H. G., and Goldman, A., The α/β hydrolase fold. Protein Eng., 5, 197-211 (1992).
38. c and PBAD, in the L-Arabinose regulatory region of Escherichia coli. Proc. Natl. Acad. Sci. U.S.A., 78, 752-756 (1981).
39. Saraste, M., Sibbald, P. R., and Wittinghofer, A., The p-loop - a common motif in ATP- and GTP-binding proteins. Trends Biochem. Sci., 15, 430-434 (1990).
40. Sugimoto, K., Aoshima, H., Senda, T., Masai, E., Fukuda, M., and Mitsui, Y., Purification and crystallization of a protocatechuate 4,5-dioxygenase LigAB from Sphingomonas paucimobilis SYK-6. Protein Peptide Lett., 6, 55-58 (1999).
41. Wierenga, R. K., and Hol, W. G. J., Predicted nucleotide-binding properties of p21 protein and its cancer-associated variant. Nature, 302, 842-844 (1983).
42. Brinkmann, U., Mattes, R. E., and Buckel, P., High-level expression of recombinant genes in Escherichia coli is dependent on the availability of the dnaY gene product. Gene, 85, 109-114 (1989).
43. Sugimoto, K., Senda, T., Aoshima, H., Masai, E., Fukuda, M., and Mitsui, Y., Crystal structure of an aromatic ring opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, under aerobic conditions. Structure, 1, 953-965 (1999).