Characterization of Sphingomonas paucimobilis SYK-6 genes involved in degradation of lignin-related compounds

Journal of Industrial Microbiology and Biotechnology

Volumn 23, Issue 4-5, 1999, Pages 364-373

  Masai, E ^a   Katayama, Y ^b   Nishikawa, S ^c   Fukuda, M ^a  

^a NAGAOKA UNIVERSITY OF TECHNOLOGY   (Japan)

^b TOKYO UNIVERSITY OF AGRICULTURE AND TECHNOLOGY   (Japan)

^c New Products and Technology Laboratory   (Japan)

Author keywords

Biphenyl degradation; Lignin degradation; O demethylation; Protocatechuate 4,5 cleavage pathway; Sphingomonas paucimobilis; aryl ether cleavage

Indexed keywords

BIPHENYL DERIVATIVE; ETHER DERIVATIVE; GLUTATHIONE PEROXIDASE; GLUTATHIONE TRANSFERASE; HYDROGEN; LIGNIN; OXYGENASE; VANILLIC ACID;

AMINO ACID SEQUENCE; ARTICLE; CATABOLISM; DEGRADATION; DEMETHYLATION; ENZYME MECHANISM; ENZYME MODIFICATION; GENE DISRUPTION; NONHUMAN; NUCLEOTIDE SEQUENCE; SPHINGOMONAS PAUCIMOBILIS;

NEGIBACTERIA; PROKARYOTA; SPHINGOMONAS PAUCIMOBILIS;

EID: 0033383704     PISSN: 13675435     EISSN: None     Source Type: Journal    
DOI: 10.1038/sj.jim.2900747     Document Type: Article

References (64)

1. 1 Asturias JA, LD Eltis, M Prucha and KN Timmis. 1994. Analysis of three 2,3-dihydroxybiphenyl 1,2-dioxygenases found in Rhodococcus globerulus P6. Identification of a new family of extradiol dioxygenases. J Biol Chem 269: 7807-7815.
2. 2 Bader R and T Leisinger. 1994. Isolation and characterization of the Methylophilus sp strain DM11 gene encoding dichloromethane dehalogenase/glutathione S-transferase. J Bacteriol 176: 3466-3473.
3. 3 Barnes MR, WA Duetz and PA Williams. 1997. A 3-(3-hydroxyphenyl) propionic acid catabolic pathway in Rhodococcus globerulus PWD1: cloning and characterization of the hpp operon. J Bacteriol 179: 6145-6153.
4. 4 Blocki FA, LBM Ellis and LP Wackett. 1993. MIF proteins are theta-class glutathione S-transferase homologs. Protein Sci 2: 2095-2102.
5. 5 Board PG, M Coggan, MCJ Wilce and MW Parker. 1995. Evidence for an essential serine residue in the active site of the theta class glutathione transferases. Biochem J 311: 247-250.
6. 6 Brunel F and J Davison. 1988. Cloning and sequencing of Pseudomonas genes encoding vanillate demethylase. J Bacteriol 170: 4924-4930.
7. 7 Cullen D. 1997. Recent advances on the molecular genetics of lignolytic fungi. J Biotechnol 53: 273-289.
8. 8 Dirr H, P Reinemer and R Huber. 1994. Refined crystal structure of porcine class Pi glutathione S-transferase (pGST P1-1) at 2.1 resolution. J Mol Biol 243: 72-92.
9. 9 Donnelly MI and S Dagley. 1981. Bacterial degradation of 3,4,5-trimethoxycinnamic acid with production of methanol. J Bacteriol 147: 471-476.
10. 10 Eltis LD and JT Bolin. 1996. Evolutionary relationships among extradiol dioxygenases. J Bacteriol 178: 5930-5937.
11. 11 Han S, LD Eltis, KN Timmis, SW Muchmore and JT Bolin. 1995. Crystal structure of the biphenyl-cleaving extradiol dioxygenase from a PCB-degrading pseudomonad. Science 270: 976-980.
12. 12 Harayama S, M Rekik, K-L Ngai and LN Ornston. 1989. 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 171: 6251-6258.
13. 13 Harwood CS and RE Parales. 1996. The β-ketoadipate pathway and the biology of self-identity. Annu Rev Microbiol 50: 553-590.
14. 14 Itzhaki H and WR Woodson. 1993. Characterization of an ethylene-responsive glutathione S-transferase gene cluster in carnation. Plant Mol Biol 22: 43-58.
15. 15 Ji X, P Zhang, RN Armstrong and GL Gilliland. 1992. The three-dimensional structure of a glutathione S-transferase from the mu gene class. Structural analysis of the binary complex of isozyme 3-3 and glutathione at 2.2-Å resolution. Biochemistry 31: 10169-10184.
16. 16 Ji X, EC von Rosenvinge, WW Johnson, SL Tomarev, J Piatigorsky, RN Armstrong and GL Gilliland. 1995. Three-dimensional structure, catalytic properties, and evolution of a sigma class glutathione transferase from squid, a progenitor of the lens S-crystallins of cephalopods. Biochemistry 34: 5317-5328.
17. 17 Kabisch M and P Fortnagel. 1990. Nucleotide sequence of metapyrocatechase I (catechol 2,3-oxygenase I) gene mpcI from Alcaligenes eutrophus JMP222. Nucleic Acids Res 18: 3405-3406.
18. 18 Kamoda S and Y Saburi. 1993. Cloning, expression, and sequence analysis of a lignostilbene-α,β-dioxygenase gene from Pseudomonas paucimobilis TMY 1009. Biosci Biotechnol Biochem 57: 926-930.
19. 19 Kamoda S and Y Saburi. 1995. Cloning of a lignostilbene-α,β-dioxygenase isozyme gene from Pseudomonas paucimobilis TMY 1009. Biosci Biotechnol Biochem 59: 1866-1868.
20. 20 Katayama Y, S Nishikawa, A Murayama, M Yamasaki, N Morohoshi and T Haraguchi. 1988. The metabolism of biphenyl structures in lignin by the soil bacterium (Pseudomonas paucimobilis SYK-6). FEBS Lett 233: 129-133.
21. 21 Katayama Y, S Nishikawa, M Nakamura, K Yano, M Yamasaki, N Morohoshi and T Haraguchi. 1987. Cloning and expression of Pseudomonas paucimobilis SYK-6 genes involved in the degradation of vanillate and protocatechuate in P. putida. Mokuzai Gakkaishi 33: 77-79.
22. 22 Kaufmann F, G Wohlfarth and G Diekert. 1998. O-demethylase from Acetobacterium dehalogenans. Substrate specificity and function of the participating proteins. Eur J Biochem 253: 706-711.
23. 23 Kersten PJ, S Dagley, JW Whittaker, DM Arciero and JD Lipscomb. 1982. 2-pyrone-4,6-dicarboxylate, a catabolite of gallates in Pseudomonas species. J Bacteriol. 152: 1154-1162.
24. 24 Kulakov LA, VA Delcroix, MJ Larkin, VN Ksenzenko and AN Kulakova. 1998. Cloning of new Rhodococcus extradiol dioxygenase genes and study of their distribution in different Rhodococcus strains. Microbiology 144: 955-963.
25. 25 Laurie AD and G Lloyd-Jones. 1999. The phn genes of Burkholderia sp strain RP007 constitute a divergent gene cluster for polycyclic aromatic hydrocarbon catabolism. J Bacteriol 181: 531-540.
26. 26 Lovell CR, A Prazybyla and LG Ljungdahl. 1990. Primary structure of thermostable formyltetrahydrofolate synthetase from Clostridium thermoaceticum. Biochemistry 29: 5687-5694.
27. 27 Maruyama K. 1979. Isolation and identification of the reaction product of α-hydroxy-γ-carboxymuconic-∈-semialdehyde dehydrogenase. J Biochem 86: 1671-1677.
28. 28 Maruyama K. 1983. Purification and properties of 2-pyrone-4,6-dicarboxylate hydrolase. J Biochem 93: 557-565.
29. 29 Maruyama K. 1985. Purification and properties of γ-oxalmesaconate hydratase from Pseudomonas ochraceae grown with phthalate. J Biochem 93: 567-574.
30. 30 Maruyama K. 1990. Purification and properties of 4-hydroxy-4-methyl-2-oxo-glutarate aldolase from Pseudomonas ochraceae grown on phthalate. J Biochem 108: 327-333.
31. 31 Maruyama K, N Ariga, M Tsuda and K Deguchi. 1978. Purification and properties of α-hydroxy-γ-carboxymuconic-∈-semialdehyde dehydrogenase. J Biochem 83: 1125-1134.
32. 32 Masai E, Y Katayama, S Kawai, S Nishikawa, M Yamasaki and N Morohoshi. 1991. Cloning and sequencing of the gene for a Pseudomonas paucimobilis enzyme that cleaves β-aryl ether. J Bacteriol 173: 7950-7955.
33. 33 Masai E, Y Katayama, S Kubota, S Kawai, M Yamasaki and N Morohoshi. 1993. A bacterial enzyme degrading the model lignin compound β-etherase is a member of the glutathione-S-transferase superfamily. FEBS Lett 323: 135-140.
34. 34 Masai E, Y Katayama, S Nishikawa, M Yamasaki, N Morohoshi and T Haraguchi. 1989. Detection and localization of a new enzyme catalyzing the β-aryl ether cleavage in the soil bacterium (Pseudomonas paucimobilis SYK-6). FEBS Lett 249: 348-352.
35. 35 Masai E, S Kubota, Y Katayama, S Kawai, M Yamasaki and N Morohoshi. 1993. Characterization of the Cα-dehydrogenase gene involved in the cleavage of β-aryl ether by Pseudomonas paucimobilis SYK-6. Biosci Biotech Biochem 57: 1655-1659.
36. 36 Masai E, S Shinohara, H Hara, S Nishikawa, Y Katayama and M Fukuda. 1999. 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.
37. 37 Nishida M, S Harada, S Noguchi, Y Satow, H Inoue and K Takahashi. 1998. Three-dimensional structure of Escherichia coli glutathione S-transferase complexed with glutathione sulfonate: catalytic roles of Cys10 and His106. J Mol Biol 281: 135-147.
38. 38 Nishikawa S, Y Katayama, M Yamasaki, N Morohoshi and T Haraguchi. 1991. Cloning of the genes involved in protocatechuate meta-cleavage pathway. In: Proceedings of the 6th International Symposium on Wood and Pulping Chemistry, 2nd edn, pp 311-313.
39. 39 Nishikawa S, T Sonoki, T Kasahara, T Obi, S Kubota, S Kawai, N Morohoshi and Y Katayama. 1998. Cloning and sequencing of the Sphingomonas (Pseudomonas) paucimobilis gene essential for the O demethylation of vanillate and syringate. Appl Environ Microbiol 64: 836-842.
40. 40 Noda Y, S Nishikawa, K Shiozuka, H Kadokura, H Nakajima, K Yoda, Y Katayama, N Morohoshi, T Haraguchi and M Yamasaki. 1990. Molecular cloning of the protocatechuate 4,5-dioxygenase gene of Pseudomonas paucimobilis. J Bacteriol 172: 2704-2709.
41. 41 Orser CS, J Dutton, CC Lange, PE Jablonski, L Xun and M Hargis. 1993. Characterization of a Flavobacterium glutathione S-transferase gene involved reductive dechlorination. J Bacteriol 175: 2640-2644.
42. 42 Peng X, T Egashira, K Hanashiro, E Masai, S Nishikawa, Y Katayama, K Kimbara and M Fukuda. 1998. Cloning of a Sphingomonas paucimobilis SYK-6 gene encoding a novel oxygenase that cleaves lignin-related biphenyl and characterization of the enzyme. Appl Environ Microbiol 64: 2520-2527.
43. 43 Peng X, E Masai, Y Katayama and M Fukuda. 1999. Characterization of the meta-cleavage compound hydrolase gene involved in degradation of the lignin-related biphenyl structure by Sphingomonas paucimobilis SYK-6. Appl Environ Microbiol 65: 2789-2793.
44. 44 Powlowski J, L Sahlman and V Shingler. 1993. Purification and properties of the physically associated meta-cleavage pathway enzymes 4-hydroxy-2-ketovalerate aldolase and aldehyde dehydrogenase (acylating) from Pseudomonas sp strain CF600. J Bacteriol 175: 377-385.
45. 45 Priefert H, J Rabenhorst and A Steinbuchel. 1997. Molecular characterization of genes of Pseudomonas sp strain HR199 involved in bioconversion of vanillin to protocatechuate. J Bacteriol 179: 2595-2607.
46. 46 Rankin CA, GC Haslam and RH Himes. 1993. Sequence and expression of the gene for N10-formyltetrahydrofolate synthetase from Clostridium cylindrosporum. Protein Sci 2: 197-205.
47. 47 Reinemer P, L Prade, P Hof, T Neueffind, R Huber, R Zettl, K Palme, J Schell, I Koelln, HD Bartunik and B Bieseler. 1996. Three-dimensional structure of glutathione S-transferase from Arabidopsis thaliana at 2.2-Å resolution: structural characterization of herbicide-conjugating plant glutathione S-transferases and a novel active site architecture. J Mol Biol 255: 289-309.
48. 48 Sato S, N Ouchiyama, T Kimura, H Nojiri, H Yamane and T Omori. 1997. Cloning of genes involved in carbazole degradation of Pseudomonas sp strain CA10: nucleotide sequences of genes and characterization of meta-cleavage enzymes and hydrolase. J Bacteriol 179: 4841-4849.
49. 49 Senda T, K Sugiyama, H Narita, T Yamamoto, K Kimbara, M Fukuda, M Sato, K Yano and Y Mitsui. 1996. Three-dimensional structures of free form and two substrate complexes of an extradiol ring-cleavage type dioxygenase, the BphC enzyme from Pseudomonas sp strain KKS102. J Mol Biol 255: 735-752.
50. 50 Shigehara K, C Seki, N Okamura, M Matsumoto, Y Katayama and S Nishikawa. 1998. Synthesis of polymers with 2H-pyran-2-one-4,6-dicarboxylate (PDC). Nuclei Polymer Preprints, Japan. English edition 47: 415.
51. 51 Sinning I, GJ Kleywegt, SW Cowan, P Reinemer, HW Dirr, R Huber, GL Gilliland, RN Armstrong. X Ji, PG Board, B Olin, B Mannervik and TA Jones. 1993. Structure determination and refinement of human alpha class glutathione transferase A1-1, and a comparison with the Mu and Pi class enzymes. J Mol Biol 232: 192-212.
52. 52 Spence EL, M Kawamukai, J Sanvoisin, H Braven and TD Bugg. 1996. Catechol dioxygenases from Escherichia coli (MhpB) and Alcaligenes eutrophus (MpcI): sequence analysis and biochemical properties of a third family of extradiol dioxygenases. J Bacteriol 178: 5249-5256.
53. 53 Sugimoto K, T Senda, H Aoshima, E Masai, M Fukuda and Y Mitsui. 1999. Crystal structure of an aromatic-ring-opening dioxygenase LigAB which is a protocatechuate 4,5-dioxygenase. Structure Fold Des 15: 953-965.
54. 54 Tack BF, PJ Chapman and S Dagley. 1972. Purification and properties of 4-hydroxy-4-methyl-2-oxoglutarate aldolase. J Biol Chem 247: 6444-6449.
55. 55 van der Zaal EJ, FNJ Droog, CJM Boot, LAM Hensgens, JHC Hoge, RA Schilperoort and KR Libbenga. 1991. Promoters of auxin-induced genes from tobacco can lead to auxin-inducible and root tip-specific expression. Plant Mol Biol 16: 983-998.
56. 56 Vicña R. 1988. Bacterial degradation of lignin. Enzyme Microb Technol 10: 646-655.
57. 57 Vuilleumier S. 1997. Bacterial glutathione S-transferase: what are they good for? J Bacteriol 179: 1431-1441.
58. 58 Vuilleumier S and T Leisinger. 1996. Protein engineering studies of dichloromethane dehalogenase/glutathione S-transferase from Methylophilus sp strain DM11. Ser12 but not Tyr6 is required for enzyme activity. Eur J Biochem 239: 410-417.
59. 59 Werwath J, HA Arfmann, DH Pieper, KN Timmis and RM Wittich. 1998. Biochemical and genetic characterisation of a gentisate 1,2-dioxygenase from Sphingomonas sp strain RW5. J Bacteriol 180: 4171-4176.
60. 1-tetrahydrofolate synthase from Saccharomyces cerevisiae. J Bacteriol 170: 3255-3261.
61. 61 Wilce MCJ, PG Board, SC Feil and MW Parker. 1995. Crystal structure of a theta-class glutathione transferase. EMBO J 14: 2133-2143.
62. 62 Wilce MCJ and MW Parker. 1994. Structure and function of glutathione S-transferases. Biochim Biophys Acta 1205: 1-18.
63. 63 Wolgel SA, JE Dege, PE Perkins-Olson, CH Jaurez-Garcia, RL Crawford, E Munck and JD Lipscomb. 1993. Purification and characterization of protocatechuate 2,3-dioxygenase from Bacillus macerans: a new extradiol catecholic dioxygenase. J Bacteriol 175: 4414-4426.
64. 64 Zimmermann W. 1990. Degradation of lignin by bacteria. J Biotechnol 13: 119-130.