Aerobic Degradation of Aromatic Hydrocarbons

  • D. Pérez-Pantoja
  • B. González
  • Dietmar H. PieperEmail author
Reference work entry
Part of the Handbook of Hydrocarbon and Lipid Microbiology book series (HHLM)


Aromatic hydrocarbons are widely distributed in nature. They are found as lignin components, aromatic amino acids and xenobiotic compounds, among others. Microorganisms, mostly bacteria, degrade an impressive variety of such chemical structures. The major principle of aromatic hydrocarbon biodegradation is that a broad range of aromatic hydrocarbons are transformed by peripheral reactions to a restricted range of central intermediates, which are subject to ring-cleavage and funneling into the Krebs cycle. Key enzymes in aerobic aromatic degradation are oxygenases, preparing aromatics for ring-cleavage by the introduction of hydroxyl functions and catalyzing cleavage of the aromatic ring. The diverse monooxygenases and dioxygenases involved in hydroxylations, a significant proportion of them possessing relaxed substrate specificity, are discussed as well as the broad diversity of side chain processing transformations involved in the formation of ring-cleavage central intermediates. Ring cleavage dioxygenases, covering intradiol ring cleavage of ortho dihydroxylated intermediates, and a large number of diverse but mechanistically related extradiol dioxygenases participating in ring cleavage of ortho and para dihydroxylated intermediates are also discussed. CoA dependent aerobic routes to allow ring-cleavage of aromatic hydrocarbons without involvement of dihydroxylated aromatic intermediates have been described in the last years and are also reviewed. The degradation of heteroarenes will not be described in this chapter.


  1. Abe T, Masai E, Miyauchi K, Katayama Y, Fukuda M (2005) A tetrahydrofolate-dependent O-demethylase, LigM, is crucial for catabolism of vanillate and syringate in Sphingomonas paucimobilis SYK-6. J Bacteriol 187:2030–2037PubMedPubMedCentralCrossRefGoogle Scholar
  2. Altenschmidt U, Fuchs G (1992) Novel aerobic 2-aminobenzoate metabolism. Purification and characterization of 2-aminobenzoate-CoA ligase, localization of the genes on a 8-kbp plasmid, and cloning and sequencing of the genes from a denitrifying Pseudomonas sp. Eur J Biochem 205:721–727PubMedCrossRefGoogle Scholar
  3. Altenschmidt U, Oswald B, Steiner E, Herrmann H, Fuchs G (1993) New aerobic benzoate oxidation pathway via benzoyl-Coenzyme A and 3-hydroxybenzoyl-Coenzyme A in a denitrifying Pseudomonas sp. J Bacteriol 175:4851–4858PubMedPubMedCentralCrossRefGoogle Scholar
  4. Arias-Barrau E, Olivera ER, Luengo JM, Fernandez C, Galan B, Garcia JL, Diaz E, Minambres B (2004) The homogentisate pathway: a central catabolic pathway involved in the degradation of L-phenylalanine, L-tyrosine, and 3-hydroxyphenylacetate in Pseudomonas putida. J Bacteriol 186:5062–5077PubMedPubMedCentralCrossRefGoogle Scholar
  5. Arias-Barrau E, Sandoval A, Naharro G, Olivera ER, Luengo JM (2005) A two-component hydroxylase involved in the assimilation of 3-hydroxyphenylacetate in Pseudomonas putida. J Biol Chem 280:26435–26447PubMedCrossRefGoogle Scholar
  6. Armengaud J, Timmis KN, Wittich RM (1999) A functional 4-hydroxysalicylate/hydroxyquinol degradative pathway gene cluster is linked to the initial dibenzo-p-dioxin pathway genes in Sphingomonas sp strain RW1. J Bacteriol 181:3452–3461PubMedPubMedCentralGoogle Scholar
  7. Assinder SJ, Williams PA (1990) The TOL plasmids: determinants of the catabolism of toluene and the xylenes. Adv Microb Physiol 31:1–69PubMedCrossRefPubMedCentralGoogle Scholar
  8. Babbitt PC, Hasson MS, Wedekind JE, Palmer DRJ, Barrett WC, Reed GH, Rayment I, Ringe D, Kenyon GL, Gerlt JA (1996) The enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids. Biochemistry 35:16489–16501PubMedCrossRefPubMedCentralGoogle Scholar
  9. Bains J, Boulanger MJ (2007) Biochemical and structural characterization of the paralogous benzoate CoA ligases from Burkholderia xenovorans LB400: defining the entry point into the novel benzoate oxidation (box) pathway. J Mol Biol 373:965–977PubMedCrossRefPubMedCentralGoogle Scholar
  10. Ballou DP, Entsch B, Cole LJ (2005) Dynamics involved in catalysis by single-component and two-component flavin-dependent aromatic hydroxylases. Biochem Biophys Res Commun 338:590–598PubMedCrossRefGoogle Scholar
  11. Barnes MR, Duetz WA, Williams PA (1997) A 3-(3-hydroxyphenyl)propionic acid catabolic pathway in Rhodococcus globerulus PWD1: cloning and characterization of the hpp operon. J Bacteriol 179:6145–6153PubMedPubMedCentralCrossRefGoogle Scholar
  12. Batie CJ, LaHaie E, Ballou DP (1987) Purification and characterization of phthalate oxygenase and phthalate oxygenase reductase from Pseudomonas cepacia. J Biol Chem 262:1510–1518PubMedGoogle Scholar
  13. Beltrametti F, Marconi AM, Bestetti G, Colombo C, Galli E, Ruzzi M, Zennaro E (1997) Sequencing and functional analysis of styrene catabolism genes from Pseudomonas fluorescens ST. Appl Environ Microbiol 63:2232–2239PubMedPubMedCentralGoogle Scholar
  14. Bertoni G, Martino M, Galli E, Barbieri P (1998) Analysis of the gene cluster encoding toluene/o-xylene monooxygenase from Pseudomonas stutzeri OX1. Appl Environ Microbiol 64:3626–3632PubMedPubMedCentralGoogle Scholar
  15. Bosch R, Moore ERB, GarciaValdes E, Pieper DH (1999) NahW, a novel, inducible salicylate hydroxylase involved in mineralization of naphthalene by Pseudomonas stutzeri AN10. J Bacteriol 181:2315–2322PubMedPubMedCentralGoogle Scholar
  16. Bruce NC, Cain RB, Pieper DH, Engesser K-H (1989) Purification and characterization of 4-methylmuconolactone methyl-isomerase, a novel enzyme of the modified 3-oxoadipate pathway in nocardioform actionomycetes. Biochem J 262:303–312PubMedPubMedCentralCrossRefGoogle Scholar
  17. Buder R, Fuchs G (1989) 2-Aminobenzoyl-CoA monooxygenase/reductase, a novel type of flavoenzyme. Purification and some properties of the enzyme. Eur J Biochem 185:629–635PubMedCrossRefGoogle Scholar
  18. Bundy BM, Campbell AL, Neidle EL (1998) Similarities between the antABC-encoded anthranilate dioxygenase and the benABC-encoded benzoate dioxygenase of Acinetobacter sp. strain ADP1. J Bacteriol 180:4466–4474PubMedPubMedCentralGoogle Scholar
  19. Buswell JA, Ribbons DW (1988) Vanillate O-demethylase from Pseudomonas species. Methods Enzymol 161:294–301PubMedCrossRefPubMedCentralGoogle Scholar
  20. Cafaro V, Izzo V, Scognamiglio R, Notomista E, Capasso P, Casbarra A, Pucci P, Di Donato A (2004) Phenol hydroxylase and toluene/o-xylene monooxygenase from Pseudomonas stutzeri OX1: interplay between two enzymes. Appl Environ Microbiol 70:2211–2219PubMedPubMedCentralCrossRefGoogle Scholar
  21. Camara B, Bielecki P, Kaminski F, dos Santos VM, Plumeier I, Nikodem P, Pieper DH (2007) A gene cluster involved in degradation of substituted salicylates via ortho cleavage in Pseudomonas sp. strain MT1 encodes enzymes specifically adapted for transformation of 4-methylcatechol and 3-methylmuconate. J Bacteriol 189:1664–1674PubMedCrossRefPubMedCentralGoogle Scholar
  22. Catelani D, Fiecchi A, Galli E (1971) (+)-γ-Carboxymethyl-γ-methyl-Δα-butenolide. A 1,2 ring-fission product of 4-methylcatechol by Pseudomonas desmolyticum. Biochem J 121:89–92PubMedPubMedCentralCrossRefGoogle Scholar
  23. Cha CJ, Cain RB, Bruce NC (1998) The modified beta-ketoadipate pathway in Rhodococcus rhodochrous N75: enzymology of 3-methylmuconolactone metabolism. J Bacteriol 180:6668–6673PubMedPubMedCentralGoogle Scholar
  24. Chang HK, Zylstra GJ (1998) Novel organization of the genes for phthalate degradation from Burkholderia cepacia DBO1. J Bacteriol 180:6529–6537PubMedPubMedCentralGoogle Scholar
  25. Chang HK, Mohseni P, Zylstra GJ (2003) Characterization and regulation of the genes for a novel anthranilate 1,2-dioxygenase from Burkholderia cepacia DBO1. J Bacteriol 185:5871–5881PubMedPubMedCentralCrossRefGoogle Scholar
  26. Crawford RL (1976) Degradation of homogentisate by strains of Bacillus and Moraxella. Can J Microbiol 22:276–280PubMedCrossRefGoogle Scholar
  27. Crawford RL (1978) Hydroxylation of 4-hydroxyphenoxyacetate by a Bacillus sp. FEMS Microbiol Lett 4:233–234CrossRefGoogle Scholar
  28. Crawford RL, Frick TD (1977) Rapid spectrophotometric differentiation between glutathione-dependent and glutathione-independent gentisate and homogentisate pathways. Appl Environ Microbiol 34:170–174PubMedPubMedCentralGoogle Scholar
  29. Crawford RL, Hutton SW, Chapman PJ (1975) Purification and properties of gentisate 1,2-dioxygenase from Moraxella osloensis. J Bacteriol 121:794–799PubMedPubMedCentralGoogle Scholar
  30. Cronin CN, Kim J, Fuller JH, Zhang X, McIntire WS (1999) Organization and sequences of p-hydroxybenzaldehyde dehydrogenase and other plasmid-encoded genes for early enzymes of the p-cresol degradative pathway in Pseudomonas putida NCIMB 9866 and 9869. DNA Seq 10:7–17PubMedCrossRefGoogle Scholar
  31. Darby JM, Taylor DG, Hopper DJ (1987) Hydroquinone as a ring-fission substrate in the catabolism of 4-ethylphenol and 4-hydroxyacetophenone by Pseudomonas putida JD1. J Gen Microbiol 133:2137–2146Google Scholar
  32. DeFrank JJ, Ribbons DW (1976) The p-cymene pathway in Pseudomonas putida PL: isolation of a dihydrodiol accumulated by a mutant. Biochem Biophys Res Commun 70:1129–1135PubMedCrossRefGoogle Scholar
  33. Diaz E, Ferrandez A, Prieto MA, Garcia JL (2001) Biodegradation of aromatic compounds by Escherichia coli. Microbiol Mol Biol Rev 65:523–569PubMedPubMedCentralCrossRefGoogle Scholar
  34. Duarte M, Jauregui R, Vilchez-Vargas R, Junca H, Pieper DH (2014) AromaDeg, a novel database for phylogenomics of aerobic degradation of aromatics. Database 2014; bau118Google Scholar
  35. Dunwell JM, Khuri S, Gane PJ (2000) Microbial relatives of the seed storage proteins of higher plants: conservation of structure and diversification of function during evolution of the cupin superfamily. Microbiol Mol Biol Rev 64:153–179PubMedPubMedCentralCrossRefGoogle Scholar
  36. Eaton RW (1996) p-Cumate catabolic pathway in Pseudomonas putida F1: cloning and characterization of DNA carrying the cmt operon. J Bacteriol 178:1351–1362PubMedPubMedCentralCrossRefGoogle Scholar
  37. Eaton RW (1997) p-Cymene catabolic pathway in Pseudomonas putida F1: cloning and characterization of DNA encoding conversion of p-cymene to p-cumate. J Bacteriol 179:3171–3180PubMedPubMedCentralCrossRefGoogle Scholar
  38. Eaton RW (2001) Plasmid-encoded phthalate catabolic pathway in Arthrobacter keyseri 12B. J Bacteriol 183:3689–3703PubMedPubMedCentralCrossRefGoogle Scholar
  39. Eby DM, Beharry ZM, Coulter ED, Kurtz DM, Neidle EL (2001) Characterization and evolution of anthranilate 1,2-dioxygenase from Acinetobacter sp. strain ADP1. J Bacteriol 183:109–118PubMedPubMedCentralCrossRefGoogle Scholar
  40. Eltis LD, Bolin JT (1996) Evolutionary relationships among extradiol dioxygenases. J Bacteriol 178:5930–5937PubMedPubMedCentralCrossRefGoogle Scholar
  41. Entsch B, van Berkel WJ (1995) Structure and mechanism of para-hydroxybenzoate hydroxylase. FASEB J 9:476–483PubMedCrossRefGoogle Scholar
  42. Entsch B, Massey V, Claiborne A (1987) p-Hydroxybenzoate hydroxylase containing 6-hydroxy-FAD is an effective enzyme with modified reaction mechanisms. J Biol Chem 262:6060–6068PubMedGoogle Scholar
  43. Eulberg D, Golovleva LA, Schlomann M (1997) Characterization of catechol catabolic genes from Rhodococcus erythropolis 1CP. J Bacteriol 179:370–381PubMedPubMedCentralCrossRefGoogle Scholar
  44. Eulberg D, Lakner S, Golovleva LA, Schlomann M (1998) Characterization of a protocatechuate catabolic gene cluster from Rhodococcus opacus 1CP: evidence for a merged enzyme with 4-carboxymuconolactone-decarboxylating and 3-oxoadipate enol-lactone-hydrolyzing activity. J Bacteriol 180:1072–1081PubMedPubMedCentralGoogle Scholar
  45. Farrow JM, Pesci EC (2007) Two distinct pathways supply anthranilate as a precursor of the Pseudomonas quinolone signal. J Bacteriol 189:3425–3433PubMedPubMedCentralCrossRefGoogle Scholar
  46. Fernandez C, Ferrandez A, Minambres B, Diaz E, Garcia JL (2006) Genetic characterization of the phenylacetyl-coenzyme A oxygenase from the aerobic phenylacetic acid degradation pathway of Escherichia coli. Appl Environ Microbiol 72:7422–7426PubMedPubMedCentralCrossRefGoogle Scholar
  47. Ferrández A, Garciá JL, Díaz E (1997) Genetic characterization and expression in heterologous hosts of the 3-(3-hydroxyphenyl)propionate catabolic pathway of Escherichia coli K-12. J Bacteriol 179:2573–2581PubMedPubMedCentralCrossRefGoogle Scholar
  48. Ferrandez A, Minambres B, Garcia B, Olivera ER, Luengo JM, Garcia JL, Diaz E (1998) Catabolism of phenylacetic acid in Escherichia coli – Characterization of a new aerobic hybrid pathway. J Biol Chem 273:25974–25986PubMedCrossRefGoogle Scholar
  49. Ferraroni M, Seifert J, Travkin VM, Thiel M, Kaschabek S, Scozzafava A, Golovleva L, Schlomann M, Briganti F (2005) Crystal structure of the hydroxyquinol 1,2-dioxygenase from Nocardioides simplex 3E, a key enzyme involved in polychlorinated aromatics biodegradation. J Biol Chem 280:21144–21154PubMedCrossRefPubMedCentralGoogle Scholar
  50. Fishman A, Tao Y, Wood TK (2004) Toluene 3-monooxygenase of Ralstonia pickettii PKO1 is a para-hydroxylating enzyme. J Bacteriol 186:3117–3123PubMedPubMedCentralCrossRefGoogle Scholar
  51. Fishman A, Tao Y, Rui L, Wood TK (2005) Controlling the regiospecific oxidation of aromatics via active site engineering of toluene para-monooxygenase of Ralstonia pickettii PKO1. J Biol Chem 280:506–514PubMedCrossRefPubMedCentralGoogle Scholar
  52. Fitzpatrick PF (2003) Mechanism of aromatic amino acid hydroxylation. Biochemistry 42:14083–14091PubMedPubMedCentralCrossRefGoogle Scholar
  53. Fu WJ, Oriel P (1998) Gentisate 1,2-dioxygenase from Haloferax sp. D1227. Extremophiles 2:439–446PubMedCrossRefGoogle Scholar
  54. Fuenmayor SL, Wild M, Boyes AL, Williams PA (1998) A gene cluster encoding steps in conversion of naphthalene to gentisate in Pseudomonas sp. strain U2. J Bacteriol 180:2522–2530PubMedPubMedCentralGoogle Scholar
  55. Fujisawa H, Hayaishi O (1968) Protocatechuate 3,4-dioxygenase. I. Crystallization and characterization. J Biol Chem 243:2673–2681PubMedGoogle Scholar
  56. Fukumori F, Saint CP (1997) Nucleotide sequences and regulational analysis of genes involved in conversion of aniline to catechol in Pseudomonas putida UCC22(pTDN1). J Bacteriol 179:399–408PubMedPubMedCentralCrossRefGoogle Scholar
  57. Gasson MJ, Kitamura Y, McLauchlan WR, Narbad A, Parr AJ, Lindsay E, Parsons H, Payne J, Rhodes MJC, Walton NJ (1998) Metabolism of ferulic acid to vanillin – A bacterial gene of the enoyl-SCoA hydratase/isomerase superfamily encodes an enzyme for the hydration and cleavage of a hydroxycinnamic acid SCoA thioester. J Biol Chem 273:4163–4170PubMedCrossRefGoogle Scholar
  58. Gerlt JA, Babbitt PC (2001) Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies. Annu Rev Biochem 70:209–246PubMedCrossRefGoogle Scholar
  59. Gescher J, Eisenreich W, Worth J, Bacher A, Fuchs G (2005) Aerobic benzoyl-CoA catabolic pathway in Azoarcus evansii: studies on the non-oxygenolytic ring cleavage enzyme. Mol Microbiol 56:1586–1600PubMedCrossRefGoogle Scholar
  60. Gescher J, Ismail W, Olgeschlager E, Eisenreich W, Worth J, Fuchs G (2006) Aerobic benzoyl-coenzyme A (CoA) catabolic pathway in Azoarcus evansii: conversion of ring cleavage product by 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase. J Bacteriol 188:2919–2927PubMedPubMedCentralCrossRefGoogle Scholar
  61. Gibson DT, Parales RE (2000) Aromatic hydrocarbon dioxygenases in environmental biotechnology. Curr Opin Biotechnol 11:236–243PubMedCrossRefPubMedCentralGoogle Scholar
  62. Gibson DT, Koch JR, Kallio RE (1968) Oxidative degradation of aromatic hydrocarbons by microorganisms. 1. Enzymatic formation of catechol from benzene. Biochemistry 7:2653–2662PubMedCrossRefGoogle Scholar
  63. Gobel M, Kassel-Cati K, Schmidt E, Reineke W (2002) Degradation of aromatics and chloroaromatics by Pseudomonas sp. strain B13: cloning, characterization, and analysis of sequences encoding 3-oxoadipate: succinyl-coenzyme A (CoA) transferase and 3-oxoadipyl-CoA thiolase. J Bacteriol 184:216–223PubMedPubMedCentralCrossRefGoogle Scholar
  64. Gu W, Song J, Bonner CA, Xie G, Jensen RA (1998) PhhC is an essential aminotransferase for aromatic amino acid catabolism in Pseudomonas aeruginosa. Microbiology 144:3127–3134PubMedCrossRefGoogle Scholar
  65. Halak S, Basta T, Burger S, Contzen M, Wray V, Pieper DH, Stolz A (2007) 4-Sulfomuconolactone hydrolases from Hydrogenophaga intermedia S1 and Agrobacterium radiobacter S2. J Bacteriol 189:6998–7006PubMedPubMedCentralCrossRefGoogle Scholar
  66. Hara H, Masai E, Katayama Y, Fukuda M (2000) 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 182:6950–6957PubMedPubMedCentralCrossRefGoogle Scholar
  67. Harayama S, Rekik M (1989) Bacterial aromatic ring-cleavage enzymes are classified into two different gene families. J Biol Chem 264:15328–15333PubMedPubMedCentralGoogle Scholar
  68. Harayama S, Leppik RA, Rekik M, Mermod M, Lehrbach PR, Reineke W, Timmis KN (1986) Gene order of the TOL catabolic plasmid upper pathway operon and oxidation of both toluene and benzyl alcohol by the xylA product. J Bacteriol 167:455–461PubMedPubMedCentralCrossRefGoogle Scholar
  69. Harayama S, Mermod N, Rekik M, Lehrbach PR, Timmis KN (1987) Roles of the divergent branches of the meta-cleavage pathway in the degradation of benzoate and substituted benzoates. J Bacteriol 169:558–564PubMedPubMedCentralCrossRefGoogle Scholar
  70. Hareland WA, Crawford RL, Chapman PJ, Dagley S (1975) Metabolic function and properties of 4-hydroxyphenylacetic acid 1-hydroxylase from Pseudomonas acidovorans. J Bacteriol 121:272–285PubMedPubMedCentralGoogle Scholar
  71. Harpel MR, Lipscomb JD (1990) Gentisate 1,2-dioxygenase from Pseudomonas. Substrate coordination of the active site Fe2+ and mechanism of turnover. J Biol Chem 265:22187–22196PubMedGoogle Scholar
  72. Harwood CS, Parales RE (1996) The beta-ketoadipate pathway and the biology of self-identity. Annu Rev Microbiol 50:553–590PubMedCrossRefGoogle Scholar
  73. Hatta T, Mukerjee-Dhar G, Damborsky J, Kiyohara H, Kimbara K (2003) Characterization of a novel thermostable Mn(II)-dependent 2,3-dihydroxybiphenyl 1,2-dioxygenase from a polychlorinated biphenyl- and naphthalene-degrading Bacillus sp. JF8. J Biol Chem 278:21483–21492PubMedCrossRefPubMedCentralGoogle Scholar
  74. He ZG, Spain JC (1998) A novel 2-Aminomuconate deaminase in the nitrobenzene degradation pathway of Pseudomonas pseudoalcaligenes JS45. J Bacteriol 180:2502–2506PubMedPubMedCentralGoogle Scholar
  75. He ZQ, Davis JK, Spain JC (1998) Purification, characterization, and sequence analysis of 2-aminomuconic 6-semialdehyde dehydrogenase from Pseudomonas pseudoalcaligenes JS45. J Bacteriol 180:4591–4595PubMedPubMedCentralGoogle Scholar
  76. Hintner JP, Lechner C, Riegert U, Kuhm AE, Storm T, Reemtsma T, Stolz A (2001) Direct ring fission of salicylate by a salicylate 1,2- dioxygenase activity from Pseudaminobacter salicylatoxidans. J Bacteriol 183:6936–6942PubMedPubMedCentralCrossRefGoogle Scholar
  77. Hiromoto T, Fujiwara S, Hosokawa K, Yamaguchi H (2006) Crystal structure of 3-hydroxybenzoate hydroxylase from Comamonas testosteroni has a large tunnel for substrate and oxygen access to the active site. J Mol Biol 364:878–896PubMedCrossRefGoogle Scholar
  78. Hopper DJ (1976) The hydroxylation of p-cresol and its conversion to p-hydroxybenzaldehyde in Pseudomonas putida. Biochem Biophys Res Commun 69:462–468PubMedCrossRefGoogle Scholar
  79. Hopper D, Taylor DG (1977) The purification and properties of p-cresol-(acceptor) oxidoreductase (hydroxylating), a flavocytochrome from Pseudomonas putida. Biochem J 187:155–162CrossRefGoogle Scholar
  80. Hopper D, Chapman PJ, Dagley S (1971) The enzymatic degradation of alkyl-substituted gentisates, maleates and malates. Biochem J 122:29–40PubMedPubMedCentralCrossRefGoogle Scholar
  81. Huang Y, Zhao KX, Shen XH, Chaudhry MT, Jiang CY, Liu SJ (2006) Genetic characterization of the resorcinol catabolic pathway in Corynebacterium glutamicum. Appl Environ Microbiol 72:7238–7245PubMedPubMedCentralCrossRefGoogle Scholar
  82. Hugo N, Armengaud J, Gaillard J, Timmis KN, Jouanneau Y (1998) A novel [2Fe-2S] ferredoxin from Pseudomonas putida mt-2 promotes the reductive reactivation of catechol 2,3-dioxygenase. J Biol Chem 273:9622–9629PubMedCrossRefPubMedCentralGoogle Scholar
  83. Ishiyama D, Vujaklija D, Davies J (2004) Novel pathway of salicylate degradation by Streptomyces sp. strain WA46. Appl Environ Microbiol 70:1297–1306PubMedPubMedCentralCrossRefGoogle Scholar
  84. Ismail W, El-Said Mohamed M, Wanner BL, Datsenko KA, Eisenreich W, Rohdich F, Bacher A, Fuchs G (2003) Functional genomics by NMR spectroscopy. Phenylacetate catabolism in Escherichia coli. Eur J Biochem 270:3047–3054PubMedCrossRefGoogle Scholar
  85. Iwabuchi T, Harayama S (1998) Biochemical and molecular characterization of 1-hydroxy-2-naphthoate dioxygenase from Nocardioides sp. KP7. J Biol Chem 273:8332–8336PubMedCrossRefPubMedCentralGoogle Scholar
  86. Jouanneau Y, Micoud J, Meyer C (2007) Purification and characterization of a three-component salicylate 1-hydroxylase from Sphingomonas sp. strain CHY-1. Appl Environ Microbiol 73:7515–7521PubMedPubMedCentralCrossRefGoogle Scholar
  87. Karlson U, Dwyer DF, Hooper SW, Moore ERB, Timmis KN, Eltis LD (1993) Two independently regulated cytochromes P-450 in a Rhodococcus rhodochrous strain that degrades 2-ethoxyphenol and 4-methoxybenzoate. J Bacteriol 175:1467–1474PubMedPubMedCentralCrossRefGoogle Scholar
  88. Kasai D, Masai E, Miyauchi K, Katayama Y, Fukuda M (2004) Characterization of the 3- O-methylgallate dioxygenase gene and evidence of multiple 3- O-methylgallate catabolic pathways in Sphingomonas paucimobilis SYK-6. J Bacteriol 186:4951–4959PubMedPubMedCentralCrossRefGoogle Scholar
  89. Kasai D, Masai E, Miyauchi K, Katayama Y, Fukuda M (2005) Characterization of the gallate dioxygenase gene: three distinct ring cleavage dioxygenases are involved in syringate degradation by Sphingomonas paucimobilis SYK-6. J Bacteriol 187:5067–5074PubMedPubMedCentralCrossRefGoogle Scholar
  90. Keat MJ, Hopper DJ (1978) p-Cresol and 3,5-xylenol methylhydroxylases in Pseudomonas putida N.C.I.B. 9869. Biochem J 175:649–658PubMedPubMedCentralCrossRefGoogle Scholar
  91. Kirk TK, Farrell RL (1987) Enzymatic “combustion”: the microbial degradation of lignin. Annu Rev Microbiol 41:465–505PubMedCrossRefGoogle Scholar
  92. Kurnasov O, Jablonski L, Polanuyer B, Dorrestein P, Begley T, Osterman A (2003a) Aerobic tryptophan degradation pathway in bacteria: novel kynurenine formamidase. FEMS Microbiol Lett 227:219–227PubMedCrossRefGoogle Scholar
  93. Kurnasov O, Goral V, Colabroy K, Gerdes S, Anantha S, Osterman A, Begley TP (2003b) NAD biosynthesis: identification of the tryptophan to quinolinate pathway in bacteria. Chem Biol 10:1195–1204PubMedCrossRefGoogle Scholar
  94. Lam WWY, Bugg TDH (1997) Purification, characterization, and stereochemical analysis of a C-C hydrolase: 2-hydroxy-6-keto-nona-2,4-diene-1,9-dioic acid 5,6-hydrolase. Biochemistry 36:12242–12251PubMedCrossRefGoogle Scholar
  95. Leahy JG, Batchelor PJ, Morcomb SM (2003) Evolution of the soluble diiron monooxygenases. FEMS Microbiol Rev 27:449–479PubMedCrossRefPubMedCentralGoogle Scholar
  96. Lee J-H, Omori T, Kodama T (1994) Identification of the metabolic intermediates of phthalate by Tn5 mutants of Pseudomonas testosteroni and analysis of the 4,5-dihydroxyphthalate decarboxylase gene. J Ferment Bioeng 77:583–590CrossRefGoogle Scholar
  97. Lehrbach PR, Zeyer J, Reineke W, Knackmuss HJ, Timmis KN (1984) Enzyme recruitment in vitro: use of cloned genes to extend the range of haloaromatics degraded by Pseudomonas sp. strain B13. J Bacteriol 158:1025–1032PubMedPubMedCentralGoogle Scholar
  98. Liang Q, Takeo M, Chen M, Zhang W, Xu Y, Lin M (2005) Chromosome-encoded gene cluster for the metabolic pathway that converts aniline to TCA-cycle intermediates in Delftia tsuruhatensis AD9. Microbiology 151:3435–3446PubMedCrossRefGoogle Scholar
  99. Lipscomb JD, Orville AM (1992) Mechanistic aspects of dihydroxybenzoate dioxygenases. In: Sigel H, Sigel A (eds) Metal ions in biological systems. Marcel Dekker Inc., New York, pp 243–298Google Scholar
  100. Liu L, Wu JF, Ma YF, Wang SY, Zhao GP, Liu SJ (2007) A novel deaminase involved in chloronitrobenzene and nitrobenzene degradation with Comamonas sp. strain CNB-1. J Bacteriol 189:2677–2682PubMedPubMedCentralCrossRefGoogle Scholar
  101. Marin M, Perez-Pantoja D, Donoso R, Wray V, Gonzalez B, Pieper DH (2010). Modified 3-oxoadipate pathway for the biodegradation of methylaromatics in Pseudomonas reinekei MT1. J Bacteriol 192:1543–1552PubMedPubMedCentralCrossRefGoogle Scholar
  102. Maruyama K (1983) Purification and properties of 2-pyrone-4,6-dicarboxylate hydrolase. J Biochem 93:557–565PubMedCrossRefPubMedCentralGoogle Scholar
  103. Masai E, Katayama Y, Nishikawa S, Fukuda M (1999a) Characterization of Sphingomonas paucimobilis SYK-6 genes involved in degradation of lignin-related compounds. J Ind Microbiol Biotechnol 23:364–373PubMedCrossRefPubMedCentralGoogle Scholar
  104. Masai E, Shinohara S, Hara H, Nishikawa S, Katayama Y, Fukuda M (1999b) 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 181:55–62PubMedPubMedCentralGoogle Scholar
  105. Masai E, Sasaki M, Minakawa Y, Abe T, Sonoki T, Miyauchi K, Katayama Y, Fukuda M (2004) A novel tetrahydrofolate-dependent O-demethylase gene is essential for growth of Sphingomonas paucimobilis SYK-6 with syringate. J Bacteriol 186:2757–2765PubMedPubMedCentralCrossRefGoogle Scholar
  106. Matera I, Ferraroni M, Bürger S, Scozzafava A, Stolz A, Briganti F (2008) Salicylate 1,2-dioxygenase from Pseudaminobacter salicylatoxidans: crystal structure of a peculiar ring-cleaving dioxygenase. J Mol Biol 380:856–868PubMedCrossRefPubMedCentralGoogle Scholar
  107. McIntire W, Hopper DJ, Singer TP (1985) p-Cresol methylhydroxylase. Biochem J 228:325–335PubMedPubMedCentralCrossRefGoogle Scholar
  108. Mohamed ME (2000) Biochemical and molecular characterization of phenylacetate-coenzyme A ligase, an enzyme catalyzing the first step in aerobic metabolism of phenylacetic acid in Azoarcus evansii. J Bacteriol 182:286–294CrossRefGoogle Scholar
  109. Moonen MJ, Kamerbeek N, Westphal AH, Boeren SA, Janssen DB, Fraaije MW, van Berkel WJ (2008a) Elucidation of the 4-hydroxyacetophenone catabolic pathway in Pseudomonas fluorescens ACB. J Bacteriol 190:5190–5198PubMedPubMedCentralCrossRefGoogle Scholar
  110. Moonen MJ, Synowsky SA, van den Berg WA, Westphal AH, Heck AJ, van den Heuvel RH, Fraaije MW, van Berkel WJ (2008b) Hydroquinone dioxygenase from Pseudomonas fluorescens ACB: a novel member of the family of nonheme-iron(II)-dependent dioxygenases. J Bacteriol 190:5199–5209PubMedPubMedCentralCrossRefGoogle Scholar
  111. Moran GR (2005) 4-Hydroxyphenylpyruvate dioxygenase. Arch Biochem Biophys 433:117–128PubMedCrossRefPubMedCentralGoogle Scholar
  112. Morawski B, Segura A, Ornston LN (2000) Substrate range and genetic analysis of Acinetobacter vanillate demethylase. J Bacteriol 182:1383–1389PubMedPubMedCentralCrossRefGoogle Scholar
  113. Murakami S, Sawami Y, Takenaka S, Aoki K (2004) Cloning of a gene encoding 4-amino-3-hydroxybenzoate 2,3-dioxygenase from Bordetella sp. 10d. Biochem Biophys Res Commun 314:489–494PubMedCrossRefGoogle Scholar
  114. Muraki T, Taki M, Hasegawa Y, Iwaki H, Lau PCK (2003) Prokaryotic homologs of the eukaryotic 3-hydroxyanthranilate 3,4-dioxygenase and 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase in the 2-nitrobenzoate degradation pathway of Pseudomonas fluorescens strain KU-7. Appl Environ Microbiol 69:1564–1572PubMedPubMedCentralCrossRefGoogle Scholar
  115. Nakata H, Yamauchi T, Fujisawa H (1979) Phenylalanine hydroxylase from Chromobacterium violaceum Purification and characterization. J Biol Chem 254:1829–1833PubMedGoogle Scholar
  116. Nakazawa T, Hayashi E (1978) Phthalate and 4-hydroxyphthalate metabolism in Pseudomonas testosteroni: purification and properties of 4,5-dihydroxyphthalate decarboxylase. Appl Environ Microbiol 36:264–269PubMedPubMedCentralGoogle Scholar
  117. Newman LM, Wackett LP (1995) Purification and characterization of toluene 2-monooxygenase from Burkholderia cepacia G4. Biochemistry 34:14066–14076PubMedCrossRefGoogle Scholar
  118. Ng LC, Shingler V, Sze CC, Poh CL (1994) Cloning and sequences of the first eight genes of the chromosomally encoded (methyl) phenol degradation pathway from Pseudomonas putida P35X. Gene 151:29–36PubMedCrossRefGoogle Scholar
  119. Nogales J, Canales A, Jimenez-Barbero J, Garcia JL, Diaz E (2005) Molecular characterization of the gallate dioxygenase from Pseudomonas putida KT2440. The prototype of a new subgroup of extradiol dioxygenases. J Biol Chem 280:35382–35390PubMedCrossRefGoogle Scholar
  120. Nogales J, Macchi R, Franchi F, Barzaghi D, Fernández C, García JL, Bertoni G, Díaz E (2007) Characterization of the last step of the aerobic phenylacetic acid degradation pathway. Microbiology 153:357–365PubMedCrossRefPubMedCentralGoogle Scholar
  121. Nurk A, Kasak L, Kivisaar M (1991) Sequence of the gene (pheA) encoding phenol monooxygenae from Pseudomonas sp. EST1001: expression in Escherichia coli and Pseudomonas putida. Gene 102:13–18PubMedCrossRefPubMedCentralGoogle Scholar
  122. Olivera ER, Minambres B, Garcia B, Muniz C, Moreno MA, Ferrandez A, Diaz E, Garcia JL, Luengo JM (1998) Molecular characterization of the phenylacetic acid catabolic pathway in Pseudomonas putida U: the phenylacetyl-CoA catabolon. Proc Natl Acad Sci USA 95:6419–6424PubMedCrossRefGoogle Scholar
  123. Olsen RH, Kukor JJ, Kaphammer B (1994) A novel toluene-3-monooxygenase pathway cloned from Pseudomonas pickettii PKO1. J Bacteriol 176:3749–3756PubMedPubMedCentralCrossRefGoogle Scholar
  124. Ono K, Nozaki M, Hayaishi O (1970) Purification and some properties of protocatechuate 4,5-dioxygenase. Biochim Biophys Acta 220:224–238PubMedCrossRefPubMedCentralGoogle Scholar
  125. Orii C, Takenaka S, Murakami S, Aoki K (2004) A novel coupled enzyme assay reveals an enzyme responsible for the deamination of a chemically unstable intermediate in the metabolic pathway of 4-amino-3-hydroxybenzoic acid in Bordetella sp. strain 10d. Eur J Biochem 271:3248–3254PubMedCrossRefPubMedCentralGoogle Scholar
  126. Overhage J, Priefert H, Steinbuchel A (1999) Biochemical and genetic analyses of ferulic acid catabolism in Pseudomonas sp strain HR199. Appl Environ Microbiol 65:4837–4847PubMedPubMedCentralGoogle Scholar
  127. Peng X, Masai E, Kitayama H, Harada K, Katayama Y, Fukuda M (2002) Characterization of the 5-carboxyvanillate decarboxylase gene and its role in lignin-related biphenyl catabolism in Sphingomonas paucimobilis SYK-6. Appl Environ Microbiol 68:4407–4415PubMedPubMedCentralCrossRefGoogle Scholar
  128. Peng X, Masai E, Kasai D, Miyauchi K, Katayama Y, Fukuda M (2005) A second 5-carboxyvanillate decarboxylase gene, ligW2, is important for lignin-related biphenyl catabolism in Sphingomonas paucimobilis SYK-6. Appl Environ Microbiol 71:5014–5021PubMedPubMedCentralCrossRefGoogle Scholar
  129. Perez-Pantoja D, De la Iglesia R, Pieper DH, Gonzalez B (2008) Metabolic reconstruction of aromatic compounds degradation from the genome of the amazing pollutant degrading bacterium Cupriavidus necator JMP134. FEMS Microbiol Rev 32:736–794PubMedCrossRefPubMedCentralGoogle Scholar
  130. Pieper DH, Engesser K-H, Don RH, Timmis KN, Knackmuss H-J (1985) Modified ortho-cleavage pathway in Alcaligenes eutrophus JMP134 for the degradation of 4-methylcatechol. FEMS Microbiol Lett 29:63–67CrossRefGoogle Scholar
  131. Pieper DH, Stadler-Fritzsche K, Knackmuss H-J, Engesser KH, Bruce NC, Cain RB (1990) Purification and characterization of 4-methylmuconolactone methylisomerase, a novel enzyme of the modified 3-oxoadipate pathway in the Gram-negative bacterium Alcaligenes eutrophus JMP 134. Biochem J 271:529–534PubMedPubMedCentralCrossRefGoogle Scholar
  132. Pinyakong O, Habe H, Yoshida T, Nojiri H, Omori T (2003) Identification of three novel salicylate 1-hydroxylases involved in the phenanthrene degradation of Sphingobium sp strain P2. Biochem Biophys Res Commun 301:350–357PubMedCrossRefGoogle Scholar
  133. Plaggenborg R, Steinbuchel A, Priefert H (2001) The coenzyme A-dependent, non-beta-oxidation pathway and not direct deacetylation is the major route for ferulic acid degradation in Delftia acidovorans. FEMS Microbiol Lett 205:9–16PubMedGoogle Scholar
  134. Powell JA, Archer JA (1998) Molecular characterisation of a Rhodococcus ohp operon. Antonie Van Leeuwenhoek 74:175–188PubMedCrossRefGoogle Scholar
  135. Powlowski J, Shingler V (1994) Genetics and biochemistry of phenol degradation by Pseudomonas sp. CF600. Biodegradation 5:219–236PubMedCrossRefGoogle Scholar
  136. Powlowski J, Sealy J, Shingler V, Cadieux E (1997) On the role of DmpK, an auxiliary protein associated with multicomponent phenol hydroxylase from Pseudomonas sp. CF600. J Biol Chem 272:945–951PubMedCrossRefGoogle Scholar
  137. Priefert H, Rabenhorst J, Steinbüchel A (2001) Biotechnological production of vanillin. Appl Microbiol Biotechnol 56:296–314PubMedCrossRefGoogle Scholar
  138. Prucha M, Peterseim A, Pieper DH (1997) Evidence for an isomeric muconolactone isomerase involved in the metabolism of 4-methylmuconolactone by Alcaligenes eutrophus JMP134. Arch Microbiol 168:33–38PubMedCrossRefGoogle Scholar
  139. Pujar BG, Ribbons DW (1985) Phthalate metabolism in Pseudomonas fluorescens PHK: purification and properties of 4,5-dihydroxyphthalate decarboxylase. Appl Environ Microbiol 49:374–376PubMedPubMedCentralGoogle Scholar
  140. Ranjith NK, Sasikala C, Ramana Ch V (2007) Catabolism of L-phenylalanine and L-tyrosine by Rhodobacter sphaeroides OU5 occurs through 3,4-dihydroxyphenylalanine. Res Microbiol 158:506–511PubMedCrossRefGoogle Scholar
  141. Reeve D, Carver MA, Hopper DJ (1989) The purification and characterization of 4-ethylphenol methylenehydroxylase, a flavocytochrome from Pseudomonas putida JD1. Biochem J 263:431–437PubMedPubMedCentralCrossRefGoogle Scholar
  142. Reineke W, Knackmuss H-J (1978) Chemical structure and biodegradability of halogenated aromatic compounds. Substituent effects on 1,2-dioxygenation of benzoic acid. Biochim Biophys Acta 532:412–423CrossRefGoogle Scholar
  143. Reiner AM (1972) Purification and properties of the catechol-forming enzyme 3,5-cyclohexadiene-1,2-diol-1-carboxylic acid (NAD+) oxidoreductase (decarboxylating). J Biol Chem 247:4960–4965PubMedGoogle Scholar
  144. Reiner A, Hegeman G (1971) Metabolism of benzoic acid by bacteria. Accumulation of (−)-3,5-cyclohexadiene-1,2-diol-1-carboxylic acid by mutant strain of Alcaligenes eutrophus. Biochemistry 10:2530–2536PubMedCrossRefGoogle Scholar
  145. Roper DI, Cooper RA (1990) Purification, some properties and nucleotide sequence of 5-carboxymethyl-2-hydroxymuconate isomerase of Escherichia coli C. Fed Eur Biochem Soc Lett 266:63–66CrossRefGoogle Scholar
  146. Sasoh M, Masai E, Ishibashi S, Hara H, Kamimura N, Miyauchi K, Fukuda M (2006) Characterization of the terephthalate degradation genes of Comamonas sp. strain E6. Appl Environ Microbiol 72:1825–1832PubMedPubMedCentralCrossRefGoogle Scholar
  147. Sauret-Ignazi G, Dardas A, Pelmont J (1988) Purification and properties of cytochrome P-450 from Moraxella sp. Biochimie 70:1385–1395PubMedCrossRefGoogle Scholar
  148. Schläfli HR, Weiss MA, Leisinger T, Cook AM (1994) Terephthalate 1,2-dioxygenase system from Comamonas testosteroni T-2: purification and some properties of the oxygenase component. J Bacteriol 176:6644–6652PubMedPubMedCentralCrossRefGoogle Scholar
  149. Schlömann M (1994) Evolution of chlorocatechol catabolic pathways. Biodegradation 5:301–321PubMedCrossRefPubMedCentralGoogle Scholar
  150. Schuhle K, Jahn M, Ghisla S, Fuchs G (2001) Two similar gene clusters coding for enzymes of a new type of aerobic 2-aminobenzoate (anthranilate) metabolism in the bacterium Azoarcus evansii. J Bacteriol 183:5268–5278PubMedPubMedCentralCrossRefGoogle Scholar
  151. Shen XH, Jiang CY, Huang Y, Liu ZP, Liu SJ (2005) Functional identification of novel genes involved in the glutathione-independent gentisate pathway in Corynebacterium glutamicum. Appl Environ Microbiol 71:3442–3452PubMedPubMedCentralCrossRefGoogle Scholar
  152. Shields MS, Montgomery SO, Chapman PJ, Cuskey SM, Pritchard PH (1989) Novel pathway of toluene catabolism in the trichloroethylene-degrading bacterium G4. Appl Environ Microbiol 55:1624–1629PubMedPubMedCentralGoogle Scholar
  153. Shingler V, Powlowski J, Marklund U (1992) Nucleotide sequence and functional analysis of the complete phenol/3,4-dimethylphenol catabolic pathway of Pseudomonas sp. strain CF600. J Bacteriol 174:711–724PubMedPubMedCentralCrossRefGoogle Scholar
  154. Smith MA, Weaver VB, Young DM, Ornston LN (2003) Genes for chlorogenate and hydroxycinnamate catabolism (hca) are linked to functionally related genes in the dca-pca-qui-pob-hca chromosomal cluster of Acinetobacter sp strain ADP1. Appl Environ Microbiol 69:524–532PubMedPubMedCentralCrossRefGoogle Scholar
  155. Spence EL, Kawamukai M, Sanvoisin J, Braven H, Bugg TD (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 178:5249–5256PubMedPubMedCentralCrossRefGoogle Scholar
  156. Suemori A, Kurane R, Tomizuka N (1993) Purification and properties of gentisate 1,2-dioxygenase from Rhodococcus erythropolis S-1. Biosci Biotechnol Biochem 57:1781–1783CrossRefGoogle Scholar
  157. Suemori A, Nakajima K, Kurane R, Nakamura Y (1996) Purification and characterization of o-hydroxyphenylacetate 5-hydroxylase, m-hydroxyphenylacetate 6-hydroxylase and p-hydroxyphenylacetate 1-hydroxylase from Rhodococcus erythropolis. J Ferment Bioeng 81:133–137CrossRefGoogle Scholar
  158. Sugimoto K, Senda T, Aoshima H, Masai E, Fukuda M, Mitsui Y (1999) Crystal structure of an aromatic ring opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, under aerobic conditions. Structure 7:953–965PubMedCrossRefGoogle Scholar
  159. Suske WA, Held M, Schmid A, Fleischmann T, Wubbolts MG, Kohler HPE (1997) Purification and characterization of 2-hydroxybiphenyl 3-monooxygenase, a novel NADH-dependent, FAD-containing aromatic hydroxylase from Pseudomonas azelaica HBP1. J Biol Chem 272:24257–24265PubMedCrossRefGoogle Scholar
  160. Sutherland JB (1986) Demethylation of veratrole by cytochrome P-450 in Streptomyces setonii. Appl Environ Microbiol 52:98–100PubMedPubMedCentralGoogle Scholar
  161. Tago K, Sato J, Takesa H, Kawagishi H, Hayatsu M (2005) Characterization of methylhydroquinone-metabolizing oxygenase genes encoded on plasmid in Burkholderia sp. NF100. J Biosci Bioeng 100:517–523PubMedCrossRefGoogle Scholar
  162. Taguchi K, Motoyama M, Kudo T (2004) Multiplicity of 2,3-dihydroxybiphenyl dioxygenase genes in the Gram-positive polychlorinated biphenyl degrading bacterium Rhodococcus rhodochrous K37. Biosci Biotechnol Biochem 68:787–795PubMedCrossRefGoogle Scholar
  163. Takenaka S, Murakami S, Shinke R, Hatakeyama K, Yukawa H, Aoki K (1997) Novel genes encoding 2-aminophenol 1,6-dioxygenase from Pseudomonas species AP-3 growing on 2-aminophenol and catalytic properties of the purified enzyme. J Biol Chem 272:14727–14732PubMedCrossRefGoogle Scholar
  164. Takenaka S, Murakami S, Kim YJ, Aoki K (2000) Complete nucleotide sequence and functional analysis of the genes for 2-aminophenol metabolism from Pseudomonas sp. AP-3. Arch Microbiol 174:265–272PubMedCrossRefGoogle Scholar
  165. Takenaka S, Asami T, Orii C, Murakami S, Aoki K (2002) A novel meta-cleavage dioxygenase that cleaves a carboxyl-group substituted 2-aminophenol – Purification and characterization of 4-amino-3-hydroxybenzoate 2,3-dioxygenase from Bordetella sp. strain 10d. Eur J Biochem 269:5871–5877PubMedCrossRefGoogle Scholar
  166. Takenaka S, Okugawa S, Kadowaki M, Murakami S, Aoki K (2003) The metabolic pathway of 4-aminophenol in Burkholderia sp. strain AK-5 differs from that of aniline and aniline with C-4 substituents. Appl Environ Microbiol 69:5410–5413PubMedPubMedCentralCrossRefGoogle Scholar
  167. Tao Y, Fishman A, Bentley WE, Wood TK (2004a) Altering toluene 4-monooxygenase by active-site engineering for the synthesis of 3-methoxycatechol, methoxyhydroquinone, and methylhydroquinone. J Bacteriol 186:4705–4713PubMedPubMedCentralCrossRefGoogle Scholar
  168. Tao Y, Fishman A, Bentley WE, Wood TK (2004b) Oxidation of benzene to phenol, catechol, and 1,2,3-trihydroxybenzene by toluene 4-monooxygenase of Pseudomonas mendocina KR1 and toluene 3-monooxygenase of Ralstonia pickettii PKO1. Appl Environ Microbiol 70:3814–3820PubMedPubMedCentralCrossRefGoogle Scholar
  169. Titus GP, Mueller HA, Burgner J, Rodríguez de Córdoba S, Peñalva MA, Timm DE (2000) Crystal structure of human homogentisate dioxygenase. Nat Struct Biol 7:542–546PubMedCrossRefGoogle Scholar
  170. Vaillancourt FH, Labbe G, Drouin NM, Fortin PD, Eltis LD (2002) The mechanism-based inactivation of 2,3-dihydroxybiphenyl 1,2-dioxygenase by catecholic substrates. J Biol Chem 277:2019–2027PubMedCrossRefPubMedCentralGoogle Scholar
  171. Vaillancourt FH, Bolin JT, Eltis LD (2004) Ring-cleavage dioxygenases. In: Ramos JL (ed) Pseudomonas. Kluwer Academic/Plenum Publishers, New York, pp 359–395CrossRefGoogle Scholar
  172. Vaillancourt FH, Bolin JT, Eltis LD (2006) The ins and outs of ring-cleaving dioxygenases. Crit Rev Biochem Mol Biol 41:241–267PubMedCrossRefGoogle Scholar
  173. van Berkel WJ, Kamerbeek NM, Fraaije MW (2006) Flavoprotein monooxygenases, a diverse class of oxidative biocatalysts. J Biotechnol 124:670–689PubMedCrossRefPubMedCentralGoogle Scholar
  174. Vardar G, Wood TK (2004) Protein engineering of toluene- o-xylene monooxygenase from Pseudomonas stutzeri OX1 for synthesizing 4-methylresorcinol, methylhydroquinone, and pyrogallol. Appl Environ Microbiol 70:3253–3262PubMedPubMedCentralCrossRefGoogle Scholar
  175. Vederas JC, Schleicher E, Tsai MD, Floss HG (1978) Stereochemistry and mechanism of reactions catalyzed by tryptophanase Escherichia coli. J Biol Chem 253:5350–5354PubMedGoogle Scholar
  176. Vetting MW, Wackett LP, Que L, Lipscomb JD, Ohlendorf DH (2004) Crystallographic comparison of manganese- and iron-dependent homoprotocatechuate 2,3-dioxygenases. J Bacteriol 186:1945–1958PubMedPubMedCentralCrossRefGoogle Scholar
  177. Wang L-H, Hamzah RY, Yu Y, Tu S-C (1987) Pseudomonas cepacia 3-hydroxybenzoate 6-hydroxylase: induction, purification, and characterization. Biochemistry 26:1099–1104PubMedCrossRefGoogle Scholar
  178. Wang YZ, Zhou Y, Zylstra GJ (1995) Molecular analysis of isophthalate and terephthalate degradation by Comamonas testosteroni YZW-D. Environ Health Perspect 103(Suppl 5):9–12PubMedPubMedCentralCrossRefGoogle Scholar
  179. Whited GM, Gibson DT (1991) Toluene-4-monooxygenase, a three-component enzyme system that catalyzes the oxidation of toluene to p-cresol in Pseudomonas mendocina KR1. J Bacteriol 173:3010–3016PubMedPubMedCentralCrossRefGoogle Scholar
  180. Williams SE, Woodridge EM, Ransom SC, Landro JA, Babbitt PC, Kozarich JW (1992) 3-carboxy- cis, cis-muconate lactonizing enzymes from Pseudomonas putida is homologous to the class 2 fumarase family: a new reaction in the evolution of a mechanistic motif. Biochemistry 31:9768–9776PubMedCrossRefPubMedCentralGoogle Scholar
  181. Wolfe MD, Altier DJ, Stubna A, Popescu CV, Munck E, Lipscomb JD (2002) Benzoate 1,2-dioxygenase from Pseudomonas putida: single turnover kinetics and regulation of a two-component Rieske dioxygenase. Biochemistry 41:9611–9626PubMedCrossRefGoogle Scholar
  182. Wolgel SA, Dege JE, Perkins-Olson PE, Juarez-Garcia CH, Crawford RL, Münck E, Lipscomb JD (1993) Purification and characterization of protocatechuate 2,3-dioxygenase from Bacillus macerans: a new extradiol catecholic dioxygenase. J Bacteriol 175:4414–4426PubMedPubMedCentralCrossRefGoogle Scholar
  183. Yamaguchi M, Fujisawa H (1980) Purification and characterization of an oxygenase component in benzoate 1,2-dioxygenase system from Pseudomonas arvilla C-1. J Biol Chem 255:5058–5063PubMedPubMedCentralGoogle Scholar
  184. Yamamoto S, Katagiri M, Maeno H, Hayaishi O (1965) Salicylate hydroxylase, a monooxygenase requiring flavin adenine dinucleotide. I. Purification and general properties. J Biol Chem 240:3408–3413PubMedPubMedCentralGoogle Scholar
  185. Yoshida R, Hori K, Fujiwara M, Saeki Y, Kagamiyama H (1976) Non-identical subunits of protocatechuate 3,4-dioxygenase. Biochemistry 15:4048–4053PubMedCrossRefPubMedCentralGoogle Scholar
  186. Yoshida T, Hayakawa Y, Matsui T, Nagasawa T (2004) Purification and characterization of 2,6-dihydroxybenzoate decarboxylase reversibly catalyzing nonoxidative decarboxylation. Arch Microbiol 181:391–397PubMedCrossRefPubMedCentralGoogle Scholar
  187. Zaar A, Gescher J, Eisenreich W, Bacher A, Fuchs G (2004) New enzymes involved in aerobic benzoate metabolism in Azoarcus evansii. Mol Microbiol 54:223–238PubMedCrossRefGoogle Scholar
  188. Zhang Y, Colabroy KL, Begley TP, Ealick SE (2005) Structural studies on 3-hydroxyanthranilate-3,4-dioxygenase: the catalytic mechanism of a complex oxidation involved in NAD biosynthesis. Biochemistry 44:7632–7643PubMedCrossRefPubMedCentralGoogle Scholar
  189. Zhou NY, Al-Dulayymi J, Baird MS, Williams PA (2002) Salicylate 5-hydroxylase from Ralstonia sp. strain U2: a monooxygenase with close relationships to and shared electron transport proteins with naphthalene dioxygenase. J Bacteriol 184:1547–1555PubMedPubMedCentralCrossRefGoogle Scholar
  190. Zhuang Z, Song F, Takami H, Dunaway-Mariano D (2004) The BH1999 protein of Bacillus halodurans C-125 is gentisyl-coenzyme A thioesterase. J Bacteriol 186:393–399PubMedPubMedCentralCrossRefGoogle Scholar

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© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • D. Pérez-Pantoja
    • 1
  • B. González
    • 2
  • Dietmar H. Pieper
    • 3
    Email author
  1. 1.Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias BiológicasUniversidad de ConcepciónConcepciónChile
  2. 2.Facultad de Ingeniería y CienciasUniversidad Adolfo IbáñezSantiagoChile
  3. 3.Microbial Interactions and Processes Research GroupHZI – Helmholtz Centre for Infection ResearchBraunschweigGermany

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