User menu

Accès à distance ? S'identifier sur le proxy UCLouvain

Characterization of a ring-hydroxylating dioxygenase from phenanthrene-degrading Sphingomonas sp. strain LH128 able to oxidize benz[a]anthracene.

  1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
  2. Armengaud J, Happe B, Timmis KN (1998) Genetic analysis of dioxin dioxygenase of Sphingomonas sp. strain RW1: catabolic genes dispersed on the genome. J Bacteriol 180:3954–3966
  3. Bastiaens L, Springael D, Wattiau P, Harms H, deWachter R, Verachtert H, Diels L (2000) Isolation of adherent polycyclic aromatic hydrocarbon (PAH)-degrading bacteria using PAH-sorbing carriers. Appl Environ Microbiol 66:1834–1843
  4. Boyd DR, Sharma ND, Allen CCR (2001) Aromatic dioxygenases: molecular biocatalysis and applications. Curr Opin Biotechnol 12:564–573
  5. Boyd DR, Sharma ND, Sbircea L, Murphy D, Belhocine T, Malone JF, James SL, Allen CCR, Hamilton JTG (2008) Azaarene cis-dihydrodiol-derived 2,2′-bipyridine ligands for asymmetric allylic oxidation and cyclopropanation. Chem Commun 43:5535–5537
  6. Bunz PV, Cook AM (1993) Dibenzofuran 4,4a-dioxygenase from Sphingomonas sp. strain RW1: angular dioxygenation by a three-component enzyme system. J Bacteriol 175:6467–6475
  7. Butler CS, Mason JR (1997) Structure–function analysis of the bacterial aromatic ring-hydroxylating dioxygenases. Adv Microb Physiol 38:47–84
  8. Cai M, Xun L (2002) Organization and regulation of pentachlorophenol-degrading genes in Sphingobium chlorophenolicum ATCC 39723. J Bacteriol 184:4672–4680
  9. Cerniglia CE (1992) Biodegradation of polycyclic aromatic hydrocarbons. Biodegradation 3:351–368
  10. de Lorenzo V, Eltis L, Kessler B, Timmis KN (1993) Analysis of Pseudomonas gene products using lacI q/Ptrp-lac plasmids and transposons that confer conditional phenotypes. Gene 123:17–24
  11. Demaneche S, Meyer C, Micoud J, Louwagie M, Willison JC, Jouanneau Y (2004) Identification and functional analysis of two aromatic-ring-hydroxylating dioxygenases from a Sphingomonas strain that degrades various polycyclic aromatic hydrocarbons. Appl Environ Microbiol 70:6714–6725
  12. Dimitriou-Christidis P, Autenrieth RL, McDonald TJ, Desai AM (2007) Measurement of biodegradability parameters for single unsubstituted and methylated polycyclic aromatic hydrocarbons in liquid bacterial suspensions. Biotechnol Bioeng 97:922–932
  13. Feng X, Ou LT, Ogram A (1997) Plasmid-mediated mineralization of carbofuran by Sphingomonas sp. strain CF06. Appl Environ Microbiol 63:1332–1337
  14. Ferraro DJ, Gakhar L, Ramaswamy S (2005) Rieske business: structure–function of rieske non-heme oxygenases. Biochem Biophys Res Commun 338:175–190
  15. Fortnagel P, Harms H, Wittich RM, Krohn S, Meyer H, Sinnwell V, Wilkes H, Francke W (1990) Metabolism of dibenzofuran by Pseudomonas sp. strain HH69 and the mixed culture HH27. Appl Environ Microbiol 56:1148–1156
  16. Fujii K, Satomi M, Morita N, Motomura T, Tanaka T, Kikuchi S (2003) Novosphingobium tardaugens sp. nov., an oestradiol-degrading bacterium isolated from activated sludge of a sewage treatment plant in Tokyo. Int J Syst Evol Microbiol 53:47–52
  17. Furukawa K, Suenaga H, Goto M (2004) Biphenyl dioxygenases: functional versatilities and directed evolution. J Bacteriol 186:5189–5196
  18. Gakhar L, Malik ZA, Allen CCR, Lipscomb DA, Larkin MJ, Ramaswamy S (2005) Structure and increased thermostability of Rhodococcus sp. naphthalene 1,2-dioxygenase. J Bacteriol 197:7222–7231
  19. Happe B, Eltis LD, Poth H, Hedderich R, Timmis KN (1993) Characterization of 2,2′,3-trihydroxybiphenyl dioxygenase, an extradiol dioxygenase from the dibenzofuran- and dibenzo-p-dioxin-degrading bacterium Sphingomonas sp. strain RW1. J Bacteriol 175:7313–7320
  20. Hong HB, Chang YS, Nam IH, Fortnagel P, Schmidt S (2002) Biotransformation of 2,7-dichloro- and 1,2,3,4-tetrachlorodibenzo-p-dioxin by Sphingomonas wittichii RW1. Appl Environ Microbiol 68:2584–2588
  21. Jakoncic J, Jouanneau Y, Meyer C, Stojanoff V (2007a) The catalytic pocket of the ring-hydroxylating dioxygenase from Sphingomonas CHY-1. Biochem Biophys Res Commun 352:861–866
  22. Jakoncic J, Jouanneau Y, Meyer C, Stojanoff V (2007b) The crystal structure of the ring-hydroxylating dioxygenase from Sphingomonas CHY-1. FEBS J 274:2470–2481
  23. Johannesen H, Sorensen SR, Aamand J (2003) Mineralization of soil-aged isoproturon and isoproturon metabolites by Sphingomonas sp. strain SRS2. J Environ Qual 32:1250–1257
  24. Johnsen AR, Wick LY, Harms H (2005) Principles of microbial PAH-degradation in soil. Environ Pollut 133:71–84
  25. Jouanneau Y, Meyer C, Jakoncic J, Stojanoff V, Gaillard J (2006) Characterization of a naphthalene dioxygenase endowed with an exceptionally broad substrate specificity toward polycyclic aromatic hydrocarbons. Biochemistry 45:12380–12391
  26. Kauppi B, Lee K, Carredano E, Parales RE, Gibson DT, Eklund H, Ramaswamy S (1998) Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2-dioxygenase. Structure 6:571–586
  27. Kim E, Zylstra GJ (1999) Functional analysis of genes involved in biphenyl, naphthalene, phenanthrene, and m-xylene degradation by Sphingomonas yanoikuyae B1. J Ind Microbiol Biotechnol 23:294–302
  28. Kim S. J., Chun J., Bae K. S., Kim Y. C., Polyphasic assignment of an aromatic-degrading Pseudomonas sp., strain DJ77, in the genus Sphingomonas as Sphingomonas chungbukensis sp. nov, 10.1099/00207713-50-4-1641
  29. Kim IS, Ryu JY, Hur HG, Gu MB, Kim SD, Shim JH (2004) Sphingomonas sp. strain SB5 degrades carbofuran to a new metabolite by hydrolysis at the furanyl ring. J Agric Food Chem 52:2309–2314
  30. Krivobok S, Kuony S, Meyer C, Louwagie M, Willison JC, Jouanneau Y (2003) Identification of pyrene-induced proteins in Mycobacterium sp. strain 6PY1: evidence for two ring-hydroxylating dioxygenases. J Bacteriol 185:3828–3841
  31. Leys NM, Ryngaert A, Bastiaens L, Verstraete W, Top EM, Springael D (2004) Occurrence and phylogenetic diversity of Sphingomonas strains in soils contaminated with polycyclic aromatic hydrocarbons. Appl Environ Microbiol 70:1944–1955
  32. McIver AM, Janardhan Garikipati SVB, Bankole KS, Gyamerah M, Peeples TL (2008) Microbial oxidation of naphthalene to cis-1,2-naphthalene dihydrodiol using naphthalene dioxygenase in biphasic media. Biotechnol Prog 24:593–598
  33. Mergeay M, Nies D, Schlegel HG, Gerits J, Charles P, Van Gijsegem F (1985) Alcaligenes eutrophus CH34 is a facultative chemolithotroph with plasmid-bound resistance to heavy metals. J Bacteriol 162:328–334
  34. Ni Chadhain SM, Moritz EM, Kim E, Zylstra GJ (2007) Identification, cloning, and characterization of a multicomponent biphenyl dioxygenase from Sphingobium yanoikuyae strain B1. J Ind Microbiol Biotechnol 34:605–613
  35. Parales RE (2003) The role of active-site residues in naphthalene dioxygenase. J Ind Microbiol Biotechnol 30:271–278
  36. Parales RE, Parales JV, Gibson DT (1999) Aspartate 205 in the catalytic domain of naphthalene dioxygenase is essential for activity. J Bacteriol 181:1831–1837
  37. Parales RE, Lee K, Resnick SM, Jiang H, Lessner DJ, Gibson DT (2000a) Substrate specificity of naphthalene dioxygenase: effect of specific amino acids at the active site of the enzyme. J Bacteriol 182:1641–1649
  38. Parales RE, Resnick SM, Yu CL, Boyd DR, Sharma ND, Gibson DT (2000b) Regioselectivity and enantioselectivity of naphthalene dioxygenase during arene cis-dihydroxylation: control by phenylalanine 352 in the alpha subunit. J Bacteriol 182:5495–5504
  39. 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 68:4407–4415
  40. Pinyakong O, Habe H, Supaka N, Pinpanichkarn P, Juntongjin K, Yoshida T, Furihata K, Nojiri H, Yamane H, Omori T (2000) Identification of novel metabolites in the degradation of phenanthrene by Sphingomonas sp. strain P2. FEMS Microbiol Lett 191:115–121
  41. Pinyakong O, Habe H, Omori T (2003a) The unique aromatic catabolic genes in sphingomonads degrading polycyclic aromatic hydrocarbons (PAHs). J Gen Appl Microbiol 49:1–19
  42. Pinyakong O, Habe H, Yoshida T, Nojiri H, Omori T (2003b) Identification of three novel salicylate 1-hydroxylases involved in the phenanthrene degradation of Sphingobium sp. strain P2. Biochem Biophys Res Commun 301:350–357
  43. Resnick SM, Torok DS, Gibson DT (1993) Oxidation of carbazole to 3-hydroxycarbazole by naphthalene 1,2-dioxygenase and biphenyl 2,3-dioxygenase. FEMS Microbiol Lett 113:297–302
  44. Romine MF, Stillwell LC, Wong KK, Thurston SJ, Sisk EC, Sensen C, Gaasterland T, Fredrickson JK, Saffer JD (1999) Complete sequence of a 184-kilobase catabolic plasmid from Sphingomonas aromaticivorans F199. J Bacteriol 181:1585–1602
  45. Sambrook J, Fritsch EF, Maniatis T (1990) Molecular cloning: a laboratory manual. Cold Spring Laboratory Harbor Press, Cold Spring Harbor, NY
  46. Schuler L, Ni Chadhain SM, Jouanneau Y, Meyer C, Zylstra GL, Hols P, Agathos SN (2008) Characterization of a novel angular dioxygenase from fluorene-degrading Sphingomonas sp. strain LB126. Appl Environ Microbiol 74:1050–1057
  47. Sorensen SR, Ronen Z, Aamand J (2001) Isolation from agricultural soil and characterization of a Sphingomonas sp. able to mineralize the phenylurea herbicide isoproturon. Appl Environ Microbiol 67:5403–5409
  48. Stolz A (1999) Degradation of substituted naphthalenesulfonic acids by Sphingomonas xenophaga BN6. J Ind Microbiol Biotechnol 23:391–399
  49. Story SP, Parker SH, Hayasaka SS, Riley MB, Kline EL (2001) Convergent and divergent points in catabolic pathways involved in utilization of fluoranthene, naphthalene, anthracene, and phenanthrene by Sphingomonas paucimobilis var. EPA505. J Ind Microbiol Biotechnol 26:369–382
  50. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882
  51. van Herwijnen R, de Graaf C, Govers HA, Parsons JR (2004) Estimation of kinetic parameter for the biotransformation of three-ring azaarenes by the phenanthrene-degrading strain Sphingomonas sp. LH128. Environ Toxicol Chem 23:331–338
  52. Wackett LP (2002) Mechanism and application of Rieske non-heme iron dioxygenases. Enzyme Microb Technol 31:577–587
  53. Willison JC (2004) Isolation and characterization of a novel sphingomonad capable of growth with chrysene as sole carbon and energy source. FEMS Microbiol Lett 241:143–150
  54. Yrjala K, Paulin L, Kilpi S, Romantschuk M (1994) Cloning of cmpE, a plasmid-borne catechol 2,3-dioxygenase-encoding gene from the aromatic- and chloroaromatic-degrading Pseudomonas sp. HV3. Gene 138:119–121
  55. Yu CL, Liu W, Ferraro DJ, Brown EN, Parales JV, Ramaswamy S, Zylstra GJ, Gibson DT, Parales RE (2007) Purification, characterization, and crystallization of the components of a biphenyl dioxygenase system from Sphingobium yanoikuyae B1. J Ind Microbiol Biotechnol 34:311–324
  56. Zielinski M, Kahl S, Hecht HJ, Hofer B (2003) Pinpointing biphenyl dioxygenase residues that are crucial for substrate interaction. J Bacteriol 185:6976–6980
  57. Zielinski M, Kahl S, Standfuss-Gabisch C, Camara B, Seeger M, Hofer B (2006) Generation of novel-substrate-accepting biphenyl dioxygenases through segmental random mutagenesis and identification of residues involved in enzyme specificity. Appl Environ Microbiol 72:2191–2199
  58. Zylstra GJ, Kim E (1997) Aromatic hydrocarbon degradation by Sphingomonas yanoikuyae B1. J Ind Microbiol Biotechnol 19:408–414
Bibliographic reference Schuler, Luc ; Jouanneau, Yves ; Ní Chadhain, Sinéad ; Meyer, Christine ; Pouli, Maria ; et. al. Characterization of a ring-hydroxylating dioxygenase from phenanthrene-degrading Sphingomonas sp. strain LH128 able to oxidize benz[a]anthracene.. In: Applied Microbiology and Biotechnology, Vol. 83, no. 3, p. 465-475 (2009)
Permanent URL http://hdl.handle.net/2078.1/21328