1932

Abstract

Oxygenases, which catalyze the reductive activation of O and incorporation of oxygen atoms into substrates, are widely distributed in aerobes. They function by switching the redox states of essential cofactors that include flavin, heme iron, Rieske non-heme iron, and Fe(II)/α-ketoglutarate. This review summarizes the catalytic features of flavin-dependent monooxygenases, heme iron–dependent cytochrome P450 monooxygenases, Rieske non-heme iron–dependent oxygenases, Fe(II)/α-ketoglutarate-dependent dioxygenases, and ring-cleavage dioxygenases, which are commonly involved in pesticide degradation. Heteroatom release (hydroxylation-coupled hetero group release), aromatic/heterocyclic ring hydroxylation to form ring-cleavage substrates, and ring cleavage are the main chemical fates of pesticides catalyzed by these oxygenases. The diversity of oxygenases, specificities for electron transport components, and potential applications of oxygenases are also discussed. This article summarizes our current understanding of the catalytic mechanisms of oxygenases and a framework for distinguishing the roles of oxygenases in pesticide degradation.

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2022-09-08
2024-06-21
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Literature Cited

  1. 1.
    Alfieri A, Fersini F, Ruangchan N, Prongjit M, Chaiyen P, Mattevi A. 2007. Structure of the monooxygenase component of a two-component flavoprotein monooxygenase. PNAS 104:1177–82
    [Google Scholar]
  2. 2.
    Behrens MR, Mutlu N, Chakraborty S, Dumitru R, Jiang WZ et al. 2007. Dicamba resistance: enlarging and preserving biotechnology-based weed management strategies. Science 316:1185–88
    [Google Scholar]
  3. 3.
    Bers K, Leroy B, Breugelmans P, Albers P, Lavigne R et al. 2011. A novel hydrolase identified by genomic-proteomic analysis of phenylurea herbicide mineralization by Variovorax sp. strain SRS16. Appl. Environ. Microbiol. 77:8754–64
    [Google Scholar]
  4. 4.
    Cai S, Chen LW, Ai YC, Qiu JG, Wang CH et al. 2017. Degradation of diphenyl ether in Sphingobium phenoxybenzoativorans SC_3 is initiated by a novel ring cleavage dioxygenase. Appl. Environ. Microbiol. 83:e00104–17
    [Google Scholar]
  5. 5.
    Cao L, Xu J, Wu G, Li M, Jiang J et al. 2013. Identification of two combined genes responsible for dechlorination of 3,5,6-trichloro-2-pyridinol (TCP) in Cupriavidus pauculus P2. J. Hazard Mater. 260:700–6
    [Google Scholar]
  6. 6.
    Chauvaux S, Chevalier F, Le Dantec C, Fayolle F, Miras I et al. 2001. Cloning of a genetically unstable cytochrome P-450 gene cluster involved in degradation of the pollutant ethyl tert-butyl ether by Rhodococcus ruber. J. Bacteriol. 183:6551–57
    [Google Scholar]
  7. 7.
    Chekan JR, Ongpipattanakul C, Wright TR, Zhang B, Bollinger JM Jr. et al. 2019. Molecular basis for enantioselective herbicide degradation imparted by aryloxyalkanoate dioxygenases in transgenic plants. PNAS 116:13299–304
    [Google Scholar]
  8. 8.
    Chen K, Huang L, Xu C, Liu X, He J et al. 2013. Molecular characterization of the enzymes involved in the degradation of a brominated aromatic herbicide. Mol. Microbiol. 89:1121–39
    [Google Scholar]
  9. 9.
    Chen K, Mu Y, Jian S, Zang X, Chen Q et al. 2018. Comparative transcriptome analysis reveals the mechanism underlying 3,5-dibromo-4-hydroxybenzoate catabolism via a new oxidative decarboxylation pathway. Appl. Environ. Microbiol. 84:e02467–17
    [Google Scholar]
  10. 10.
    Chen Q, Wang CH, Deng SK, Wu YD, Li Y et al. 2014. Novel three-component Rieske non-heme iron oxygenase system catalyzing the N-dealkylation of chloroacetanilide herbicides in sphingomonads DC-6 and DC-2. Appl. Environ. Microbiol. 80:5078–85
    [Google Scholar]
  11. 11.
    Chen X, Ji J, Zhao L, Qiu J, Dai C et al. 2017. Molecular mechanism and genetic determinants of buprofezin degradation. Appl. Environ. Microbiol. 83:e00868–17
    [Google Scholar]
  12. 12.
    Cheng M, Meng Q, Yang Y, Chu C, Chen Q et al. 2017. The two-component monooxygenase MeaXY initiates the downstream pathway of chloroacetanilide herbicide catabolism in sphingomonads. Appl. Environ. Microbiol. 83:e03241–16
    [Google Scholar]
  13. 13.
    Chu CW, Liu B, Li N, Yao SG, Cheng D et al. 2017. A novel aerobic degradation pathway for thiobencarb is initiated by the TmoAB two-component flavin mononucleotide-dependent monooxygenase system in Acidovorax sp. strain T1. Appl. Environ. Microbiol. 83:e01490–17
    [Google Scholar]
  14. 14.
    Danganan CE, Shankar S, Ye RW, Chakrabarty AM. 1995. Substrate diversity and expression of the 2,4,5-trichlorophenoxyacetic acid oxygenase from Burkholderia cepacia AC1100. Appl. Environ. Microbiol. 61:4500–4
    [Google Scholar]
  15. 15.
    Danganan CE, Ye RW, Daubaras DL, Xun L, Chakrabarty AM. 1994. Nucleotide sequence and functional analysis of the genes encoding 2,4,5-trichlorophenoxyacetic acid oxygenase in Pseudomonas cepacia AC1100. Appl. Environ. Microbiol. 60:4100–6
    [Google Scholar]
  16. 16.
    Dehmel U, Engesser KH, Timmis KN, Dwyer DF. 1995. Cloning, nucleotide sequence, and expression of the gene encoding a novel dioxygenase involved in metabolism of carboxydiphenyl ethers in Pseudomonas pseudoalcaligenes POB310. Arch. Microbiol. 163:35–41
    [Google Scholar]
  17. 17.
    Dong W, Chen Q, Hou Y, Li S, Zhuang K et al. 2015. Metabolic pathway involved in 2-methyl-6-ethylaniline degradation by Sphingobium sp. strain MEA3-1 and cloning of the novel flavin-dependent monooxygenase system meaBA. Appl. Environ. Microbiol. 81:8254–64
    [Google Scholar]
  18. 18.
    D'Ordine RL, Rydel TJ, Storek MJ, Sturman EJ, Moshiri F et al. 2009. Dicamba monooxygenase: structural insights into a dynamic Rieske oxygenase that catalyzes an exocyclic monooxygenation. J. Mol. Biol. 392:481–97
    [Google Scholar]
  19. 19.
    Dunning Hotopp JC, Auchtung TA, Hogan DA, Hausinger RP 2003. Intrinsic tryptophan fluorescence as a probe of metal and α-ketoglutarate binding to TfdA, a mononuclear non-heme iron dioxygenase. J. Inorg. Biochem. 93:66–70
    [Google Scholar]
  20. 20.
    Emerson JP, Kovaleva EG, Farquhar ER, Lipscomb JD, Que L Jr. 2008. Swapping metals in Fe- and Mn-dependent dioxygenases: evidence for oxygen activation without a change in metal redox state. PNAS 105:7347–52
    [Google Scholar]
  21. 21.
    Entsch B, van Berkel WJ. 1995. Structure and mechanism of para-hydroxybenzoate hydroxylase. FASEB J 9:476–83
    [Google Scholar]
  22. 22.
    Fang L, Shi T, Chen Y, Wu X, Zhang C et al. 2019. Kinetics and catabolic pathways of the insecticide chlorpyrifos, annotation of the degradation genes, and characterization of enzymes TcpA and Fre in Cupriavidus nantongensis X1T. J. Agric. Food Chem. 67:2245–54
    [Google Scholar]
  23. 23.
    Ferraro DJ, Gakhar L, Ramaswamy S. 2005. Rieske business: structure-function of Rieske non-heme oxygenases. Biochem. Biophys. Res. Commun. 338:175–90
    [Google Scholar]
  24. 24.
    Fetzner S. 2012. Ring-cleaving dioxygenases with a cupin fold. Appl. Environ. Microbiol. 78:2505–14
    [Google Scholar]
  25. 25.
    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. 180:2522–30
    [Google Scholar]
  26. 26.
    Fukumori F, Hausinger RP. 1993. Alcaligenes eutrophus JMP134 “2,4-dichlorophenoxyacetate monooxygenase” is an α-ketoglutarate-dependent dioxygenase. J. Bacteriol. 175:2083–86
    [Google Scholar]
  27. 27.
    Fukumori F, Hausinger RP. 1993. Purification and characterization of 2,4-dichlorophenoxyacetate/α-ketoglutarate dioxygenase. J. Biol. Chem. 268:24311–17
    [Google Scholar]
  28. 28.
    Gatti DL, Palfey BA, Lah MS, Entsch B, Massey V et al. 1994. The mobile flavin of 4-OH benzoate hydroxylase. Science 266:110–14
    [Google Scholar]
  29. 29.
    Gisi MR, Xun L. 2003. Characterization of chlorophenol 4-monooxygenase (TftD) and NADH:flavin adenine dinucleotide oxidoreductase (TftC) of Burkholderia cepacia AC1100. J. Bacteriol. 185:2786–92
    [Google Scholar]
  30. 30.
    Griffin SL, Godbey JA, Oman TJ, Embrey SK, Karnoup A et al. 2013. Characterization of aryloxyalkanoate dioxygenase-12, a nonheme Fe(II)/α-ketoglutarate-dependent dioxygenase, expressed in transgenic soybean and Pseudomonas fluorescens. J. Agric. Food Chem. 61:6589–96
    [Google Scholar]
  31. 31.
    Grzyska PK, Appelman EH, Hausinger RP, Proshlyakov DA. 2010. Insight into the mechanism of an iron dioxygenase by resolution of steps following the FeIV=O species. PNAS 107:3982–87
    [Google Scholar]
  32. 32.
    Gu T, Zhou C, Sorensen SR, Zhang J, He J et al. 2013. The novel bacterial N-demethylase PdmAB is responsible for the initial step of N,N-dimethyl-substituted phenylurea herbicide degradation. Appl. Environ. Microbiol. 79:7846–56
    [Google Scholar]
  33. 33.
    Guengerich FP. 2018. Mechanisms of cytochrome P450-catalyzed oxidations. ACS Catal. 8:10964–76
    [Google Scholar]
  34. 34.
    Guo Y, Li DF, Ji H, Zheng J, Zhou NY. 2020. Hexachlorobenzene monooxygenase substrate selectivity and catalysis: structural and biochemical insights. Appl. Environ. Microbiol. 87:e01965–20
    [Google Scholar]
  35. 35.
    Hausinger RP. 2004. Fe(II)/α-ketoglutarate-dependent hydroxylases and related enzymes. Crit. Rev. Biochem. Mol. Biol. 39:21–68
    [Google Scholar]
  36. 36.
    Herman PL, Behrens M, Chakraborty S, Chrastil BM, Barycki J, Weeks DP. 2005. A three-component dicamba O-demethylase from Pseudomonas maltophilia, strain DI-6: gene isolation, characterization, and heterologous expression. J. Biol. Chem. 280:24759–67
    [Google Scholar]
  37. 37.
    Hlouchova K, Rudolph J, Pietari JM, Behlen LS, Copley SD. 2012. Pentachlorophenol hydroxylase, a poorly functioning enzyme required for degradation of pentachlorophenol by Sphingobium chlorophenolicum. Biochemistry 51:3848–60
    [Google Scholar]
  38. 38.
    Hou YJ, Guo Y, Li DF, Zhou NY. 2021. Structural and biochemical analysis reveals a distinct catalytic site of salicylate 5-monooxygenase NagGH from Rieske dioxygenases. Appl. Environ. Microbiol. 87:e01629–20
    [Google Scholar]
  39. 39.
    Huang H, Pandya C, Liu C, Al-Obaidi NF, Wang M et al. 2015. Panoramic view of a superfamily of phosphatases through substrate profiling. PNAS 112:E1974–83
    [Google Scholar]
  40. 40.
    Huang J, Chen D, Jiang J 2020. Preferential catabolism of the (S)-enantiomer of the herbicide napropamide mediated by the enantioselective amidohydrolase SnaH and the dioxygenase Snpd in Sphingobium sp. strain B2. Environ. Microbiol. 22:286–96
    [Google Scholar]
  41. 41.
    Huang J, Chen D, Kong X, Wu S, Chen K, Jiang J 2021. Coinducible catabolism of 1-naphthol via synergistic regulation of the initial hydroxylase genes in Sphingobium sp. strain B2. Appl. Environ. Microbiol. 87:e00170–21
    [Google Scholar]
  42. 42.
    Hubner A, Danganan CE, Xun L, Chakrabarty AM, Hendrickson W. 1998. Genes for 2,4,5-trichlorophenoxyacetic acid metabolism in Burkholderia cepacia AC1100: characterization of the tftC and tftD genes and locations of the tft operons on multiple replicons. Appl. Environ. Microbiol. 64:2086–93
    [Google Scholar]
  43. 43.
    Huijbers MM, Montersino S, Westphal AH, Tischler D, van Berkel WJ. 2014. Flavin dependent monooxygenases. Arch. Biochem. Biophys. 544:2–17
    [Google Scholar]
  44. 44.
    Janssen DB, Oppentocht JE, Poelarends GJ. 2001. Microbial dehalogenation. Curr. Opin. Biotechnol. 12:254–58
    [Google Scholar]
  45. 45.
    Ji J, Zhang J, Liu Y, Zhang Y, Liu Y, Yan X 2019. The substrate specificity of aniline dioxygenase is mainly determined by two of its components: glutamine synthetase-like enzyme and oxygenase. Appl. Microbiol. Biotechnol. 103:6333–44
    [Google Scholar]
  46. 46.
    John CW, Hausinger RP, Proshlyakov DA. 2019. Structural origin of the large redox-linked reorganization in the 2-oxoglutarate dependent oxygenase, TauD. J. Am. Chem. Soc. 141:15318–26
    [Google Scholar]
  47. 47.
    Kal S, Que L. 2017. Dioxygen activation by nonheme iron enzymes with the 2-His-1-carboxylate facial triad that generate high-valent oxoiron oxidants. J. Biol. Inorg. Chem. 22:339–65
    [Google Scholar]
  48. 48.
    Karlsson A, Parales JV, Parales RE, Gibson DT, Eklund H, Ramaswamy S. 2003. Crystal structure of naphthalene dioxygenase: side-on binding of dioxygen to iron. Science 299:1039–42
    [Google Scholar]
  49. 49.
    Kijima K, Mita H, Kawakami M, Amada K 2018. Role of CadC and CadD in the 2,4-dichlorophenoxyacetic acid oxygenase system of Sphingomonas agrestis 58–1. J. Biosci. Bioeng. 125:649–53
    [Google Scholar]
  50. 50.
    Kitagawa W, Kimura N, Kamagata Y. 2004. A novel p-nitrophenol degradation gene cluster from a gram-positive bacterium, Rhodococcus opacus SAO101. J. Bacteriol. 186:4894–902
    [Google Scholar]
  51. 51.
    Kitagawa W, Takami S, Miyauchi K, Masai E, Kamagata Y et al. 2002. Novel 2,4-dichlorophenoxyacetic acid degradation genes from oligotrophic Bradyrhizobium sp. strain HW13 isolated from a pristine environment. J. Bacteriol. 184:509–18
    [Google Scholar]
  52. 52.
    Knoot CJ, Purpero VM, Lipscomb JD. 2015. Crystal structures of alkylperoxo and anhydride intermediates in an intradiol ring-cleaving dioxygenase. PNAS 112:388–93
    [Google Scholar]
  53. 53.
    Kovaleva EG, Lipscomb JD. 2007. Crystal structures of Fe2+ dioxygenase superoxo, alkylperoxo, and bound product intermediates. Science 316:453–57
    [Google Scholar]
  54. 54.
    Kumar P, Lindeman SV, Fiedler AT. 2019. Cobalt superoxo and alkylperoxo complexes derived from reaction of ring-cleaving dioxygenase models with O2. J. Am. Chem. Soc. 141:10984–87
    [Google Scholar]
  55. 55.
    Ledger T, Pieper DH, Gonzalez B. 2006. Chlorophenol hydroxylases encoded by plasmid pJP4 differentially contribute to chlorophenoxyacetic acid degradation. Appl. Environ. Microbiol. 72:2783–92
    [Google Scholar]
  56. 56.
    Li N, Yao L, He Q, Qiu J, Cheng D et al. 2018. 3,6-Dichlorosalicylate catabolism is initiated by the DsmABC cytochrome P450 monooxygenase system in Rhizorhabdus dicambivorans Ndbn-20. Appl. Environ. Microbiol. 84:e02133–17
    [Google Scholar]
  57. 57.
    Li S, Du L, Bernhardt R. 2020. Redox partners: function modulators of bacterial P450 enzymes. Trends Microbiol 28:445–54
    [Google Scholar]
  58. 58.
    Liu T, Chapman PJ. 1984. Purification and properties of a plasmid-encoded 2,4-dichlorophenol hydroxylase. FEBS Lett 173:314–18
    [Google Scholar]
  59. 59.
    Malmström BG. 1982. Enzymology of oxygen. Annu. Rev. Biochem. 51:21–59
    [Google Scholar]
  60. 60.
    Matthews A, Saleem-Batcha R, Sanders JN, Stull F, Houk KN, Teufel R. 2020. Aminoperoxide adducts expand the catalytic repertoire of flavin monooxygenases. Nat. Chem. Biol. 16:556–63
    [Google Scholar]
  61. 61.
    Min J, Lu Y, Hu X, Zhou NY. 2016. Biochemical characterization of 3-methyl-4-nitrophenol degradation in Burkholderia sp. strain SJ98. Front. Microbiol. 7:791
    [Google Scholar]
  62. 62.
    Müller TA, Byrde SM, Werlen C, van der Meer JR, Kohler HP. 2004. Genetic analysis of phenoxyalkanoic acid degradation in Sphingomonas herbicidovorans MH. Appl. Environ. Microbiol. 70:6066–75
    [Google Scholar]
  63. 63.
    Müller TA, Fleischmann T, van der Meer JR, Kohler HP. 2006. Purification and characterization of two enantioselective α-ketoglutarate-dependent dioxygenases, RdpA and SdpA, from Sphingomonas herbicidovorans MH. Appl. Environ. Microbiol. 72:4853–61
    [Google Scholar]
  64. 64.
    Nagano S, Poulos TL. 2005. Crystallographic study on the dioxygen complex of wild-type and mutant cytochrome P450cam: implications for the dioxygen activation mechanism. J. Biol. Chem. 280:31659–63
    [Google Scholar]
  65. 65.
    Nagy I, Compernolle F, Ghys K, Vanderleyden J, De Mot R. 1995. A single cytochrome P-450 system is involved in degradation of the herbicides EPTC (S-ethyl dipropylthiocarbamate) and atrazine by Rhodococcus sp. strain NI86/21. Appl. Environ. Microbiol. 61:2056–60
    [Google Scholar]
  66. 66.
    Nagy I, Schoofs G, Compernolle F, Proost P, Vanderleyden J, de Mot R. 1995. Degradation of the thiocarbamate herbicide EPTC (S-ethyl dipropylcarbamothioate) and biosafening by Rhodococcus sp. strain NI86/21 involve an inducible cytochrome P-450 system and aldehyde dehydrogenase. J. Bacteriol. 177:676–87
    [Google Scholar]
  67. 67.
    Nickel K, Suter MJ, Kohler HP. 1997. Involvement of two α-ketoglutarate-dependent dioxygenases in enantioselective degradation of (R)- and (S)-mecoprop by Sphingomonas herbicidovorans MH. J. Bacteriol. 179:6674–79
    [Google Scholar]
  68. 68.
    Ohlendorf DH, Lipscomb JD, Weber PC. 1988. Structure and assembly of protocatechuate 3,4-dioxygenase. Nature 336:403–5
    [Google Scholar]
  69. 69.
    Orville AM, Lipscomb JD, Ohlendorf DH. 1997. Crystal structures of substrate and substrate analog complexes of protocatechuate 3,4-dioxygenase: endogenous Fe3+ ligand displacement in response to substrate binding. Biochemistry 36:10052–66
    [Google Scholar]
  70. 70.
    Perry LL, Zylstra GJ. 2007. Cloning of a gene cluster involved in the catabolism of p-nitrophenol by Arthrobacter sp. strain JS443 and characterization of the p-nitrophenol monooxygenase. J. Bacteriol. 189:7563–72
    [Google Scholar]
  71. 71.
    Price JC, Barr EW, Glass TE, Krebs C, Bollinger JM Jr. 2003. Evidence for hydrogen abstraction from C1 of taurine by the high-spin Fe(IV) intermediate detected during oxygen activation by taurine:α-ketoglutarate dioxygenase (TauD). J. Am. Chem. Soc. 125:13008–9
    [Google Scholar]
  72. 72.
    Rogers MS, Lipscomb JD. 2019. Salicylate 5-hydroxylase: intermediates in aromatic hydroxylation by a Rieske monooxygenase. Biochemistry 58:5305–19
    [Google Scholar]
  73. 73.
    Schleinitz KM, Kleinsteuber S, Vallaeys T, Babel W. 2004. Localization and characterization of two novel genes encoding stereospecific dioxygenases catalyzing 2(2,4-dichlorophenoxy)propionate cleavage in Delftia acidovorans MC1. Appl. Environ. Microbiol. 70:5357–65
    [Google Scholar]
  74. 74.
    Schlichting I, Berendzen J, Chu K, Stock AM, Maves SA et al. 2000. The catalytic pathway of cytochrome P450cam at atomic resolution. Science 287:1615–22
    [Google Scholar]
  75. 75.
    Schuster J, Purswani J, Breuer U, Pozo C, Harms H et al. 2013. Constitutive expression of the cytochrome P450 EthABCD monooxygenase system enables degradation of synthetic dialkyl ethers in Aquincola tertiaricarbonis L108. Appl. Environ. Microbiol. 79:2321–27
    [Google Scholar]
  76. 76.
    Shao ZQ, Behki R. 1996. Characterization of the expression of the thcB gene, coding for a pesticide-degrading cytochrome P-450 in Rhodococcus strains. Appl. Environ. Microbiol. 62:403–7
    [Google Scholar]
  77. 77.
    Smidt H, de Vos WM. 2004. Anaerobic microbial dehalogenation. Annu. Rev. Microbiol. 58:43–73
    [Google Scholar]
  78. 78.
    Sucharitakul J, Tinikul R, Chaiyen P. 2014. Mechanisms of reduced flavin transfer in the two-component flavin-dependent monooxygenases. Arch. Biochem. Biophys. 555–56:33–46
    [Google Scholar]
  79. 79.
    Takeo M, Murakami M, Niihara S, Yamamoto K, Nishimura M et al. 2008. Mechanism of 4-nitrophenol oxidation in Rhodococcus sp. strain PN1: characterization of the two-component 4-nitrophenol hydroxylase and regulation of its expression. J. Bacteriol. 190:7367–74
    [Google Scholar]
  80. 80.
    Takeo M, Ohara A, Sakae S, Okamoto Y, Kitamura C et al. 2013. Function of a glutamine synthetase-like protein in bacterial aniline oxidation via γ-glutamylanilide. J. Bacteriol. 195:4406–14
    [Google Scholar]
  81. 81.
    Takeo M, Yamamoto K, Sonoyama M, Miyanaga K, Kanbara N et al. 2018. Characterization of the 3-methyl-4-nitrophenol degradation pathway and genes of Pseudomonas sp. strain TSN1. J. Biosci. Bioeng. 126:355–62
    [Google Scholar]
  82. 82.
    Toplak M, Matthews A, Teufel R. 2021. The devil is in the details: the chemical basis and mechanistic versatility of flavoprotein monooxygenases. Arch. Biochem. Biophys. 698:108732
    [Google Scholar]
  83. 83.
    Trivedi VD, Jangir PK, Sharma R, Phale PS. 2016. Insights into functional and evolutionary analysis of carbaryl metabolic pathway from Pseudomonas sp. strain C5pp. Sci. Rep. 6:38430
    [Google Scholar]
  84. 84.
    Uemura T, Kita A, Watanabe Y, Adachi M, Kuroki R, Morimoto Y. 2016. The catalytic mechanism of decarboxylative hydroxylation of salicylate hydroxylase revealed by crystal structure analysis at 2.5 Å resolution. Biochem. Biophys. Res. Commun. 469:158–63
    [Google Scholar]
  85. 85.
    Vaillancourt FH, Bolin JT, Eltis LD. 2006. The ins and outs of ring-cleaving dioxygenases. Crit. Rev. Biochem. Mol. Biol. 41:241–67
    [Google Scholar]
  86. 86.
    Visitsatthawong S, Chenprakhon P, Chaiyen P, Surawatanawong P. 2015. Mechanism of oxygen activation in a flavin-dependent monooxygenase: a nearly barrierless formation of C4a-hydroperoxyflavin via proton-coupled electron transfer. J. Am. Chem. Soc. 137:9363–74
    [Google Scholar]
  87. 87.
    Wang C, Chen Q, Wang R, Shi C, Yan X et al. 2014. A novel angular dioxygenase gene cluster encoding 3-phenoxybenzoate 1′,2′-dioxygenase in Sphingobium wenxiniae JZ-1. Appl. Environ. Microbiol. 80:3811–18
    [Google Scholar]
  88. 88.
    Wang F, Zhou J, Li Z, Dong W, Hou Y et al. 2015. Involvement of the cytochrome P450 system EthBAD in the N-deethoxymethylation of acetochlor by Rhodococcus sp. strain T3–1. Appl. Environ. Microbiol. 81:2182–88
    [Google Scholar]
  89. 89.
    Wang J, Ortiz-Maldonado M, Entsch B, Massey V, Ballou D, Gatti DL. 2002. Protein and ligand dynamics in 4-hydroxybenzoate hydroxylase. PNAS 99:608–13
    [Google Scholar]
  90. 90.
    Wang X, Li B, Herman PL, Weeks DP. 1997. A three-component enzyme system catalyzes the O-demethylation of the herbicide dicamba in Pseudomonas maltophilia DI-6. Appl. Environ. Microbiol. 63:1623–26
    [Google Scholar]
  91. 91.
    Wang Y, Li J, Liu A. 2017. Oxygen activation by mononuclear nonheme iron dioxygenases involved in the degradation of aromatics. J. Biol. Inorg. Chem. 22:395–405
    [Google Scholar]
  92. 92.
    Wang Z, Shaik S, Wang B. 2021. Conformational motion of ferredoxin enables efficient electron transfer to heme in the full-length P450TT. J. Am. Chem. Soc. 143:1005–16
    [Google Scholar]
  93. 93.
    Warman AJ, Robinson JW, Luciakova D, Lawrence AD, Marshall KR et al. 2012. Characterization of Cupriavidus metallidurans CYP116B1—a thiocarbamate herbicide oxygenating P450-phthalate dioxygenase reductase fusion protein. FEBS J 279:1675–93
    [Google Scholar]
  94. 94.
    Webb BN, Ballinger JW, Kim E, Belchik SM, Lam KS et al. 2010. Characterization of chlorophenol 4-monooxygenase (TftD) and NADH:FAD oxidoreductase (TftC) of Burkholderia cepacia AC1100. J. Biol. Chem. 285:2014–27
    [Google Scholar]
  95. 95.
    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 41:9611–26
    [Google Scholar]
  96. 96.
    Wolfe MD, Parales JV, Gibson DT, Lipscomb JD. 2001. Single turnover chemistry and regulation of O2 activation by the oxygenase component of naphthalene 1,2-dioxygenase. J. Biol. Chem. 276:1945–53
    [Google Scholar]
  97. 97.
    Wright TR, Shan G, Walsh TA, Lira JM, Cui C et al. 2010. Robust crop resistance to broadleaf and grass herbicides provided by aryloxyalkanoate dioxygenase transgenes. PNAS 107:20240–45
    [Google Scholar]
  98. 98.
    Xun L. 1996. Purification and characterization of chlorophenol 4-monooxygenase from Burkholderia cepacia AC1100. J. Bacteriol. 178:2645–49
    [Google Scholar]
  99. 99.
    Xun L, Orser CS. 1991. Purification and properties of pentachlorophenol hydroxylase, a flavoprotein from Flavobacterium sp. strain ATCC 39723. J. Bacteriol. 173:4447–53
    [Google Scholar]
  100. 100.
    Xun L, Topp E, Orser CS. 1992. Confirmation of oxidative dehalogenation of pentachlorophenol by a Flavobacterium pentachlorophenol hydroxylase. J. Bacteriol. 174:5745–47
    [Google Scholar]
  101. 101.
    Xun L, Topp E, Orser CS. 1992. Diverse substrate range of a Flavobacterium pentachlorophenol hydroxylase and reaction stoichiometries. J. Bacteriol. 174:2898–902
    [Google Scholar]
  102. 102.
    Yadid I, Rudolph J, Hlouchova K, Copley SD. 2013. Sequestration of a highly reactive intermediate in an evolving pathway for degradation of pentachlorophenol. PNAS 110:E2182–90
    [Google Scholar]
  103. 103.
    Yan X, Gu T, Yi Z, Huang J, Liu X et al. 2016. Comparative genomic analysis of isoproturon-mineralizing sphingomonads reveals the isoproturon catabolic mechanism. Environ. Microbiol. 18:4888–906
    [Google Scholar]
  104. 104.
    Yan X, Huang J, Xu X, Chen D, Xie X et al. 2018. Enhanced and complete removal of phenylurea herbicides by combinational transgenic plant-microbe remediation. Appl. Environ. Microbiol. 84:e00273–18
    [Google Scholar]
  105. 105.
    Yan X, Jin W, Wu G, Jiang W, Yang Z et al. 2018. Hydrolase CehA and monooxygenase CfdC are responsible for carbofuran degradation in Sphingomonas sp. strain CDS-1. Appl. Environ. Microbiol. 84:e00805–18
    [Google Scholar]
  106. 106.
    Yoshinaga M, Rosen BP. 2014. A C·As lyase for degradation of environmental organoarsenical herbicides and animal husbandry growth promoters. PNAS 111:7701–6
    [Google Scholar]
  107. 107.
    Zhang H, Yu T, Li J, Wang YR, Wang GL et al. 2018. Two dcm gene clusters essential for the degradation of diclofop-methyl in a microbial consortium of Rhodococcus sp. JT-3 and Brevundimonas sp. JT-9. J. Agric. Food Chem. 66:12217–26
    [Google Scholar]
  108. 108.
    Zhang JJ, Liu H, Xiao Y, Zhang XE, Zhou NY. 2009. Identification and characterization of catabolic para-nitrophenol 4-monooxygenase and para-benzoquinone reductase from Pseudomonas sp. strain WBC-3. J. Bacteriol. 191:2703–10
    [Google Scholar]
  109. 109.
    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. 184:1547–55
    [Google Scholar]
  110. 110.
    Zhou Y, Ke Z, Ye H, Hong M, Xu Y et al. 2020. Hydrolase CehA and a novel two-component 1-naphthol hydroxylase CehC1C2 are responsible for the two initial steps of carbaryl degradation in Rhizobium sp. X9. J. Agric. Food Chem. 68:14739–47
    [Google Scholar]
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