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Chapter 23 : Metabolism of Aromatic Compounds

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Abstract:

There has been a long-standing fundamental and practical interest in microbial metabolism of aromatic compounds. The goal of this chapter is to provide an overview of the generally used, well-established methods that are the hallmark of aromatic metabolism studies. Growing cells in large liquid volumes such as in a fermentor or chemostat is a challenge as well. The high aeration rate of these cultures strips volatile aromatic substrates out of the medium. Toluene and related aromatic compounds have long been used as models for the analysis of aromatic hydrocarbon degradation due to the fact that there are several catabolic pathways known for its degradation, illustrating the many possible ways by which aromatic hydrocarbons can be metabolized. Bacterial metabolism of aromatic hydrocarbons can result in a variety of chemically different compounds, resulting from the ring oxidation and the later ring cleavage steps. These metabolites can be either neutral or charged and either chemically stable or unstable, and thus, care must be taken in the extraction process to stabilize and competently extract the chemicals. If one can identify a -dihydrodiol intermediate in culture supernatants, then a priori the pathway proceeds via an initial dioxygenase attack of the aromatic nucleus. However, if one detects only phenolic or dihydroxylated products in the culture medium then it is uncertain whether the catabolic pathway proceeds by an initial dioxygenase or by two initial monooxygenases.

Citation: Kukor J, Wawrik B, Zylstra G. 2007. Metabolism of Aromatic Compounds, p 586-595. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch23

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Aromatic Hydrocarbon Degradation
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High-Performance Liquid Chromatography
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FIGURE 1

Method for growing bacteria in the presence of volatile liquid aromatic hydrocarbons either in a shake flask (A) or on a solid medium (B).

Citation: Kukor J, Wawrik B, Zylstra G. 2007. Metabolism of Aromatic Compounds, p 586-595. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch23
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Image of FIGURE 2
FIGURE 2

Photograph of bacterial colonies on a plate that has phenanthrene applied to it by the spray plate technique. As the colonies grow, they form clear zones, indicating that the substrate is being utilized. This photograph was kindly provided by J. Philp, Napier University, Edinburgh, United Kingdom.

Citation: Kukor J, Wawrik B, Zylstra G. 2007. Metabolism of Aromatic Compounds, p 586-595. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch23
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Image of FIGURE 3
FIGURE 3

Representative known pathways for the degradation of toluene illustrating typical reactions catalyzed by enzymes that act on aromatic compounds.

Citation: Kukor J, Wawrik B, Zylstra G. 2007. Metabolism of Aromatic Compounds, p 586-595. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch23
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References

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1. Alley, J. F.,, and L. R. Brown. 2000. Use of sublimation to prepare solid microbial media with water-insoluble substrates. Appl. Environ. Microbiol. 66: 439 442.
2. Arciero, D. M.,, A. M. Orville,, and J. D. Lipscomb. 1990. Protocatechuate 4,5-dioxygenase from Pseudomonas testosteroni. Methods Enzymol. 188: 89 95.
3. Batie, C. J.,, E. LaHaie,, and D. P. Ballou. 1987. Purification and characterization of phthalate oxygenase and phthalate oxygenase reductase from Pseudomonas cepacia. J. Biol. Chem. 262: 1510 1518.
4. Bayly, R. C.,, S. Dagley,, and D. T. Gibson. 1966. The metabolism of cresols by species of Pseudomonas. Biochem. J. 101: 293 301.
5. Bayly, R. C.,, and G. J. Wigmore. 1973. Metabolism of phenol and cresols by mutants of Pseudomonas putida. J. Bacteriol. 113: 1112 1120.
6. Blau, K.,, and J. Halket. 1993. Handbook of Derivatives for Chromatography, 2nd ed. John Wiley & Sons, New York, N.Y..
7. Bogardt, A. H.,, and B. B. Hemmingsen. 1992. Enumeration of phenanthrene-degrading bacteria by an overlayer technique and its use in evaluation of petroleumcontaminated sites. Appl. Environ. Microbiol. 58: 2579 2582.
8. Brown, E. J.,, and J. F. Braddock. 1990. Sheen Screen, a miniaturized most-probable-number method for enumeration of oil-degrading microorganisms. Appl. Environ. Microbiol. 56: 3895 3896.
9. Chapman, P. J.,, and D. W. Ribbons. 1976. Metabolism of resorcinylic compounds by bacteria: orcinol pathway in Pseudomonas putida. J. Bacteriol. 125: 975 984.
10. Dorn, E.,, and H. J. Knackmuss. 1978. Chemical structure and biodegradability of halogenated aromatic compounds. Two catechol 1,2-dioxygenases from a 3-chlorobenzoategrown pseudomonad. Biochem. J. 174: 73 84.
11. Ensley, B. D.,, and D. T. Gibson. 1983. Naphthalene dioxygenase: purification and properties of a terminal oxygenase component. J. Bacteriol. 155: 505 511.
12. Ensley, B. D.,, D. T. Gibson,, and A. L. Laborde. 1982. Oxidation of naphthalene by a multicomponent enzyme system from Pseudomonas sp. strain NCIB 9816. J. Bacteriol. 149: 948 954.
13. Entsch, B. 1990. Hydroxybenzoate hydroxylase. Methods Enzymol. 188: 138 147.
14. Fujisawa, H. 1970. Protocatechuate-3,4-dioxygenase ( Pseudomonas). Methods Enzymol. 17A: 526 529.
15. Gibson, D. T.,, G. E. Cardini,, F. C. Maseles,, and R. E. Kallio. 1970. Incorporation of oxygen-18 into benzene by Pseudomonas putida. Biochemistry 9: 1631 1635.
16. Gibson, D. T.,, M. Hensley,, H. Yoshioka,, and T. J. Mabry. 1970. Formation of (_)-cis-2,3-dihydroxy-1- methylcyclohexa-4,6-diene from toluene by Pseudomonas putida. Biochemistry 9: 1626 1630.
17. Gibson, D. T.,, R. L. Roberts,, M. C. Wells,, and V. M. Kobal. 1973. Oxidation of biphenyl by a Beijerinckia species. Biochem. Biophys. Res. Commun. 50: 211 219.
18. Gibson, D. T.,, G. J. Zylstra,, and S. Chauhan,. 1990. Biotransformations catalyzed by toluene dioxygenase from Pseudomonas putita F1, p. 121 132. In S. Silver,, A. M. Chakrabarty,, B. Iglewski,, and S. Kaplan (ed.), Pseudomonas: Biotransformations, Pathogenesis, and Evolving Biotechnology. American Society for Microbiology, Washington, D.C..
19. Gottschalk, G. 1986. Bacterial Metabolism, 2nd ed. Springer-Verlag, New York, N.Y..
20. Habe, H.,, J. S. Chung,, J. H. Lee,, K. Kasuga,, T. Yoshida,, H. Nojiri,, and T. Omori. 2001. Degradation of chlorinated dibenzofurans and dibenzo- p-dioxins by two types of bacteria having angular dioxygenases with different features. Appl. Environ. Microbiol. 67: 3610 3617.
21. Haddock, J. D.,, and D. T. Gibson. 1995. Purification and characterization of the oxygenase component of biphenyl 2,3-dioxygenase from Pseudomonas sp. strain LB400. J. Bacteriol. 177: 5834 5839.
22. Haddock, J. D.,, L. M. Nadim,, and D. T. Gibson. 1993. Oxidation of biphenyl by a multicomponent enzyme system from Pseudomonas sp. strain LB400. J. Bacteriol. 175: 395 400.
23. Haigler, B. E.,, and J. C. Spain. 1991. Biotransformation of nitrobenzene by bacteria containing toluene degradative pathways. Appl. Environ. Microbiol. 57: 3156 3162.
24. Hartmans, S.,, M. J. van der Werf,, and J. A. de Bont. 1990. Bacterial degradation of styrene involving a novel flavin adenine dinucleotide-dependent styrene monooxygenase. Appl. Environ. Microbiol. 56: 1347 1351.
25. Heipieper, J. H.,, F. J. Weber,, J. Sikkema,, H. Keweloh,, and J. A. M. de Bont. 1994. Mechanisms of resistance of whole cells to toxic organic solvents. Trends Biotechnol. 12: 409 415.
26. Heitkamp, M. A.,, and C. E. Cerniglia. 1987. Effects of chemical structure and exposure on the microbial degradation of polycyclic aromatic hydrocarbons in freshwater and estuarine ecosystems. Environ. Toxicol. Chem. 6: 535 546.
27. Kahng, H. Y.,, J. C. Malinverni,, M. M. Majko,, and J. J. Kukor. 2001. Genetic and functional analysis of the tbc operons for catabolism of alkyl- and chloroaromatic compounds in Burkholderia sp. strain JS150. Appl. Environ. Microbiol. 67: 4805 4816.
28. Kaphammer, B.,, J. J. Kukor,, and R. H. Olsen. 1990. Regulation of tfdCDEF by tfdR of the 2,4-dichlorophenoxyacetic acid degradation plasmid pJP4. J. Bacteriol. 172: 2280 2286.
29. Kataeva, I. A.,, and L. A. Golovleva. 1990. Catechol 2,3- dioxygenases from Pseudomonas aeruginosa 2x. Methods Enzymol. 188: 115 121.
30. Kieboom, J.,, J. J. Dennis,, J. A. de Bont,, and G. J. Zylstra. 1998. Identification and molecular characterization of an efflux pump involved in Pseudomonas putida S12 solvent tolerance. J. Biol. Chem. 273: 85 91.
31. Kim, E.,, and G. J. Zylstra. 1995. Molecular and biochemical characterization of two meta-cleavage dioxygenases involved in biphenyl and m-xylene degradation by Beijerinckia sp. strain B1. J. Bacteriol. 177: 3095 3103.
32. Kiyohara, H.,, K. Nagao,, and K. Yana. 1982. Rapid screen for bacteria degrading water-insoluble, solid hydrocarbons on agar plates. Appl. Environ. Microbiol. 43: 454 457.
33. Knapp, D. R. 1979. Handbook of Analytical Derivatization Reactions. John Wiley & Sons, New York, N.Y..
34. Kukor, J. J.,, and R. H. Olsen. 1991. Genetic organization and regulation of a meta cleavage pathway for catechols produced from catabolism of toluene, benzene, phenol, and cresols by Pseudomonas pickettii PKO1. J. Bacteriol. 173: 4587 4594.
35. Kukor, J. J.,, R. H. Olsen,, and J. S. Siak. 1989. Recruitment of a chromosomally encoded maleylacetate reductase for degradation of 2,4-dichlorophenoxyacetic acid by plasmid pJP4. J. Bacteriol. 171: 3385 3390.
36. Lessner, D. J.,, G. R. Johnson,, R. E. Parales,, J. C. Spain,, and D. T. Gibson. 2002. Molecular characterization and substrate specificity of nitrobenzene dioxygenase from Comamonas sp. strain JS765. Appl. Environ. Microbiol. 68: 634 641.
37. Liu, T.,, and P. J. Chapman. 1984. Purification and properties of a plasmid-encoded 2,4-dichlorophenol hydroxylase. FEBS Lett. 173: 314 318.
38. Nakagawa, H.,, H. Inoue,, and Y. Takeda. 1963. Characteristics of catechol oxygenase from Brevibacterium fuscum. J. Biochem. (Tokyo) 54: 65 74.
39. Neujahr, H. Y.,, and A. Gaal. 1973. Phenol hydroxylase from yeast. Purification and properties of the enzyme from Trichosporon cutaneum. Eur. J. Biochem. 35: 386 400.
40. Ngai, K. L.,, E. L. Neidle,, and L. N. Ornston. 1990. Catechol and chlorocatechol 1,2-dioxygenases. Methods Enzymol. 188: 122 126.
41. Ngai, K. L.,, and L. N. Ornston. 1988. Abundant expression of Pseudomonas genes for chlorocatechol metabolism. J. Bacteriol. 170: 2412 2413.
42. Nishino, S. F.,, G. C. Paoli,, and J. C. Spain. 2000. Aerobic degradation of dinitrotoluenes and pathway for bacterial degradation of 2,6-dinitrotoluene. Appl. Environ. Microbiol. 66: 2139 2147.
43. Nozaki, M. 1970. Metapyrocatechase. Methods Enzymol. 17A: 522 525.
44. Pieper, D. H.,, K.-H. Engesser,, and H.-J. Knackmuss. 1989. Regulation of catabolic pathways of phenoxyacetic acids and phenol in Alcaligenes eutrophus JMP134. Arch. Microbiol. 151: 365 371.
45. Pollmann, K.,, S. Beil,, and D. H. Pieper. 2001. Transformation of chlorinated benzenes and toluenes by Ralstonia sp. strain PS12 tecA (tetrachlorobenzene dioxygenase) and tecB (chlorobenzene dihydrodiol dehydrogenase) gene products. Appl. Environ. Microbiol. 67: 4057 4063.
46. Ramos, J. L.,, E. Duque,, J. J. Rodriguez-Herva,, P. Godoy,, A. Haidour,, F. Reyes,, and A. Fernandez- Barrero. 1997. Mechanisms for solvent tolerance in bacteria. J. Biol. Chem. 272: 3887 3890.
47. Reineke, W.,, and H. J. Knackmuss. 1984. Microbial metabolism of haloaromatics: isolation and properties of a chlorobenzene-degrading bacterium. Appl. Environ. Microbiol. 47: 395 402.
48. Resnick, S. M.,, and D. T. Gibson. 1996. Regio- and stereospecific oxidation of fluorene, dibenzofuran, and dibenzothiophene by naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816-4. Appl. Environ. Microbiol. 62: 4073 4080.
49. Rosenberg, E., 1992. The hydrocarbon-oxidizing bacteria, p. 446 459. In A. Balows,, H. G. Truper,, M. Dworkin,, W. Harder,, and K.-H. Schleifer (ed.), The Prokaryotes, 2nd ed. Springer-Verlag, New York, N.Y..
50. Schmidt, E.,, and H. J. Knackmuss. 1980. Chemical structure and biodegradability of halogenated aromatic compounds. Conversion of chlorinated muconic acids into maleoylacetic acid. Biochem. J. 192: 339 347.
51. Seeger, M.,, B. Camara,, and B. Hofer. 2001. Dehalogenation, denitration, dehydroxylation, and angular attack on substituted biphenyls and related compounds by a biphenyl dioxygenase. J. Bacteriol. 183: 3548 3555.
52. Seeger, M.,, K. N. Timmis,, and B. Hofer. 1995. Conversion of chlorobiphenyls into phenylhexadienoates and benzoates by the enzymes of the upper pathway for polychlorobiphenyl degradation encoded by the bph locus of Pseudomonas sp. strain LB400. Appl. Environ. Microbiol. 61: 2654 2658.
53. Spain, J. C.,, and S. F. Nishino. 1987. Degradation of 1,4- dichlorobenzene by a Pseudomonas sp. Appl. Environ. Microbiol. 53: 1010 1019.
54. Spain, J. C.,, G. J. Zylstra,, C. K. Blake,, and D. T. Gibson. 1989. Monohydroxylation of phenol and 2,5- dichlorophenol by toluene dioxygenase in Pseudomonas putida F1. Appl. Environ. Microbiol. 55: 2648 2652.
55. Subramanian, V.,, T. N. Liu,, W. K. Yeh,, and D. T. Gibson. 1979. Toluene dioxygenase: purification of an iron-sulfur protein by affinity chromatography. Biochem. Biophys. Res. Commun. 91: 1131 1139.
56. Warhurst, A. M.,, K. F. Clarke,, R. A. Hill,, R. A. Holt,, and C. A. Fewson. 1994. Metabolism of styrene by Rhodococcus rhodochrous NCIMB 13259. Appl. Environ. Microbiol. 60: 1137 1145.
57. Whited, G. M.,, and D. T. Gibson. 1991. Separation and partial characterization of the enzymes of the toluene-4- monooxygenase catabolic pathway in Pseudomonas mendocina KR1. J. Bacteriol. 173: 3017 3020.
58. Whited, G. M.,, and D. T. Gibson. 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 3016.
59. Whittaker, J. W.,, A. M. Orville,, and J. D. Lipscomb. 1990. Protocatechuate 3,4-dioxygenase from Brevibacterium fuscum. Methods Enzymol. 188: 82 88.
60. Williams, P. A.,, and K. Murray. 1974. Metabolism of benzoate and the methylbenzoates by Pseudomonas putida (arvilla) mt-2: evidence for the existence of a TOL plasmid. J. Bacteriol. 120: 416 423.
61. Wolgel, S. A.,, and J. D. Lipscomb. 1990. Protocatechuate 2,3-dioxygenase from Bacillus macerans. Methods Enzymol. 188: 95 101.
62. Wrenn, B. A.,, and A. D. Venosa. 1996. Selective enumeration of aromatic and aliphatic hydrocarbon degrading bacteria by a most-probable-number procedure. Can. J. Microbiol. 42: 252 258.
63. Wright, A.,, and R. H. Olsen. 1994. Self-mobilization and organization of the genes encoding the toluene metabolic pathway of Pseudomonas mendocina KR1. Appl. Environ. Microbiol. 60: 235 242.
64. Yeh, W. K.,, D. T. Gibson,, and T. N. Liu. 1977. Toluene dioxygenase: a multicomponent enzyme system. Biochem. Biophys. Res. Commun. 78: 401 410.
65. Yen, K. M.,, and M. R. Karl. 1992. Identification of a new gene, tmoF, in the Pseudomonas mendocina KR1 gene cluster encoding toluene-4-monooxygenase. J. Bacteriol. 174: 7253 7261.
66. Yen, K. M.,, M. R. Karl,, L. M. Blatt,, M. J. Simon,, R. B. Winter,, P. R. Fausset,, H. S. Lu,, A. A. Harcourt,, and K. K. Chen. 1991. Cloning and characterization of a Pseudomonas mendocina KR1 gene cluster encoding toluene-4-monooxygenase. J. Bacteriol. 173: 5315 5327.
67. Zylstra, G. J., 1995. Molecular analysis of aromatic hydrocarbon degradation, p. 83 115. In S. J. Garte (ed.), Molecular Environmental Biology. Lewis Publishers, Boca Raton, F.L..
68. Zylstra, G. J.,, and D. T. Gibson,. 1997. Aromatic hydrocarbon degradation: a molecular approach, p. 183 203. In J. K. Setlow (ed.), Genetic Engineering: Principles and Methods. Plenum Press, New York, N.Y..
69. Zylstra, G. J.,, and D. T. Gibson. 1989. Toluene degradation by Pseudomonas putida F1. Nucleotide sequence of the todC1C2BADE genes and their expression in Escherichia coli. J. Biol. Chem. 264: 14940 14946.
70. Zylstra, G. J.,, R. H. Olsen,, and D. P. Ballou. 1989. Cloning, expression, and regulation of the Pseudomonas cepacia protocatechuate 3,4-dioxygenase genes. J. Bacteriol. 171: 5907 5914.

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