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Genomic Insights in the Metabolism of Aromatic Compounds in Pseudomonas

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Pseudomonas

Abstract

Pseudomonads are ubiquitous γ-proteobacteria with a remarkable degree of physiological and genetic adaptability. Members of the genus Pseudomonas are found in large numbers in different natural environments (soil, freshwater, marine) as well as in association with plants and animals. These bacteria are involved in important metabolic activities in the environment, being element cycling and degradation of biogenic and xenobiotic pollutants some of their major tasks56, 64, 90, 96. The metabolic versatility of Pseudomonas strains has been used for biotechnological applications, mainly to degrade waste (bioremediation) and to synthesize specialty chemicals (biocatalysis)69, 99.

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References

  1. Aranda-Olmedo, I., Tobes, R., Manzanera, M., Ramos, J.L., and Marqués, S., 2002, Species-specific repetitive extragenic palindromic (REP) sequences in Pseudomonas putida. Nucleic Acids Res., 30:1826–1833

    Article  PubMed  CAS  Google Scholar 

  2. Assinder, S.J. and Williams, P.A., 1990, The TOL plasmids: Determinants of the catabolism of toluene and the xylenes. Adv. Microbiol. Physiol., 31:1–69.

    Article  CAS  Google Scholar 

  3. Bagdasarian, M., Lurz, R., Rückert, B., Franklin, F.C.H., Bagdasarian, M.M., and Timmis, K.N., 1981, Specific-purpose plasmid cloning vectors. II. Broad host range, high copy number, RSFlOlO-derived vectors, and a host-vector system for gene cloning in Pseudomonas. Gene, 16:237–247.

    Article  PubMed  CAS  Google Scholar 

  4. Bayley, S.A., Duggleby, C.J., Worsey, M.J., Williams, P.A., Hardy, K.G., and Broda, P., 1977, Two modes of loss of the TOL function from Pseudomonas putida mt-2. Mol. Gen. Genet., 154:203–204.

    Article  PubMed  CAS  Google Scholar 

  5. Beil, S., Kehrli, H., James, P., Staudenmann, W., Cook, A.M., Leisinger, T., and Kertesz, M.A., 1995, Purification and characterization of the arylsulfatase synthesized by Pseudomonas aeruginosa PAO during growth in sulfate-free medium and cloning of the arylsulfatase gene (atsA). Eur. J. Biochem., 229:385–394.

    Article  PubMed  CAS  Google Scholar 

  6. Bertani, I., Kojic, M., and Venturi, V., 2001, Regulation of the p-hydroxybenzoic acid hydro-xylase gene (pobA) in plant-growth-promoting Pseudomonas putida WCS358. Microbiology, 147:1611–1620.

    PubMed  CAS  Google Scholar 

  7. Bundy, B.M., Campbell, A.L., and Neidle, E.L., 1998, Similarities between the antABC-encoded anthranilate dioxygenase and the benABC-encoded benzoate dioxygenase of Acinetobacter sp. strain ADP1. J. Bacteriol., 180:4466–4474.

    PubMed  CAS  Google Scholar 

  8. Cases, I. and de Lorenzo, V., 2001, The black cat/white cat principle of signal integration in bacterial promoters. EMBO J., 20:1–11.

    Article  PubMed  CAS  Google Scholar 

  9. Collier, L.S., Gaines, G.L.I., and Neidle, E.L., 1998, Regulation of benzoate degradation in Acinetobacter sp. strain ADP1 by BenM, a LysR-type transcriptional activator. J. Bacteriol., 180:2493–2501.

    PubMed  CAS  Google Scholar 

  10. Cooper, R.A. and Skinner, M.A., 1980, Catabolism of 3-and 4-hydroxyphenylacetate by the 3,4-dihydroxyphenylacetate pathway in Escherichia coli. J. Bacteriol., 143:302–306

    PubMed  CAS  Google Scholar 

  11. Cowles, C.E., Nichols, N.N., and Harwood, C.S., 2000, BenR, a XylS homologue, regulates three different pathways of aromatic acid degradation in Pseudomonas putida. J. Bacteriol., 182:6339–6346.

    Article  PubMed  CAS  Google Scholar 

  12. Cuskey, S.M. and Olsen, R.H., 1988, Catabolism of aromatic biogenic amines by Pseudomonas aeruginosa PAO1 via meta cleavage of homoprotocatechuic acid. J. Bacteriol., 170:393–399.

    PubMed  CAS  Google Scholar 

  13. Cuskey, S.M., Peccoraro, V., and Olsen, R.H., 1987, Initial catabolism of aromatic biogenic amines by Pseudomonas aeruginosa PAO: Pathway description, mapping of mutations, and cloning of essential genes. J. Bacteriol., 169:2398–2404.

    PubMed  CAS  Google Scholar 

  14. Dagley, S., 1986, Biochemistry of aromatic hydrocarbon degradation in Pseudomonads. In J. Sokatch and J.L. Ornston (eds), The Bacteria, vol. 10, pp. 527–555. Academic Press Inc., Orlando, FL.

    Google Scholar 

  15. D’Argenio, D.A., Segura, A., Coco, W.M., Bünz, P.V., and Ornston, L.N., 1999, The physiological contribution of Acinetobacter PcaK, a transport system that acts upon protocatechuate, can be masked by the overlapping specificity of VanK. J. Bacteriol., 181:3505–3515.

    PubMed  Google Scholar 

  16. Diaz, E., Ferrández, A., Prieto, M.A., and García, J.L., 2001, Biodegradation of aromatic compounds by Escherichia coli. Microbiol. Mol. Biol. Rev., 65:523–569.

    Article  PubMed  CAS  Google Scholar 

  17. Durham, D.R. and Perry, J.J., 1978, Purification and characterization of a heme-containing amine dehydrogenase from Pseudomonas putida. J. Bacteriol., 134:837–843.

    PubMed  CAS  Google Scholar 

  18. Eaton, R.W., 2001, Plasmid-encoded phthalate catabolic pathway in Arthrobacter keyseri 12B. J. Bacteriol., 183:3689–3703.

    Article  PubMed  CAS  Google Scholar 

  19. Elsemore, D.A. and Ornston, L.N., 1995, Unusual ancestry of dehydratases associated with quinate catabolism in Acinetobacter calcoaceticus. J. Bacteriol., 177:5971–5978.

    PubMed  CAS  Google Scholar 

  20. Entsch, B., Nan, Y., Weaich, K., and Scott, K.F., 1988, Sequence and organization of pobA, the gene coding for p-hydroxybenzoate hydroxylase, an inducible enzyme from Pseudomonas aeruginosa. Gene, 71:279–291.

    Article  PubMed  CAS  Google Scholar 

  21. Eulberg, D., Lakner, S., Golovleva, L.A., and Schlömann, 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., 180:1072–1081.

    PubMed  CAS  Google Scholar 

  22. Fernández-Cañón, J. and Peñalva, M.A., 1998, Characterization of a fungal maleylaceto-acetate isomerase gene and identification of its human homologue. J. Biol Chem., 273:329–337.

    Article  PubMed  Google Scholar 

  23. Ferrández, A., Miñambres, B., García, B., Olivera, E.R., Luengo, J.M., García, J.L., and Díaz, E., 1998, Catabolism of phenylacetic acid in Escherichia coli. Characterization of a new aerobic hybrid pathway. J. Biol. Chem., 273:25974–25986.

    Article  PubMed  Google Scholar 

  24. Fetzner, S., 1998, Bacterial degradation of pyridine, indole, quinoline, and their derivatives under different redox conditions. Appl. Microbiol. Biotechnol., 49:237–250.

    Article  CAS  Google Scholar 

  25. Franklin, F.C.H., Bagdasarian, M., Bagdasarian, M.M., and Timmis, K.N., 1981, Molecular and functional analysis of the TOL plasmid pWWO from Pseudomonas putida and cloning of genes for the entire regulated aromatic ring meta cleavage pathway. Proc. Nad. Acad. Sci. USA, 78:7458–7462.

    Article  CAS  Google Scholar 

  26. Fukimori, F., Hirayama, H., Takami, H., Inoue, A., and Horikoshi, K., 1998, Isolation and transposon mutagenesis of a Pseudomonas putida KT2442 toluene-resistant variant: Involvement of an efflux system in solvent resistance. Extremophiles, 2:395–400.

    Article  Google Scholar 

  27. Garcia, B., Olivera, E.R., Mifiambres, B., Carnicero, D., Muñiz, C., Naharro, G., and Luengo, J.M., 2000, Phenylacetyl-coenzyme A is the true inducer of the phenylacetic acid catabolism pathway in Pseudomonas putida U. Appl. Environ. Microbiol., 66:4575–4578.

    Article  PubMed  CAS  Google Scholar 

  28. Gou, Z. and Houghton, J.E., 1999, PcaR-mediated activation and repression of pca genes from Pseudomonas putida are propagated by its binding to both the — 35 and the-10 promoter elements. Mol. Microbiol., 32:253–263.

    Article  Google Scholar 

  29. Greated, A., Lambertsen, L., Williams, P.A., and Thomas, CM., 2002, Complete sequence of the IncP-9 TOL plasmid pWWO from Pseudomonas putida. Environ. Microbiol., 4:856–87

    Article  PubMed  CAS  Google Scholar 

  30. Gu, W., Song, J., Bonner, CA., Xie, G., and Jensen, R.A., 1998, PhhC is an essential aminotransferase for aromatic amino acid catabolism in Pseudomonas aeruginosa. Microbiology, 144:3127–3134.

    Article  PubMed  CAS  Google Scholar 

  31. Hacisalihoglu, A., Jongejan, J.A., and Duine, J.A., 1997, Distribution of amine oxidases and amine dehydrogenases in bacteria grown on primary amines and characterization of the amine oxidase from Klebsiella oxytoca. Microbiology, 143:505–512.

    Article  PubMed  CAS  Google Scholar 

  32. Harayama, S. and Timmis, K.N., 1989, Catabolism of aromatic hydrocarbons by Pseudomonas. In A. Hopwood and K.F. Chater (eds), Genetics of bacterial diversity. Academic Press, London.

    Google Scholar 

  33. Harayama, S. and Timmis, K.N., 1992, Aerobic biodegradation of aromatic hydrocarbons by bacteria. In H. Sigel and A. Sigel (eds), Metal Ions in Biological Systems. Marcel Dekker, Inc., New York, NY.

    Google Scholar 

  34. Harwood, C.S., Burchhardt, G., Herrmann, H., and Fuchs, G., 1999, Anaerobic metabolism of aromatic compounds via the benzoyl-CoA pathway. FEMS Microbiol. Rev., 22:439–458.

    Article  Google Scholar 

  35. Harwood, C.S., Nichols, N.N., Kim, M.-K., Ditty, J.L., and Parales, R.E., 1994, Identification of the pcaRKF gene cluster from Pseudomonas putida: Involvement in chemotaxis, biodegradation, and transport of 4-hydroxybenzoate. J. Bacteriol., 176:6479–6488.

    PubMed  CAS  Google Scholar 

  36. Harwood, C.S. and Parales, R.E., 1996, The β-ketoadipate pathway and the biology of self-identity. Annu. Rev. Microbiol., 50:553–590.

    Article  PubMed  CAS  Google Scholar 

  37. Hawkins, A.R., Lamb, H.K., Smith, M., Keyte, J.W., and Roberts, CF., 1988, Molecular organisation of the quinic acid utilization (QUT) gene cluster in Aspergillus nidulans. Mol. Gen. Genet., 214:224–231.

    Article  PubMed  CAS  Google Scholar 

  38. Hickey, W.J., Sabat, G., Yuroff, A.S., Arment, A.R., and Pérez-Lesher, J., 2001, Cloning, nucleotide sequencing, and functional analysis of a novel, mobile cluster of biodegradation genes from Pseudomonas aeruginosa strain JB2. Appl. Environ. Microbiol., 67:4603–4609.

    Article  PubMed  CAS  Google Scholar 

  39. Hirano, S.S. and Upper, CD., 2000, Bacteria in the leaf ecosystem with emphasis on Pseudomonas syringae—a pathogen, ice nucleus and epiphyte. Microbiol. Mol. Biol. Rev., 64:624–6

    Article  PubMed  CAS  Google Scholar 

  40. Hoet, P.P. and Stanier, R.Y., 1970, Existence and functions of the two enzymes with β-ketoadipate:Succinyl-CoA transferase activity in Pseudomonas fluorescens. Eur. J. Biochem., 13:71–76.

    Article  PubMed  CAS  Google Scholar 

  41. Houghton, J.E., Brown, T.M., Appel, A.J., Hughes, E.J., and Ornston, L.N., 1995, Discontinuities in the evolution ofPseudomonas putida cat genes. J. Bacteriol., 177:401–412.

    PubMed  CAS  Google Scholar 

  42. Ingledew, W.M. and Tai, C.C., 1972, Quinate metabolism in Pseudomonas aeruginosa. Can. J. Microbiol., 18:1817–1824.

    Article  PubMed  CAS  Google Scholar 

  43. Iwaki, M., Yagi, T., Horiike, K., Saeki, Y., Ushijima, T., and Nozaki, M., 1983, Crystallization and properties of aromatic amine dehydrogenase from Pseudomonas sp. Arch. Biochem. Biophys., 220:253–262.

    Article  PubMed  CAS  Google Scholar 

  44. Jeffrey, W.H., Cuskey, S.M., Chapman, P.J., Resnick, S., and Olsen, R.H., 1992, Characterization of Pseudomonas putida mutants unable to catabolize benzoate: Cloning and characterization of Pseudomonas genes involved in benzoate catabolism and isolation of a chromosomal DNA fragment able to substitute for xylS in activation of the TOL lower-pathway promoter. J. Bacteriol., 174:4986–4996.

    PubMed  CAS  Google Scholar 

  45. Jiménez, J.I., Miñambres, B., García, J.L., and Díaz, E., 2002, Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440. Environ. Microbiol., 4:824–841.

    Article  PubMed  Google Scholar 

  46. Knackmuss, H.-J., 1996, Basic knowledge and perspectives of bioelimination of xenobiotic compounds. J. Biotechnol., 51:287–295.

    Article  CAS  Google Scholar 

  47. Kukor, J.J., Olsen, R.H., and Ballou, D.P., 1988, Cloning and expression of the catAand catBC gene clusters from Pseudomonas aeruginosa PAO. J. Bacteriol., 170:4458–4465.

    PubMed  CAS  Google Scholar 

  48. Luengo, J.M., Garcia, J.L., and Olivera, E.R., 2001, The phenylacetyl-CoA catabolon: A complex catabolic unit with broad biotechnological applications. Mol. Microbiol., 39:1434–1442.

    Article  PubMed  CAS  Google Scholar 

  49. Mallavarapu, M., Möhler, I., Krüger, M., Hosseini, M., Bartels, F., Timmis, K.N., and Holtel, A., 1998, Genetic requirements for the expression of benzylamine dehydrogenase activity in Pseudomonas putida. FEMS Microbiol. Lett., 166:109–114.

    Article  CAS  Google Scholar 

  50. McLeish, M.J., Kneen, M.M., Gopalakrishna, K.N., Koo, C.W., Babbitt, P.C., Gerlt, J.A., and Kenyon, G.L., 2003, Identification and characterization of a mandelamide hydrolase and an NAD(P)+-dependent benzaldehyde dehydrogenase from Pseudomonas putida ATCC 12633. J. Bacteriol., 185:2451–2456.

    Article  PubMed  CAS  Google Scholar 

  51. Milcamps, A. and de Bruijn, F.J., 1999, Identification of a novel nutrient-deprivation-induced Sinorhizobium meliloti gene (hmgA) involved in the degradation of tyrosine. Microbiology, 145:935–947.

    Article  PubMed  CAS  Google Scholar 

  52. Mitra, A., Kitamura, Y., Gasson, M.J., Narbad, A., Parr, A.J., Payne, J., Rhodes, M.J.C., Sewter, C., and Walton, N.J., 1999, 4-Hydroxycinnamoyl-CoA hydratase/lyase (HCHL)— an enzyme of phenylpropanoid chain cleavage from Pseudomonas. Arch. Biochem. Biophys., 365:10–16.

    Article  PubMed  CAS  Google Scholar 

  53. Mohamed, M.E., Ismail, W., Heider, J., and Fuchs, G., 2002, Aerobic metabolism of pheny-lacetic acids in Azoarcus evansii. Arch. Microbiol., 178:180–192.

    Article  CAS  Google Scholar 

  54. Morawski, B., Segura, A., and Ornston, L.N., 2000, Repression of Acinetobacter vanillate demethylase synthesis by VanR, a member of the GntR family of transcriptional regulators. FEMS Microbiol. Lett., 187:65–68.

    Article  PubMed  CAS  Google Scholar 

  55. Nakai, C., Horiike, K., Kuramitsu, S., Kagamiyama, H., and Nozaki, M., 1990, Three isoenzymes of catechol 1,2-dioxygenase (pyrocatechase), αα, αβ, and β β, from Pseudomonas arvilla C-1. αJ. Biol. Chem., 265:660–665.

    CAS  Google Scholar 

  56. Nelson, K.E., Weinel, C., Paulsen, I.T., Dodson, R.J., Hilbert, H., Martins dos Santos, V.A.P., Fouts, D.E., Gill, S.R., Pop, M., Holmes, M., Brinkac, L., Beanan, M., DeBoy, R.T., Daugherty, S., Kolonay, J., Madupu, R., Nelson, W., White, O., Peterson, J., Khouri, H., Hance, I., Chris Lee, P., Holtzapple, E., Scanlan, D., Tran, K., Moazzez, A., Utterback, T., Rizzo, M., Lee, K., Kosack, D., Moestl, D., Wedler, H., Lauber, J., Stjepandic, D., Hoheisel, J., Straetz, M., Heim, S., Kiewitz, C., Eisen, J., Timmis, K.N., Düsterhöft, A., Tümmler, B., and Fraser, CM., 2002, Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ. Microbiol., 4:799–808.

    Article  PubMed  CAS  Google Scholar 

  57. Nichols, N.N. and Harwood, C.S., 1997, PcaK, a high-affinity permease for the aromatic compounds 4-hydroxybenzoate and protocatechuate from Pseudomonas putida. J. Bacteriol., 179:5056–5061.

    PubMed  CAS  Google Scholar 

  58. Nishi, A., Tominaga, K., and Furukawa, K., 2000, A 90-kilobase conjugative chromosomal element coding for biphenyl and salicylate catabolism in Pseudomonas putida KF715. J. Bacteriol., 182:1949–1955.

    Article  PubMed  CAS  Google Scholar 

  59. Nozaki, M., Kagamiyama, H., and Hayaishi, O., 1963, Crystallization and some properties of metapyrocatechase. Biochem. Biophys. Res. Commun., 11:65–70.

    Article  PubMed  CAS  Google Scholar 

  60. Olivera, E.R., Carnicero, D., García, B., Miñambres, B., Moreno M.A., Cañedo, L., DiRusso, C.C., Naharro, G., and Luengo, J.M., 2001, Two different pathways are involved in the β-oxidation of n-alkanoic and n-phenylalkanoic acids in Pseudomonas putida U: Genetic studies and biotechnological applications. Mol. Microbiol., 39:863–874.

    Article  PubMed  CAS  Google Scholar 

  61. Olivera, E.R., Reglero, A., Martínez-Blanco, H., Fernández-Medarde, A., Moreno, M.A., and Luengo, J.M., 1994, Catabolism of aromatics in Pseudomonas putida U. Formal evidence that phenylacetic acid and 4-hydroxyphenylacetic acid are catabolized by two unrelated pathways. Eur. J. Biochem., 221:375–381.

    Article  PubMed  CAS  Google Scholar 

  62. Ornston, L.N., 1971, Regulation of catabolic pathways in Pseudomonas. Bacteriol Rev., 35:87–116.

    PubMed  CAS  Google Scholar 

  63. Overhage, J., Priefert, H., and Steinbüchel, A., 1999, Biochemical and genetic analyses of ferulic acid catabolism in Pseudomonas sp. strain HR199. Appl. Environ. Microbiol., 65:4837–4847.

    PubMed  CAS  Google Scholar 

  64. Palleroni, N.J., 2003, Prokaryote taxonomy of the 20th century and the impact of studies on the genus Pseudomonas: A personal view. Microbiology, 149:1–7.

    Article  PubMed  CAS  Google Scholar 

  65. Parales, R.E. and Harwood, C.S., 2002, Bacterial chemotaxis to pollutants and plant-derived aromatic molecules. Curr. Opin. Microbiol., 5:266–273.

    Article  PubMed  CAS  Google Scholar 

  66. Parke, D., 1996, Characterization of PcaQ, a LysR-type transcriptional activator required for catabolism of phenolic compounds, from Agrobacterium tumefaciens. J. Bacteriol., 178:266–272.

    PubMed  CAS  Google Scholar 

  67. Parke, D., D’Argenio, D.A., and Ornston, L.N., 2000, Bacteria are not what they eat: That is why they are so diverse. J. Bacteriol., 182:257–263.

    Article  PubMed  CAS  Google Scholar 

  68. Parke, D., Garcia, M.A., and Ornston, L.N., 2001, Cloning and genetic characterization of dca genes required for β-oxidation of straight-chain dicarboxylic acids in Acinetobacter sp. strain ADP1. Appl. Environ. Microbiol., 67:4817–4827.

    Article  PubMed  CAS  Google Scholar 

  69. Pieper, D.H. and Reineke, W., 2000, Engineering bacteria for bioremediation. Curr. Opin. Biotechnol., 11:262–270.

    Article  PubMed  CAS  Google Scholar 

  70. Plaggenborg, R., Overhage, J., Steinbuchel, A., and Priefert, H., 2003, Functional analyses of genes involved in the metabolism of ferulic acid in Pseudomonas putida KT2440. Appl. Microbiol. Biotechnol., 61:528–535.

    PubMed  CAS  Google Scholar 

  71. Powlowski, J. and Shingler, V., 1994, Genetics and biochemistry of phenol degradation by Pseudomonas sp. CF600. Biodegradation, 5:219–236.

    Article  PubMed  CAS  Google Scholar 

  72. Priefert, H., Rabenhorst, J., and Steinbüchel, A., 1997, Molecular characterization of genes of Pseudomonas sp. strain HR199 involved in bioconversion of vanillin to protocatechuate. J. Bacteriol., 179:2595–2607.

    PubMed  CAS  Google Scholar 

  73. Priefert, H., Rabenhorst, J., and Steinbüchel, A., 2001, Biotechnological production of vanillin. Appl. Microbiol. Biotechnol., 56:296–314.

    Article  PubMed  CAS  Google Scholar 

  74. Ramos, J.L., Díaz, E., Dowling, D., de Lorenzo, V., Molin, S., O’Gara, F., Ramos, C., and Timmis, K.N., 1994, The behaviour of bacteria designed for biodegradation. Biotechnology, 12:1349–1356.

    Article  PubMed  CAS  Google Scholar 

  75. Ramos, J.L., Duque, E., Godoy, P., and Segura, A., 1998, Efflux pumps involved in toluene tolerance in Pseudomonas putida DOT-TIE. J. Bacteriol., 180:3323–3329.

    PubMed  CAS  Google Scholar 

  76. Ravatn, R., Studer, S., Springael, D., Zehnder, A.J.B., van der Meer, J.R., 1998, Chromosomal integration, tandem amplification, and deamplification in Pseudomonas putida Fl of a 105-kilobase genetic element containing the chlorocatechol degradative genes from Pseudomonas sp. strain B13. J. Bacteriol., 180:4360–4369.

    PubMed  CAS  Google Scholar 

  77. Reineke, W., 1998, Development of hybrid strains for the mineralization of chloroaromatics by patchwork assembly. Annu. Rev. Microbiol., 52:287–331.

    Article  PubMed  CAS  Google Scholar 

  78. Rosenberg, S.L., 1971, Regulation of the mandelate pathway in Pseudomonas aeruginosa. J. Bacteriol., 108:1257–1269

    PubMed  CAS  Google Scholar 

  79. Rosenberg, S.L. and Hegeman, G.D., 1971, Genetics of the mandelate pathway in Pseudomonas aeruginosa. J. Bacteriol., 108:1270–1276.

    PubMed  CAS  Google Scholar 

  80. Rothmel, R.K., Aldrich, T.L., Houghton, J.E., Coco, W.M., Ornston, L.N., and Chakrabarty, A.M., 1990, Nucleotide sequencing and characterization of Pseudomonas putida catR: A positive regulator of the catBC operon is a member of the LysR family. J. Bacteriol., 172:922–931.

    PubMed  CAS  Google Scholar 

  81. Saier, M.H., Jr, 1998, Molecular phylogeny as a basis for the classification of transport proteins from bacteria, archaea, and eukarya. Adv. Microb. Physiol., 40:81–136.

    Article  PubMed  CAS  Google Scholar 

  82. Segura, A., Bünz, P.V, D’Argenio, D.A., and Ornston, L.N., 1999, Genetic analysis of a chromosomal region containing vanA and vanB, genes required for conversion of either ferulate or vanillate to protocatechuate in Acinetobacter. J. Bacteriol., 181:3494–3504.

    PubMed  CAS  Google Scholar 

  83. Serre, L., Sailland, A., Sy, D., Boudec, P., Rolland, A., Pebay-Peyroula, E., and Cohen-Addad, C., 1999, Crystal structure of Pseudomonas fluorescens 4-hydroxyphenylpyruvate dioxygenase: An enzyme involved in the tyrosine degradation pathway. Structure, 7:977–988.

    Article  PubMed  CAS  Google Scholar 

  84. Smith, M.A., Weaver, VB., Young, D.M., and Ornston, L.N., 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., 69:524–532.

    Article  PubMed  CAS  Google Scholar 

  85. Song, J. and Jensen, R.A., 1996, PhhR, a divergently transcribed activator of the phenylalanine hydroxylase gene cluster of Pseudomonas aeruginosa. Mol. Microbiol., 22:497–507.

    Article  PubMed  CAS  Google Scholar 

  86. Song, J., Xia, T., and Jensen, R.A., 1999, PhhB, a Pseudomonas aeruginosa homolog of mammalian pterin 4a-carbinolamine dehydratase/DcoH, does not regulate expression of phenylalanine hydroxylase at the transcriptional level. J. Bacteriol., 181:2789–2796.

    PubMed  CAS  Google Scholar 

  87. Spain, J.C., 1995, Biodegradation of nitroaromatic compounds. Annu. Rev. Microbiol., 49:523–555.

    Article  PubMed  CAS  Google Scholar 

  88. Sparnins, VL., Chapman, P.J., and Dagley, S., 1974, Bacterial degradation of 4-hydroxy-phenylacetic acid and homoprotocatechuic acid. J. Bacteriol., 120:159–167.

    PubMed  CAS  Google Scholar 

  89. Stanier, R.Y., Palleroni, N.J., and Doudoroff, M., 1966, The aerobic pseudomonads: A taxonomic study. J. Gen. Microbiol., 43:159–271.

    Article  PubMed  CAS  Google Scholar 

  90. Spiers, A.J., Buckling, A., and Rainey, P.B., 2000, The causes of Pseudomonas diversity. Microbiology, 146:2345–2350.

    PubMed  CAS  Google Scholar 

  91. Stover, C.K., Pham, X.Q., Erwin, A.L., Mizoguchi, S.D., Warrener, P., Hickey, M.J., Brinkman, F.S.L., Hufhagle, W.O., Kowalik, D.J., Lagrou, M., Garber, R.L., Goltry, L., Tolentino, E., Westbrock-Wadman, S., Yuan, Y., Brody, L.L., Coulter, S.N., Folger, K.R., Kas, A., Larbig, K., Lim. L., Smith, K., Spencer, D., Wong, G.K.-S., Wu, Z., Paulsen, I.T., Reizer, J., Saier, M.H., Hancock, R.E.W, Lory, S., and Olson, M.V, 2000, Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature, 406:959–964.

    Article  PubMed  CAS  Google Scholar 

  92. Suzuki, K., Ichimura, A., Ogawa, N., Hasebe, A., and Miyashita, K., 2002, Differential expression of two catechol 1,2-dioxygenases in Burkholderia sp. strain TH2. J. Bacteriol., 184:5714–5722.

    Article  PubMed  CAS  Google Scholar 

  93. Tan, H.-M., 1999, Bacterial catabolic transposons. Appl. Microbiol. Biotechnol., 51:1–12.

    Article  PubMed  CAS  Google Scholar 

  94. Timmis, K.N., 2002, Pseudomonas putida: A cosmopolitan opportunist par excellence. Environ. Microbiol., 4:779–781.

    Article  PubMed  Google Scholar 

  95. Turner, J.E., Allison, N., and Fewson, CA., 1996, Metabolic characterisation of a novel vanillylmandelate-degrading bacterium. Arch. Microbiol., 166:252–259.

    Article  PubMed  CAS  Google Scholar 

  96. van der Meer, J.R., de Vos, W.M., Harayama, S., and Zehnder, A.J.B., 1992, Molecular mechanisms of genetic adaptation to xenobiotic compounds. Microbiol. Rev., 56:677–694.

    PubMed  Google Scholar 

  97. van der Meer, J.R., van Neerven, A.R.W., de Vries, E.J., de Vos, W.M., and Zehnder, A.J.B., 1991, Cloning and characterization of plasmid-encoded genes for the degradation of 1,2-dichloro-, 1,4-dichloro-, and 1,2,4-trichlorobenzene of Pseudomonas sp. strain P51. J. Bacteriol., 173:6–15.

    PubMed  Google Scholar 

  98. Venturi, V., Zennaro, F., Degrassi, G., Okeke, B.C., and Bruschi, C.V, 1998, Genetics of ferulic acid bioconversion to protocatechuic acid in plant-growth-promoting Pseudomonas putida WCS358. Microbiology, 144:965–973.

    Article  PubMed  CAS  Google Scholar 

  99. Wackett, L.P., 2003, Pseudomonas putida— a versatile biocatalyst. Nat. Biotechnol., 21:136–138.

    Article  PubMed  CAS  Google Scholar 

  100. Walsh, U.F., Morrissey, J.P., and O’Gara, E, 2001, Pseudomonas for biocontrol of phytopathogens: From functional genomics to commercial exploitation. Curr. Opin. Biotechnol., 12:289–295.

    Article  PubMed  CAS  Google Scholar 

  101. Wang, J., Ortiz-Maldonado, M., Entsch, B., Massey, V., Ballou, D., and Gatti, D.L., 2002, Protein and ligand dynamics in 4-hydroxybenzoate hydroxylase. Proc. Natl. Acad. Sci. USA., 99:608–613.

    Article  PubMed  CAS  Google Scholar 

  102. Yen, K.-M. and Serdar, CM., 1988, Genetics of naphthalene catabolism in pseudomonads. Crit. Rev. Microbiol., 15:247–268.

    Article  PubMed  CAS  Google Scholar 

  103. Yeo, C.C., Tham, J.M., Yap, M.W-C., and Poh, C.L., 1997, Group II intron from Pseudomonas alcaligenes NCIB 9867 (P25X): Entrapment in plasmid RP4 and sequence analysis. Microbiology, 143:2833–2840.

    Article  PubMed  CAS  Google Scholar 

  104. Zhang, C., Huang, M., and Holloway, B.W., 1993, Mapping of the ben, ant and cat genes of Pseudomonas aeruginosa and evolutionary relationship of the ben region of P. aeruginosa and P. putida. FEMS Microbiol. Lett., 108:303–310.

    Article  PubMed  CAS  Google Scholar 

  105. Zhou, N.-Y., Fuenmayor, S.L., and Williams, P.A., 2001, nag genes of Ralstonia (formerly Pseudomonas) sp. strain U2 encoding enzymes for gentisate catabolism. J. Bacteriol., 183:700–708.

    Article  PubMed  CAS  Google Scholar 

  106. Zylstra, GJ. and Gibson, D.T., 1989, Toluene degradation by Pseudomonas putida Fl: Nucleotide sequence of the todClC2BADE genes and their expression in Escherichia coli. J. Biol. Chem., 264:14940–14946.

    PubMed  CAS  Google Scholar 

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Jiménez, J.I., Miñambres, B., García, J.L., Díaz, E. (2004). Genomic Insights in the Metabolism of Aromatic Compounds in Pseudomonas . In: Ramos, JL. (eds) Pseudomonas. Springer, Boston, MA. https://doi.org/10.1007/978-1-4419-9088-4_15

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