Abstract
Pseudomonas sp. strain CF600 is an efficient degrader of phenol and methylsubstituted phenols. These compounds are degraded by the set of enzymes encoded by the plasmid locateddmpoperon. The sequences of all the fifteen structural genes required to encode the nine enzymes of the catabolic pathway have been determined and the corresponding proteins have been purified. In this review the interplay between the genetic analysis and biochemical characterisation of the catabolic pathway is emphasised. The first step in the pathway, the conversion of phenol to catechol, is catalysed by a novel multicomponent phenol hydroxylase. Here we summarise similarities of this enzyme with other multicomponent oxygenases, particularly methane monooxygenase (EC 1.14.13.25). The other enzymes encoded by the operon are those of the well-knownmeta-cleavage pathway for catechol, and include the recently discoveredmeta-pathway enzyme aldehyde dehydrogenase (acylating) (EC 1.2.1.10). The known properties of thesemeta-pathway enzymes, and isofunctional enzymes from other aromatic degraders, are summarised. Analysis of the sequences of the pathway proteins, many of which are unique to themeta-pathway, suggests new approaches to the study of these generally little-characterised enzymes. Furthermore, biochemical studies of some of these enzymes suggest that physical associations betweenmeta-pathway enzymes play an important role. In addition to the pathway enzymes, the specific regulator of phenol catabolism, DmpR, and its relationship to the XylR regulator of toluene and xylene catabolism is discussed.
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References
Abril M-A, Michan C, Timmis KN & Ramos JL (1989) Regulator and enzyme specificities of the TOL plasmid-encoded upper pathway for degradation of aromatic hydrocarbons and expansion of the substrate range of the pathway. J. Bacteriol. 171:6782–6790
Andrews SC, Shipley D, Keen JN, Findley JBC, Harrison PM & Guest JR (1992) The haemoglobin-like protein (HMP) ofEscherichia coli has ferrisiderophore reductase activity and its C-terminal domain shares homology with ferredoxin NADP+ reductases. FEBS Lett. 302:247–252
Anonymous (1993) Facts and figures for the chemical industry. Chem. Engineer. News 71:38–82
Assinder S & Williams PA (1990) The TOL plasmids: determinants of the catabolism of toluene and xylenes. Adv. Microbial Physiol. 31:1–39
Ballou DP (1982) Flavoprotein monooxygenases. In: Massey V & Williams CH (Eds) Flavins and Flavoproteins (pp 301–310). Elsevier Science Publishing, Amsterdam
Bartilson M, Nordlund I & Shingler V (1990) Location and organization of the dimethylphenol catabolising genes ofPseudomonas CF600. Mol. Gen. Genet. 220:294–300
Bartilson M & Shingler V (1989) Nucleotide sequence and expression of the catechol 2,3-dioxygenase-encoding gene of phenolcatabolizingPseudomonas CF600. Gene 85:233–238
Bayly RC & Barbour MG (1984) The degradation of aromatic compounds. In: Gibson DT (Ed) Microbial Degradation of Organic Compounds (pp 253–294). Marcel Dekker, New York
Bayly RC & Wigmore GJ (1973) Metabolism of phenol and cresols by mutants ofPseudomonas putida. J. Bacteriol. 113:1112–1126
Burton RM & Stadman ER (1953) The oxidation of acetaldehyde to acetyl coenzyme A. J. Biol. Chem. 202:873–890
Carlson J, Fuchs JA & Messing J (1984) Primary structure of theEscherichia coli ribonucleoside diphosphate reductase operon. Proc. Natl. Acad. Sci. U.S.A. 81:4294–4297
Carrington B, Lowe A & Williams PA (1994) The lower pathway operon for benzoate catabolism in biphenyl-utilisingPseudomonas sp. strain IC and the nucleotide sequence of thebphE gene for catechol 2,3-dioxygenase. Microbiology 140:499–508
Chen LH, Kenyon GL, Curtin F, Harayama S, Bembenek ME, Hajipour G & Whitman CP (1992) 4-Oxalocrotonate tautomerase, an enzyme composed of 62 amino acid residues per monomer. J. Biol. Chem. 267:17716–17721
Coco WM, Rothmel RK, Henikoff S & Chakrabarty AM (1993) Nucleotide sequence and initial functional analysis of theclcR gene encoding a LysR Family activator of theclcABD chlorocatechol operon inPseudomonas putida. J. Bacteriol. 175:417–427
Collinsworth WL, Chapman PJ & Dagley S (1972) Stereospecific enzymes in the degradation of aromatic compounds byPseudomonas putida. J. Bacteriol. 113:922–931
Dagley S (1975) A biochemical approach to some problems of environmental pollution. Essays Biochem. 11:81–138
Dagley S (1986) Biochemistry of aromatic hydrocarbon degradation in pseudomonads. In: Sokatch JR (Ed) The Bacteria, Vol 10 (pp 527–556). Academic Press, New York
Dagley S & Gibson DT (1965) The bacterial degradation of catechol. Biochemistry 95:466–474
Davenport RC & Whitman CP (1993) Preliminary analysis of crystals of 4-oxalocrotonate tautomerase, an enzyme composed of unusually small monomers. J. Mol. Biol. 231:509–512
Derewenda ZS & Sharp AM (1993) News from the interface: the molecular structure of triacylglyceride lipases. Trends Biochem. Sci. 18:20–25
Entsch B, Ballou DP & Massey V (1976) Flavin-oxygen derivatives involved in hydroxylation byp-hydroxybenzoate hydroxylase. J. Biol. Chem. 251:2550–2563
Ericson A, Hedman B, Hodgson KO, Green J, Dalton H, Bentsen JG, Beers RH & Lippard SJ (1988) Structural characterization by EXAFS spectroscopy of the binuclear iron centre in protein A of methane monooxygenase fromMethylococcus capsulatus (Bath). J. Amer. Chem. Soc. 110:2330–2332
Feller G, Thiry M & Gerday C (1991) Nucleotide sequence of the lipase genelip3 from the antarctic psychotrophMoraxella TA144. Biochim. Biophys. Acta 1088:323–324
Fennewald M, Prevatt W, Meyer R & Shapiro J (1978) Isolation of IncP-2 DNA fromPseudomonas aeruginosa. Plasmid 1:164–173
Fox BG, Surerus KK, Münck E & Lipscomb JD (1988) Evidence for a μ-oxo-bridged binuclear iron cluster in the hydroxylase component of methane monooxygenase. J. Biol. Chem. 263:10553–10556
Froland WA, Andersson KK, Lee S-K & Lipscomb JD (1992) Methane monooxygenase component B and reductase alter the regioselectivity of the hydroxylase-catalyzed reaction. J. Biol. Chem. 267:17588–17597
Green J & Dalton H (1985) Protein B of soluble methane monooxygenase fromMethylococcus capsulatus (Bath). J. Biol. Chem. 260:15795–15801
Gurujeyalakshmi G & Oriel P (1989) Isolation of phenol-degradingBacillus stearothermophilus. Appl. Environ. Microbiol. 55:500–502
Happold FC & Key A (1932) The bacterial purification of gas-works liquors. The action of liquors on the bacterial flora of sewage. J. Hygiene 32:573–580
Harayama S, Kok M & Neidle EL (1992) Functional and evolutionary relationships amoung divers oxygenases. Annu. Rev. Microbiol. 46:565–601
Harayama S, Polissi A & Rekik M (1991) Divergent evolution of chloroplast-type ferredoxins. FEBS Lett. 285:85–88
Harayama S & Rekik M (1993) Comparison of the nucleotide sequence of themeta-cleavage pathway genes of TOL plasmid pWW0 fromPseudomonas putida with othermeta-cleavage genes suggests that both single and multiple nucleotide substitutions contribute to enzyme evolution. Mol. Gen. Genet. 239:81–89
Harayama S, Rekik M, Ngai K-l & Ornston LN (1989) Physically associated enzymes produce and metabolize 2-hydroxy-2,4-dienoate, a chemically unstable intermediate formed in catechol metabolism viameta-cleavage inPseudomonas putida. J. Bacteriol. 171:6251–6258
Hempel J & Jörnvall H (1989) Aldehyde dehydrogenases-structure. In: Crow KE & Batt RD (Eds) Human Metabolism of Alcohol, Vol II, Regulation, Enzymology and Metabolites of Ethanol (pp 77–88). CRC Press, Boca Raton, FL
Horn JA, Harayama S & Timmis KN (1991) DNA sequence determination of the TOL plasmidxylGFH genesPseudomonas putida: implications for the evolution of aromatic catabolism. Mol. Microbiol. 5:2459–2474
Howard PH, Boethling RS, Jarvis WF, Meylan WM & Michalenko EM (1991) Handbook of Environmental Degradation Rates. Lewis Publishers Inc, Chelsea, MI
Inouye S, Nakazawa A & Nakazawa T (1986) Nucleotide sequence of the regulatory genexylS on thePseudomonas putida TOL plasmid and identification of the protein product. Gene 44:235–242
Inouye S, Nakazawa A & Nakazawa T (1988) Nucleotide sequence of the regulatory genexylR of the TOL plasmid fromPseudomonas putida. Gene 66:301–306
Johansson J, Von Bahr-Lindström J, Jeck R, Woenckhaus C & Jörnvall H (1988) Mitochondrial aldehyde dehydrogenase from horse liver: correlation of the same species variants for both the cytosolic and mitochondrial forms of an enzyme. Eur. J. Biochem. 172:527–533
Kedishvili NY, Popov KM, Rougraff PM, Zhao Y, Crab DW & Harris RA (1992) CoA dependent methylmalonate-semialdehyde dehydrogenase, a unique member of the aldehyde dehydrogenase superfamily. J. Biol. Chem. 267:19724–19729
Kikuchi K, Yasukochi Y, Nagata Y, Koana T, Fukuda M, Yano K & Takagi M (1993) Analysis of gene structure for biphenyl and polychlorinated biphenys (PCBs) degradation inPseudomonas sp. KKS102 (Abstract). The Fourth International Symposium onPseudomonas: Biotechnology and Molecular Biology, Vancouver, August 1993
Kimbara K, Hashimoto T, Fukuda M, Koana T, Takagi M, Oishi M & Yano K (1989) Cloning and sequencing of two tandem genes involved in degradation of 2,3-dihydroxybiphenol to benzoic acid in the polychlorinated biphenyl-degrading soil bacteriumPseudomonas sp. strain KKS102. J. Bacteriol. 171:2740–2747
Kukor JJ & Olsen RH (1991) Genetic organization and regulation of ameta cleavage pathway for catechols produced from catabolism of toluene, benzene, phenol, and cresols byPseudomonas pickettii PKO1. J. Bacteriol. 173:4587–4594
Kukor JJ & Olsen RH (1992) Complete nucleotide sequence oftbuD, the gene encoding phenol/cresol hydroxylase fromPseudomonas. pickettii PKO1, and functional analysis of the encoded enzymes. J. Bacteriol. 174:6518–6526
Kumagai H, Yamada H, Matsui H, Ohkishi H & Ogata H (1970) Tyrosine phenol lyase I. Purification, crystalization, and properties. J. Biol. Chem. 245:1767–1777
Lau PCK, Wang Y, Rawlings M, Labbé D, Bergeron H, Brousseau R & Gibson DT (1993) Regulation of toluene degradation inPseudomonas putida F1 by an unusual sensor-regulator protein (Abstract) The Fourth International Symposium onPseudomonas: Biotechnology and Molecular Biology, Vancouver, August 1993
Lister J (1867) On a new method of treating compound fracture, abscess, etc.: with observations on the conditions of suppuration. Lancet (March 16):326–329
Loomes KM, Midwinter GG, Blackwell LF & Buckley PD (1990) Evidence for reactivity of serine-74 withtrans-(N, N-dimethylamino)cinnamaldehyde during oxidation by the cytoplasmic aldehyde dehydrogenase from sheep liver. Biochemistry 29:2070–2075
Marcotte P & Walsh C (1978) Sequence of reactions which follows enzymatic oxidation of allylglycine. Biochemistry 17:5620–5626
Mason JR & Cammack R (1992) The electron-transport proteins of hydroxylating bacterial dioxygenases. Annu. Rev. Microbiol. 46:277–305
McGrew RE (1985) Encyclopedia of Medical History (pp 20–24). MacMillan Reference Books, MacMillan Press, London
Menn F-M, Zylstra GJ & Gibson DT (1991) Location and sequence of thetodF gene encoding 2-hydroxy-6-oxohepta-2,4-dienoate hydrolase inPseudomonas putida F1. Gene 104:91–94
Nakai C, Kagamiyama H & Nozaki M (1983) Complete nucleotide sequence of the metapyrocatachase gene of the TOL plasmid ofPseudomonas putida mt-2. J. Biol. Chem. 258:2923–2928
Neujahr HY & Gaal A (1973) Phenol hydroxylase from yeast. Purification and properties of the enzyme fromTrichosporon cutaneum. Eur. J. Biochem. 35:386–400
Ng LC, Sze CC & Poh CL (1993) Cloning, nucleotide sequence and expression of chromosomally-encoded phenol hydroxylase degradative genes inPseudomonas putida P35X (Abstract) The Fourth International Symposium onPseudomonas: Biotechnology and Molecular Biology, Vancouver, August 1993
Nordlund I & Shingler V (1990) Nucleotide sequence of themeta-cleavage pathway enzymes 2-hydroxymuconic semialdehyde dehydrogenase and 2-hydroxymuconic semialdehyde hydrolase fromPseudomonas CF600. Biochim. Biophys. Acta 1049:227–230
Nordlund I, Powlowski J, Hagström Å & Shingler V (1993) Conservation of regulatory and structural genes for a multicomponent phenol hydroxylase within phenol-catabolizing bacteria that utilize ameta-cleavage pathway. J. Gen. Microbiol. 139:2695–2703
Nordlund I, Powlowski J & Shingler V (1990a) Complete nucleotide sequence and polypeptide analysis of multicomponent phenol hydroxylase fromPseudomonas sp. strain CF600. J. Bacteriol. 172:6826–6833
Nordlund P, Sjöberg B-M & Eklund H (1990b) Three-dimensional structure of the free radical protein of ribonucleotide reductase. Nature 345:593–598
Nordlund P, Dalton H & Eklund H (1992) The active site structure of methane monooxygenase is closely related to the binuclear iron centre of ribonucleotide reductase. FEBS Lett. 307:257–262
North AK, Klose KE, Stedman KM & Kustu S (1993) Prokayotic enhancer-binding proteins reflect eukaryote-like modularity: the puzzle of nitrogen regulatory protein C. J. Bacteriol. 175:4267–4273
Nurk A, Kasak L & Kivisaar M (1991) Sequence of the gene (pheA) encoding phenol monooxygenase fromPseudomonas EST1001: expression inEscherichia coli andPseudomonas putida. Gene 102:13–18
Nunn WP (1987) Two-carbon compounds and fatty acids as carbon sources. In: Neidhardt FC, Ingraham JL, Low KB, Maganasik B, Schaechter M & Umbarger HE (Eds)Escherichia Coli andSalmonella Typhimurium: Cellular and Molecular Biology (pp 285–301). American Society for Microbiology, Washington, D.C.
Ornston LN & Yeh W-K (1982) Recurring themes and repeated sequences in metabolic evolution. In: Chakrabarty AM (Ed) Biodegradation and Detoxification of Environmental Pollutants (pp 105–126). CRC Press, Boca Raton, FL
Pathak D & Ollis D (1990) The refined structure of dienelactone hydrolase at 1.8 Å. J. Mol. Biol. 214:497–525
Polissi A & Harayama S (1993)In vivo reactivation of catechol 2,3-dioxygenase mediated by a chloroplast-type ferredoxin: a bacterial strategy to expand the substrate specificity of aromatic degradative pathways. EMBO J. 12:3339–3347
Powlowski J, Sahlman L & Shingler V (1993) Purification and properties of the physically associatedmeta-cleavage pathway enzymes 4-hydroxy-2-ketovalerate aldolase and aldehyde dehydrogenase (acylating) fromPseudomonas sp. strain CF600. J. Bacteriol. 175:377–385
Powlowski J & Shingler V (1990) In vitro analysis of polypeptide requirements of multicomponent phenol hydroxylase fromPseudomonas sp. strain CF600. J. Bacteriol. 172:6834–6840
Ramos JL, Stolz, A Reineke W & Timmis KN (1986) Altered effector specificities in regulators of gene expression: TOL plasmidxylS mutants and their use to engineer expansion of the range of aromatics degraded by bacteria. Proc. Natl. Acad. Sci. U.S.A. 83:8467–8471
Ramos JL, Michan C, Rojo F, Dwyer D & Timmis KN (1990) Signal-regulator interactions. Genetic analysis of the effector binding site ofxylS, the benzoate-activated positive regulator ofPseudomonas TOL plasmidmeta-cleavage pathway operon. J. Mol. Biol. 211:373–382
Rheinwald JG, Chakrabarty AM & Gunsalus IC (1973) A transmissible plasmid controlling camphor oxidation inPseudomonas putida. Proc. Natl. Acad. Sci. U.S.A. 70:885–889
Rosenzweig AC, Fredrick CA, Lippard SJ & Nordlund P (1993) Crystal structure of a bacterial non-haem iron hydroxylase that catalyses the biological oxidation of methane. Nature 366:537–543
Sala-Trepat JM, Murray K & Williams PA (1972) The metabolic divergence in themeta cleavage of catechols byPseudomonas putida. Eur. J. Biochem. 28:347–356
Sala-Trepat JM & Evans WC (1971) Themeta-cleavage of catechol byAzotobacter species: 4-oxalocrotonate pathway. Eur. J. Biochem. 20:400–413
Shingler V, Bartilson M & Moore T (1993) Cloning and nucleotide sequence of the gene encoding the positive regulator (DmpR) of the phenol catabolic pathway encoded by pVI150 and identification of DmpR as a member of the NtrC family of transcriptional activators. J. Bacteriol. 175:1596–1604
Shingler V, Franklin FCH, Tsuda M, Holroyd D & Bagdasarian M (1989) Molecular analysis of a plasmid-encoded phenol hydroxylase fromPseudomonas CF600. J. Gen. Microbiol. 135:1083–1092
Shingler V & Moore T (1994) Sensing of aromatic compounds by the transcriptional activator of phenol-catabolisingPseudomonas sp. strain CF600. J. Bacteriol. 176:1555–1560
Shingler V, Powlowski J & Marklund U (1992) Nucleotide sequence and functional analysis of the complete phenol/3,4-dimethylphenol catabolic pathway ofPseudomonas sp. strain CF600. J. Bacteriol. 174:711–724
Spain JC & Gibson DT (1988) Oxidation of substituted phenols byPseudomonas putida F1 andPseudomonas sp. strain JS6. Appl. Environ. Microbiol. 54:1399–1404
Spoelstra SF (1977) Degradation of tyrosine in anaerobically stored piggery wastes and pig faeces. Appl. Environ. Microbiol. 36:631–638
Stainthorpe AC, Lees V, Salmond GPC, Dalton H & Murrell JC (1990) The methane monooxygenase gene cluster ofMethylococcus capsulatus (Bath). Gene 91:27–34
Stainthorpe AC, Murrell JC, Salmond GPC, Dalton H & Lees V (1989) Molecular analysis of methane monooxygenase fromMethylococcus capsulatus (Bath). Arch. Microbiol. 152:154–159
Steele MI, Lorenz D, Hatter K, Park A & Sokatch (1992) Characterization of themmsAB operon ofPseudomonas aeruginosa PAO encoding methylmalonate-semialdehyde dehydrogenase and 3-hydroxyisobutyrate dehydrogenase. J. Biol. Chem. 267:13585–13592
Walsh C (1979) Enzymatic Reaction Mechanisms (pp 745–759). Freeman and Company, San Francisco
Wasserfallen A, Rekik M & Harayama S (1991) APseudomonas strain able to degradem-toluate in the presence of 3-chlorocatechol. Bio/Technol. 9:296–298
Whitman CP, Aird BA, Gillespie WR & Stolowich NJ (1991) Chemical and enzymatic ketonization of 2-hydroxymuconate, a conjugated enol. J. Amer. Chem. Soc. 113:3154–3162
Wierenga RK, Terpstra P & Hol WGJ (1986) Prediction of the occurrence of the ADP-binding β-α-β fold in proteins using an amino acid sequence finger print. J. Mol. Biol. 187:101–107
Wigmore GJ, Bayly RC & Berardino D (1974)Pseudomonas putida mutants defective in metabolism of the products ofmeta-fisson of catechol and its methyl analogues. J. Bacteriol. 120:31–37
Williams PA, Assinder SJ & Shaw LE (1990) Construction of hybridxylE genes between the two duplicate homologous genes from TOL plasmid pWW53: comparison of the kinetic properties of the gene product. J. Gen. Microbiol. 136:1583–1589
Williams PA & Sayers JR (1994) The evolution of pathways for aromatic hydrocarbon oxidation inPseudomonas. This Volume
Yamamoto S & Ishimura Y (1991) Dioxygenases and monooxygenases. In: Kuby J (Ed) A Study of Enzymes (pp 315–344). CRC Press, Boca Raton, FL
Yen K-M & Karl MR (1992) Identification of a new gene,tmoF, in thePseudomonas mendocinaKR1 gene cluster encoding toluene-4-monooxygenase. J. Bacteriol. 174:7253–7261
Yen K-M, Karl MR, Blatt LM, Simon MJ, Winter RB, Fausset PR, Lu HS, Harcourt AA & Chen KK (1991) Cloning and characterization of aPseudomonas mendocina KR1 gene cluster encoding toluene-4-monooxygenase. J. Bacteriol. 173:5315–5327
You I-S, Ghosal D & Gunsalus IC (1991) Nucleotide sequence analysis of thePseudomonas putida PpG7 salicylate hydroxylase gene (nahG) and its 3′-flanking region. Biochemistry 30:1635–1641
Zylstra GJ & Gibson DT (1989) Toluene degradation by Pseudomonas F1: nucleotide sequence of thetodC1C2BADE genes and their expression inEscherichia coli. J. Biol. Chem. 264:14940–14946
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Powlowski, J., Shingler, V. Genetics and biochemistry of phenol degradation byPseudomonas sp. CF600. Biodegradation 5, 219–236 (1994). https://doi.org/10.1007/BF00696461
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DOI: https://doi.org/10.1007/BF00696461