Abstract
Many Pseudomonads are able to use linear alkanes as sole carbon and energy source. The genetics and enzymology of alkane metabolism have been investigated in depth forPseudomonas oleovorans, which is able to oxidize C5-C12 n-alkanes by virtue of two gene regions, localized on the OCT-plasmid. The so-calledalk-genes have been cloned in pLAFR1, and were subsequent analyzed using minicell expression experiments, DNA sequencing and deletion analysis. This has led to the identification and characterization of thealkBFGHJKL andalkST genes which encode all proteins necessary to convert alkanes to the corresponding acyl-CoA derivatives. These then enter the β-oxidation-cycle, and can be utilized as carbon- and energy sources. Medium (C6-C12)- or long-chain (C13-C20) n-alkanes can be utilized by many strains, some of which have been partially characterized. The alkane-oxidizing enzymes used by some of these strains (e.g. twoP. aeruginosa strains, aP. denitrificans strain and a marinePseudomonas sp.) appear to be closely related to those encoded by the OCT-plasmid.
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Arnold FC & Haymore BL (1991) Engineered metal-binding proteins: purification to protein folding. Science 252: 1796–1797
Atlas RM & Bartha R (1992) Hydrocarbon biodegradation and oil spill bioremediation. Adv. Microb. Ecol. 12: 287–338
Azoulay E, Chouteau J & Davidovics G (1963) Isolement et characterisation des enzymes responsables de l'oxydation des hydrocarbures. Biochim. Biophys. Acta 77: 554–567
Babbitt PC, Kenyon GL, Martin BM, Charest H, Sylvestre M, Scholten JD, Chang K-H, Liang P-H & Dunaway-Mariano D (1992) Ancestry of the 4-chlorobenzoate dehalogenase: Analysis of amino acid sequence identities among families of acyl: adenyl ligases, enoyl-CoA hydratases/isomerases, and acyl-CoA thioesterases. Biochemistry 31: 5594–5604
Bairoch A (1992) PROSITE: a dictionary of sites and patterns in proteins. Nucl. Acids Res. 20: 2013–2018
Baptist JN, Gholson RK & Coon MJ (1963) Hydrocarbon oxidation by a bacterial enzyme system. I. Products of octane oxidation. Biochim. Biophys. Acta 69: 40–47
Benson A, Tomoda K, Chang J, Matsueda G, Lode ET, Coon MJ & Yasunobu KT (1971) Evolutionary and phylogenetic relationships of rubredoxin-containing microbes. Biochem. Biophys. Res. Commun. 42: 640–646
Benson S & Shapiro J (1975) Induction of alkane hydroxylase proteins by unoxidized alkane inPseudomonas putida. J. Bacteriol. 123: 759–760
—— (1976) Plasmid determined alcohol dehydrogenase activity in alkane-utilizing strain ofPseudomonas putida. J. Bacteriol. 126: 794–798
Benson S, Fennewald M, Shapiro J & Huettner C (1977) Fractionation of inducible alkane hydroxylase activity inPseudomonas putida and characterization of hydroxylase-negative plasmid mutations. J. Bacteriol. 132: 614–621
Benson S, Oppici M, Shapiro J & Fennewald M (1979) Regulation of membrane peptides by thePseudomonas plasmidalk regulon. J. Bacteriol. 140: 754–762
Bertrand JC, Doux HJM & Azoulay E (1976) Métabolisme des hydrocarbures chez une bactérie marine. Biochimie 58: 843–854
Bird CW & Molton P (1967) The metabolism of n-decane by aPseudomonas. Biochem. J. 104: 987–990
Bird CW & Lynch JM (1974) Formation of hydrocarbons by Microorganisms. Chem. Soc. Rev. 3: 309–328
Bonamy AMJ, Yon JM & Vandecasteele JP (1983) Purification and catalytic properties of a membrane-bound alcohol dehydrogenase involved in the oxidation of alkanes byPseudomonasaeruginosa. Biol. Cell. 47: 219–226
Bosetti A, Van Beilen JB, Preusting H, Lageveen RG & Witholt B (1992) Production of primary aliphatic alcohols with a recombinantPseudomonas strain, encoding the alkane hydroxylase enzyme system. Enzyme Microb. Technol. 14: 702–708
Boulton CA & Ratledge C (1984) The physiology of hydrocarbonutilizing microorganisms. Topics in Enz. Ferment Biotechnol. 9: 11–77
Bradow JM & Connick WJ (1990) Volatile seed germination inhibitors from plant residues. J. Chem. Ecol. 16: 645–666
Britton LN (1984) Microbial degradation of aliphatic hydrocarbons. In: Gibson DT (Ed.) Microbiology Series. Microbial degradation of organic compounds, Vol. 13 (pp 89–129). Marcel Dekker, New York
Bühler M & Schindler J (1984) Aliphatic hydrocarbons. In: Kieslich K (Ed.) Biotechnology, Vol. 6a (pp 329–385). Verlag Chemie, Weinheim
Cao X, Kolonay J, Saxton KA & Hartline RA (1993) The OCT plasmid encodes D-lysine membrane transport and catabolic enzymes inPseudomonas putida. Plasmid 30: 83–89
Chakrabarty AM (1973) Genetic fusion of incompatible plasmids inPseudomonas. Proc. Natl. Acad. Sci. USA 70: 1641–1644
Chakrabarty AM, Chou G & Gunsalus IC (1973) Genetic regulation of octane dissimulation plasmid inPseudomonas. Proc. Natl. Acad. Sci. USA 70: 1137–1140
Chakrabarty AM (1974) Dissociation of a degradative plasmid aggregate inPseudomonas. J. Bacteriol. 118: 815–820
—— (1985) Genetically-manipulated microorganisms and their products in the oil service industries. TIBS 3: 32–38
Claus R, Asperger O & Kleber H-P (1980) Influence of growth phase and carbon source on the content of rubredoxin inAcinetobacter calcoaceticus. Arch. Microbiol. 128: 263–265
Cooney JJ & Kula TJ (1970) Growth and survival of organisms isolated from hydrocarbon fuel systems. Int. Biodeterior Bull. 6: 109–114
De Lorenzo V, Fernández S, Herrero M, Jakubzik U & Timmis KN (1993) Engineering of alkyl- and haloaromatic-responsive gene expression with mini-transposons containing regulated promoters of biodegradative pathways ofPseudomonas. Gene 130: 41–46
Eggink G, Van Lelyveld PH & Witholt B (1984) The construction of a gene bank fromPseudomonas oleovorans. Molecular cloning of thealk sequences of the OCT plasmid coding for the alkane oxidizing enzymes. In: Houwink EH & Van der Meer RR (Eds) Progress in Industrial Microbiology, Vol 20 (pp 373–380). Elsevier, Amsterdam
Eggink G (1987) Genetics of alkane degradation inPseudomonas oleovorans. Cell Engineering for biotechnological applications. Ph.D. Thesis, University of Groningen, The Netherlands
Eggink G, Van Lelyveld PH, Arnberg A, Arfman N, Witteveen C & Witholt B (1987a) Structure of thePseudomonas putida alkBAC operon. Identification of transcription and translation products. J. Biol. Chem. 262: 6400–6406
Eggink G, Lageveen RG, Altenburg B & Witholt B (1987b) Controlled and functional expression of thePseudomonas oleovorans alkane utilization system inPseudomonas putida andEscherichia coli. J. Biol. Chem. 262: 17712–17718
Eggink G, Engel H, Meijer W, Otten J, Kingma J & Witholt B (1988) Alkane utilization inPseudomonas oleovorans. Structure and function of the regulatory locusalkR. J. Biol. Chem. 263: 13400–13405
Eggink G, Engel H, Vriend G, Terpstra P & Witholt B (1990) Rubredoxin reductase ofPseudomonas oleovorans. Structural relationship to other flavoprotein oxidoreductases based on one NAD and two FAD fingerprints. J. Mol. Biol. 212: 135–142
Favre-Bulle O (1992)Escherichia coli as a potential hydrocarbon conversion microorganism. Ph.D. Thesis. University of Groningen, the Netherlands
Favre-Bulle O, Weenink E, Vos T, Preusting P & Witholt B (1993) Continuous bioconversion of n-octane to octanoic acid by a recombinant Escherichia coli (Alk+) growing in a two-liquid phase bioreactor. Biotechnol. Bioeng. 41: 263–272
Fennewald M & Shapiro J (1977) Regulatory mutations of thePseudomonas plasmidalk regulon. J. Bacteriol. 132: 622–627
Fennewald M, Prevatt W, Meyer R & Shapiro J (1978) Isolation of Inc P-2 plasmid DNA fromPseudomonas aeruginosa. Plasmid 1: 164–173
Fennewald M & Shapiro J (1979) Transposition of Tn7 inPseudomonas aeruginosa and isolation ofalk::Tn7 mutations. J. Bacteriol. 139: 264–269
Fennewald M, Benson S, Oppici M & Shapiro J (1979) Insertion element analysis and mapping of thePseudomonas plasmidalk regulon. J. Bacteriol. 139: 940–952
Frantz B & Chakrabarty AM (1986) Degradative plasmids inPseudomonas. In: Sokatch JR (Ed) The Bacteria, Vol X, The Biology ofPseudomonas (pp 295–323). Academic Press, New York
Fu H, Newcomb M & Wong CH (1991)Pseudomonas oleovorans monooxygenase catalyzed asymmetric epoxidation of allyl alcohol derivatives and hydroxylation of a hypersensitive radical probe with the radical ring opening state exceeding the oxygen rebound state. J. Am. Chem. Soc. 113: 5878–5880
Fukuda M, Nishi T, Igarashi M, Kondo T, Takagi M & Yano K (1989) Degradation of ethylbenzene byPseudomonas putida harboring OCT plasmid. Agric. Biol. Chem. 53: 3293–3299
Gholson RK, Baptist JN & Coon MJ (1963) Hydrocarbon oxidation by a bacterial enzyme system. II. Cofactor requirements for octanol formation from octane. Biochemistry 2: 1155–1159
Gross R, Aricó B & Rappuoli R (1989) Families of bacterial signaltransducing proteins. Mol. Microbiol. 3: 1661–1667
Grund A, Shapiro J, Fennewald M, Bacha P, Leahy J, Markbreiter K, Nieder M & Toepfer M (1975) Regulation of alkane oxidation inPseudomonas putida. J. Bacteriol. 123: 546–556
Hammer KD & Liemann F (1976) Primäre Oxydationsmechanismen beim Abbau aliphatischer Kohlenwasserstoffe durch bakterielle Enzymsysteme. Zbl. Bakt. Hyg. 1 Abt. Orig. B. 162: 169–179
Hansen JB & Olsen RH (1978) IncP2 group ofPseudomonas, a class of uniquely large plasmids. Nature 274: 715–717
Harder PA & Kunz DA (1986) Characterization of the OCT-plasmid encoding alkane oxidation and mercury resistance inPseudomonas putida. J. Bacteriol. 165: 650–653
Henikoff S, Wallace JC & Brown JP (1990) Finding protein similarities with nucleotide sequence databases. Meth. Enzymol. 183: 111–132
Horn JM, Harayama S & Timmis KN (1991) DNA sequence determination of the TOL-plasmid (pWWO)xylGFJ genes ofPseudomonas putida: implication for the evolution of aromatic catabolism. Mol. Microbiol. 5: 2459–2474
Inoue A & Horikoshi K (1991) Estimation of solvent-tolerance of bacteria by the solvent parameter LogP. J. Ferm. Bioeng. 71: 194–196
Johnstone SL, Phillips GT, Robertson BW, Watts PD, Bertola MA, Koger HS & Marx AF (1986) Stereoselective synthesis of s-(-)-β-blockers via microbially produced epoxide intermediates. In: Laane C, Tramper J & Lilly MD (Eds) Biocatalysis in Organic Media (pp 387–392). Elsevier, Amsterdam
Katopodis AG, Smith HA & May SW (1988) New oxyfunctionalization capabilities for θ-hydroxylases: asymmetric aliphatic sulfoxidation and branched ether demethylation. J. Am. Chem. Soc. 110: 897–899
Kleber H-P, Schöpp W & Aurich H (1973) Verwertung von n-Alkanen durch einen Stamm vonAcinetobacter calcoaceticus. Z. Allg. Mikrobiol. 13: 445–447
Kok M, Oldenhuis R, Van der Linden MPG, Raatjes P, Kingma J, Van Lelyveld PH & Witholt B (1989a). ThePseudomonas oleovorans alkane hydroxylase gene. Sequence and expression. J. Biol. Chem. 264: 5435–5441
Kok M, Oldenhuis R, Van der Linden MPG, Meulenberg CHC, Kingma J & Witholt B (1989b) ThePseudomonas oleovorans alkBAC operon encodes two structurally related rubredoxins and an aldehyde dehydrogenase. J. Biol. Chem. 264: 5442–5451
Kusunose M, Kusunose E & Coon MJ (1964) Enzymatic θ-oxidation of fatty acids. II. Substrate specificity and other properties of the enzyme system. J. Biol. Chem. 239: 2135–2139
Kusunose M, Matsumoto J, Ichihara K, Kusunose E & Nozaka J (1967) Requirement for three proteins for hydrocarbon oxidation. J. Biochem. 61: 665–667
Laane C, Boeren S, Vos K & Veeger C (1987) Rules of optimization of biocatalysis in organic solvents. Biotechnol. Bioeng. 30: 81–87
Lageveen RG (1986) Oxidation of aliphatic compounds byPseudomonas oleovorans. Biotechnological applications of the alkane-hydroxylase system. Ph.D. Thesis. University of Groningen, The Netherlands
Lee M & Chandler AC (1941) A study of the nature, growth and control of bacteria in cutting compounds. J. Bacteriol. 41: 373–386
Linder P, Lasko PF, Ashburner M, Leroy P, Nielsen PJ, Nishi K, Schnier J & Slonimski PP (1989) Birth of the DEAD box. Nature 337: 121–122
Lode ET & Coon MJ (1971) Enzymatic θ-oxidation. V. Forms ofPseudomonas oleovorans rubredoxin containing one or two iron atoms: structure and function in θ-hydroxylation. J. Biol. Chem. 246: 791–802
Lovenberg W & Sobel BE (1965) Rubredoxin: A new electron transfer protein fromClostridium Pasteurianum. Proc. Natl. Acad. Sci. USA 54: 193–199
Macham LP & Heydeman MT (1974)Pseudomonas aeruginosa mutants defective in heptane oxidation. J. Gen. Microbiol. 85: 77–84
Mandel M (1966) Deoxyribonucleic acid base composition in the genusPseudomonas. J. Gen. Microbiol. 43: 273–292
Martínez-Zapater JM, Marin A & Oliver JL (1993) Evolution of base composition in T-DNA genes fromAgrobacterium. Mol. Biol. Evol. 10: 437–448
May SW & Abbott BJ (1972) Enzymatic epoxidation. I. Alkane epoxidation by the θ-hydroxylation system ofPseudomonas oleovorans. Biochem. Biophys. Res. Comm. 48: 1230–1234
—— (1973) Enzymatic epoxidation. II. Comparison between the epoxidation and hydroxylation reactions catalyzed by the θ-hydroxylation system ofPseudomonas oleovorans. J. Biol. Chem. 248: 1725–1730
May SW, Schwartz RD, Abbott BJ & Zaborsky OR (1975) Structural effects on the reactivity of substrates and inhibitors in the epoxidation system ofPseudomonas oleovorans. Biochim. Biophys. Acta 403: 245–255
May SW, Lee LG, Katopodis AG, Kuo J-Y, Wimalasena K & Thowsen JR (1984) Rubredoxin fromPseudomonas oleovorans: effects of selective chemical modification and metal substitution. Biochemistry 23: 2187–2192
McKenna EJ & Coon MJ (1970) Enzymatic θ-oxidation. IV. Purification and properties of the θ-hydroxylase ofPseudomonas oleovorans. J. Biol. Chem. 245: 3882–3889
Nieboer M, Kingma J & Witholt B (1993) The alkane oxidation system ofPseudomonasoleovorans: induction of thealk-genes inEscherichia coli W3110 affects membrane biogenesis and results in overexpression of alkane hydroxylase in a distinct cytoplasmic membrane subfraction. Mol. Microbiol. 8: 1039–1051
Nieder M & Shapiro J (1975) Physiological function of thePseudomonas putida PpG6 (Pseudomonas oleovorans) alkane hydroxylase: monoterminal oxidation of alkane and fatty acids. J. Bacteriol. 122: 93–98
Owen DJ, Eggink G, Hauer B, Kok M, McBeth DL, Yang YL & Shapiro JA (1984) Physical structure, genetic content and expression of thealkBAC operon. Mol. Gen. Genet. 197: 373–383
Owen DJ (1986) Molecular cloning and characterization of sequences from the regulatory cluster of thePseudomonas plasmidalk system. Mol. Gen. Genet. 203: 64–72
Palchaudchuri S (1977) Molecular characterization of hydrocarbon degradative plasmids inPseudomonasputida. Biochem. Biophys. Res. Commun. 77: 518–525
Peterson JA, Basu D & Coon MJ (1966) Enzymatic θ-oxidation. I. Electron carriers in fatty acid and hydrocarbon hydroxylation. J. Biol. Chem. 241: 5162–5164
Peterson JA, Kusunose M, Kusunose E & Coon MJ (1967) Enzymatic θ-oxidation II. Function of rubredoxin as the electron-carrier in θ-hydroxylation. J. Biol. Chem. 242: 4334–4340
Peterson JA & Coon MJ (1968) Enzymatic θ-oxidation. III. Purification and properties of rubredoxin, a component of the θ-hydroxylation system ofPseudomonas oleovorans. J. Biol. Chem. 243: 329–334
Richet E & Raibaud O (1989) MalT, the regulatory protein of theEscherichia coli maltose system, is an ATP-dependent transcriptional activator. EMBO J. 8: 981–987
Robinson DS (1964) Oxidation of selected alkanes and related compounds by aPseudomonas strain. Antonie van Leeuwenhoek 30: 303–316
Ruettinger RT, Olson ST, Boyer RF & Coon MJ (1974) Identification of the θ-hydroxylase ofPseudomonas oleovorans as a nonheme iron protein requiring phospholipid for catalytic activity. Biochem. Biophys. Res. Commun. 57: 1011–1017
Ruettinger RT, Griffith GR & Coon MJ (1977) Characterization of the θ-hydroxylase ofPseudomonas oleovorans as a non-heme iron protein. Arch. Biochem. Biophys. 183: 528–537
Sariaslani IS (1989) Microbial enzymes for oxydation of organic molecules. Crit. Rev. Biotechnol. 9: 171–257
Schoner B & Kahn M (1981) The nucleotide sequence of IS5 fromEscherichia coli. Gene 14: 165–174
Schwartz M (1987) The maltose regulon. In: Niedhardt FC, Low KB, Magasanik B, Schaechter M & Umbacher HE (Eds)Escherichia coli andSalmonella typhimurium: cellular and molecular biology, Vol. 2 (pp 1482–1502). American Society for Microbiology, Washington, D.C.
Schwartz RD & Leathen WW (1976) Petroleum microbiology. In: Miller BM & Litsky W (Eds) Industrial Microbiology (pp 384–411). McGraw-Hill, New York
Schwartz RD & McCoy CJ (1973)Pseudomonas oleovorans hydroxylation-epoxidation system: additional strain improvements. Appl. Microbiol. 26: 217–218
Soby S, Kirkpatrick B & Kosuge T (1993) Characterization of an insertion sequence (IS53) located within IS51 on theiaa-containing palsmid ofPseudomonas syringae pv.savastanoi. Plasmid 29: 135–141
Stanier RY, Palleroni NJ & Doudoroff M (1966) The aerobic Pseudomonads: a taxonomic study. J. Gen. Microbiol. 43: 159–271
Struyvé M, Moons M & Tommassen J (1991) Carboxy-terminal phenylalanine is essential for the correct assembly of a bacterial outer membrane protein. J. Mol. Biol. 218: 141–148
Suzuki M, Hayakawa T, Shaw JP, Rekik M & Harayama S (1991) Primary structure of xylene monooxygenase: similarities to and differences from the alkane hydroxylation system. J. Bacteriol. 173: 1690–1695
Taylor SE & Calvin M (1987) Hydrocarbons from plants: Biosynthesis and utilization. Comments Agric. & Food Chem. 1: 1–26
Thysse GJE & Van der Linden AC (1958) N-alkane oxidation by aPseudomonas. Studies on the intermediate metabolism. Antonie van Leeuwenhoek 24: 298–308
Traxler RW & Bernard JM (1969) The utilization of n-alkanes byP. aeruginosa under conditions of anaerobiosis. I. Preliminary observation. Int. Biodeterior. Bull. 5: 21–25
Turgay K, Krause M & Marahiel MA (1992) Four homologous domains in the primary structure of GrsB are related to domains in a superfamily of adenylate-forming enzymes. Mol. Microbiol. 6: 529–546
Ueda T, Lode ET & Coon MJ (1972a) Enzymatic θ-oxidation. VI. Isolation of homogeneous reduced diphosphopyridine nucleotide-rubredoxin reductase. J. Biol. Chem. 247: 2109–2116
Ueda T & Coon MJ (1972b) Enzymatic θ-oxidation. VII. Reduced diphosphopyridine nucleotide-rubredoxin reductase: properties and function as an electron carrier in θ-hydroxylation. J. Biol. Chem. 247: 5010–5016
Van Beilen JB, Penninga D & Witholt B (1992a) Topology of the membrane-bound alkane hydroxylase ofPseudomonas oleovorans. J. Biol. Chem. 267: 9194–9201
Van Beilen JB, Eggink G, Enequist H, Bos R & Witholt B (1992b) DNA sequence determination and functional characterization of the OCT-plasmid encodedalkJKL genes ofPseudomonas oleovorans. Mol. Microbiol. 6: 3121–3136
Van der Meer JR, De Vos WM, Harayama S & Zehnder AJB (1992) Molecular mechanisms of genetic adaptation to xenobiotic compounds. Microbiol. Revs. 56: 677–694
Van Eyk J & Bartels TJ (1968) Paraffin oxidation inPseudomonas aeruginosa. I. Induction of paraffin oxidation. J. Bacteriol. 96: 706–712
—— (1970) Paraffin oxidation inPseudomonas aeruginosa. II. Gross fractionation of the enzyme system into soluble and particulate components. J. Bacteriol. 104: 1065–1073
Van Ravenswaay Claasen JC & Van der Linden AC (1971) Substrate specificity of the paraffin hydroxylase ofPseudomonas aeruginosa. Antonie van Leeuwenhoek 37: 339–352
Vandecasteele JP, Blanchet D, Tassin JP, Bonamy AM & Guerrilot L (1983) Enzymology of alkane degradation inPseudomonas aeruginosa. Acta Biotechnol. 3: 339–344
Watkinson RJ & Morgan P (1990) Physiology of aliphatic hydrocarbon-degrading micro-organisms. Biodegradation 1: 79–92
Williams GR, Cumins E, Gardener AC, Palmier M, Rubidge T (1981) The growth ofPseudomonas putida in AVTUR aviation turbine fuel. J. Appl. Bacteriol. 50: 551–557
Witholt B, De Smet M-J, Kingma J, Van Beilen JB, Kok M, Lageveen RG & Eggink G (1990) Bioconversions of aliphatic compounds byPseudomonas oleovorans in multiphase bioreactors: background and economic potential. Trends Biotechnol 8: 46–52
Yamada T, Lee PD & Kosuge T (1986) Insertion sequence elements ofPseudomonas savastanoi: nucleotide sequence and homology withAgrobacterium tumefaciens transfer DNA. Proc. Natl. Acad. Sci. USA 83: 8263–8267
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van Beilen, J.B., Wubbolts, M.G. & Witholt, B. Genetics of alkane oxidation byPseudomonas oleovorans . Biodegradation 5, 161–174 (1994). https://doi.org/10.1007/BF00696457
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DOI: https://doi.org/10.1007/BF00696457