Biopetrochemicals via Biocatalysis by Hydrocarbons Microbes and their Enzymes

Reference work entry
Part of the Handbook of Hydrocarbon and Lipid Microbiology book series (HHLM)

Abstract

Hydrocarbon-degrading organisms are an important source for industrial relevant reactions. The respective degradation pathways harbor oxidoreductases, an enzyme class catalyzing highly interesting reactions for the production of high value added compounds and fine chemicals. Exploiting these reactions for biocatalysis requires the development of different reaction concepts, as hydrocarbons are often problematic substrates in terms of toxicity and solubility. This chapter will present the development of various reaction concepts for the technical utilization of hydrocarbon degrading organisms and their respective enzymes as biocatalysts.

References

  1. Abril MA, 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 171:6782–6790CrossRefPubMedPubMedCentralGoogle Scholar
  2. Alexander AK, Biedermann D, Fink MJ, Mihovilovic MD, Mattes TE (2012) Enantioselective oxidation by a cyclohexanone monooxygenase from the xenobiotic-degrading Polaromonas sp. strain JS666. J Mol Catal B Enzym 78:105–110CrossRefGoogle Scholar
  3. Baldwin CVF, Wohlgemuth R, Woodley JM (2008) The first 200-l scale asymmetric Baeyer-Villiger oxidation using a whole-cell biocatalyst. Org Process Res Dev 12:660–665CrossRefGoogle Scholar
  4. Banat IM, Makkar RS, Cameotra SS (2000) Potential commercial applications of microbial surfactants. Appl Microbiol Biotechnol 53:495–508CrossRefPubMedGoogle Scholar
  5. Blank LM, Ionidis G, Ebert BE, Buehler B, Schmid A (2008) Metabolic response of Pseudomonas putida during redox biocatalysis in the presence of a second octanol phase. FEBS J 275:5173–5190CrossRefPubMedGoogle Scholar
  6. Bosetti A, van Beilen JB, Preusting H, Lageveen RG, Witholt B (1992) Production of primary aliphatic-alcohols with a recombinant Pseudomonas strain, encoding the alkane hydroxylase enzyme-system. Enzym Microb Technol 14:702–708CrossRefGoogle Scholar
  7. Branda SS, Vik A, Friedman L, Kolter R (2005) Biofilms: the matrix revisited. Trends Microbiol 13:20–26CrossRefPubMedGoogle Scholar
  8. Coleman NV, Mattes TE, Gossett JM (2002) Biodegradation of cis -Dichloroethene as the sole carbon source by a β biodegradation of cis -Dichloroethene as the sole carbon source by a β -Proteobacterium. Appl Environ Microbiol 68:2726–2730CrossRefPubMedPubMedCentralGoogle Scholar
  9. Conrado RJ, Gonzalez R (2014) Envisioning the bioconversion of methane to liquid fuels. Science 343:621–623CrossRefPubMedGoogle Scholar
  10. Dalvi S, Nicholson C, Najar F, Roe BA, Canaan P, Hartson SD, Fathepure BZ (2014) Arhodomonas sp. strain seminole and its genetic potential to degrade aromatic compounds under high-salinity conditions. Appl Environ Microbiol 80:6664–6676CrossRefPubMedPubMedCentralGoogle Scholar
  11. de Smet MJ, Wynberg H, Witholt B (1981) Synthesis of 1,2-epoxyoctane by Pseudomonas oleovorans during growth in a two-phase system containing high concentrations of 1-octene. Appl Environ Microbiol 42:811–816PubMedPubMedCentralGoogle Scholar
  12. de Smet MJ, Kingma J, Wynberg H, Witholt B (1983) Pseudomonas oleovorans as a tool in bioconversions of hydrocarbons: growth, morphology and conversion characteristics in different two-phase systems. Enzym Microb Technol 5:352–360CrossRefGoogle Scholar
  13. Dobslaw D, Engesser KH (2012) Degradation of 2-chlorotoluene by Rhodococcus sp. OCT 10. Appl Microbiol Biotechnol 93:2205–2214CrossRefPubMedGoogle Scholar
  14. Doig SD, Avenell PJ, Bird PA, Gallati P, Lander KS, Lye GJ, Wohlgemuth R, Woodley JM (2002) Reactor operation and scale-up of whole cell Baeyer-Villiger catalyzed lactone synthesis. Biotechnol Prog 18:1039–1046CrossRefPubMedGoogle Scholar
  15. Doig SD, Simpson H, Alphand V, Furstoss R, Woodley JM (2003) Characterization of a recombinant Escherichia coli top10 [pqr239] whole-cell biocatalyst for stereoselective Baeyer-Villiger oxidations. Enzym Microb Technol 32:347–355CrossRefGoogle Scholar
  16. Fuchs G (2008) Anaerobic metabolism of aromatic compounds. Ann N Y Acad Sci 1125:82–99CrossRefPubMedGoogle Scholar
  17. Furuhashi K (1986) A fermentation process for the production of optically active epoxides. Chem Econ Eng Rev 18:21–26Google Scholar
  18. Furuhashi K, Taoka A, Uchida S, Karube I, Suzuki A (1981) Production of 1,2-epoxyalkanes from 1-alkenes by Nocardia Corallina B-276. Eur J Appl Microbiol Biotechnol 12:39–45CrossRefGoogle Scholar
  19. Gibson DT, Subramanian V (1984) Microbial degradation of aromatic hydrocarbons. In: Gibson DT (ed) Microbial degradation of organic compounds. Marcel Dekker, Inc., New York, pp 181–252Google Scholar
  20. Gross R, Hauer B, Otto K, Schmid A (2007) Microbial biofilms: new catalysts for maximizing productivity of long-term biotransformations. Biotechnol Bioeng 98:1123–1134CrossRefPubMedGoogle Scholar
  21. Harayama S, Rekik M, Wubbolts M, Rose K, Leppik RA, Timmis KN (1989) Characterization of five genes in the upper-pathway operon of TOL plasmid pww0 from Pseudomonas putida and identification of the gene products. J Bacteriol 171:5048–5055CrossRefPubMedPubMedCentralGoogle Scholar
  22. Hilker I, Alphand W, Wohlgemuth R, Furstoss R (2004) Microbial transformations, 56. Preparative scale asymmetric Baeyer-Villiger oxidation using a highly productive “two-in-one” resin-based in situ SFPR concept. Adv Synth Catal 346:203–214CrossRefGoogle Scholar
  23. Hilker I, Wohlgemuth R, Alphand V, Furstoss R (2005) Preparative scale asymmetric microbial Baeyer-Villiger oxidation with optimized productivity using a resin-based in situ SFPR strategy. Biotechnol Bioeng 92:702–710CrossRefPubMedGoogle Scholar
  24. Hüsken LE, Beeftink R, de Bont JA, Wery J (2001a) High-rate 3-methylcatechol production in Pseudomonas putida strains by means of a novel expression system. Appl Microbiol Biotechnol 55:571–577CrossRefPubMedGoogle Scholar
  25. Hüsken LE, Dalm MCF, Tramper J, Wery J, de Bont JA, Beeftink R (2001b) Integrated bioproduction and extraction of 3-methylcatechol. J Biotechnol 88:11–19CrossRefPubMedGoogle Scholar
  26. Hüsken LE, de Bont JAM, Beeftink R, Tramper J, Wery J (2002) Optimisation of microbial 3-methylcatechol production as affected by culture conditions. Biocatal Biotransform 20:57–61CrossRefGoogle Scholar
  27. Karande R, Halan B, Schmid A, Buehler K (2014) Segmented flow is controlling growth of catalytic biofilms in continuous multiphase microreactors. Biotechnol Bioeng 111:1831–1840CrossRefPubMedGoogle Scholar
  28. Karande R, Debor L, Salamanca D, Bogdahn F, Engesser KH, Buehler K, Schmid A (2016) Continuous cyclohexane oxidation to cyclohexanol using a novel cytochrome P450 monooxygenase from Acidovorax sp. CHX100 in recombinant P. taiwanensis VLB120 biofilms. Biotechnol Bioeng 113:52–61CrossRefPubMedGoogle Scholar
  29. Kiener A (1992) Enzymatic oxidation of methyl groups on aromatic heterocycles: a versatile method for the preparation of heteroaromatic carboxylic acids. Angew Chem Int Ed Eng 31:774–775CrossRefGoogle Scholar
  30. Ladkau N, Assmann M, Schrewe M, Julsing MK, Schmid A, Bühler B (2016) Efficient production of the nylon 12 monomer ω-aminododecanoic acid methyl ester from renewable dodecanoic acid methyl ester with engineered Escherichia coli. Metab Eng 36:1–9CrossRefPubMedGoogle Scholar
  31. Li XZ, Webb JS, Kjelleberg S, Rosche B (2006) Enhanced benzaldehyde tolerance in Zymomonas mobilis biofilms and the potential of biofilms in fine-chemical production. Appl Environ Microbiol 72:1639–1644CrossRefPubMedPubMedCentralGoogle Scholar
  32. Lode ET, Coon MJ (1971) Enzymatic ω-oxidation. J Biol Chem 246:791–802PubMedGoogle Scholar
  33. Mathys RG, Schmid A, Witholt B (1999) Integrated two-liquid phase bioconversion and product-recovery processes for the oxidation of alkanes: process design and economic evaluation. Biotechnol Bioeng 64:459–477CrossRefPubMedGoogle Scholar
  34. Mattes TE, Alexander AK, Richardson PM, Munk AC, Han CS, Stothard P, Coleman NV (2008) The genome of Polaromonas sp. strain JS666: insights into the evolution of a hydrocarbon- and xenobiotic-degrading bacterium, and features of relevance to biotechnology. Appl Environ Microbiol 74:6405–6416CrossRefPubMedPubMedCentralGoogle Scholar
  35. McKenna EJ, Coon MJ (1970) Enzymatic ω-oxidation. J Biol Chem 245:3882–3889PubMedGoogle Scholar
  36. Miura A, Dalton H (1995) Purification and characterization of the alkene monooxygenase from Nocardia corallina B-276. Biosci Biotechnol Biochem 59:853–859CrossRefGoogle Scholar
  37. Nishino SF, Shin KA, Gossett JM, Spain JC (2013) Cytochrome P450 initiates degradation of cis-dichloroethene by Polaromonas sp. strain JS666. Appl Environ Microbiol 79:2263–2272CrossRefPubMedPubMedCentralGoogle Scholar
  38. Otto K, Hofstetter K, Roethlisberger M, Witholt B, Schmid A (2004) Biochemical characterization of StyAB from Pseudomonas sp. strain VLB120: a two-component flavin-diffusible monooxygenase. J Bacteriol 186:5292–5302CrossRefPubMedPubMedCentralGoogle Scholar
  39. Panke S, Witholt B, Schmid A, Wubbolts MG (1998) Towards a biocatalyst for (S)-styrene oxide production: characterization of the styrene degradation pathway of Pseudomonas sp. strain VLB120. Appl Environ Microbiol 64:2032–2043PubMedPubMedCentralGoogle Scholar
  40. Park JB, Bühler B, Panke S, Witholt B, Schmid A (2007) Carbon metabolism and product inhibition determine the epoxidation efficiency of solvent-tolerant Pseudomonas sp. strain VLB120ΔC. Biotechnol Bioeng 98:1219–1229CrossRefPubMedGoogle Scholar
  41. Peterson JA, Coon MJ (1968) Enzymatic ω-oxidation. III. Purification and properties of rubredoxin, a component of the ω-hydroxylation system of Pseudomonas oleovorans. J Biol Chem 243:329–334PubMedGoogle Scholar
  42. Peterson JA, Kusunose M, Kusunose E, Coon MJ (1967) Enzymatic ω-oxidation II Function of rubredoxin as the electron carrier in ω-hydroxylation. J Biol Chem 242:4334–4340PubMedGoogle Scholar
  43. Ramos JL, Duque E, Gallegos MT, Godoy P, Ramos-Gonzalez MI, Rojas A, Teran W, Segura A (2002) Mechanisms of solvent tolerance in gram-negative bacteria. Annu Rev Microbiol 56:743–768CrossRefPubMedGoogle Scholar
  44. Rogers EJ, Gibson DT (1977) Purification and properties of cis-toluene dihydrodiol dehydrogenase from Pseudomonas putida. J Bacteriol 130:1117–1124PubMedPubMedCentralGoogle Scholar
  45. Rosenberg E, Rubinovitz C, Legmann R, Ron EZ (1988) Purification and chemical properties of Acinetobacter calcoaceticus A2 biodispersan. Appl Environ Microbiol 54:323–326PubMedPubMedCentralGoogle Scholar
  46. Rothen SA, Sauer M, Sonnleitner B, Witholt B (1998) Biotransformation of octane by E. coli HB101[pGEc47] on defined medium: octanoate production and product inhibition. Biotechnol Bioeng 58:356–365CrossRefPubMedGoogle Scholar
  47. Ruettinger T, Olson ST, Boyer R, Coon MJ (1974) Identification of the ω-hydroxylase of Pseudomonas oleovorans as a nonheme iron protein requiring phospholipid for catalytic activity. Biochem Biophys Res Commun 57:1011–1017CrossRefPubMedGoogle Scholar
  48. Ruettinger T, Griffith GR, Coon MJ (1977) Characterization of the ω-hydroxylase of Pseudomonas oleovorans as a nonheme iron protein. Arch Biochem Biophys 183:528–537CrossRefPubMedGoogle Scholar
  49. Salamanca D, Engesser KH (2014) Isolation and characterization of two novel strains capable of using cyclohexane as carbon source. Environ Sci Pollut Res 21:12757–12766CrossRefGoogle Scholar
  50. Salamanca D, Karande R, Schmid A, Dobslaw D (2015) Novel cyclohexane monooxygenase from Acidovorax sp. CHX100. Appl Microbiol Biotechnol 99:6889–6897CrossRefPubMedGoogle Scholar
  51. Salamanca D, Dobslaw D, Engesser K-H (2017) Removal of cyclohexane gaseous emissions using a biotrickling filter system. Chemosphere 176:97–107CrossRefPubMedGoogle Scholar
  52. Scheps D, Malca SH, Hoffmann H, Nestl BM, Hauer B (2011) Regioselective omega-hydroxylation of medium-chain n-alkanes and primary alcohols by CYP153 enzymes from Mycobacterium marinum and Polaromonas sp. strain JS666. Org Biomol Chem 9:6727–6733CrossRefPubMedGoogle Scholar
  53. Schmutzler K, Kupitz K, Schmid A, Buehler K (2016) Hyperadherence of Pseudomonas taiwanensis VLB120dC increases productivity of (S)-styrene oxide formation. Microb Biotechnol 10:735–744Google Scholar
  54. Schwartz RD (1973) Octene epoxidation by a cold-stable alkane-oxidizing isolate of Pseudomonas oleovorans. Appl Microbiol 25:574–577PubMedPubMedCentralGoogle Scholar
  55. Schwartz RD, McCoy CJ (1973) Pseudomonas oleovorans hydroxylation-epoxidation system: additional strain improvements. Appl Microbiol 26:217–218PubMedPubMedCentralGoogle Scholar
  56. Schwartz RD, McCoy CJ (1977) Epoxidation of 1,7-octadiene by Pseudomonas oleovorans: fermentation in the presence of cyclohexane. Appl Environ Microbiol 34:47–49PubMedPubMedCentralGoogle Scholar
  57. Shennan JL (2006) Utilisation of C2-C4 gaseous hydrocarbons and isoprene by microorganisms. J Chem Technol Biotechnol 81:237–256CrossRefGoogle Scholar
  58. Sikkema J, Poolman B, Konings WN, de Bont JA (1992) Effects of the membrane action of tetralin on the functional and structural properties of artificial and bacterial membranes. J Bacteriol 174:2986–2992CrossRefPubMedPubMedCentralGoogle Scholar
  59. Simpson HD, Alphand V, Furstoss R (2001) Microbiological transformations 49. Asymmetric biocatalysed Baeyer-Villiger oxidation: improvement using a recombinant Escherichia coli whole cell biocatalyst in the presence of an adsorbent resin. J Mol Catal B Enzym 16:101–108CrossRefGoogle Scholar
  60. Staijen IE, Hatzimanikatis V, Witholt B (1997) The AlkB monooxygenase of Pseudomonas oleovorans. Synthesis, stability and level in recombinant Escherichia coli and the native host. J Biochem 244:462–470Google Scholar
  61. Subramanian V, Liu TN, Yeh WK, Narro M, Gibson DT (1981) Purification and properties of NADH-ferredoxin TOL reductase. A component of toluene dioxygenase from Pseudomonas putida. J Biol Chem 256:2723–2730PubMedGoogle Scholar
  62. Subramanian V, Liu TN, Yeh WK, Serdar CM, Wackett LP, Gibson DT (1985) Purification and properties of ferredoxinTOL. a component of toluene dioxygenase from Pseudomonas putida F1. J Biol Chem 260:2355–2363PubMedGoogle Scholar
  63. Taggart MS (1946) Utilization of hydrocarbons. U.S. patent office no. 2396900Google Scholar
  64. Ueda T, Coon MJ (1972) Enzymatic ω-oxidation. VII Reduced diphosphopyridine nucleotide-rubredoxin reductase: properties and function as an electron carrier in ω-hydroxylation. J Biol Chem 247:5010–5016PubMedGoogle Scholar
  65. van Beilen J, Penninga D, Witholt B (1992a) Topology of the membrane-bound alkane hydroxylase of Pseudomonas oleovorans. J Biol Chem 267:9194–9201PubMedGoogle Scholar
  66. van Beilen JB, Eggink G, Enequist H, Bos R, Witholt B (1992b) DNA sequence determination and functional characterization of the oct-plasmid-encoded alkjkl genes of Pseudomonas oleovorans. Mol Microbiol 6:3121–3126CrossRefPubMedGoogle Scholar
  67. van Beilen JB, Panke S, Lucchini S, Franchini AG, Rothlisberger M, Witholt B (2001) Analysis of Pseudomonas putida alkane-degradation gene clusters and flanking insertion sequences: evolution and regulation of the alk genes. Microbiology 147:1621–1630CrossRefPubMedGoogle Scholar
  68. van Hamme JD, Singh A, Ward OP (2003) Recent advances in petroleum microbiology. Microbiol Mol Biol Rev 67:503–549CrossRefPubMedPubMedCentralGoogle Scholar
  69. Widdel F, Rabus R (2001) Anaerobic biodegradation of saturated and aromatic hydrocarbons. Curr Opin Biotechnol 12:259–276CrossRefPubMedGoogle Scholar
  70. Willrodt C, Halan B, Karthaus L, Rehdorf J, Julsing MK, Buehler K, Schmid A (2016) Continuous multistep synthesis of perillic acid from limonene by catalytic biofilms under segmented flow. Biotechnol Bioeng 114:281–290CrossRefPubMedGoogle Scholar
  71. Witholt B, de Smet M-J, Kingma J, van Beilen JB, Lageveen RG, Eggink G (1990) Bioconversions of aliphatic compounds by Pseudomonas oleovorans in multiphase bioreactors: background and economic potential. Trends Biotechnol 8:46–52CrossRefPubMedGoogle Scholar
  72. Worsey MJ, Williams PA (1975) Metabolism of toluene and xylenes by Pseudomonas putida (arvilla) mt-2: evidence for a new function of the TOL plasmid. J Bacteriol 124:7–13PubMedPubMedCentralGoogle Scholar
  73. Wubbolts MG, FavreBulle O, Witholt B (1996) Biosynthesis of synthons in two-liquid-phase media. Biotechnol Bioeng 52:301–308CrossRefPubMedGoogle Scholar
  74. Yeh WK, Gibson DT, Liu T-N (1977) Toluene dioxygenase: a multicomponent enzyme system. Biochem Biophys Res Commun 78:401–410CrossRefPubMedGoogle Scholar
  75. Zylstra GJ, Gibson DT (1989) Toluene degradation by pseudomonas putida F1 - nucleotide-sequence of the todc1c2bade genes and their expression in Escherichia coli. J Biol Chem 264:14940–14946PubMedGoogle Scholar
  76. Zylstra GJ, Mccombie WR, Finette BA (1988) Toluene degradation by Pseudomonas putida F1: genetic organization of the tod operon. Appl Environ Microbiol 54:1498–1503PubMedPubMedCentralGoogle Scholar

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© Springer International Publishing AG, part of Springer Nature 2017

Authors and Affiliations

  1. 1.Department of Solar MaterialsHelmholtz Center for Environmental Research Leipzig (UFZ)LeipzigGermany

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