Abstract
DNA family shuffling is a relatively new method of directed evolution used to create novel enzymes in order to improve their existing properties or to develop new features. This method of evolution in vitro has one basic requirement: a high similarity of initial parental sequences. Cytochrome P450 enzymes are relatively well conserved in their amino acid sequences. Members of the same family can have more than 40% of sequence identity at the protein level and are therefore good candidates for DNA family shuffling. These xenobiotic-metabolising enzymes have an ability to metabolise a wide range of chemicals and produce a variety of products including blue pigments such as indigo. By applying the specifically designed DNA family shuffling approach, catalytic properties of cytochrome P450 enzymes were further extended in the chimeric progeny to include a new range of blue colour formations. This mini-review evokes the possibility of exploiting directed evolution of cytochrome P450s and the novel enzymes created by DNA family shuffling for the production of new dyes.
Similar content being viewed by others
References
Abecassis V, Pompon D, Truan G (2000) High efficiency family shuffling based on multi-step PCR and in vivo DNA recombination in yeast: statistical and functional analysis of a combinatorial library between human cytochrome P450 1A1 and 1A2. Nucleic Acids Res 28:E88
Adachi J, Mori Y, Matsui S, Takigami H, Fujino J, Kitagawa H, Miller CA, Kato T, Saeki K, Matsuda T (2001) Indirubin and indigo are potent aryl hydrocarbon receptor ligands present in human urine. J Biol Chem 276(34):31475–31478
Ahmad N, Mukhtar H (2004) Cytochrome p450: a target for drug development for skin diseases. J Invest Dermatol 123:417–425
Alcalde M, Farinas ET, Arnold FH (2004) Colorimetric high-throughput assay for alkene epoxidation catalyzed by cytochrome P450 BM-3 variant 139-3. J Biomol Screen 9:141–146
Andersen JF, Tatsuta K, Gunji H, Ishiyama T, Hutchinson CR (1993) Substrate specificity of 6-deoxyerythronolide B hydroxylase, a bacterial cytochrome P450 of erythromycin A biosynthesis. Biochemistry 32:1905–1913
Anh DH, Ullrich R, Benndorf D, Svatos A, Muck A, Hofrichter M (2007) The coprophilous mushroom Coprinus radians secretes a haloperoxidase that catalyzes aromatic peroxygenation. Appl Environ Microbiol 73:5477–5485
Barnes HJ, Arlotto MP, Waterman MR (1991) Expression and enzymatic activity of recombinant cytochrome P450 17 alpha-hydroxylase in Escherichia coli. Proc Natl Acad Sci USA 88:5597–5601
Bell SG, Stevenson JA, Boyd HD, Campbell S, Riddle AD, Orton EL, Wong LL (2002) Butane and propane oxidation by engineered cytochrome P450cam. Chem Commun (Camb) 2002:490–491
Bell SG, Chen X, Sowden RJ, Xu F, Williams JN, Wong LL, Rao Z (2003a) Molecular recognition in (+)-alpha-pinene oxidation by cytochrome P450cam. J Am Chem Soc 125:705–714
Bell SG, Chen X, Xu F, Rao Z, Wong LL (2003b) Engineering substrate recognition in catalysis by cytochrome P450cam. Biochem Soc Trans 31:558–562
Bernhardt R (2006) Cytochromes P450 as versatile biocatalysts. J Biotechnol 124:128–145
Bershtein S, Tawfik DS (2008) Advances in laboratory evolution of enzymes. Curr Opin Chem Biol 12:151–158
Bischoff D, Bister B, Bertazzo M, Pfeifer V, Stegmann E, Nicholson GJ, Keller S, Pelzer S, Wohlleben W, Sussmuth RD (2005) The biosynthesis of vancomycin-type glycopeptide antibiotics—a model for oxidative side-chain cross-linking by oxygenases coupled to the action of peptide synthetases. Chembiochem 6:267–272
Blanz J, Ehninger G, Zeller KP (1989) The isolation and identification of indigo and indirubin from urine of a patient with leukemia. Res Commun Chem Pathol Pharmacol 64:145–156
Brodie AM (1994) Aromatase inhibitors in the treatment of breast cancer. J Steroid Biochem Mol Biol 49:281–287
Brown CM, Reisfeld B, Mayeno AN (2008) Cytochromes P450: a structure-based summary of biotransformations using representative substrates. Drug Metab Rev 40:1–100
Estabrook RW, Cooper DY, Rosenthal O (1963) The light reversible carbon monoxide inhibition of the steroid C21-hydroxylase system of the adrenal cortex. Biochem Z 338:741–755
Farinas ET, Bulter T, Arnold FH (2001) Directed enzyme evolution. Curr Opin Biotechnol 12:545–551
Fujita K, Kamataki T (2002) Genetically engineered bacterial cells co-expressing human cytochrome P450 with NADPH-cytochrome P450 reductase: prediction of metabolism and toxicity of drugs in humans. Drug Metab Pharmacokinet 17:1–22
Gillam EM (1998) Human cytochrome P450 enzymes expressed in bacteria: reagents to probe molecular interactions in toxicology. Clin Exp Pharmacol Physiol 25:877–886
Gillam EM, Aguinaldo AM, Notley LM, Kim D, Mundkowski RG, Volkov AA, Arnold FH, Soucek P, DeVoss JJ, Guengerich FP (1999) Formation of indigo by recombinant mammalian cytochrome P450. Biochem Biophys Res Commun 265:469–472
Gillam EM, Notley LM, Cai H, De Voss JJ, Guengerich FP (2000) Oxidation of indole by cytochrome P450 enzymes. Biochemistry 39:13817–13824
Glieder A, Farinas ET, Arnold FH (2002) Laboratory evolution of a soluble, self-sufficient, highly active alkane hydroxylase. Nat Biotechnol 20:1135–1139
Gorren AC, Mayer B (2007) Nitric-oxide synthase: a cytochrome P450 family foster child. Biochim Biophys Acta 1770:432–445
Groves JT, Han Y-Z (1995) Models and mechanisms of cytochrome P450 action. In: Ortiz de Montellano PR (ed) Cytochrome P450: structure, mechanism and biochemistry. Plenum, New York, pp 3–48
Guengerich FP (1995a) Cytochrome P450 proteins and potential utilization in biodegradation. Environ Health Perspect 103(Suppl 5):25–28
Guengerich FP (1995b) Human cytochrome P450 enzymes. In: Ortiz de Montellano PR (ed) Cytochrome P450: structure, mechanism and biochemistry. Plenum, New York, pp 473–535
Guengerich FP (2001) Common and uncommon cytochrome P450 reactions related to metabolism and chemical toxicity. Chem Res Toxicol 14:611–650
Guengerich FP (2002) Cytochrome P450 enzymes in the generation of commercial products. Nat Rev Drug Discov 1:359–366
Guengerich FP, Gillam EM, Shimada T (1996) New applications of bacterial systems to problems in toxicology. Crit Rev Toxicol 26:551–583
Guengerich FP, Parikh A, Turesky RJ, Josephy PD (1999) Inter-individual differences in the metabolism of environmental toxicants: cytochrome P450 1A2 as a prototype. Mutat Res 428:115–124
Guengerich FP, Miller GP, Hanna IH, Martin MV, Leger S, Black C, Chauret N, Silva JM, Trimble LA, Yergey JA, Nicoll-Griffith DA (2002) Diversity in the oxidation of substrates by cytochrome P450 2D6: lack of an obligatory role of aspartate 301-substrate electrostatic bonding. Biochemistry 41:11025–11034
Guengerich FP, Hanna IH, Martin MV, Gillam EM (2003) Role of glutamic acid 216 in cytochrome P450 2D6 substrate binding and catalysis. Biochemistry 42:1245–1253
Guengerich FP, Martin MV, McCormick WA, Nguyen LP, Glover E, Bradfield CA (2004a) Aryl hydrocarbon receptor response to indigoids in vitro and in vivo. Arch Biochem Biophys 423:309–316
Guengerich FP, Sorrells JL, Schmitt S, Krauser JA, Aryal P, Meijer L (2004b) Generation of new protein kinase inhibitors utilizing cytochrome p450 mutant enzymes for indigoid synthesis. J Med Chem 47:3236–3241
Guo Z, Gillam EM, Ohmori S, Tukey RH, Guengerich FP (1994) Expression of modified human cytochrome P450 1A1 in Escherichia coli: effects of 5′ substitution, stabilization, purification, spectral characterization, and catalytic properties. Arch Biochem Biophys 312:436–446
Hanna IH, Kim MS, Guengerich FP (2001) Heterologous expression of cytochrome P450 2D6 mutants, electron transfer, and catalysis of bufuralol hydroxylation: the role of aspartate 301 in structural integrity. Arch Biochem Biophys 393:255–261
Hoessel R, Leclerc S, Endicott JA, Nobel MEM, Lawrie A, Tunnah P, Leost M, Damiens E, Marie D, Marko D, Niederberg E, Tang W, Eisenbrand G, Meijer L (1999) Indirubin, the active constituent of a Chinese antileukaemia medicine, inhibits cyclin-dependent kinases. Nature Cell Biology 1:60–67
Hofrichter M, Ullrich R (2006) Heme-thiolate haloperoxidases: versatile biocatalysts with biotechnological and environmental significance. Appl Microbiol Biotechnol 71:276–288
Hogg JA (1992) Steroids, the steroid community, and Upjohn in perspective: a profile of innovation. Steroids 57:593–616
Huang W, Johnston WA, Hayes MA, De Voss JJ, Gillam EM (2007) A shuffled CYP2C library with a high degree of structural integrity and functional versatility. Arch Biochem Biophys 467:193–205
Isin EM, Guengerich FP (2007) Complex reactions catalyzed by cytochrome P450 enzymes. Biochim Biophys Acta 1770:314–329
Jackson AH, Jenkins RT, Grinstein M, Ferramola de Sancovich AM, Sancovich HA (1988) The isolation and identification of indigoid pigments from urine. Clin Chim Acta 172:245–252
Jennewein S, Croteau R (2001) Taxol: biosynthesis, molecular genetics, and biotechnological applications. Appl Microbiol Biotechnol 57:13–19
Jennewein S, Rithner CD, Williams RM, Croteau RB (2001) Taxol biosynthesis: taxane 13 alpha-hydroxylase is a cytochrome P450-dependent monooxygenase. Proc Natl Acad Sci USA 98:13595–13600
Jennewein S, Park H, DeJong JM, Long RM, Bollon AP, Croteau RB (2005) Coexpression in yeast of Taxus cytochrome P450 reductase with cytochrome P450 oxygenases involved in Taxol biosynthesis. Biotechnol Bioeng 89:588–598
Joern JM, Meinhold P, Arnold FH (2002) Analysis of shuffled gene libraries. J Mol Biol 316:643–656
Johnston WA, Huang W, De Voss JJ, Hayes MA, Gillam EM (2007) A shuffled CYP1A library shows both structural integrity and functional diversity. Drug metabolism and disposition: the biological fate of chemicals 35:2177–2185
Jones JP, O’Hare EJ, Wong LL (2001) Oxidation of polychlorinated benzenes by genetically engineered CYP101 (cytochrome P450(cam)). Eur J Biochem 268:1460–1467
Joo H, Lin Z, Arnold FH (1999) Laboratory evolution of peroxide-mediated cytochrome P450 hydroxylation. Nature 399:670–673
Kellner DG, Maves SA, Sligar SG (1997) Engineering cytochrome P450s for bioremediation. Curr Opin Biotechnol 8:274–278
Kim D, Guengerich FP (2004) Selection of human cytochrome P450 1A2 mutants with enhanced catalytic activity for heterocyclic amine N-hydroxylation. Biochemistry 43:981–988
Kitazume T, Takaya N, Nakayama N, Shoun H (2000) Fusarium oxysporum fatty-acid subterminal hydroxylase (CYP505) is a membrane-bound eukaryotic counterpart of Bacillus megaterium cytochrome P450BM3. J Biol Chem 275:39734–39740
Kluge MG, Ullrich R, Scheibner K, Hofrichter M (2007) Spectrophotometric assay for detection of aromatic hydroxylation catalyzed by fungal haloperoxidase-peroxygenase. Appl Microbiol Biotechnol 75:1473–1478
Kumar S, Halpert JR (2005) Use of directed evolution of mammalian cytochromes P450 for investigating the molecular basis of enzyme function and generating novel biocatalysts. Biochem Biophys Res Commun 338:456–464
Leclerc S, Garnier M, Hoessel R, Marko D, Bibb JA, Snyder GL, Greengard P, Biernat J, Wu YZ, Mandelkow EM, Eisenbrand G, Meijer L (2001) Indirubins inhibit glycogen synthase kinase-3 beta and CDK5/p25, two protein kinases involved in abnormal tau phosphorylation in Alzheimer’s disease. A property common to most cyclin-dependent kinase inhibitors. J Biol Chem 276:251–260
Manoj KM, Hager LP (2001) Utilization of peroxide and its relevance in oxygen insertion reactions catalyzed by chloroperoxidase. Biochim Biophys Acta 1547:408–417
Manoj KM, Yi X, Rai GP, Hager LP (1999) A kinetic epoxidation assay for chloroperoxidase. Biochem Biophys Res Commun 266:301–303
Murdock D, Ensley BD, Serdar C, Thalen M (1993) Construction of metabolic operons catalyzing the de novo biosynthesis of indigo in Escherichia coli. Biotechnology (N Y) 11:381–386
Nakamura K, Martin MV, Guengerich FP (2001) Random mutagenesis of human cytochrome p450 2A6 and screening with indole oxidation products. Arch Biochem Biophys 395:25–31
Nebert DW, Nelson DR, Adesnik M, Coon MJ, Estabrook RW, Gonzalez FJ, Guengerich FP, Gunsalus IC, Johnson EF, Kemper B et al (1989) The P450 superfamily: updated listing of all genes and recommended nomenclature for the chromosomal loci. DNA 8:1–13
Nebert DW, Nelson DR, Coon MJ, Estabrook RW, Feyereisen R, Fujii-Kuriyama Y, Gonzalez FJ, Guengerich FP, Gunsalus IC, Johnson EF et al (1991) The P450 superfamily: update on new sequences, gene mapping, and recommended nomenclature. DNA Cell Biol 10:1–14
Nelson DR, Kamataki T, Waxman DJ, Guengerich FP, Estabrook RW, Feyereisen R, Gonzalez FJ, Coon MJ, Gunsalus IC, Gotoh O et al (1993) The P450 superfamily: update on new sequences, gene mapping, accession numbers, early trivial names of enzymes, and nomenclature. DNA Cell Biol 12:1–51
Nelson DR, Koymans L, Kamataki T, Stegeman JJ, Feyereisen R, Waxman DJ, Waterman MR, Gotoh O, Coon MJ, Estabrook RW, Gunsalus IC, Nebert DW (1996) P450 superfamily: update on new sequences, gene mapping, accession numbers and nomenclature. Pharmacogenetics 6:1–42
Omura T (2005) Heme-thiolate proteins. Molec Cell Biol Res Commun 338:404–409
Omura T, Sato R (1962) A new cytochrome in liver microsomes. J Biol Chem 237:1375–1376
Parikh A, Gillam EM, Guengerich FP (1997) Drug metabolism by Escherichia coli expressing human cytochromes P450. Nat Biotechnol 15:784–788
Parikh A, Josephy PD, Guengerich FP (1999) Selection and characterization of human cytochrome P450 1A2 mutants with altered catalytic properties. Biochemistry 38:5283–5289
Peters MW, Meinhold P, Glieder A, Arnold FH (2003) Regio- and enantioselective alkane hydroxylation with engineered cytochromes P450 BM-3. J Am Chem Soc 125:13442–13450
Puchalska M, Polec-Pawlak K, Zadrozna I, Hryszko H, Jarosz M (2004) Identification of indigoid dyes in natural organic pigments used in historical art objects by high-performance liquid chromatography coupled to electrospray ionization mass spectrometry. J Mass Spectrom 39:1441–1449
Roberts GC (1999) The power of evolution: accessing the synthetic potential of P450s. Chem Biol 6:R269–R272
Roberts GA, Grogan G, Greter A, Flitsch SL, Turner NJ (2002) Identification of a new class of cytochrome P450 from a Rhodococcus sp. J Bacteriol 184:3898–3908
Rosic N (2005) Molecular breeding of cytochrome P450s for indigoid pigment production. School of Biomedical Sciences. University of Queensland, Brisbane, pp 1–160
Rosic N, Lonhienne TGA, DeVoss JJ, Gillam EMJ (2003) Directed evolution of mammalian cytochrome P450 enzymes involved in xenobiotic metabolism. Drug Metabolism Reviews 35:46–46
Rosic NN, Huang W, Johnston WA, DeVoss JJ, Gillam EM (2007) Extending the diversity of cytochrome P450 enzymes by DNA family shuffling. Gene 395:40–48
Seng Wong T, Arnold FH, Schwaneberg U (2004) Laboratory evolution of cytochrome p450 BM-3 monooxygenase for organic cosolvents. Biotechnol Bioeng 85:351–358
Shafiee A, Hutchinson CR (1988) Purification and reconstitution of the electron transport components for 6-deoxyerythronolide B hydroxylase, a cytochrome P-450 enzyme of macrolide antibiotic (erythromycin) biosynthesis. J Bacteriol 170:1548–1553
Sowden RJ, Yasmin S, Rees NH, Bell SG, Wong LL (2005) Biotransformation of the sesquiterpene (+)-valencene by cytochrome P450cam and P450BM-3. Org Biomol Chem 3:57–64
Strobel HW, Hodgson AV, Shen S (1995) NADPH cytochrome P450 reductase and its structural and functional domains. In: Ortiz de Montellano PR (ed) Cytochrome P450: structure, mechanism and biochemistry. Plenum, New York, pp 225–244
Tompkins LM, Wallace AD (2007) Mechanisms of cytochrome P450 induction. J Biochem Mol Toxicol 21:176–181
Ullrich R, Nuske J, Scheibner K, Spantzel J, Hofrichter M (2004) Novel haloperoxidase from the agaric basidiomycete Agrocybe aegerita oxidizes aryl alcohols and aldehydes. Appl Environ Microbiol 70:4575–4581
Urban P, Truan G, Pompon D (2008) High-throughput enzymology and combinatorial mutagenesis for mining cytochrome P450 functions. Expert Opin Drug Metab Toxicol 4:733–747
Urlacher V, Schmid RD (2002) Biotransformations using prokaryotic P450 monooxygenases. Curr Opin Biotechnol 13:557–564
VonWachenfeldt C, Johnson EF (1995) Structures of eukaryotic cytochrome P450 enzymes. In: Ortiz de Montellano PR (ed) Cytochrome P450: structure, mechanism and biochemistry. Plenum, New York, pp 183–223
Yang J, Liao M, Shou M, Jamei M, Yeo KR, Tucker GT, Rostami-Hodjegan A (2008) Cytochrome p450 turnover: regulation of synthesis and degradation, methods for determining rates, and implications for the prediction of drug interactions. Curr Drug Metab 9:384–394
Yun CH, Miller GP, Guengerich FP (2000) Rate-determining steps in phenacetin oxidations by human cytochrome P450 1A2 and selected mutants. Biochemistry 39:11319–11329
Acknowledgments
The author would like to thank Drs. Elizabeth Gillam, James De Voss, Pavel Soucek, Robert Kinobe, Deanne Mitchell, Shona Osborne and Iris Depaz for their help with different aspects of this research. International Postgraduate Research Scholarship and University of Queensland Graduate School Award (N. R.) also supported this project.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Rosic, N.N. Versatile capacity of shuffled cytochrome P450s for dye production. Appl Microbiol Biotechnol 82, 203–210 (2009). https://doi.org/10.1007/s00253-008-1812-8
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00253-008-1812-8