DyP-type peroxidases: A promising and versatile class of enzymes

Journal of Industrial Microbiology and Biotechnology

Volumn 41, Issue 1, 2014, Pages 1-7

  Colpa, Dana I ^a   Fraaije, Marco W ^a   Van Bloois, Edwin ^a  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

Author keywords

Biocatalysis; Dye decolorization; Heme; Lignin degradation; Peroxidase

Indexed keywords

ASPARTIC ACID; BACTERIAL ENZYME; BETA CAROTENE; DYP PEROXIDASE; FERRIC ION; FUNGAL ENZYME; HYDROLASE; LIGNIN; LIGNIN PEROXIDASE; PEROXIDASE; SULFIDE; UNCLASSIFIED DRUG;

AURICULARIA AURICULA-JUDAE; BIOCATALYSIS; BIOCATALYST; BJERKANDERA; CRYSTAL STRUCTURE; DECOLORIZATION; ENZYMATIC DEGRADATION; ENZYME SPECIFICITY; ENZYME STRUCTURE; EPOXIDATION; HETEROLOGOUS EXPRESSION; HORSERADISH; HUMAN; HYDROLYSIS; NONHUMAN; PHANEROCHAETE; PHYLOGENY; REVIEW; RHODOCOCCUS; SEQUENCE ANALYSIS; THERMOBIFIDA FUSCA;

ANIMALIA; FUNGI;

BIOCATALYSIS; HYDROLYSIS; LIGNIN; OXIDATION-REDUCTION; PEROXIDASES;

EID: 84891879043     PISSN: 13675435     EISSN: 14765535     Source Type: Journal    
DOI: 10.1007/s10295-013-1371-6     Document Type: Review

References (51)

1. Adav SS, Ng CS, Arulmani M, Sze SK (2010) Quantitative iTRAQ secretome analysis of cellulolytic Thermobifida fusca. J Proteome Res 9:3016-3024
2. Ahmad M, Roberts JN, Hardiman EM, Singh R, Eltis LD, Bugg TD (2011) Identification of DypB from Rhodococcus jostii RHA1 as a lignin peroxidase. Biochemistry 50:5096-5107
3. Amini S, Tavazoie S (2011) Antibiotics and the post-genome revolution. Curr Opin Microbiol 14:513-518
4. Banci L (1997) Structural properties of peroxidases. J Biotechnol 53:253-263 (Pubitemid 27286441)
5. Brown ME, Barros T, Chang MC (2012) Identification and characterization of a multifunctional dye peroxidase from a lignin-reactive bacterium. ACS Chem Biol 7:2074-2081
6. Bugg TD, Ahmad M, Hardiman EM, Singh R (2011) The emerging role for bacteria in lignin degradation and bio-product formation. Curr Opin Biotechnol 22:394-400
7. Burner U, Krapfenbauer G, Furtmuller PG, Regelsberger G, Obinger C (2000) Oxidation of hydroquinone, 2,3-dimethylhydroquinone and 2,3,5- trimethylhydroquinone by human myeloperoxidase. Redox Rep 5:185-190
8. Chen H (2006) Recent advances in azo dye degrading enzyme research. Curr Protein Pept Sci 7:101-111
9. Choinowski T, Blodig W, Winterhalter KH, Piontek K (1999) The crystal structure of lignin peroxidase at 1.70-A resolution reveals a hydroxy group on the cbeta of tryptophan 171: a novel radical site formed during the redox cycle. J Mol Biol 286:809-827 (Pubitemid 29106220)
10. Dailey HA et al (2011) The Escherichia coli protein YfeX functions as a porphyrinogen oxidase, not a heme dechelatase. MBio 2. doi: 10.1128/mBio.00248- 11
11. Davies MJ, Hawkins CL, Pattison DI, Rees MD (2008) Mammalian heme peroxidases: from molecular mechanisms to health implications. Antioxid Redox Signal 10:1199-1234 (Pubitemid 351634397)
12. Doyle WA, Blodig W, Veitch NC, Piontek K, Smith AT (1998) Two substrate interaction sites in lignin peroxidase revealed by site-directed mutagenesis. Biochemistry 37:15097-15105 (Pubitemid 28503237)
13. Faraco V, Piscitelli A, Sannia G, Giardina P (2007) Identification of a new member of the dye-decolorizing peroxidase family from Pleurotus ostreatus. World J Microbiol Biotechnol 23:889-893 (Pubitemid 46742104)
14. Johjima T, Ohkuma M, Kudo T (2003) Isolation and cDNA cloning of novel hydrogen peroxide-dependent phenol oxidase from the basidiomycete Termitomyces albuminosus. Appl Microbiol Biotechnol 61:220-225 (Pubitemid 36570741)
15. Jongbloed JD, Grieger U, Antelmann H, Hecker M, Nijland R, Bron S, van Dijl JM (2004) Two minimal Tat translocases in Bacillus. Mol Microbiol 54:1319-1325 (Pubitemid 39578274)
16. Kim SJ, Shoda M (1999) Purification and characterization of a novel peroxidase from Geotrichum candidum dec 1 involved in decolorization of dyes. Appl Environ Microbiol 65:1029-1035 (Pubitemid 29111167)
17. Klibanov AM (2003) Asymmetric enzymatic oxidoreductions in organic solvents. Curr Opin Biotechnol 14:427-431 (Pubitemid 37011324)
18. Kong L, Guo D, Zhou S, Yu X, Hou G, Li R, Zhao B (2010) Cloning and expression of a toxin gene from Pseudomonas fluorescens GcM5-1A. Arch Microbiol 192:585-593
19. Li J, Liu C, Li B, Yuan H, Yang J, Zheng B (2012) Identification and molecular characterization of a novel DyP-type peroxidase from Pseudomonas aeruginosa PKE117. Appl Biochem Biotechnol 166:774-785
20. Liers C, Bobeth C, Pecyna M, Ullrich R, Hofrichter M (2010) DyP-like peroxidases of the jelly fungus Auricularia auricula-judae oxidize nonphenolic lignin model compounds and high-redox potential dyes. Appl Microbiol Biotechnol 85:1869-1879
21. Liers C, Pecyna MJ, Kellner H, Worrich A, Zorn H, Steffen KT, Hofrichter M, Ullrich R (2013) Substrate oxidation by dye-decolorizing peroxidases (DyPs) from wood- and litter-degrading agaricomycetes compared to other fungal and plant heme-peroxidases. Appl Microbiol Biotechnol 97:5839-5849
22. Liers C, Ullrich R, Hofrichter M, Minibayeva FV, Beckett RP (2011) A heme peroxidase of the ascomyceteous lichen Leptogium saturninum oxidizes high-redox potential substrates. Fungal Genet Biol 48:1139-1145
23. Liu X et al (2011) Crystal structure and biochemical features of EfeB/YcdB from Escherichia coli O157: ASP235 plays divergent roles in different enzyme-catalyzed processes. J Biol Chem 286:14922-14931
24. Ogola HJ, Kamiike T, Hashimoto N, Ashida H, Ishikawa T, Shibata H, Sawa Y (2009) Molecular characterization of a novel peroxidase from the cyanobacterium Anabaena sp. strain PCC 7120. Appl Environ Microbiol 75:7509-7518
25. Passardi F, Cosio C, Penel C, Dunand C (2005) Peroxidases have more functions than a Swiss army knife. Plant Cell Rep 24:255-265 (Pubitemid 41116471)
26. Puhse M, Szweda RT, Ma Y, Jeworrek C, Winter R, Zorn H (2009) Marasmius scorodonius extracellular dimeric peroxidase - exploring its temperature and pressure stability. Biochim Biophys Acta 1794:1091-1098
27. Regalado C, García-Almendárez BE, Duarte-Vázquez MA (2004) Biotechnological applications of peroxidases. Phytochem Rev 3:243-256 (Pubitemid 41184553)
28. Reszka KJ, McCormick ML, Britigan BE (2001) Peroxidase- and nitrite-dependent metabolism of the anthracycline anticancer agents daunorubicin and doxorubicin. Biochemistry 40:15349-15361 (Pubitemid 33151950)
29. Reszka KJ, Wagner BA, Burns CP, Britigan BE (2005) Effects of peroxidase substrates on the Amplex red/peroxidase assay: antioxidant properties of anthracyclines. Anal Biochem 342:327-337 (Pubitemid 40884583)
30. Roberts JN, Singh R, Grigg JC, Murphy ME, Bugg TD, Eltis LD (2011) Characterization of dye-decolorizing peroxidases from Rhodococcus jostii RHA1. Biochemistry 50:5108-5119
31. Salvachua D, Prieto A, Martinez AT, Martinez MJ (2013) Characterization of a novel dye-decolorizing peroxidase (DyP)-type enzyme from Irpex lacteus and its application in enzymatic hydrolysis of wheat straw. Appl Environ Microbiol 79:4316-4324
32. Santos A, Mendes S, Brissos V, Martins LO (2013) New dye-decolorizing peroxidases from Bacillus subtilis and Pseudomonas putida MET94: towards biotechnological applications. Appl Microbiol Biotechnol. doi: 10.1007/s00253-013-5041-4
33. Scheibner M, Hulsdau B, Zelena K, Nimtz M, de Boer L, Berger RG, Zorn H (2008) Novel peroxidases of Marasmius scorodonius degrade beta-carotene. Appl Microbiol Biotechnol 77:1241-1250
34. Sezer M, Santos A, Kielb P, Pinto T, Martins LO, Todorovic S (2013) Distinct structural and redox properties of the heme active site in bacterial dye decolorizing peroxidase-type peroxidases from two subfamilies: resonance Raman and electrochemical study. Biochemistry 52:3074-3084
35. Singh R, Grigg JC, Armstrong Z, Murphy ME, Eltis LD (2012) Distal heme pocket residues of B-type dye-decolorizing peroxidase: arginine but not aspartate is essential for peroxidase activity. J Biol Chem 287:10623-10630
36. Stolz A (2001) Basic and applied aspects in the microbial degradation of azo dyes. Appl Microbiol Biotechnol 56:69-80 (Pubitemid 32661539)
37. Strittmatter E, Liers C, Ullrich R, Wachter S, Hofrichter M, Plattner DA, Piontek K (2013) First crystal structure of a fungal high-redox potential dye-decolorizing peroxidase: substrate interaction sites and long-range electron transfer. J Biol Chem 288:4095-4102
38. Strittmatter E, Wachter S, Liers C, Ullrich R, Hofrichter M, Plattner DA, Piontek K (2013) Radical formation on a conserved tyrosine residue is crucial for DyP activity. Arch Biochem Biophys. doi: 10.1016/j.abb.2013.07.007
39. Sturm A, Schierhorn A, Lindenstrauss U, Lilie H, Bruser T (2006) YcdB from Escherichia coli reveals a novel class of Tat-dependently translocated hemoproteins. J Biol Chem 281:13972-13978 (Pubitemid 43848323)
40. Sugano Y (2009) DyP-type peroxidases comprise a novel heme peroxidase family. Cell Mol Life Sci 66:1387-1403
41. Sugano Y, Ishii Y, Shoda M (2004) Role of H164 in a unique dye-decolorizing heme peroxidase DyP. Biochem Biophys Res Commun 322:126-132 (Pubitemid 39093849)
42. Sugano Y, Muramatsu R, Ichiyanagi A, Sato T, Shoda M (2007) DyP, a unique dye-decolorizing peroxidase, represents a novel heme peroxidase family: ASP171 replaces the distal histidine of classical peroxidases. J Biol Chem 282:36652-36658
43. Sutter M et al (2008) Structural basis of enzyme encapsulation into a bacterial nanocompartment. Nat Struct Mol Biol 15:939-947
44. van Bloois E, Torres Pazmino DE, Winter RT, Fraaije MW (2010) A robust and extracellular heme-containing peroxidase from Thermobifida fusca as prototype of a bacterial peroxidase superfamily. Appl Microbiol Biotechnol 86:1419-1430
45. van Rantwijk F, Sheldon RA (2000) Selective oxygen transfer catalysed by heme peroxidases: synthetic and mechanistic aspects. Curr Opin Biotechnol 11:554-564
46. Veitch NC (2004) Horseradish peroxidase: a modern view of a classic enzyme. Phytochemistry 65:249-259 (Pubitemid 38147341)
47. Welinder KG, Mauro JM, Norskov-Lauritsen L (1992) Structure of plant and fungal peroxidases. Biochem Soc Trans 20:337-340
48. Yoshida T, Tsuge H, Konno H, Hisabori T, Sugano Y (2011) The catalytic mechanism of dye-decolorizing peroxidase DyP may require the swinging movement of an aspartic acid residue. FEBS J 278:2387-2394
49. Zamocky M, Jakopitsch C, Furtmuller PG, Dunand C, Obinger C (2008) The peroxidase-cyclooxygenase superfamily: reconstructed evolution of critical enzymes of the innate immune system. Proteins 72:589-605 (Pubitemid 351928514)
50. Zubieta C et al (2007) Identification and structural characterization of heme binding in a novel dye-decolorizing peroxidase, TyrA. Proteins 69:234-243 (Pubitemid 47429287)
51. Zubieta C et al (2007) Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif. Proteins 69:223-233 (Pubitemid 47429286)