Cited by 158

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

New dye-decolorizing peroxidases from Bacillus subtilis and Pseudomonas putida MET94: towards biotechnological applications

Santos, Ana, Mendes, Sónia, Brissos, Vânia, Martins, Lígia O.·2014·Applied Microbiology and Biotechnology

Abstract

This work provides spectroscopic, catalytic, and stability fingerprints of two new bacterial dye-decolorizing peroxidases (DyPs) from Bacillus subtilis (BsDyP) and Pseudomonas putida MET94 (PpDyP). DyPs are a family of microbial heme-containing peroxidases with wide substrate specificity, including high redox potential aromatic compounds such as synthetic dyes or phenolic and nonphenolic lignin units. The genes encoding BsDyP and PpDyP, belonging to subfamilies A and B, respectively, were cloned and heterologously expressed in Escherichia coli. The recombinant PpDyP is a 120-kDa homotetramer while BsDyP enzyme consists of a single 48-kDa monomer. The optimal pH of both enzymes is in the acidic range (pH 4-5). BsDyP has a bell-shape profile with optimum between 20 and 30 °C whereas PpDyP shows a peculiar flat and broad (10-30 °C) temperature profile. Anthraquinonic or azo dyes, phenolics, methoxylated aromatics, and also manganese and ferrous ions are substrates used by the enzymes. In general, PpDyP exhibits higher activities and accepts a wider scope of substrates than BsDyP; the spectroscopic data suggest distinct heme microenvironments in the two enzymes that might account for the distinctive catalytic behavior. However, the Bs enzyme with activity lasting for up to 53 h at 40 °C is more stable towards temperature or chemical denaturation than the PpDyP. The results of this work will guide future optimization of the biocatalytis towards their utilization in the fields of e…

Overview

Integrity signals

Registry

Crossref · 10.1007/s00253-013-5041-4

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Verification

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 49

  1. 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 · DOI
  2. Ayala M (2010) Redox potential of peroxidases. Springer, Heidelberg
  3. Banci L, Bertini I, Turano P, Tien M, Kirk TK (1991) Proton NMR investigation into the basis for the relatively high redox potential of lignin peroxidase. Proc Natl Acad Sci U S A 88:6956–6960 · DOI
  4. Berry EA, Trumpower BL (1987) Simultaneous determination of hemes a, b, and c from pyridine hemochrome spectra. Anal Biochem 161:1–15 · DOI
  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 · DOI
  6. Cao J, Woodhall MR, Alvarez J, Cartron ML, Andrews SC (2007) EfeUOB (YcdNOB) is a tripartite, acid-induced and CpxAR-regulated, low-pH Fe2+ transporter that is cryptic in Escherichia coli K-12 but functional in E. coli O157:H7. Mol Microbiol 65:857–875 · DOI · Paper page
  7. Chung N, Aust SD (1995) Veratryl alcohol-mediated indirect oxidation of phenol by lignin peroxidase. Arch Biochem Biophys 316:733–737 · DOI
  8. Durão P, Bento I, Fernandes AT, Melo EP, Lindley PF, Martins LO (2006) Perturbations of the T1 copper site in the CotA laccase from Bacillus subtilis: structural, biochemical, enzymatic and stability studies. J Biol Inorg Chem 11:514–526 · DOI
  9. Fernandes AT, Martins LO, Melo EP (2009) The hyperthermophilic nature of the metallo-oxidase from Aquifex aeolicus. Biochim Biophys Acta 1794:75–83 · DOI
  10. Hewson WD, Hager LP (1979) Oxidation of horseradish peroxidase compound II to compound I. J Biol Chem 254:3182–3186 · DOI
  11. Hiner AN, Hernandez-Ruiz J, Rodriguez-Lopez JN, Garcia-Canovas F, Brisset NC, Smith AT, Arnao MB, Acosta M (2002) Reactions of the class II peroxidases, lignin peroxidase and Arthromyces ramosus peroxidase, with hydrogen peroxide. Catalase-like activity, compound III formation, and enzyme inactivation. J Biol Chem 277:26879–26885 · DOI
  12. Hofrichter M, Ullrich R, Pecyna MJ, Liers C, Lundell T (2010) New and classic families of secreted fungal heme peroxidases. Appl Microbiol Biotechnol 87:871–897 · DOI · Paper page
  13. 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 · DOI
  14. Kandelbauer A, Gübitz GM (2005) Bioremediation for the decolorization of textile dyes—a review. In: Lichtfouse E, Schwarzbauer J, Robert D (eds) Environmental chemistry. Springer, Berlin, pp 269–288 · DOI
  15. Kelley LA, Sternberg MJ (2009) Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc 4:363–371 · DOI
  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 · DOI · Paper page
  17. Krishnappa L, Monteferrante CG, van Dijl JM (2012) Degradation of the twin-arginine translocation substrate YwbN by extracytoplasmic proteases of Bacillus subtilis. Appl Environ Microbiol 78:7801–7804 · DOI
  18. Kuan I-C, Johnson K, Tien M (1993) Kinetic analysis of manganese peroxidase. J Biol Chem 268:20064–20070 · DOI
  19. 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 · DOI
  20. 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 · DOI
  21. Liu X, Du Q, Wang Z, Zhu D, Huang Y, Li N, Wei T, Xu S, Gu L (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 · DOI
  22. Martinez AT, Ruiz-Duenas FJ, Martinez MJ, Del Rio JC, Gutierrez A (2009) Enzymatic delignification of plant cell wall: from nature to mill. Curr Opin Biotechnol 20:348–357 · DOI
  23. Martins LO, Soares CM, Pereira MM, Teixeira M, Costa T, Jones GH, Henriques AO (2002) Molecular and biochemical characterization of a highly stable bacterial laccase that occurs as a structural component of the Bacillus subtilis endospore coat. J Biol Chem 277:18849–18859 · DOI
  24. Mendes S, Farinha A, Ramos CG, Leitao JH, Viegas CA, Martins LO (2011a) Synergistic action of azoreductase and laccase leads to maximal decolourization and detoxification of model dye-containing wastewaters. Bioresour Technol 102:9852–9859 · DOI
  25. Mendes S, Pereira L, Batista C, Martins LO (2011b) Molecular determinants of azo reduction activity in the strain Pseudomonas putida MET94. Appl Microbiol Biotechnol 92:393–405 · DOI
  26. 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 · DOI · Paper page
  27. Pereira L, Coelho A, Viegas AC, Ganachaud C, Lacazio G, Tron T, Robalo M, Martins LO (2009a) On the mechanism of biotransformation of the anthraquinonic dye Acid Blue 62 by laccases. Adv Synth Catal 351:1857–1865 · DOI
  28. Pereira L, Coelho AV, Viegas CA, Santos MM, Robalo MP, Martins LO (2009b) Enzymatic biotransformation of the azo dye sudan orange G with bacterial CotA-laccase. J Biotechnol 139:68–77 · DOI
  29. Poulos TL, Kraut J (1980) The stereochemistry of peroxidase catalysis. J Biol Chem 255:8199–8205 · DOI
  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 · DOI
  31. Rodriguez-Couto S (2009) Enzymatic biotransformation of synthetic dyes. Curr Drug Metab 10:1048–1054 · DOI
  32. Scheibner M, Hulsdau B, Zelena K, Nimtz M, de Boer L, Berger RG, Zorn H (2008) Novel peroxidases of Marasmius scorodonius degrade β-carotene. Appl Microbiol Biotechnol 77:1241–1250 · DOI
  33. Sezer S, Genebra T, Mendes S, Martins LO, Todorovic S (2012) A DyP-type peroxidase at a bio-compatible interface: structural and mechanistic insights. Soft Matter 8:10314–10321 · DOI · Paper page
  34. Sezer S, Santos A, Kielb P, Pinto T, Martins LO, Todorovic S (2013) Distinct structural and redox properties of heme active in bacterial DyP-type peroxidases from two subfamilies: resonance Raman and electrochemistry study. Biochemistry 52:3074–3084 · DOI
  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 · DOI
  36. Strittmatter E, Liers C, Ullrich R, Wachter S, Hofrichter M, Plattner DA, Piontek K (2012) 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 · DOI
  37. 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 · DOI
  38. Sugano Y (2009) DyP-type peroxidases comprise a novel heme peroxidase family. Cell Mol Life Sci 66:1387–1403 · DOI
  39. Sugano Y, Matsushima Y, Shoda M (2006) Complete decolorization of the anthraquinone dye reactive blue 5 by the concerted action of two peroxidases from Thanatephorus cucumeris Dec 1. Appl Microbiol Biotechnol 73:862–871 · DOI
  40. 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 · DOI
  41. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739 · DOI
  42. Valderrama B, Ayala M, Vazquez-Duhalt R (2002) Suicide inactivation of peroxidases and the challenge of engineering more robust enzymes. Chem Biol 9:555–565 · DOI
  43. 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 · DOI · Paper page
  44. van der Ploeg R, Barnett JP, Vasisht N, Goosens VJ, Pother DC, Robinson C, van Dijl JM (2011) Salt sensitivity of minimal twin arginine translocases. J Biol Chem 286:43759–43770 · DOI
  45. van der Ploeg R, Monteferrante CG, Piersma S, Barnett JP, Kouwen TR, Robinson C, van Dijl JM (2012) High-salinity growth conditions promote Tat-independent secretion of Tat substrates in Bacillus subtilis. Appl Environ Microbiol 78:7733–7744 · DOI
  46. Wong DW (2009) Structure and action mechanism of ligninolytic enzymes. Appl Biochem Biotechnol 157:174–209 · DOI
  47. 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 · DOI
  48. Zubieta C, Joseph R, Krishna SS, McMullan D, Kapoor M, Axelrod HL, Miller MD, Abdubek P, Acosta C, Astakhova T, Carlton D, Chiu HJ, Clayton T, Deller MC, Duan L, Elias Y, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Kumar A, Marciano D, Morse AT, Murphy KD, Nigoghossian E, Okach L, Oommachen S, Reyes R, Rife CL, Schimmel P, Trout CV, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA (2007a) Identification and structural characterization of heme binding in a novel dye-decolorizing peroxidase, TyrA. Proteins 69:234–243 · DOI
  49. Zubieta C, Krishna SS, Kapoor M, Kozbial P, McMullan D, Axelrod HL, Miller MD, Abdubek P, Ambing E, Astakhova T, Carlton D, Chiu HJ, Clayton T, Deller MC, Duan L, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Hampton E, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kumar A, Marciano D, Morse AT, Nigoghossian E, Okach L, Oommachen S, Reyes R, Rife CL, Schimmel P, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA (2007b) Crystal structures of two novel dye-decolorizing peroxidases reveal a β-barrel fold with a conserved heme-binding motif. Proteins 69:223–233 · DOI

Cited by

Sorted by citations

Metadata

Authors
Santos, A., Mendes, S., Brissos, V., & Martins, L. O.
Venue
Applied Microbiology and Biotechnology
Published
2013-07-03
Volume
98
Issue
5
Pages
2053-2065
ISSN
  • 0175-7598
  • 1432-0614
Cited by
158
References
1
Language
en

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review