[en] The cloning and sequencing of the rbpa gene coding for a versatile peroxidase from a novel Bjerkandera strain is hereby reported. The 1777 bp isolated fragment contained a 1698 bp peroxidase-encoding gene, interrupted by 11 introns. The 367 amino acid-deduced sequence includes a 27 amino acid-signal peptide. The molecular model, built via homology modelling with crystal structures of four fungal peroxidases, highlighted the amino acid residues putatively involved in manganese binding and aromatic substrate oxidation. The potential heme pocket residues (R44, F47, H48, E79, N85, H177, F194 and D239) include both distal and proximal histidines (H48 and H177). RBP possesses potential calcium-binding residues (D49, G67, D69, S71, S178, D195, T197, I200 and D202) and eight cysteine residues (C3, C15, C16, C35, C121, C250, C286, C316). In addition, RIBP includes residues involved in substrate oxidation: three acidic residues (E37, E41 and D183)-putatively involved in manganese binding and H83 and W172-potentially involved in oxidation of aromatic substrates. Characterisation of nucleotide and amino acid sequences include RBP in versatile peroxidase group sharing catalytic properties of both UP and MnP. In addition, the RBP enzyme appears to be closely related with the ligninolytic peroxidases from the Trametes versicolor strain. (C) 2005 Published by Elsevier B.V.
Disciplines :
Microbiology Biotechnology
Author, co-author :
Moreira, Patricia R.
Duez, Colette ; Université de Liège - ULiège > Centre d'ingénierie des protéines
Dehareng, Dominique ; Université de Liège - ULiège > Centre d'ingénierie des protéines
Antunes, Antonio; Université de Liège - ULiège > Chimie générale et Physique > Spectrométrie de masse
Almeida-Vara, E.; INETI, Lisboa Portugal > Biotecnologia
Frère, Jean-Marie ; Université de Liège - ULiège > Département des sciences de la vie > Département des sciences de la vie
Malcata, F.Xavier; Universidade Catolica Portuguesa, Porto > Escola superior de biotecnologia
Duarte, J. C.; INETI, Lisboa Portugal > Biotecnologia
Language :
English
Title :
Molecular characterisation of a versatile peroxidase from a Bjerkandera strain
Publication date :
10 September 2005
Journal title :
Journal of Biotechnology
ISSN :
0168-1656
eISSN :
1873-4863
Publisher :
Elsevier Science Bv, Amsterdam, Netherlands
Volume :
118
Issue :
4
Pages :
339-352
Peer reviewed :
Peer Reviewed verified by ORBi
Funders :
BELSPO - SPP Politique scientifique - Service Public Fédéral de Programmation Politique scientifique F.R.S.-FNRS - Fonds de la Recherche Scientifique FCT - Fundação para a Ciência e a Tecnologia
S.F. Altschul, T.L. Madden, A.A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25 1997 3389 3402
L. Banci Structural properties of peroxidases J. Biotechnol 53 1997 253 263
Bernstein, H., 2003. Program RasMol Molecular Rendering. Distributed by author.
Biosym Technologies I., 1993a. Program InsightII.
Biosym Technologies I., 1993b. Program Discover.
U. Burkert, and N.L. Allinger Molecular Mechanics 1982 American Chemical Society Washington, DC, USA
S. Camarero, B. Bockle, M.J. Martinez, and A.T. Martinez Manganese-mediated lignin-degradation by Pleurotus pulmonarius Appl. Environ. Microbiol. 62 1996 1070 1072
S. Camarero, S. Sarkar, F.J. Ruiz-Duenas, M.J. Martinez, and A.T. Martinez Description of a versatile peroxidase involved in the natural degradation of lignin that has both manganese peroxidase and lignin peroxidase substrate interaction sites J. Biol. Chem. 274 1999 10324 10330
S. Camarero, F.J. Ruiz-Duenas, S. Sarkar, M.J. Martinez, and A.T. Martinez The cloning of a new peroxidase found in lignocellulose cultures of Pleurotus eryngii and sequence comparison with other fungal peroxidases FEMS Microbiol. Lett. 191 2000 37 43
Felsenstein, J., 1993. Phylogeny Inference Package (PHYLIP). Distributed by author.
B.C. Finzel, T.L. Poulos, and J. Kraut Crystal structure of yeast cytochrome C peroxidase refined at 1.7 Å resolution J. Biol. Chem. 259 1984 3027 3036
E. Gianazza Isoelectric focusing as a tool for the investigation of posttranslational processing and chemical modifications of proteins J. Chromatogr. A 705 1995 67 87
P. Giardina, G. Palmieri, B. Fontanella, V. Rivieccio, and G. Sannia Manganese peroxidase isoenzymes produced by Pleurotus ostreatus grown on wood sawdust Arch. Biochem. Biophys. 376 2000 171 179
M.H. Gold, and M. Alic Molecular biology of the lignin degrading basidiomycete Phanerochaete chrysosporium Microbiol. Rev. 57 1993 605 622
N. Guex, and M.C. Peitsch Swiss-model and the Swiss-PdbViewer: an environment for comparative protein modelling Electrophoresis 18 1997 2714 2723
T.A. Hall BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT Nucleic Acids Symp. Ser. 41 1999 95 98
A. Heinfling, M.J. Martinez, A.T. Martinez, M. Bergbauer, and U. Szewzyk Purification and characterization of peroxidases from the dye-decolorizing fungus Bjerkandera adusta FEMS Microbiol. Lett. 165 1998 43 50
A. Heinfling, M.J. Martinez, A.T. Martinez, M. Bergbauer, and U. Szewzyk Transformation of industrial dyes by manganese peroxidases from Bjerkandera adusta and Pleurotus eryngii in a manganese-independent reaction Appl. Environ. Microbiol. 64 1998 2788 2793
A. Heinfling, F.J. Ruiz-Duenas, M.J. Martinez, M. Bergbauer, U. Szewzyk, and A.T. Martinez A study on reducing substrates of manganese-oxidizing peroxidases from Pleurotus eryngii and Bjerkandera adusta FEBS Lett. 428 1998 141 146
Y. Kimura, Y. Asada, T. Oka, and M. Kuwahara Molecular analysis of a Bjerkandera adusta lignin peroxidase gene Appl. Microbiol. Biotechnol. 35 1991 510 514
A.T. Martinez Molecular biology and structure-function of lignin degrading heme peroxidases Enzyme Microb. Technol. 30 2002 425 444
A. Matagne, B. Joris, and J.M. Frere Anomalous behaviour of a protein during SDS/PAGE corrected by chemical modification of carboxylic groups Biochem. J. 280 1991 553 556
T. Mester, and J.A. Field Characterization of a novel manganese peroxidase-lignin peroxidase hybrid isozyme produced by Bjerkandera species strain BOS55 in the absence of manganese J. Biol. Chem. 273 1998 15412 15417
P.R. Moreira, E. Almeida-Vara, G. Sena-Martins, I. Polonia, F.X. Malcata, and J.C. Duarte Decolourisation of Remazol Brilliant Blue R via a novel Bjerkandera sp. strain J. Biotechnol. 89 2001 107 111
H. Nielsen, S. Brunak, and G. von Heijne Machine learning approaches for the prediction of signal peptides and other protein sorting signals Protein Eng. 12 1999 3 9
C. Palma, A.T. Martinez, J.M. Lema, and M.J. Martinez Different fungal manganese-oxidizing peroxidases: a comparison between Bjerkandera sp. and Phanerochaete chrysosporium J. Biotechnol. 77 2000 235 245
M.C. Peitsch Protein modeling by e-mail Biotechnology 13 1995 658 660
M.C. Peitsch ProMod and Swiss-model: internet-based tools for automated comparative protein modelling Biochem. Soc. Trans. 24 1996 274 279
D.G. Pitcher, N.A. Saunders, and R.J. Owen Rapid extraction of bacterial genomic DNA with guanidium thiocyanate Lett. Appl. Microbiol. 8 1989 151 156
F.J. Ruiz-Duenas, M.J. Martinez, and A.T. Martinez Heterologous expression of Pleurotus eryngii peroxidase confirms its ability to oxidize Mn2+ and different aromatic substrates Appl. Environ. Microbiol. 65 1999 4705 4707
F.J. Ruiz-Duenas, M.J. Martinez, and A.T. Martinez Molecular characterization of a novel peroxidase isolated from the ligninolytic fungus Pleurotus eryngii Mol. Microbiol. 31 1999 223 235
F.J. Ruiz-Duenas, S. Camarero, M. Perez-Boada, M.J. Martinez, and A.T. Martinez A new versatile peroxidase from Pleurotus Biochem. Soc. Trans. 29 2001 116 122
A. Shevchenko, I. Chernushevich, M. Wilm, and M. Mann De novo peptide sequencing by nanoelectrospray tandem mass spectrometry using triple quadrupole and quadrupole/time-of-flight instruments J.R. Chapman Protein and Peptide Analysis 2000 Humana Press Totowa, NJ 1 16
S.E. Unkles Gene organization in industrial filamentous fungi J.R. Kinghorn G. Turner Applied Molecular Genetics of Filamentous Fungi 1992 London University Press Cambridge 28 53
S. Weiner, and P.A. Kollman AMBER: assisted model building with energy refinement. A general program for modeling molecules and their interactions J. Comp. Chem. 2 1981 287 303
S. Weiner, P.A. Kollman, D.T. Nguyen, and D.A. Case An all atom force field for simulations of proteins and nucleic acids J. Comp. Chem. 7 1986 230 252
H. Zorn, S. Langhoff, M. Scheibner, M. Nimtz, and R.G. Berger A peroxidase from Lepista irina cleaves beta-carotene to flavor compounds Biol. Chem. 384 2003 1049 1056