In silico characterization of laccase gene isoforms of edible and medicinal basidiomycetes
DOI:
https://doi.org/10.33448/rsd-v9i12.10388Keywords:
Agaricus; Isogenes; Lentinus; Pleurotus; White-rot fungi.Abstract
Laccases are part of the family of ligninolytic enzymes and have played essential roles in several biological filamentous fungi processes, including fruiting body formation and lignin degradation. This study aimed to identify and characterize laccase genes in silico of several basidiomycete strains. The applied guaiacol oxidation test allowed the selection of seven out of 11 strains with ligninase activity, which were used for DNA extraction and amplification of the copper-binding region. A single amplicon of approximately 450 bp, was produced by all selected strains and they were further sequenced. Sequence analysis has suggested the presence of a new subdivision of the laccase genes. Clustering analysis confirmed the existence of two groups: cluster A with six strains and singleton B with U8-11 strain. The structural predictions of the U8-11 protein were dissimilar compared to other proteins described in our study due to the absence of the ALAVIN motif and, therefore, the U8-11 amino acid sequence was separated in a different cluster.
References
Baldrian, P. (2006). Fungal laccases - occurrence and properties. FEMS Microbiology Reviews 30 (2), 215-242. https://doi.org/10.1111/j.1574-4976.2005.00010.x
Bleve, G., Lezzi, C., Mita, G., Rampino, P., Perrotta, C., Villanova, L., & Grieco, F. (2008). Molecular cloning and heterologous expression of a laccase gene from Pleurotus eryngii in free and immobilized Saccharomyces cerevisiae cells. Applied Microbiology and Biotechnology, 79, 731. https://doi.org/10.1007/s00253-008-1479-1
Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I.N., & Bourne, P.E. (2000). The protein data bank. Nucleic Acids Research, 28(1), 235-242. https://doi.org/10.1093/nar/28.1.235
Cannatelli, M. D., & Ragauskas, A. J. (2017). Two decades of laccases: advancing sustainability in the chemical industry. The Chemical Record, 17(1), 122-140. https://doi.org/10.1002/tcr.201600033
Cázares-García, S. V., Vázquez-Garciduenas, M. S., & Vázquez-Marrufo, G. (2013). Structural and phylogenetic analysis of laccases from Trichoderma: a bioinformatic approach. PLOS One, 8(1), e55295. https://doi.org/10.1371/journal.pone.0055295
Chojnacki, S., Cowley, A., Lee, J., Foix, A., & Lopez, R. (2017). Programmatic access to bioinformatics tools from EMBL-EBI update: 2017. Nucleic Acids Research, 45 (W1), W550-W553. https://doi.org/10.1093/nar/gkx273
Garnier, J., Gibrat, J. F., & Robson, B. (1996). GOR method for predicting protein secondary structure from amino acid sequence. Methods in Enzymology, 266, 540-553. https://doi.org/10.1016/S0076-6879(96)66034-0
Grandes-Blanco, A. I., Tlecuitl-Beristain, S., Díaz, R., Sánchez, C., Téllez-Téllez, M., Márquez-Domínguez, L., Santos-López, G., & Diaz-Godinez, G. (2017). Heterologous expression of laccase (LACP83) of Pleurotus ostreatus. BioResources, 12(2), 3211-3221. https://doi.org/10.15376/biores.12.2.3211-3221
Gupta, V., Balda, S., Gupta, N. K., Capalashe, N., & Sharma, P. (2019). Functional substitution of domain 3 (T1 copper center) of a novel laccase with Cu ions. International Journal of Biological Macromolecules, 123, 1052-1061. https://doi.org/10.1016/j.ijbiomac.2018.11.174
Hall, T. (2011). BioEdit: an important software for molecular biology. GERF Bulletin of Bioscience, 2 (1), 60-61.
Jiao, X., Li, G., Wang, Y., Nie, F., Cheng, X., Abdullah, M., Lin, Y., & Cai, Y. (2018). Systematic analysis of the Pleurotus ostreatus laccase gene (PoLac) family and functional characterization of PoLac2 involved in the degradation of cotton-straw lignin. Molecules, 23 (4), 880. https://doi.org/10.3390/molecules23040880
Kataoka, K., Hirota, S., Maeda, Y., Kogi, H., Shinohara, N., Sekimoto, M., & Sakurai, T. (2010). Enhancement of laccase activity through the construction and breakdown of a hydrogen bond at the type I copper center in Escherichia coli CueO and the deletion mutant Δα5− 7 CueO. Biochemistry, 50 (4), 558-565. https://doi.org/10.1021/bi101107c
Katoh, K., Rozewicki, J., & Yamada, K. D. (2019). MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Briefings in Bioinformatics, 20 (4), 1160-1166. https://doi.org/10.1093/bib/bbx108.
Kiiskinen, L‐L., Rättö, M., & Kruus, K. (2004). Screening for novel laccase‐producing microbes. Journal of Applied Microbiology, 97 (3), 640-646. https://doi.org/10.1111/j.1365-2672.2004.02348.x
Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16, 111-120. https://doi.org/10.1007/BF01731581
Kües, U., & Rühl, M. (2011). Multiple multi-copper oxidase gene families in basidiomycetes-what for? Current Genomics, 12 (2), 72-94. https://doi.org/10.2174/138920211795564377
Lira, R. K. de S., & Orlanda, J. F. F. (2020). Biodegradação do inseticida carbofuran por Syncephalastrum racemosum. Research, Society and Development, 9(7), e824974932. https://doi.org/10.33448/rsd-v9i7.4932
Mantovani, T. R. A., Tanaka, H. S., Umeo, S. H., Zaghi, Jr. L. L., Valle, J. S., Paccola-Meirelles, L. D., Linde, G. A., & Colauto, N. B. (2012). Cryopreservation at −20 and −70 ◦C of Pleurotus ostreatus on grains. Indian Journal of Microbiology, 52 (3), 484-488. https://dx.doi.org/10.1007%2Fs12088-012-0289-4
Marchler-Bauer, A., Bo, Y., Han, L., He, J., Lanczycki, C. J., Lu, S., Chitsaz, F., Derbyshire, M. K., Geer, R. C., Gonzales, N. R., Gwadz, M., Hurwitz, D. I., Lu, F., Marchler, G. H., Song, J. S., Thanki, N., Wang, Z., Yamashita, R. A., Zhang, D., Zheng, C,. Geer, L. Y., & Bryant, S. H. (2017). CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Research, 45(D1), D200-D203.
https://doi.org/10.1093/nar/gkw1129
Mate, D. M., & Alcalde, M. (2017). Laccase: a multi‐purpose biocatalyst at the forefront of biotechnology. Microbial Biotechnology, 10 (6), 1457-1467. https://doi.org/10.1111/1751-7915.12422
Piscitelli, A., Giardina, P., Lettera, V., Pezzella, C., Sannia, G., & Faraco, V. (2011a). Induction and transcriptional regulation of laccases in fungi. Current Genomics, 12(2), 104-112. https://doi.org/10.2174/138920211795564331
Piscitelli, A., Vecchio, C. D., Faraco, V., Giardina, P., Macellaro, G., Miele, A., Pezzella, C., & Sannia, G. (2011b). Fungal laccases: versatile tools for lignocellulose transformation. Comptes Rendus Biologies, 334 (11), 789-794. https://doi.org/10.1016/j.crvi.2011.06.007
Rivera-Hoyos, C. M., Morales-Álvarez, E. D., Poutou-Piñales, R. A., Pedroza-Rodríguez, A. M., Rodríguez-Vázquez, R., & Delgado-Boada, J. M. (2013). Fungal laccases. Fungal Biology Reviews, 27 (3), 67-82. https://doi.org/10.1016/j.fbr.2013.07.001
Rodgers, C. J., Blandford, C. F., Giddens, S. R., Skamnioti, P., Armstrong, F. A., & Gurr, S. J. (2010). Designer laccases: a vogue for high-potential fungal enzymes? Trends in Biotechnology, 28 (2), 63-72. https://doi.org/10.1016/j.tibtech.2009.11.001
Shraddha, R. S., Sehgal, S., Kamthania, M., & Kumar, A. (2011). Laccase: microbial sources, production, purification, and potential biotechnological applications.
Enzyme Research, Article ID 217861, 11 p. https://doi.org/10.4061/2011/217861
Sharma, D, Singh, V. P., & Singh, N. K. (2018). A review on phytochemistry and pharmacology of medicinal as well as poisonous mushrooms. Mini-Reviews in Medicinal Chemistry, 18(13), 1095-1109. https://doi.org/10.2174/1389557517666170927144119
Sirim, D., Wagner, F., Wang, L., Schmid, R. D., & Pleiss, J. (2011). The laccase engineering; Database: a classification and analysis system for laccases and related multicopper oxidases. Database, 2011, bar006. https://doi.org/10.1093/database/bar006
Soden, D. M., & Dobson, A. D. W. (2001). Differential regulation of laccase gene expression in Pleurotus sajor-caju. Microbiology, 147 (7), 1755-1763. https://doi.org/10.1099/00221287-147-7-1755
Tamura, K., Stecher, G., Peterson, D., Filipski, A., & Kumar, S. (2013). MEGA 6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30 (12), 2725-2729. https://doi.org/10.1093/molbev/mst197
Téllez-Téllez, M., Diaz-Godinez, G., Aguilar, M. B., Sánchez, C., & Fernández, F. J. (2012). Description of a laccase gene from Pleurotus ostreatus expressed under submerged fermentation conditions. Bioresources, 7 (2), 2038-2050.
Valasatava, Y., Rosato, A., Furnham, N., Thornton, J. M., & Andreini, C. (2018). To what extent do structural changes in catalytic metal sites affect enzyme function? Journal of Inorganic Biochemistry, 179, 40-53. https://doi.org/10.1016/j.jinorgbio.2017.11.002
Volpini, ,A. F. N., Thomazine, T., Umeo, S. H., Pereira, G. A., Linde, G. A., Valle, J. S., Colauto, N. B., Barcellos, F. G., & Souza, S. G. H. (2016). Identification and characterization of genes related to cellulolytic activity in basidiomycetes. Genetics and Molecular Research, 15 (3), gmr.15038722. https://doi.org/10.4238/gmr.15038722
Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F. T., de Beer, T. A. P., Rempfer, C., Bordoli, L., Lepore, R., & Schwede, T. (2018). SWISS-MODEL: homology modeling of protein structures and complexes. Nucleic Acids Research, 46 (W1), W296-W303. https://doi.org/10.1093/nar/gky427
Zaghi, Jr. L. L., Lopes, A. D., Cordeiro, F. A., Colla, I. M., Bertéli, M. B. D., Valle, J. S., Linde, G. A., & Colauto, N. B. (2018). Cryopreservation at −75 ◦C of Agaricus subrufescens on wheat grains with sucrose. Brazilian Journal of Microbiology, 49 (2), 370-377. https://doi.org/10.1016/j.bjm.2017.08.003
Yan, L., Xu, R., Bian, Y., Li, H., & Zhou, Y. (2019). Expression profile of Laccase ene family in white-rot basidiomycete Lentinula edodes under different environmental stresses. Genes, 10, 1045. https://dx.doi.org/10.3390%2Fgenes10121045
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Copyright (c) 2020 Aline Franciele Navarro Volpini-Klein; Gilberto de Aguiar Pereira; Thiago Teodoro Santana; Giani Andrea Linde; Juliana Silveira do Valle; Nelson Barros Colauto; Fernando Gomes Barcellos; Silvia Graciele Hülse de Souza
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