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http://dx.doi.org/10.14480/JM.2021.19.4.285

Identification and characterization of laccase genes in the Flammulina velutipes var. lupinicola genome  

Yu, Hye-Won (Department of Medicinal Biosciences, Konkuk University)
Park, Young-Jin (Department of Medicinal Biosciences, Konkuk University)
Publication Information
Journal of Mushroom / v.19, no.4, 2021 , pp. 285-293 More about this Journal
Abstract
The purpose of this study was to identify and characterize the laccase genes of Flammulina velutipes var. lupinicola. Five laccase genes (g1934, g1937, g2415, g2539, g5858) were selected based on the copper binding site and signal peptide analysis results using the laccase gene selected from the F. velutipes var. lupinicola genome. The size of the laccase genes of F. velutipes var. lupinicola were 1,488 bp~1,662 bp. As a result of cDNA sequence analysis, 14 to 17 introns were identified in the laccase genes. The cleavage site predicted as the signal peptide of the laccase gene was found to be located between 20 bp and 34 bp from the N-terminus. In addition, separation and purification were performed to characterize the F. velutipes var. lupinicola laccases, and the optimal activity of the separated and purified proteins were analyzed by pH, temperature and time. Five bands with laccase activity were found from zymogram analysis. The optimal pH of the reaction was 5.5, the optimal temperature was found to be 40℃. Therefore, characterization of the laccase genes identified in this study should help in better understanding the biomass decomposition of F. velutipes var. lupinicola.
Keywords
Bioinformatics; Flammulina velutipes var. lupinicola; Genome; Laccase;
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1 Bertrand T, Jolivalt C, Briozzo P, Caminade E, Joly N, Madzak C, Mougin C. 2002. Crystal structure of a four-copper laccase complexed with an arylamine: insights into substrate recognition and correlation with kinetics. Biochemistry 41: 7325-7333.   DOI
2 Cho NS, Chow HY, Shin SJ, Choi YJ, Leonowicz A, Ohga S. 2008. Production of Fungal Laccase and Its Immobilization and Stability. J Fac Agr 53: 13-18.
3 Edward IS, Uma MS, Timothy EM. 1996. Multicopper Oxidases and Oxygenases. Chem Rev 96: 2563-2606.   DOI
4 Eriksson K, Blanchette RA, Ander P. 1990. Morphological aspects of wood degradation by fungi and bacteria. In Microbial and Ezymatic Degradation of Wood and Wood Components. Germany: Spinge. ISBN 978-3-642-46687-8.
5 Kumar A, Singh D, Sharma KK, Arora S, Singh AK, Gill SS, Singhal B. 2017. Gel-Based Purification and Biochemical Study of Laccase Isozymes from Ganoderma sp. and Its Role in Enhanced Cotton Callogenesis. Front Microbiol 8: 674.   DOI
6 Lipman DJ, Wilbur WJ, Smith TF, Waterman MS. 1984. On the statistical significance of nucleic acid similarities. Nucleic Acids Res 12: 215-226.   DOI
7 Lombard V, Golaconda Ramulu H, Drual E, Coutinho PM, Henrissat B. 2014. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res 42: D490-D495.   DOI
8 Kim HI, Kwon OC, Kong WS, Lee CS, Park YJ. 2014. Genome-Wide Identification and Characterization of Novel Laccase Genes in the White-Rot Fungus Flammulina velutipes. Mycobiology 42: 322-330.   DOI
9 Bento I, Carrondo MA, Lindley PF. 2006. Reduction of dioxygen by enzymes containing copper. J Biol Inorg Chem 11: 539-547.   DOI
10 Buchfink B, Xie C, Huson D. 2015. Fast and sensitive protein alignment using DIAMOND Nat Methods 12: 59-60.   DOI
11 Eduardo B, Liliana M, Juan MS. 2015. Inconsistencies and ambiguities in calculating enzyme activity: The case of laccase. J Microbiol Methods 119: 126-131.   DOI
12 Haberle V, Stark A. 2018. Eukaryotic core promoters and the functional basis of transcription initiation. Nat Rev Mol Cell Biol 19: 621-637.   DOI
13 Palmer JM and Stajich JE. 2020. Funannotate: Eukaryotic Genome Annotation Pipeline. Available online: http://funannotate.readthedocs.io.
14 Lin Y, Zhang Z, Tian Y, Zhao W, Zhu B, Xu Z, Peng R, Yao Q. 2013. Purification and characterization of a novel laccase from Coprinus cinereus and decolorization of different chemically dyes. Mol Biol Rep 40: 1487-1494.   DOI
15 Smale ST, Kadonaga JT. 2003. The RNA polymerase II core promoter. Annu Rev Biochem 72: 449-479.   DOI
16 Kumar SV, Phale PS, Durani S, Wangikar PP. 2003. Combined sequence and structure analysis of the fungal laccase family. Biotechnol Bioeng 83: 386-394.   DOI
17 Christopher FT. 1994. The structure and function of fungal laccase. Microbiology 140: 19-26.   DOI
18 Lee CS, Kong WS, Park YJ. 2018. Genome sequencing and genome-wide identification of carbohydrate-active enzymes (CAZymes) in the white rot fungus Flammulina fennae. Microbiol Biotechnol Lett 46: 300-312.   DOI
19 Rytioja J, Hilden K, Yuzon J, Hatakka A, de Vries RP, Makela MR. 2014. Plant-polysaccharide-degrading enzymes from basidiomycetes. Microbiol Mol Biol Rev 78: 614-649.   DOI
20 Sista Kameshwar AK, Qin W. 2018. Comparative study of genome-wide plant biomass-degrading CAZymes in white rot, brown rot and soft rot fungi. Mycology 9: 93-105.   DOI
21 Strange RW, Reinhammer B, Murphy LM, Hasnain SS. 1995. Structural and spectroscopic studies of the copper site of stellacyanin. Biochemistry 34: 220-231.   DOI
22 Sun J, Chen QJ, Cao QQ, Wu YY, Xu LJ, Zhu MJ, Ng TB, Wang HX, Zhang GQ. 2012. A laccase with antiproliferative and HIV-I reverse transcriptase inhibitory activities from the mycorrhizal fungus agaricus placomyces. J Biopmed Biotech 2012: 736472.
23 Tien M, Kirk TK. 1988. Lignin peroxidase of Phanerochaete chtysosporium. Method Enzymol 46: 220-225.
24 Tomoko M, Hitomi I, TaKanori F, Wataru O, Koji T, Satoshi K. 2013. Ethanol prodution from high cellulose concentration by the basidiomycete fungus Flammulina velutipes. Fungal Biol 117: 220-226.   DOI
25 Upadhyay P, Shrivastava R, Agrawal PK. 2016. Bioprospecting and biotechnological applications of fungal laccase. 3 Biotech 6(1): 15.   DOI
26 Zhang H, Zhang Y, Huang F, Gao P, Chen J. 2009. Purification and characterization of a thermostable laccase with unique oxidative characterisitcs from Trametes hirusta. Biotechnol Letters 31: 837-843.   DOI
27 Petr B. 2006. Fungal laccases-occurrence and properties. FEMS Microbiol Rev 30: 215-242.   DOI
28 Ning YJ, Wang SS, Chen QJ, Ling ZR, Wang SN, Wang WP, Zhang GQ, Zhe MJ. 2016. An extracellular yellow laccase with potent dye decolorizing ability from the fungus Leucoagaricus naucinus LAC-04. Biological Mactromolecules 93: 837-842.   DOI
29 Park YJ,Kong WS. 2018. Genome-wide comparison of carbohydrate-active enzymes (CAZymes) repertoire of Flammulina ononidis. Mycobiology 46: 349-360.   DOI
30 Park YJ, Baek JH, Lee S, Kim C, Rhee H, Kim H, Seo JS, Park HR, Yoon DE, Nam JY, Kim HI, Kim JG, Yoon HJ, Kang HW, Cho JY, Song ES, Sung GH, Yoo YB, Lee CS. 2014. Whole genome and global gene expression analyses of the model mushroom Flammulina velutipes reveal a high capacity for lignocellulose degradation. PLoS ONE 9: e93560.   DOI
31 Redhead SA, Petersen RH. 1999. New species, varieties and combinations in the genus Flammulina. Mycotaxon 71: 285-294.
32 Scott CD, Davison BH, Scott TC, Woodward J, Dees C, Rothrock DS. 1994. An advanced bioprocessing concept for the conversion of waste paper to ethanol. Appl Biochem Biotechnol 45: 641-653.   DOI
33 Simpson JT, Kim W, Shaun DJ, Jacqueline ES, Steven JMJ, Inanc B. 2009. ABySS: a parallel assembler for short read sequence data. Genome Res 19: 1117-1123.   DOI
34 Bolger A.M, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114-2120.   DOI
35 Park YJ, Jeong YU, Kong WS. 2018. Genome sequencing and carbohydrate-active enzyme (CAZyme) repertoire of the white rot fungus Flammulina elastica. Int J Mol Sci 19: 2379.   DOI
36 Sun J, Chen QJ, Zhu MJ, Wang HX, Zhang GQ. 2014. An extracellular laccase with antiproliferative activity from the sanghuang mushroom Inonotus baumii. J Biopmed Biotech 99: 20-25.
37 Zhou YJ, Wang HX, Ng TB, Huang CY, Zhang JX. 2012. Purification and characterization of a novel laccase from the edible mushroom Hericium coralloides. J Microbiol 50: 72-78.   DOI
38 Altschul SF and Erickson BW. 1985. Significance of nucleotide sequence alignments: a method for random sequence permutation that preserves dinucleotide and codon usage. Mol Biol Evol 2: 526-538.
39 Baldrian P. 2006. Fungal laccase: occurrence and properties. FEMS Microbiol Rev 30: 215-242.   DOI