猴头菌MnP1基因全长cDNA克隆及生物信息学分析

doi:10.11707/j.1001-7488.20150508

Abstract

Abstract:

【Objective】 The cDNA gene sequences of Manganese peroxidase (MnP) were isolated from H. erinaceum CB1, and used for analyzing structure and function of the He-mnp 1.【Method】Degenerate primers were designed according to conservative domain of white-rot fungi MnPs gene cDNA sequences reported in GenBank, the full-length cDNA gene sequence was obtained by using the methods of PCR, Reverse transcription-PCR and Rapid Amplification of cDNA Ends (RACE) and named as He-mnp 1 (GenBank No. HM116841.3), and the bioinformatics of He-mnp 1 gene were analyzed. BLAST homology search was conducted through the NCBI database; ORF Finder was used to look up the complete open reading frame of the gene; The Expasy database and BioEdit software were used to predict physicochemical properties and amino acid composition of He-mnp 1 protein, and analyze the hydrophilicity/hydrophobicity and transmembrane region; The SignalP 4.1 software was used to predict protein signal peptide; The clustal W with MEGA 5.1 software was adopted to complete the He-mnp1 protein sequence homology alignment and to construct the phylogenetic trees of white rot fungi MnPs, respectively. The CDD database was used to predict protein conserved domains, and check the He-mnp1 heme, substrate and manganese, calcium binding site etc. The PredictProtein software and SWISS-MODEL software were used to complete the He-mnp1 protein secondary structure prediction and to construct homologous 3D modeling, respectively.【Result】The full-length cDNA of He-mnp 1 was 1 279 bp, the ORF of 1 080 bp with starting codon of ATG and stopping codon of TAA, including 5'UTR of 68 bps and 3'UTR of 131 bps and encoded 359 amino acids. Bioinformatics analysis showed that the He-mnp1 protein has the highest content of Ala, without Tyr, and the Mw 38.18 is kDa, with the pI of 4.35. The He-nmp1 protein has an obvious hydrophilic region and two hydrophobic regions in the area of 81-105 and 121-141, and belongs to hydrophilic protein. He-mnp1 protein precursor polypeptides consists of a 18 aa signal peptide and a 5 aa the intermediate leader peptide.【Conclusion】Protein phylogenetic analysis revealed that He-mnp1 is distributed in Group II, and has closely evolutionary relationship to MnPs of Pleurotus ostreatus, Polyporus brumalis, and Trametes versicolor. He-mnp 1 has a conserved domain, and belongs to Class II fungal heme-dependent peroxidase superfamily, predicting that the protein secondary structure accounts for α-helix of 30.99%, β-sheet of 3.38% and random coil of 65.63%, and it is a stable protein. He-mnp1 protein 3D modeling showed that there are 1 Fe heme, 2 Ca²⁺, 1 Mn²⁺ binding sites and the histidine residues.

Key words: Hericium erinaceum, manganese peroxidase, genomic clone, bioinformatics analysis, sequence analysis

CLC Number:

S718.81

Yin Liwei, Chi Yujie. Cloning and Bioinformatics Analysis of MnP 1 cDNA Gene from Hericium erinaceum[J]. Scientia Silvae Sinicae, 2015, 51(5): 68-77.

References

池玉杰, 伊洪伟. 2007. 木材白腐菌分解木质素的酶系统-锰过氧化物酶、漆酶和木质素过氧化物酶催化分解木质素的机制. 菌物学报, 26 (1): 153-160.(Chi Y J, Yi H W.2007. Lignin degradation mechanisms of ligninolytic enzyme system,manganese peroxidase, laccase and lignin peroxidase, produced by wood white rot fungi. Mycosystema, 26(1): 153-160.[in Chinese])
戴玉成, 徐梅卿, 杨忠, 等. 2008. 中国储木及建筑木材腐朽菌(Ⅰ).林业科学研究, 21 (1): 49-54.(Dai Y C, Xu M Q, Yang Z, et al. 2008. Wood-decaying fungi on timber or wooden constructions in China(I). Forest Research, 21 (1): 49-54.[in Chinese])
严东辉, 姚一建. 2003. 菌物在森林生态系统中的功能和作用研究进展.植物生态学报, 27 (2): 143-150.(Yan D H, Yao Y J. 2003.Recent advance of research on fungi in forest ecosystem. Acta Phytoecologica Sinica, 27 (2): 143-150.[in Chinese])
曾祥谓, 崔宝凯, 徐梅卿, 等. 2008. 中国储木及建筑木材腐朽菌(Ⅱ). 林业科学研究, 21 (6): 783-791.(Zeng X W, Cui B K, Xu M Q, et al. 2008. Wood-decaying fungi on timber or wooden constructions in China(Ⅱ). Forest Research, 21(6): 783-791.[in Chinese])
朱刚, 吴林, 陈明杰, 等. 2013. 草菇锰过氧化物酶编码基因生物信息学分析及其转录水平和酶活性的测定.菌物学报, 32 (5): 919-927.[in Chinese])(Zhu G, Wu L, Chen M J, et al. 2013. Bioinformatic, gene expression and enzyme activity analyses of manganese peroxidases in Volvariella volvacea. Mycosystema, 32 (5): 919-927.[in Chinese])
Blodig W, Smith A T, Doyle W A, et al. 2001.Crystal structures of pristine and oxidatively processed lignin peroxidase expressed in Escherichia coli and of the W171F variant that eliminates the redox active tryptophan 171. Implications for the reaction mechanism. J Mol Biol, 305 (4): 851-861.
Canales M, Lobos S, Vicuйa R. 1998. Molecular modeling of manganese peroxidase from the lignin-degrading fungus Ceriporiopsis subvermispora and structural comparison with other peroxidases. Elec J Biotech, 1 (2): 96-102.
Hakala T, Hilden K, Maijala P, et al. 2006. Differential regulation of manganese peroxidases and characterization of two variable MnP encoding genes in the white rot fungus Physisporinus rivulosus. Appl Microbiol Biotechnol, 73 (4): 839-849.
Hildén K, Martinez A T,Hatakka A, et al. 2005. The two manganese peroxidases Pr-MnP2 and Pr-MnP3 of Phlebia radiata, a lignin-degrading basidiomycete, are phylogenetically and structurally divergent. Fungal Genetics and Biology, 42 (5): 403-419.
Hirofumi H, Kenta M, Tomohiro S, et al. 2013. Improvement of manganese peroxidase production by the hyper lignin-degrading fungus Phanerochaete sordida YK-624 by recombinant expression of the 5-aminolevulinic acid synthase gene.Current Microbiology, 67: 708-711.
Janusza G, Katarzyna K H, Pawlik A, et al. 2012. Fungal laccase, manganese peroxidase and lignin peroxidase: Gene expression and regulation. Enzyme and Microbial Technology, 52 (1): 1-12.
Johansson T, Nymann P, Cullen D. 2002. Differential regulation of mnp2, a new manganese peroxidase encoding gene from the ligninolytic fungus Trametes versicolor PRL572. Appl Environ Microbiol, 68 (4): 2077-2080.
Kazumichi F, Mari U, Chie H, et al. 2013. Environmental control of lignin peroxidase, manganese peroxidase, and laccase activities in forest floor layers in humid Asia.Soil Biology and Biochemistry, 57: 109-115.
Kum H, Lee S, Ryu S, et al. 2011. Degradation of endocrine disrupting chemicals by genetic transformants with two lignin degrading enzymes in Phlebia tremellosa. J Microbiol, 49 (5): 824-827.
Mancilla R A,Canessa P, Manubens A, et al. 2010. Effect of manganese on the secretion of manganese-peroxidase by the basidiomycete Ceriporiopsis subvermispora. Fungal Genetics and Biology, 47 (7): 656-661.
Manubens A, Avila M, Canessa P, et al. 2003. Differential regulation of genes encoding manganese peroxidase (MnP) in the basidiomycete Ceriporiopsis subvermispora. Curr Genet, 43 (6): 433-438.
Morgenstern I, Klopman S, Hibbett D S. 2008. Molecular evolution and diversity of lignin degrading heme peroxidases in the agaricomycetes. J Mol Evol, 66 (3): 243-257.
Morgenstern I, Robertson D L, Hibbett D S. 2010. Characterization of three mnp genes of Fomitiporia mediterrane and report of additional class Ⅱ Peroxidases in the order hymenochaetales. Applied and Environmental Microbiology, 76 (19): 6431-6440.
Muhammad A,Bazgha A,Hafiz M N I. 2013. Novel catalytic and effluent decolorization functionalities of sol-gel immobilized Pleurotus ostreatus IBL-02 manganese peroxidase produced from bio-processing of wheat straw. Chinese Journal of Catalysis, 34 (9): 1756-1761.
Nagai M, Sakamoto Y, Nakade K, et al. 2007. Isolation and characterization of the gene encoding a manganese peroxidase from Lentinula edodes. Mycoscience, 48 (2): 125-130.
Orth A, Rzhetskaya M, Cullen D, et al. 1994. Characterization of a cDNA encoding a manganese peroxidase from Phanerochaete chrysosporium: genomic organization of lignin and manganese peroxidase genes. Gene, 148 (1): 161-165.
Phil K, Dan C. 2007. Extracellular oxidative systems of the lignin-degrading basidiomycete Phanerochaete chrysosporium. Fungal Genetics and Biology, 44 (2): 77-87.
Pribnow D, Mayfield M B, Nipper V J, et al. 1989. Characterization of a cDNA encoding a manganese peroxidase, from the lignin-degrading basidiomycete Phanerochaete chrysosporium. J Biol Chem, 264 (9): 5036-5040.
Ruiz-Dueйas F J, Morales M, Garcia E, et al. 2009. Substrate oxidation sites in versatile peroxidase and other basidiomycete peroxidases. J Exp Bot, 60 (2): 441-452.
Ryu S H, Kim B, Kim M, et al. 2014. Molecular characterization of manganese peroxidases from white-rot fungus Polyporus brumalis. Bioprocess Biosyst Eng, 37 (3): 393-400.
Sangcheol J, Kyunghoon K, Hyoung C T, et al. 2004. Characterization of Mn-peroxidase isoenzymes from the white-rot fungus Trametes versicolor in Korea. Journal of Huazhong Agricultural University, 23 (1): 146-149.
Sundaramoorthy M, Kishi K, Gold M H, et al. 1994.The crystal structure of manganese peroxidase from Phanerochaete chrysosporium at 2.06-A resolution. J Biol Chem, 269 (52): 32759-32767.
Sundaramoorthy M, Youngs H L, Gold M H, et al. 2005. High-resolution crystal structure of manganese peroxidase: substrate and inhibitor complexes. Biochemistry, 44 (17): 6463-64670.
Yeo S, Park N, Song H G, et al. 2007. Generation of a transformant showing higher manganese peroxidase (MnP) activity by overexpression of MnP gene in Trametes versicolor.J Microbiol, 45 (3): 213-218.

[1]	Li Hui, Gu Tianzi, Chen Changyu, Huang Kairu, Tian Shuo, Zhao Xudong, Hao Dejun. cDNA Cloning, Sequence Analysis and Expression Profile of a Chemosensory Protein from the Clostera restitura (Lepidoptera: Notodontidae) [J]. Scientia Silvae Sinicae, 2018, 54(4): 67-75.
[2]	Zhang Yulong, Chi Yujie, Feng Lianrong. Enzymology Characteristics and Dye Decolorization of Manganese Peroxidase from Lenzites gibbosa [J]. Scientia Silvae Sinicae, 2017, 53(9): 73-80.
[3]	Zhang Yulong, Chi Yujie, Feng Lianrong. Grading Purification of Manganese Peroxidases from Lenzites gibbosa [J]. Scientia Silvae Sinicae, 2017, 53(8): 64-70.
[4]	Yu Shaoshuai, Li Yong, Ren Zhengguang, Song Chuansheng, Lin Caili, Piao Chungen, Tian Guozhong. Multilocus Sequence Analysis for Revealing Finer Genetic Variation and Phylogenetic Interrelatedness of Phytoplasma Strains in 16SrI Group in China [J]. Scientia Silvae Sinicae, 2017, 53(3): 105-118.
[5]	Wang Fengjuan, Li Weiqing, Mu Zhimei, Wang Yanwen, Liu Qingxin, Gao Huiju. Enzymological Characteristics of Ligninolytic Enzyme from Paraconiothyrium variabile GHJ-4 [J]. Scientia Silvae Sinicae, 2017, 53(1): 94-100.
[6]	Sun Shina, Chi Yujie, Yu Cun, Li Yue. Optimization of Culture Conditions to Produce MnP and Dye Decolorization of TN02A7-He-mnp1 and TN02A7-He-mnp2 [J]. Scientia Silvae Sinicae, 2016, 52(4): 75-82.
[7]	Yu Xianmei, Hou Changming, Wang Jie, Wang Hairong, An Miao, Ai Chengxiang. Identification of Pathogen Causing Beef Heart Persimmon Anthracnose in Shandong and Its Pathogenicity [J]. Scientia Silvae Sinicae, 2015, 51(4): 126-133.
[8]	Li Yanyan, Yang Yanfang, Wang Junqing, Wang Shuai, Liu Hongwei, Qiu Deyou. Cloning and Expression of Lateral Organ Boundaries Domain Genes (TcLBDs) in Taxus chinensis [J]. Scientia Silvae Sinicae, 2015, 51(10): 126-133.
[9]	Yu Cun, Chi Yujie. Optimization of Culture Conditions of MnP Produced by Cerrena unicolor and Its Decolorization to 5 Kinds of Dyes [J]. Scientia Silvae Sinicae, 2014, 50(7): 121-127.
[10]	Yu Cun, Chi Yujie. Detection on Manganese Peroxidase Activity and Cloning of Cu-mnp1 of Cerena unicolor [J]. Scientia Silvae Sinicae, 2014, 50(3): 109-116.
[11]	Yin Liwei, Chi Yujie. Phylogenetic Analysis and Detection on the Major Ligninolytic Enzymes of Hericium erinaceum Strain CB 1 [J]. Scientia Silvae Sinicae, 2013, 49(6): 129-134.
[12]	Hu Jiaxu;Song Chuansheng;Lin Caili;Geng Xiansheng;Tian Guozhong. Sequencing the Full-Length DNA and the Molecular Characterization of Four Plasmids from Plant Pathogens of Phytoplasma Disease [J]. Scientia Silvae Sinicae, 2013, 49(4): 90-97.
[13]	Li Jing;Yuan Huwei;Li Wei. Isolation, Expression and Single Nucleotide Polymorphisms Analysis of Dehydration Responsive Element Binding Gene (LpDREB) in Lespedeza potaninii [J]. Scientia Silvae Sinicae, 2012, 48(6): 40-46.
[14]	Zhang Yulong;Chi Yujie;Yan Hongbo. Optimization of Ferment Conditions of Manganese Peroxidase Produced by Trametes gibbosa [J]. Scientia Silvae Sinicae, 2011, 47(8): 88-94.
[15]	Wang Meng;Cao Fuxiang;Long Jiangxue. Cloning and Prokaryotic Expression of the Light Harvesting Chlorophyll a/b Binding Protein Gene from Pinus massoniana [J]. Scientia Silvae Sinicae, 2010, 46(9): 172-177.

Cloning and Bioinformatics Analysis of MnP 1 cDNA Gene from Hericium erinaceum

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments