Expression and analysis of zinc finger family gene in Lenzites gibbosa

Abstract

Zinc finger transcription factors play significant roles in the growth and development of plant and animal, but their function remains obscure in fungi. Lenzites gibbosa mycelia were extracted and sequenced by transcriptome analysis after growing on sawdust at different times to support mycelial growth of L. gibbosa in a nutrient matrix. Data bases used for analysis were the Kyoto encyclopedia of genes and genomes (KEGG) annotation, the cluster of orthologous groups of proteins (COG) and gene ontology (GO) annotation. Zinc finger class genes related to the growth and development of L. gibbosa were screened. GO annotation and enrichment analysis of differentially expressed genes were carried out. A total of 114.55 Gb Clean Data were obtained from the L. gibbosa transcriptome. The average Clean Data in each sample was 6.16 Gb. The relative efficiency of reads between each sample and the reference genome was 88.5% to 91.4%. The COG analysis showed that most zinc finger protein genes were related to replication, recombination and repair function. GO enrichment analysis showed that the expressed genes involved in cellular process, cell part and binding. We identified seventy-two expressed genes including seven up-regulated genes and sixty-five down-regulated genes by applying DESeq2 data analysis software. By comparing the significantly expressed genes with KEGG database, 66 annotated sequences were obtained, and 35 primary metabolic pathways were annotated. Pathway enrichment analysis showed that differentially expressed genes were significantly enriched in protein processing in endoplasmic reticulum and ubiquitin-mediated proteolysis pathways. Gene_11750 and gene_5266 are highly correlated with the growth and development of L. gibbosa and are closely related to protein processing in endoplasmic reticulum and ubiquitin-mediated proteolysis pathway. According to gene functional analysis, seven important differentially expressed genes related to the growth and development of L. gibbosa were identified.

Keywords

Lenzites gibbosa / Differently expressed genes / The transcriptome / Zinc finger

References

[1] Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. Nat Genet, 2000, 25(1): 25-29.

[2] Berg JM, Shi Y. The galvanization of biology: a growing appreciation for the roles of zinc. Science, 1996, 271: 1081-1085.

[3] Bowman JL, Sakai H, Jack T, Weigel D, Mayer U, Meyerowitz EM. SUPERMAN, a regulator of floral homeotic genes in Arabidopsis. Development, 1992, 114: 599-615.

[4] Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M. Pfam: the protein family database. Nucleic Acids Res, 2009, 42: D222-D230.

[5] Huang J, Zhang HS, Cao YJ, Wand D, Wang JF, Yang JS. Cloning and sequence analysis of a new novel C2H2 zinc finger cDNA from rice (Oryza sativa L.). J Nanjing Agric Univ, 2002, 25(2): 110-112. (with abstract in English)

[6] Jia CL, Zhang Y, Zhu L, Zhang R. Application progress of transcriptome sequencing technology in biological sequencing. Mol Plant Breeding, 2015, 13(10): 2388-2394. (with abstract in English)

[7] Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res, 2004, 32: D277-D280.

[8] Kapoor S, Kobayashi A, Takatsuji H. Silencing of the tapetum-specific zinc finger gene TAZ1 causes premature degeneration of tapetum and pollen abortion in petunia. Plant Cell, 2002, 14: 2353-2367.

[9] Kim JC, Lee SH, Cheong YH, Yoo CM, Lee SI, Chun HJ, Yun DJ, Hong HC, Lee SY, Lim CO, Cho MJ. A novel cold-inducible zinc finger protein from soybean. Plant J, 2001, 25: 247-259.

[10] Kirk TK, Jeffries TW (1996) Roles for microbial enzymes in pulp and paper processing. Enzymes for pulp and paper processing ACS symposium series, vol 655, pp 2–14

[11] Kobayashi A, Sakmoto A, Kubo K, Rybka Z, Kanno Y, Takatsuji H. Seven zinc-finger transcription factors are expressed sequentially during the development of anthers in petunia. Plant J, 1998, 13(4): 571-576.

[12] Koonin EV, Fedorova ND, Jackson JD, Jacobs AR, Krylov DM, Makarova KS, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Rogozin IB, Smirnov S, Sorokin AV, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol, 2004 5 2 R7

[13] Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Dolyle M, Fitzhugh W, Funke R. Initial sequencing and analysis of the human genome. Nature, 2001, 409(6822): 860-921.

[14] Lippuner V, Cyert MS, Gasser CS. Two classes of plant cDNA clones differentially complement yeast calcineurin mutants and increase salt tolerance of wild-type yeast. J Biol Chem, 1996, 271: 12859-12866.

[15] Miller J, McLachlan AD, Klug A. Repetitive zinc-binding domains in the protein transcription factor III A from Xenopus oocytes. EMBO J, 1985, 4(6): 1609-1614.

[16] Peng B, Li BJ, Guan WQ, Lin Q. Transcription sequencing of Agaricus bisporus and mining of genes involved in browing. Food Sci, 2019, 40(2): 126-132. (with abstract in English)

[17] Qi YX, Liu YB, Rong WH. RNA-sep and its applications: a new technology for transcriptomics. Hereditas, 2011, 33(11): 1191-1202.

[18] Sakai H, Medrano LJ, Meyerowitz EM. Role of SUPERMAN in maintaining Arabidopsis floral whorl boundaries. Nature, 1995, 378: 199-203.

[19] Sakamoto A, Minami M, Huh GH, Iwabuchi M. The putative zinc-finger protein WZF1 interacts with a cis-acting element of wheat histone genes. Eur J Biochem, 1993, 217: 1049-1056.

[20] Sakamoto H, Araki T, Meshi T, Iwabuchi M. Expression of a subset of the Arabidopsis Cys2/His2-type zinc-finger protein gene family under water stress. Gene, 2000, 248: 23-32.

[21] Shi HR (2016) Comparison of transcription analysis methods based on next-generation sequencing technologies. Dissertation of Sichuan Agricultural University, Yaan, pp 10–18 (in Chinese with abstract in English)

[22] Takatsuji H, Mori M, Benfey PN, Ren L, Chua NH. Characterization of a zinc finger DNA-binding protein expressed specifically in Petunia petals and seedlings. EMBO J, 1992, 11: 241-249.

[23] Tang LH, Jian HH, Song CY, Bao DP, Shang XD, Wu DQ, Tan Q, Zhang XH. Transcriptome analysis of candidate genes and signaling pathways associated with light-induced brown film formation Lentinula edodes. Appl Microbiol Biotechnol, 2013, 97(11): 4977-4989.

[24] Tatusov RL, Galperin MY, Natale DA. The COG database: a tool for genome scale analysis of protein functions and evolution. Nucleic Acids Res, 2000, 28(1): 33-36.

[25] Wang D, Yang JS. Cloning and characterization of cDNA encoding cotton STZ-like protein. J Fudan Univ (Nat Sci), 2002, 4(4): 42-46. (with abstract in English)

[26] Wu XM, Zhang X, Li NY. Transcriptome analysis of Agaricus bisporus fruiting at different stages. Mycosystema, 2017, 36(2): 193-203. (in Chinese with abstract in English)

[27] Xu B, Zhang WQ, Feng XX, Wang CY, Zhang HS, Xu HT, Wang YH, Zhang JH. Application progress of transcriptome sequencing technology in maize. J Maize Sci, 2014, 22(1): 67-72. (in Chinese with abstract in English)

[28] Yan HB (2009) Molecular cloning of cDNA gene encoding a manganese peroxidase from Pseudotrametes gibbosa and heterologous expression of this gene in Pichis pastoris. Dissertation of Northeast Forestry University, Harbin, pp 10–26 (in Chinese with abstract in English)

[29] Yi LL (2015) Sequencing of transcription and screening of genes involved in cell wall degradation in shiitaki mushroom. Dissertation of Zhejiang University, Zhejiang, pp 12–20 (in Chinese with abstract in English)

[30] Yun JY, Weigel D, Lee I. Ectopic expression of SUPERMAN suppresses development of petals and stamens. Plant Cell Physiol, 2002, 43: 52-57.

[31] Zhao QQ, Chi YJ, Zhang J, Feng LR. Transcription construction and related gene expression analysis of Lenzites gibbosa in woody environment. Sci Silvae Sin, 2019, 55(4): 185-195. (in Chinese with abstract in English)

[32] Zhou H, Zhang X, Liu TY, Yu FX. Data processing and gene discovery of high-throughput transcriptome sequencing. Jiangxi Sci, 2012, 30(5): 607-611. (in Chinese with abstract in English)