Please wait a minute...
Journal of Zhejiang University (Agriculture and Life Sciences)  2023, Vol. 49 Issue (6): 776-786    DOI: 10.3785/j.issn.1008-9209.2022.10.261
Biological sciences & biotechnologies     
Bioinformatics and expression analysis of heat shock protein genes in Trametes gibbosa
Xuxin YANG1(),Lianrong FENG1,2(),Yujie CHI1(),Shuying HAN1,3
1.School of Forestry, Northeast Forestry University, Harbin 150040, Heilongjiang, China
2.Liaoning Provincial Institute of Poplar, Yingkou 115000, Liaoning, China
3.School of Life Sciences and Agronomy, Zhoukou Normal University, Zhoukou 466001, Henan, China
Download: HTML   HTML (   PDF(6767KB)
Export: BibTeX | EndNote (RIS)      

Abstract  

To investigate the function and structure of the heat shock protein (HSP) family in Trametes gibbosa,a cDNA library was constructed by collecting mycelial samples at different time under the sawdust treatment.All the HSP genes in this strain were screened by analyzing their transcriptome data; subsequently, bioinformatics analysis was performed for all the HSPs. Gene cloning and sequence structure analysis were performed for the HSP100 family, and the expression levels of the HSP100 genes were verified under the sawdust treatment by real-time fluorescent quantitative polymerase chain reaction (qRT-PCR). The results were as follows: A total of 32 HSP genes were screened and divided into five subclasses in T. gibbosa. Among the 32 HSPs, there were two HSP100, two HSP90, seven HSP70, one HSP60 and twenty small HSPs (sHSPs). In growth regulation, they had important functions, such as protein posttranslational modification, protein folding, and chaperonin. In T. gibbosa, HSPs were hydrophobic proteins with distinct physicochemical properties for different subclasses. The HSP100 family consist of an N-terminus, nucleotide-binding domain 1 (NBD1), NBD2, and the linker between the two NBDs. The NBDs had highly conserved Walker A and Walker B motifs and arginine finger residues. The qRT-PCR amplification results showed that there was obvious upregulation expression of HSP100 gene in T. gibbosa under the sawdust treatment. In summary, the classification of the HSP family in T. gibbosa is diverse and complex. Under stress conditions, the HSP100 family plays an important role in protein depolymerization, and its sequence and structure are relatively conserved. The above results can provide a theoretical basis for the study of T. gibbosa under stress.



Key wordsTrametes gibbosa      white-rot fungi      heat shock protein      heat shock protein 104 (HSP104)      gene cloning      bioinformatics     
Received: 26 October 2022      Published: 25 December 2023
CLC:  S718.81  
Corresponding Authors: Yujie CHI     E-mail: Green_m10@163.com;fenglianrong@163.com;chiyujienefu@126.com
Cite this article:

Xuxin YANG,Lianrong FENG,Yujie CHI,Shuying HAN. Bioinformatics and expression analysis of heat shock protein genes in Trametes gibbosa. Journal of Zhejiang University (Agriculture and Life Sciences), 2023, 49(6): 776-786.

URL:

https://www.zjujournals.com/agr/10.3785/j.issn.1008-9209.2022.10.261     OR     https://www.zjujournals.com/agr/Y2023/V49/I6/776


迷宫栓孔菌热激蛋白基因的生物信息学与表达分析

为了探究迷宫栓孔菌(Trametes gibbosa)热激蛋白(heat shock proteins, HSPs)家族的功能及结构,对经木屑处理不同时间点的菌丝样品进行cDNA建库,然后根据转录组数据筛选该菌株的所有HSPs基因并进行生物信息学分析;针对HSP100家族进行基因克隆和序列结构分析,并利用实时荧光定量聚合酶链反应(real-time fluorescent quantitative polymerase chain reaction, qRT-PCR)对其在木屑处理下的表达量进行验证。结果如下:在迷宫栓孔菌中共筛选出32个HSPs基因,其编码的蛋白分为5个亚类,分别为HSP100(2个)、HSP90(2个)、HSP70(7个)、HSP60(1个)和小分子热激蛋白[small HSPs(sHSPs),20个],它们在菌体生长调控中具有蛋白翻译后修饰、蛋白质折叠、伴侣蛋白等重要功能。这些HSPs都为疏水蛋白,不同亚类的HSPs理化性质有所差异。HSP100由N-端、核苷酸结合域1(nucleotide-binding domain 1, NBD1)、NBD2、2个NBDs间的接头构成,其中,NBDs具有十分保守的Walker A、Walker B基序及精氨酸指残基。qRT-PCR扩增结果表明,在木屑处理下迷宫栓孔菌HSP100基因表达量有明显上调趋势。综上所述,迷宫栓孔菌中HSPs家族种类多且复杂,在应激情况下HSP100家族承担了重要的蛋白质解聚功能,其序列及结构相对保守。本研究结果为迷宫栓孔菌在胁迫应激方面的研究提供了理论依据。


关键词: 迷宫栓孔菌,  白腐菌,  热激蛋白,  热激蛋白104,  基因克隆,  生物信息学 

KEGG通路名称

KEGG pathway name

通路标识符

Pathway ID

基因数

Number of genes

校正后p

Adjusted p-value

富集因子

Rich factor

内质网中蛋白质加工

Protein processing in endoplasmic reticulum

ko04141167.07×10-2122.122 222 220
RNA降解 RNA degradationko0301820.434.022 222 222
内吞作用 Endocytosisko0414420.703.030 441 400
蛋白质输出 Protein exportko0306010.915.027 777 778
剪接体 Spliceosomeko0304021.002.257 369 615
Table 1 KEGG pathway enrichment of HSP genes in T. gibbosa
Fig. 1 Phylogenetic tree of HSP genes in T. gibbosa (NJ method)
Fig. 2 GO enrichment of HSP genes in T. gibbosaA. Biological process; B. Cellular component; C. Molecular function.
Fig. 3 Tertiary structures of different classes of HSPs in T. gibbosa
Fig. 4 Electrophoretogram of HSP100 genes by PCR amplificationM: DL15000 DNA marker; 1: Tg-hsp104-1 with 2 663 bp in length; 2: Tg-hsp104-2 with 2 789 bp in length.
Fig. 5 Sequence structures of HSP100 genes in T. gibbosa
Fig. 6 Amino acid sequence structures of HSP100 in T. gibbosaA. Amino acid sequence structure of Tg-HSP104-1;B. Amino acid sequence structure of Tg-HSP104-2.
Fig. 7 Tertiary structure analysis of Tg-HSP104-2 in T. gibbosaA. Top view of Tg-HSP104-2 hexamer; B. Side view of Tg-HSP104-2 hexamer; C. Tg-HSP104-2 monomer (red represents NBD1, and blue represents NBD2, and orange represents the N-terminal domain, and green represents the other sequences including linkers); D. Tertiary structure of NBD1; E. Tertiary structure of NBD2. R414 and R804 are Arg-finger residues.
Fig. 8 Gene expression levels at different time under the sawdust treatmentA. Tg-hsp104-1; B. Tg-hsp104-2. Different lowercase letters above bars indicate significant differences at the 0.05 probability level, and n=9.
[1]   翁锦周,洪月云.植物热激转录因子在非生物逆境中的作用[J].分子植物育种,2006,4(1):88-94. DOI:10.3969/j.issn.1672-416X.2006.01.016
WENG J Z, HONG Y Y. The roles of plant heat shock transcription factors in abiotic stress[J]. Molecular Plant Breeding, 2006, 4(1): 88-94. (in Chinese with English abstract)
doi: 10.3969/j.issn.1672-416X.2006.01.016
[2]   MORISHIMA N. Control of cell fate by Hsp70: more than an evanescent meeting[J]. The Journal of Biochemistry, 2005, 137(4): 449-453. DOI: 10.1093/jb/mvi057
doi: 10.1093/jb/mvi057
[3]   邢淑莲,周益林,段霞瑜,等.生物热激蛋白及真菌HSP70的研究进展[C]//植保科技创新与病虫防控专业化:中国植物保护学会2011年学术年会论文集.北京:中国农业科学技术出版社,2011.
XING S L, ZHOU Y L, DUAN X Y, et al. Research progress on biological heat shock proteins and fungal HSP70[C]//Plant Protection Science and Technology Innovation and Specialization of Disease and Pest Control: The 2011 Academic Annual Meeting of China Plant Protection Society. Beijing: China Agricultural Science and Technology Press, 2011. (in Chinese)
[4]   王敏,江彪,林毓娥,等.小分子热激蛋白参与植物抗逆性方面的研究进展[J].安徽农业科学,2018,46(18):29-32. DOI:10.3969/j.issn.0517-6611.2018.18.009
WANG M, JIANG B, LIN Y E, et al. Advances of small heat shock proteins participating in plant resistance[J]. Journal of Anhui Agricultural Sciences, 2018, 46(18): 29-32. (in Chinese with English abstract)
doi: 10.3969/j.issn.0517-6611.2018.18.009
[5]   栗振义,龙瑞才,张铁军,等.植物热激蛋白研究进展[J].生物技术通报,2016,32(2):7-13. DOI:10.13560/j.cnki.biotech.bull.1985.2016.02.003
LI Z Y, LONG R C, ZHANG T J, et al. Research progress on plant heat shock protein[J]. Biotechnology Bulletin, 2016, 32(2): 7-13. (in Chinese with English abstract)
doi: 10.13560/j.cnki.biotech.bull.1985.2016.02.003
[6]   WATERS E R, LEE G J, VIERLING E. Evolution, structure and function of the small heat shock proteins in plants[J]. Journal of Experimental Botany, 1996, 47(3): 325-338. DOI: 10.1093/jxb/47.3.325
doi: 10.1093/jxb/47.3.325
[7]   NAGY M, AKOEV V, ZOLKIEWSKI M. Domain stability in the AAA+ ATPase ClpB from Escherichia coli [J]. Archives of Biochemistry and Biophysics, 2006, 453(1): 63-69. DOI: 10.1016/j.abb.2006.03.004
doi: 10.1016/j.abb.2006.03.004
[8]   LEE S, SOWA M E, WATANABE Y H, et al. The structure of ClpB: a molecular chaperone that rescues proteins from an aggregated state[J]. Cell, 2003, 115(2): 229-240. DOI: 10.1016/s0092-8674(03)00807-9
doi: 10.1016/s0092-8674(03)00807-9
[9]   LEE S, SOWA M E, CHOI J M, et al. The ClpB/Hsp104 molecular chaperone: a protein disaggregating machine[J]. Journal of Structural Biology, 2004, 146(1/2): 99-105. DOI: 10.1016/j.jsb.2003.11.016
doi: 10.1016/j.jsb.2003.11.016
[10]   杨金莹,孙爱清,刘箭.热激蛋白ClpB的结构和功能[J].植物生理学通讯,2006,42(2):326-330. DOI:10.13592/j.cnki.ppj.2006.02.051
YANG J Y, SUN A Q, LIU J. The structure and function of heat shock protein ClpB[J]. Plant Physiology Journal, 2006, 42(2): 326-330. (in Chinese)
doi: 10.13592/j.cnki.ppj.2006.02.051
[11]   ZHANG G, LI S, CHENG K W, et al. AAA ATPases as therapeutic targets: structure, functions, and small-molecule inhibitors[J]. European Journal of Medicinal Chemistry, 2021, 219: 113446. DOI: 10.1016/j.ejmech.2021.113446
doi: 10.1016/j.ejmech.2021.113446
[12]   SCHIRMER E C, GLOVER J R, SINGER M A, et al. HSP100/Clp proteins: a common mechanism explains diverse functions[J]. Trends in Biochemical Sciences, 1996, 21(8): 289-296. DOI: 10.1016/S0968-0004(96)10038-4
doi: 10.1016/S0968-0004(96)10038-4
[13]   李姝璇,池玉杰.木屑处理迷宫栓孔菌Zn(Ⅱ)-Cys(6)转录因子差异表达分析[J].菌物学报,2022,41(4):546-560. DOI:10.13346/j.mycosystema.210397
LI S X, CHI Y J. Analysis of the differentially expressed Zn(Ⅱ)-Cys(6) transcription factors in Trametes gibbosa treated with sawdust[J]. Mycosystema, 2022, 41(4): 546-560. (in Chinese with English abstract)
doi: 10.13346/j.mycosystema.210397
[14]   李玉,李泰辉,杨祝良,等.中国大型菌物资源图鉴[M].河南,郑州:中原农民出版社,2015:658.
LI Y, LI T H, YANG Z L, et al. Atlas of Chinese Macrofungal Resources[M]. Zhengzhou, Henan: Central China Farmers Publishing House, 2015: 658. (in Chinese)
[15]   池玉杰,闫洪波.红平菇木质素降解酶系统漆酶、锰过氧化物酶及木质素过氧化物酶的检测[J].林业科学,2009,45(12):154-158. DOI:10.3321/j.issn:1001-7488.2009.12.027
CHI Y J, YAN H B. Detection on laccase, manganese peroxidase and lignin peroxidase in ligninolytic enzymes of Pleurotus djamor [J]. Scientia Silvae Sinicae, 2009, 45(12): 154-158. (in Chinese with English abstract)
doi: 10.3321/j.issn:1001-7488.2009.12.027
[16]   CHI Y J, ZHANG J. Gene expression of the white-rot fungus Lenzites gibbosa during wood degradation[J]. Mycologia, 2022, 114(5): 841-856. DOI: 10.1080/00275514.2022.2072148
doi: 10.1080/00275514.2022.2072148
[17]   BASCOS N A D, LANDRY S J. A history of molecular chaperone structures in the protein data bank[J]. International Journal of Molecular Sciences, 2019, 20(24): 6195. DOI: 10.3390/ijms20246195
doi: 10.3390/ijms20246195
[18]   GATES S N, YOKOM A L, LIN J B, et al. Ratchet-like polypeptide translocation mechanism of the AAA+ dis-aggregase Hsp104[J]. Science, 2017, 357(6348): 273-279. DOI: 10.1126/science.aan1052
doi: 10.1126/science.aan1052
[19]   BIEBL M M, BUCHNER J. Structure, function, and regulation of the Hsp90 machinery[J]. Cold Spring Harbor Perspectives in Biology, 2019, 11(9): a034017. DOI: 10.1101/cshperspect.a034017
doi: 10.1101/cshperspect.a034017
[20]   WU C C, NAVEEN V, CHIEN C H, et al. Crystal structure of DnaK protein complexed with nucleotide exchange factor GrpE in DnaK chaperone system[J]. Journal of Biological Chemistry, 2012, 287(25): 21461-21470. DOI: 10.1074/jbc.M112.344358
doi: 10.1074/jbc.M112.344358
[21]   张景霞,杨颖,张权,等.核苷酸转换因子的特性及其在植物中的研究现状[J].植物生理学报,2011,47(3):218-222. DOI:10.13592/j.cnki.ppj.2011.03.012
ZHANG J X, YANG Y, ZHANG Q, et al. Characteristic of the nucleotide exchange factors and recent studies in plants[J]. Plant Physiology Journal, 2011, 47(3): 218-222. (in Chinese with English abstract)
doi: 10.13592/j.cnki.ppj.2011.03.012
[22]   VIERLING E. The roles of heat shock proteins in plants[J]. Annual Review of Plant Physiology and Plant Molecular Biology, 1991, 42: 579-620.
[23]   LEIPE D D, WOLF Y I, KOONIN E V, et al. Classification and evolution of P-loop GTPases and related ATPases[J]. Journal of Molecular Biology, 2002, 317(1): 41-72. DOI: 10.1006/jmbi.2001.5378
doi: 10.1006/jmbi.2001.5378
[24]   WALLDÉN K, WILLIAMS R, YAN J, et al. Structure of the VirB4 ATPase, alone and bound to the core complex of a type Ⅳ secretion system[J]. PNAS, 2012, 109(28): 11348-11353. DOI: 10.1073/pnas.1201428109
doi: 10.1073/pnas.1201428109
[25]   ZHAO Z Y, DE-DONATIS G M, SCHWARTZ C, et al. An arginine finger regulates the sequential action of asymmetrical hexameric ATPase in the double-stranded DNA translocation motor[J]. Molecular and Cellular Biology, 2016, 36(19): 2514-2523. DOI: 10.1128/MCB.00142-16
doi: 10.1128/MCB.00142-16
[26]   SNIDER J, THIBAULT G, HOURY W A. The AAA+ super-family of functionally diverse proteins[J]. Genome Biology, 2008, 9(4): 216. DOI: 10.1186/gb-2008-9-4-216
doi: 10.1186/gb-2008-9-4-216
[27]   SNIDER J, HOURY W A. AAA+ proteins: diversity in function, similarity in structure[J]. Biochemical Society Transactions, 2008, 36(Pt 1): 72-77. DOI: 10.1042/BST0360072
doi: 10.1042/BST0360072
[28]   CHOW I T, BARNETT M E, ZOLKIEWSKI M, et al. The N-terminal domain of Escherichia coli ClpB enhances chaperone function[J]. FEBS Letters, 2005, 579(20): 4242-4248. DOI: 10.1016/j.febslet.2005.06.055
doi: 10.1016/j.febslet.2005.06.055
[29]   杜甫佑.白腐菌木质纤维素降解次序研究[D].湖北,武汉:华中科技大学,2004.
DU F Y. Study on law of degradation sequence in lignocellulose by white-rot fungi[D]. Wuhan, Hubei: Huazhong University of Science and Technology, 2004. (in Chinese with English abstract)
[1] Attached Table S1 and S2 Download
[1] Fengyan LI,Fangqian QU,Fangmeng ZHAO,Qi WANG,Hong ZHOU,Liangsheng ZHANG,Yiping XIA,Xiuyun WANG. Bioinformatics and expression analyses of heat shock protein 90 gene family in Rhododendron ovatum[J]. Journal of Zhejiang University (Agriculture and Life Sciences), 2023, 49(5): 708-718.
[2] Yang LI,Fan LI,Danchen MENG,Linju LI,Chunmei WEI,Meijuan HUANG,Haiquan HUANG. Cloning and expression analysis of petal spur development related gene TCP4 in Impatiens uliginosa[J]. Journal of Zhejiang University (Agriculture and Life Sciences), 2023, 49(3): 341-348.
[3] Xin HAO,Ruina TAN,Jie CHEN,Yang LI,Jingxin CAO,Jian DIAO,Zhen DENG,Ping ZHANG,Ling MA. Analysis of structures and expression patterns of the flavin-containing monooxygenase family genes in Bursaphelenchus xylophilus[J]. Journal of Zhejiang University (Agriculture and Life Sciences), 2023, 49(2): 191-199.
[4] Hui LI,Wei FENG,Junjie YU,Mingyin ZHANG,Chunmiao ZHOU,Yongkai TANG. Research progress of peroxiredoxingene in crustaceans[J]. Journal of Zhejiang University (Agriculture and Life Sciences), 2021, 47(3): 284-294.
[5] Youxuan WANG,Mengyu WANG,Yubo LI,Han TAO,Chuchu XIA,Kaimei HUANG,Qiaomei WANG. Bioinformatics and expression analysis of Aux/IAA family gene in Chinese kale[J]. Journal of Zhejiang University (Agriculture and Life Sciences), 2021, 47(3): 314-324.
[6] Faxiang WAN,Lianzhen WANG,Jun GAO. Bioinformatics of 1-aminocyclopropane-1-carboxylic acid synthase gene from eggplant and its expression analysis in response to adversity stresses[J]. Journal of Zhejiang University (Agriculture and Life Sciences), 2021, 47(3): 325-334.
[7] Huichun LIU,Jiaqiang ZHANG,Guangying MA,Jianghua ZHOU,Wenting XU,Kaiyuan ZHU. Cloning of PsDHN1 gene of Paeonia suffruticosa and waterlogging tolerance analysis of transgenic Arabidopsis with PsDHN1 gene[J]. Journal of Zhejiang University (Agriculture and Life Sciences), 2021, 47(3): 335-346.
[8] Zhuo LI,Lang CHEN,Tao JIANG,Lixia LIU,Li ZHANG,Rui WANG,Yaodong LI. Single nucleotide polymorphism and bioinformatics analysis of DQA2 gene in yak[J]. Journal of Zhejiang University (Agriculture and Life Sciences), 2020, 46(3): 376-382.
[9] Li ZHANG,Weilun NONG,Jianxiong LU,Guohua ZHANG,Lixia LIU. Single nucleotide polymorphism screening and bioinformatics analysis of the main family genes of FABPs in Bamei pig[J]. Journal of Zhejiang University (Agriculture and Life Sciences), 2019, 45(1): 109-118.
[10] ZHANG Li, LIU Lixia, DAI Hongwei, CHEN Hong, WANG Rui, YUE Binghui. Single nucleotide polymorphism screening and bioinformatics analysis of myostatin gene in Jingning chicken[J]. Journal of Zhejiang University (Agriculture and Life Sciences), 2018, 44(5): 629-637.
[11] XU Kangkang, DING Tianbo, YAN Yi, LI Can, YANG Wenjia. Expression analysis of glutathione S-transferase genes in Lasioderma serricorne (Coleoptera: Anobiidae) subjected to CO2-enriched atmosphere[J]. Journal of Zhejiang University (Agriculture and Life Sciences), 2017, 43(5): 599-607.
[12] ZHENG Qunyan, PAN Xiaoyi, SHEN Jinyu, CHEN Shaobo, XU Yang, XU Ting. Molecular cloning and tissue expression analysis of glutamate dehydrogenase gene from Macrobrachium rosenbergii under MrTV infection stress[J]. Journal of Zhejiang University (Agriculture and Life Sciences), 2017, 43(5): 639-648.
[13] MA Guangying, ZHU Kaiyuan, SHI Xiaohua, ZOU Qingcheng, LIU Huichun, ZHAN Jing, TIAN Danqing. Cloning, sequence and expression analysis of two SOC1 genes from Anthurium[J]. Journal of Zhejiang University (Agriculture and Life Sciences), 2017, 43(3): 289-297.
[14] WANG Jiaqing, DONG Huiming, LI Zhengang, LI Shaoming, WANG Ruonan, FU Yujie. Cloning and function prediction of full-length cDNA for cathepsin E derived from medaka (Oryzias latipes).[J]. Journal of Zhejiang University (Agriculture and Life Sciences), 2017, 43(2): 183-191.
[15] Shen Enhui, Liu Yang, Ye Chuyu, Fan Longjiang. Recent studies on non-coding small RNAs in plants[J]. Journal of Zhejiang University (Agriculture and Life Sciences), 2014, 40(4): 370-378.