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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
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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:;;
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.

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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 pathway name


Pathway ID


Number of genes


Adjusted p-value


Rich factor


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.
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