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浙江大学学报(农业与生命科学版)  2023, Vol. 49 Issue (6): 776-786    DOI: 10.3785/j.issn.1008-9209.2022.10.261
生物科学与技术     
迷宫栓孔菌热激蛋白基因的生物信息学与表达分析
杨旭欣1(),冯连荣1,2(),池玉杰1(),韩树英1,3
1.东北林业大学林学院, 黑龙江 哈尔滨 150040
2.辽宁省杨树研究所, 辽宁 营口 115000
3.周口师范学院生命科学与农学学院, 河南 周口 466001
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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摘要:

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    
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 words: Trametes gibbosa    white-rot fungi    heat shock protein    heat shock protein 104 (HSP104)    gene cloning    bioinformatics
收稿日期: 2022-10-26 出版日期: 2023-12-25
CLC:  S718.81  
基金资助: 国家自然科学基金项目(30671700);黑龙江省自然科学基金项目(C2016006);中央高校基本科研业务费专项资金项目(2572016AA04)
通讯作者: 池玉杰     E-mail: Green_m10@163.com;fenglianrong@163.com;chiyujienefu@126.com
作者简介: 杨旭欣(https://orcid.org/0000-0002-6234-5392),E-mail:Green_m10@163.com|冯连荣(https://orcid.org/0000-0002-5325-8502),E-mail:fenglianrong@163.com
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引用本文:

杨旭欣,冯连荣,池玉杰,韩树英. 迷宫栓孔菌热激蛋白基因的生物信息学与表达分析[J]. 浙江大学学报(农业与生命科学版), 2023, 49(6): 776-786.

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.

链接本文:

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

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
表1  迷宫栓孔菌热激蛋白基因的KEGG通路富集
图1  迷宫栓孔菌热激蛋白基因系统发育树(NJ法)
图2  迷宫栓孔菌热激蛋白基因的GO富集A. 生物过程;B.细胞组分;C.分子功能。
图3  迷宫栓孔菌不同类别热激蛋白的三级结构
图4  HSP100基因PCR扩增电泳图M:DL15000 DNA标志物;1:Tg-hsp104-1,长度为2 663 bp;2:Tg-hsp104-2,长度为2 789 bp。
图5  迷宫栓孔菌HSP100基因序列结构
图6  迷宫栓孔菌HSP100氨基酸序列结构A. Tg-HSP104-1的氨基酸序列结构;B. Tg-HSP104-2的氨基酸序列结构。
图7  迷宫栓孔菌Tg-HSP104-2的三级结构分析A. Tg-HSP104-2六聚体的俯视图;B. Tg-HSP104-2六聚体的侧视图;C. Tg-HSP104-2单体(红色为NBD1,蓝色为NBD2,橙色为N-端结构域,绿色为包括接头在内的其他序列);D. NBD1的三级结构;E. NBD2的三级结构。R414和R804为精氨酸指残基。
图8  木屑处理不同时间的基因表达情况A. Tg-hsp104-1;B. Tg-hsp104-2。短栅上不同小写字母表示在P<0.05水平差异有统计学意义,n=9。
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