谷子泛素连接酶U-box E3基因家族的鉴定及响应非生物胁迫分析

doi:10.13560/j.cnki.biotech.bull.1985.2024-0983

生物技术通报 ›› 2025, Vol. 41 ›› Issue (5): 104-118.doi: 10.13560/j.cnki.biotech.bull.1985.2024-0983

• 研究报告 •

谷子泛素连接酶U-box E3基因家族的鉴定及响应非生物胁迫分析

何卫¹^,²(), 李俊怡¹^,², 李新妮¹^,², 马雪华², 邢媛¹^,², 曹晓宁¹^,², 乔治军¹^,²(), 刘思辰¹^,²()

^1.山西农业大学农业基因资源研究中心农业农村部黄土高原作物基因资源与种质创制重点实验室，太原 030031
^2.山西农业大学农学院，太谷 030801

收稿日期:2024-10-08 出版日期:2025-05-26 发布日期:2025-06-05
通讯作者: 刘思辰，女，副研究员，研究方向：谷子种质资源评价利用；E-mail: lsch@163.com
乔治军，男，研究员，研究方向：旱作栽培与逆境生理；E-mail: qiaozhijun@sxau.edu.cn
作者简介:何卫，男，硕士，研究方向：作物遗传育种；E-mail: hwysyyds@163.com
基金资助:
中央引导地方科技发展资金项目(YDZJSX20231A040);山西农业大学校科技提升工程(CXGC2023094);国家重点研发计划(2023YFD120270505);现代农业产业技术体系建设专项(CARS-06-14.5-A16)

Genome-wide Identification of U-box E3 Ubiquitin Ligase Gene Family in Setaria italica and Response Analysis to Abiotic Stress

HE Wei¹^,²(), LI Jun-yi¹^,², LI Xin-ni¹^,², MA Xue-hua², XING Yuan¹^,², CAO Xiao-ning¹^,², QIAO Zhi-ju¹^,²(), LIU Si-chen¹^,²()

^1.Center for Agricultural Genetic Resources Research, College of Agronomy, Shanxi Agricultural University, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau of the Ministry of Agriculture and Rural Affairs, Taiyuan 030031
^2.College of Agriculture, Shanxi Agricultural University, Taigu 030801

Received:2024-10-08 Published:2025-05-26 Online:2025-06-05

摘要/Abstract

摘要：

目的基于全基因组水平对谷子（Setaria italica）泛素连接酶U-box（plant U-box protein, PUB）基因家族（SiPUB）进行系统鉴定，为谷子泛素连接酶U-box基因家族的生物学功能研究提供理论支撑。方法利用U-box保守Pfam序列全基因组鉴定谷子U-box基因家族成员，采用系统进化树构建、亚细胞定位预测、预测蛋白的相对分子质量与等电点等理化性质、绘制家族成员Scaffold定位图等分析，利用实时荧光定量PCR技术（RT-qPCR）对不同胁迫处理下的谷子U-box基因家族成员表达情况进行研究。结果谷子基因组中有71个PUB基因家族成员，不均匀地分布在8条染色体上。系统进化分析表明，SiPUB基因分布在Ⅰ-Ⅸ亚家族中。启动子顺式作用元件分析显示，U-box基因与植物生长发育、胁迫和激素调控相关。荧光定量PCR结果表明，SiPUBs在谷子的各个部位差异表达，对谷子U-box基因家族不同结构域在胁迫下的表达模式分析，含U-box结构域基因在低温和干旱下表达量变化显著、茉莉酸下特定时段表达，含U-box+HEAT_2结构域基因在3种胁迫下变化不显著，含U-box+Pkinase等结构域基因在不同胁迫下表达量有升有降，表明各结构域在植物环境应答及基因调控中有不同作用，植株可通过调控SiPUBs表达响应非生物胁迫。结论鉴定出71个SiPUBs基因，不同亚家族在非生物胁迫下的表达模式存在差异，表明SiPUBs对谷子响应非生物胁迫起重要的调控作用。

关键词: 谷子, E3泛素连接酶, U-box基因家族, 低温胁迫, 干旱胁迫, 茉莉酸胁迫

Abstract:

Objective The ubiquitin ligase U-box (plant U-box protein, PUB) gene family (SiPUB) of Setaria italica was systematically identified based on the whole genome level, which may provide theoretical support for the study of the biological function of the ubiquitin ligase U-box gene family of S. italica. Method The U-box gene family members of S. italica were identified by the whole genome of the U-box conserved Pfam sequence. The phylogenetic tree construction, subcellular localization prediction, physical and chemical properties such as relative molecular mass and isoelectric point of the predicted protein, and Scaffold localization map of the family were analyzed. The expressions of U-box gene family members in S. italica under different stress treatments were studied by real-time fluorescence quantitative PCR (RT-qPCR). Result There were 71 PUB gene family members in the genome of S. italica, which were unevenly distributed on 8 chromosomes. Phylogenetic analysis showed that SiPUB genes were distributed in subfamilies I to Ⅸ. Promoter cis-acting element analysis showed that U-box genes were related to plant growth and development, stress and hormone regulation. The results of fluorescence quantitative PCR showed that SiPUBs were differentially expressed in various parts of S. italica. The expression patterns of different domains of S. italicaU-box gene family under stress were analyzed. The expressions of genes containing U-box domain changed significantly under low temperature and drought, and the expressions of genes containing U-box+HEAT_2 domain did not change significantly under three stresses. The expressions of genes containing U-box+Pkinase and other domains increased and decreased under different stresses, indicating that each domain played different roles in plant environmental response and gene regulation. Plants responded to abiotic stress by regulating the expression of SiPUBs. Conclusion A total of 71 SiPUBs genes are identified, and the expression patterns of different subfamilies under abiotic stress are different, indicating that SiPUBs play an important regulatory role in the response of S. italica to abiotic stress. The results of this study can provide reference for the analysis of stress resistance function of SiPUBs.

Key words: Setaria italica, E3 ubiquitin ligase, U-box gene family, low temperature stress, drought stress, MeJA stress

何卫, 李俊怡, 李新妮, 马雪华, 邢媛, 曹晓宁, 乔治军, 刘思辰. 谷子泛素连接酶U-box E3基因家族的鉴定及响应非生物胁迫分析[J]. 生物技术通报, 2025, 41(5): 104-118.

HE Wei, LI Jun-yi, LI Xin-ni, MA Xue-hua, XING Yuan, CAO Xiao-ning, QIAO Zhi-ju, LIU Si-chen. Genome-wide Identification of U-box E3 Ubiquitin Ligase Gene Family in Setaria italica and Response Analysis to Abiotic Stress[J]. Biotechnology Bulletin, 2025, 41(5): 104-118.

图/表 12

表1 引物序列

Table 1 Sequences of primers

引物名称 Primer name	基因序列 Gene sequence （5′‒3′）
25S-F	AGGCAACAGAAACTCCATACG
25S-R	ATGGCATAGCATTCATCACG
SiPUB2-F	GGAGTCACTGCTCCGCAAT
SiPUB2-R	CTTCTCGTCAGCGGGGC
SiPUB3-F	ACAGCGGAAAGAGGCTCATC
SiPUB3-R	CGAGCGACATCAAGTTTGGC
SiPUB8-F	CGGGCTTGAAGAGAAGCTGA
SiPUB8-R	ACTCGTGCAGGAGAAAGTCG
SiPUB24-F	GTTACTCCTGAGGTCACTTG
SiPUB24-R	TCCACCTGTAACATTGTCTG
SiPUB29-F	CCATTGGTGGTTCAGACATA
SiPUB29-R	AGGGAGTCCAAATATCCGTA
SiPUB38-F	TCAGATTCATTCTCCCAAGC
SiPUB38-R	CCTGAACTTTCTGAAGCAAC
SiPUB46-F	TCAGAGAAATTGACGAGGAG
SiPUB46-R	ATAATCCTGTCAGCAGGTTG
SiPUB49-F	GGAGCGAGATGATGCGGTTA
SiPUB49-R	AGTGAACGGCTGAAGACCTG
SiPUB55-F	CCAGCATCGAGTCCTGGGTC
SiPUB55-R	ACGCACCACTCCTGGATGA
SiPUB59-F	CAACAAGCCCAAGAGGGACT
SiPUB59-R	GCTGGCTTCCCAGTTACCAT
SiPUB64-F	CTCACAGGAACAAAGCGTGC
SiPUB64-R	CACGCCTCAATGTGCTGTTC
SiPUB70-F	CTGTTCCTGTGCCCCATCTC
SiPUB70-R	CCGTACCCGAAGATCCACTG

图1 谷子U-box基因家族的系统发育（A）、保守结构域（B）与基因结构分析（C）

Fig. 1 Phylogenetic relationship (A), gene structure (B) and conserved motif analyses (C) of U-box genes

表2 谷子U-box基因家族蛋白质结构域

Table 2 U-box gene family protein domains in Setaria italica

分类名称	蛋白名称	基因
Classification name	Protein name	Gene
Ⅰ	U-box+ARM	SiPUB5， SiPUB10， SiPUB12， SiPUB14， SiPUB25， SiPUB31， SiPUB32， SiPUB33， SiPUB35， SiPUB37， SiPUB43， SiPUB47， SiPUB48， SiPUB64， SiPUB65， SiPUB71
Ⅱ	U-box	SiPUB2， SiPUB15， SiPUB16， SiPUB19， SiPUB20， SiPUB21， SiPUB22， SiPUB26， SiPUB27， SiPUB34， SiPUB40， SiPUB42， SiPUB45， SiPUB55， SiPUB57， SiPUB62， SiPUB66， SiPUB67， SiPUB70
Ⅲ	U-box	SiPUB17， SiPUB18， SiPUB58
Ⅲ	U-box+KAP	SiPUB50
Ⅳ	U-box	SiPUB28
Ⅳ	U-box+ARM	SiPUB9， SiPUB28， SiPUB54
Ⅴ	U-box	SiPUB13， SiPUB23， SiPUB56
	U-box+ARM	SiPUB39
	U-box+HEAT_2	SiPUB3
Ⅵ	U-box	SiPUB8
Ⅵ	Pro_isomerase+U-box	SiPUB44
Ⅶ	U-box	SiPUB6， SiPUB61
	U-box+Pkinase	SiPUB1， SiPUB36， SiPUB38， SiPUB46， SiPUB52， SiPUB68
	U-box+Pkinase+Usp	SiPUB7， SiPUB59， SiPUB63
	U-box+Pkinase_Tyr+Usp	SiPUB11， SiPUB41， SiPUB51， SiPUB69
	TPR_11+U-box+Pkinase	SiPUB30， SiPUB60
Ⅸ	Prp19+WD40+U-box	SiPUB29

图2 谷子（Si）、水稻（Os）、拟南芥（At）U-box基因家族系统进化树五角星表示谷子U-box基因家族成员

Fig. 2 Phylogenetic tree of S. italica (Si), Oryza sativa (Os) and Arabidopsis thaliana (At) U-box genesfamilyThe pentagram indicates the members of the U-box gene family in S. italica

图3 谷子U-box基因的启动子分析

Fig. 3 Promoter analysis of U-box gene family in S. italica

图4 谷子U-box基因家族成员在谷子染色体上的分布五角星表示串联基因簇

Fig. 4 Distribution of U-box gene family members on chromosomes in S. italicaThe pentagram indicates the tandem gene cluster

图5 谷子种内U-box基因家族共线性分析1‒9代表谷子第1-9染色体；染色体内部以基因密度填充，颜色由蓝到红代表基因密度由小到大

Fig. 5 Synteny analysis of U-box gene family in S. italica1‒9 indicates chromosome 1‒9 in S. italica. The interior of the chromosome is filled with gene density,with colors ranging from blue to red indicating a gradual increase in gene density

图6 谷子U-box基因家族成员与拟南芥（A）、玉米（B）和水稻（C） U-box基因共线性分析

Fig. 6 Synteny analysis of U-box gene between S. italicaA., thaliana (A), Z. mays (B) and O. sativa (C)

图7 谷子U-box基因家族在不同组织部位中的表达分析

Fig. 7 Expression analysis of U-box gene family members in the different tissues of S. italica

图8 低温处理下不同基因的表达水平不同字母表示差异显著（P<0.05）。下同

Fig. 8 Expressions of different genes under low-temperature treatmentThe different letters indicate significant differences (P<0.05). The same below

图9 干旱处理下不同基因的表达水平

Fig. 9 Expressions of different genes under drought treatment

图10 MeJA处理下不同基因的表达水平

Fig. 10 Expressions of different genes under MeJA treatment

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谷子泛素连接酶U-box E3基因家族的鉴定及响应非生物胁迫分析

Genome-wide Identification of U-box E3 Ubiquitin Ligase Gene Family in Setaria italica and Response Analysis to Abiotic Stress

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