谷子SiGeBP基因家族生物信息学及表达分析

doi:10.13560/j.cnki.biotech.bull.1985.2025-1439

摘要/Abstract

摘要：

目的无表皮毛增强子结合蛋白（glabrous-enhancer binding protein, GeBP）是植物特有的转录调控因子，参与生长发育调控及逆境胁迫应答。明确谷子SiGeBP基因家族的成员组成、分子特征及表达响应模式，为解析该家族基因功能奠定基础。方法以谷子为试材，利用TBtools、MEGA 11.0、PlantCARE等生物信息学工具及NCBI、Pfam等相关数据库，鉴定SiGeBP基因家族成员，并系统分析其染色体定位、理化性质、系统发育关系、蛋白结构、基因结构和顺式作用元件；采用RT-qPCR技术，检测部分家族基因在4种非生物胁迫和4种激素处理下的表达特征。结果鉴定到16个SiGeBP基因，不均匀地分布在8条染色体上。理化性质分析表明，SiGeBP蛋白均为不稳定性亲水蛋白，具有较高热稳定性，9个成员为偏碱性蛋白。基因结构分析显示，SiGeBP基因含0‒2个内含子，呈典型“内含子缺乏型”特征。经系统发育分析，将16个SiGeBP蛋白划分为5个亚家族，同一亚家族成员具有高度相似的蛋白保守基序和功能结构域，所有成员均含DUF573结构域。顺式作用元件预测发现，SiGeBP基因启动子区域富集多种非生物胁迫响应元件及激素应答元件。RT-qPCR结果显示，SiGeBP基因家族成员在非生物胁迫与外源激素处理下，相较于对照组均呈现显著差异化表达：SiGeBP-1和SiGeBP-2的相对表达水平在4种激素处理下均显著升高；SiGeBP-6和SiGeBP-13的表达水平在4种非生物胁迫处理下均显著下调。结论谷子SiGeBP基因家族具有保守的结构特征及多样的表达响应模式，推测其可能通过参与激素调控网络及逆境应答通路，协同调控谷子抗逆性及生长发育进程。

关键词: 谷子, SiGeBP基因家族, 生物信息学分析, 非生物胁迫, 激素

Abstract:

Objective Glabrous-enhancer binding proteins (GeBPs) are a class of plant-specific transcriptional regulators that participate in the regulation of growth and development and the responses to abiotic stress. This study aimed to clarify the member composition, molecular characteristics, and expression response patterns of the SiGeBP gene family in Setaria italica, thereby laying a foundation for elucidating the functions of this gene family. Method S. italica was used as the experimental material. Bioinformatics tools, including TBtools, MEGA 11.0, and PlantCARE, together with relevant databases such as NCBI and Pfam, were employed to identify the members of the SiGeBP gene family, followed by systematic analyses of their chromosomal localization, physicochemical properties, phylogenetic relationships, protein conserved motifs, functional domains, gene^{structures, and cis-acting elements. Additionally, quantitative real-time polymerase chain reaction (RT-qPCR) was performed to detect the expression characteristics of the SiGeBP gene family under four types of abiotic stress and four types of hormone treatment conditions. Result A total of 16 SiGeBP genes were identified and they unevenly distributed across 8 chromosomes. Physicochemical property analysis revealed that all SiGeBP proteins were unstable hydrophilic proteins with high thermal stability, and 9 members were alkaline proteins. Gene structure analysis indicated that SiGeBP genes contained 0-2 introns, exhibiting a typical intron-poor feature. Phylogenetic analysis clustered the 16 SiGeBP proteins into 5 subfamilies. Members within the same subfamily shared highly similar conserved motifs and functional domains, and all members possessed the DUF573 domain. The prediction of cis-acting elements showed that the promoter regions of SiGeBP genes were enriched with various abiotic stress-responsive elements and hormone-responsive elements. RT-qPCR results demonstrated that members of the SiGeBP gene family exhibited significant differential expression patterns, compared with the control group under abiotic stresses and exogenous hormone treatments; the relative expressions of SiGeBP-1 and SiGeBP-2 were significantly upregulated under all four hormone treatments; the expressions of SiGeBP-6 and SiGeBP-13 were significantly downregulated under all four abiotic stresses. Conclusion The SiGeBP gene family in S. italica exhibits conserved structural characteristics and diverse expression response patterns, implying that it may synergistically regulate the stress resistance and growth and development processes of S. italica by participating in hormone regulatory networks and stress response pathways.}

Key words: Setaria italica, SiGeBP gene family, bioinformation analysis, abiotic stresses, hormones

曹海艳, 张子彤, 孟子钰, 宋继策, 郝雪峰, 金竹萍. 谷子SiGeBP基因家族生物信息学及表达分析[J]. 生物技术通报, 2026, 42(10): 67-76.

CAO Hai-yan, ZHANG Zi-tong, MENG Zi-yu, SONG Ji-ce, HAO Xue-feng, JIN Zhu-ping. Bioinformatic and Expression Analysis of the SiGeBP Gene Family in Setaria italica[J]. Biotechnology Bulletin, 2026, 42(10): 67-76.

图/表 7

图1 SiGeBP基因家族染色体定位

Fig. 1 Chromosomal localization of SiGeBP gene family

图2 谷子、拟南芥、水稻GeBP蛋白的系统发育树

Fig. 2 Phylogenetic tree of GeBP proteins from Setaria italica, Arabidopsis thaliana and Oryza sativa

图3 SiGeBP蛋白保守基序（A）及功能结构域预测（B）

Fig. 3 Prediction of conserved motifs (A) and functional domain (B) of SiGeBP proteins

图4 谷子SiGeBP基因家族基因结构预测

Fig. 4 Prediction of gene structure of SiGeBP gene family in S. italica

图5 谷子SiGeBP基因家族的顺式作用元件分析

Fig. 5 Analysis of cis-acting elements of the SiGeBP gene family in S. italica

图6 SiGeBP基因家族在非生物胁迫下的表达模式分析*：在P<0.05水平差异显著，**：在P<0.01水平差异极显著，ns：差异不显著。下同

Fig. 6 Expression pattern analysis of the SiGeBP gene family under abiotic stresses*: Significant difference at the P<0.05 level. **: Highly significant difference at the P<0.01 level. ns: No significant difference. The same below

图7 SiGeBP基因家族在外源激素处理下的表达模式分析

Fig. 7 Expression pattern analysis of the SiGeBP gene family under exogenous hormone treatments

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