茶树ZF-HD转录因子基因家族的鉴定及表达分析

Identification and expression analysis of ZF-HD transcription factor gene family in Camellia sinensis

  • 摘要: 【目的】搜索鉴定茶树ZF-HD(Zinc finger homeodomain)转录因子基因家族成员,并对其进行生物信息学分析及在不同组织及非生物胁迫和激素处理下的表达模式,为茶树ZF-HD基因家族的功能研究及茶树遗传性状改良提供理论依据。【方法】通过隐马尔可夫模型预测和序列比对从茶树基因组中筛选鉴定出茶树ZF-HD基因家族成员,利用在线生物信息学分析软件对其基因结构、启动子元件,以及编码蛋白的理化性质、氨基酸序列、结构特征、进化关系等进行预测分析,并基于转录组测序(RNA-Seq)数据分析其在不同组织及在干旱胁迫、盐胁迫和茉莉酸甲酯(MeJA)处理下的表达模式。【结果】从茶树基因组中鉴定出17个ZF-HD基因家族成员(CsZHD1~CsZHD17),其编码区(CDS)序列长度为369~2187 bp,编码122~728个氨基酸残基,蛋白分子量13.51~80.42 kD,理论等电点为6.09~9.19,均属于亲水性不稳定蛋白,蛋白二级结构均由β-转角、延伸链、α-螺旋和无规则卷曲构成。除CsZHD2、CsZHD5和CsZHD7蛋白定位于细胞质,CsZHD9蛋白定位于细胞外,其他13个蛋白均定位于细胞核。仅CsZHD2CsZHD7CsZHD9CsZHD10CsZHD12基因含外显子和内含子,其他12个CsZHDs基因均无内含子。除CsZHD7蛋白具有2个ZF-HD_dimer结构域外,其他16个蛋白均具有1个ZF-HD_dimer结构域。CsZHD1~CsZHD17蛋白具有2~5个保守基序(motif),其中motif 1和motif 3为共有的保守基序。茶树ZF-HD家族蛋白可分为5个亚族(ZHDⅠ、ZHDⅡ、ZHDⅢ、ZHDⅣ和MIF),较拟南芥少了ZHDⅤ亚族。除CsZHD2CsZHD12CsZHD17基因在8个组织中不表达或表达量极低外,其他14个CsZHDs基因在8个组织中呈差异性表达;除CsZHD2CsZHD12CsZHD17基因外,其他15个CsZHDs基因在顶芽或花中表达量较高。在干旱胁迫和盐胁迫处理下,除CsZHD1CsZHD2CsZHD5CsZHD12CsZHD14CsZHD17基因的表达量始终处于较低水平外,其他CsZHDs基因均呈不同的变化趋势;在MeJA处理下,除CsZHD2CsZHD5CsZHD12基因表达量极低外,多数CsZHDs基因呈下调表达的趋势。【结论】从茶树基因组中鉴定出17个ZH-HD基因家族成员,其编码蛋白具有保守的锌指结构域和同源异型盒结构域;茶树与拟南芥ZH-HD基因家族相比缺少ZHDⅤ亚族;CsZHDs基因的表达具有组织特异性,且大多数成员的表达受非生物胁迫和MeJA的影响。

     

    Abstract: 【Objective】Identification and analysis of ZF-HD(zinc finger homeodomain) gene family members by bioinformatics methods and detection of their expression patterns under different tissues, abiotic stresses and hormone induction were conducted, which laid theoretical basis for the functional study of tea plant ZF-HD(ZFD) family gene and improvement of tea genetic traits.【Method】ZF-HD gene family members of tea plant were identified from tea plant genome by HMMER program prediction and sequence alignment. A variety of bioinformatics analysis tools were used to analyze gene structure, promoter elements, and the physical and chemical properties, amino acid sequences, structural characteristics, evolutionary relationships, of the encoded protein. Based on RNA-Seq data, the expression patterns of members of the ZF-HD gene family in different tissues under drought stress, salt stress, and methyl jasmonate(MeJA) were analyzed.【Result】Seventeen ZF-HD gene family members(CsZHD1-CsZHD17) were identified from tea plant genome database. Coding region sequence(CDS) length was 369-2187 bp, encoding 122-728 amino acid residues. CsZHD encoded proteins with molecular weights ranging from 13.51 to 80.42 kD and theoretical isoelectric points of 6.09 to 9.19, which were all hydrophilic and unstable proteins. The secondary structure consisted of beta-turn, extended strand, alpha-helix and random-coil state. The results of subcellular localization showed that except CsZHD2, CsZHD5, and CsZHD7 proteins were localized in the cytoplasmic and CsZHD9 was localized in the extracellular, all other CsZHD proteins were localized in the nuclears. Only CsZHD2, CsZHD7, CsZHD9, CsZHD10 and CsZHD12 contained exons and introns, and the other 12 CsZHDs had no introns. CsZHD7 protein had two ZF-HD_dimer domains and the other 16 proteins had one ZF-HD_dimer domain. CsZHD1-CsZHD17 had 2-5 conserved motifs, and motif 1 and motif 3 were shared conserved motifs in CsZHDs. Tea ZH-HD family proteins could be divided into 5 subfamilies(ZHDⅠ, ZHDⅡ, ZHDⅢ, ZHDⅣand MIF), but the tea plant lacked the ZHDⅤsubfamily compared to Arabidopsis thaliana. The expression profile of the ZHD genes using RNA-Seq data showed that except for CsZHD2, CsZHD12, and CsZHD17, which were not expressed in these eight tissues or the expression levels were low, other CsZHDs genes were differentially expressed in the 8 tissues. The expression levels of CsZHD1, CsZHD2, CsZHD5, CsZHD12, CsZHD14 and CsZHD17 were always at a low level, and other CsZHDs genes showed different expressional trends under drought and salt stresses. Under MeJA treatment, most CsZHDs genes showed a downward-regulated expression except for the extremely low expression of CsZHD2, CsZHD5 and CsZHD12.【Conclusion】Seventeen members of the ZH-HD gene family were identified from the tea tree genome, and the encoded proteins have conserved zinc finger domain and homotype box domain. Tea trees lack ZHDⅤsubgroups compared to the A. thaliana ZH-HD gene family;the expression of the CsZHDs gene is tissue-specific, and most members are affected by ambiotic stress and MeJA.

     

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