十字花科植物SOM基因的鉴定及分析

Identification and Analysis of SOM Gene of Brassicaceae

SOMNUS(SOM)基因编码一个CCCH型锌指蛋白,是PHYTOCHROME INTERACTING FACTOR3-LIKE5(PIL5)下游的关键负调控因子,参与调控种子的萌发。本研究从十字花科12个物种的全基因组数据库中鉴定了17个SOM基因,其中芸薹属物种白菜、甘蓝和甘蓝型油菜中均包含2个及以上的SOM基因。预测这17个SOM蛋白的等电点和分子量,结果显示La SOM蛋白明显不同于其他的SOM蛋白。氨基酸序列比对显示La SOM蛋白缺失了部分氨基酸序列,但所有的SOM蛋白均包含保守的3个锌指基序,其中2个CCCH型的锌指基序。对这些SOM基因的组织结构进行分析,结果显示:只有La SOM基因存在一个内含子,其他SOM基因均没有内含子,暗示La SOM基因在进化过程中获得了内含子,并导致La SOM蛋白缺失部分序列。启动子分析显示每个SOM基因起始密码子上游1 000 bp的启动子中至少有2个E-box元件。白菜RNA-seq数据显示Br SOM1在根、茎、叶、花和角果中均不表达,仅在胚胎发育阶段的早期子叶胚和成熟胚中有表达。而Br SOM2在根、茎、叶和花中均有表达,Br SOM2在胚胎发育阶段中的表达类似于Br SOM1,只是在表达水平上比Br SOM1低。研究结果可为深入研究SOM基因奠定基础。

SOMNUS(SOM) gene encodes a CCCH-type zinc finger protein, which is a key downstream negative regulator of PHYTOCHROMEINTERACTING FACTOR3-LIKE5(PIL5) and involves in the regulation of seed germination. This study identified 17 SOM genes from the genomes of 12 Brassicaceae species. Each of Brassica rapa, B. oleracea and B. napus from Brassica had at least 2 SOM genes. Molecular weight(MW) and isoelectric point(p I) of the 17 SOM proteins were predicted by bioinformatics, showing that La SOM protein was significantly different from the other SOM proteins both in molecular weight and isoelectric point. Amino acid sequence alignment showed that La SOM protein missed a part of amino acid sequence. However, all of the 17 SOM proteins had three conserved zinc finger motifs, including 2 CCCH-type zinc finger motifs. Gene structure analysis of 17 SOM genes indicated that one intron existed in La SOM gene, while, no intron was present in the rest SOM genes.The result suggested that the La SOM gene could gain one intron during the evolutionary process, causing lack of partial amino acid sequence in La SOM protein. Promoter sequence analysis demonstrated that each SOM gene had at least 2 E-box elements in promoter of 1 000 bp upstream of initiation codon. Based on RNA-seq data of B. rapa,Br SOM1 was not expressed in roots, stems, leaves, flowers and siliques, but in early cotyledon embryo and matureembryo of the embryonic stage. However, Br SOM2 was expressed in roots, stems, leaves and flowers. In embryonic development, the expression profile of Br SOM2 was similar to that of Br SOM1, while, Br SOM2 showed lower expression level than Br SOM1. The results can lay the foundation for further research on SOM genes.