甘蓝型油菜GPDH基因克隆及其生物信息学分析

发布时间：2018-10-30 20:24

【摘要】：为了进一步研究甘蓝型油菜GPDH基因,通过从拟南芥GPDH基因与甘蓝型油菜的共线性分析发现:拟南芥GPDH基因(At2g41540)在甘蓝型油菜A基因组和C基因组中有4个拷贝,分别为:GSBRNA2T00132785001、GSBRNA2T00024258001、GSBRNA2T00058395001、GSBRNA2T00019118001。从Gen Bank分别下载了它们的DNA序列和c DNA序列,c DNA序列依次命名为GPDH1、GPDH2、GPDH3、GPDH4。根据序列信息设计了4对不同的引物,从甘蓝型油菜湘油15号c DNA全长序列中扩增出了4条片段,分别命名为Bn GPDH1、Bn GPDH2、Bn GPDH3、Bn GPDH4。利用生物信息学软件和在线系统进行核苷酸序列分析和蛋白进化分析。结果显示:4条片段大小依次为1 395,1 395,1 389,1 536 bp。其中,Bn GPDH4翻译成氨基酸时序列中间出现终止密码子,不能合成有效蛋白。3个Bn GPDH蛋白的氨基酸数目为464,464和462个,理论分子量为51.584 4~51.829 7 k Da,二级结构α螺旋和无规则卷曲所占比例在42%左右,其次是延伸链所占比例约为15%。三者的跨膜结构总体来说是相同的。3个蛋白都由保守结构Gps A、NADB_Rossmann superfamily和NAD_Gly3P_dh_C superfamily组成,属于GPDH超基因家族。同源建模分析表明3个蛋白均能适用甘油3磷酸脱氢酶(Glycerol-3-phosphate dehydrogenase,GPDH)模型。对其进行亚细胞定位预测在细胞质膜的概率为79.0%。从序列分析、核苷酸聚类、理化性质预测、二级、三级结构预测、亚细胞定位预测、氨基酸聚类分析得出结论,它们具有GPDH基因家族的特征,为甘蓝型油菜GPDH基因家族中的成员。
[Abstract]:In order to further study the GPDH gene of Brassica napus, the co-linear analysis of Arabidopsis GPDH gene and Brassica napus showed that the GPDH gene (At2g41540) of Arabidopsis thaliana had four copies in the genome A and C of Brassica napus, which were GSBRNA2T00132785001, respectively. GSBRNA2T00024258001,GSBRNA2T00058395001,GSBRNA2T00019118001. Their DNA sequence and c DNA sequence, c DNA sequence are downloaded from Gen Bank and named GPDH1,GPDH2,GPDH3,GPDH4. in turn According to the sequence information, four pairs of primers were designed and four fragments were amplified from the full-length sequence of Hunan oil 15 c DNA in Brassica napus, named Bn GPDH1,Bn GPDH2,Bn GPDH3,Bn GPDH4.. Nucleotide sequence analysis and protein evolution analysis were performed using bioinformatics software and online system. The results showed that the size of the four fragments was 1 395 bp.. When Bn GPDH4 was translated into amino acids, terminating codon appeared in the middle of the sequence and could not synthesize effective protein. The number of amino acids of three Bn GPDH proteins was 464464 and 462, and the theoretical molecular weight was 51.584 4 ~ 51.829 7 k Da,. The proportion of secondary structure 伪 -helix and irregular crimp is about 42%, followed by the proportion of extended chain is about 15%. The transmembrane structure of the three proteins is the same in general, and the three proteins are composed of conserved Gps superfamily and NAD_Gly3P_dh_C superfamily, which belong to the GPDH supergene family. Homology modeling analysis showed that the three proteins were suitable for glycerol 3 phosphate dehydrogenase (Glycerol-3-phosphate dehydrogenase,GPDH) model. The probability of subcellular localization in cytoplasmic membrane was 79.0%. From sequence analysis, nucleotide clustering, physicochemical properties prediction, secondary and tertiary structure prediction, subcellular localization prediction and amino acid cluster analysis, it is concluded that they possess the characteristics of GPDH gene family. It is a member of GPDH gene family in Brassica napus L.
【作者单位】： 湖南农业大学作物基因工程湖南省重点实验室;
【基金】：国家“973”计划项目(2015CB150200) 湖南省科技计划项目(2014FJ1006-3)
【分类号】：S565.4
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本文编号：2301079