甘藍(lán)型油菜GPDH基因克隆及其生物信息學(xué)分析
發(fā)布時(shí)間：2018-10-30 20:24
【摘要】：為了進(jìn)一步研究甘藍(lán)型油菜GPDH基因,通過從擬南芥GPDH基因與甘藍(lán)型油菜的共線性分析發(fā)現(xiàn):擬南芥GPDH基因(At2g41540)在甘藍(lán)型油菜A基因組和C基因組中有4個(gè)拷貝,分別為:GSBRNA2T00132785001、GSBRNA2T00024258001、GSBRNA2T00058395001、GSBRNA2T00019118001。從Gen Bank分別下載了它們的DNA序列和c DNA序列,c DNA序列依次命名為GPDH1、GPDH2、GPDH3、GPDH4。根據(jù)序列信息設(shè)計(jì)了4對(duì)不同的引物,從甘藍(lán)型油菜湘油15號(hào)c DNA全長(zhǎng)序列中擴(kuò)增出了4條片段,分別命名為Bn GPDH1、Bn GPDH2、Bn GPDH3、Bn GPDH4。利用生物信息學(xué)軟件和在線系統(tǒng)進(jìn)行核苷酸序列分析和蛋白進(jìn)化分析。結(jié)果顯示:4條片段大小依次為1 395,1 395,1 389,1 536 bp。其中,Bn GPDH4翻譯成氨基酸時(shí)序列中間出現(xiàn)終止密碼子,不能合成有效蛋白。3個(gè)Bn GPDH蛋白的氨基酸數(shù)目為464,464和462個(gè),理論分子量為51.584 4~51.829 7 k Da,二級(jí)結(jié)構(gòu)α螺旋和無規(guī)則卷曲所占比例在42%左右,其次是延伸鏈所占比例約為15%。三者的跨膜結(jié)構(gòu)總體來說是相同的。3個(gè)蛋白都由保守結(jié)構(gòu)Gps A、NADB_Rossmann superfamily和NAD_Gly3P_dh_C superfamily組成,屬于GPDH超基因家族。同源建模分析表明3個(gè)蛋白均能適用甘油3磷酸脫氫酶(Glycerol-3-phosphate dehydrogenase,GPDH)模型。對(duì)其進(jìn)行亞細(xì)胞定位預(yù)測(cè)在細(xì)胞質(zhì)膜的概率為79.0%。從序列分析、核苷酸聚類、理化性質(zhì)預(yù)測(cè)、二級(jí)、三級(jí)結(jié)構(gòu)預(yù)測(cè)、亞細(xì)胞定位預(yù)測(cè)、氨基酸聚類分析得出結(jié)論,它們具有GPDH基因家族的特征,為甘藍(lán)型油菜GPDH基因家族中的成員。
[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 偽 -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.
【作者單位】： 湖南農(nóng)業(yè)大學(xué)作物基因工程湖南省重點(diǎn)實(shí)驗(yàn)室;
【基金】：國(guó)家“973”計(jì)劃項(xiàng)目(2015CB150200) 湖南省科技計(jì)劃項(xiàng)目(2014FJ1006-3)
【分類號(hào)】：S565.4
，
本文編號(hào)：2301079
[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 偽 -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.
【作者單位】： 湖南農(nóng)業(yè)大學(xué)作物基因工程湖南省重點(diǎn)實(shí)驗(yàn)室;
【基金】：國(guó)家“973”計(jì)劃項(xiàng)目(2015CB150200) 湖南省科技計(jì)劃項(xiàng)目(2014FJ1006-3)
【分類號(hào)】：S565.4
，
本文編號(hào)：2301079
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