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中国农学通报

中国农学通报 ›› 2011, Vol. 27 ›› Issue (25): 193-199.

所属专题： 生物技术； 园艺

• 林学 园艺 园林 • 上一篇    下一篇

葡萄AMT基因家族生物信息学分析

丛郁 杨顺瑛 宋志忠 郝东利 苏彦华   

  • 收稿日期:2011-04-11 修回日期:2011-04-29 出版日期:2011-10-05 发布日期:2011-10-05
  • 基金资助:

    国家973项目;国家转基因重大专项课题;中国博士后基金项目

Bioinformatics Analysis of AMT Protein Family in Grape

  • Received:2011-04-11 Revised:2011-04-29 Online:2011-10-05 Published:2011-10-05

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摘要：

运用隐马尔柯夫模型，对葡萄的蛋白质数据库进行搜索，共找到12个AMT蛋白同源序列。利用生物信息学方法对葡萄12个AMT基因进行染色体定位，进而预测它们的氨基酸组成成分、理化性质以及二级结构，并分析葡萄与拟南芥、水稻和杨树AMT基因家族之间的联系。基因组定位结果发现12个AMT基因分布在6条染色体上，较拟南芥AMT基因在染色体上的分布更为集中。12个葡萄AMT蛋白序列可分成2个亚族，AMT1亚族有3个成员，其余为AMT2亚族成员。本研究发现不同成员间氨基酸数目、氨基酸序列间的疏水性存在一定的差异；二级结构预测结果显示，12个AMT氨基酸序列以α-螺旋和无规则卷曲为主要组成部分。基因结构分析表明，仅有2个葡萄AMT基因家族成员不含内含子，其余10个AMT基因含有1~4个内含子。对葡萄AMT蛋白的亚细胞定位分析表明：12个VvAMT均定位于膜结构上。对获得的12个葡萄AMT基因进行EST分析，只有5个有对应的EST序列，而仅有2个有相应的电子表达谱。

关键词: 白头翁素, 白头翁素, 轮状病毒, 大肠杆菌, 腹泻, 小鼠肠道, 超微结构

Abstract:

12 AMT proteins were identified in grape genome by searching the protein database using Hidden Markov model (HMM) scan strategy. Using bioinformatics methods, genome localizations of 12 VvAMTs were analyzed firstly, and then predicted their amino acid composition, physical and chemical characteristics, as well as secondary structures. Meanwhile the relation of AMT gene family between Vitis vinifera, Arabidopsis thaliana, Oryza sativa and Populus trichocarpa was assayed. Genetic mapping of AMT genome localization found that they could be distributed on six chromosomes, which locations were more focus than their in Arabidopsis thaliana. 12 VvAMTs sequences could be divided into two sub-families, AMT1 sub-family had three members, and the rest belonged to AMT2 sub-family. The research still found that the amino acid number and sequence hydrophobic in 12 members of AMT gene family presented some differences. Furthermore, the main composition of 12 amino acid sequences were alpha helix and random coil via secondary structure predicted. Structural analysis of extrons and introns showed that only two members of VvAMT family had no intron, others had one, two, three or four introns. Protein subcellular localization analysis showed that all members of VvAMT were located in the membrane structure. EST analysis of VvAMT displayed that only five members had corresponding EST sequences, and only two members among them had a corresponding electronic expression profiles.