葡萄基因组中 KUP 蛋白的生物信息学分析(英文)  

In silico Analyses of KUP Proteins Based on Grape Genomic Data

作　　者：宋志忠[1,2] 丛郁[1] 韩蕾[1,2] 王莉[1,2] 苏彦华[1] 

机构地区：[1]土壤与农业可持续发展国家重点实验室,中国科学院南京土壤研究所,南京210008 [2]中国科学院研究生院,北京100049

出　　处：《基因组学与应用生物学》2011年第6期728-737,共10页Genomics and Applied Biology

基　　金：the National Special Program of Transgenic Plants Research and Development (2009ZX080-09-129B);National Natural Science Foundation of China (30971857)

摘　　要：植物钾（K＋）转运体蛋白在K＋的跨膜运输中起重要作用，进而维持植物体正常生长和代谢活动。本研究中，通过隐马尔科夫模型（HMM）和葡萄蛋白质库搜索，共找到18个葡萄钾转运体蛋白（VvKUPs）。利用生物信息学方法，我们对葡萄家族12条KUP蛋白序列的系统发生和KUP基因组定位进行分析，然后对其氨基酸组成成分、理化性质以及二级结构进行预测和分析，同时还分析了葡萄与拟南芥、水稻和杨树的K卯基因家族之间的联系。基因组定位结果发现其分布在至少9条染色体上。二级结构预测结果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；仅一螺旋和无规则卷曲为主要二级结构组成部分。基因结构分析表明，KUP基因家族成员分别含有7～10个内含子。葡萄KUP蛋白的亚细胞定位分析表明VvKUP主要定位于膜结构上。电子表达图谱分析结果表明：12条K卯基因有对应的EST序列，其中的11条KUP有相应的电子表达谱，并主要在花、果实、花序和花蕾等组织部位表达。Potassium （K＋） transporter plays an important role in the K＋ transmembrane transport of plants to maintain normal growth and metabolic activities. In this paper 18 potassium uptake proteins （VvKUPs） were identified from the genome of grape （Vitis vinifera, hereafter V. vinifera） by using Hidden Markov model （HMM） scanning strategy and searching the protein database. With the aids of in silico approaches of bioinformatics, we conducted phylogenic analysis and genomic localization for the selected 12 KUP proteins, and analyzed their amino acid composition, physical and chemical characteristics as well as secondary structure prediction. Moreover, we also predicted the evolutionary relationships of KUP gene families derived from grape （V. vinifera）, Arabidopsis （A. thaliana）, rice （Oryza sativa） and poplar （Populus trichocarpa）. The results of genomic localization indicated that KUPs might be preferable distribution and scatter on at least 9 chromosomes. Secondary structure simulations revealed that hydrophobic amino acid sequences varied among the different VvKUPs and the dominant patterns were predicted to alpha helix and random coil. ORF structure analysis showed that the selected VvKUPs had variable numbers of introns from seven to ten, respectively, while subcellular localization of these proteins indicated that members of VvAMT mainly located in the plasma membrane. In silieo expression analyses showed that the 12 VvKUPs had their EST sequences and 11 VvKUPs of them had in silico expression profiles, that showed the genes possible expressed in flower, fruit, inflorescence, and bud.

关 键 词：葡萄 K+转运体 生物信息学分析 

分 类 号：S663.1[农业科学—果树学] Q943[农业科学—园艺学]