2019年10月17日 星期四
葡萄Actin基因家族的鉴定及进化和表达分析
Identification, evolution and expression analyses of Actin gene family of Vitis vinifera
2017年 第26卷 第3期 页码[1-10]    下载全文[3.1MB]  
摘要

采用生物信息学方法从葡萄(Vitis vinifera Linn.)全基因组中鉴定Actin基因家族,并对各基因的染色体定位和结构特征,编码蛋白质的理化性质、亚细胞定位、二级结构、三级结构和系统进化,以及不同组织的基因表达进行研究。结果表明:葡萄Actin基因家族16个基因分布在12条染色体上。16个基因的结构特征及其编码蛋白质的理化性质差异较大。16个基因的长度及其内含子总长度的变化范围较大,编码序列(CDS)和外显子总长度的变化范围较小。除登录号GSVIVG01008254001和GSVIVG01014035001的基因外,其他14个基因的GC含量均低于其CDS的GC含量。除登录号GSVIVG01008254001的基因外,其他15个基因编码的蛋白质的理论相对分子质量为12 534.54~82 612.33,理论等电点为pI 4.92~pI 9.13。16个基因编码蛋白质的消光系数为14 105~73 645,脂肪族氨基酸指数为65.54~92.06,其中9个为稳定蛋白,7个为不稳定蛋白。除登录号GSVIVG01014035001的基因外,其他15个基因编码的蛋白质均为亲水性蛋白。登录号GSVIVG01016517001的基因编码的蛋白质定位于细胞质和细胞核,其他15个基因编码的蛋白质定位于细胞质。二级结构和三级结构显示:葡萄Actin基因家族16个基因编码的蛋白质均由α螺旋、无规则卷曲和延伸链构成,且总体以无规则卷曲为主。系统进化分析和不同组织的基因表达分析结果显示:与拟南芥〔Arabidopsis thaliana (Linn.) Heynh.〕相似,葡萄Actin基因家族16个基因编码的蛋白质分为3个亚家族,ClassⅡ亚家族(营养型)包括登录号GSVIVG01003099001和GSVIVG01026580001的基因编码的蛋白质,这2个基因在所有组织中的表达均较高;ClassⅢ亚家族(生殖型)包括登录号GSVIVG01033494001、GSVIVG01024980001和GSVIVG01016550001的基因编码的蛋白质,这3个基因在花粉、雄蕊和花中的表达均较高;ClassⅠ亚家族包括其他11个基因编码的蛋白质,这11个基因在各组织中的表达总体上较低。研究结果显示:葡萄Actin基因家族的表达具有组织特异性。

Abstract

 Actin gene family was identified from the whole genome of Vitis vinifera Linn. by bioinformatics method, and chromosome localization and structural characteristics of each gene, physicochemical property, subcellular localization, secondary structure, tertiary structure and phylogeny of proteins encoded, and gene expression in different tissues were researched. The results show that sixteen genes in Actin gene family of V. vinifera are distributed on twelve chromosomes. There are great differences in structural characteristics of sixteen genes and physicochemical property of their proteins encoded. Variation ranges of length of sixteen genes and their total length of introns are large, and those of total length of coding sequences (CDSs) and exons are small. Except genes with accession number of GSVIVG01008254001 and GSVIVG01014035001, GC contents in other fourteen genes are lower than those in their CDSs. Except gene with accession number of GSVIVG01008254001, theoretical relative molecular mass of proteins encoded by other fifteen genes is 12 534.54-82 612.33, and their theoretical isoelectric point is pI 4.92-pI 9.13. Extinction coefficient of proteins encoded by sixteen genes is 14 105-73 645, their aliphatic amino acid index is 65.54-92.06, in which, there are nine stable proteins and seven instable proteins. Except gene with accession number of GSVIVG01014035001, proteins encoded by other fifteen genes are hydrophilic proteins. Protein encoded by gene with accession number of GSVIVG01016517001 is located in cytoplasm and nucleus, and those encoded by other fifteen genes are located in cytoplasm. The secondary and tertiary structures show that proteins encoded by sixteen genes in Actin gene family of V. vinifera are composed with α helix, random coil and extended strand, and in general, random coil is the main component. Analysis results of phylogeny and gene expression in different tissues show that being similar to Arabidopsis thaliana (Linn.) Heynh., proteins encoded by sixteen genes in Actin gene family of V. vinifera can be divided into three subfamilies. Class Ⅱ subfamily (vegetative type) includes proteins encoded by genes with accession number of GSVIVG01003099001 and GSVIVG01026580001, and the expression of these two genes in all tissues is higher. Class Ⅲ subfamily (reproductive type) includes proteins encoded by genes with accession number of GSVIVG01033494001, GSVIVG01024980001 and GSVIVG01016550001, and the expression of these three genes in pollen, stamen and flower is higher. Class Ⅰ subfamily includes proteins encoded by the rest of eleven genes, and the expression of these eleven genes in all tissues is generally low. The results of gene expression analysis show that there is tissue specificity in expression of Actin gene family of V. vinifera.
 

关键词葡萄; Actin基因家族; 系统进化; 基因表达
Key wordsVitis vinifera Linn.; Actin gene family; phylogeny; gene expression
作者崔力文, 郑婷, 张克坤, 张川, 上官凌飞, 房经贵
所在单位南京农业大学园艺学院, 江苏 南京 210095
点击量470
基金项目国家自然科学基金资助项目(31672131)