毛果杨HMA基因家族的生物信息学分析

王晓桐, 李昊阳, 徐吉臣*
北京林业大学林木育种国家工程实验室, 北京100083

通信作者:徐吉臣;E-mail: jcxu282@sina.com;Tel: 010-62336628

摘 要:

重金属转运ATP酶(heavy metal transporting ATPase, HMA)是一种通过水解ATP跨膜运送重金属阳离子的转运蛋白, 属于P-ATPase家族中一个亚类。不同HMA蛋白对重金属离子的转运具有选择性, 在植物修复重金属污染土壤方面起着重要作用。依据毛果杨全基因组测序的结果, 以及HMA基因蛋白的序列和功能特征, 从毛果杨基因组中鉴定了13个HMA基因家族成员, 分属于Zn亚类(Zn2+/Co2+/Cd2+/Pb2+P1B-ATPase)和Cu亚类(Cu+/Ag+P1B-ATPase)两个亚家族, 主要分布于1、3号染色体上。生物信息学分析表明, 毛果杨HMA基因的氨基酸序列一致性介于21.3%~89.3%, 且具有保守的基序CPC、HP、DKTGT、TGEx、GDG、PxD和CxxC等。蛋白理化特征分析显示, 多数毛果杨HMA蛋白稍偏酸性, 结构稳定性较好, 蛋白脂溶指数高, 稍具疏水性。密码子偏好性分析显示, 毛果杨HMA蛋白14个氨基酸中存在16个高频密码子, 另有1个终止密码子为高频密码子, 显示出毛果杨的种属特征。研究结果展示了毛果杨HMA基因家族的基本信息和特点, 为深入研究毛果杨HMA基因的功能搭建了基础平台。

关键词:杨树; 重金属转运ATP酶; 植物修复; 基因家族; 生物信息学<

收稿:2014-02-12   修定:2014-04-15

资助:北京市自然科学基金项目(5122019)。

Bioinformatics Analysis of the Heavy Metal Transporting ATPase Gene Family in Poplar Genome

WANG Xiao-Tong, LI Hao-Yang, XU Ji-Chen*
National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China

Corresponding author: XU Ji-Chen; E-mail: jcxu282@sina.com; Tel: 010-62336628

Abstract:

Heavy metal transporting ATPases (HMA) is a kind of protein transporting the heavy metal ions across membranes through ATP hydrolysis, which belong to the large P-type ATPase family. Each HMA protein transports the heavy metal ions selectively. They might play an important role in phytoremediation for contaminated soil. Based on the sequence and function characteristics of HMA, 13 HMA genes members were identified from the sequence database of Populus trichocarpa, those were classified into Zn (Zn2+/Co2+/Cd2+/Pb2+) and Cu (Cu+/Ag+) subfamily, respectively. Most of the genes were anchored on the chromosome 1 and 3. Sequence alignment showed that the identity of amino acid among HMA genes is between 21.3% and 89.3%, also with several conserved motifs such as CPC, HP, DKTGT, TGEx, GDG, PxD and CxxC. Most of HMA proteins have a little acidic and hydrophobic, stable space structure and higher aliphatic index. The codon usage of HMA genes in Populus trichocarpa also displayed the feature in space, which having 16 codons for 14 amino acids and 1 codon for termination as the high-frequency codons. The results here revealed the basic information of poplar HMA family that would be a well platform for the further gene function study in future.

Key words: poplus; heavy metal transporting ATPases (HMA); phytoremediation; gene family; bioinformatics

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