拟南芥和水稻金属蛋白酶ftsH基因家族的基因组比较分析

Genome-wide comparative analysis of the metalloprotease ftsH gene families between Arabidopsis thaliana and rice

摘要:

FtsH (Filamentation temperature-sensitive H)是一种广泛存在于原核生物和真核生物中的ATP依赖型金属蛋白酶。同源性分析表明, 在拟南芥和水稻基因组中分别有12个和9个ftsH基因。ftsH基因在染色体上的分布有明显的偏爱性, 如拟南芥的1、2、5号染色体和水稻的1、5号染色体。亚细胞定位分析表明, 所有FtsH蛋白均定位于叶绿体或线粒体中。系统进化分析表明, 21个FtsH蛋白成员可分为8个类群, 其中AtFtsH12在水稻中没有发现种间同源物。每个类群成员的蛋白序列高度保守, 种内同源物显示出大于80%的相似性, 而种间同源物的相似性也大于70%。类群内的同源基因并非平行进化产生的, 拟南芥基因组中进化出AtftsH1/5、AtftsH2/8、AtftsH3/10和AtftsH7/9共4个同源基因对, 而水稻基因组中只有OsftsH3/8和OsftsH4/5 两个同源基因对。每一类群中的成员在基因外显子-内含子边界分布上表现出高度保守性, 在蛋白功能结构域的可变残基上具有偏爱性, 而内含子在碱基组成和序列长度上表现出广泛的变异。拟南芥和水稻ftsH基因家族的比较分析为其他物种ftsH基因的特性和功能研究奠定了基础。

Abstract:

Filamentation temperature-sensitive H (FtsH) is an ATP-dependent metalloprotease in prokaryotes and eukaryotes. Homology-based analysis was applied to determine 12 ftsH genes in Arabidopsis genome and 9 members in rice genome. Distribution of these ftsH genes on each chromosome displayed a clear preference for some chromosomes such as chromosome 1, 2, 5 of Arabidopsis and chromosome 1, 5 of rice. All 21 FtsH proteins were subcellularly targeted to chloroplast or mitochondria. These members could be phylogenetically assorted as eight groups, of which no ortholog of AtFtsH12 in rice was detected. Paralogs in each group shared similarity higher than 80% and orthologs higher than 70%. This strongly indicated that the members from single group were descended from a common ancestral gene. Four pairs of paralogs, AtftsH1/5, AtftsH2/8, AtftsH7/9 and AtftsH3/10 were found in Arabidopsis genome. However, only two pairs of ftsH paralogs, OsftsH3/8 and OsftsH4/5, resided in rice genome. The highly homologous members in each group performed striking conservation of exon-intron boundaries and preference for the variable residues in function domains. By contrast, there was significant difference in base composition and sequence length of introns. The comparative analysis of the ftsH gene families of Arabidopsis and rice provided the basis for characteristic and function research of ftsH genes in other plants.