Conservation, diversification and expansion of C2H2 zinc finger proteins in the Arabidopsis thaliana genome.
Conservation, diversification and expansion of C2H2 zinc finger proteins in the Arabidopsis thaliana genome.
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DOI：
10.1186/1471-2164-5-39
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发表时间：
2004-07-05
期刊：
影响因子：
4.4
通讯作者：
Böhm S
中科院分区：
文献类型：
--
作者：
Englbrecht CC;Schoof H;Böhm S
经典的C2H2锌指结构域具有广泛的功能，可以与DNA、RNA和蛋白质结合。锌指蛋白在几种真核生物中的比较表明，锌指蛋白存在着许多谱系特异性的多样化和扩增。尽管携带经典C2H2锌指基序的植物蛋白的数量正在增加，但对植物基因组锌指基因集的系统分类和分析仍然缺乏。通过硅分析，我们在拟南芥中发现了176个锌指蛋白，从而构成了该植物中最丰富的推定转录调节因子家族。33种拟南螺旋藻锌指蛋白中只有少数在其他真核生物中保守。相比之下，这些蛋白质中的大多数（81%）是植物特异性的。它们起源于广泛的重复事件，形成了扩展的家族。我们将这些蛋白质分配到不同的亚群和家族中，并特别关注了两个最大的、进化上最年轻的家族（A1和C1），它们被认为主要参与转录调控。新定义的家族A1（24个成员）包括串联排列锌指结构域的蛋白质。家族C1（64个成员），早前被描述为牵牛epf家族，由一个分离的或两到五个分散的指状蛋白和锌指螺旋中一个基本不变的QALGGH基序列组成。根据这些螺旋中的氨基酸模式，我们可以描述C1锌指结构域中普遍存在的五种不同的特征序列。我们还发现了一些非手指结构域在这些家族中是保守的。我们对拟南芥中少数进化上保守的锌指蛋白的分析表明，它们中的大多数可能参与了RNA代谢和染色质重塑等古老的生物过程。相比之下，大多数独特的拟南芥锌指蛋白已知或被认为参与转录调控。与动物锌指蛋白相比，它们在锌指序列和锌指排列特征上表现出显著差异。我们在家族C1中发现的不同锌指螺旋特征可能对序列特异性DNA识别具有重要意义，并允许对该家族成员的进化进行推断。
The classical C2H2 zinc finger domain is involved in a wide range of functions and can bind to DNA, RNA and proteins. The comparison of zinc finger proteins in several eukaryotes has shown that there is a lot of lineage specific diversification and expansion. Although the number of characterized plant proteins that carry the classical C2H2 zinc finger motifs is growing, a systematic classification and analysis of a plant genome zinc finger gene set is lacking. We found through in silico analysis 176 zinc finger proteins in Arabidopsis thaliana that hence constitute the most abundant family of putative transcriptional regulators in this plant. Only a minority of 33 A. thaliana zinc finger proteins are conserved in other eukaryotes. In contrast, the majority of these proteins (81%) are plant specific. They are derived from extensive duplication events and form expanded families. We assigned the proteins to different subgroups and families and focused specifically on the two largest and evolutionarily youngest families (A1 and C1) that are suggested to be primarily involved in transcriptional regulation. The newly defined family A1 (24 members) comprises proteins with tandemly arranged zinc finger domains. Family C1 (64 members), earlier described as the EPF-family in Petunia, comprises proteins with one isolated or two to five dispersed fingers and a mostly invariant QALGGH motif in the zinc finger helices. Based on the amino acid pattern in these helices we could describe five different signature sequences prevalent in C1 zinc finger domains. We also found a number of non-finger domains that are conserved in these families. Our analysis of the few evolutionarily conserved zinc finger proteins of A. thaliana suggests that most of them could be involved in ancient biological processes like RNA metabolism and chromatin-remodeling. In contrast, the majority of the unique A. thaliana zinc finger proteins are known or suggested to be involved in transcriptional regulation. They exhibit remarkable differences in the features of their zinc finger sequences and zinc finger arrangements compared to animal zinc finger proteins. The different zinc finger helix signatures we found in family C1 may have important implications for the sequence specific DNA recognition and allow inferences about the evolution of the members in this family.
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