Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada.
Ann Bot. 2011 May;107(7):1141-57. doi: 10.1093/aob/mcr034. Epub 2011 Mar 7.
The cell cycle is controlled by cyclin-dependent kinases (CDKs), and CDK inhibitors are major regulators of their activities. The ICK/KRP family of CDK inhibitors has been reported in several plants, with seven members in arabidopsis; however, the phylogenetic relationship among members in different species is unknown. Also, there is a need to understand how these genes and proteins are regulated. Furthermore, little information is available on the functional differences among ICK/KRP family members.
We searched publicly available databases and identified over 120 unique ICK/KRP protein sequences from more than 60 plant species. Phylogenetic analysis was performed using 101 full-length sequences from 40 species and intron-exon organization of ICK/KRP genes in model species. Conserved sequences and motifs were analysed using ICK/KRP protein sequences from arabidopsis (Arabidopsis thaliana), rice (Oryza sativa) and poplar (Populus trichocarpa). In addition, gene expression was examined using microarray data from arabidopsis, rice and poplar, and further analysed by RT-PCR for arabidopsis.
Phylogenetic analysis showed that plant ICK/KRP proteins can be grouped into three major classes. Whereas the C-class contains sequences from dicotyledons, monocotyledons and gymnosperms, the A- and B-classes contain only sequences from dicotyledons or monocotyledons, respectively, suggesting that the A- and B-classes might have evolved from the C-class. This classification is also supported by exon-intron organization. Genes in the A- and B- classes have four exons, whereas genes in the C-class have only three exons. Analysis of sequences from arabidopsis, rice and poplar identified conserved sequence motifs, some of which had not been described previously, and putative functional sites. The presence of conserved motifs in different family members is consistent with the classification. In addition, gene expression analysis showed preferential expression of ICK/KRP genes in certain tissues. A model has been proposed for the evolution of this gene family in plants.
细胞周期受细胞周期蛋白依赖性激酶（CDKs）的调控，而 CDK 抑制剂是其活性的主要调节剂。已经在几种植物中报道了 CDK 抑制剂的 ICK/KRP 家族，在拟南芥中有 7 个成员；然而，不同物种成员之间的系统发育关系尚不清楚。此外，需要了解这些基因和蛋白质是如何被调控的。此外，关于 ICK/KRP 家族成员之间的功能差异的信息很少。
我们搜索了公开可用的数据库，从 60 多种植物中鉴定出了 120 多个独特的 ICK/KRP 蛋白序列。使用来自 40 个物种的 101 个全长序列和模型物种中 ICK/KRP 基因的内含子-外显子组织进行了系统发育分析。使用来自拟南芥（Arabidopsis thaliana）、水稻（Oryza sativa）和杨树（Populus trichocarpa）的 ICK/KRP 蛋白序列分析了保守序列和基序。此外，使用来自拟南芥、水稻和杨树的微阵列数据检查了基因表达，并进一步通过 RT-PCR 对拟南芥进行了分析。
系统发育分析表明，植物 ICK/KRP 蛋白可以分为三大类。C 类包含来自双子叶植物、单子叶植物和裸子植物的序列，而 A 类和 B 类仅包含来自双子叶植物或单子叶植物的序列，这表明 A 类和 B 类可能是从 C 类进化而来的。这种分类也得到了内含子-外显子组织的支持。A 类和 B 类的基因有四个外显子，而 C 类的基因只有三个外显子。对来自拟南芥、水稻和杨树的序列分析鉴定了保守的序列基序，其中一些以前没有描述过，还有一些假定的功能位点。不同家族成员中保守基序的存在与分类一致。此外，基因表达分析表明，ICK/KRP 基因在某些组织中优先表达。提出了一个模型，用于解释该基因家族在植物中的进化。
