Phylogenetic analysis and classification of the Brassica rapa SET-domain protein family.
Phylogenetic analysis and classification of the Brassica rapa SET-domain protein family.
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甘蓝SET结构域蛋白家族的系统发育分析和分类
DOI：
10.1186/1471-2229-11-175
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发表时间：
2011-12-14
影响因子：
5.3
通讯作者：
Ruan Y
中科院分区：
文献类型：
--
作者：
Huang Y;Liu C;Shen WH;Ruan Y
SET(SU(Var)3-9，Enhancer-of-Zust，Trithorax)结构域是一个进化保守的序列，大约由130-150个氨基酸组成，是赖氨酸甲基转移酶(KMTs)的催化部位。KMT通过染色质的组蛋白甲基化发挥许多重要的生物学功能。组蛋白甲基化标记根据组蛋白类型(即H3或H4)、赖氨酸位置(例如H3K4、H3K9、H3K27、H3K36或H4K20)和添加的甲基数目(即ME1、ME2或ME3)的不同而有不同的解释。例如，H3K4me3和H3K36me3与转录激活有关，而H3K9me2和H3K27me3与基因沉默有关。KMT的底物特异性和活性由蛋白质的SET结构域和其他区域内的序列决定。在这里，我们从最近测序的白菜基因组中鉴定了49个SET-DOMAIN蛋白。我们进行了这些蛋白质的序列相似性和蛋白质结构域组织分析，以及来自双子叶拟南芥、单子叶水稻和短柄短臂以及绿藻Ostreorics tauri的SET结构域蛋白质。我们发现植物SET结构域蛋白可以分为6个不同的类别，即KMT1、KMT2、KMT3、KMT6、KMT7和S-ET。除了具有中断的SET结构域并可能参与非组蛋白蛋白甲基化的S-ET类外，其他类都具有组蛋白甲基转移酶的特征，表现出不同的底物特异性：H3K9的KMT1，H3K4的KMT2，H3K36的KMT3，H3K27的KMT6和H3K4的KMT7。我们还提出了一个连贯而合理的植物SET结构域蛋白命名法。通过对白菜型油菜和甘蓝型油菜集合域蛋白的序列相似性和同源性的比较，揭示了最近发生的一些KMT的基因重复事件。本研究首次对白菜型油菜的SET结构域KMT蛋白进行了鉴定。系统发育分析数据允许对植物和动物中的这一重要蛋白质家族进行连贯和合理的命名。本研究的结果将为其他植物的KMT命名提供基础，并有助于这些重要的表观遗传调控基因在十字花科作物中的功能鉴定。
The SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain is an evolutionarily conserved sequence of approximately 130-150 amino acids, and constitutes the catalytic site of lysine methyltransferases (KMTs). KMTs perform many crucial biological functions via histone methylation of chromatin. Histone methylation marks are interpreted differently depending on the histone type (i.e. H3 or H4), the lysine position (e.g. H3K4, H3K9, H3K27, H3K36 or H4K20) and the number of added methyl groups (i.e. me1, me2 or me3). For example, H3K4me3 and H3K36me3 are associated with transcriptional activation, but H3K9me2 and H3K27me3 are associated with gene silencing. The substrate specificity and activity of KMTs are determined by sequences within the SET domain and other regions of the protein. Here we identified 49 SET-domain proteins from the recently sequenced Brassica rapa genome. We performed sequence similarity and protein domain organization analysis of these proteins, along with the SET-domain proteins from the dicot Arabidopsis thaliana, the monocots Oryza sativa and Brachypodium distachyon, and the green alga Ostreococcus tauri. We showed that plant SET-domain proteins can be grouped into 6 distinct classes, namely KMT1, KMT2, KMT3, KMT6, KMT7 and S-ET. Apart from the S-ET class, which has an interrupted SET domain and may be involved in methylation of nonhistone proteins, the other classes have characteristics of histone methyltransferases exhibiting different substrate specificities: KMT1 for H3K9, KMT2 for H3K4, KMT3 for H3K36, KMT6 for H3K27 and KMT7 also for H3K4. We also propose a coherent and rational nomenclature for plant SET-domain proteins. Comparisons of sequence similarity and synteny of B. rapa and A. thaliana SET-domain proteins revealed recent gene duplication events for some KMTs. This study provides the first characterization of the SET-domain KMT proteins of B. rapa. Phylogenetic analysis data allowed the development of a coherent and rational nomenclature of this important family of proteins in plants, as in animals. The results obtained in this study will provide a base for nomenclature of KMTs in other plant species and facilitate the functional characterization of these important epigenetic regulatory genes in Brassica crops.
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