phylogenetic analysis and classification of the brassica rapa set-domain protein family系统发育分析和芸苔属植物的分类拉伯set-domain蛋白质家族.pdf

Huang et al. BMC Plant Biology 2011, 11:175 /1471-2229/11/175 RESEARCH ARTICLE Open Access Phylogenetic analysis and classification of the Brassica rapa SET-domain protein family 1,2 1 3* 1,2* Yong Huang , Chunlin Liu , Wen-Hui Shen and Ying Ruan Abstract Background: 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. Results: 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 differ