Pandey Ritu, Müller Andreas, Napoli Carolyn A, Selinger David A, Pikaard Craig S, Richards Eric J, Bender Judith, Mount David W, Jorgensen Richard A
Department of Plant Sciences, University of Arizona, Tucson, AZ 85721-0036, USA.
Nucleic Acids Res. 2002 Dec 1;30(23):5036-55. doi: 10.1093/nar/gkf660.
Sequence similarity and profile searching tools were used to analyze the genome sequences of Arabidopsis thaliana, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Caenorhabditis elegans and Drosophila melanogaster for genes encoding three families of histone deacetylase (HDAC) proteins and three families of histone acetyltransferase (HAT) proteins. Plants, animals and fungi were found to have a single member of each of three subfamilies of the GNAT family of HATs, suggesting conservation of these functions. However, major differences were found with respect to sizes of gene families and multi-domain protein structures within other families of HATs and HDACs, indicating substantial evolutionary diversification. Phylogenetic analysis identified a new class of HDACs within the RPD3/HDA1 family that is represented only in plants and animals. A similar analysis of the plant-specific HD2 family of HDACs suggests a duplication event early in dicot evolution, followed by further diversification in the lineage leading to Arabidopsis. Of three major classes of SIR2-type HDACs that are found in animals, fungi have representatives only in one class, whereas plants have representatives only in the other two. Plants possess five CREB-binding protein (CBP)-type HATs compared with one to two in animals and none in fungi. Domain and phylogenetic analyses of the CBP family proteins showed that this family has evolved three distinct types of CBPs in plants. The domain architecture of CBP and TAF(II)250 families of HATs show significant differences between plants and animals, most notably with respect to bromodomain occurrence and their number. Bromodomain-containing proteins in Arabidopsis differ strikingly from animal bromodomain proteins with respect to the numbers of bromodomains and the other types of domains that are present. The substantial diversification of HATs and HDACs that has occurred since the divergence of plants, animals and fungi suggests a surprising degree of evolutionary plasticity and functional diversification in these core chromatin components.
利用序列相似性和谱搜索工具，对拟南芥、酿酒酵母、粟酒裂殖酵母、秀丽隐杆线虫和黑腹果蝇的基因组序列进行分析，以寻找编码三类组蛋白去乙酰化酶（HDAC）蛋白和三类组蛋白乙酰转移酶（HAT）蛋白的基因。研究发现，植物、动物和真菌中各有GNAT家族三个亚家族中的一个成员，这表明这些功能具有保守性。然而，在HAT和HDAC其他家族的基因家族大小和多结构域蛋白结构方面发现了重大差异，这表明存在大量的进化分化。系统发育分析在RPD3/HDA1家族中鉴定出一类新的HDAC，仅存在于植物和动物中。对植物特有的HDAC的HD2家族进行的类似分析表明，在双子叶植物进化早期发生了一次复制事件，随后在导致拟南芥的谱系中进一步分化。在动物中发现的三类主要的SIR2型HDAC中，真菌仅在其中一类中有代表，而植物仅在另外两类中有代表。与动物中的一到两个和真菌中没有相比，植物拥有五个CREB结合蛋白（CBP）型HAT。对CBP家族蛋白的结构域和系统发育分析表明，该家族在植物中进化出了三种不同类型的CBP。HAT的CBP和TAF(II)250家族的结构域结构在植物和动物之间存在显著差异，最明显的是在含溴结构域的出现及其数量方面。拟南芥中含溴结构域的蛋白在溴结构域的数量和其他存在的结构域类型方面与动物含溴结构域的蛋白有显著差异。自植物、动物和真菌分化以来，HAT和HDAC发生的大量分化表明，这些核心染色质成分具有惊人程度的进化可塑性和功能多样性。
