植物PHD结构域蛋白的结构与功能特性

doi:10.16288/j.yczz.20-412

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Hereditas(Beijing) ›› 2021, Vol. 43 ›› Issue (4): 323-339.doi: 10.16288/j.yczz.20-412

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Structural and functional characteristics of plant PHD domain-containing proteins

Tianyi Wang, Yingxiang Wang, Chenjiang You()

Institute of Plant Science, College of Life Science, Fudan University, Shanghai 200433, China

Received:2020-12-01 Revised:2021-02-09 Online:2021-04-20 Published:2021-04-20
Contact: You Chenjiang E-mail:cjyou@fudan.edu.cn
Supported by:
Supported by the National Natural Science Foundation of China No(31925005)

Abstract

Abstract:

Plant homeodomain (PHD) is a class of transcription factor in the Zinc finger domain family. The most important function of which is to recognize various histone modifications, including histone methylation and acetylation, etc. They can also bind to DNA. Proteins with PHD domains, some of which possess histone modification enzyme activity, or can interact with histone modification enzymes, and some are associated with DNA methylation, with E3 ubiquitin ligase activity, or even can be chromatin remodeling factors. As transcriptional regulators, they play an important role in plant growth and development. In this review, we summarize the structural features and substrate binding specificity of PHD domains (including H3K4me3/0, H3K9me3, H3R2, H3K14ac) and DNA, the conservation of plant PHD domain in evolution, the molecular mechanism of known PHD domain-containing proteins in plants, providing a reference for further understanding of the involvement of these proteins during plant growth and development.

Key words: plant homeodomain (PHD), histone code, histone modification reader, transcriptional regulation, epigenetics

Tianyi Wang, Yingxiang Wang, Chenjiang You. Structural and functional characteristics of plant PHD domain-containing proteins[J]. Hereditas(Beijing), 2021, 43(4): 323-339.

Figures/Tables 5

Fig. 1

Fig. 2

Fig. 3

Table 1

The characteristics and functions of PHD proteins studied in Arabidopsis"

分类依据		蛋白名称	其他包含的结构域	识别的配体	作用特点	在植物中的功能	参考文献
本身具有组蛋白修饰酶活性	本身具有组蛋白甲基转移酶活性	ATX1	ePHD结构域、SET结构域	H3K4me3	使H3K4三甲基化	根系、叶片和花器官的发育以及一些逆境胁迫基因的转录调控	[29~31]
		ATX2	ePHD结构域、SET结构域	H3K4me2	使H3K4三甲基化	与ATX1拥有相似的序列,但是在调控基因转录方面具有非冗余的功能	[32]
		ATX3/4/5	编码了一个可能的H3K4甲基转移酶	H3K4me2/3	是迄今为止在拟南芥基因组中发现的具有H3K4me2甲基转移酶活性的蛋白	ATX3/4/5具有冗余的功能,可以调控一系列作用于营养生长和生殖生长的基因	[33,34]
		ATXR	SET结构域	H3K4me0	PHD结构域作用于SET结构域结合辅因子以及促进H3K27me1的过程	作用于植物中染色质结构、基因沉默和异染色质的DNA复制过程	[35]
	本身具有组蛋白乙酰基转移酶活性	IDM1/ ROS4	MBD结构域、乙酰基转移酶结构域	H3K4me0	PHD结构域影响IDM1乙酰转移酶的活性	对于DNA去甲基化具有负面调控,阻止高度同源的多拷贝基因和其他重复序列的DNA高度甲基化	[36,37]
与组蛋白修饰酶相互作用	与组蛋白去乙酰化酶相互作用	EBS/SHL	BAH结构域	H3K4me2/3	PHD结构域结合HDA6	作用于开花调控和种子休眠	[38,39]
	与组蛋白甲基转移酶相互作用	MMD1	MMD结构域	H3K4me2/3	与组蛋白去甲基化酶JMJ16相互作用	植物减数分裂,调控浓缩等过程的蛋白	[40~42]
		AL		除AL3以外所有AL蛋白都结合H3K4me2/3	是植物中特有的一类转录因子,PHD结构域与PRC1蛋白相互作用,招募PRC2从而积累H3K27me3	调控植物的生长发育,以及应对低温、干旱、高盐等非生物胁迫	[43~46]
		VIN3		H3K9me2和H3K4me2	PHD结构域与PRC2的相互作用,PHD-PRC2复合体使H3K27me3水平升高	作用于春化作用所需的FLC表观遗传学基因沉默过程	[47~51]
与DNA甲基化相关	结合甲基化的DNA	MBD9	MBD结构域 Bromo结构域	DNA甲基化	MBD结构域结合甲基化的DNA,Bromo结构域可能发挥了催化组蛋白乙酰化反应的作用	通过DNA甲基化和组蛋白乙酰基化,分别间接和直接调控基因的表达,影响拟南芥的生长发育	[52,53]
与DNA甲基化相关	结合甲基化的DNA	ORTH	RING结构域、SRA结构域	DNA甲基化	SRA结构域作用于结合甲基化的DNA	作用于调控DNA甲基化	[54,55]
具有E3泛素连接酶活性		SIZ1	RING、SAP、SXS、PINIT 结构域	H3R2me2和H3K4me3	PHD结构域与染色质重塑复合体有关,也可能作为一个E3泛素连接酶	通过调控基因的表达,作用于植物的生长发育以及应对干旱、低盐的胁迫的过程	[56~58]
是染色质重塑因子		CHR4	Chromodomain结构域		是依赖于ATP的染色质重塑因子	植物的生长发育和DNA损伤应答	[59,60]
是染色质重塑因子		PKL	Chromodomain结构域		是依赖于ATP的染色质重塑因子	DNA损伤应答,以及调控植物生长和响应胁迫基因的表达	[61,62]
与bHLH型的转录因子相互作用		OBE		可能结合 bHLH型的转录因子	促进依赖于转录因子MP的基因的激活表达	在生长素介导的调控发育过程中,作用于根系和顶端分生组织的维持和建立	[63~65]
其他		SCC2	在陆地植物有PHD,动物和真菌中没有	未修饰及甲基化的H3、H4和H2A		作用于减数分裂过程,介导染色质黏连蛋白cohesin的招募过程	[66]
		ORC	只有植物的ORC1中含有PHD结构域	H3K4me3,更倾向于结合未修饰的H3	通过PHD结构域识别靶基因启动子区域的H3K4me3来激活基因的转录表达	作用于DNA复制的起始,在细胞周期中调控转录过程	[67,68]
		MS1				调控作用于花粉外壁形成,花粉细胞溶质和绒毡层的基因的表达,对于减数分裂后的花粉和绒毡层的发育具有重要作用	[69]
		PTM	DDT 结构域	H3K4me3	结合到ABI4的启动子上,以激活ABI4基因的表达。	结合叶绿体被膜的转录调控因子,作用于将叶绿体信号传递到细胞膜	[70]

Table 1

Fig. 4

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Structural and functional characteristics of plant PHD domain-containing proteins

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