中国农业科学  2015,48(增刊):16-22
Scientia Agricultura Sinica
doi: 10.3864/j.issn.0578-1752.2015.S.002
收稿日期：2015-09-21；接受日期：2015-10-16 基金项目：中国博士后科学基金（2014M550108）
：耿帅锋，E-mail ：*********************。通信作者毛龙，E-mail ：***************
RNA 介导的DNA 甲基化路径在植物抗病中的研究进展
耿帅锋，李爱丽，毛  龙
（中国农业科学院作物科学研究所/国家农作物基因资源与基因改良重大科学工程，北京 100081）
摘要：在植物中，小分子RNA 介导的DNA 甲基化（RNA-directed DNA methylation，RdDM）是一个表观修饰过程，主要依赖两个核心蛋白：切割长双链RNA 产生小分子干扰RNA（siRNA）的Dicer-Like 3（DCL3）蛋白和结合siRNA 发挥功能的Argonaute 4（AGO4）蛋白。同时，RdDM 的转录机制主要依赖两个植物特有的RNA 聚合酶Pol  IV 和Pol  V。近来，越来越多的研究表明RdDM 路径参与植物防御反
应。文章主要综述RdDM 及其相关基因与植物抗病的最新研究进展，以期对作物抗病分子机制和育种提供有益的借鉴。
关键词：RdDM；siRNA；表观修饰；植物抗病
Research Progress on the Roles of RNA-Directed DNA
Methylation Pathway in Plant Defense
GENG Shuai-feng, LI Ai-li, MAO Long
(Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic
Improvement, Beijing 100081)
Abstract: RNA-directed DNA methylation (RdDM) is an epigenetic process in plants that relies on two core proteins: Dicer-Like 3 (DCL3), which processes long double-stranded RNAs (dsRNAs) into siRNAs, and Argonaute 4 (AGO4), which is involved in siRNA effector functions. RdDM also depends on a specialized transcriptional machinery that is centred around two plant-specific RNA polymerase II
(Pol II)-related enzymes called Pol IV and Pol V. Recently, RdDM is found to be involved in plant defense. In this paper, we present an up-to-date overview on RdDM and its related genes during plant defense. We also provide opinions on future research directions for crop defense and breeding.
Key words: RdDM; siRNA; epigenetic modification; plant defense
1  植物免疫反应
病害严重影响作物的产量和质量，因此对其抗病分子机理的研究能够对作物抗病和分子育种提供借鉴。由于植物不能像动物那样通过移动躲避病害，故其进化出两道防线抵御病原菌的侵染[1]。其中第一道防线是病原物激发的免疫反应（pathogen-associated molecular patterns-triggered immunity ，PTI ），主要依靠植物膜上的分子模式识别受体（pattern recognition receptors ，PRRs ）识别病原物，进而激活免疫反应；
第二道防线是效应子激发的免疫反应（effector-triggered immunity ，ETI ），主要通过植物抗病基因（resistant gene ，R ）编码的蛋白，间接或直接识别病原菌产生的效应蛋白，从而激活R 蛋白介导植物的抗性，并伴有过敏反应（hypersencitive reaction ，HR ）和程序性的细胞死亡[1-3]。
免疫反应能激活一系列防御反应信号，诸如细胞分裂原激活的蛋白激酶（mitogen-activated protein kina
se ，MAPK ）信号级联反应、活性氧迸发（reactive oxygen species ，ROS ）以及众多免疫响应基因的差异
增刊耿帅锋等：RNA介导的DNA甲基化路径在植物抗病中的研究进展 17
表达。其中也包括在植物免疫反应中扮演重要角的小干扰RNAs（small interfering RNAs，siRNAs）和microRNAs（miRNAs）的差异表达[4-14]。例如，miR393可通过对其靶基因生长素受体基因TIR（toll/ interleukin-1 receptor）的调控参与拟南芥抗病反应[15]；miRNA393*通过调节病程相关蛋白（pathogenesis- related protein 1，PR1）的分泌，参与抗病基因介导的防御反应[16]；miR160a、miR398b和miR773通过调控胼胝质沉积，参与拟南芥对细菌病害的基础防御[17]。miRNA还可以通过调节植物免疫受体基因（NB-LRR）的表达参与植物抗病反应[18]。至于siRNA，拟南芥中发现天然反义转录本来源的nat-siRNAAATGB2和长siRNA（lsiRNA-1）被细菌病原Pseudomonas syringae pv. tomato DC3000（Pst）诱导并参与植物免疫反应[19-20]；RPP4位点产生的内源siRNA使拟南芥对Ps pv. maculicola和oomycetes Hyaloperonospora均产生抗性[21]。因此，小分子RNA（small RNA，sRNA）介导的基因沉默是植物和动物寄主免疫反应最为重要的调节机制之一[22-25]。
2  DNA甲基化及其相关基因
表观修饰通过DNA甲基化、组蛋白修饰和某些方面的siRNA路径影响染质结构和基因组稳定，进而正
确的传递遗传信息和产生表型[26-28]。在植物中，DNA甲基化是通过胞嘧啶添加一个甲基而实现基因沉默的表观遗传沉默机制，主要发生在转座子和其他DNA重复元件上[29-32]。动物DNA甲基化主要发生在对称的CG位点，而植物的DNA甲基化发生在所有的胞嘧啶位点，包括对称的CG和CHG（H 代表A、C、T）位点，及非对称的CHH（H代表A、C、T）位点[26,32]。在拟南芥基因组中，CG、CHG和CHH的甲基化水平分别为24%、6.7%和1.7%[33-34]。在大豆根系中，CG、CHG和CHH的甲基化水平分别为81%、59.3%和  5.5%[35]。在植物中，甲基化由DOMAINS REARRANGED METHYLTRA NSFERASE2（DRM2）起始催化，并通过不同的途径维持，其中CG和CHG分别通过METHYLTRANSFER ASE1（MET1）和CHROMOMETHYLASE3（CMT3）维持，非对称的CHH甲基化通过DRM2催化持久的起始甲基化维持[31-32]。
3  RdDM路径及其相关基因
新的研究表明RNA干扰产生的siRNA能通过RdDM（RNA-directed DNA methylation）路径，识别同源基因组DNA序列发生甲基化，在这个过程中，24 nt siRNA指导的起始甲基化转移酶DRM2到同源序列位点建立甲基化，进而产生基因沉默[26,32,36-38]。植物编码许多RdDM组分，其中重要的有DCL3（Dicer-Like 3）蛋白、AGO4（Argonaute 4）蛋白和两个植物特有的RNA聚合酶Pol IV 和Pol V[39-43]。在植物中，SHH1（Sawadee homeodomain homolog 1）结合H3K4和H3K9m区域[44-45]，招募植物特有的RNA聚合酶Pol IV到目标转录区启动转录，产生长单链非编码RNA（long noncoding RNA，l
ncRNA）[46]，在ATP依赖的Chromatin-remodeler CLASSY1（CLSY1）蛋白的帮助下[47]，经RNA聚合酶RDR2复制，合成双链siRNA 前体[16]，经DCL3切割，产生24 nt siRNAs[48-49]。DCL3切割产生的24 nt siRNA 双链，随后被甲基转移酶HEN 1（Hua enhancer1）识别，甲基化双链siRNA[50]。甲基化的双链24 nt siRNAs中的一条在细胞质中被AGO4或AGO6选择包装，形成沉默复合体（RNA-induced silencing complex，RISC）[51-53]。再经HSP90蛋白的帮助，结合的双链siRNA降解其中一条链，形成成熟的RISC，后被转运到细胞核内[54]。同时植物特有的RNA聚合酶Pol V在一系列转录因子的帮助下，从沉默位点附近转录[55-57]。通过AGO4包裹的siRNA与转录产生的RNA配对和AGO4与Pol V的CTD （C-terminal domain）尾巴上的WG/GW-rich 结构域相互作用的机制确保RISC被准确募集到Pol V转录的沉默位点[58-59]。然后甲基转移酶DRM2也被募集到沉默位点，介导转座子（transposable element，TE）和重复序列的DNA甲基化[32]。
另外，除了siRNA介导DNA甲基化，组蛋白甲基化也与DNA甲基化相关[60-62]。不同的DNA甲基化类型和位置与不同的组蛋白甲基化相关[63-64]。基因区的DNA甲基化伴随高度的H3K4m1（Histone 3 lysine 4 monomethylation），相反非基因区的DNA甲基化伴随高度的H3K9m2（histone 3 lysine 9 dimethylation）和低度的H3K4m2/m3（histone 3 lysine 4 di-/ trimethylation）[65-66]。其中H3K9m2与CMT3路径的CHG甲基化相关[64,67]，H3K4m2/m3与RdDM路径相关[68]。在拟南芥中，组蛋白去甲基化酶JMJ14（Jumonji 14）和LDL（lysine-specific demethylase 1-like）能通过中和附近基因H3K4的活
性，而增强小分子介导的DNA甲基化[62,69]。包含JmjC 结构域的组蛋白去甲基化酶IBM1（increase in bonsai
18 中国农业科学48卷
methylation 1）能通过RdDM路径间接调控基因表达[70]。
4  DNA甲基化与植物抗病
DNA甲基化是一个表观遗传修饰，通过沉默TE 和重复序列产生功能。目前有关DNA甲基化参与植物抗病的研究，主要是病原菌通过影响植物基因组DNA甲基化水平，引起基因表达水平的表达变化，使植物产生相应的生理反应，从而参与抗病反应[71]。在拟南芥中，通过DNA甲基化图谱发现，Pst的侵染会导致拟南芥基因组CG和CHH位点的DNA甲基化水平降低，引起防御相关基因的高水平表达[72]。在水稻中，对甲基化分析发现，突变株系Line-2中基因Xa21G 的启动子区域发生了去甲基化，从而激活该基因，最终导致植株抗病性增强[73]。另外，成株期水稻品种Wase Aikoku 3的全基因组DNA甲基化水平显著高于幼苗期，抗病相关基因的甲基化水平则相反，进而导致该品种成株期对白叶枯病菌抗性强于幼苗期，因此暗示DNA甲基化水平影响水稻的成株期抗病性[74]。在烟草中，病毒感染能够导致抗病性相关的亮氨酸重复序列区域发生去甲基化[75]，增强基因表达，进而提高植物抗病性。在拟南芥细菌防御中，一些转座子通过DNA去甲基化被转录激活，同时这个过程伴随关键转录沉默因子的下降，并部分依
赖去甲基化的激活，暗示DNA去甲基化是植物诱导免疫反应的一部分，主要通过激活一些TE或者重复序列相关抗病基因的转录[71]。在大豆中根系中，胞囊线虫侵染后，甲基化下调显著多于甲基化上调，同时全基因组CHH甲基化下降，暗示CHH甲基化在抗虫中起重要作用[35]。
5  RdDM路径基因与植物抗病
RdDM路径的表观调控机制，主要通过siRNA影响基因产生功能[76-84]。但RdDM路径基因突变体在不同病原菌诱导后，表现出不一致的抗性。例如非CG 甲基化转移酶的ddc（drm1-2/drm2-2/cmt3-11）三突变体，Pol IV大亚基的nrpd1突变体，染质重塑蛋白drd-1突变体，dcl2/dcl3/dcl4三突变体，都对Pst的抗病性增强[72]；相反rdd（ros1/dml2/dml3）三突变体，RdDM 路径ago4和nrpe1突变体，对Fusarium oxysporum的敏感性增强[85]。突变体ago4、drd1、rdr2、drm1、drm2和nrpd2对死体营养型真菌Botrytis cinerea和Plectospherella cucumerina的敏感性增强[82]。此外，在细菌病原物flg22诱导后，RdDM路径的许多基因下调表达，即在细菌诱导后，RdDM路径基因的表达被抑制，引起抗病基因的去甲基化，造成抗病基因激活。进一步研究发现，尽管ROS1（repressor of silencing 1）在细菌诱导后被抑制，ros1突变体对Pst的敏感性增强，但能启动抗病基因的DNA去甲基化，暗示在病原菌侵染中，启动DNA去甲基化是激活抗病基因路径的一部分[71]。通过芯片分析发现，RdDM的nrpd1和nrpe1突变体中差异表达的基因多于rdd突变体中，说明RdDM或者去甲基化调控抗病基因的转录状态[82]。对RdDM组分突变体的遗传学分析表明RdDM路径参与植物免疫反应[82]，但是直接还是间接作用于抗病相
关基因还不清楚。另外，拟南芥世代抗性的获得依赖RdDM路径调控非CG位点的去甲基化[86]。
6  展望
RdDM路径通过小分子RNA介导DNA甲基化来参与抗病性，对其分子机制的深入研究，能够为育种提供借鉴意义。同时，表观修饰变化能够遗传给后代[87]，将促进DNA甲基化等表观修饰变化在作物育种中的应用。例如利用DNA甲基化抑制剂处理植物的种子或者幼苗，然后选择优良性状用于育种[88-89]。另外也可以开发表观遗传学标记，如DNA甲基化标记，进而辅助育种。随着RdDM抗病路径分子机理的深入研究，将为抗病品种的选育和品质改良提供表观遗传修饰方面的理论依据。
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