Kapoor Meenu, Arora Rita, Lama Tenisha, Nijhawan Aashima, Khurana Jitendra P, Tyagi Akhilesh K, Kapoor Sanjay
Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi-110021, India.
BMC Genomics. 2008 Oct 1;9:451. doi: 10.1186/1471-2164-9-451.
Important developmental processes in both plants and animals are partly regulated by genes whose expression is modulated at the post-transcriptional level by processes such as RNA interference (RNAi). Dicers, Argonautes and RNA-dependent RNA polymerases (RDR) form the core components that facilitate gene silencing and have been implicated in the initiation and maintenance of the trigger RNA molecules, central to process of RNAi. Investigations in eukaryotes have revealed that these proteins are encoded by variable number of genes with plants showing relatively higher number in each gene family. To date, no systematic expression profiling of these genes in any of the organisms has been reported.
In this study, we provide a complete analysis of rice Dicer-like, Argonaute and RDR gene families including gene structure, genomic localization and phylogenetic relatedness among gene family members. We also present microarray-based expression profiling of these genes during 14 stages of reproductive and 5 stages of vegetative development and in response to cold, salt and dehydration stress. We have identified 8 Dicer-like (OsDCLs), 19 Argonaute (OsAGOs) and 5 RNA-dependent RNA polymerase (OsRDRs) genes in rice. Based on phylogeny, each of these genes families have been categorized into four subgroups. Although most of the genes express both in vegetative and reproductive organs, 2 OsDCLs, 14 OsAGOs and 3 OsRDRs were found to express specifically/preferentially during stages of reproductive development. Of these, 2 OsAGOs exhibited preferential up-regulation in seeds. One of the Argonautes (OsAGO2) also showed specific up-regulation in response to cold, salt and dehydration stress.
This investigation has identified 23 rice genes belonging to DCL, Argonaute and RDR gene families that could potentially be involved in reproductive development-specific gene regulatory mechanisms. These data provide an insight into probable domains of activity of these genes and a basis for further, more detailed investigations aimed at understanding the contribution of individual components of RNA silencing machinery during reproductive phase of plant development.
植物和动物的重要发育过程部分受基因调控，这些基因的表达在转录后水平通过RNA干扰（RNAi）等过程进行调节。Dicer、Argonaute和RNA依赖性RNA聚合酶（RDR）构成了促进基因沉默的核心组件，并与触发RNA分子的起始和维持有关，而触发RNA分子是RNAi过程的核心。对真核生物的研究表明，这些蛋白质由数量可变的基因编码，植物在每个基因家族中的数量相对较多。迄今为止，尚未有关于这些基因在任何生物体中的系统表达谱分析的报道。
在本研究中，我们对水稻中类Dicer、Argonaute和RDR基因家族进行了全面分析，包括基因结构、基因组定位以及基因家族成员之间的系统发育相关性。我们还展示了这些基因在生殖发育的14个阶段、营养发育的5个阶段以及对冷、盐和脱水胁迫响应过程中的基于微阵列的表达谱分析。我们在水稻中鉴定出8个类Dicer（OsDCLs）、19个Argonaute（OsAGOs）和5个RNA依赖性RNA聚合酶（OsRDRs）基因。基于系统发育，这些基因家族中的每一个都被分为四个亚组。尽管大多数基因在营养器官和生殖器官中都有表达，但发现2个OsDCLs、14个OsAGOs和3个OsRDRs在生殖发育阶段特异性/优先表达。其中，2个OsAGOs在种子中表现出优先上调。其中一个Argonaute（OsAGO2）在响应冷、盐和脱水胁迫时也表现出特异性上调。
本研究鉴定出23个属于DCL、Argonaute和RDR基因家族的水稻基因，它们可能参与生殖发育特异性基因调控机制。这些数据为了解这些基因可能的活性域提供了见解，并为进一步更详细的研究奠定了基础，旨在了解RNA沉默机制的各个组件在植物发育生殖阶段的作用。
