Conservation of tRNA and rRNA 5-methylcytosine in the kingdom Plantae.
Conservation of tRNA and rRNA 5-methylcytosine in the kingdom Plantae.
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DOI：
10.1186/s12870-015-0580-8
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发表时间：
2015-08-14
影响因子：
5.3
通讯作者：
Searle IR
中科院分区：
文献类型：
--
作者：
Burgess AL;David R;Searle IR
RNA胞嘧啶残基转录后甲基化为5-甲基胞嘧啶（m5 C）是调节RNA代谢的重要修饰，并且在真核生物和原核生物中都发生。然而，到目前为止，没有转录组范围内的m5 C位点的鉴定已在植物中进行。植物为研究m5 C的起源和进化提供了一个独特的比较系统，因为它们包含三个不同的基因组，细胞核，线粒体和叶绿体。在这里，我们使用RNA的亚硫酸氢盐转化结合高通量Illumina测序（RBS-seq）来鉴定六种不同物种的所有三种亚细胞转录组的非编码核糖体RNA和转移RNA中m5 C位点的单核苷酸分辨率，所述六种不同物种包括单细胞藻类Nannochloropsis oculata，大型藻类Caulerpa taxifolia和多细胞高等植物拟南芥，芜菁，小麦和银杏。使用植物模型拟南芥，我们确定了总共39个高度甲基化的m5 C位点的预测结构位置的核tRNA和7个m5 C位点的rRNA从核，叶绿体和线粒体转录组。tRNA和rRNAm 5C位点的核苷酸位置和甲基化百分比在所有分析的物种中都是保守的，从单细胞藻N.到多细胞植物。有趣的是，线粒体和叶绿体编码的tRNA在A. thaliana，这在植物界是普遍保守的。这表明动物和植物中细胞器甲基化的独立进化，因为动物线粒体tRNA具有m5 C位点。在这里，我们描述了5个成员的RNA 5-甲基胞嘧啶家族在拟南芥和扩展TRDMT 1和NOP 2A/OLI 2的功能特性。我们证明，核tRNA甲基化需要两个进化上保守的甲基转移酶，TRDMT 1和TRM 4 B。trdmt 1 trm 4 B双突变体对抗生素潮霉素B高度敏感，证明了tRNA甲基化在调节翻译中的功能。此外，我们证明，核大亚基25 S rRNA甲基化需要保守的RNA甲基转移酶NSUN 5。我们的研究结果还表明，至少有两个在拟南芥中的NOP 2旁系同源的功能冗余。我们的数据表明，在植物界广泛发生和保护的非编码RNA甲基化，这表明重要的和高度保守的作用，这种转录后修饰。本文的在线版本（doi：10.1186/s12870-015-0580-8）包含补充材料，可供授权用户使用。
Post-transcriptional methylation of RNA cytosine residues to 5-methylcytosine (m5C) is an important modification that regulates RNA metabolism and occurs in both eukaryotes and prokaryotes. Yet, to date, no transcriptome-wide identification of m5C sites has been undertaken in plants. Plants provide a unique comparative system for investigating the origin and evolution of m5C as they contain three different genomes, the nucleus, mitochondria and chloroplast. Here we use bisulfite conversion of RNA combined with high-throughput IIlumina sequencing (RBS-seq) to identify single-nucleotide resolution of m5C sites in non-coding ribosomal RNAs and transfer RNAs of all three sub-cellular transcriptomes across six diverse species that included, the single-celled algae Nannochloropsis oculata, the macro algae Caulerpa taxifolia and multi-cellular higher plants Arabidopsis thaliana, Brassica rapa, Triticum durum and Ginkgo biloba. Using the plant model Arabidopsis thaliana, we identified a total of 39 highly methylated m5C sites in predicted structural positions of nuclear tRNAs and 7 m5C sites in rRNAs from nuclear, chloroplast and mitochondrial transcriptomes. Both the nucleotide position and percent methylation of tRNAs and rRNAs m5C sites were conserved across all species analysed, from single celled algae N. oculata to multicellular plants. Interestingly the mitochondrial and chloroplast encoded tRNAs were devoid of m5C in A. thaliana and this is generally conserved across Plantae. This suggests independent evolution of organelle methylation in animals and plants, as animal mitochondrial tRNAs have m5C sites. Here we characterize 5 members of the RNA 5-methylcytosine family in Arabidopsis and extend the functional characterization of TRDMT1 and NOP2A/OLI2. We demonstrate that nuclear tRNA methylation requires two evolutionarily conserved methyltransferases, TRDMT1 and TRM4B. trdmt1 trm4b double mutants are hypersensitive to the antibiotic hygromycin B, demonstrating the function of tRNA methylation in regulating translation. Additionally we demonstrate that nuclear large subunit 25S rRNA methylation requires the conserved RNA methyltransferase NSUN5. Our results also suggest functional redundancy of at least two of the NOP2 paralogs in Arabidopsis. Our data demonstrates widespread occurrence and conservation of non-coding RNA methylation in the kingdom Plantae, suggesting important and highly conserved roles of this post-transcriptional modification. The online version of this article (doi:10.1186/s12870-015-0580-8) contains supplementary material, which is available to authorized users.