Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, 430070, China.
College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
BMC Plant Biol. 2017 Dec 21;17(1):261. doi: 10.1186/s12870-017-1206-0.
Modification of nucleosides on transfer RNA (tRNA) is important either for correct mRNA decoding process or for tRNA structural stabilization. Nucleoside methylations catalyzed by MTase (methyltransferase) are the most common type among all tRNA nucleoside modifications. Although tRNA modified nucleosides and modification enzymes have been extensively studied in prokaryotic systems, similar research remains preliminary in higher plants, especially in crop species, such as rice (Oryza sativa). Rice is a monocot model plant as well as an important cereal crop, and stress tolerance and yield are of great importance for rice breeding.
In this study, we investigated how the composition and abundance of tRNA modified nucleosides could change in response to drought, salt and cold stress, as well as in different tissues during the whole growth season in two model plants-O. sativa and Arabidopsis thaliana. Twenty two and 20 MTase candidate genes were identified in rice and Arabidopsis, respectively, by protein sequence homology and conserved domain analysis. Four methylated nucleosides, Am, Cm, mA and mG, were found to be very important in stress response both in rice and Arabidopsis. Additionally, three nucleosides,Gm, mU and mC, were involved in plant development. Hierarchical clustering analysis revealed consistency on Am, Cm, mA and mG MTase candidate genes, and the abundance of the corresponding nucleoside under stress conditions. The same is true for Gm, mU and mC modifications and corresponding methylation genes in different tissues during different developmental stages.
We identified candidate genes for various tRNA modified nucleosides in rice and Arabidopsis, especially on MTases for methylated nucleosides. Based on bioinformatics analysis, nucleoside abundance assessments and gene expression profiling, we propose four methylated nucleosides (Am, Cm, mA and mG) that are critical for stress response in rice and Arabidopsis, and three methylated nucleosides (Gm, mU and mC) that might be important during development.
转移 RNA（tRNA）核苷的修饰对于正确的 mRNA 解码过程或 tRNA 结构稳定性都很重要。在所有 tRNA 核苷修饰中，甲基转移酶（MTase）催化的核苷甲基化是最常见的类型。尽管在原核系统中已经广泛研究了 tRNA 修饰核苷和修饰酶，但在高等植物中，特别是在作物物种中，如水稻（Oryza sativa），类似的研究仍处于初步阶段。水稻是单子叶模式植物，也是一种重要的谷类作物，对水稻的选育来说，胁迫耐受性和产量非常重要。
在这项研究中，我们调查了在两种模式植物水稻和拟南芥中，tRNA 修饰核苷的组成和丰度如何在整个生长季节的不同组织中，以及在干旱、盐和冷胁迫下发生变化。通过蛋白质序列同源性和保守结构域分析，在水稻和拟南芥中分别鉴定出 22 个和 20 个 MTase 候选基因。在水稻和拟南芥中，发现 Am、Cm、mA 和 mG 这四个甲基化核苷在胁迫反应中非常重要。此外，Gm、mU 和 mC 这三个核苷参与了植物的发育。层次聚类分析显示，Am、Cm、mA 和 mG 的 MTase 候选基因及其在胁迫条件下对应的核苷的丰度在水稻和拟南芥中具有一致性。在不同发育阶段的不同组织中，Gm、mU 和 mC 的修饰及其对应的甲基化基因也是如此。
我们鉴定了水稻和拟南芥中各种 tRNA 修饰核苷的候选基因，特别是在甲基化核苷的 MTase 上。基于生物信息学分析、核苷丰度评估和基因表达谱分析，我们提出了 Am、Cm、mA 和 mG 这四个对水稻和拟南芥胁迫反应至关重要的甲基化核苷，以及 Gm、mU 和 mC 这三个在发育过程中可能很重要的甲基化核苷。
