Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, China.
BMC Plant Biol. 2010 Sep 14;10:201. doi: 10.1186/1471-2229-10-201.
In all domains of life, transfer RNA (tRNA) molecules contain modified nucleosides. Modifications to tRNAs affect their coding capacity and influence codon-anticodon interactions. Nucleoside modification deficiencies have a diverse range of effects, from decreased virulence in bacteria, neural system disease in human, and gene expression and stress response changes in plants. The purpose of this study was to identify genes involved in tRNA modification in the model plant Arabidopsis thaliana, to understand the function of nucleoside modifications in plant growth and development.
In this study, we established a method for analyzing modified nucleosides in tRNAs from the model plant species, Arabidopsis thaliana and hybrid aspen (Populus tremula × tremuloides). 21 modified nucleosides in tRNAs were identified in both species. To identify the genes responsible for the plant tRNA modifications, we performed global analysis of the Arabidopsis genome for candidate genes. Based on the conserved domains of homologs in Sacccharomyces cerevisiae and Escherichia coli, more than 90 genes were predicted to encode tRNA modifying enzymes in the Arabidopsis genome. Transcript accumulation patterns for the genes in Arabidopsis and the phylogenetic distribution of the genes among different plant species were investigated. Transcripts for the majority of the Arabidopsis candidate genes were found to be most abundant in rosette leaves and shoot apices. Whereas most of the tRNA modifying gene families identified in the Arabidopsis genome was found to be present in other plant species, there was a big variation in the number of genes present for each family.Through a loss of function mutagenesis study, we identified five tRNA modification genes (AtTRM10, AtTRM11, AtTRM82, AtKTI12 and AtELP1) responsible for four specific modified nucleosides (m1G, m2G, m7G and ncm5U), respectively (two genes: AtKTI12 and AtELP1 identified for ncm5U modification). The AtTRM11 mutant exhibited an early-flowering phenotype, and the AtELP1 mutant had narrow leaves, reduced root growth, an aberrant silique shape and defects in the generation of secondary shoots.
Using a reverse genetics approach, we successfully isolated and identified five tRNA modification genes in Arabidopsis thaliana. We conclude that the method established in this study will facilitate the identification of tRNA modification genes in a wide variety of plant species.
在所有生命领域中，转移 RNA（tRNA）分子都含有修饰核苷。tRNA 的修饰会影响其编码能力，并影响密码子-反密码子相互作用。核苷修饰缺陷的影响范围广泛，从细菌毒力下降、人类神经系统疾病到植物基因表达和应激反应改变等。本研究旨在鉴定模式植物拟南芥中参与 tRNA 修饰的基因，以了解核苷修饰在植物生长发育中的作用。
在这项研究中，我们建立了一种分析模式植物物种拟南芥和杂种白杨（Populus tremula× tremuloides）中 tRNA 修饰核苷的方法。在这两个物种中鉴定出了 21 种修饰核苷。为了鉴定负责植物 tRNA 修饰的基因，我们对拟南芥基因组进行了全局分析以寻找候选基因。基于酿酒酵母和大肠杆菌同源物的保守结构域，预测拟南芥基因组中超过 90 个基因编码 tRNA 修饰酶。研究了拟南芥和不同植物物种中基因的转录物积累模式和基因的系统发育分布。发现大多数拟南芥候选基因的转录物在莲座叶和茎尖中最丰富。虽然在拟南芥基因组中鉴定的大多数 tRNA 修饰基因家族在其他植物物种中都存在，但每个家族的基因数量存在很大差异。通过功能丧失诱变研究，我们鉴定了五个 tRNA 修饰基因（AtTRM10、AtTRM11、AtTRM82、AtKTI12 和 AtELP1），分别负责四个特定修饰核苷（m1G、m2G、m7G 和 ncm5U）的修饰（两个基因：AtKTI12 和 AtELP1 鉴定用于修饰 ncm5U）。AtTRM11 突变体表现出早花表型，AtELP1 突变体叶片狭窄，根生长减少，荚果形状异常，次生枝生成缺陷。
使用反向遗传学方法，我们成功分离并鉴定了拟南芥中的五个 tRNA 修饰基因。我们得出结论，本研究建立的方法将有助于鉴定各种植物物种中的 tRNA 修饰基因。
