Wang Han, Zhang Jingjing, Yao Sheng, Cheng Xiang, Ji Kongshu, Yu Qiong
State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China.
Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China.
Plants (Basel). 2024 Dec 23;13(24):3589. doi: 10.3390/plants13243589.
-methyladenosine (mA) is a widespread post-transcriptional modification of RNA in eukaryotes. The conserved YTH-domain-containing RNA binding protein has been widely reported to serve as a typical mA reader in various species. However, no studies have reported the mA readers in (). In this study, a systematic analysis of the mA reader (YTH) gene family was performed on , identifying 10 genes in its genome. Phylogenetic analysis of protein-coding sequences revealed that genes from could be classified into two subgroups: and in and in , each with similar motifs and gene structures. In , the predicated aromatic cage pocket of the YTH domains in the gene family is uniformly composed of tryptophan residues (WWW). Subcellular localization experiments verified that is indeed localized in the nucleus, while is localized in both the nucleus and the cytoplasm. The expression patterns of the identified mA reader genes showed a wide distribution but were tissue-specific. Most genes were highly expressed in leaves, followed by the stem, while the lowest expression tendency was found in the roots. Cis-regulatory element analysis predicted the possible functions of genes in , which were mainly responsive to plant hormones such as ABA and MeJA, as well as stress responses. Furthermore, the expression levels of genes indeed changed significantly after ABA, MeJA, and NaCl treatments, suggesting that they can be affected by these abiotic factors. In addition, the PLAAC prediction results indicate that prion domains exist in , , , , , , , and , and phase separation is possible. This study provides a foundation for further investigation of the effects of mA methylation on gene expression regulation in and other forest trees.
N6-甲基腺苷（mA）是真核生物中一种广泛存在的RNA转录后修饰。保守的含YTH结构域的RNA结合蛋白在各种物种中作为典型的mA识别蛋白已被广泛报道。然而，尚无研究报道（某物种）中的mA识别蛋白。在本研究中，对（某物种）的mA识别蛋白（YTH）基因家族进行了系统分析，在其基因组中鉴定出10个基因。蛋白质编码序列的系统发育分析表明，来自（某物种）的基因可分为两个亚组：（具体亚组1）中的（具体基因1）和（具体基因2），以及（具体亚组2）中的（具体基因3），每个亚组都具有相似的基序和基因结构。在（某物种）中，YTH结构域基因家族预测的芳香笼口袋均由色氨酸残基（WWW）组成。亚细胞定位实验证实（具体基因）确实定位于细胞核，而（具体基因）定位于细胞核和细胞质。所鉴定的mA识别蛋白基因的表达模式分布广泛但具有组织特异性。大多数基因在叶片中高表达，其次是茎，而在根中的表达趋势最低。顺式作用元件分析预测了（某物种）中基因的可能功能，这些基因主要对脱落酸（ABA）和茉莉酸甲酯（MeJA）等植物激素以及应激反应作出响应。此外，在ABA、MeJA和NaCl处理后，基因的表达水平确实发生了显著变化，表明它们会受到这些非生物因素的影响。此外，基于氨基酸组成的朊病毒样结构域预测结果表明，（具体基因1）、（具体基因2）、（具体基因3）、（具体基因4）、（具体基因5）、（具体基因6）、（具体基因7）和（具体基因8）中存在朊病毒结构域，并且可能发生相分离。本研究为进一步研究mA甲基化对（某物种）和其他林木基因表达调控的影响奠定了基础。
