Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, China.
Int J Mol Sci. 2022 Apr 20;23(9):4522. doi: 10.3390/ijms23094522.
Advanced knowledge of messenger RNA (mRNA) -methyladenosine (mA) and DNA -methyldeoxyadenosine (6 mA) redefine our understanding of these epigenetic modifications. Both mA and 6mA carry important information for gene regulation, and the corresponding catalytic enzymes sometimes belong to the same gene family and need to be distinguished. However, a comprehensive analysis of the mA gene family in tomato remains obscure. Here, 24 putative mA genes and their family genes in tomato were identified and renamed according to BLASTP and phylogenetic analysis. Chromosomal location, synteny, phylogenetic, and structural analyses were performed, unravelling distinct evolutionary relationships between the MT-A70, ALKBH, and YTH protein families, respectively. Most of the 24 genes had extensive tissue expression, and 9 genes could be clustered in a similar expression trend. Besides, and showed a different expression pattern in leaf and fruit development. Additionally, qPCR data revealed the expression variation under multiple abiotic stresses, and LC-MS/MS determination exhibited that the cold stress decreased the level of 2'-O dimethyladenosine (mAm). Notably, the orthologs of newly identified single-strand DNA (ssDNA) 6mA writer-eraser-reader also existed in the tomato genome. Our study provides comprehensive information on mA components and their family proteins in tomato and will facilitate further functional analysis of the tomato -methyladenosine modification genes.
高级信使 RNA（mRNA）-甲基腺嘌呤（mA）和 DNA-甲基脱氧腺嘌呤（6mA）知识重新定义了我们对这些表观遗传修饰的理解。mA 和 6mA 都为基因调控携带重要信息，相应的催化酶有时属于同一个基因家族，需要加以区分。然而，番茄中 mA 基因家族的综合分析仍不清楚。在这里，根据 BLASTP 和系统发育分析，鉴定并重新命名了番茄中的 24 个假定 mA 基因及其家族基因。进行了染色体定位、同线性、系统发育和结构分析，分别揭示了 MT-A70、ALKBH 和 YTH 蛋白家族之间不同的进化关系。24 个基因中的大多数在广泛的组织中有表达，并且 9 个基因可以聚类在相似的表达趋势中。此外，和在叶片和果实发育中表现出不同的表达模式。此外，qPCR 数据显示在多种非生物胁迫下表达的变化，并且 LC-MS/MS 测定表明冷胁迫降低了 2'-O 二甲氨基腺苷（mAm）的水平。值得注意的是，新鉴定的单链 DNA（ssDNA）6mA 写入器-擦除器-读取器的同源物也存在于番茄基因组中。我们的研究提供了番茄中 mA 成分及其家族蛋白的全面信息，将有助于进一步对番茄 -甲基腺嘌呤修饰基因的功能分析。
