State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China.
Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China.
Planta. 2021 Dec 23;255(1):25. doi: 10.1007/s00425-021-03752-8.
This study systematically identifies 112 U2A genes from 80 plant species by combinatory bioinformatics analysis, which is important for understanding their phylogenetic history, expression profiles and for predicting specific functions. In eukaryotes, a pre-mRNA can generate multiple transcripts by removing certain introns and joining corresponding exons, thus greatly expanding the transcriptome and proteome diversity. The spliceosome is a mega-Dalton ribonucleoprotein (RNP) complex that is essential for the process of splicing. In spliceosome components, the U2 small nuclear ribonucleoprotein (U2 snRNP) forms the pre-spliceosome by association with the branch site. An essential component that promotes U2 snRNP assembly, named U2A, has been extensively identified in humans, yeast and nematodes. However, studies examining U2A genes in plants are scarce. In this study, we performed a comprehensive analysis and identified a total of 112 U2A genes from 80 plant species representing dicots, monocots, mosses and algae. Comparisons of the gene structures, protein domains, and expression patterns of 112 U2A genes indicated that the conserved functions were likely retained by plant U2A genes and important for responses to internal and external stimuli. In addition, analysis of alternative transcripts and splice sites of U2A genes indicated that the fifth intron contained a conserved alternative splicing event that might be important for its molecular function. Our work provides a general understanding of this splicing factor family in terms of genes and proteins, and it will serve as a fundamental resource that will contribute to further mechanistic characterization in plants.
本研究通过组合生物信息学分析，从 80 种植物物种中系统地鉴定出 112 个 U2A 基因，这对于了解其系统发育历史、表达谱以及预测特定功能非常重要。在真核生物中，通过去除某些内含子并连接相应的外显子，前体 mRNA 可以产生多个转录本，从而极大地扩展了转录组和蛋白质组的多样性。剪接体是一种大型的核蛋白核糖核蛋白（RNP）复合物，对于剪接过程至关重要。在剪接体成分中，U2 小核核糖核蛋白（U2 snRNP）通过与分支位点结合形成前剪接体。一种促进 U2 snRNP 组装的必需成分，称为 U2A，已在人类、酵母和线虫中得到广泛鉴定。然而，关于植物 U2A 基因的研究却很少。在本研究中，我们对 80 种植物物种进行了全面分析，共鉴定出 112 个 U2A 基因，这些物种代表了双子叶植物、单子叶植物、苔藓植物和藻类。对 112 个 U2A 基因的结构、蛋白质结构域和表达模式进行比较表明，植物 U2A 基因可能保留了保守的功能，对于应对内外刺激非常重要。此外，对 U2A 基因的可变转录本和剪接位点的分析表明，第五内含子包含一个保守的可变剪接事件，这可能对其分子功能很重要。我们的工作提供了对这个剪接因子家族在基因和蛋白水平上的全面理解，它将作为一个基本资源，为植物中的进一步机制特征提供帮助。
