Yue Liu1,2,3, Yuan Tian1, Lan-Xiang Wang4,3, Tao Fan1, Jianhua Zhang5, Mo-Xian Chen6,7,8, Ying-Gao Liu9. 1. State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China. 2. Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China. 3. Shenzhen Institutes of Advanced Technology, Shenzhen Institute of Synthetic Biology, Chinese Academy of Sciences, Shenzhen, 518055, People's Republic of China. 4. Guangdong Provincial Key Laboratory of Seed and Seedling Health Management Technology, Guangdong Province, Shenzhen Noposion Agrochemical Co. Ltd, Shenzhen, 518102, China. 5. Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong. 6. Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China. cmx2009920734@gmail.com. 7. Guangdong Provincial Key Laboratory of Seed and Seedling Health Management Technology, Guangdong Province, Shenzhen Noposion Agrochemical Co. Ltd, Shenzhen, 518102, China. cmx2009920734@gmail.com. 8. Shenzhen Institutes of Advanced Technology, Shenzhen Institute of Synthetic Biology, Chinese Academy of Sciences, Shenzhen, 518055, People's Republic of China. cmx2009920734@gmail.com. 9. State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China. liuyg@sdau.edu.cn.
Abstract
MAIN CONCLUSION: 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.
MAIN CONCLUSION: 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.