Phylogenetic comparison of 5′ splice site determination in central spliceosomal proteins of the U1‐70K gene family, in response to developmental cues and stress conditions

• Published in: The Plant journal : for cell and molecular biology Vol. 103; no. 1; pp. 357 - 378
• Main Authors: Chen, Mo‐Xian, Zhang, Kai‐Lu, Gao, Bei, Yang, Jing‐Fang, Tian, Yuan, Das, Debatosh, Fan, Tao, Dai, Lei, Hao, Ge‐Fei, Yang, Guang‐Fu, Zhang, Jianhua, Zhu, Fu‐Yuan, Fang, Yan‐Ming
• Format: Journal Article
• Language: English
• Published: England Blackwell Publishing Ltd 01.07.2020
• Subjects: Algae; Alternative splicing; Angiosperms; Conserved Sequence - genetics; Deoxyribonucleic acid; DNA; DNA, Plant - genetics; Environmental stress; Gene expression; Genes; Genes, Plant - genetics; Genetic analysis; Genome-Wide Association Study; Genomes; Insertion; Isoforms; Macromolecules; Osmotic stress; Phylogenetics; Phylogeny; plants; Plants - genetics; Plants - metabolism; promoter; Promoter Regions, Genetic - genetics; Proteins; Proteomes; Ribonucleoprotein, U1 Small Nuclear - classification; Ribonucleoprotein, U1 Small Nuclear - genetics; Ribonucleoprotein, U1 Small Nuclear - metabolism; Ribonucleoproteins (small nuclear); RNA Splice Sites - genetics; Spliceosomes - genetics; Spliceosomes - metabolism; Splicing; Splicing factors; stress response; Stress, Physiological; Synteny - genetics; Transcription; U1‐snRNP; Yeasts; stress response; alternative splicing; plants; phylogenetics; promoter; gene expression; U1-snRNP
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/tpj.14735

SUMMARY Intron‐containing genes have the ability to generate multiple transcript isoforms by splicing, thereby greatly expanding the eukaryotic transcriptome and proteome. In eukaryotic cells, precursor mRNA (pre‐mRNA) splicing is performed by a mega‐macromolecular complex defined as a spliceosome. Among its splicing components, U1 small nuclear ribonucleoprotein (U1 snRNP) is the smallest subcomplex involved in early spliceosome assembly and 5′‐splice site recognition. Its central component, named U1‐70K, has been extensively characterized in animals and yeast. Very few investigations on U1‐70K genes have been conducted in plants, however. To this end, we performed a comprehensive study to systematically identify 115 U1‐70K genes from 67 plant species, ranging from algae to angiosperms. Phylogenetic analysis suggested that the expansion of the plant U1‐70K gene family was likely to have been driven by whole‐genome duplications. Subsequent comparisons of gene structures, protein domains, promoter regions and conserved splicing patterns indicated that plant U1‐70Ks are likely to preserve their conserved molecular function across plant lineages and play an important functional role in response to environmental stresses. Furthermore, genetic analysis using T‐DNA insertion mutants suggested that Arabidopsis U1‐70K may be involved in response to osmotic stress. Our results provide a general overview of this gene family in Viridiplantae and will act as a reference source for future mechanistic studies on this U1 snRNP‐specific splicing factor. Significance Statement This study describes a comprehensive analysis to systematically name and identify 115 U1‐70K genes from 67 plant species, ranging from algae to angiosperms.