Phylogenetic Analysis of the Plant U2 snRNP Auxiliary Factor Large Subunit A Gene Family in Response to Developmental Cues and Environmental Stimuli

Abstract

In all organisms, splicing occurs through the formation of spliceosome complexes, and splicing auxiliary factors are essential during splicing. U2AF65 is a crucial splicing cofactor, and the two typical RNA-recognition motifs at its center recognize and bind the polypyrimidine sequence located between the intron branch site and the 3′-splice site. U2AF65A is a member of the U2AF65 gene family, with pivotal roles in diseases in mammals, specifically humans; however, few studies have investigated plant U2AF65A, and its specific functions are poorly understood. Therefore, in the present study, we systematically identified U2AF65A in plant species from algae to angiosperms. Based on 113 putative U2AF65A sequences from 33 plant species, phylogenetic analyses were performed, followed by basic bioinformatics, including the comparisons of gene structure, protein domains, promoter motifs, and gene expression levels. In addition, using rice as the model crop, we demonstrated that the OsU2AF65A protein is localized to the nucleus and cytoplasm, and it is involved in responses to various stresses, such as drought, high salinity, low temperature, and heavy metal exposure (e.g., cadmium). Using Arabidopsis thaliana and rice mutants, we demonstrated that U2AF65A is involved in the accumulation of plant biomass, growth of hypocotyl upon thermal stimulation, and reduction of tolerance of high temperature stress. These findings offer an overview of the U2AF65 gene family and its stress response functions, serving as the reference for further comprehensive functional studies of the essential specific splicing cofactor U2AF65A in the plant kingdom.

The OsCBL8–OsCIPK17 Module Regulates Seedling Growth and Confers Resistance to Heat and Drought in Rice

“…The growth and stress treatments of NIP were performed according to the procedure published by Lu et al [ 55 ] with minor modifications. Seedlings were cultivated hydroponically with Mucun B nutrient solution, in a climate chamber (QY-14; Quanyou Electronic Technology Co., Ltd., Nanjing, China) at 22 °C/20 °C under a 16 h/8 h light/dark cycle at a light intensity of 100 μmol m −2 s −1 .…”

Differential alternative splicing genes and isoform co-expression networks of Brassica napus under multiple abiotic stresses

“…In addition, we also found that U2 snRNP auxiliary factor encoding gene, U2AF65A ( MSTRG.17488 ), was DAS by A3SS event under 4 h of cold. OsU2AF65A was certificated to mediate response to various stresses, such as drought, cold, high salt, and heavy metal exposure in rice ( Lu et al., 2021 ).…”

“…OsU2AF65A was certificated to mediate response to various stresses, such as drought, cold, high salt, and heavy metal exposure in rice (Lu et al, 2021).…”

Phylogenetic analysis and stress response of the plant U2 small nuclear ribonucleoprotein B″ gene family

“…The CDS of OsU2B″ (LOC_Os03g18720.1) was amplified using gene-specific primers (5'-CCT GTT GTT TGG TGT TAC TTA AGC TTA TGT TGT CCG GCG ACA TACC-3' and 5'-TCC TCG CCC TTG CTC ACC ATG GAT CCT CAC TTC TTT GCG TAG GAT ATA GCC-3') and inserted into the GFP (pGreen II-UBI-GFP) vector to generate a fusion construct according to Lu et al [1]. NLS − mCherry (SV40 large − T antigen NLS, a signal peptide guiding GFP into the nucleus) was selected as a marker for nuclear localisation [54].…”

“…In contrast to the model of the 1 gene-1 polypeptide in prokaryotes, eukaryotic genes contain exons and introns. They generate mature mRNAs via splicing, which is an important post-transcriptional regulatory link during pre-mRNA splicing [ 1 ]. In the splicing process, the U1 snRNP identifies and binds to the 5'-terminal splicing site of the intron [ 2 ].…”