Brassica Rapa SR45a Regulates Drought Tolerance via the Alternative Splicing of Target Genes

Abstract

The emerging evidence has shown that plant serine/arginine-rich (SR) proteins play a crucial role in abiotic stress responses by regulating the alternative splicing (AS) of key genes. Recently, we have shown that drought stress enhances the expression of SR45a (also known as SR-like 3) in Brassica rapa. Herein, we unraveled the hitherto unknown functions of BrSR45a in drought stress response by comparing the phenotypes, chlorophyll a fluorescence and splicing patterns of the drought-responsive genes of Arabidopsis BrSR45a overexpressors (OEs), homozygous mutants (SALK_052345), and controls (Col-0). Overexpression and loss of function did not result in aberrant phenotypes; however, the overexpression of BrSR45a was positively correlated with drought tolerance and the stress recovery rate in an expression-dependent manner. Moreover, OEs showed a higher drought tolerance index during seed germination (38.16%) than the control lines. Additionally, the overexpression of BrSR45a induced the expression of the drought stress-inducible genes RD29A, NCED3, and DREB2A under normal conditions. To further illustrate the molecular linkages between BrSR45a and drought tolerance, we investigated the AS patterns of key drought-tolerance and BrSR45a interacting genes in OEs, mutants, and controls under both normal and drought conditions. The splicing patterns of DCP5, RD29A, GOLS1, AKR, U2AF, and SDR were different between overexpressors and mutants under normal conditions. Furthermore, drought stress altered the splicing patterns of NCED2, SQE, UPF1, U4/U6-U5 tri-snRNP-associated protein, and UPF1 between OEs and mutants, indicating that both overexpression and loss of function differently influenced the splicing patterns of target genes. This study revealed that BrSR45a regulates the drought stress response via the alternative splicing of target genes in a concentration-dependent manner.

Analysis of Whole Transcriptome RNA-seq Data Reveals Many Alternative Splicing Events in Soybean Roots under Drought Stress Conditions

“…Interestingly, plant SPF-related genes themselves also undergo AS in a developmental and tissue-specific manner as well as in response to various hormones and abiotic stresses [ 10 , 12 , 51 ]. Overexpression of BrSR45a in Arabidopsis not only increased the abundance of the drought stress-inducible genes but also influenced the splicing patterns of target genes [ 52 ]. The transcript abundance and the ratio of exon-skipped transcripts of AtSR45a were promoted by heat and drought stress in Arabidopsis [ 53 ].…”

“…AS has been studied extensively in several plant species. The concept of deep learning and gene editing technology (Clusters of Regularly Interspaced Short Palindromic Repeats, CRISPR) have been used to identify AS events and gene function [ 52 , 56 , 57 ]. Moreover, differences in the recognition sequences of splice sites have been reported between plants and animals [ 26 , 58 , 59 ].…”

Characterization of the Gene Expression Profile Response to Drought Stress in Populus ussuriensis Using PacBio SMRT and Illumina Sequencing

“…Some mRNA precursors of eukaryotic genes produce different mRNA splicing isoforms through different splicing methods, which produce proteome and genetic diversity in eukaryotes [ 19 , 20 ]. There have been reports that AS mediates drought response, for example, maize plants overexpressing three different ZmCCA1 isoforms distinguished by AS events showed different tolerance to drought stress [ 21 ], and BrSR45a regulates drought stress response by influencing AS of target genes [ 22 ]. Although many AS events have been identified in this study, different functions of these AS events on drought stress need to be further investigated.…”

Plant RNA Binding Proteins as Critical Modulators in Drought, High Salinity, Heat, and Cold Stress Responses: An Updated Overview

“…Further, it was shown that SR45a is essentially important for alternative splicing and mRNA maturation of several salt-tolerance genes. In B. rapa, BrSR45a was induced by drought stress, and the overexpression of BrSR45a improved drought tolerance in Arabidopsis [45]. Further analysis revealed that BrSR45a overexpression resulted in alternative splicing of drought-stress response genes and BrSR45a interacting genes.…”

“…Of these, three subfamilies (SR, SC, and RSZ) were found only in plants. Additionally, a few SR-like genes (e.g., SR45, SR45a) were found to have two RS domains instead of the one found in typical SR proteins [45,100,101]. Genome-wide identification of SR proteins in Brassica rapa [20], wheat, Brachypodium distachyon [44], tomato [36], and Cassava [43] resulted in 28, 40, 18, 19, and 18 SR genes, respectively.…”