Identification and Regulation of Tomato Serine/Arginine-Rich Proteins Under High Temperatures

Abstract

Alternative splicing is an important mechanism for the regulation of gene expression in eukaryotes during development, cell differentiation or stress response. Alterations in the splicing profiles of genes under high temperatures that cause heat stress (HS) can impact the maintenance of cellular homeostasis and thermotolerance. Consequently, information on factors involved in HS-sensitive alternative splicing is required to formulate the principles of HS response. Serine/arginine-rich (SR) proteins have a central role in alternative splicing. We aimed for the identification and characterization of SR-coding genes in tomato (Solanum lycopersicum), a plant extensively used in HS studies. We identified 17 canonical SR and two SR-like genes. Several SR-coding genes show differential expression and altered splicing profiles in different organs as well as in response to HS. The transcriptional induction of five SR and one SR-like genes is partially dependent on the master regulator of HS response, HS transcription factor HsfA1a. Cis-elements in the promoters of these SR genes were predicted, which can be putatively recognized by HS-induced transcription factors. Further, transiently expressed SRs show reduced or steady-state protein levels in response to HS. Thus, the levels of SRs under HS are regulated by changes in transcription, alternative splicing and protein stability. We propose that the accumulation or reduction of SRs under HS can impact temperature-sensitive alternative splicing.

Alternative Splicing Dynamics During the Lifecycle of Salvia miltiorrhiza Root Revealed the Fine Tuning in Root Development and Ingredients Biosynthesis

“…Chr3 contained five SR proteins, chr2, chr6, and chr7 contained two SR proteins, and the other four chromosomes contained one SR protein. They were clustered into six subgroups according to a phylogenetic tree that includes 52 SR proteins (18 in A. thaliana, and 19 in Oryza sativa) (Figure 5A), which was consistent with the known sub-families in plants (SCL, SR, SC, RSZ, RS2Z, and RS) (Rosenkranz et al, 2021). All SR genes showed variant gene structures with different introns numbers from 4 to 14.…”

“…As molecular adaptors, SR proteins modulate the constitutive and AS of pre-mRNAs, which play critical roles in the RNA metabolism of higher eukaryotes (Palusa and Reddy, 2010). They are characterized by the presence of one or two terminal RNA recognition motif (RRM) and a C-terminal domain rich in arginine-serine dipeptides (RS domain) (Rosenkranz et al, 2021). The RRM motif could recognize and bind with the target sequence, the RS domain is involved in the interaction between proteins, subnuclear location, and regulation of RNA binding, modulated by the phosphorylation status (Ngo et al, 2005;Palusa et al, 2007;Sahebi et al, 2016).…”

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

“…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. Of these, the expression of 22 and alternative splicing patterns of 17 genes in B. rapa were significantly altered in response to cold, heat, or oxidative stresses [20].…”

“…Although the precise mechanism responsible for stress-responsive RBP activation is limited, multiple lines of available evidence suggest that stress-responsive alternative splicing at post-transcriptional levels decides the activation/deactivation of RBPs under adverse conditions [34,36,37]. The early stress-response regulators are expected to perceive the primary stress signals and transduce them to the nucleus, where the upstream abiotic stress response cis-elements of RBP genes were targeted for its regulation [20,36,38] (Figure 1). The activity of existing RBPs can be transiently regulated by post-translational modifications and, indeed, RBPs are enriched in post-translational modification (PTM) sites [5,7].…”

“…SR proteins are non-small nuclear ribonucleoproteins (non-snRNP) which form complex spliceosome machinery that mediates numerous events in pre-mRNA splicing [20,97]. The canonical SR domain proteins consist of one or two N-terminal RNA recognition motifs (RRMs), which bind to the RNA targets, and a serine-arginine or arginine-serine dipeptide-rich C-terminal-terminal region (RS domain) with a variable length [36,43,97]. Based on the domain organization structures and the presence of amino acid sequence motifs, SR proteins can be classified into six subfamilies: SR (two RRM), RS (two RRM, but the second RRM lacks SWQDLKD motif), SC (with just 1 RRM), SCL (SC-like with charged N terminal AA residues), RSZ (CCHC zinc knuckle), and RS2Z (two CCHC zinc knuckles) [44,98,99].…”