The DEAD-box RNA helicase SHI2 functions in repression of salt-inducible genes and regulation of cold-inducible gene splicing

Abstract

Gene regulation is central for growth, development, and adaptation to environmental changes in all living organisms. Many genes are induced by environmental cues, and the expression of these inducible genes is often repressed under normal conditions. Here, we show that the SHINY2 (SHI2) gene is important for repressing salt-inducible genes and also plays a role in cold response. The shi2 mutant displayed hypersensitivity to cold, abscisic acid (ABA), and LiCl. Map-based cloning demonstrates that SHI2 encodes a DEAD- (Asp-Glu-Ala-Asp) box RNA helicase with similarity to a yeast splicing factor. Transcriptomic analysis of the shi2 mutant in response to cold revealed that the shi2 mutation decreased the number of cold-responsive genes and the magnitude of their response, and resulted in the mis-splicing of some cold-responsive genes. Under salt stress, however, the shi2 mutation increased the number of salt-responsive genes but had a negligible effect on mRNA splicing. Our results suggest that SHI2 is a component in a ready-for-transcription repressor complex important for gene repression under normal conditions, and for gene activation and transcription under stress conditions. In addition, SHI2 also serves as a splicing factor required for proper splicing of cold-responsive genes and affects 5' capping and polyadenylation site selection.

Modulation of plant development and chilling stress responses by alternative splicing events under control of the spliceosome protein SmEb in Arabidopsis

“…The increased chilling sensitivity of the smeb mutants are restored by the hy5 mutation, indicating that HY5 may be involved in mediating chilling responses downstream of SmEb. Previous studies have shown that certain mutants with altered sensitivity to cold stress are involved in pre-mRNA splicing (Guan et al, 2013;Nakaminami & Seki, 2018;Wang et al, 2020;Zhu et al, 2020). In addition, the previously published mutants are defective in not only splicing but also other RNA processing events.…”

“…Previous studies have shown that certain mutants with altered sensitivity to cold stress are involved in pre‐mRNA splicing (Guan et al, 2013; Nakaminami & Seki, 2018; Wang et al, 2020; Zhu et al, 2020). In addition, the previously published mutants are defective in not only splicing but also other RNA processing events.…”

DEAD-Box RNA Helicase Family in Physic Nut (Jatropha curcas L.): Structural Characterization and Response to Salinity

“…An RNA-Seq of A. thaliana plants from NaCl-treated seeds disclosed that 49% of genes with introns underwent splicing alterations, with 10% undergoing differential alternative splicing (SAD) [ 83 ]. In addition, after salinity exposure, plants of Gossypium davidsonii exhibited a significant increase (32%) in genes undergoing splicing alterations [ 84 ], while a crucial role in the stress response was played particularly by the SHI2 gene, with its DEAD-box activity in splicing cold response genes [ 85 ]. Another distinct cluster highlighted the biosynthesis of histidine, an amino acid crucial for plant growth, development, and responses to environmental factors, including salinity.…”

Mapping Quantitative Trait Loci for Cold Tolerance in Rice under Germination Stage by Whole Genome Resequencing and Analysis of Candidate Genes

“…Taken together, the results suggested that AtRH7 affects rRNA biogenesis and plays an important role in plant growth under cold stress (Yuelin Liu, 2016). Wang reported that SHINY2 encodes a DEAD-(Asp-Glu-Ala-Asp) box RNA helicase that serves as a splicing factor required for proper splicing of cold-responsive genes (Wang et al 2019).…”