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

Abstract

Cold stress resulting from chilling and freezing temperatures substantially inhibits plant growth and reduces crop production worldwide. Tremendous research efforts have been focused on elucidating the molecular mechanisms of freezing tolerance in plants. However, little is known about the molecular nature of chilling stress responses in plants. Here we found that two allelic mutants in a spliceosome component gene SmEb (smeb‐1 and smeb‐2) are defective in development and responses to chilling stress. RNA‐seq analysis revealed that SmEb controls the splicing of many pre‐messenger RNAs (mRNAs) under chilling stress. Our results suggest that SmEb is important to maintain proper ratio of the two COP1 splicing variants (COP1a/COP1b) to fine tune the level of HY5. In addition, the transcription factor BES1 shows a dramatic defect in pre‐mRNA splicing in the smeb mutants. Ectopic expression of the two BES1 splicing variants enhances the chilling sensitivity of the smeb‐1 mutant. Furthermore, biochemical and genetic analysis showed that CBFs act as negative upstream regulators of SmEb by directly suppressing its transcription. Together, our results demonstrate that proper alternative splicing of pre‐mRNAs controlled by the spliceosome component SmEb is critical for plant development and chilling stress responses.

The Sm core protein SmEb regulates salt stress responses through maintaining proper splicing of RCD1 pre‐mRNA in Arabidopsis

“…However, overexpression of SmEb is unable to improve salt resistance in transgenic plants (Figure S6), suggesting a possible tissuespecific function of SmEb required for salt stress response. This notion is in accordance with the finding that the phenotype of smeb mutant plants can be recovered by expressing SmEb promoter-driven SmEa gene which encodes for another SmE protein (Wang et al, 2022). LSM8 and SmD3b are two spliceosome proteins essential for plants, but only SmD3b plays a role in salt stress response (Figure 2C, D).…”

“…To elucidate the role of SmEb in salt stress response, we performed transcriptome analysis using smeb‐1 , smeb‐2 , and Col‐0 seedlings treated with 150 mM NaCl for 6 h. Under normal growth conditions, 55 differential alternative splicing events of 27 genes were identified in smeb mutants compared to the wild type (Wang et al, 2022). Under salt stress condition, 634 differential alternative splicing events of 375 genes were identified in smeb mutants, while 497 differential alternative splicing events of 441 unique genes occurred in the Col‐0 plants (Figure 3A, B).…”

“…Heptameric ring of Sm proteins assembled by SmB, SmD1, SmD2, SmD3, SmE, SmF, and SmG directly binds to U‐rich snRNAs as core components of snRNPs. In plants, SmE proteins (two paralogous proteins named SmEa and SmEb) have been considered as the interactors of SmFb, SmGa, and SmGb in the heptameric Sm ring (Wang et al, 2022). The splice site recognition begins from U1 snRNP interacting with the 5' splice site and U2 auxiliary factor recognizing the 3' splice site, and then U2 snRNP integrates into the branch point.…”

Alternative Splicing Plays a Crucial Role in the Salt Tolerance of Foxtail Millet

“…16 Furthermore, the AS of SmEb has been associated with plant cold stress. 17 Previous research categorizes AS into seven main types: Alternative 3′ splice site (A3), Alternative 5′ splice site (A5), Alternative First exon (AF), Alternative Last exon (AL), Mutually exclusive exon (MX), Retained intron (RI), and Skipping exon (SE). 18 Cyclophilins (CYPs) are members of the peptidyl-prolyl cistrans isomerase family.…”

“…Another study demonstrated that the AS-related gene Sm core protein SmEb enhances salt tolerance in Arabidopsis thaliana by regulating the AS of pre-mRNA of RCD1 . Furthermore, the AS of SmEb has been associated with plant cold stress . Previous research categorizes AS into seven main types: Alternative 3′ splice site (A3), Alternative 5′ splice site (A5), Alternative First exon (AF), Alternative Last exon (AL), Mutually exclusive exon (MX), Retained intron (RI), and Skipping exon (SE) …”