Abstract
BackgroundSm-like proteins are highly conserved proteins that form the core of the U6 ribonucleoprotein and function in several mRNA metabolism processes, including pre-mRNA splicing. Despite their wide occurrence in all eukaryotes, little is known about the roles of Sm-like proteins in the regulation of splicing.ResultsHere, through comprehensive transcriptome analyses, we demonstrate that depletion of the Arabidopsis supersensitive to abscisic acid and drought 1 gene (SAD1), which encodes Sm-like protein 5 (LSm5), promotes an inaccurate selection of splice sites that leads to a genome-wide increase in alternative splicing. In contrast, overexpression of SAD1 strengthens the precision of splice-site recognition and globally inhibits alternative splicing. Further, SAD1 modulates the splicing of stress-responsive genes, particularly under salt-stress conditions. Finally, we find that overexpression of SAD1 in Arabidopsis improves salt tolerance in transgenic plants, which correlates with an increase in splicing accuracy and efficiency for stress-responsive genes.ConclusionsWe conclude that SAD1 dynamically controls splicing efficiency and splice-site recognition in Arabidopsis, and propose that this may contribute to SAD1-mediated stress tolerance through the metabolism of transcripts expressed from stress-responsive genes. Our study not only provides novel insights into the function of Sm-like proteins in splicing, but also uncovers new means to improve splicing efficiency and to enhance stress tolerance in a higher eukaryote.
Highlights
Sm-like proteins are highly conserved proteins that form the core of the U6 ribonucleoprotein and function in several mRNA metabolism processes, including pre-mRNA splicing
RNA sequencing of wild-type, sad1 mutant and SAD1-overexpressing plants The Arabidopsis sad1 mutant was isolated in our previous genetic screen for components that regulate the expression of stress-responsive genes [14]
The transgenic plants in both backgrounds had similar physiological and molecular phenotypes, here we mainly focus on SAD1-overexpressing plants (SAD1-OE) in the sad1 mutant background
Summary
Sm-like proteins are highly conserved proteins that form the core of the U6 ribonucleoprotein and function in several mRNA metabolism processes, including pre-mRNA splicing. Following transcription, many eukaryotic precursor messenger RNAs (pre-mRNA) are subjected to a series of modifications that are essential for the maturation, nuclear export and subsequent translation of these transcripts One such modification, the removal (splicing) of non-protein-coding sequences from pre-mRNA, is an important step in gene regulation that contributes to increased protein diversity from a limited number of genes. The LSm2-8 heptameric complex is located in the nucleus This complex directly binds and stabilizes the 3′-terminal poly(U) tract of U6 small nuclear RNA, forms the core of the U6 small nuclear ribonucleoproteins (RNPs) and functions in pre-mRNA splicing [12,13]. Recent studies suggested that the depletion of SAD1 and the other LSm protein (LSm8) reduced the stability of U6 RNPs and resulted in defects in pre-mRNA splicing that lead to intron retention in Arabidopsis [15,16]. It is still unclear if the depletion of SAD1 or other LSm proteins has any effect on the selection of splice sites and alternative splicing (AS), and whether overexpression of these LSm proteins could affect splicing efficiency or accuracy
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