AUTHOR=Ma Hui , Cai Lingling , Lin Juncheng , Zhou Kaiyue , Li Qingshun Q. 

TITLE=Divergence in the Regulation of the Salt Tolerant Response Between Arabidopsis thaliana and Its Halophytic Relative Eutrema salsugineum by mRNA Alternative Polyadenylation

JOURNAL=Frontiers in Plant Science

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.866054

DOI=10.3389/fpls.2022.866054

ISSN=1664-462X

ABSTRACT=<p>Salt tolerance is an important mechanism by which plants can adapt to a saline environment. To understand the process of salt tolerance, we performed global analyses of mRNA alternative polyadenylation (APA), an important regulatory mechanism during eukaryotic gene expression, in <italic>Arabidopsis thaliana</italic> and its halophytic relative <italic>Eutrema salsugineum</italic> with regard to their responses to salt stress. Analyses showed that while APA occurs commonly in both <italic>Arabidopsis</italic> and <italic>Eutrema</italic>, <italic>Eutrema</italic> possesses fewer APA genes than <italic>Arabidopsis</italic> (47% vs. 54%). However, the proportion of APA genes was significantly increased in <italic>Arabidopsis</italic> under salt stress but not in <italic>Eutrema</italic>. This indicated that <italic>Arabidopsis</italic> is more sensitive to salt stress and that <italic>Eutrema</italic> exhibits an innate response to such conditions. Both species utilized distal poly(A) sites under salt stress; however, only eight genes were found to overlap when their 3′ untranslated region (UTR) lengthen genes were compared, thus revealing their distinct responses to salt stress. In <italic>Arabidopsis</italic>, genes that use distal poly(A) sites were enriched in response to salt stress. However, in <italic>Eutrema</italic>, the use of poly(A) sites was less affected and fewer genes were enriched. The transcripts with upregulated poly(A) sites in <italic>Arabidopsis</italic> showed enriched pathways in plant hormone signal transduction, starch and sucrose metabolism, and fatty acid elongation; in <italic>Eutrema</italic>, biosynthetic pathways (stilbenoid, diarylheptanoid, and gingerol) and metabolic pathways (arginine and proline) showed enrichment. APA was associated with 42% and 29% of the differentially expressed genes (DE genes) in <italic>Arabidopsis</italic> and <italic>Eutrema</italic> experiencing salt stress, respectively. Salt specific poly(A) sites and salt-inducible APA events were identified in both species; notably, some salt tolerance-related genes and transcription factor genes exhibited differential APA patterns, such as <italic>CIPK21</italic> and <italic>LEA4-5</italic>. Our results suggest that adapted species exhibit more orderly response at the RNA maturation step under salt stress, while more salt-specific poly(A) sites were activated in <italic>Arabidopsis</italic> to cope with salinity conditions. Collectively, our findings not only highlight the importance of APA in the regulation of gene expression in response to salt stress, but also provide a new perspective on how salt-sensitive and salt-tolerant species perform differently under stress conditions through transcriptome diversity.</p>