Bypassing miRNA-mediated gene regulation under drought stress: alternative splicing affects CSD1 gene expression

The binding site for miR398 in an isoform of Cu/Zn superoxide dismutase (CSD1) is eliminated by alternative splicing to bypass miR398-mediated gene down-regulation under drought stress. MicroRNA (miRNA) binding sites (MBSs) are frequently interrupted by introns and therefore require proper splicing to generate functional MBSs in target transcripts. MBSs can also be excluded during splicing of pre-messenger RNA, leading to different regulation among isoforms. Previous studies have shown that levels of Cu/Zn superoxide dismutase (CSD) are down-regulated by miR398. In this study, sequences and transcript levels of peanut CSD1 isoforms (AhCSD1-1, AhCSD1-2.1, and AhCSD1-2.2) were analyzed under the drought stress. Results demonstrated that a miR398 binding site is eliminated in AhCSD1-2.2 as a consequence of alternative splicing, which bypasses miRNA-mediated down-regulation under drought stress. This alternative isoform was not only identified in peanut but also in soybean and Arabidopsis. In addition, transgenic Arabidopsis plants expressing AhCSD1 were more tolerant to osmotic stress. We hypothesize that the level of AhCSD1 is increased to allow diverse plant responses to overcome environmental challenges even in the presence of increased miR398 levels. These findings suggest that studies on the role of alternatively spliced MBSs affecting transcript levels are important for understanding plant stress responses.