<i>Arabidopsis</i> PP6 phosphatases dephosphorylate PIF proteins to repress photomorphogenesis

Abstract

The PHYTOCHROME-INTERACTING FACTORs (PIFs) play a central role in repressing photomorphogenesis, and phosphorylation mediates the stability of PIF proteins. Although the kinases responsible for PIF phosphorylation have been extensively studied, the phosphatases that dephosphorylate PIFs remain largely unknown. Here, we report that seedlings with mutations in <i>FyPP1</i> and <i>FyPP3</i>, 2 genes encoding the catalytic subunits of protein phosphatase 6 (PP6), exhibited short hypocotyls and opened cotyledons in the dark, which resembled the photomorphogenic development of dark-grown <i>pifq</i> mutants. The hypocotyls of dark-grown sextuple mutant <i>fypp1 fypp3</i> (<i>f1 f3</i>) <i>pifq</i> were shorter than those of parental mutants <i>f1 f3</i> and <i>pifq</i>, indicating that PP6 phosphatases and PIFs function synergistically to repress photomorphogenesis in the dark. We showed that FyPPs directly interacted with PIF3 and PIF4, and PIF3 and PIF4 proteins exhibited mobility shifts in <i>f1 f3</i> mutants, consistent with their hyperphosphorylation. Moreover, PIF4 was more rapidly degraded in <i>f1 f3</i> mutants than in wild type after light exposure. Whole-genome transcriptomic analyses indicated that PP6 and PIFs coregulated many genes, and PP6 proteins may positively regulate PIF transcriptional activity. These data suggest that PP6 phosphatases may repress photomorphogenesis by controlling the stability and transcriptional activity of PIF proteins via regulating PIF phosphorylation.