HEMERA Couples the Proteolysis and Transcriptional Activity of PHYTOCHROME INTERACTING FACTORs in Arabidopsis Photomorphogenesis

Abstract

Phytochromes (phys) are red and far-red photoreceptors that control plant development and growth by promoting the proteolysis of a family of antagonistically acting basic helix-loop-helix transcription factors, the PHYTOCHROME-INTERACTING FACTORs (PIFs). We have previously shown that the degradation of PIF1 and PIF3 requires HEMERA (HMR). However, the biochemical function of HMR and the mechanism by which it mediates PIF degradation remain unclear. Here, we provide genetic evidence that HMR acts upstream of PIFs in regulating hypocotyl growth. Surprisingly, genomewide analysis of HMR-and PIF-dependent genes reveals that HMR is also required for the transactivation of a subset of PIF direct-target genes. We show that HMR interacts with all PIFs. The HMR-PIF interaction is mediated mainly by HMR's N-terminal half and PIFs' conserved active-phytochrome B binding motif. In addition, HMR possesses an acidic nine-aminoacid transcriptional activation domain (9aaTAD) and a loss-of-function mutation in this 9aaTAD impairs the expression of PIF target genes and the destruction of PIF1 and PIF3. Together, these in vivo results support a regulatory mechanism for PIFs in which HMR is a transcriptional coactivator binding directly to PIFs and the 9aaTAD of HMR couples the degradation of PIF1 and PIF3 with the transactivation of PIF target genes.

Phytochromes and Phytochrome Interacting Factors

“…DNA binding is not necessary for the light-induced degradation of PIFs (Al-Sady et al, 2008;Shen et al, 2008). However, HEMERA has been shown to couple PIF degradation with PIF transactivation of their target genes (Qiu et al, 2015). HEMERA is necessary for PIF degradation only under light-grown seedlings (Chen et al, 2010).…”

A Negative Feedback Loop between PHYTOCHROME INTERACTING FACTORs and HECATE Proteins Fine-Tunes Photomorphogenesis in Arabidopsis

“…Light signals induce rapid phosphorylation of PIFs (Leivar and Quail, 2011) and the lightinduced phosphorylation is necessary for PIF3 degradation (Ni et al, 2013). A polyubiquitin-recognizing factor (HEMERA) is also necessary for degradation of PIF1 and PIF3 under deetiolated conditions possibly by coupling PIFs transcriptional activation activity with proteasomal degradation (Chen et al, 2010;Galvão et al, 2012;Qiu et al, 2015). PIF1 and PIF4 are phosphorylated by Arabidopsis Casein Kinase 2 and BRASSINOSTEROID INSENSITIVE2, respectively, and this phosphorylation affects the light-induced degradation of PIF1 and PIF4 (Bu et al, 2011b;Bernardo-García et al, 2014).…”

Mechanism of Dual Targeting of the Phytochrome Signaling Component HEMERA/pTAC12 to Plastids and the Nucleus

“…PIF1, PIF3, and PIF5 inhibit chloroplast development by repressing nuclear-encoded photosynthetic genes Moon et al, 2008;Shin et al, 2009;Stephenson et al, 2009;Kim et al, 2011). Most PIFs accumulate to high levels in dark-grown seedlings, and photoactivated phys mediate photomorphogenetic reprogramming by interacting directly with PIFs and repressing their stability and activity in the light (Shen et al, 2005;Al-Sady et al, 2006;Oh et al, 2006;Lorrain et al, 2008;Leivar and Quail, 2011;Park et al, 2012;Qiu et al, 2015).…”

“…One of the first light responses at the cellular level is the translocation of photoactivated phys from the cytoplasm to the nucleus, where phys are further compartmentalized to subnuclear photosensory domains named photobodies (Sakamoto and Nagatani, 1996;Kircher et al, 1999;Yamaguchi et al, 1999;Chen et al, 2003Chen et al, , 2005Chen et al, , 2010Van Buskirk et al, 2012. A central mechanism by which phys control gene expression, possibly at photobodies, is by regulating the stability and activity of a group of nodal basic helix-loop-helix transcriptional regulators, the Phytochrome-Interacting Factors (PIFs; Shen et al, 2005;Al-Sady et al, 2006;Oh et al, 2006;Lorrain et al, 2008;Leivar and Quail, 2011;Park et al, 2012;Kaiserli et al, 2015;Qiu et al, 2015). Eight PIFs have been reported, including PIF1, PIF3-8, and PIL1 (PIF3-Like1), which perform overlapping and distinct antagonistic roles in photomorphogenesis (Ni et al, 1998;Huq and Quail, 2002;Huq et al, 2004;Khanna et al, 2004;Leivar et al, 2008a;Li et al, 2012;Luo et al, 2014).…”

“…The hmr mutant represents the founding member of a new class of photomorphogenetic mutants that show a combination of long hypocotyl and albino phenotypes (Chen et al, 2010;Chen and Chory, 2011). HMR transduces light signals by interacting directly with photoactivated phys and all PIFs, and it acts as a transcriptional coactivator that regulates the degradation and activity of PIF1 and PIF3 (Galvão et al, 2012;Qiu et al, 2015). Knocking out PIF1, PIF3, PIF4, and PIF5 rescues hmr's long hypocotyl phenotype but not its albino phenotype, indicating that HMR plays two separable roles: a PIF-dependent role in regulating hypocotyl elongation and a PIF-independent role in chloroplast biogenesis (Chen et al, 2010;Qiu et al, 2015).…”