Light regulation and functional characterization of Phytochrome Interacting Factor 1 (PIF1) in Arabidopsis

Plants sense light intensity, quality and direction through a group of photoreceptors to modulate their growth and development. One family of photoreceptor is called phytochromes (phys) that perceives red and far red light. Phys transduce light signals via a sub-family of the basic Helix-Loop-Helix (bHLH) transcription factors called Phytochrome Interacting Factors (PIFs). PIFs function as negative regulators in the phy-mediated light signaling pathways. In darkness, PIFs regulate downstream gene expressions to inhibit photomorphogenesis. Upon light exposure, PIFs are phosphorylated and poly-ubiquitylated prior to their rapid degradation through the 26S proteasome pathway. One of the PIFs, PIF1, has the highest affinity for both phyA and phyB and also displayed the fastest degradation kinetics under both red and far red light. Here we showed that PIF1 directly and indirectly regulates key genes involved in chlorophyll biosynthesis to optimize the greening process in Arabidopsis. PIF1 binds to a G-box (CACGTG) DNA sequence element present in its direct target genes (e.g., protochlorophyllide oxidoreductase C, PORC) in darkness and regulates their expression. Structure-function studies revealed two separate regions called APB and APA necessary for binding to phyB and phyA, respectively, located at the amino-terminus and a novel phosphorylation site at the carboxy-terminus of PIF1. Both amino- and carboxy-terminal regions are necessary for the light-induced degradation of PIF1. However, the DNA binding is not necessary for the light-induced degradation of PIF1. Using a targeted systems biology approach, we identified new factors, HECATE proteins that promote photomorphogenesis by negatively regulating the function of PIF1. Moreover, we employed an unbiased genetic screening using luciferase imaging system to identify new mutants defective in the light-induced degradation of PIF1. The cloning and characterization of these mutants will help identify the factors, such as the kinase and E3 ligase, responsible for the light-induced degradation of PIF1. Taken together, these data revealed detail mechanisms of how PIF1 negatively regulates photomorphogenesis and how light induces rapid degradation of PIF1 to promote photomorphogenesis.