PIF1 directly and indirectly regulates chlorophyll biosynthesis to optimize the greening process in Arabidopsis

Abstract

Plants depend on light signals to modulate many aspects of their development and optimize their photosynthetic capacity. Phytochromes (phys), a family of photoreceptors, initiate a signal transduction pathway that alters expression of a large number of genes to induce these responses. Recently, phyA and phyB were shown to bind members of a basic helix-loop-helix family of transcription factors called phy-interacting factors (PIFs). PIF1 negatively regulates chlorophyll biosynthesis and seed germination in the dark, and lightinduced degradation of PIF1 relieves this negative regulation to promote photomorphogenesis. Here, we report that PIF1 regulates expression of a discrete set of genes in the dark, including protochlorophyllide oxidoreductase (POR), ferrochelatase (FeChII), and heme oxygenase (HO3), which are involved in controlling the chlorophyll biosynthetic pathway. Using ChIP and DNA gel-shift assays, we demonstrate that PIF1 directly binds to a G-box (CACGTG) DNA sequence element present in the PORC promoter. Moreover, in transient assays, PIF1 activates transcription of PORC in a G-boxdependent manner. These data strongly suggest that PIF1 directly and indirectly regulates key genes involved in chlorophyll biosynthesis to optimize the greening process in Arabidopsis.basic helix-loop-helix transcription factors ͉ photomorphogenesis ͉ phytochrome signaling ͉ transcriptional regulation ͉ G-box

PIFs: Systems Integrators in Plant Development

“…Microarray studies using dark-grown single mutants for PIF3 (Monte et al, 2004;Leivar et al, 2009;Sentandreu et al, 2011) or PIF1 (Moon et al, 2008), and double mutants for PIF4 and PIF5 , showed relatively modest contributions of individual PIFs in regulating gene expression genome wide, consistent with the absence of robust morphological phenotypes of these mutants in the dark due to genetic redundancy (Leivar et al, 2008b(Leivar et al, , 2012bShin et al, 2009). In sharp contrast, the transcriptomic profile of pifq mutants in the dark largely resemble that of wild-type seedlings grown in the light (Leivar et al, 2009;Shin et al, 2009).…”

“…The defined binding sites for these PIFs are located predominantly in promoter regions of target genes and are strongly enriched in the DNA motif G-box (CACGTG) and the E-box variant (CACATG and CATGTG) that has been called the PBE-box (for PIF binding E-box), suggesting that these PIFs have similar sequence recognition requirements in terms of DNA binding (Hornitschek et al, 2012;Oh et al, 2012;Zhang et al, 2013). In vitro assays have shown specific binding to the G-box for all the PIFs tested (PIF1, PIF3, PIF4, PIF5, and PIF7) (Martínez-García et al, 2000;Huq and Quail, 2002;Leivar et al, 2008a;Moon et al, 2008;Hornitschek et al, 2009) and to the PBE-box for PIF1, PIF3, and PIF4 (Kim et al, 2008;Hornitschek et al, 2012;Zhang et al, 2013).…”

“…During seedling deetiolation, PIFs promote cotyledon greening and prevent photodamage by regulating the production of chlorophyll precursors and carotenoids in the dark. This action involves direct PIF repression of genes like PORC (which encodes the Pchlide reductase C enzyme that catalyzes the conversion of Pchlide to chlorophyll), CHLH, and PSY Moon et al, 2008;Shin et al, 2009;ToledoOrtiz et al, 2010;Cheminant et al, 2011). Evidence also indicates that, in etiolated seedlings, DELLAs accumulate in the cotyledons and work in antagonistic fashion with the PIFs to derepress chlorophyll and carotenoid biosynthesis, at least in part by inhibiting PIF binding to their targets (Cheminant et al, 2011).…”

Phytochromes and Phytochrome Interacting Factors

“…2; Shi et al, 2013;Lee et al, 2015). PIF1 also regulates chlorophyll biosynthesis and plastid development by modulating the expression of a number of genes Moon et al, 2008;Kim et al, 2016c). PIF2 (more commonly known as PIL1) also interacts with COP1 and phyB in vivo ( Fig.…”

NO FLOWERING IN SHORT DAY (NFL) is a bHLH transcription factor that promotes flowering specifically under short-day in Arabidopsis

“…The qRT-PCR was performed as previously described (Kim and Sung, 2010;Moon et al, 2008). Briefly, apical tissues including meristem were harvested from 60-day-old wt and nfl mutant plants grown under SD conditions at T0 ( just prior to turning on light at dawn) and total RNA was isolated as described above.…”