Circadian Waves of Transcriptional Repression Shape PIF-Regulated Photoperiod-Responsive Growth in Arabidopsis

Abstract

Plants coordinate their growth and development with the environment through integration of circadian clock and photosensory pathways. In Arabidopsis thaliana, rhythmic hypocotyl elongation in short days (SD) is enhanced at dawn by the basic-helix-loop-helix (bHLH) transcription factors PHYTOCHROME-INTERACTING FACTORS (PIFs) directly inducing expression of growth-related genes [1-6]. PIFs accumulate progressively during the night and are targeted for degradation by active phytochromes in the light, when growth is reduced. Although PIF proteins are also detected during the day hours [7-10], their growth-promoting activity is inhibited through unknown mechanisms. Recently, the core clock components and transcriptional repressors PSEUDO-RESPONSE REGULATORS PRR9/7/5 [11, 12], negative regulators of hypocotyl elongation [13, 14], were described to associate to G boxes [15], the DNA motifs recognized by the PIFs [16, 17], suggesting that PRR and PIF function might converge antagonistically to regulate growth. Here we report that PRR9/7/5 and PIFs physically interact and bind to the same promoter region of pre-dawn-phased, growth-related genes, and we identify the transcription factor CDF5 [18, 19] as target of this interplay. In SD, CDF5 expression is sequentially repressed from morning to dusk by PRRs and induced pre-dawn by PIFs. Consequently, CDF5 accumulates specifically at dawn, when it induces cell elongation. Our findings provide a framework for recent TIMING OF CAB EXPRESSION 1 (TOC1/PRR1) data [5, 20] and reveal that the long described circadian morning-to-midnight waves of the PRR transcriptional repressors (PRR9, PRR7, PRR5, and TOC1) [21] jointly gate PIF activity to dawn to prevent overgrowth through sequential regulation of common PIF-PRR target genes such as CDF5.

Circadian Rhythms in Plants

“…The circadian clock also regulates hypocotyl elongation via control of PIF transactivation activity through other core clock components. TOC1 and the other repressive PRR proteins physically interact with the transactivating PIF proteins to inhibit the induction of growth-promoting genes (Liu et al 2016;Soy et al 2016;Zhu et al 2016;Martín et al 2018). Thus, the circadian clock and lightsignaling pathways facilitate late-night/earlyday phased hypocotyl elongation via multiple mechanisms.…”

Phytochrome light receptors control metabolic flux, and their action during seedling development sets the trajectory for biomass production

“…Interestingly, increased ABA levels and high expression of ABA synthetic genes have been reported for the prr975 mutant which also over-accumulates amino acids and organic acids (Fukushima et al 2009). Since PIFs and PRRs mutually repress each other (Martìn et al 2018), we speculate that ABA up-regulation is caused either by low PRR or high PIF levels.…”

The DOF Transcription Factors in Seed and Seedling Development

“…In addition to being involved in the negative control of clock-dependent photoperiodic flowering response [94,95], it was recently shown that CDF5 promotes cell expansion and hypocotyl elongation in a light-and clock-dependent manner [96]. CDF5 acts downstream of both the PIFs and the PRR9/7/5 (PSEUDO-RESPONSE REGULATORS 9/7/5) antagonistic pathway, which promote and, respectively, inhibit hypocotyl growth.…”

“…CDF5 acts downstream of both the PIFs and the PRR9/7/5 (PSEUDO-RESPONSE REGULATORS 9/7/5) antagonistic pathway, which promote and, respectively, inhibit hypocotyl growth. Both PIFs and PRRs target CDF5: PIFs induce pre-dawn expression of CDF5 to promote hypocotyl growth, whereas PRRs directly repress CDF5 from morning to dusk to prevent overgrowth of the hypocotyl [96] (Figure 2). Similarly, DAG1 has been recently shown to promote cell expansion and hypocotyl elongation [97]: light-grown dag1 mutant seedlings have hypocotyls significantly shorter than the wild-type, suggesting that DAG1 is a negative regulator in the light-mediated inhibition of hypocotyl elongation [73].…”

“…PRRs inhibit the activity of PIFs in post-dusk phase, gating the hypocotyl elongation to pre-dawn (upper panel). Schematic representation of the PRRs, PIFs and CDF5 proteins temporal activity (lower panel)[96]. CDF5 (CYCLING DOF FACTOR 5), PRRs (PSEUDO-RESPONSE REGULATORS), PIFs (PHYTOCHROME INTERACTING FACTORS).…”