Identification of Primary Target Genes of Phytochrome Signaling. Early Transcriptional Control during Shade Avoidance Responses in Arabidopsis

Abstract

The phytochrome (phy) photoreceptors modulate plant development after perception of light. Upon illumination of etiolated seedlings, phys initiate a transcriptional cascade by directly transducing light signals to the promoters of genes encoding regulators of morphogenesis. In light-grown plants, however, little is known about the transcriptional cascade modulated by phys in response to changes in light. The phy entry points in this cascade are completely unknown. We are particularly interested in the shade avoidance syndrome (SAS). Here we describe a subset of six genes whose expression is rapidly modulated by phys during both deetiolation and SAS in Arabidopsis (Arabidopsis thaliana). Using cycloheximide, we provide evidence that four of these phy rapidly regulated (PAR) genes are direct targets of phy signaling during SAS, revealing these genes as upstream components of the transcriptional cascade. Promoter-b-glucuronidase fusions confirmed that PAR genes are photoregulated at the transcriptional level. Analysis of gene expression in light signal transduction mutants showed that COP1 and DET1 (but not DET2 or HY5) play a role in modulating PAR expression in response to shade in light-grown seedlings. Moreover, genetic analyses showed that one of the genes identified as a direct target of phy signaling was phy-interacting factor 3-like-1 (PIL1). PIL1 has previously been implicated in SAS in response to transient shade, but we show here that it also plays a key role in response to long-term shade. The action of PIL1 was particularly apparent in a phyB background, suggesting an important negative role for PIL1 under dense vegetation canopies.

Dynamic Antagonism between Phytochromes and PIF Family Basic Helix-Loop-Helix Factors Induces Selective Reciprocal Responses to Light and Shade in a Rapidly Responsive Transcriptional Network in Arabidopsis

“…We define those genes with FIR values >1.5 as being moderately to robustly dependent on the four PIFs for shade responsiveness (Table 1) and those with FIR values <1.5 as being marginally to minimally dependent on these PIFs for shade responsiveness (see Supplemental Data Set 18 online). Several genes previously well documented as rapidly shadeinduced marker genes, including ARABIDOPSIS THALIANA HOMEOBOX PROTEIN2 (ATHB2), XTR7, HFR1, PHY RAPIDLY REGULATED1 (PAR1), and INDOLE-3-ACETIC ACID INDUC-IBLE29 (IAA29) (Roig-Villanova et al, 2006, 2007Carabelli et al, 2007;Lorrain et al, 2008), are identified here as being robustly dependent on the PIF quartet for this rapid shade responsiveness (Table 1; see Supplemental Data Set 18 online).…”

Phytochrome‐mediated inhibition of shade avoidance involves degradation of growth‐promoting bHLH transcription factors

“…Analysis of phytochrome mutants has demonstrated that, in Arabidopsis, phyB, phyD and phyE are the major phytochromes inhibiting shade avoidance (Devlin et al, 1998;Franklin et al, 2003). The search for genes up-regulated in response to shade led to the identification of several transcription factors that are very rapidly induced in response to low R/FR ratios (Carabelli et al, 1993;Devlin et al, 2003;Roig-Villanova et al, 2006;Salter et al, 2003;Sessa et al, 2005). Functional characterization of these genes indicated that, while ATHB-2 promotes growth responses associated with shade, HFR1 is part of a negative branch preventing 'over-reaction' in response to canopy light (Roig-Villanova et al, 2006;Salter et al, 2003;Sessa et al, 2005;Steindler et al, 1999).…”

“…The search for genes up-regulated in response to shade led to the identification of several transcription factors that are very rapidly induced in response to low R/FR ratios (Carabelli et al, 1993;Devlin et al, 2003;Roig-Villanova et al, 2006;Salter et al, 2003;Sessa et al, 2005). Functional characterization of these genes indicated that, while ATHB-2 promotes growth responses associated with shade, HFR1 is part of a negative branch preventing 'over-reaction' in response to canopy light (Roig-Villanova et al, 2006;Salter et al, 2003;Sessa et al, 2005;Steindler et al, 1999). As ATHB-2 and PIL1 expression is constitutively high in phy mutants, especially in the phyB phyD phyE triple mutants, the high level of their mRNA during shade conditions may result from a phytochrome-dependent de-repression mechanism (Salter et al, 2003).…”

Green Light Induces Shade Avoidance Symptoms

“…On the other hand, PHYB transcripts did accumulate with the addition of green light, consistent with the increases observed by Devlin et al (2003) in response to far-red light. The HY5 transcript has been well described in photomorphogenic responses, yet it is not required for transducing shade-triggered signals (Roig-Villanova et al, 2006). Here, this transcript serves as an additional non-shade-associated message that is sensitive to changing light environments, and its levels also increase.…”

“…PIL1 encodes a bHLH transcription factor and is a member of the PIF transcription factor family. It has been described to play an important negative role in long-term shade avoidance syndrome in a phyB background, aside from its effect on shade stimulation (Roig-Villanova et al, 2006). The transcript levels of HAT4 and PIL1 are welldescribed molecular signatures of the shade response.…”