REP1, a basic helix-loop-helix protein, is required for a branch pathway of phytochrome A signaling in arabidopsis

Integration of light signaling with photoperiodic flowering and circadian rhythm

Plants become photosynthetic through de-etiolation, a developmental process regulated by red/far-red light-absorbing phytochromes and blue/ultraviolet A light-absorbing cryptochromes. Genetic screens have identified in the last decade many far-red light signaling mutants and several red and blue light signaling mutants, suggesting the existence of distinct red, far-red, or blue light signaling pathways downstream of phytochromes and cryptochromes. However, genetic screens have also identified mutants with defective de-etiolation responses under multiple wavelengths. Thus, the optimal de-etiolation responses of a plant depend on coordination among the different light signaling pathways. This review intends to discuss several recently identified signaling components that have a potential role to integrate red, far-red, and blue light signalings. This review also highlights the recent discoveries on proteolytic degradation in the desensitization of light signal transmission, and the tight connection of light signaling with photoperiodic flowering and circadian rhythm. Studies on the controlling mechanisms of de-etiolation, photoperiodic flowering, and circadian rhythm have been the fascinating topics in Arabidopsis research. The knowledge obtained from Arabidopsis can be readily applied to food crops and ornamental species, and can be contributed to our general understanding of signal perception and transduction in all organisms.

Repression of light signaling by Arabidopsis SPA1 involves post-translational regulation of HFR1 protein accumulation

Arabidopsis uses two major classes of photoreceptors to mediate seedling de-etiolation. The cryptochromes (cry1 and cry2) absorb blue/ultraviolet-A light, whereas the phytochromes (phyA-phyE) predominantly regulate responses to red/far-red light. Arabidopsis COP1 represses light signaling by acting as an E3 ubiquitin ligase in the nucleus, and is responsible for targeted degradation of a number of photomorphogenesis-promoting factors, including HY5, LAF1, phyA, and HFR1. Distinct light signaling pathways initiated by multiple photoreceptors (including both phytochromes and cryptochromes) eventually converge on COP1, causing its inactivation and nuclear depletion. Arabidopsis SPA1, which encodes a protein structurally related to COP1, also represses light signaling under various light conditions. In this study, we present genetic evidence supporting that HFR1, which encodes a photomorphogenesis-promoting bHLH transcription factor, acts downstream of SPA1 and is required for different subsets of branch pathways of light signaling controlled by SPA1 under different light conditions. We show that SPA1 physically interacts with HFR1 in a yeast two-hybrid assay and an in vitro co-immunoprecipitation assay. We demonstrate that higher levels of HFR1 protein accumulate in the spa1 mutant background under various light conditions, including far-red, red, blue, and white light, whereas a marginal increase in HFR1 transcript level is only seen in dark- and far-red light-grown spa1-100 mutants. Together, our data suggest that repression of light signaling by Arabidopsis SPA1 likely involves post-translational regulation of HFR1 protein accumulation.

A basic helix-loop-helix transcription factor in Arabidopsis, MYC2, acts as a repressor of blue light-mediated photomorphogenic growth

The crosstalk of light signaling pathways with other signaling cascades has just started to be revealed. Here, we report the identification and functional characterization of a Z-box binding factor (ZBF1) in light signaling pathways. Arabidopsis thaliana ZBF1 encodes AtMYC2/JIN1, a basic helix-loop-helix transcription factor, which has recently been shown to be involved in abscisic acid (ABA), jasmonic acid (JA), and jasmonate-ethylene signaling pathways. We demonstrate that AtMYC2 interacts with the Z- and G-box light-responsive elements of minimal light-regulated promoters. AtMYC2 is expressed in various light-grown seedlings, including in red, far red, and blue light. Genetic analyses suggest that AtMYC2 acts as a negative regulator of blue light-mediated photomorphogenic growth and blue and far-red-light-regulated gene expression; however, it functions as a positive regulator of lateral root formation. Our results further demonstrate that atmyc2 mutants have compromised sensitivity to ABA- and JA-mediated responses. Taken together, these results demonstrate that AtMYC2 is a common transcription factor of light, ABA, and JA signaling pathways in Arabidopsis.

New Arabidopsis recombinant inbred lines (Landsberg erecta x Nossen) reveal natural variation in phytochrome-mediated responses

We used 52 Arabidopsis (Arabidopsis thaliana) accessions and developed a new set of 137 recombinant inbred lines between Landsberg erecta (Ler) and Nossen (No-0) to explore the genetic basis of phytochrome-mediated responses during deetiolation. Unexpectedly, most accessions showed weak or moderate hypocotyl growth and cotyledon unfolding responses to pulses of far-red light (FR). Crosses between Columbia and No-0, two accessions with poor response, segregated seedlings with unfolded cotyledons under pulsed FR, suggesting the occurrence of accession-specific loci in the repression of morphological responses to weak light signals. Confirming the latter expectation, mapping of responses to pulsed FR in the Ler x No-0 lines identified novel loci. Despite its weak response to pulsed FR, No-0 showed a response to continuous FR stronger than that observed in Ler. By mapping the differential effect of pulsed versus continuous FR, we identified two high-irradiance response loci that account for the steeper response to continuous FR in No-0. This underscores the potential of the methodology to identify loci involved in the regulation of the shape of signal input-output relationships. Loci specific for a given phytochrome-mediated response were more frequent than pleiotropic loci. Segregation of these specific loci is predicted to yield different combinations of seedling responsivity to light. Such flexibility in combination of responses is observed among accessions and could aid in the adjustment to different microenvironments.

The degradation of HFR1, a putative bHLH class transcription factor involved in light signaling, is regulated by phosphorylation and requires COP1

All developmental transitions throughout the life cycle of a plant are influenced by light. In Arabidopsis, multiple photoreceptors including the UV-A/blue-sensing cryptochromes (cry1-2) and the red/far-red responsive phytochromes (phyA-E) monitor the ambient light conditions. Light-regulated protein stability is a major control point of photomorphogenesis. The ubiquitin E3 ligase COP1 (constitutively photomorphogenic 1) regulates the stability of several light-signaling components. HFR1 (long hypocotyl in far-red light) is a putative transcription factor with a bHLH domain acting downstream of both phyA and the cryptochromes. HFR1 is closely related to PIF1, PIF3, and PIF4 (phytochrome interacting factor 1, 3 and 4), but in contrast to the latter three, there is no evidence for a direct interaction between HFR1 and the phytochromes. Here, we show that the protein abundance of HFR1 is tightly controlled by light. HFR1 is an unstable phosphoprotein, particularly in the dark. The proteasome and COP1 are required in vivo to degrade phosphorylated HFR1. In addition, HFR1 can interact with COP1, consistent with the idea of COP1 directly mediating HFR1 degradation. We identify a domain, conserved among several bHLH class proteins involved in light signaling , as a determinant of HFR1 stability. Our physiological experiments indicate that the control of HFR1 protein abundance is important for a normal de-etiolation response.

Light regulates COP1-mediated degradation of HFR1, a transcription factor essential for light signaling in Arabidopsis

Arabidopsis thaliana seedlings undergo photomorphogenesis in the light and etiolation in the dark. Long Hypocotyl in Far-Red 1 (HFR1), a basic helix-loop-helix transcription factor, is required for both phytochrome A-mediated far-red and cryptochrome 1-mediated blue light signaling. Here, we report that HFR1 is a short-lived protein in darkness and is degraded through a 26S proteasome-dependent pathway. Light, irrespective of its quality, enhances HFR1 protein accumulation via promoting its stabilization. We demonstrate that HFR1 physically interacts with Constitutive Photomorphogenesis 1 (COP1) and that COP1 exhibits ubiquitin ligase activity toward HFR1 in vitro. In addition, we show that COP1 is required for degradation of HFR1 in vivo. Furthermore, plants overexpressing a C-terminal 161-amino acid fragment of HFR1 (CT161) display enhanced photomorphogenesis, suggesting an autonomous function of CT161 in promoting light signaling. This truncated HFR1 gene product is more stable than the full-length HFR1 protein in darkness, indicating that the COP1-interacting N-terminal portion of HFR1 is essential for COP1-mediated destabilization of HFR1. These results suggest that light enhances HFR1 protein accumulation by abrogating COP1-mediated degradation of HFR1, which is necessary and sufficient for promoting light signaling. Additionally, our results substantiate the E3 ligase activity of COP1 and its critical role in desensitizing light signaling.

HFR1 is targeted by COP1 E3 ligase for post-translational proteolysis during phytochrome A signaling

Upon activation by far-red light, phytochrome A signals are transduced through several pathways to promote photomorphogenesis. The COP1 E3 ligase represses photomorphogenesis in part by targeting transcription activators such as LAF1 and HY5 for destruction. Another positive regulator of photomorphogenesis is HFR1, a basic helix-loop-helix (bHLH) transcription factor. Here, we show that HFR1 colocalizes with COP1 in nuclear bodies, and that the HFR1 N-terminal region (amino acids 1-131) interacts with the COP1 WD40 domain. HFR1(DeltaN), an HFR1 mutant lacking the two N-terminal, COP1-interacting motifs, still localizes in nuclear bodies and retains weak affinity for COP1. Both HFR1 and HFR1(DeltaN) can be ubiquitinated by COP1, although with different efficiencies. Expression of 35S-HFR1(DeltaN) in wild-type plants confers greater hypersensitivity to FR than 35S-HFR1 expression, and only seedlings expressing 35S-HFR1(DeltaN) display constitutive photomorphogenesis. These phenotypic differences can be attributed to the instability of HFR1 compared with HFR1(DeltaN). In transgenic plants, HFR1 levels are significantly elevated upon induced expression of a dominant-negative COP1 mutant that interferes with endogenous COP1 E3 activity. Moreover, induced expression of wild-type COP1 in transgenic plants accelerates post-translational degradation of HFR1 under FR light. Taken together, our results show that HFR1 is ubiquitinated by COP1 E3 ligase and marked for post-translational degradation during photomorphogenesis.

bHLH class transcription factors take centre stage in phytochrome signalling

The phytochrome family of photoreceptors (there are five phytochromes in Arabidopsis, named phyA to phyE) maximally absorbs red and far-red light and plays important functions throughout the life cycle of plants. Several recent studies have shown that multiple related bHLH (basic helix-loop-helix) class transcription factors play key roles in phytochrome signal transduction. Somewhat surprisingly these transcription factors primarily act as negative regulators of phytochrome signalling. Moreover, in some cases, the phytochromes inhibit those negative regulators.

The Dof transcription factor OBP3 modulates phytochrome and cryptochrome signaling in Arabidopsis

Plants perceive subtle changes in light quality and quantity through a set of photoreceptors, including phytochromes and cryptochromes. Upon perception, these photoreceptors initiate signal transduction pathways leading to photomorphogenic changes in development. Using activation-tagging mutagenesis to identify novel light-signaling components, we have isolated a gain-of-function mutant, sob1-D (suppressor of phytochrome B-4 [phyB-4] dominant), which suppresses the long-hypocotyl phenotype of the phyB missense allele, phyB-4. The sob1-D mutant phenotype is caused by the overexpression of a Dof (DNA binding with one finger) transcription factor, OBF4 Binding Protein 3 (OBP3). A translational fusion between OBP3 and green fluorescent protein is nuclear localized in onion (Allium cepa) cells. Tissue-specific accumulation of an OBP3:OBP3-beta-glucuronidase translational fusion is regulated by light in Arabidopsis thaliana. Hypocotyls of transgenic lines with reduced OBP3 expression are less responsive to red light. This aberrant phenotype in red light requires functional phyB, suggesting that OBP3 is a positive regulator of phyB-mediated inhibition of hypocotyl elongation. Furthermore, these partial-loss-of-function lines have larger cotyledons. This light-dependent cotyledon phenotype is most dramatic in blue light and requires functional cryptochrome 1 (cry1), indicating that OBP3 is a negative regulator of cry1-mediated cotyledon expansion. These results suggest a model where OBP3 is a component in both phyB and cry1 signaling pathways, acting as a positive and negative regulator, respectively. An alternate, though not mutually exclusive, model places OBP3 as a general inhibitor of tissue expansion with phyB and cry1, differentially modulating OBP3's role in this response.

Arabidopsis HAF2 Gene Encoding TATA-binding Protein (TBP)-associated Factor TAF1, Is Required to Integrate Light Signals to Regulate Gene Expression and Growth

Plant growth and development are sensitive to light. Light-responsive DNA-binding transcription factors have been functionally identified. However, how transcription initiation complex integrates light signals from enhancer-bound transcription factors remains unknown. In this work, we characterized mutations within the Arabidopsis HAF2 gene encoding TATA-binding protein-associated factor TAF1 (or TAF(II)250). The mutation of HAF2 induced decreases on chlorophyll accumulation, light-induced mRNA levels, and promoter activity. Genetic analysis indicated that HAF2 is involved in the pathways of both red/far-red and blue light signals. Double mutants between haf2-1 and hy5-1, a mutation of a light signaling positive DNA-binding transcription factor gene, had a synergistic effect on photomorphogenic traits and light-activated gene expression under different light wavelengths, suggesting that HAF2 is required for interaction with additional light-responsive DNA-binding transcription factors to fully respond to light induction. Chromatin immunoprecipitation assays showed that the mutation of HAF2 reduced acetylation of histone H3 in light-responsive promoters. In addition, transcriptome analysis showed that the mutation altered the expression of about 9% of genes in young leaves. These data indicate that TAF1 encoded by the Arabidopsis HAF2 gene functions as a coactivator capable of integrating light signals and acetylating histones to activate light-induced gene transcription.

PIL5, a phytochrome-interacting basic helix-loop-helix protein, is a key negative regulator of seed germination in Arabidopsis thaliana

The first decision made by an angiosperm seed, whether to germinate or not, is based on integration of various environmental signals such as water and light. The phytochromes (Phys) act as red and far-red light (Pfr) photoreceptors to mediate light signaling through yet uncharacterized pathways. We report here that the PIF3-like 5 (PIL5) protein, a basic helix-loop-helix transcription factor, is a key negative regulator of phytochrome-mediated seed germination. PIL5 preferentially interacts with the Pfr forms of Phytochrome A (PhyA) and Phytochrome B (PhyB). Analyses of a pil5 mutant in conjunction with phyA and phyB mutants, a pif3 pil5 double mutant, and PIL5 overexpression lines indicate that PIL5 is a negative factor in Phy-mediated promotion of seed germination, inhibition of hypocotyl negative gravitropism, and inhibition of hypocotyl elongation. Our data identify PIL5 as the first Phy-interacting protein that regulates seed germination.

The nuclear localization signal and the C-terminal region of FHY1 are required for transmission of phytochrome A signals

Plants use the family of phytochrome photoreceptors to sense their light environment in the red/far-red region of the spectrum. Phytochrome A (phyA) is the primary photoreceptor that regulates germination and early seedling development. This phytochrome mediates seedling de-etiolation for the developmental transition from heterotrophic to photoauxotrophic growth. High intensity far-red light provides a way to specifically assess the role of phyA in this process and was used to isolate phyA-signaling intermediates. fhy1 and pat3 (renamed fhy1-3) are independently isolated alleles of a gene encoding a phyA signal transduction component. FHY1 is a small 24 kDa protein that shows no homology to known functional motifs, besides a small conserved septin-related domain at the C-terminus, a putative nuclear localization signal (NLS) and a putative nuclear exclusion signal (NES). Here we demonstrate that the septin-related domain is important for FHY1 to transmit phyA signals. Moreover, the putative NLS and NES of FHY1 are indeed involved in its nuclear localization and exclusion. Nuclear localization of FHY1 is needed for it to execute responses downstream of phyA. Together with the results from global expression analysis, our findings point to an important role of FHY1 in phyA signaling through its nuclear translocation and induction of gene expression.

Overexpression of a mutant basic helix-loop-helix protein HFR1, HFR1-deltaN105, activates a branch pathway of light signaling in Arabidopsis

The HFR1, a basic helix-loop-helix protein, is required for a subset of phytochrome A-mediated photoresponses in Arabidopsis. Here, we show that overexpression of the HFR1-deltaN105 mutant, which lacks the N-terminal 105 amino acids, confers exaggerated photoresponses even in darkness. Physiological analysis implied that overexpression of HFR1-deltaN105 activated constitutively a branch pathway of light signaling that mediates a subset of photomorphogenic responses, including germination, de-etiolation, gravitropic hypocotyl growth, blocking of greening, and expression of some light-regulated genes such as CAB, DRT112, PSAE, PSBL, PORA, and XTR7, without affecting the light-responsiveness of anthocyanin accumulation and expression of other light-regulated genes such as CHS and PSBS. Although the end-of-day far-red light response and petiole elongation were suppressed in the HFR1-deltaN105-overexpressing plants, flowering time was not affected by HFR1-deltaN105. In addition, the HFR1-deltaN105-overexpressing plants showed hypersensitive photoresponses in the inhibition of hypocotyl elongation, dependently on phytochrome A, FHY1, and FHY3 under FR light or phyB under R light, respectively. Moreover, our double mutant analysis suggested that the hypersensitive photoresponse is due to functional cooperation between HFR1-deltaN105 and other light-signaling components including HY5, a basic leucine zipper protein. Taken together, our results of gain-of-function approach with HFR1-deltaN105 suggest the existence of a complex and important basic helix-loop-helix protein-mediated transcriptional network controlling a branch pathway of light signaling and provide a useful framework for further genetic dissection of light-signaling network in Arabidopsis.

LAF3, a novel factor required for normal phytochrome A signaling

Phytochrome A (phyA) is the photolabile plant light receptor that mediates broad spectrum very low-fluence responses and high irradiance responses to continuous far-red light (FRc). An Arabidopsis mutant laf3-1 (long after far-red 3) was recovered from a screen for transposon-tagged mutants that exhibit reduced inhibition of hypocotyl elongation in FRc. The laf phenotype correlated well with a strongly attenuated disappearance of XTR7 transcript in FRc. The effects of laf3-1 on phyA-controlled CAB, CHS, and PET H expression were more subtle, and the mutation had no clear effects on PET E and ASN1 transcript levels in FRc. The use of two alternative transcription initiation sites in the LAF3 gene generates two isoforms that differ only at their N termini. Transcripts encoding both isoforms were induced during germination and were present at slightly higher levels in de-etiolated seedlings than in those grown in darkness. No significant differential regulation of the two isoforms was observed upon exposure to either FRc or continuous red light. Transcripts encoding the shorter isoform (LAF3ISF2) always appear to be more abundant than those encoding the longer isoform (LAF3ISF1). However, both isoforms were capable of full complementation of the laf3-1 hypocotyl phenotype in FRc. When fused to a yellow fluorescent protein, both isoforms localize to the perinuclear region, suggesting that LAF3 encodes a product that might regulate nucleo-cytoplasmic trafficking of an intermediate(s) involved in phyA signal transduction.

Analysis of the Arabidopsis nuclear proteome and its response to cold stress

The nucleus is the subcellular organelle that contains nearly all the genetic information required for the regulated expression of cellular proteins. In this study, we comprehensively characterized the Arabidopsis nuclear proteome. Nuclear proteins were isolated and analyzed using two-dimensional (2D) gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Approximately 500-700 spots were detected in reference 2D gels of nuclear proteins. Proteomic analyses led to the identification of 184 spots corresponding to 158 different proteins implicated in a variety of cellular functions. We additionally analyzed the changes in the nuclear proteome in response to cold stress. Of the 184 identified proteins, 54 were up- or downregulated with a greater than twofold change in response to cold treatment. Among these, six proteins were selected for further characterization. Northern analysis data revealed that gene expression of these proteins was also altered by cold stress. Following transient expression in BY-2 protoplasts, two proteins were detected in both the cytoplasm and the nucleus and four others were detected exclusively in the nucleus, which correlates well with the nuclear localization patterns of the proteomic data. Our study provides an initial insight into the Arabidopsis nuclear proteome and its response to cold stress.

Functional characterization of phytochrome interacting factor 3 in phytochrome-mediated light signal transduction

Phytochromes regulate various light responses through their interactions with different signaling proteins, such as phytochrome interacting factor 3 (PIF3). However, the physiological functions of PIF3 in light signaling are not yet fully understood. To increase our understanding of these roles, we characterized a T-DNA insertional pif3 mutant and transgenic plants overexpressing the full-length PIF3. Transgenic overexpressing lines displayed longer hypocotyls and smaller cotyledons under red light and reduced cotyledon opening under both red and far-red light, whereas the pif3 mutant showed the opposite phenotypes. The accumulation of anthocyanin and chlorophyll further indicated complicated features of PIF3 function. The accumulation of anthocyanin was increased and the content of chlorophyll was decreased in the overexpression lines. Our data indicate that PIF3 plays complex roles depending on the type of light response and the light conditions.

Light-mediated regulation defines a minimal promoter region of TOP2

Light signaling has been demonstrated to be an important factor for plant growth and development; however, its role in the regulation of DNA replication and cell cycle has just started to be unraveled. In this work, we have demonstrated that the TOP2 promoter of Pisum sativum (pea) is activated by a broad spectrum of light including far-red light (FR), red light (RL) and blue light (BL). Deletion analyses of the TOP2 promoter in transformed plants, Arabidopsis thaliana and Nicotiana tobaccum (tobacco), define a minimal promoter region that is induced by RL, FR and BL, and is essential and sufficient for light-mediated activation. The minimal promoter of TOP2 follows the phytochrome- mediated low-fluence response similar to complex light regulated promoters. DNA-protein interaction studies reveal the presence of a DNA binding activity specific to a 106 bp region of the minimal promoter that is crucial for light-mediated activation. These results altogether indicate a direct involvement of light signaling in the regulation of expression of TOP2, one of the components of the DNA replication/cell cycle machinery.

HFR1, a putative bHLH transcription factor, mediates both phytochrome A and cryptochrome signalling

Plants are very sensitive to their light environment. They use cryptochromes and phytochromes to scan the light spectrum. Those two families of photoreceptors mediate a number of similar physiological responses. The putative bHLH (basic Helix Loop Helix) transcription factor long hypocotyl in far-red (HFR1) is important for a subset of phytochrome A (phyA)-mediated light responses. Interestingly, hfr1 alleles also have reduced de-etiolation responses, including hypocotyl growth, cotyledon opening and anthocyanin accumulation, when grown in blue light. This phenotype is particularly apparent under high fluence rates. The analysis of double mutants between hfr1 and different blue light photoreceptor mutants demonstrates that, in addition to its role in phyA signalling, HFR1 is a component of cryptochrome 1 (cry1)-mediated light signalling. Moreover, HFR1 mRNA levels are high both in blue and in far-red light but low in red light. These results identify HFR1 as a positively acting component of cry1 signalling and indicate that HFR1 integrates light signals from both phyA and cry1.

Light, phytochrome signalling and photomorphogenesis in Arabidopsis

The phytochromes is a family of plant photoreceptors that control growth and development in response to environmental cues. Red and far-red light are the most efficient wavebands to induce conformational changes of phytochromes and consequently modify their kinetics, nuclear/cytoplasmic partitioning, ability to phosphorylate substrates, and physical interaction with proteins that bind DNA. Many players in phytochrome signalling have been identified and a complex, highly regulated network is envisaged. Here we describe the connection between different features of the phytochrome signalling network and the versatile relationship between light signals and physiological outputs shown by phytochromes.

Phylogenetic analysis of plant basic helix-loop-helix proteins

The basic helix-loop-helix (bHLH) family of proteins is a group of functionally diverse transcription factors found in both plants and animals. These proteins evolved early in eukaryotic cells before the split of animals and plants, but appear to function in 'plant-specific' or 'animal-specific' processes. In animals bHLH proteins are involved in regulation of a wide variety of essential developmental processes. On the contrary, bHLH proteins have not been extensively studied in plants. Those that have been characterized function in anthocyanin biosynthesis, phytochrome signaling, globulin expression, fruit dehiscence, carpel and epidermal development. We have identified 118 different bHLH genes in the completely sequenced Arabidopsis thaliana genome and 131 bHLH genes in the rice genome. Here we report a phylogenetic analysis of these genes, including 46 genes from other plant species and a classification of these proteins into 15 distinct plant clades. Results imply a polyphyletic origin for the plant bHLH proteins related only by their bHLH DNA binding motif. We suggest that plant bHLH proteins are under weaker selective constraints than their animal counterparts and that lineage specific expansions and subfunctionalization have fashioned regulatory proteins for plant specific functions.

FIN5 positively regulates far-red light responses in Arabidopsis thaliana

We report the characterization of a semi-dominant mutation fin5-1 (far-red insensitive 5-1) of Arabidopsis, which was isolated from genetic screening of phytochrome A (phyA) signaling components. Plants with the fin5-1 mutation exhibited a long hypocotyl phenotype when grown under far-red (FR) light, but not under red light. Physiological analyses implied that FIN5 might be differentially involved in diverse responses that are regulated by phyA under continuous FR light. Anthocyanin accumulation, gravitropic response of hypocotyl growth, and FR light-preconditioned blocking of greening were also impaired in the fin5-1 mutant, whereas photoperiodic floral induction was not, if at all, significantly affected. Moreover, light-regulated expression of the CHS, PORA and PsbS genes was attenuated in fin5-1 mutant plants, while the light-induced expression of CAB was normal. The mutation exhibited semi-dominance regarding control of hypocotyl growth in FR light. We suggest that FIN5 defines a novel branch in the network of phyA signaling in Arabidopsis.

The Arabidopsis COG1 gene encodes a Dof domain transcription factor and negatively regulates phytochrome signaling

Light is a critical environmental factor that influences almost all developmental aspects of plants, including seed germination, seedling morphogenesis, and transition to reproductive growth. Plants have therefore developed an intricate network of mechanisms to perceive and process environmental light information. To further characterize the molecular basis of light-signaling processes in plants, we screened an activation tagging pool of Arabidopsis for altered photoresponses. A dominant mutation, cog1-D, attenuated various red (R) and far-red (FR) light-dependent photoresponses. The mutation was caused by overexpression of a gene encoding a member of the Dof family of transcription factors. The photoresponses in Arabidopsis were inversely correlated with the expression levels of COG1 mRNA. When the COG1 gene was overexpressed in transgenic plants, the plants exhibited hyposensitive responses to R and FR light in a manner inversely dependent on COG1 mRNA levels. On the other hand, transgenic lines expressing antisense COG1 were hypersensitive to R and FR light. Expression of the COG1 gene is light inducible and requires phytochrome A (phyA) for FR light-induced expression and phytochrome B (phyB) for R light-induced expression. Thus, the COG1 gene functions as a negative regulator in both the phyA- and phyB-signaling pathways. We suggest that these phytochromes positively regulate the expression of COG1, a negative regulator, as a mechanism for fine tuning the light-signaling pathway.

Dissecting the phytochrome A-dependent signaling network in higher plants

Plants monitor their ambient light environment using a network of photoreceptors. In Arabidopsis, phytochrome A (phyA) is the primary photoreceptor responsible for perceiving and mediating various responses to far-red light. Several breakthroughs in understanding the signaling network mediating phyA-activated responses have been made in recent years. Here, we highlight several key advances: the demonstration that light regulates nuclear translocation of phyA and its associated kinase activity; the revelation of a transcriptional cascade controlling phyA-regulated gene expression; the detection of a direct interaction between phyA and a transcription factor; and the identification and characterization of many phyA-specific signaling intermediates, some of them suggesting the involvement of the ubiquitin-proteasome pathway.

Analysis of far-red light-regulated genome expression profiles of phytochrome A pathway mutants in Arabidopsis

Phytochrome A (phyA) is the primary photoreceptor responsible for various far-red (FR) light-mediated responses. Previous studies have identified multiple phyA signaling mutants, including both positive and negative regulators of the phyA-mediated responses. How these defined intermediates act to mediate FR light responses is largely unknown. Here a cDNA microarray was used to examine effects of those mutations on the far-red light control of genome expression. Clustering analysis of the genome expression profiles supports the notion that phyA signaling may entail a network with multiple paths, controlling overlapping yet distinct sets of gene expression. FHY1, FAR1 and FHY3 most likely act upstream in the phyA signaling network, close to the phyA photoreceptor itself. FIN219, SPA1 and REP1 most likely act somewhere more downstream in the network and control the expression of smaller sets of genes. Further, this study also provides genomics evidence for the partial functional redundancy between FAR1 and FHY3. These two homologous proteins control the expression of a largely overlapping set of genes, and likely act closely together in the phyA-mediated FR light responses.

Phytochrome-mediated signal transduction pathways in plants

Phytochromes are photoreceptors that regulate plant growth and development in response to the solar radiation environment. Recent studies reveal how phytochrome-mediated light signals can be transduced to the cells for their responses. The possible signal transduction pathways of phytochromes include: (a) direct regulation of gene transcription and (b) typical kinase-involved signaling pathways and its regulation by phosphorylation, dephosphorylation, and proteolytic degradation. This review highlights some of the recent findings.

Mutations affecting light regulation of nuclear genes encoding chloroplast glyceraldehyde-3-phosphate dehydrogenase in Arabidopsis

Expression of nuclear genes that encode the A and B subunits of chloroplast glyceraldehyde-3-phosphate dehydrogenase (GAPA and GAPB) of Arabidopsis is known to be regulated by light. We used a negative selection approach to isolate mutants that were defective in light-regulated expression of the GAPA gene. Two dominant mutants belonging to the same complementation group, uga1-1 and uga1-2, were then characterized. These two mutants showed a dramatic reduction in GAPA mRNA level in both mature plants and seedlings. Surprisingly, mutations in uga1-1 and uga1-2 had no effect on the expression of GAPB and several other light-regulated genes. In addition, we found that the chloroplast glyceraldehyde-3-phosphate dehydrogenase enzyme activity of the mutants was only slightly lower than that of the wild type. Western-blot analysis showed that the GAPA protein level was nearly indistinguishable between the wild-type and the uga mutants. These results suggested that posttranscriptional control was involved in the up-regulation of the GAPA protein in the mutants. The uga1-1 mutation was mapped to the bottom arm of chromosome V of the Arabidopsis genome.

Three redundant brassinosteroid early response genes encode putative bHLH transcription factors required for normal growth

Brassinosteroids (BRs) are a class of polyhydroxylated steroids that are important regulators of plant growth and development. We have identified three closely related basic helix-loop-helix (bHLH) transcription factors, BEE1, BEE2, and BEE3, as products of early response genes required for full BR response. Comparison of the phenotypes of plants that overexpress BEE1 with bee1 bee2 bee3 triple-knockout mutant plants suggests that BEE1, BEE2, and BEE3 are functionally redundant positive regulators of BR signaling. Expression of BEE1, BEE2, and BEE3 is also regulated by other hormones, notably abscisic acid (ABA), a known antagonist of BR signaling. Reduced ABA response in plants overexpressing BEE1 suggests that BEE proteins may function as signaling intermediates in multiple pathways.

Light regulated modulation of Z-box containing promoters by photoreceptors and downstream regulatory components, COP1 and HY5, in Arabidopsis

The Z-box is one of the light-responsive elements (LREs) found in the promoters of light inducible genes. We have studied the light responsive characteristics of Z-box containing synthetic as well as native promoters. We show that promoters with Z-box as a single LRE or paired with another LRE can respond to a broad spectrum of light. The response is primarily mediated by phyA, phyB and CRY1 photoreceptors at their respective wavelengths of light. We have demonstrated that CAB1 and Z-GATA containing promoters are down-regulated in hy5 mutants in the light. On the other hand, a promoter with Z-box alone is down-regulated in hy5 mutants both in dark and in light conditions, suggesting involvement of a similar regulatory system in the regulation of the promoter in two distinct developmental pathways: skotomorphogenesis and photomorphogenesis. Furthermore, similar to the CAB1 promoter, a Z-GATA containing promoter is derepressed in cop1 mutants in the dark. DNA-protein interaction studies reveal the presence of a DNA-binding activity that is specific to Z-box. These results provide insights into the regulation of the Z-box LRE mediated by various light signaling components.

The cell biology of phytochrome signalling

Phytochrome signal transduction has in the past often been viewed as being a nonspatially separated linear chain of events. However, through a combination of molecular, genetic and cell biological approaches, it is becoming increasingly evident that phytochrome signalling constitutes a highly ordered multidimensional network of events. The discovery that some phytochromes and signalling intermediates show light-dependent nucleo-cytoplasmic partitioning has not only led to the suggestion that early signalling events take place in the nucleus, but also that subcellular localization patterns most probably represent an important signalling control point. Moreover, detailed characterization of signalling intermediates has demonstrated that various branches of the signalling network are spatially separated and take place in different cellular compartments including the nucleus, cytosol, and chloroplasts. In addition, proteasome-mediated degradation of signalling intermediates most probably act in concert with subcellular partitioning events as an integrated checkpoint. An emerging view from this is that phytochrome signalling is separated into several subcellular organelles and that these are interconnected in order to execute accurate responses to changes in the light environment. By integrating the available data, both at the cellular and subcellular level, we should be able to construct a solid foundation for further dissection of phytochrome signal transduction in plants. Contents Summary 553 I. Introduction 554 II. Nucleus vs cytoplasm 556 III. The nucleus 562 IV. The cytoplasm 571 V. Interactions with other signalling pathways 577 VI. Conclusions and the future 582 Acknowledgements 583 References 583.

HFR1, a phytochrome A-signalling component, acts in a separate pathway from HY5, downstream of COP1 in Arabidopsis thaliana

HFR1, a basic helix-loop-helix protein, is known to be required for a subset of phytochrome A (phyA)-dependent photoresponses. To investigate the role of HFR1 in light signalling, we have examined the genetic interaction between HFR1 and HY5, a positive regulator of light signalling, and COP1, a repressor of photomorphogenesis. Double mutant analysis suggests that HFR1 mediates phyA-dependent inhibition of hypocotyl elongation independently of HY5. HFR1 was shown to be necessary for a subset of cop1-triggered photomorphogenic phenotypes in the dark, including inhibition of hypocotyl elongation, gravitropic hypocotyl growth, and expression of the light-inducible genes CAB and RBCS. Phenotypic analysis of the triple mutant cop1hy5hfr1 indicated that both HFR1 and HY5 are required for cop1-mediated photomorphogenic seedling development in darkness, consistent with their additive roles in phyA-dependent signalling. Taken together, these results suggest that HFR1 might act downstream of COP1, in a separate pathway from HY5, to mediate photomorphogenesis in Arabidopsis.

Two interacting bZIP proteins are direct targets of COP1-mediated control of light-dependent gene expression in Arabidopsis

Arabidopsis COP1 acts to repress photomorphogenesis in the absence of light. It was shown that in the dark, COP1 directly interacts with the bZIP transcription factor HY5, a positive regulator of photomorphogenesis, and promotes its proteasome-mediated degradation. Here we identify a novel bZIP protein HYH, as a new target of COP1. We identify a physical and genetic interaction between HYH and COP1 and show that this interaction results in dark-specific degradation of HYH. Genetic analysis indicates that HYH is predominantly involved in blue-light regulation of development and gene expression, and that the function of HYH in part overlaps with that of HY5. The accumulation of HYH protein, not the mRNA, is dependent on the presence of HY5. Our data suggest that HYH and HY5 can, respectively, act as heterodimers and homodimers, thus mediating light-regulated expression of overlapping as well as distinct target genes. We propose that COP1 mediates light control of gene expression through targeted degradation of multiple photomorphogenesis-promoting transcription factors in the nucleus.

Two interacting bZIP proteins are direct targets of COP1-mediated control of light-dependent gene expression in Arabidopsis

Arabidopsis COP1 acts to repress photomorphogenesis in the absence of light. It was shown that in the dark, COP1 directly interacts with the bZIP transcription factor HY5, a positive regulator of photomorphogenesis, and promotes its proteasome-mediated degradation. Here we identify a novel bZIP protein HYH, as a new target of COP1. We identify a physical and genetic interaction between HYH and COP1 and show that this interaction results in dark-specific degradation of HYH. Genetic analysis indicates that HYH is predominantly involved in blue-light regulation of development and gene expression, and that the function of HYH in part overlaps with that of HY5. The accumulation of HYH protein, not the mRNA, is dependent on the presence of HY5. Our data suggest that HYH and HY5 can, respectively, act as heterodimers and homodimers, thus mediating light-regulated expression of overlapping as well as distinct target genes. We propose that COP1 mediates light control of gene expression through targeted degradation of multiple photomorphogenesis-promoting transcription factors in the nucleus.

Photosensory perception and signalling in plant cells: new paradigms?

Plants monitor informational light signals using three sensory photoreceptor families: the phototropins, cryptochromes and phytochromes. Recent advances suggest that the phytochromes act transcriptionally by targeting light signals directly to photoresponsive promoters through binding to a transcriptional regulator. By contrast, the cryptochromes appear to act post-translationally, by disrupting extant proteosome-mediated degradation of a key transcriptional activator through direct binding to a putative E3 ubiquitin ligase, thereby elevating levels of the activator and consequently of target gene expression.

The negatively acting factors EID1 and SPA1 have distinct functions in phytochrome A-specific light signaling

EID1 (empfindlicher im dunkelroten Licht) and SPA1 (suppressor of phytochrome A[phyA]-105) function as negatively acting components in phyA-specific light signaling. Mutants in the respective genes led to very similar phenotypes under weak-light conditions. To examine whether both genes are functionally redundant, detailed physiological and genetic analyses were performed with eid1 and spa1 mutants isolated from the same wild-type background. Measurements of hypocotyl elongation, anthocyanin accumulation, and Lhcb1-transcript accumulation under different light treatments demonstrated that SPA1 has a strong influence on the regulation of very low fluence responses and a weaker influence on high-irradiance responses. In contrast, EID1 severely altered high-irradiance responses and caused almost no change on very low fluence responses. Analyses on eid1 phyA-105 double mutants demonstrated that EID1 could not suppress the phenotype of the weak phyA allele under continuous far-red light. Measurements on eid1 spa1 double mutants exhibited a strong interference of both genes in the regulation of hypocotyl elongation. These results indicate that EID1 and SPA1 are involved in different but interacting phyA-dependent signal transduction chains.

Phytochrome photosensory signalling networks

Light is life for plants. To continuously assess and adapt to fluctuations in the quality and quantity of this essential commodity, plants deploy sensory photoreceptors, including the phytochromes. Having captured an incoming photon, the activated phytochrome molecule must relay this information to nuclear genes that are poised to respond by directing appropriate adjustments in growth and development. Defining the intricate intracellular signalling networks through which this sensory information is transduced is an area of intense research activity.

Environmental cues affecting development

Multiple receptors connect environmental cues to developmental genes via shortcuts and more tortuous pathways, creating a network of interactive signals in which negative regulators play a key role. The elements of the circuitry, their connections, and their functional significance are being uncovered thanks to the analysis of genetic interactions, protein-protein interactions, sub-cellular localisation and transcriptome patterns.

Phytochromes control photomorphogenesis by differentially regulated, interacting signaling pathways in higher plants

In this review the kinetic properties of both phytochrome A and B measured by in vivo spectroscopy in Arabidopsis are described. Inactivation of phyA is mediated by destruction and that of phyB by fast dark reversion. Recent observations, describing a complex interaction network of various phytochromes and cryptochromes, are also discussed. The review describes recent analysis of light-dependent nuclear translocation of phytochromes and genetic and molecular dissection of phyA- and phyB-mediated signal transduction. After nuclear transport, both phyA- and phyB-mediated signal transduction probably include the formation of light-dependent transcriptional complexes. Although this hypothesis is quite attractive and probably true for some responses, it cannot account for the complex network of phyA-mediated signaling and the interaction with the circadian clock. In addition, the biological function of phytochromes localized in the cytosol remains to be elucidated.

FHY1: a phytochrome A-specific signal transducer

Phytochromes are plant photoreceptors that regulate plant growth and development with respect to the light environment. Following the initial light-perception event, the phytochromes initiate a signal-transduction process that eventually results in alterations in cellular behavior, including gene expression. Here we describe the molecular cloning and functional characterization of Arabidopsis FHY1. FHY1 encodes a product (FHY1) that specifically transduces signals downstream of the far-red (FR) light-responsive phytochrome A (PHYA) photoreceptor. We show that FHY1 is a novel light-regulated protein that accumulates in dark (D)-grown but not in FR-grown hypocotyl cells. In addition, FHY1 transcript levels are regulated by light, and by the product of FHY3, another gene implicated in FR signaling. These observations indicate that FHY1 function is both FR-signal transducing and FR-signal regulated, suggesting a negative feedback regulation of FHY1 function. Seedlings homozygous for loss-of-function fhy1 alleles are partially blind to FR, whereas seedlings overexpressing FHY1 exhibit increased responses to FR, but not to white (WL) or red (R) light. The increased FR-responses conferred by overexpression of FHY1 are abolished in a PHYA-deficient mutant background, showing that FHY1 requires a signal from PHYA for function, and cannot modulate growth independently of PHYA.

The phytochrome A specific signaling component PAT3 is a positive regulator of Arabidopsis photomorphogenesis

Phytochrome A plays a major role in early seedling development by triggering the transition from etiolated growth to greening. Seedlings germinated under constant far-red (FR) light show a partially de-etiolated phenotype that is not seen in phyA mutants. This phytochrome A specific response was used to screen a population of T-DNA mutagenized Arabidopsis seedlings. One mutant line, pat3 (phytochrome A signal transduction3), which showed no inhibition of hypocotyl elongation under FR light conditions and no FR-induced killing response, contained a T-DNA insertion in a 609-bp ORF. The recessive mutation co-segregated with the T-DNA resistance marker and could be allelic to fhy1. A 2,248-bp genomic fragment of the PAT3 locus can complement the pat3 mutant phenotype. PAT3 transcript peaked 3 d after germination and was downregulated by light. PAT3 has no significant homology to any known protein and shows no preferential cellular localization. The protein can activate transcription in yeast when fused to the GAL4 DNA-binding domain. Our results show that PAT3 is a positive regulator of phytochrome A signal transduction.

The phytochrome A-specific signaling intermediate SPA1 interacts directly with COP1, a constitutive repressor of light signaling in Arabidopsis

SPA1 is a phytochrome A (phyA)-specific signaling intermediate that acts as a light-dependent repressor of photomorphogenesis in Arabidopsis seedlings. It contains a WD-repeat domain that shows high sequence similarity to the WD-repeat region of the constitutive repressor of light signaling, COP1. Here, using yeast two-hybrid and in vitro interaction assays, we show that SPA1 strongly and selectively binds to COP1. Domain mapping studies indicate that the putative coiled-coil domain of SPA1 is necessary and sufficient for binding to COP1. Conversely, similar deletion analyses of the COP1 protein suggest that SPA1 interacts with the presumed coiled-coil domain of COP1. To further investigate SPA1 function in the phyA signaling pathway, we tested whether SPA1, like COP1, mediates changes in gene expression in response to light. We show that spa1 mutations increase the photoresponsiveness of certain light-regulated genes within 2 h of light treatment. Taken together, the results suggest that SPA1 may function to link the phytochrome A-specific branch of the light signaling pathway to COP1. Hence, our data provide molecular support for the hypothesis that COP1 is a convergence point for upstream signaling pathways dedicated to individual photoreceptors.

Photocontrol of stem growth

Rapid and measurable growth rate changes that occur in seedling stems upon illumination serve as an excellent means to analyze signal transduction. Growth kinetic studies have shown how red, far-red and blue light signals are transduced via the solitary and/or coordinated action of known plant photoreceptors. These reports are consistent with current findings describing light-induced photoreceptor interaction and compartmentation.

LAF1, a MYB transcription activator for phytochrome A signaling

The photoreceptor phytochrome (phy) A has a well-defined role in regulating gene expression in response to specific light signals. Here, we describe a new Arabidopsis mutant, laf1 (long after far-red light 1) that has an elongated hypocotyl specifically under far-red light. Gene expression studies showed that laf1 has reduced responsiveness to continuous far-red light but retains wild-type responses to other light wavelengths. As far-red light is only perceived by phyA, our results suggest that LAF1 is specifically involved in phyA signal transduction. Further analyses revealed that laf1 is affected in a subset of phyA-dependent responses and the phenotype is more severe at low far-red fluence rates. LAF1 encodes a nuclear protein with strong homology with the R2R3-MYB family of DNA-binding proteins. Experiments using yeast cells identified a transactivation domain in the C-terminal portion of the protein. LAF1 is constitutively targeted to the nucleus by signals in its N-terminal portion, and the full-length protein accumulates in distinct nuclear speckles. This accumulation in speckles is abolished by a point mutation in a lysine residue (K258R), which might serve as a modification site by a small ubiquitin-like protein (SUMO).

Light-induced growth promotion by SPA1 counteracts phytochrome-mediated growth inhibition during de-etiolation

Previous evidence has suggested that SPA1 is a signal transduction component that appears to require phytochrome A for function in seedling photomorphogenesis. Using digital image analysis, we examined the time course of growth inhibition induced by red light in spa1 mutants to test the interpretation that SPA1 functions early in a phyA-specific signaling pathway. By comparing wild-type and mutant responses, we found that SPA1 caused an increase in hypocotyl growth rate after approximately 2 h of continuous red light, whereas the onset of phyA-mediated inhibition was detected within several minutes. Thus, SPA1-dependent growth promotion began after phyA started to inhibit growth. The action of SPA1 persisted for approximately 2 d of red light, a period well beyond the time when the phyA photoreceptor and its influence on growth have both decayed to undetectable levels. Also, SPA1 promoted growth for many hours in the complete absence of a light stimulus when red-light-grown seedlings were shifted to darkness. We propose that SPA1 functions in a light-induced mechanism that promotes growth and thereby counteracts growth inhibition mediated by phyA and phyB. Our finding that spa1 seedlings do not display growth promotion in response to end-of-day pulses of far-red light, even in a phyA-null background, supports this interpretation. Combined, these results lead us to the view that the rate of hypocotyl elongation in light is determined by at least two independent, opposing processes; an inhibition of growth by the phytochromes and a promotion of growth by light-activated SPA1.

Overexpression of the heterotrimeric G-protein alpha-subunit enhances phytochrome-mediated inhibition of hypocotyl elongation in Arabidopsis

Plant heterotrimeric G-proteins have been implicated in a number of signaling processes. However, most of these studies are based on biochemical or pharmacological approaches. To examine the role of heterotrimeric G-proteins in plant development, we generated transgenic Arabidopsis expressing the Galpha subunit of the heterotrimeric G-protein under the control of a glucocorticoid-inducible promoter. With the conditional overexpression of either the wild type or a constitutively active version of Arabidopsis Galpha, transgenic seedlings exhibited a hypersensitive response to light. This enhanced light sensitivity was more exaggerated in a relatively lower intensity of light and was observed in white light as well as far-red, red, and blue light conditions. The enhanced responses in far-red and red light required functional phytochrome A and phytochrome B, respectively. Furthermore, the response to far-red light depended on functional FHY1 but not on FIN219 and FHY3. This dependence on FHY1 indicates that the Arabidopsis Galpha protein may act only on a discrete branch of the phytochrome A signaling pathway. Thus, our results support the involvement of a heterotrimeric G-protein in the light regulation of Arabidopsis seedling development.

Overexpression of the heterotrimeric G-protein alpha-subunit enhances phytochrome-mediated inhibition of hypocotyl elongation in Arabidopsis

Plant heterotrimeric G-proteins have been implicated in a number of signaling processes. However, most of these studies are based on biochemical or pharmacological approaches. To examine the role of heterotrimeric G-proteins in plant development, we generated transgenic Arabidopsis expressing the Galpha subunit of the heterotrimeric G-protein under the control of a glucocorticoid-inducible promoter. With the conditional overexpression of either the wild type or a constitutively active version of Arabidopsis Galpha, transgenic seedlings exhibited a hypersensitive response to light. This enhanced light sensitivity was more exaggerated in a relatively lower intensity of light and was observed in white light as well as far-red, red, and blue light conditions. The enhanced responses in far-red and red light required functional phytochrome A and phytochrome B, respectively. Furthermore, the response to far-red light depended on functional FHY1 but not on FIN219 and FHY3. This dependence on FHY1 indicates that the Arabidopsis Galpha protein may act only on a discrete branch of the phytochrome A signaling pathway. Thus, our results support the involvement of a heterotrimeric G-protein in the light regulation of Arabidopsis seedling development.

shygrl1 is a mutant affected in multiple aspects of photomorphogenesis

We have used a counter-selection strategy based on aberrant phytochrome regulation of an Lhcb gene to isolate an Arabidopsis mutant designated shygrl1 (shg1). shg1 seedlings have reduced phytochrome-mediated induction of the Lhcb gene family, but normal phytochrome-mediated induction of several other genes, including the rbcS1a gene. Additional phenotypes observed in shg1 plants include reduced chlorophyll in leaves and additional photomorphogenic abnormalities when the seedlings are grown on medium containing sucrose. Mutations in the TATA-proximal region of the Lhcb1*3 promoter that are known to be important for phytochrome regulation affected reporter gene expression in a manner similar to the shg1 mutation. Our results are consistent with the possibility that the mutation either leads to defective chloroplast development or to aberrant phytochrome regulation. They also add to the evidence of complex interactions between light- and sucrose-regulated pathways.

EID1, an F-box protein involved in phytochrome A-specific light signaling

To perceive red and far-red light, plants have evolved specific photoreceptors called phytochromes. Even though the spectral properties of all phytochromes are very similar, they show a distinct mode of action. Here we describe EID1, a negatively acting component of the signaling cascade that shifts the responsiveness of the phytochrome A (phyA) signaling system associated with hypocotyl elongation from red to far-red wavelengths. EID1 is a novel nuclear F-box protein that contains a leucine zipper whose integrity is necessary for its biological function. EID1 most probably acts by targeting activated components of the phyA signaling pathway to ubiquitin-dependent proteolysis.