Photoreceptor Specificity in the Light-Induced and COP1-Mediated Rapid Degradation of the Repressor of Photomorphogenesis SPA2 in Arabidopsis

S-nitrosylation may inhibit the activity of COP1 in plant photomorphogenesis

Protein S-nitrosylation, which is defined by the covalent attachment of nitric oxide (NO) to the thiol group of cysteine residues, is known to play critical roles in plant development and stress responses. NO promotes seedling photomorphogenesis and NO emission is enhanced by light. However, the function of protein S-nitrosylation in plant photomorphogenesis is largely unknown. E3 ligase CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) and transcription factor ELONGATED HYPOCOTYL 5 (HY5) antagonistically regulate seedling photomorphogenesis. COP1 inhibits plant photomorphogenesis by targeting photomorphogenic promoters like HY5 for 26S proteasome degradation. Here, we report that COP1 is S-nitrosylated in vitro. Mass spectrometry analyses revealed that two evolutionarily well conserved residues, cysteine 425 and cysteine 607, in the WD40 domain of COP1 are S-nitrosylated. S-nitrosylated glutathione (GSNO) is an important physiological NO donor for protein S-nitrosylation. The Arabidopsis (Arabidopsis thaliana) gsnor1-3 mutant, which accumulates higher level of GSNO, accumulated higher HY5 levels than wildtype (WT), indicating that COP1 activity is inhibited. Protein S-nitrosylation can be reversed by Thioredoxin-h5 (TRXh5) in plants. Indeed, COP1 interacts directly with TRXh5 and its close homolog TRXh3. Moreover, catalase 3 (CAT3) acts as a transnitrosylase that transfers NO to its target proteins like GSNO reductase (GSNOR). We found that CAT3 interacts with COP1 in plants. Taken together, our data indicate that the activity of COP1 is likely inhibited by NO via S-nitrosylation to promote the accumulation of HY5 and photomorphogenesis.

What is going on inside of phytochrome B photobodies?

Plants exhibit an enormous phenotypic plasticity to adjust to changing environmental conditions. For this purpose, they have evolved mechanisms to detect and measure biotic and abiotic factors in their surroundings. Phytochrome B exhibits a dual function, since it serves as a photoreceptor for red and far-red light as well as a thermosensor. In 1999, it was first reported that phytochromes not only translocate into the nucleus but also form subnuclear foci upon irradiation by red light. It took more than 10 years until these phytochrome speckles received their name; these foci were coined photobodies to describe unique phytochrome-containing subnuclear domains that are regulated by light. Since their initial discovery, there has been much speculation about the significance and function of photobodies. Their presumed roles range from pure experimental artifacts to waste deposits or signaling hubs. In this review, we summarize the newest findings about the meaning of phyB photobodies for light and temperature signaling. Recent studies have established that phyB photobodies are formed by liquid-liquid phase separation via multivalent interactions and that they provide diverse functions as biochemical hotspots to regulate gene expression on multiple levels.

CRISPR/Cas9-Mediated HY5 Gene Editing Reduces Growth Inhibition in Chinese Cabbage (Brassica rapa) under ER Stress

Various stresses can affect the quality and yield of crops, including vegetables. In this study, CRISPR/Cas9 technology was employed to examine the role of the ELONGATED HYPOCOTYL 5 (HY5) gene in influencing the growth of Chinese cabbage (Brassica rapa). Single guide RNAs (sgRNAs) were designed to target the HY5 gene, and deep-sequencing analysis confirmed the induction of mutations in the bZIP domain of the gene. To investigate the response of Chinese cabbage to endoplasmic reticulum (ER) stress, plants were treated with tunicamycin (TM). Both wild-type and hy5 mutant plants showed increased growth inhibition with increasing TM concentration. However, the hy5 mutant plants displayed less severe growth inhibition compared to the wild type. Using nitroblue tetrazolium (NBT) and 3,3'-diaminobenzidine (DAB) staining methods, we determined the amount of reactive oxygen species (ROS) produced under ER stress conditions, and found that the hy5 mutant plants generated lower levels of ROS compared to the wild type. Under ER stress conditions, the hy5 mutant plants exhibited lower expression levels of UPR- and cell death-related genes than the wild type. These results indicate that CRISPR/Cas9-mediated editing of the HY5 gene can mitigate growth inhibition in Chinese cabbage under stresses, improving the quality and yield of crops.

Arabidopsis SPA2 represses seedling de-etiolation under multiple light conditions

In Arabidopsis, phytochrome (phy) A, phyB, and cryptochrome 1 (cry1) are representative far-red, red, and blue light photoreceptors, respectively. Members of the SUPPRESSOR OF PHYA-105 (SPA) protein family (SPA1-SPA4) form E3 ubiquitin ligase complexes with CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1), which mediates the degradation of photomorphogenesis-promoting factors to desensitize light signaling. SPA2 has been reported to promote seedling etiolation in the dark. However, the unique roles of SPA2 and its three functional domains in suppressing photomorphogenesis under different light conditions are largely unknown. Here, we demonstrate that overexpression of the full-length or the central coiled-coil and C-terminal WD-repeat domains of SPA2 cause hyper-etiolation phenotypes under several light conditions. The SPA2 central coiled-coil and C-terminal WD-repeat domains are necessary and sufficient for repressing seedling de-etiolation, cotyledon unfolding, and promoting hypocotyl negative gravitropism under several light conditions. Furthermore, phyA, phyB, cry1, and COP1 repress protein accumulation or nuclear translocation of SPA2 through direct interactions with its kinase-like and coiled-coil domains located in the N-terminus in response to far-red, red, and blue light treatments, respectively. Taken together, our results demonstrate that SPA2 functions under multiple light conditions; moreover, light-activated photoreceptors rapidly suppress SPA2 activity via direct interactions in response to different light treatments.

Signaling Mechanisms by Arabidopsis Cryptochromes

Cryptochromes (CRYs) are blue light photoreceptors that regulate growth, development, and metabolism in plants. In Arabidopsis thaliana (Arabidopsis), CRY1 and CRY2 possess partially redundant and overlapping functions. Upon exposure to blue light, the monomeric inactive CRYs undergo phosphorylation and oligomerization, which are crucial to CRY function. Both the N- and C-terminal domains of CRYs participate in light-induced interaction with multiple signaling proteins. These include the COP1/SPA E3 ubiquitin ligase, several transcription factors, hormone signaling intermediates and proteins involved in chromatin-remodeling and RNA N6 adenosine methylation. In this review, we discuss the mechanisms of Arabidopsis CRY signaling in photomorphogenesis and the recent breakthroughs in Arabidopsis CRY research.

Functions of COP1/SPA E3 Ubiquitin Ligase Mediated by MpCRY in the Liverwort Marchantia polymorpha under Blue Light

COP1/SPA1 complex in Arabidopsis inhibits photomorphogenesis through the ubiquitination of multiple photo-responsive transcription factors in darkness, but such inhibiting function of COP1/SPA1 complex would be suppressed by cryptochromes in blue light. Extensive studies have been conducted on these mechanisms in Arabidopsis whereas little attention has been focused on whether another branch of land plants bryophyte utilizes this blue-light regulatory pathway. To study this problem, we conducted a study in the liverwort Marchantia polymorpha and obtained a MpSPA knock-out mutant, in which Mpspa exhibits the phenotype of an increased percentage of individuals with asymmetrical thallus growth, similar to MpCRY knock-out mutant. We also verified interactions of MpSPA with MpCRY (in a blue light-independent way) and with MpCOP1. Concomitantly, both MpSPA and MpCOP1 could interact with MpHY5, and MpSPA can promote MpCOP1 to ubiquitinate MpHY5 but MpCRY does not regulate the ubiquitination of MpHY5 by MpCOP1/MpSPA complex. These data suggest that COP1/SPA ubiquitinating HY5 is conserved in Marchantia polymorpha, but dissimilar to CRY in Arabidopsis, MpCRY is not an inhibitor of this process under blue light.

Integration of Light and Brassinosteroid Signaling during Seedling Establishment

Light and brassinosteroid (BR) are external stimuli and internal cue respectively, that both play critical roles in a wide range of developmental and physiological process. Seedlings grown in the light exhibit photomorphogenesis, while BR promotes seedling etiolation. Light and BR oppositely control the development switch from shotomorphogenesis in the dark to photomorphogenesis in the light. Recent progress report that substantial components have been identified as hubs to integrate light and BR signals. Photomorphogenic repressors including COP1, PIFs, and AGB1 have been reported to elevate BR response, while photomorphogenesis-promoting factors such as HY5, BZS1, and NF-YCs have been proven to repress BR signal. In addition, BR components also modulate light signal. Here, we review the current research on signaling network associated with light and brassinosteroids, with a focus on the integration of light and BR signals enabling plants to thrive in the changeable environment.

Light-induced degradation of SPA2 via its N-terminal kinase domain is required for photomorphogenesis

Arabidopsis (Arabidopsis thaliana) CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1) and members of the SUPPRESSOR OF PHYTOCHROMEA-105 (SPA) protein family form an E3 ubiquitin ligase that suppresses light signaling in darkness by polyubiquitinating positive regulators of the light response. COP1/SPA is inactivated by light to allow photomorphogenesis to proceed. Mechanisms of inactivation include light-induced degradation of SPA1 and, in particular, SPA2, corresponding to a particularly efficient inactivation of COP1/SPA2 by light. Here, we show that SPA3 and SPA4 proteins are stable in the light, indicating that light-induced destabilization is specific to SPA1 and SPA2, possibly related to the predominant function of SPA1 and SPA2 in dark-grown etiolating seedlings. SPA2 degradation involves cullin and the COP10-DEETIOLATED-DAMAGED-DNA BINDING PROTEIN (DDB1) CDD complex, besides COP1. Consistent with this finding, light-induced SPA2 degradation required the DDB1-interacting Trp-Asp (WD)-repeat domain of SPA2. Deletion of the N-terminus of SPA2 containing the kinase domain led to strong stabilization of SPA2 in darkness and fully abolished light-induced degradation of SPA2. This prevented seedling de-etiolation even in very strong far-red and blue light and reduced de-etiolation in red light, indicating destabilization of SPA2 through its N-terminal domain is essential for light response. SPA2 is exclusively destabilized by phytochrome A in far-red and blue light. However, deletion of the N-terminal domain of SPA2 did not abolish SPA2-phytochrome A interaction in yeast nor in vivo. Our domain mapping suggests there are two SPA2-phytochrome A interacting domains, the N-terminal domain and the WD-repeat domain. Conferring a light-induced SPA2-phyA interaction only via the WD-repeat domain may thus not lead to COP1/SPA2 inactivation.

DET1-mediated COP1 regulation avoids HY5 activity over second-site gene targets to tune plant photomorphogenesis

DE-ETIOLATED 1 (DET1) and CONSTITUTIVE PHOTOMORPHOGENESIS 1 (COP1) are two essential repressors of Arabidopsis photomorphogenesis. These proteins can associate with CULLIN4 to form independent CRL4-based E3 ubiquitin ligases that mediate the degradation of several photomorphogenic transcription factors, including ELONGATED HYPOCOTYL 5 (HY5), thereby controlling multiple gene-regulatory networks. Despite extensive biochemical and genetic analyses of their multi-subunit complexes, the functional links between DET1 and COP1 have long remained elusive. Here, we report that DET1 associates with COP1 in vivo, enhances COP1-HY5 interaction, and promotes COP1 destabilization in a process that dampens HY5 protein abundance. By regulating its accumulation, DET1 avoids HY5 association with hundreds of second-site genomic loci, which are also frequently targeted by the skotomorphogenic transcription factor PHYTOCHROME-INTERACTING FACTOR 3. Accordingly, ectopic HY5 chromatin enrichment favors local gene repression and can trigger fusca-like phenotypes. This study therefore shows that DET1-mediated regulation of COP1 stability tunes down the HY5 cistrome, avoiding hyper-photomorphogenic responses that might compromise plant viability.

DET1-mediated COP1 regulation avoids HY5 activity over second-site gene targets to tune plant photomorphogenesis

DE-ETIOLATED 1 (DET1) and CONSTITUTIVE PHOTOMORPHOGENESIS 1 (COP1) are two essential repressors of Arabidopsis photomorphogenesis. These proteins can associate with CULLIN4 to form independent CRL4-based E3 ubiquitin ligases that mediate the degradation of several photomorphogenic transcription factors, including ELONGATED HYPOCOTYL 5 (HY5), thereby controlling multiple gene-regulatory networks. Despite extensive biochemical and genetic analyses of their multi-subunit complexes, the functional links between DET1 and COP1 have long remained elusive. Here, we report that DET1 associates with COP1 in vivo, enhances COP1-HY5 interaction, and promotes COP1 destabilization in a process that dampens HY5 protein abundance. By regulating its accumulation, DET1 avoids HY5 association with hundreds of second-site genomic loci, which are also frequently targeted by the skotomorphogenic transcription factor PHYTOCHROME-INTERACTING FACTOR 3. Accordingly, ectopic HY5 chromatin enrichment favors local gene repression and can trigger fusca-like phenotypes. This study therefore shows that DET1-mediated regulation of COP1 stability tunes down the HY5 cistrome, avoiding hyper-photomorphogenic responses that might compromise plant viability.

Illuminating the COP1/SPA Ubiquitin Ligase: Fresh Insights Into Its Structure and Functions During Plant Photomorphogenesis

CONSTITUTIVE PHOTOMORPHOGENIC 1 functions as an E3 ubiquitin ligase in plants and animals. Discovered originally in Arabidopsis thaliana, COP1 acts in a complex with SPA proteins as a central repressor of light-mediated responses in plants. By ubiquitinating and promoting the degradation of several substrates, COP1/SPA regulates many aspects of plant growth, development and metabolism. In contrast to plants, human COP1 acts as a crucial regulator of tumorigenesis. In this review, we discuss the recent important findings in COP1/SPA research including a brief comparison between COP1 activity in plants and humans.

Molecular pathways regulating elongation of aerial plant organs: a focus on light, the circadian clock, and temperature

Organs such as hypocotyls and petioles rapidly elongate in response to shade and temperature cues, contributing to adaptive responses that improve plant fitness. Growth plasticity in these organs is achieved through a complex network of molecular signals. Besides conveying information from the environment, this signaling network also transduces internal signals, such as those associated with the circadian clock. A number of studies performed in Arabidopsis hypocotyls, and to a lesser degree in petioles, have been informative for understanding the signaling networks that regulate elongation of aerial plant organs. In particular, substantial progress has been made towards understanding the molecular mechanisms that regulate responses to light, the circadian clock, and temperature. Signals derived from these three stimuli converge on the BAP module, a set of three different types of transcription factors that interdependently promote gene transcription and growth. Additional key positive regulators of growth that are also affected by environmental cues include the CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and SUPPRESSOR OF PHYA-105 (SPA) E3 ubiquitin ligase proteins. In this review we summarize the key signaling pathways that regulate the growth of hypocotyls and petioles, focusing specifically on molecular mechanisms important for transducing signals derived from light, the circadian clock, and temperature. While it is clear that similarities abound between the signaling networks at play in these two organs, there are also important differences between the mechanisms regulating growth in hypocotyls and petioles.

COP1 and BBXs-HY5-mediated light signal transduction in plants

Light is one of the most essential environmental factors affecting many aspects of growth and developmental processes in plants. Plants undergo skotomorphogenic or photomorphogenic development dependent on the absence or presence of light. These two developmental programs enable a germinated seed to become a healthy seedling at the early stage of the plant life cycle. CULLIN 4-DNA DAMAGE-BINDING PROTEIN 1 (DDB1)-based CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1)-SUPPRESSOR OF PHYA and COP10-DEETIOLATED 1-DDB1 E3 ubiquitin ligase complexes promote the skotomorphogenesis by ubiquitinating and degrading a number of photomorphogenic-promoting factors in darkness. Photoreceptors sense and transduce light information to downstream signaling, thereby initiating a set of molecular events and subsequent photomorphogenesis. These processes are precisely modulated by a group of components including various photoreceptors, E3 ubiquitin ligase, and transcription factors at the molecular level. This review provides an overview of the current understanding of the COP1, ELONGATED HYPOCOTYL 5, and B-BOX CONTAINING PROTEINs-mediated light signal transduction pathway and highlights still open questions in the field.

Distinct Responses to Light in Plants

The development of almost every living organism is, to some extent, regulated by light. When discussing light regulation on biological systems, one is referring to the sun that has long been positioned in the center of the solar system. Through light regulation, all life forms have evolved around the presence of the sun. As soon our planet started to develop an atmospheric shield against most of the detrimental solar UV rays, life invaded land, and in the presence of water, it thrived. Especially for plants, light (solar radiation) is the source of energy that controls a high number of developmental aspects of growth, a process called photomorphogenesis. Once hypocotyls reach soil′s surface, its elongation deaccelerates, and the photosynthetic apparatus is established for an autotrophic growth due to the presence of light. Plants can sense light intensities, light quality, light direction, and light duration through photoreceptors that accurately detect alterations in the spectral composition (UV-B to far-red) and are located throughout the plant. The most well-known mechanism promoted by light occurring on plants is photosynthesis, which converts light energy into carbohydrates. Plants also use light to signal the beginning/end of key developmental processes such as the transition to flowering and dormancy. These two processes are particularly important for plant´s yield, since transition to flowering reduces the duration of the vegetative stage, and for plants growing under temperate or boreal climates, dormancy leads to a complete growth arrest. Understanding how light affects these processes enables plant breeders to produce crops which are able to retard the transition to flowering and avoid dormancy, increasing the yield of the plant.

Molecular mechanisms suppressing COP1/SPA E3 ubiquitin ligase activity in blue light

Arabidopsis CONSTITUTIVE PHOTOMORPHOGENIC1/SUPPRESSOR OF PHYA-105 (COP1/SPA) is an E3 ubiquitin ligase complex that prevents photomorphogenesis in darkness by ubiquitinating and subsequently degrading light-responsive transcription factors. Upon light perception, photoreceptors directly interact with the COP1/SPA complex to suppress its activity. In blue light (450-500 nm of visible spectrum), COP1/SPA activity is inhibited by the cryptochrome photoreceptors (CRY1 and CRY2), FKF1 from the ZEITLUPE family as well as phytochrome A. Together, these photoreceptors regulate vital aspects of plant growth and development from seedling stage to the induction of flowering. This review presents and discusses the recent advances in blue light-mediated suppression of COP1/SPA activity.

CONSTITUTIVELY PHOTOMORPHOGENIC1 promotes ABA-mediated inhibition of post-germination seedling establishment

Under acute stress conditions, precocious seedling development may result in the premature death of young seedlings, before they switch to autotrophic growth. The phytohormone abscisic acid (ABA) inhibits seed germination and post-germination seedling establishment under unfavorable conditions. Various environmental signals interact with the ABA pathway to optimize these early developmental events under stress. Here, we show that light availability critically influences ABA sensitivity during early seedling development. In dark conditions, the ABA-mediated inhibition of post-germination seedling establishment is strongly enhanced. COP1, a central regulator of seedling development in the dark, is necessary for this enhanced post-germination ABA sensitivity in darkness. Despite their slower germination, cop1 seedlings establish faster than wild type in the presence of ABA in both light and dark. PHY and CRY photoreceptors that inhibit COP1 activity in light modulate ABA-mediated inhibition of seedling establishment in light. Genetically, COP1 acts downstream to ABI5, a key transcriptional regulator of ABA signaling, and does not influence the transcriptional and protein levels of ABI5 during the early post-germination stages. COP1 promotes post-germination growth arrest independent of the antagonistic interaction between ABA and cytokinin signaling pathways. COP1 facilitates the binding of ABI5 on its target promoters and the ABA-mediated upregulation of these target genes is reduced in cop1-4. Together, our results suggest that COP1 positively regulates ABA signaling to inhibit post-germination seedling establishment under stress.

The Photomorphogenic Central Repressor COP1: Conservation and Functional Diversification during Evolution

Green plants on the earth have evolved intricate mechanisms to acclimatize to and utilize sunlight. In Arabidopsis, light signals are perceived by photoreceptors and transmitted through divergent but overlapping signaling networks to modulate plant photomorphogenic development. COP1 (CONSTITUTIVE PHOTOMORPHOGENIC 1) was first cloned as a central repressor of photomorphogenesis in higher plants and has been extensively studied for over 30 years. It acts as a RING E3 ubiquitin ligase downstream of multiple photoreceptors to target key light-signaling regulators for degradation, primarily as part of large protein complexes. The mammalian counterpart of COP1 is a pluripotent regulator of tumorigenesis and metabolism. A great deal of information on COP1 has been derived from whole-genome sequencing and functional studies in lower green plants, which enables us to illustrate its evolutionary history. Here, we review the current understanding about COP1, with a focus on the conservation and functional diversification of COP1 and its signaling partners in different taxonomic clades.

Genetic and molecular basis of floral induction in Arabidopsis thaliana

Many plants synchronize their life cycles in response to changing seasons and initiate flowering under favourable environmental conditions to ensure reproductive success. To confer a robust seasonal response, plants use diverse genetic programmes that integrate environmental and endogenous cues and converge on central floral regulatory hubs. Technological advances have allowed us to understand these complex processes more completely. Here, we review recent progress in our understanding of genetic and molecular mechanisms that control flowering in Arabidopsis thaliana.

Photoexcited phytochrome B interacts with brassinazole resistant 1 to repress brassinosteroid signaling in Arabidopsis

Photoreceptor phytochrome B (phyB) mediates a variety of light responses in plants. To further elucidate the molecular mechanisms of phyB-regulated hypocotyl elongation, we performed firefly luciferase complementation imaging (LCI) screening for phyB-interacting transcription factors (TFs). LCI assays showed that phyB possibly interacts with brassinazoleresistant 1 (BZR1), BZR2, AUXIN RESPONSE FACTOR 6 (ARF6), and several WRKY DNA-binding TFs in a red light-dependent manner. Furthermore, biochemical assays demonstrated that photoexcited phyB specifically interacts with non-phosphorylated BZR1, the physiologically active form of a master TF in brassinosteroid (BR) signaling, and this interaction can be competitively interfered by phytochrome-interacting factor 4. Furthermore, we showed that phyB can directly interact with the DNA-binding domain of BZR1 and affect the enrichment of BZR1 on the chromatin of target genes. Moreover, our genetic evidence and RNA-seq analysis demonstrated that phyB negatively regulates BR signaling. Together, we revealed that photoexcited phyB directly interacts with the TF BZR1 to repress BR signaling in Arabidopsis.

PHYTOCHROME INTERACTING FACTOR8 Inhibits Phytochrome A-Mediated Far-Red Light Responses in Arabidopsis

PHYTOCHROME INTERACTING FACTORs (PIFs) are a group of basic helix-loop-helix (bHLH) transcription factors that repress plant light responses. PIF8 is one of the less-characterized Arabidopsis (Arabidopsis thaliana) PIFs, whose putative orthologs are conserved in other plant species. PIF8 possesses a bHLH motif and an active phytochrome B motif but not an active phytochrome A motif. Consistent with this motif composition, PIF8 binds to G-box elements and interacts with the Pfr form of phyB but only very weakly, if at all, with that of phyA. PIF8 differs, however, from other PIFs in its protein accumulation pattern and functional roles in different light conditions. First, PIF8 inhibits phyA-induced seed germination, suppression of hypocotyl elongation, and randomization of hypocotyl growth orientation in far-red light, but it does not inhibit phyB-induced red light responses. Second, PIF8 protein accumulates more in far-red light than in darkness or red light. This is distinct from the pattern observed with PIF3, which accumulates more in darkness. This PIF8 accumulation pattern requires degradation of PIF8 by CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1) in darkness, inhibition of COP1 by phyA in far-red light, and promotion of PIF8 degradation by phyB in red light. Together, our results indicate that PIF8 is a genuine PIF that represses phyA-mediated light responses.

Cell wall structure and composition is affected by light quality in tomato seedlings

Light affects many aspects of cell development. Tomato seedlings growing at different light qualities (white, blue, green, red, far-red) and in the dark displayed alterations in cell wall structure and composition. A strong and negative correlation was found between cell wall thickness and hypocotyl growth. Cell walls was thicker under blue and white lights and thinner under far-red light and in the dark, while intermediate values was observed for red or green lights. Additionally, the inside layer surface of cell wall presented random deposited microfibrillae angles under far-red light and in the dark. However, longitudinal transmission electron microscopy indicates a high frequency of microfibrils close to parallels related to the elongation axis in the outer layer. This was confirmed by ultra-high resolution small angle X-ray scattering. These data suggest that cellulose microfibrils would be passively reoriented in the longitudinal direction. As the cell expands, the most recently deposited layers (inside) behave differentially oriented compared to older (outer) layers in the dark or under FR lights, agreeing with the multinet growth hypothesis. High Ca and pectin levels were found in the cell wall of seedlings growing under blue and white light, also contributing to the low extensibility of the cell wall. Low Ca and pectin contents were found in the dark and under far-red light. Auxins marginally stimulated growth in thin cell wall circumstances. Hypocotyl growth was stimulated by gibberellins under blue light.

Cryptochrome 2 competes with COP1 substrates to repress COP1 ubiquitin ligase activity during Arabidopsis photomorphogenesis

In plants, the cryptochrome photoreceptors suppress the activity of the COP1/SPA ubiquitin ligase to initiate photomorphogenesis in blue light. Both CRY1 and CRY2 interact with the COP1/SPA complex in a blue light-dependent manner. The mechanisms underlying the inhibition of COP1 activity through direct interactions with photoactivated CRYs are not fully understood. Here we tested the hypothesis that CRY2 inhibits COP1 by displacing the degradation substrates from COP1. To this end, we analyzed the role of a conserved valine-proline (VP) motif in the C-terminal domain of CRY2 (CCT2), which resembles the core COP1-WD40-binding sequences present in the substrates of COP1. We show that the VP motif in CRY2 is essential for the interaction of CRY2 with COP1 in yeast two-hybrid assays and in planta Mutations in the VP motif of CRY2 abolished the CRY2 activity in photomorphogenesis, indicating the importance of VP. The interaction between COP1 and its VP-containing substrate PAP2 was prevented in the presence of coexpressed CRY2, but not in the presence of CRY2 carrying a VP mutation. Thus, since both PAP2 and CRY2 engage VP motifs to bind to COP1, these results demonstrate that CRY2 outcompetes PAP2 for binding to COP1. We further found that the previously unknown interaction between SPA1-WD and CCT2 occurs via the VP motif in CRY2, suggesting structural similarities in the VP-binding pockets of COP1-WD40 and SPA1-WD40 domains. A VP motif present in CRY1 is also essential for binding to COP1. Thus, CRY1 and CRY2 might share this mechanism of COP1 inactivation.

Characterization of spa mutants in the moss Physcomitrella provides evidence for functional divergence of SPA genes during the evolution of land plants

The Arabidopsis COP1/SPA complex is a key repressor of photomorphogenesis that suppresses light signaling in the dark. Both COP1 and SPA proteins are essential components of this complex. Although COP1 also exists in humans, SPA genes are specific to the green lineage. To elucidate the evolution of SPA genes we analyzed SPA functions in the moss Physcomitrella patens by characterizing knockout mutants in the two Physcomitrella SPA genes PpSPAa and PpSPAb. Light-grown PpspaAB double mutants exhibit smaller gametophores than the wild-type. In the dark, PpspaAB mutant gametophores show enhanced continuation of growth but etiolate normally. Gravitropism in the dark is reduced in PpspaAB mutant protonemata. The expression of light-regulated genes is mostly not constitutive in PpspaAB mutants. PpSPA and PpCOP1 interact; PpCOP1 also interacts with the transcription factor PpHY5 and, indeed, PpHY5 is destabilized in dark-grown Physcomitrella. Degradation of PpHY5 in darkness, however, does not require PpSPAa and PpSPAb. The data suggest that COP1/SPA-mediated light signaling is only partially conserved between Arabidopsis and Physcomitrella. Whereas COP1/SPA interaction and HY5 degradation in darkness is conserved, the role of SPA proteins appears to have diverged. PpSPA genes, unlike their Arabidopsis counterparts, are only required to suppress a subset of light responses in darkness.

Phenotypic and genome-wide association with the local environment of Arabidopsis

The environment imposes critical selective forces on all living organisms, and the sessile nature of plants makes them particularly useful for investigating the relationship between genetic variation and environmental adaptation. In the model plant Arabidopsis thaliana, extensive information on phenotypic and genotypic variation is available, but comparable information on environmental variation within the native range of the species is lacking. Here, we compile 204 geoclimatic variables to describe the local environments of Arabidopsis accessions with known collection sites encompassing a wide geo-environmental range, and fully sequenced genomes from the 1001 Genomes Project. We identify candidate adaptive genetic variation associated with these environmental variables, and validate this approach through comparison with previous experimental studies, and by targeted confirmation of a role of the heterotrimeric G-protein γ subunit, AGG3, in cold tolerance, as newly predicted from our environmental genome wide association study (GWAS). To facilitate identification of adaptive variation, we created Arabidopsis CLIMtools : interactive web-based databases of the environment × genome associations and correlations between the local environments and 131 phenotypes compiled from previous experimental GWASs. Our study presents an extensive analysis of the local environments, landscape genomics and phenotypic variation of Arabidopsis, and illustrates how 'in silico GWAS' approaches can inform and complement experimental phenomics studies.

Photoreceptor-mediated regulation of the COP1/SPA E3 ubiquitin ligase

Plants have evolved specific photoreceptors that capture informational cues from sunlight. The phytochrome, cryptochrome, and UVR8 photoreceptors perceive red/far-red, blue/UV-A, and UV-B light, respectively, and control overlapping photomorphogenic responses important for plant growth and development. A major repressor of such photomorphogenic responses is the E3 ubiquitin ligase formed by CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) and SUPPRESSOR OF PHYA-105 (SPA) proteins, which acts by regulating the stability of photomorphogenesis-promoting transcription factors. The direct interaction of light-activated photoreceptors with the COP1/SPA complex represses its activity via nuclear exclusion of COP1, disruption of the COP1-SPA interaction, and/or SPA protein degradation. This process enables plants to integrate different light signals at the level of the COP1/SPA complex to enact appropriate photomorphogenic responses according to the light environment.

COP1 plays a prominent role in drought stress tolerance in Arabidopsis and Pea

Constitutively photomorphogenic 1 (COP1) is an E3 ubiquitin ligase that has been studied extensively in the photomorphogenesis- and light-related processes in Arabidopsis. However, the possible role of COP1 in plant drought stress response remains unknown. Hence, in the present study, the stomatal behavior as one of the key elements in plant dehydration response was investigated in Arabidopsis cop1-4 and pea light-independent photomorphogenesis (lip1) mutants. We observed that water loss rate in the cop1-4 and lip1 detached leaves was significantly much faster than wild-type, resulting from failing to reduce the stomatal aperture by the mutants. But, interestingly, the cop1-4 and lip1 isolated leaves treated with abscisic acid (ABA) as well as cop1-4 and lip1 soil-grown under drought stress could close their stomata as wild-type. Hence, COP1 plays a fundamental role in the regulation of stomatal movements in response to dehydration and its function was conserved during evolution in both Arabidopsis and pea. Further evaluations showed the cop1-4 mutant was not significantly damaged from the oxidative stress derived from soil water limiting conditions when compared to wild-type. Similarly, the up-regulation level of several key stress-responsive genes was relatively lower in cop1-4 than wild-type. Therefore, COP1 might be considered as a potential key regulator of both short-and long-term dehydration response. Multiple stress-related cis-elements were also detected in the COP1 promoter region, which supported its up-regulation in response to drought, salt, and cold stresses. Besides, we figured out the constitutively open stomata of cop1-4 in darkness can be as a result of the reduced AtMYB61 expression.

Phytochrome B Requires PIF Degradation and Sequestration to Induce Light Responses across a Wide Range of Light Conditions

Phytochrome B (phyB) inhibits the function of phytochrome-interacting factors (PIFs) by inducing their degradation and sequestration, but the relative physiological importance of these two phyB activities is unclear. In an analysis of published Arabidopsis thaliana phyB mutations, we identified a point mutation in the N-terminal half of phyB (phyB^G111D) that abolishes its PIF sequestration activity without affecting its PIF degradation activity. We also identified a point mutation in the phyB C-terminal domain, which, when combined with a deletion of the C-terminal end (phyB990^G767R), does the opposite; it blocks PIF degradation without affecting PIF sequestration. The resulting phyB proteins, phyB990^G767R and phyB^G111D, are equally capable of inducing light responses under continuous red light. However, phyB^G111D, which exhibits only the PIF degradation activity, induces stronger light responses than phyB990^G767R under white light with prolonged dark periods (i.e., diurnal cycles). In contrast, phyB990^G767R, which exhibits only the PIF sequestration activity, induces stronger light responses in flickering light (a condition that mimics sunflecks). Together, our results indicate that both of these separable phyB activities are required for light responses in varying light conditions.

The Transcription Factor COL12 Is a Substrate of the COP1/SPA E3 Ligase and Regulates Flowering Time and Plant Architecture

The ambient light environment controls many aspects of plant development throughout a plant's life cycle. Such complex control is achieved because a key repressor of light signaling, the Arabidopsis (Arabidopsis thaliana) COP1/SPA E3 ubiquitin ligase causes the degradation of multiple regulators of endogenous developmental pathways. This includes the CONSTANS (CO) transcription factor that is responsible for photoperiodic control of flowering time. There are 16 CO-like proteins whose functions are only partly understood. Here, we show that 14 CO-like (COL) proteins bind CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1) and SUPPRESSOR OF PHYTOCHROME A-105 (SPA)1 in vitro. We subsequently focused on COL12 and show that COL12 binds COP1 and SPA proteins in vivo. The COL12 protein is degraded in darkness in a COP1-dependent fashion, indicating that COL12 is a substrate of the COP1/SPA ubiquitin ligase. Overexpression of COL12 causes late flowering specifically in long day conditions by decreasing the expression of FLOWERING LOCUS T This phenotype is genetically dependent on CO. Consistent with this finding, COL12 physically interacts with CO in vivo, suggesting that COL12 represses flowering by inhibiting CO protein function. We show that COL12 overexpression did not alter CO protein stability. It is therefore likely that COL12 represses the activity of CO rather than CO levels. Overexpression of COL12 also affects plant architecture by increasing the number of rosette branches and reducing inflorescence height. These phenotypes are CO independent. Hence, we suggest that COL12 affects plant development through CO-dependent and CO-independent mechanisms.

Molecular mechanisms and ecological function of far-red light signalling

Land plants possess the ability to sense and respond to far-red light (700-760 nm), which serves as an important environmental cue. Due to the nature of far-red light, it is not absorbed by chlorophyll and thus is enriched in canopy shade and will also penetrate deeper into soil than other visible wavelengths. Far-red light responses include regulation of seed germination, suppression of hypocotyl growth, induction of flowering and accumulation of anthocyanins, which depend on one member of the phytochrome photoreceptor family, phytochrome A (phyA). Here, we review the current understanding of the underlying molecular mechanisms of how plants sense far-red light through phyA and the physiological responses to this light quality. Light-activated phytochromes act on two primary pathways within the nucleus; suppression of the E3 ubiquitin ligase complex CUL4/DDB1^COP1/SPA and inactivation of the PHYTOCHROME INTERACTING FACTOR (PIF) family of bHLH transcription factors. These pathways integrate with other signal transduction pathways, including phytohormones, for tissue and developmental stage specific responses. Unlike other phytochromes that mediate red-light responses, phyA is transported from the cytoplasm to the nucleus in far-red light by the shuttle proteins FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1-LIKE (FHL). However, additional mechanisms must exist that shift the action of phyA to far-red light; current hypotheses are discussed.

COP1 regulates plant growth and development in response to light at the post-translational level

Photoreceptors perceive different wavelengths of light and transduce light signals downstream via a range of proteins. COP1, an E3 ubiquitin ligase, regulates light signaling by mediating the ubiquitination and subsequent proteasomal degradation of photoreceptors such as phytochromes and cryptochromes, as well as various development-related proteins including other light-responsive proteins. COP1 is itself regulated by direct interactions with several signaling molecules that modulate its activity. The control of photomorphogenesis by COP1 is also regulated by its localization to the cytoplasm in response to light. COP1 thus acts as a tightly regulated switch that determines whether development is skotomorphogenic or photomorphogenic. In this review, we discuss the effects of COP1 on the abundance and activity of various development-related proteins, including photoreceptors, and summarize the regulatory mechanisms that influence COP1 activity and stability in plants.

The blue light-induced interaction of cryptochrome 1 with COP1 requires SPA proteins during Arabidopsis light signaling

Plants constantly adjust their growth, development and metabolism to the ambient light environment. Blue light is sensed by the Arabidopsis photoreceptors CRY1 and CRY2 which subsequently initiate light signal transduction by repressing the COP1/SPA E3 ubiquitin ligase. While the interaction between cryptochromes and SPA is blue light-dependent, it was proposed that CRY1 interacts with COP1 constitutively, i.e. also in darkness. Here, our in vivo co-immunoprecipitation experiments suggest that CRY1 and CRY2 form a complex with COP1 only after seedlings were exposed to blue light. No association between COP1 and CRY1 or CRY2 was observed in dark-grown seedlings. Thus, our results suggest that cryptochromes bind the COP1/SPA complex after photoactivation by blue light. In a spa quadruple mutant that is devoid of all four SPA proteins, CRY1 and COP1 did not interact in vivo, neither in dark-grown nor in blue light-grown seedlings. Hence, SPA proteins are required for the high-affinity interaction between CRY1 and COP1 in blue light. Yeast three-hybrid experiments also show that SPA1 enhances the CRY1-COP1 interaction. The coiled-coil domain of SPA1 which is responsible for COP1-binding was necessary to mediate a CRY1-SPA1 interaction in vivo, implying that-in turn-COP1 may be necessary for a CRY1-SPA1 complex formation. Hence, SPA1 and COP1 may act cooperatively in recognizing and binding photoactivated CRY1. In contrast, the blue light-induced association between CRY2 and COP1 was not dependent on SPA proteins in vivo. Similarly, ΔCC-SPA1 interacted with CRY2, though with a much lower affinity than wild-type SPA1. In total, our results demonstrate that CRY1 and CRY2 strongly differ in their blue light-induced interaction with the COP1/SPA complex.

The blue light-induced interaction of cryptochrome 1 with COP1 requires SPA proteins during Arabidopsis light signaling

Plants constantly adjust their growth, development and metabolism to the ambient light environment. Blue light is sensed by the Arabidopsis photoreceptors CRY1 and CRY2 which subsequently initiate light signal transduction by repressing the COP1/SPA E3 ubiquitin ligase. While the interaction between cryptochromes and SPA is blue light-dependent, it was proposed that CRY1 interacts with COP1 constitutively, i.e. also in darkness. Here, our in vivo co-immunoprecipitation experiments suggest that CRY1 and CRY2 form a complex with COP1 only after seedlings were exposed to blue light. No association between COP1 and CRY1 or CRY2 was observed in dark-grown seedlings. Thus, our results suggest that cryptochromes bind the COP1/SPA complex after photoactivation by blue light. In a spa quadruple mutant that is devoid of all four SPA proteins, CRY1 and COP1 did not interact in vivo, neither in dark-grown nor in blue light-grown seedlings. Hence, SPA proteins are required for the high-affinity interaction between CRY1 and COP1 in blue light. Yeast three-hybrid experiments also show that SPA1 enhances the CRY1-COP1 interaction. The coiled-coil domain of SPA1 which is responsible for COP1-binding was necessary to mediate a CRY1-SPA1 interaction in vivo, implying that-in turn-COP1 may be necessary for a CRY1-SPA1 complex formation. Hence, SPA1 and COP1 may act cooperatively in recognizing and binding photoactivated CRY1. In contrast, the blue light-induced association between CRY2 and COP1 was not dependent on SPA proteins in vivo. Similarly, ΔCC-SPA1 interacted with CRY2, though with a much lower affinity than wild-type SPA1. In total, our results demonstrate that CRY1 and CRY2 strongly differ in their blue light-induced interaction with the COP1/SPA complex.

SPA Proteins Affect the Subcellular Localization of COP1 in the COP1/SPA Ubiquitin Ligase Complex during Photomorphogenesis

The Arabidopsis (Arabidopsis thaliana) COP1/SPA ubiquitin ligase is a central repressor that suppresses light signaling in darkness by targeting positive regulators of the light response, mainly transcription factors, for degradation. Light inactivates COP1/SPA, in part by excluding COP1 from the nucleus. SPA proteins are essential cofactors of COP1, but their exact role in the COP1/SPA complex is thus far unknown. To unravel a potential role of SPA proteins in COP1 nucleocytoplasmic partitioning, we monitored the subcellular localization of COP1 in a spa1234 quadruple mutant (spaQn). We analyzed a YFP-COP1-expressing transgenic line and endogenous COP1 after subcellular fractionation. In dark-grown seedlings, both YFP-COP1 and endogenous COP1 accumulated in the nucleus in the absence and presence of SPA proteins, indicating that SPA proteins are not required for nuclear localization of COP1 in darkness. In contrast, in white light-grown seedlings, spaQn mutants failed to relocalize COP1 from the nucleus to the cytoplasm. Hence, SPA proteins are necessary for the light-controlled change in COP1 subcellular localization. We conclude that SPA proteins have a dual role: (1) they are required for light-responsiveness of COP1 subcellular localization, and (2) they promote COP1 activity in darkness in a fashion that is independent of the nuclear import/nuclear retention of COP1.

SINAT E3 Ligases Control the Light-Mediated Stability of the Brassinosteroid-Activated Transcription Factor BES1 in Arabidopsis

The plant hormones brassinosteroids (BRs) participate in light-mediated regulation of plant growth, although the underlying mechanisms are far from being fully understood. In addition, the function of the core transcription factor in the BR signaling pathway, BRI1-EMS-SUPPRESSOR 1 (BES1), largely depends on its phosphorylation status and its protein stability, but the regulation of BES1 is not well understood. Here, we report that SINA of Arabidopsis thaliana (SINATs) specifically interact with dephosphorylated BES1 and mediate its ubiquitination and degradation. Our genetic data demonstrated that SINATs inhibit BR signaling in a BES1-dependent manner. Interestingly, we found that the protein levels of SINATs were decreased in the dark and increased in the light, which changed BES1 protein levels accordingly. Thus, our study not only uncovered a new mechanism of BES1 degradation but also provides significant insights into how light conditionally regulates plant growth through controlling accumulation of different forms of BES1.

The activities of the E3 ubiquitin ligase COP1/SPA, a key repressor in light signaling

Light is a critical signal to integrate plant growth and development with the environment. Downstream of photoreceptors, the E3 ubiquitin ligase COP1/SPA is a key repressor of photomorphogenesis which targets many positive regulators of light signaling, mainly transcription factors, for degradation in darkness. In light-grown plants COP1/SPA activity is repressed, allowing light responses to occur. This review provides an overview on our current knowledge on COP1/SPA repressor function, focusing in particular on the roles of the respective protein domains and the mechanisms of light-induced inactivation of COP1/SPA. Moreover, we summarize how COP1 activity is regulated by other interacting proteins, such as a SUMO E3 ligase and Phytochrome-Interacting Factors (PIFs), as well as by hormones. At last, several novel functions of COP1 that were recently revealed are included.

Jasmonate inhibits COP1 activity to suppress hypocotyl elongation and promote cotyledon opening in etiolated Arabidopsis seedlings

A germinating seedling undergoes skotomorphogenesis to emerge from the soil and reach for light. During this phase, the cotyledons are closed, and the hypocotyl elongates. Upon exposure to light, the seedling rapidly switches to photomorphogenesis by opening its cotyledons and suppressing hypocotyl elongation. The E3 ubiquitin ligase CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) is critical for maintaining skotomorphogenesis. Here, we report that jasmonate (JA) suppresses hypocotyl elongation and stimulates cotyledon opening in etiolated seedlings, partially phenocopying cop1 mutants in the dark. We also find that JA stabilizes several COP1-targeted transcription factors in a COP1-dependent manner. RNA-seq analysis further defines a JA-light co-modulated and cop1-dependent transcriptome, which is enriched for auxin-responsive genes and genes participating in cell wall modification. JA suppresses COP1 activity through at least two distinct mechanisms: decreasing COP1 protein accumulation in the nucleus; and reducing the physical interaction between COP1 and its activator, SUPPRESSOR OF PHYTOCHROME A-105 1 (SPA1). Our work reveals that JA suppresses COP1 activity to stabilize COP1 targets, thereby inhibiting hypocotyl elongation and stimulating cotyledon unfolding in etiolated Arabidopsis seedlings.

Light Controls Cytokinin Signaling via Transcriptional Regulation of Constitutively Active Sensor Histidine Kinase CKI1

In plants, the multistep phosphorelay (MSP) pathway mediates a range of regulatory processes, including those activated by cytokinins. The cross talk between cytokinin response and light has been known for a long time. However, the molecular mechanism underlying the interaction between light and cytokinin signaling remains elusive. In the screen for upstream regulators we identified a LONG PALE HYPOCOTYL (LPH) gene whose activity is indispensable for spatiotemporally correct expression of CYTOKININ INDEPENDENT1 (CKI1), encoding the constitutively active sensor His kinase that activates MSP signaling. lph is a new allele of HEME OXYGENASE1 (HY1) that encodes the key protein in the biosynthesis of phytochromobilin, a cofactor of photoconvertible phytochromes. Our analysis confirmed the light-dependent regulation of the CKI1 expression pattern. We show that CKI1 expression is under the control of phytochrome A (phyA), functioning as a dual (both positive and negative) regulator of CKI1 expression, presumably via the phyA-regulated transcription factors (TF) PHYTOCHROME INTERACTING FACTOR3 and CIRCADIAN CLOCK ASSOCIATED1. Changes in CKI1 expression observed in lph/hy1-7 and phy mutants correlate with misregulation of MSP signaling, changed cytokinin sensitivity, and developmental aberrations that were previously shown to be associated with cytokinin and/or CKI1 action. Besides that, we demonstrate a novel role of phyA-dependent CKI1 expression in the hypocotyl elongation and hook development during skotomorphogenesis. Based on these results, we propose that the light-dependent regulation of CKI1 provides a plausible mechanistic link underlying the well-known interaction between light- and cytokinin-controlled plant development.

Phytochrome-interacting factor from Arabidopsis to liverwort

Phytochromes are red and far-red light photoreceptors that regulate the responses of plants to light throughout their life cycles. Phytochromes do this in part by inhibiting the function of a group of basic helix-loop-helix transcription factors called phytochrome-interacting factors (PIFs). Arabidopsis has eight PIFs that function sometimes redundantly and sometimes distinctively depending on their expression patterns and protein stability, as well as on variations in the promoters they target in vivo. PIF-like proteins exist in other seed plants and non-vascular plants where they also regulate light responses. The mechanism by which phytochrome regulates light responses by promoting the degradation of the PIFs is conserved in liverwort, suggesting it must have evolved some time before the last common ancestor shared by seed plants and non-vascular plants.

Cryptochromes Orchestrate Transcription Regulation of Diverse Blue Light Responses in Plants

Blue light affects many aspects of plant growth and development throughout the plant lifecycle. Plant cryptochromes (CRYs) are UV-A/blue light photoreceptors that play pivotal roles in regulating blue light-mediated physiological responses via the regulated expression of more than one thousand genes. Photoactivated CRYs regulate transcription via two distinct mechanisms: indirect promotion of the activity of transcription factors by inactivation of the COP1/SPA E3 ligase complex or direct activation or inactivation of at least two sets of basic helix-loop-helix transcription factor families by physical interaction. Hence, CRYs govern intricate mechanisms that modulate activities of transcription factors to regulate multiple aspects of blue light-responsive photomorphogenesis. Here, we review recent progress in dissecting the pathways of CRY signaling and discuss accumulating evidence that shows how CRYs regulate broad physiological responses to blue light.

The Multifaceted Roles of HY5 in Plant Growth and Development

ELONGATED HYPOCOTYL5 (HY5), a member of the bZIP transcription factor family, inhibits hypocotyl growth and lateral root development, and promotes pigment accumulation in a light-dependent manner in Arabidopsis. Recent research on its role in different processes such as hormone, nutrient, abiotic stress (abscisic acid, salt, cold), and reactive oxygen species signaling pathways clearly places HY5 at the center of a transcriptional network hub. HY5 regulates the transcription of a large number of genes by directly binding to cis-regulatory elements. Recently, HY5 has also been shown to activate its own expression under both visible and UV-B light. Moreover, HY5 acts as a signal that moves from shoot to root to promote nitrate uptake and root growth. Here, we review recent advances on HY5 research in diverse aspects of plant development and highlight still open questions that need to be addressed in the near future for a complete understanding of its function in plant signaling and beyond.

Mutations in the N-terminal kinase-like domain of the repressor of photomorphogenesis SPA1 severely impair SPA1 function but not light responsiveness in Arabidopsis

The COP1/SPA complex is an E3 ubiquitin ligase that acts as a key repressor of photomorphogenesis in dark-grown plants. While both COP1 and the four SPA proteins contain coiled-coil and WD-repeat domains, SPA proteins differ from COP1 in carrying an N-terminal kinase-like domain that is not present in COP1. Here, we have analyzed the effects of deletions and missense mutations in the N-terminus of SPA1 when expressed in a spa quadruple mutant background devoid of any other SPA proteins. Deletion of the large N-terminus of SPA1 severely impaired SPA1 activity in transgenic plants with respect to seedling etiolation, leaf expansion and flowering time. This ΔN SPA1 protein showed a strongly reduced affinity for COP1 in vitro and in vivo, indicating that the N-terminus contributes to COP1/SPA complex formation. Deletion of only the highly conserved 95 amino acids of the kinase-like domain did not severely affect SPA1 function nor interactions with COP1 or cryptochromes. In contrast, missense mutations in this part of the kinase-like domain severely abrogated SPA1 function, suggesting an overriding negative effect of these mutations on SPA1 activity. We therefore hypothesize that the sequence of the kinase-like domain has been conserved during evolution because it carries structural information important for the activity of SPA1 in darkness. The N-terminus of SPA1 was not essential for light responsiveness of seedlings, suggesting that photoreceptors can inhibit the COP1/SPA complex in the absence of the SPA1 N-terminal domain. Together, these results uncover an important, but complex role of the SPA1 N-terminus in the suppression of photomorphogenesis.

The Blue Light-Dependent Polyubiquitination and Degradation of Arabidopsis Cryptochrome2 Requires Multiple E3 Ubiquitin Ligases

Cryptochromes are blue light receptors regulated by light-dependent ubiquitination and degradation in both plant and animal lineages. The Arabidopsis genome encodes two cryptochromes, CRY1 and CRY2, of which CRY2 undergoes blue light-dependent ubiquitination and 26S proteasome-dependent degradation. The molecular mechanism regulating blue light-dependent proteolysis of CRY2 is still not fully understood. We found that the F-box proteins ZEITLUPE (ZTL) and Lov Kelch Protein2 (LKP2), which mediate blue light suppression of degradation of the CRY2 signaling partner CIB1, are not required for the blue light-dependent CRY2 degradation. We further showed that the previously reported function of the COP1-SPA1 protein complex in blue light-dependent CRY2 degradation is more likely to be attributable to its cullin 4 (CUL4)-based E3 ubiquitin ligase activity than its activity as the cryptochrome signaling partner. However, the blue light-dependent CRY2 degradation is only partially impaired in the cul4 mutant, the cop1-5 null mutant and the spa1234 quadruple mutant, suggesting a possible involvement of additional E3 ubiquitin ligases in the regulation of CRY2. Consistent with this hypothesis, we demonstrated that the blue light-dependent CRY2 degradation is significantly impaired in the temperature-sensitive cul1 mutant allele (axr6-3), especially under the non-permissive temperature. Based on these and other results presented, we propose that photoexcited CRY2 undergoes Lys48-linked polyubiquitination catalyzed by the CUL4- and CUL1-based E3 ubiquitin ligases.

SPA proteins: SPAnning the gap between visible light and gene expression

In this review we focus on the role of SPA proteins in light signalling and discuss different aspects, including molecular mechanisms, specificity, and evolution. The ability of plants to perceive and respond to their environment is key to their survival under ever-changing conditions. The abiotic factor light is of particular importance for plants. Light provides plants energy for carbon fixation through photosynthesis, but also is a source of information for the adaptation of growth and development to the environment. Cryptochromes and phytochromes are major photoreceptors involved in control of developmental decisions in response to light cues, including seed germination, seedling de-etiolation, and induction of flowering. The SPA protein family acts in complex with the E3 ubiquitin ligase COP1 to target positive regulators of light responses for degradation by the 26S proteasome to suppress photomorphogenic development in darkness. Light-activated cryptochromes and phytochromes both repress the function of COP1, allowing accumulation of positive photomorphogenic factors in light. In this review, we highlight the role of the SPA proteins in this process and discuss recent advances in understanding how SPAs link light-activation of photoreceptors and downstream signaling.

The functional divergence between SPA1 and SPA2 in Arabidopsis photomorphogenesis maps primarily to the respective N-terminal kinase-like domain

BACKGROUND

Plants have evolved complex mechanisms to adapt growth and development to the light environment. The COP1/SPA complex is a key repressor of photomorphogenesis in dark-grown Arabidopsis plants and acts as an E3 ubiquitin ligase to ubiquitinate transcription factors involved in the light response. In the light, COP1/SPA activity is inhibited by photoreceptors, thereby allowing accumulation of these transcription factors and a subsequent light response. Previous results have shown that the four members of the SPA family exhibit partially divergent functions. In particular, SPA1 and SPA2 strongly differ in their responsiveness to light, while they have indistinguishable activities in darkness. The much higher light-responsiveness of SPA2 is partially explained by the much stronger light-induced degradation of SPA2 when compared to SPA1. Here, we have conducted SPA1/SPA2 domain swap experiments to identify the protein domain(s) responsible for the functional divergence between SPA1 and SPA2.

RESULTS

We have individually swapped the three domains between SPA1 and SPA2 - the N-terminal kinase-like domain, the coiled-coil domain and the WD-repeat domain - and expressed them in spa mutant Arabidopsis plants. The phenotypes of transgenic seedlings show that the respective N-terminal kinase-like domain is primarily responsible for the respective light-responsiveness of SPA1 and SPA2. Furthermore, the most divergent part of the N-terminal domain was sufficient to confer a SPA1- or SPA2-like activity to the respective SPA protein. The stronger light-induced degradation of SPA2 when compared to SPA1 was also primarily conferred by the SPA2 N-terminal domain. At last, the different affinities of SPA1 and SPA2 for cryptochrome 2 are defined by the N-terminal domain of the respective SPA protein. In contrast, both SPA1 and SPA2 similarly interacted with COP1 in light-grown seedlings.

CONCLUSIONS

Our results show that the distinct activities and protein stabilities of SPA1 and SPA2 in light-grown seedlings are primarily encoded by their N-terminal kinase-like domains. Similarly, the different affinities of SPA1 and SPA2 for cry2 are explained by their respective N-terminal domain. Hence, after a duplication event during evolution, the N-terminal domains of SPA1 and SPA2 underwent subfunctionalization, possibly to allow optimal adaptation of growth and development to a changing light environment.

Signaling mechanisms of plant cryptochromes in Arabidopsis thaliana

Cryptochromes (CRY) are flavoproteins that direct a diverse array of developmental processes in response to blue light in plants. Conformational changes in CRY are induced by the absorption of photons and result in the propagation of light signals to downstream components. In Arabidopsis, CRY1 and CRY2 serve both distinct and partially overlapping functions in regulating photomorphogenic responses and photoperiodic flowering. For example, both CRY1 and CRY2 regulate the abundance of transcription factors by directly reversing the activity of E3 ubiquitin ligase on CONSTITUTIVE PHOTOMORPHOGENIC 1 and SUPPRESSOR OF PHYA-105 1 complexes in a blue light-dependent manner. CRY2 also specifically governs a photoperiodic flowering mechanism by directly interacting with a transcription factor called CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX. Recently, structure/function analysis of CRY1 revealed that the CONSTITUTIVE PHOTOMORPHOGENIC 1 independent pathway is also involved in CRY1-mediated inhibition of hypocotyl elongation. CRY1 and CRY2 thus not only share a common pathway but also relay light signals through distinct pathways, which may lead to altered developmental programs in plants.

Arabidopsis COP1 SUPPRESSOR 2 Represses COP1 E3 Ubiquitin Ligase Activity through Their Coiled-Coil Domains Association

CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) functions as an E3 ubiquitin ligase and mediates a variety of developmental processes in Arabidopsis by targeting a number of key regulators for ubiquitination and degradation. Here, we identify a novel COP1 interacting protein, COP1 SUPPRESSOR 2 (CSU2). Loss of function mutations in CSU2 suppress the constitutive photomorphogenic phenotype of cop1-6 in darkness. CSU2 directly interacts with COP1 via their coiled-coil domains and is recruited by COP1 into nuclear speckles in living plant cells. Furthermore, CSU2 inhibits COP1 E3 ubiquitin ligase activity in vitro, and represses COP1 mediated turnover of HY5 in cell-free extracts. We propose that in csu2 cop1-6 mutants, the lack of CSU2’s repression of COP1 allows the low level of COP1 to exhibit higher activity that is sufficient to prevent accumulation of HY5 in the dark, thus restoring the etiolated phenotype. In addition, CSU2 is required for primary root development under normal light growth condition.

CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) is a key regulator of light mediated developmental processes and it works as an E3 ubiquitin ligase controlling the abundance of multiple transcription factors. In the work presented here, we identified a novel repressor of COP1, the COP1 SUPPRESSOR 2 (CSU2), via a forward genetic screen. Mutations in CSU2 completely suppress cop1-6 constitutive photomorphogenic phenotype in darkness. CSU2 interacts and co-localizes with COP1 in nuclear speckles via the coiled-coil domain association. CSU2 negatively regulates COP1 E3 ubiquitin ligase activity, and repress COP1 mediated HY5 degradation in cell-free extracts.