Phytochrome A mediates rapid red light-induced phosphorylation of Arabidopsis FAR-RED ELONGATED HYPOCOTYL1 in a low fluence response

Liquid-liquid phase separation of TZP promotes PPK-mediated phosphorylation of the phytochrome A photoreceptor

Phytochrome A (phyA) is the plant far-red (FR) light photoreceptor and plays an essential role in regulating photomorphogenic development in FR-rich conditions, such as canopy shade. It has long been observed that phyA is a phosphoprotein in vivo; however, the protein kinases that could phosphorylate phyA remain largely unknown. Here we show that a small protein kinase family, consisting of four members named PHOTOREGULATORY PROTEIN KINASES (PPKs) (also known as MUT9-LIKE KINASES), directly phosphorylate phyA in vitro and in vivo. In addition, TANDEM ZINC-FINGER/PLUS3 (TZP), a recently characterized phyA-interacting protein required for in vivo phosphorylation of phyA, is also directly phosphorylated by PPKs. We reveal that TZP contains two intrinsically disordered regions in its amino-terminal domain that undergo liquid-liquid phase separation (LLPS) upon light exposure. The LLPS of TZP promotes colocalization and interaction between PPKs and phyA, thus facilitating PPK-mediated phosphorylation of phyA in FR light. Our study identifies PPKs as a class of protein kinases mediating the phosphorylation of phyA and demonstrates that the LLPS of TZP contributes significantly to more production of the phosphorylated phyA form in FR light.

Application of Multi-Omics Technologies to the Study of Phytochromes in Plants

Phytochromes (phy) are distributed in various plant organs, and their physiological effects influence plant germination, flowering, fruiting, and senescence, as well as regulate morphogenesis throughout the plant life cycle. Reactive oxygen species (ROS) are a key regulatory factor in plant systemic responses to environmental stimuli, with an attractive regulatory relationship with phytochromes. With the development of high-throughput sequencing technology, omics techniques have become powerful tools, and researchers have used omics techniques to facilitate the big data revolution. For an in-depth analysis of phytochrome-mediated signaling pathways, integrated multi-omics (transcriptomics, proteomics, and metabolomics) approaches may provide the answer from a global perspective. This article comprehensively elaborates on applying multi-omics techniques in studying phytochromes. We describe the current research status and future directions on transcriptome-, proteome-, and metabolome-related network components mediated by phytochromes when cells are subjected to various stimulation. We emphasize the importance of multi-omics technologies in exploring the effects of phytochromes on cells and their molecular mechanisms. Additionally, we provide methods and ideas for future crop improvement.

Phytochrome B phosphorylation expanded: site-specific kinases are identified

The phytochrome B (phyB) photoreceptor is a key participant in red and far-red light sensing, playing a dominant role in many developmental and growth responses throughout the whole life of plants. Accordingly, phyB governs diverse signaling pathways, and although our knowledge about these pathways is constantly expanding, our view about their fine-tuning is still rudimentary. Phosphorylation of phyB is one of the relevant regulatory mechanisms, and - despite the expansion of the available methodology - it is still not easy to examine. Phosphorylated phytochromes have been detected using various techniques for decades, but the first phosphorylated phyB residues were only identified in 2013. Since then, concentrated attention has been turned toward the functional role of post-translational modifications in phyB signaling. Very recently in 2023, the first kinases that phosphorylate phyB were identified. These discoveries opened up new research avenues, especially by connecting diverse environmental impacts to light signaling and helping to explain some long-term unsolved problems such as the co-action of Ca2+ and phyB signaling. This review summarizes our recent views about the roles of the identified phosphorylated phyB residues, what we know about the enzymes that modulate the phospho-state of phyB, and how these recent discoveries impact future investigations.

Two Distinct Molecular Types of Phytochrome A in Plants: Evidence of Existence and Implications for Functioning

Phytochrome (phy) system in plants comprising a small number of phytochromes with phyA and phyB as major ones is responsible for acquiring light information in the red-far-red region of the solar spectrum. It provides optimal strategy for plant development under changing light conditions throughout all its life cycle beginning from seed germination and seedling establishment to fruiting and plant senescence. The phyA was shown to participate in the regulation of this cycle which is especially evident at its early stages. It mediates three modes of reactions-the very low and low fluence responses (VLFR and LFR) and the high irradiance responses (HIR). The phyA is the sole light receptor in the far-red spectral region responsible for plant's survival under a dense plant canopy where light is enriched with the far-red component. Its appearance is believed to be one of the main factors of plants' successful evolution. So far, it is widely accepted that one molecular phyA species is responsible for its complex functional manifestations. In this review, the evidence of the existence of two distinct phyA types-major, light-labile and soluble phyA' and minor, relatively light-stable and amphiphilic phyA″-is presented as what may account for the diverse modes of phyA action.

Two Distinct Molecular Types of Phytochrome A in Plants: Evidence of Existence and Implications for Functioning

Phytochrome (phy) system in plants comprising a small number of phytochromes with phyA and phyB as major ones is responsible for acquiring light information in the red—far-red region of the solar spectrum. It provides optimal strategy for plant development under changing light conditions throughout all its life cycle beginning from seed germination and seedling establishment to fruiting and plant senescence. The phyA was shown to participate in the regulation of this cycle which is especially evident at its early stages. It mediates three modes of reactions—the very low and low fluence responses (VLFR and LFR) and the high irradiance responses (HIR). The phyA is the sole light receptor in the far-red spectral region responsible for plant’s survival under a dense plant canopy where light is enriched with the far-red component. Its appearance is believed to be one of the main factors of plants′ successful evolution. So far, it is widely accepted that one molecular phyA species is responsible for its complex functional manifestations. In this review, the evidence of the existence of two distinct phyA types—major, light-labile and soluble phyA′ and minor, relatively light-stable and amphiphilic phyA″—is presented as what may account for the diverse modes of phyA action.

Regulation of Plant Photoresponses by Protein Kinase Activity of Phytochrome A

Extensive research has been conducted for decades to elucidate the molecular and regulatory mechanisms for phytochrome-mediated light signaling in plants. As a result, tens of downstream signaling components that physically interact with phytochromes are identified, among which negative transcription factors for photomorphogenesis, PHYTOCHROME-INTERACTING FACTORs (PIFs), are well known to be regulated by phytochromes. In addition, phytochromes are also shown to inactivate an important E3 ligase complex consisting of CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) and SUPPRESSORs OF phyA-105 (SPAs). This inactivation induces the accumulation of positive transcription factors for plant photomorphogenesis, such as ELONGATED HYPOCOTYL 5 (HY5). Although many downstream components of phytochrome signaling have been studied thus far, it is not fully elucidated which intrinsic activity of phytochromes is necessary for the regulation of these components. It should be noted that phytochromes are autophosphorylating protein kinases. Recently, the protein kinase activity of phytochrome A (phyA) has shown to be important for its function in plant light signaling using Avena sativa phyA mutants with reduced or increased kinase activity. In this review, we highlight the function of phyA as a protein kinase to explain the regulation of plant photoresponses by phyA.

RNA sequencing-based exploration of the effects of far-red light on microRNAs involved in the shade-avoidance response of D. officinale

Dendrobium officinale (D. officinale) has remarkable medicinal functions and high economic value. The shade-avoidance response to far-red light importantly affects the D. officinale productivity. However, the regulatory mechanism of miRNAs involved in the far-red light-avoidance response is unknown. Previous studies have found that, in D. officinale, 730 nm (far-red) light can promote the accumulation of plant metabolites, increase leaf area, and accelerate stem elongation. Here, the effects of far-red light on D. officinale were analysed via RNA-seq. KEGG analysis of miRNA target genes revealed various far-red light response pathways, among which the following played central roles: the one-carbon pool by folate; ascorbate and aldarate; cutin, suberine and wax biosynthesis; and sulfur metabolism. Cytoscape analysis of DE miRNA targets showed that novel_miR_484 and novel_miR_36 were most likely involved in the effects of far-red light on the D. officinale shade avoidance. Content verification revealed that far-red light promotes the accumulation of one-carbon compounds and ascorbic acid. Combined with qPCR validation results, the results showed that miR395b, novel_miR_36, novel_miR_159, novel_miR_178, novel_miR_405, and novel_miR_435 may participate in the far-red light signalling network through target genes, regulating the D. officinale shade avoidance. These findings provide new ideas for the efficient production of D. officinale.

Genome-wide association studies for soybean epicotyl length in two environments using 3VmrMLM

Germination of soybean seed is the imminent vital process after sowing. The status of plumular axis and radicle determine whether soybean seed can emerge normally. Epicotyl, an organ between cotyledons and first functional leaves, is essential for soybean seed germination, seedling growth and early morphogenesis. Epicotyl length (EL) is a quantitative trait controlled by multiple genes/QTLs. Here, the present study analyzes the phenotypic diversity and genetic basis of EL using 951 soybean improved cultivars and landraces from Asia, America, Europe and Africa. 3VmrMLM was used to analyze the associations between EL in 2016 and 2020 and 1,639,846 SNPs for the identification of QTNs and QTN-by-environment interactions (QEIs)".A total of 180 QTNs and QEIs associated with EL were detected. Among them, 74 QTNs (ELS_Q) and 16 QEIs (ELS_QE) were identified to be associated with ELS (epicotyl length of single plant emergence), and 60 QTNs (ELT_Q) and 30 QEIs (ELT_QE) were identified to be associated with ELT (epicotyl length of three seedlings). Based on transcript abundance analysis, GO (Gene Ontology) enrichment and haplotype analysis, ten candidate genes were predicted within nine genic SNPs located in introns, upstream or downstream, which were supposed to be directly or indirectly involved in the process of seed germination and seedling development., Of 10 candidate genes, two of them (Glyma.04G122400 and Glyma.18G183600) could possibly affect epicotyl length elongation. These results indicate the genetic basis of EL and provides a valuable basis for specific functional studies of epicotyl traits.

Optophysiology: Illuminating cell physiology with optogenetics

Optogenetics combines light and genetics to enable precise control of living cells, tissues, and organisms with tailored functions. Optogenetics has the advantages of noninvasiveness, rapid responsiveness, tunable reversibility, and superior spatiotemporal resolution. Following the initial discovery of microbial opsins as light-actuated ion channels, a plethora of naturally occurring or engineered photoreceptors or photosensitive domains that respond to light at varying wavelengths has ushered in the next chapter of optogenetics. Through protein engineering and synthetic biology approaches, genetically-encoded photoswitches can be modularly engineered into protein scaffolds or host cells to control a myriad of biological processes, as well as to enable behavioral control and disease intervention in vivo. Here, we summarize these optogenetic tools on the basis of their fundamental photochemical properties to better inform the chemical basis and design principles. We also highlight exemplary applications of opsin-free optogenetics in dissecting cellular physiology (designated "optophysiology"), and describe the current progress, as well as future trends, in wireless optogenetics, which enables remote interrogation of physiological processes with minimal invasiveness. This review is anticipated to spark novel thoughts on engineering next-generation optogenetic tools and devices that promise to accelerate both basic and translational studies.

SUMOylation of different targets fine-tunes phytochrome signaling

Plants monitor their surrounding ambient light environment by specialized photoreceptor proteins. Among them, phytochromes monitor red and far-red light. These molecules perceive photons, undergo a conformational change, and regulate diverse light signaling pathways, resulting in the mediation of key developmental and growth responses throughout the whole life of plants. Posttranslational modifications of the photoreceptors and their signaling partners may modify their function. For example, the regulatory role of phosphorylation has been investigated for decades by using different methodological approaches. In the past few years, a set of studies revealed that ubiquitin-like short protein molecules, called small ubiquitin-like modifiers (SUMOs) are attached reversibly to different members of phytochrome signaling pathways, including phytochrome B, the dominant receptor of red light signaling. Furthermore, SUMO attachment modifies the action of the target proteins, leading to altered light signaling and photomorphogenesis. This review summarizes recent results regarding SUMOylation of various target proteins, the regulation of their SUMOylation level, and the physiological consequences of SUMO attachment. Potential future research directions are also discussed.

Phytochrome Signaling Networks

The perception of light signals by the phytochrome family of photoreceptors has a crucial influence on almost all aspects of growth and development throughout a plant's life cycle. The holistic regulatory networks orchestrated by phytochromes, including conformational switching, subcellular localization, direct protein-protein interactions, transcriptional and posttranscriptional regulations, and translational and posttranslational controls to promote photomorphogenesis, are highly coordinated and regulated at multiple levels. During the past decade, advances using innovative approaches have substantially broadened our understanding of the sophisticated mechanisms underlying the phytochrome-mediated light signaling pathways. This review discusses and summarizes these discoveries of the role of the modular structure of phytochromes, phytochrome-interacting proteins, and their functions; the reciprocal modulation of both positive and negative regulators in phytochrome signaling; the regulatory roles of phytochromes in transcriptional activities, alternative splicing, and translational regulation; and the kinases and E3 ligases that modulate PHYTOCHROME INTERACTING FACTORs to optimize photomorphogenesis.

A LexA-based yeast two-hybrid system for studying light-switchable interactions of phytochromes with their interacting partners

Phytochromes are a family of photoreceptors in plants that perceive the red (R) and far-red (FR) components of their light environment. Phytochromes exist in vivo in two forms, the inactive Pr form and the active Pfr form, that are interconvertible by treatments with R or FR light. It is believed that phytochromes transduce light signals by interacting with their signaling partners. A GAL4-based light-switchable yeast two-hybrid (Y2H) system was developed two decades ago and has been successfully employed in many studies to determine phytochrome interactions with their signaling components. However, several pairs of interactions between phytochromes and their interactors, such as the phyA-COP1 and phyA-TZP interactions, were demonstrated by other assay systems but were not detected by this GAL4 Y2H system. Here, we report a modified LexA Y2H system, in which the LexA DNA-binding domain is fused to the C-terminus of a phytochrome protein. The conformational changes of phytochromes in response to R and FR light are achieved in yeast cells by exogenously supplying phycocyanobilin (PCB) extracted from Spirulina. The well-defined interaction pairs, including phyA-FHY1 and phyB-PIFs, are well reproducible in this system. Moreover, we show that our system is successful in detecting the phyA-COP1 and phyA-TZP interactions. Together, our study provides an alternative Y2H system that is highly sensitive and reproducible for detecting light-switchable interactions of phytochromes with their interacting partners.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42994-021-00034-5.

Phosphorylation-mediated signalling in flowering: prospects and retrospects of phosphoproteomics in crops

Protein phosphorylation is a major post-translational modification, regulating protein function, stability, and subcellular localization. To date, annotated phosphorylation data are available mainly for model organisms and humans, despite the economic importance of crop species and their large kinomes. Our understanding of the phospho-regulation of flowering in relation to the biology and interaction between the pollen and pistil is still significantly lagging, limiting our knowledge on kinase signalling and its potential applications to crop production. To address this gap, we bring together relevant literature that were previously disconnected to present an overview of the roles of phosphoproteomic signalling pathways in modulating molecular and cellular regulation within specific tissues at different morphological stages of flowering. This review is intended to stimulate research, with the potential to increase crop productivity by providing a platform for novel molecular tools.

Co-immunoprecipitation Assays to Detect In Vivo Association of Phytochromes with Their Interacting Partners

The red (R)/far-red (FR) light absorbing phytochromes are one of the major photoreceptor classes in plants. Phytochromes exist in two distinct but interconvertible forms: the R light-absorbing Pr form and the FR light-absorbing Pfr form. Upon photoactivation by light, phytochromes physically interact with their partners to transduce the light signal. Co-immunoprecipitation (Co-IP) is one of the most efficient techniques to study these protein-protein interactions in vivo. However, the co-IP procedure for phytochromes needs to be modified to allow their formation of Pr or Pfr form. Here, we describe a detailed co-IP procedure to examine which form of phytochrome (Pr or Pfr) is preferentially associated with their interacting partners in vivo.

Genome-wide transcriptome and proteome profiles indicate an active role of alternative splicing during de-etiolation of maize seedlings

AS events affect genes encoding protein domain composition and make the single gene produce more proteins with a certain number of genes to satisfy the establishment of photosynthesis during de-etiolation. The drastic switch from skotomorphogenic to photomorphogenic development is an excellent system to elucidate rapid developmental responses to environmental stimuli in plants. To decipher the effects of different light wavelengths on de-etiolation, we illuminated etiolated maize seedlings with blue, red, blue-red mixed and white light, respectively. We found that blue light alone has the strongest effect on photomorphogenesis and that this effect can be attributed to the higher number and expression levels of photosynthesis and chlorosynthesis proteins. Deep sequencing-based transcriptome analysis revealed gene expression changes under different light treatments and a genome-wide alteration in alternative splicing (AS) profiles. We discovered 41,188 novel transcript isoforms for annotated genes, which increases the percentage of multi-exon genes with AS to 63% in maize. We provide peptide support for all defined types of AS, especially retained introns. Further in silico prediction revealed that 58.2% of retained introns have changes in domains compared with their most similar annotated protein isoform. This suggests that AS acts as a protein function switch allowing rapid light response through the addition or removal of functional domains. The richness of novel transcripts and protein isoforms also demonstrates the potential and importance of integrating proteomics into genome annotation in maize.

Reversible SUMOylation of FHY1 Regulates Phytochrome A Signaling in Arabidopsis

In response to far-red light (FR), FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) transports the photoactivated phytochrome A (phyA), the primary FR photoreceptor, into the nucleus, where it initiates FR signaling in plants. Light promotes the 26S proteasome-mediated degradation of FHY1, which desensitizes FR signaling, but the underlying regulatory mechanism remains largely unknown. Here, we show that reversible SUMOylation of FHY1 tightly regulates this process. Lysine K32 (K32) and K103 are major SUMOylation sites of FHY1. We found that FR exposure promotes the SUMOylation of FHY1, which accelerates its degradation. Furthermore, we discovered that ARABIDOPSIS SUMO PROTEASE 1 (ASP1) interacts with FHY1 in the nucleus under FR and facilitates its deSUMOylation. FHY1 was strongly SUMOylated and its protein level was decreased in the asp1-1 loss-of-function mutant compared with that in the wild type under FR. Consistently, asp1-1 seedlings exhibited a decreased sensitivity to FR, suggesting that ASP1 plays an important role in the maintenance of proper FHY1 levels under FR. Genetic analysis further revealed that ASP1 regulates FR signaling through an FHY1- and phyA-dependent pathway. Interestingly, We found that continuous FR inhibits ASP1 accumulation, perhaps contributing to the desensitization of FR signaling. Taken together, these results indicate that FR-induced SUMOylation and ASP1-dependent deSUMOylation of FHY1 represent a key regulatory mechanism that fine-tunes FR signaling.

Molecular mechanisms underlying phytochrome-controlled morphogenesis in plants

Phytochromes are bilin-binding photosensory receptors which control development over a broad range of environmental conditions and throughout the whole plant life cycle. Light-induced conformational changes enable phytochromes to interact with signaling partners, in particular transcription factors or proteins that regulate them, resulting in large-scale transcriptional reprograming. Phytochromes also regulate promoter usage, mRNA splicing and translation through less defined routes. In this review we summarize our current understanding of plant phytochrome signaling, emphasizing recent work performed in Arabidopsis. We compare and contrast phytochrome responses and signaling mechanisms among land plants and highlight open questions in phytochrome research.

Plant Phytochromes and their Phosphorylation

Extensive research over several decades in plant light signaling mediated by photoreceptors has identified the molecular mechanisms for how phytochromes regulate photomorphogenic development, which includes degradation of phytochrome-interacting factors (PIFs) and inactivation of COP1-SPA complexes with the accumulation of master transcription factors for photomorphogenesis, such as HY5. However, the initial biochemical mechanism for the function of phytochromes has not been fully elucidated. Plant phytochromes have long been known as phosphoproteins, and a few protein phosphatases that directly interact with and dephosphorylate phytochromes have been identified. However, there is no report thus far of a protein kinase that acts on phytochromes. On the other hand, plant phytochromes have been suggested as autophosphorylating serine/threonine protein kinases, proposing that the kinase activity might be important for their functions. Indeed, the autophosphorylation of phytochromes has been reported to play an important role in the regulation of plant light signaling. More recently, evidence that phytochromes function as protein kinases in plant light signaling has been provided using phytochrome mutants displaying reduced kinase activities. In this review, we highlight recent advances in the reversible phosphorylation of phytochromes and their functions as protein kinases in plant light signaling.

Two molecular species of phytochrome A with distinct modes of action

Adaptation of plants to environmental light conditions is achieved via operation of a highly complex photoreceptor apparatus. It includes the phytochrome system comprising phytochromes A and B (phyA and phyB) as the major components. phyA differs from phyB by several properties, including its ability to mediate all three photoresponse modes – the very low and low fluence responses (VLFR and LFR respectively) and the high irradiance responses (HIR), whereas phyB is responsible for LFR. This review discusses the uniqueness of phyA in terms of its structural and functional heterogeneity. The photoreceptor is presented in monocots and dicots by two native molecular species, phyAʹ and phyAʹʹ, differing by spectroscopic, photochemical and phenomenological properties. phyA differentiation into substates includes post-translational phosphorylation of a serine residue(s) at the N-terminal extension of the molecule with phyAʹ being the phosphorylated species and phyAʹʹ, dephosphorylated. They differ also by their mode of action, which depends on the cellular context. The current working hypothesis is that phyAʹ mediates VLFR and phyAʹʹ, HIR and LFR. The content and functional activity of the two pools are regulated by light and by phosphatase/kinase equilibrium and pH in darkness, what contributes to the fine-tuning of the phytochrome system. Detection of the native pools of the cryptogamic plant fern Adiantum capillus-veneris phy1 (phy1ʹ and phy1ʹʹ) similar to those of phyA suggests that the structural and functional heterogeneity of phyA is not a unique phenomenon and may have arisen earlier in the molecular evolution of the phytochrome system than the appearance of the angiosperm phytochromes.

Detection of Phytochrome Phosphorylation in Plants

Posttranslational modification (PTM) of proteins occurs during or after translation and in most cases means covalent binding of a functional group to certain amino acid side chains. Among PTMs, phosphorylation is extensively studied for decades. During phosphorylation, a phosphate group is added to the target residue that is dominantly serine, threonine, and tyrosine in eukaryotes. The phosphate group attachment is catalyzed by kinases, whereas the removal of phosphate (dephosphorylation) is performed by phosphatases. Phosphorylation of phytochrome photoreceptors alters light signaling in multiple ways, thus the examination of this PTM is an expanding aspect of light signaling research. Although this chapter presents methods for detecting phosphorylated phytochrome B molecules, it can be applied on other phytochrome species. The first presented protocol of this chapter shows how the phosphorylation state of phytochrome photoreceptors can be monitored in a modified polyacrylamide gel electrophoresis system. The second protocol describes in detail how phosphorylated amino acids of a target molecule can be identified using mass spectrometry analysis.

Two molecular species of phytochrome A with distinct modes of action

Adaptation of plants to environmental light conditions is achieved via operation of a highly complex photoreceptor apparatus. It includes the phytochrome system comprising phytochromes A and B (phyA and phyB) as the major components. phyA differs from phyB by several properties, including its ability to mediate all three photoresponse modes - the very low and low fluence responses (VLFR and LFR respectively) and the high irradiance responses (HIR), whereas phyB is responsible for LFR. This review discusses the uniqueness of phyA in terms of its structural and functional heterogeneity. The photoreceptor is presented in monocots and dicots by two native molecular species, phyA' and phyA'', differing by spectroscopic, photochemical and phenomenological properties. phyA differentiation into substates includes post-translational phosphorylation of a serine residue(s) at the N-terminal extension of the molecule with phyA' being the phosphorylated species and phyA'', dephosphorylated. They differ also by their mode of action, which depends on the cellular context. The current working hypothesis is that phyA' mediates VLFR and phyA'', HIR and LFR. The content and functional activity of the two pools are regulated by light and by phosphatase/kinase equilibrium and pH in darkness, what contributes to the fine-tuning of the phytochrome system. Detection of the native pools of the cryptogamic plant fern Adiantum capillus-veneris phy1 (phy1' and phy1'') similar to those of phyA suggests that the structural and functional heterogeneity of phyA is not a unique phenomenon and may have arisen earlier in the molecular evolution of the phytochrome system than the appearance of the angiosperm phytochromes.

Arabidopsis phytochrome A nuclear translocation is mediated by a far-red elongated hypocotyl 1-importin complex

Phytochrome A (phyA) is a red and far-red (FR) sensing photoreceptor regulating plant growth and development. Its biologically active FR-absorbing form Pfr translocates into the nucleus and subsequently regulates gene expression. Two transport facilitators, FR elongated hypocotyl 1 (FHY1) and FHY1-like (FHL), are crucial for its cytoplasmic-nuclear translocation. FHY1 interacts preferentially with activated phyA (Pfr) in assays with recombinant phyA and FHY1 and in vivo. Nuclear translocation of the phyA-FHY1 complex depends on a nuclear localization signal (NLS) of FHY1, which is recognized by IMPαs independently of phyA. The complex is guided along the actin cytoskeleton. Additionally, FHY1 has the ability to exit the nucleus via the exportin route, thus is able to repeatedly transport phyA molecules to the nucleus, balancing the nucleo-cytoplasmic distribution. The direction of FHY1s transport appears to depend on its phosphorylation state in different compartments. Phosphorylated serins close to the NLS prevent FHY1 binding to IMPα. The work presented here elucidates key steps of the mechanism by which photoactivated phyA translocates to the nucleus.

Hinge region of Arabidopsis phyA plays an important role in regulating phyA function

Phytochrome A (phyA) is the only plant photoreceptor that perceives far-red light and then mediates various responses to this signal. Phosphorylation and dephosphorylation of oat phyA have been extensively studied, and it was shown that phosphorylation of a serine residue in the hinge region of oat phyA could regulate the interaction of phyA with its signal transducers. However, little is known about the role of the hinge region of Arabidopsis phyA. Here, we report that three sites in the hinge region of Arabidopsis phyA (i.e., S590, T593, and S602) are essential in regulating phyA function. Mutating all three of these sites to either alanines or aspartic acids impaired phyA function, changed the interactions of mutant phyA with FHY1 and FHL, and delayed the degradation of mutant phyA upon light exposure. Moreover, the in vivo formation of a phosphorylated phyA form was greatly affected by these mutations, while our data indicated that the abundance of this phosphorylated phyA form correlated well with the extent of phyA function, thus suggesting a pivotal role of the phosphorylated phyA in inducing the far-red light response. Taking these data together, our study reveals the important role of the hinge region of Arabidopsis phyA in regulating phyA phosphorylation and function, thus linking specific residues in the hinge region to the regulatory mechanisms of phyA phosphorylation.

Direct Control of SPEECHLESS by PIF4 in the High-Temperature Response of Stomatal Development

Environmental factors shape the phenotypes of multicellular organisms. The production of stomata-the epidermal pores required for gas exchange in plants-is highly plastic and provides a powerful platform to address environmental influence on cell differentiation [1-3]. Rising temperatures are already impacting plant growth, a trend expected to worsen in the near future [4]. High temperature inhibits stomatal production, but the underlying mechanism is not known [5]. Here, we show that elevated temperature suppresses the expression of SPEECHLESS (SPCH), the basic-helix-loop-helix (bHLH) transcription factor that serves as the master regulator of stomatal lineage initiation [6, 7]. Our genetic and expression analyses indicate that the suppression of SPCH and stomatal production is mediated by the bHLH transcription factor PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), a core component of high-temperature signaling [8]. Importantly, we demonstrate that, upon exposure to high temperature, PIF4 accumulates in the stomatal precursors and binds to the promoter of SPCH. In addition, we find SPCH feeds back negatively to the PIF4 gene. We propose a model where warm-temperature-activated PIF4 binds and represses SPCH expression to restrict stomatal production at elevated temperatures. Our work identifies a molecular link connecting high-temperature signaling and stomatal development and reveals a direct mechanism by which production of a specific cell lineage can be controlled by a broadly expressed environmental signaling factor.

TANDEM ZINC-FINGER/PLUS3 Is a Key Component of Phytochrome A Signaling

Phytochrome A (phyA) is the primary plant photoreceptor responsible for perceiving and mediating various responses to far-red (FR) light and is essential for survival in canopy shade. In this study, we identified two Arabidopsis thaliana mutants that grew longer hypocotyls in FR light. Genetic analyses showed that they were allelic and their FR phenotypes were caused by mutations in the gene named TANDEM ZINC-FINGER/PLUS3 (TZP), previously shown to encode a nuclear protein involved in blue light signaling and phyB-dependent regulation of photoperiodic flowering. We show that the expression of TZP is dramatically induced by light and that TZP proteins are differentially modified in different light conditions. Furthermore, we show that TZP interacts with both phyA and FAR-RED ELONGATED HYPOCOTYL1 (FHY1) and regulates the abundance of phyA, FHY1, and ELONGATED HYPOCOTYL5 proteins in FR light. Moreover, our data indicate that TZP is required for the formation of a phosphorylated form of phyA in the nucleus in FR light. Together, our results identify TZP as a positive regulator of phyA signaling required for phosphorylation of the phyA photoreceptor, thus suggesting an important role of phosphorylated phyA in inducing the FR light response.

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.

Protein Transphosphorylation During the Mutual Interaction between Phytochrome A and a Nuclear Isoform of Nucleoside Diphosphate Kinase Is Regulated by Red Light

The nuclear isoform of nucleoside diphosphate kinase isoenzyme NDPK-I_n undergoes strong catalytic activation upon its interaction with the active form of phytochrome A (Pfr) in red light. The autophosphorylation or intermolecular transphosphorylation of NDPK-I_n leads to the formation of phosphoester bonds stable in acidic solution. The phosphate residue of the phosphamide bond in the active center of NDPK-I_n can also be transferred to serine and threonine residues localized in other proteins, including phytochrome A. Phytochrome A, similarly to NDPK-I_n, undergoes autophosphorylation on serine and threonine residues and can phosphorylate some potential substrate proteins. The physical interaction between phytochrome A in the Pfr form and NDPK-I_n results in a significant increase in the kinase activity of NDPK-I_n. The results presented in this work indicate that NDPK-I_n may function as a protein kinase regulated by light.

Evidence that phytochrome functions as a protein kinase in plant light signalling

It has been suggested that plant phytochromes are autophosphorylating serine/threonine kinases. However, the biochemical properties and functional roles of putative phytochrome kinase activity in plant light signalling are largely unknown. Here, we describe the biochemical and functional characterization of Avena sativa phytochrome A (AsphyA) as a potential protein kinase. We provide evidence that phytochrome-interacting factors (PIFs) are phosphorylated by phytochromes in vitro. Domain mapping of AsphyA shows that the photosensory core region consisting of PAS-GAF-PHY domains in the N-terminal is required for the observed kinase activity. Moreover, we demonstrate that transgenic plants expressing mutant versions of AsphyA, which display reduced activity in in vitro kinase assays, show hyposensitive responses to far-red light. Further analysis reveals that far-red light-induced phosphorylation and degradation of PIF3 are significantly reduced in these transgenic plants. Collectively, these results suggest a positive relationship between phytochrome kinase activity and photoresponses in plants.

Phytochromes regulate plant responses to environmental light conditions but despite extensive research the initial events in phytochrome signaling remain uncertain. Here, Shin et al. provide evidence that phytochrome phosphorylates target proteins via kinase activity in the N-terminal core domain.

Phytochrome-interacting ankyrin repeat protein 2 modulates phytochrome A-mediated PIF3 phosphorylation in light signal transduction

Light signals recognized by phytochromes are transduced through interactions between down-stream signaling components. Phytochrome-interacting ankyrin repeat protein 2 (PIA2) was found to interact with phytochrome interacting factor 3 (PIF3), a well-known repressor of plant photomorphogenesis in response to phytochrome-mediated light signalling. Both PIA2 and PIF3 are known to be positive regulators of anthocyanin accumulation in Arabidopsis seedlings under far-red conditions. Thus, we investigated the functional relationship between PIA2 and PIF3 in light signalling. We found that PIA2 suppressed PIF3 phosphorylation by phyA. To elucidate how PIA2 modulates phyA-mediated PIF3 phosphorylation, we generated non-phosphorylation mutants and N-terminal α-helix breaking mutants of PIA2. PIF3 phosphorylation by phyA was not suppressed by α-helix breaking PIA2 mutants. The α-helix breaking mutations also resulted in remarkably decreased interactions between PIA2 and PIF3. However, the non-phosphorylation mutants exhibited no effect on phyA-mediated PIF3 phosphorylation. In addition, decreased anthocyanin accumulation in pia2 knockout plant seedlings was not rescued by overexpression of the α-helix breaking mutant in transgenic plants under far-red conditions. These results suggest that PIA2 modulates phyA-mediated PIF3 phosphorylation by physical interaction with PIF3 and that the secondary structure of the PIA2 N-terminus is important in this modulation.

Large-scale comparative phosphoprotein analysis of maize seedling leaves during greening

MAIN CONCLUSION : Large-scale comparative phosphoprotein analysis in maize seedlings reveals a complicated molecular regulation mechanism at the phosphoproteomic level during de-etiolation. In the present study we report a phosphoproteomic study conducted on Zea mays etiolated leaves harvested at three time points during greening (etiolated seedlings and seedlings exposed to light for 6 or 12 h). We identified a total of 2483 phosphopeptides containing 2389 unambiguous phosphosites from 1339 proteins. The abundance of nearly 692 phosphorylated peptides containing 783 phosphosites was reproducible and profiled with high confidence among treatments. Comparisons with other large-scale phosphoproteomic studies revealed that 473 of the phosphosites are novel to this study. Of the 783 phosphosites identified, 171, 79, and 138 were identified in 0, 6, and 12 h samples, respectively, which suggest that regulation of phosphorylation plays important roles during maize seedling de-etiolation. Our experimental methods included enrichment of phosphoproteins, allowing the identification of a great number of low abundance proteins, such as transcription factors, protein kinases, and photoreceptors. Most of the identified phosphoproteins were involved in gene transcription, post-transcriptional regulation, or signal transduction, and only a few were involved in photosynthesis and carbon metabolism. It is noteworthy that tyrosine phosphorylation and calcium signaling pathways might play important roles during maize seedling de-etiolation. Taken together, we have elucidated a new level of complexity in light-induced reversible protein phosphorylation during maize seedling de-etiolation.

Phosphorylation of CONSTANS and its COP1-dependent degradation during photoperiodic flowering of Arabidopsis

Seasonal flowering involves responses to changes in day length. In Arabidopsis thaliana, the CONSTANS (CO) transcription factor promotes flowering in the long days of spring and summer. Late flowering in short days is due to instability of CO, which is efficiently ubiquitinated in the dark by the CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) E3 ligase complex. Here we show that CO is also phosphorylated. Phosphorylated and unphosphorylated forms are detected throughout the diurnal cycle but their ratio varies, with the relative abundance of the phosphorylated form being higher in the light and lower in the dark. These changes in relative abundance require COP1, because in the cop1 mutant the phosphorylated form is always more abundant. Inactivation of the PHYTOCHROME A (PHYA), CRYPTOCHROME 1 (CRY1) and CRYPTOCHROME 2 (CRY2) photoreceptors in the phyA cry1 cry2 triple mutant most strongly reduces the amount of the phosphorylated form so that unphosphorylated CO is more abundant. This effect is caused by increased COP1 activity, as it is overcome by introduction of the cop1 mutation in the cop1 phyA cry1 cry2 quadruple mutant. Degradation of CO is also triggered in red light, and as in darkness this increases the relative abundance of unphosphorylated CO. Finally, a fusion protein containing truncated CO protein including only the carboxy-terminal region was phosphorylated in transgenic plants, locating at least one site of phosphorylation in this region. We propose that CO phosphorylation contributes to the photoperiodic flowering response by enhancing the rate of CO turnover via activity of the COP1 ubiquitin ligase.

Illuminating Progress in Phytochrome-Mediated Light Signaling Pathways

Light signals regulate a plethora of plant responses throughout their life cycle, especially the red and far-red regions of the light spectrum perceived by the phytochrome family of photoreceptors. However, the mechanisms by which phytochromes regulate gene expression and downstream responses remain elusive. Several recent studies have unraveled the details on how phytochromes regulate photomorphogenesis. These include the identification of E3 ligases that degrade PHYTOCHROME INTERACTING FACTOR (PIF) proteins, key negative regulators, in response to light, a better view of how phytochromes inhibit another key negative regulator, CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1), and an understanding of why plants evolved multiple negative regulators to repress photomorphogenesis in darkness. These advances will surely fuel future research on many unanswered questions that have intrigued plant photobiologists for decades.

Illuminating light, cytokinin, and ethylene signalling crosstalk in plant development

Integrating important environmental signals with intrinsic developmental programmes is a crucial adaptive requirement for plant growth, survival, and reproduction. Key environmental cues include changes in several light variables, while important intrinsic (and highly interactive) regulators of many developmental processes include the phytohormones cytokinins (CKs) and ethylene. Here, we discuss the latest discoveries regarding the molecular mechanisms mediating CK/ethylene crosstalk at diverse levels of biosynthetic and metabolic pathways and their complex interactions with light. Furthermore, we summarize evidence indicating that multiple hormonal and light signals are integrated in the multistep phosphorelay (MSP) pathway, a backbone signalling pathway in plants. Inter alia, there are strong overlaps in subcellular localizations and functional similarities in components of these pathways, including receptors and various downstream agents. We highlight recent research demonstrating the importance of CK/ethylene/light crosstalk in selected aspects of plant development, particularly seed germination and early seedling development. The findings clearly demonstrate the crucial integration of plant responses to phytohormones and adaptive responses to environmental cues. Finally, we tentatively identify key future challenges to refine our understanding of the molecular mechanisms mediating crosstalk between light and hormonal signals, and their integration during plant life cycles.

Molecular mechanisms for mediating light-dependent nucleo/cytoplasmic partitioning of phytochrome photoreceptors

The photoreceptors phytochromes monitor the red/far-red part of the spectrum, exist in the biologically active Pfr (far-red absorbing) or inactive Pr (red absorbing) forms, and function as red/far-red light-regulated molecular switches to modulate plant development and growth. Phytochromes are synthesized in the cytoplasm, and light induces translocation of the Pfr conformer into the nucleus. Nuclear import of phytochromes is a highly regulated process and is fine-tuned by the quality and quantity of light. It appears that phytochrome A (phyA) and phytochrome B (phyB) do not possess active endogenous nuclear import signals (NLSs), thus light-induced translocation of these photoreceptors into the nucleus requires direct protein–protein interactions with their NLS-containing signaling partners. Sub-cellular partitioning of the various phytochrome species is mediated by different molecular machineries. Translocation of phyA into the nucleus is promoted by FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1-LIKE (FHL), but the identity of nuclear transport facilitators mediating the import of phyB-E into the nucleus remains elusive. Phytochromes localized in the nucleus are associated with specific protein complexes, termed photobodies. The size and distribution of these structures are regulated by the intensity and duration of irradiation, and circumstantial evidence indicates that they are involved in fine-tuning phytochrome signaling.

phyA-GFP is spectroscopically and photochemically similar to phyA and comprises both its native types, phyA' and phyA''

Low-temperature fluorescence investigations of phyA-GFP used in experiments on its nuclear-cytoplasmic partitioning were carried out. In etiolated hypocotyls of phyA-deficient Arabidopsis thaliana expressing phyA-GFP, it was found that it is similar to phyA in spectroscopic parameters with both its native types, phyA' and phyA'', present and their ratio shifted towards phyA'. In transgenic tobacco hypocotyls, native phyA and rice phyA-GFP were also identical to phyA in the wild type whereas phyA-GFP belonged primarily to the phyA' type. Finally, truncated oat Δ6-12 phyA-GFP expressed in phyA-deficient Arabidopsis was represented by the phyA' type in contrast to full-length oat phyA-GFP with an approximately equal proportion of the two phyA types. This correlates with a previous observation that Δ6-12 phyA-GFP can form only numerous tiny subnuclear speckles while its wild-type counterpart can also localize into bigger and fewer subnuclear protein complexes. Thus, phyA-GFP is spectroscopically and photochemically similar or identical to the native phyA, suggesting that the GFP tag does not affect the chromophore. phyA-GFP comprises phyA'-GFP and phyA''-GFP, suggesting that both of them are potential participants in nuclear-cytoplasmic partitioning, which may contribute to its complexity.

Photoreceptor partner FHY1 has an independent role in gene modulation and plant development under far-red light

To incorporate the far-red light (FR) signal into a strategy for optimizing plant growth, FAR-RED ELONGATED HYPOCOTYL1 (FHY1) mediates the nuclear translocation of the FR photoreceptor phytochrome A (phyA) and facilitates the association of phyA with the promoters of numerous associated genes crucial for the response to environmental stimuli. However, whether FHY1 plays additional roles after FR irradiation remains elusive. Here, through the global identification of FHY1 chromatin association sites through ChIP-seq analysis and by the comparison of FHY1-associated sites with phyA-associated sites, we demonstrated that nuclear FHY1 can either act independently of phyA or act in association with phyA to activate the expression of distinct target genes. We also determined that phyA can act independently of FHY1 in regulating phyA-specific target genes. Furthermore, we determined that the independent FHY1 nuclear pathway is involved in crucial aspects of plant development, as in the case of inhibited seed germination under FR during salt stress. Notably, the differential presence of cis-elements and transcription factors in common and unique FHY1- and/or phyA-associated genes are indicative of the complexity of the independent and coordinated FHY1 and phyA pathways. Our study uncovers previously unidentified aspects of FHY1 function beyond its currently recognized role in phyA-dependent photomorphogenesis.

Light perception and signalling by phytochrome A

In etiolated seedlings, phytochrome A (phyA) mediates very-low-fluence responses (VLFRs), which initiate de-etiolation at the interphase between the soil and above-ground environments, and high-irradiance responses (HIR), which complete de-etiolation under dense canopies and require more sustained activation with far-red light. Light-activated phyA is transported to the nucleus by FAR-RED ELONGATED HYPOCOTYL1 (FHY1). The nuclear pool of active phyA increases under prolonged far-red light of relatively high fluence rates. This condition maximizes the rate of FHY1-phyA complex assembly and disassembly, allowing FHY1 to return to the cytoplasm to translocate further phyA to the nucleus, to replace phyA degraded in the proteasome. The core signalling pathways downstream of nuclear phyA involve the negative regulation of CONSTITUTIVE PHOTOMORPHOGENIC 1, which targets for degradation transcription factors required for photomorphogenesis, and PHYTOCHROME-INTERACTING FACTORs, which are transcription factors that repress photomorphogenesis. Under sustained far-red light activation, released FHY1 can also be recruited with active phyA to target gene promoters as a transcriptional activator, and nuclear phyA signalling activates a positive regulatory loop involving BELL-LIKE HOMEODOMAIN 1 that reinforces the HIR.

ABD1 is an Arabidopsis DCAF substrate receptor for CUL4-DDB1-based E3 ligases that acts as a negative regulator of abscisic acid signaling

Members of the DDB1-CUL4-associated factors (DCAFs) family directly bind to DAMAGED DNA BINDING PROTEIN1 (DDB1) and function as the substrate receptors in CULLIN4-based E3 (CUL4) ubiquitin ligases, which regulate the selective ubiquitination of proteins. Here, we describe a DCAF protein, ABD1 (for ABA-hypersensitive DCAF1), that negatively regulates abscisic acid (ABA) signaling in Arabidopsis thaliana. ABD1 interacts with DDB1 in vitro and in vivo, indicating that it likely functions as a CUL4 E3 ligase substrate receptor. ABD1 expression is induced by ABA, and mutations in ABD1 result in ABA- and NaCl-hypersensitive phenotypes. Loss of ABD1 leads to hyperinduction of ABA-responsive genes and higher accumulation of the ABA-responsive transcription factor ABA INSENSITIVE5 (ABI5), hypersensitivity to ABA during seed germination and seedling growth, enhanced stomatal closure, reduced water loss, and, ultimately, increased drought tolerance. ABD1 directly interacts with ABI5 in yeast two-hybrid assays and associates with ABI5 in vivo by coimmunoprecipitation, and the interaction was found in the nucleus by bimolecular fluorescence complementation. Furthermore, loss of ABD1 results in a retardation of ABI5 degradation by the 26S proteasome. Taken together, these data suggest that the DCAF-CUL4 E3 ubiquitin ligase assembled with ABD1 is a negative regulator of ABA responses by directly binding to and affecting the stability of ABI5 in the nucleus.

Gene expression regulation in photomorphogenesis from the perspective of the central dogma

Depending on the environment a young seedling encounters, the developmental program following seed germination could be skotomorphogenesis in the dark or photomorphogenesis in the light. Light signals are interpreted by a repertoire of photoreceptors followed by sophisticated gene expression networks, eventually resulting in developmental changes. The expression and functions of photoreceptors and key signaling molecules are highly coordinated and regulated at multiple levels of the central dogma in molecular biology. Light activates gene expression through the actions of positive transcriptional regulators and the relaxation of chromatin by histone acetylation. Small regulatory RNAs help attenuate the expression of light-responsive genes. Alternative splicing, protein phosphorylation/dephosphorylation, the formation of diverse transcriptional complexes, and selective protein degradation all contribute to proteome diversity and change the functions of individual proteins.

The PP6 phosphatase regulates ABI5 phosphorylation and abscisic acid signaling in Arabidopsis

The basic Leucine zipper transcription factor ABSCISIC ACID INSENSITIVE5 (ABI5) is a key regulator of abscisic acid (ABA)-mediated seed germination and postgermination seedling growth. While a family of SUCROSE NONFERMENTING1-related protein kinase2s (SnRK2s) is responsible for ABA-induced phosphorylation and stabilization of ABI5, the phosphatase(s) responsible for dephosphorylating ABI5 is still unknown. Here, we demonstrate that mutations in FyPP1 (for Phytochrome-associated serine/threonine protein phosphatase1) and FyPP3, two homologous genes encoding the catalytic subunits of Ser/Thr PROTEIN PHOSPHATASE6 (PP6), cause an ABA hypersensitive phenotype in Arabidopsis thaliana, including ABA-mediated inhibition of seed germination and seedling growth. Conversely, overexpression of FyPP causes reduced sensitivity to ABA. The ABA hypersensitive phenotype of FyPP loss-of-function mutants is ABI5 dependent, and the amount of phosphorylated and total ABI5 proteins inversely correlates with the levels of FyPP proteins. Moreover, FyPP proteins physically interact with ABI5 in vitro and in vivo, and the strength of the interaction depends on the ABI5 phosphorylation status. In vitro phosphorylation assays show that FyPP proteins directly dephosphorylate ABI5. Furthermore, genetic and biochemical assays show that FyPP proteins act antagonistically with SnRK2 kinases to regulate ABI5 phosphorylation and ABA responses. Thus, Arabidopsis PP6 phosphatase regulates ABA signaling through dephosphorylation and destabilization of ABI5.

Phosphorylation of phytochrome B inhibits light-induced signaling via accelerated dark reversion in Arabidopsis

The photoreceptor phytochrome B (phyB) interconverts between the biologically active Pfr (λmax = 730 nm) and inactive Pr (λmax = 660 nm) forms in a red/far-red-dependent fashion and regulates, as molecular switch, many aspects of light-dependent development in Arabidopsis thaliana. phyB signaling is launched by the biologically active Pfr conformer and mediated by specific protein-protein interactions between phyB Pfr and its downstream regulatory partners, whereas conversion of Pfr to Pr terminates signaling. Here, we provide evidence that phyB is phosphorylated in planta at Ser-86 located in the N-terminal domain of the photoreceptor. Analysis of phyB-9 transgenic plants expressing phospho-mimic and nonphosphorylatable phyB-yellow fluorescent protein (YFP) fusions demonstrated that phosphorylation of Ser-86 negatively regulates all physiological responses tested. The Ser86Asp and Ser86Ala substitutions do not affect stability, photoconversion, and spectral properties of the photoreceptor, but light-independent relaxation of the phyB(Ser86Asp) Pfr into Pr, also termed dark reversion, is strongly enhanced both in vivo and in vitro. Faster dark reversion attenuates red light-induced nuclear import and interaction of phyB(Ser86Asp)-YFP Pfr with the negative regulator PHYTOCHROME INTERACTING FACTOR3 compared with phyB-green fluorescent protein. These data suggest that accelerated inactivation of the photoreceptor phyB via phosphorylation of Ser-86 represents a new paradigm for modulating phytochrome-controlled signaling.

Protein Phosphatase Activity and Acidic/Alkaline Balance as Factors Regulating the State of Phytochrome A and its Two Native Pools in the Plant Cell

Phytochrome A (phyA), the most versatile plant phytochrome, exists in the two isoforms, phyA′ and phyA′′, differing by the character of its posttranslational modification, possibly, by phosphorylation at the N‐terminal extension [Sineshchekov, V. (2010) J. Botany 2010, Article ID 358372]. This heterogeneity may explain the diverse modes of phyA action. We investigated possible roles of protein phosphatases activity and pH in regulation of the phyA pools' content in etiolated seedlings of maize and their extracts using fluorescence spectroscopy and photochemistry of the pigment. The phyA′/phyA′′ ratio varied depending on the state of development of seedlings and the plant tissue/organ used. This ratio qualitatively correlated with the pH in maize root tips. In extracts, it reached a maximum at pH ≈ 7.5 characteristic for the cell cytoplasm. Inhibition of phosphatases of the PP1 and PP2A types with okadaic and cantharidic acids brought about phyA′ decline and/or concomitant increase of phyA′′ in coleoptiles and mesocotyls, but had no effect in roots, revealing a tissue/organ specificity. Thus, pH and phosphorylation status regulate the phyA′/phyA′′ equilibrium and content in the etiolated (maize) cells and this regulation is connected with alteration of the processes of phyA′ destruction and/or its transformation into the more stable phyA′′.

Photoactivated phytochromes interact with HEMERA and promote its accumulation to establish photomorphogenesis in Arabidopsis

Plant development is profoundly regulated by ambient light cues through the red/far-red photoreceptors, the phytochromes. Early phytochrome signaling events include the translocation of phytochromes from the cytoplasm to subnuclear domains called photobodies and the degradation of antagonistically acting phytochrome-interacting factors (PIFs). We recently identified a key phytochrome signaling component, HEMERA (HMR), that is essential for both phytochrome B (phyB) localization to photobodies and PIF degradation. However, the signaling mechanism linking phytochromes and HMR is unknown. Here we show that phytochromes directly interact with HMR to promote HMR protein accumulation in the light. HMR binds more strongly to the active form of phytochromes. This interaction is mediated by the photosensory domains of phytochromes and two phytochrome-interacting regions in HMR. Missense mutations in either HMR or phyB that alter the phytochrome/HMR interaction can also change HMR levels and photomorphogenetic responses. HMR accumulation in a constitutively active phyB mutant (YHB) is required for YHB-dependent PIF3 degradation in the dark. Our genetic and biochemical studies strongly support a novel phytochrome signaling mechanism in which photoactivated phytochromes directly interact with HMR and promote HMR accumulation, which in turn mediates the formation of photobodies and the degradation of PIFs to establish photomorphogenesis.

Protein phosphatase activity and acidic/alkaline balance as factors regulating the state of phytochrome A and its two native pools in the plant cell

Phytochrome A (phyA), the most versatile plant phytochrome, exists in the two isoforms, phyA' and phyA'', differing by the character of its posttranslational modification, possibly, by phosphorylation at the N-terminal extension [Sineshchekov, V. (2010) J. Botany 2010, Article ID 358372]. This heterogeneity may explain the diverse modes of phyA action. We investigated possible roles of protein phosphatases activity and pH in regulation of the phyA pools' content in etiolated seedlings of maize and their extracts using fluorescence spectroscopy and photochemistry of the pigment. The phyA'/phyA'' ratio varied depending on the state of development of seedlings and the plant tissue/organ used. This ratio qualitatively correlated with the pH in maize root tips. In extracts, it reached a maximum at pH ≈ 7.5 characteristic for the cell cytoplasm. Inhibition of phosphatases of the PP1 and PP2A types with okadaic and cantharidic acids brought about phyA' decline and/or concomitant increase of phyA'' in coleoptiles and mesocotyls, but had no effect in roots, revealing a tissue/organ specificity. Thus, pH and phosphorylation status regulate the phyA'/phyA'' equilibrium and content in the etiolated (maize) cells and this regulation is connected with alteration of the processes of phyA' destruction and/or its transformation into the more stable phyA''.

A PP6-type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis

The directional transport of the phytohormone auxin depends on the phosphorylation status and polar localization of PIN-FORMED (PIN) auxin efflux proteins. While PINIOD (PID) kinase is directly involved in the phosphorylation of PIN proteins, the phosphatase holoenzyme complexes that dephosphorylate PIN proteins remain elusive. Here, we demonstrate that mutations simultaneously disrupting the function of Arabidopsis thaliana FyPP1 (for Phytochrome-associated serine/threonine protein phosphatase1) and FyPP3, two homologous genes encoding the catalytic subunits of protein phosphatase6 (PP6), cause elevated accumulation of phosphorylated PIN proteins, correlating with a basal-to-apical shift in subcellular PIN localization. The changes in PIN polarity result in increased root basipetal auxin transport and severe defects, including shorter roots, fewer lateral roots, defective columella cells, root meristem collapse, abnormal cotyledons (small, cup-shaped, or fused cotyledons), and altered leaf venation. Our molecular, biochemical, and genetic data support the notion that FyPP1/3, SAL (for SAPS DOMAIN-LIKE), and PP2AA proteins (RCN1 [for ROOTS CURL IN NAPHTHYLPHTHALAMIC ACID1] or PP2AA1, PP2AA2, and PP2AA3) physically interact to form a novel PP6-type heterotrimeric holoenzyme complex. We also show that FyPP1/3, SAL, and PP2AA interact with a subset of PIN proteins and that for SAL the strength of the interaction depends on the PIN phosphorylation status. Thus, an Arabidopsis PP6-type phosphatase holoenzyme acts antagonistically with PID to direct auxin transport polarity and plant development by directly regulating PIN phosphorylation.

A short amino-terminal part of Arabidopsis phytochrome A induces constitutive photomorphogenic response

Phytochrome A (phyA) is the dominant photoreceptor of far-red light sensing in Arabidopsis thaliana. phyA accumulates at high levels in the cytoplasm of etiolated seedlings, and light-induced phyA signaling is mediated by a complex regulatory network. This includes light- and FHY1/FHL protein-dependent translocation of native phyA into the nucleus in vivo. It has also been shown that a short N-terminal fragment of phyA (PHYA406) is sufficient to phenocopy this highly regulated cellular process in vitro. To test the biological activity of this N-terminal fragment of phyA in planta, we produced transgenic phyA-201 plants expressing the PHYA406-YFP (YELLOW FLUORESCENT PROTEIN)-DD, PHYA406-YFP-DD-NLS (nuclear localization signal), and PHYA406-YFP-DD-NES (nuclear export signal) fusion proteins. Here, we report that PHYA406-YFP-DD is imported into the nucleus and this process is partially light-dependent whereas PHYA406-YFP-DD-NLS and PHYA406-YFP-DD-NES display the expected constitutive localization patterns. Our results show that these truncated phyA proteins are light-stable, they trigger a constitutive photomorphogenic-like response when localized in the nuclei, and neither of them induces proper phyA signaling. We demonstrate that in vitro and in vivo PHYA406 Pfr and Pr bind COP1, a general repressor of photomorphogenesis, and co-localize with it in nuclear bodies. Thus, we conclude that, in planta, the truncated PHYA406 proteins inactivate COP1 in the nuclei in a light-independent fashion.

Phosphorylation of FAR-RED ELONGATED HYPOCOTYL1 is a key mechanism defining signaling dynamics of phytochrome A under red and far-red light in Arabidopsis

Emerging plants have to adapt to a high ratio of far-red light (FR)/red light (R) light in the canopy before they reach the R-enriched direct sunlight. Phytochrome A (phyA) is the single dominant photoreceptor in young Arabidopsis thaliana seedlings that initiates photomorphogenesis in response to a FR-enriched environment and transduces increasing R signals to early responsive genes. To date, how phyA differentially transmits FR and R signals to downstream genes remains obscure. Here, we present a phyA pathway in which FAR-RED ELONGATED HYPOCOTYL1 (FHY1), an essential partner of phyA, directly guides phyA to target gene promoters and coactivates transcription. Furthermore, we identified two phosphorylation sites on FHY1, Ser-39 and Thr-61, whose phosphorylation by phyA under R inhibits phyA signaling at each step of its pathway. Deregulation of FHY1 phosphorylation renders seedlings colorblind to FR and R. Finally, we show that the weaker phyA response resulting from FHY1 phosphorylation ensures the seedling deetiolation process in response to a R-enriched light condition. Collectively, our results reveal FHY1 phosphorylation as a key mechanism for FR/R spectrum-specific responses in plants and an essential event for plant adaption to changing light conditions in nature.

Interaction with plant transcription factors can mediate nuclear import of phytochrome B

Phytochromes (phy) are red/far-red-absorbing photoreceptors that regulate the adaption of plant growth and development to changes in ambient light conditions. The nuclear transport of the phytochromes upon light activation is regarded as a key step in phytochrome signaling. Although nuclear import of phyA is regulated by the transport facilitators far red elongated hypocotyl 1 (FHY1) and fhy1-like, an intrinsic nuclear localization signal was proposed to be involved in the nuclear accumulation of phyB. We recently showed that nuclear import of phytochromes can be analyzed in a cell-free system consisting of isolated nuclei of the unicellular green algae Acetabularia acetabulum. We now show that this system is also versatile to elucidate the mechanism of the nuclear transport of phyB. We tested the nuclear transport characteristics of full-length phyB as well as N- and C-terminal phyB fragments in vitro and showed that the nuclear import of phyB can be facilitated by phytochrome-interacting factor 3 (PIF3). In vivo measurements of phyB nuclear accumulation in the absence of PIF1, -3, -4, and -5 indicate that these PIFs are the major transport facilitators during the first hours of deetiolation. Under prolonged irradiations additional factors might be responsible for phyB nuclear transport in the plant.