Far-red Photoreceptors Research Articles

Phytochrome B photobody components.

Phytochrome B (phyB) is a red and far-red photoreceptor that promotes light responses. Upon photoactivation, phyB enters the nucleus and forms a molecular condensate called a photobody through liquid-liquid phase separation. Phytochrome B photobody comprises phyB, the main scaffold molecule, and at least 37 client proteins. These clients belong to diverse functional categories enriched with transcription regulators, encompassing both positive and negative light signaling factors, with the functional bias toward the negative factors. The functionally diverse clients suggest that phyB photobody acts either as a trap to capture proteins, including negatively acting transcription regulators, for processes such as sequestration, modification, or degradation or as a hub where proteins are brought into close proximity for interaction in a light-dependent manner.

Phytochrome phosphorylation in plant light signaling.

Plant phytochromes, renowned phosphoproteins, are red and far-red photoreceptors that regulate growth and development in response to light signals. Studies on phytochrome phosphorylation postulate that the N-terminal extension (NTE) and hinge region between N- and C-domains are sites of phosphorylation. Further studies have demonstrated that phosphorylation in the hinge region is important for regulating protein-protein interactions with downstream signaling partners, and phosphorylation in the NTE partakes in controlling phytochrome activity for signal attenuation and nuclear import. Moreover, phytochrome-associated protein phosphatases have been reported, indicating a role of reversible phosphorylation in phytochrome regulation. Furthermore, phytochromes exhibit serine/threonine kinase activity with autophosphorylation, and studies on phytochrome mutants with impaired or increased kinase activity corroborate that they are functional protein kinases in plants. In addition to the autophosphorylation, phytochromes negatively regulate PHYTOCHROME-INTERACTING FACTORs (PIFs) in a light-dependent manner by phosphorylating them as kinase substrates. Very recently, a few protein kinases have also been reported to phosphorylate phytochromes, suggesting new views on the regulation of phytochrome via phosphorylation. Using these recent advances, this review details phytochrome regulation through phosphorylation and highlights their significance as protein kinases in plant light signaling.

Genome-Wide Identification and Characterization of the FAR1/FHY3 Family in Populus trichocarpa Torr. & Gray and Expression Analysis in Light Response

Light is an important environmental factor for plant growth, and in higher plants, phytochrome A (phyA) is the predominant far-red photoreceptor, involved in various photoresponses. The FAR1/FHY3 transcription factor family, derived from transposases, is able to regulate plant development in response to multiple photosensitizers phytochrome. In total, 51 PtrFRSs were identified in the poplar genome, and were divided into 4 subfamilies. Among them, 47 PtrFRSs are located on 17 chromosomes. Upstream cis-acting elements of the PtrFRS genes were classified into three categories: growth and metabolism, stress and hormone, and the hormone and stress categories contained most of the cis-acting elements. Analysis of the regulatory networks and expression patterns showed that most PtrFRSs responded to changes in light intensity and were involved in the regulation of phytochromes. In this study, 51 PtrFRSs were identified and comprehensively bioinformatically analyzed, and preliminary functional analysis and prediction of PtrFRSs was carried out.

Suppression of Phytochrome-Interacting Factors Enhances Photoresponses of Seedlings and Delays Flowering With Increased Plant Height in Brachypodium distachyon.

Phytochromes are red and far-red photoreceptors that regulate plant growth and development under ambient light conditions. During phytochrome-mediated photomorphogenesis, phytochrome-interacting factors (PIFs) are the most important signaling partners that regulate the expression of light-responsive genes. However, the function of PIFs in monocots has not been studied well. In this study, using RNA interference (RNAi), we investigated the functions of BdPIL1 and BdPIL3, two PIF-like genes identified in Brachypodium distachyon, which are closely related to Arabidopsis PIF1 and PIF3. The expression of their genes is light-inducible, and both BdPIL1 and BdPIL3 proteins interact with phytochromes in an active form-specific manner. Transgenic Brachypodium seedlings with the RNAi constructs of BdPIL1 and BdPIL3 showed decreased coleoptile lengths and increased leaf growth when exposed to both red and far-red light. In addition, the transgenic plants were taller with elongated internodes than wild-type Bd21-3 plant, exhibiting late flowering. Moreover, RNA-seq analysis revealed downregulation of many genes in the transgenic plants, especially those related to the regulation of cell number, floral induction, and chlorophyll biosynthesis, which were consistent with the phenotypes of increased plant height, delayed flowering, and pale green leaves. Furthermore, we demonstrated the DNA-binding ability of BdPIL1 and BdPIL3 to the putative target promoters and that the DNA-binding was inhibited in the presence of phytochromes. Therefore, this study determines a molecular mechanism underlying phytochrome-mediated PIF regulation in Brachypodium, i.e., sequestration, and also elucidates the functions of BdPIL1 and BdPIL3 in the growth and development of the monocot plant.

CRISPR/Cas9-mediated knockout and overexpression studies reveal a role of maize phytochrome C in regulating flowering time and plant height.

SummaryMaize is a major staple crop widely used for food, feedstocks and industrial products. Shade‐avoidance syndrome (SAS), which is triggered when plants sense competition of light from neighbouring vegetation, is detrimental for maize yield production under high‐density planting conditions. Previous studies have shown that the red and far‐red photoreceptor phytochromes are responsible for perceiving the shading signals and triggering SAS in Arabidopsis; however, their roles in maize are less clear. In this study, we examined the expression patterns of ZmPHYC1 and ZmPHYC2 and found that ZmPHYC1, but not ZmPHYC2, is highly expressed in leaves and is regulated by the circadian clock. Both ZmPHYC1 and ZmPHYC2 proteins are localized to both the nucleus and cytoplasm under light conditions and both of them can interact with themselves or with ZmPHYBs. Heterologous expression of ZmPHYCs can complement the Arabidopsis phyC‐2 mutant under constant red light conditions and confer an attenuated SAS in Arabidopsis in response to shading. Double knockout mutants of ZmPHYC1 and ZmPHYC2 created using the CRISPR/Cas9 technology display a moderate early‐flowering phenotype under long‐day conditions, whereas ZmPHYC2 overexpression plants exhibit a moderately reduced plant height and ear height. Together, these results provided new insight into the function of ZmPHYCs and guidance for breeding high‐density tolerant maize cultivars.

Quantitative Analysis of Photobodies.

Photobodies are membraneless subnuclear organelles that contain the red and far-red photoreceptors, phytochromes. Photobody biogenesis has been postulated to play important roles in early light signaling events. The size and number of photobodies are highly dynamic in response to the quality and quantity of light and correlated tightly with phytochrome-mediated seedling morphogenesis. Here, we provide a detailed protocol for characterization of the three-dimensional morphology of photobodies, including sample preparation, fluorescence microscopy, and image analysis. Although this method was developed initially for characterizing photobodies, it can be adopted to analyze other membraneless or membrane-bound subcellular organelles.

Tomato phyE Is Required for Shade Avoidance in the Absence of phyB1 and phyB2.

The phytochrome (phy) family of red and far-red photoreceptors provides plants with critical information about their surrounding environment and can signal downstream developmental and physiological changes. Neighboring plants compete for limited light resources, and their presence is detected by the phytochrome photoreceptors as a reduced ratio of red: far-red light. One common response to shade is increased elongation of petioles and internodes to compete with their neighbors. While the phytochrome family, phyB in particular, has been well studied in Arabidopsis, information about the other phytochrome family members is limited, especially in sympodial crop plants such as tomato, that have a very different architecture from that of the model plant. To study the tomato phytochrome family we took advantage of several existing mutants and generated an artificial miRNA (amiRNA) line to target SlPHYE, the remaining phytochrome B subfamily member with no currently available mutant line. Here, we characterize internode elongation and shade avoidance phenotypes of the SlPHYE amiRNA line (PHYE amiRNA). In addition, higher order phytochrome subfamily B mutants were generated with the PHYE amiRNA line to investigate the role of SlphyE within the phyB subfamily. We find that the PHYE amiRNA line has no detectable phenotype on its own, however in higher order combinations with SlphyB1 and/or SlphyB2 there are notable defects in shade avoidance. Most notably, we find that the triple mutant combination of SlPHYE amiRNA, SlphyB1, and SlphyB2 has a phenotype that is much stronger than the SlphyB1 SlphyB2 double, showing constitutive shade avoidance and little to no response to shade. This indicates that SlphyE is required for the shade avoidance response in the absence of SlphyB1 and SlphyB2.

HEMERA Couples the Proteolysis and Transcriptional Activity of PHYTOCHROME INTERACTING FACTORs in Arabidopsis Photomorphogenesis.

Phytochromes (phys) are red and far-red photoreceptors that control plant development and growth by promoting the proteolysis of a family of antagonistically acting basic helix-loop-helix transcription factors, the PHYTOCHROME-INTERACTING FACTORs (PIFs). We have previously shown that the degradation of PIF1 and PIF3 requires HEMERA (HMR). However, the biochemical function of HMR and the mechanism by which it mediates PIF degradation remain unclear. Here, we provide genetic evidence that HMR acts upstream of PIFs in regulating hypocotyl growth. Surprisingly, genome-wide analysis of HMR- and PIF-dependent genes reveals that HMR is also required for the transactivation of a subset of PIF direct-target genes. We show that HMR interacts with all PIFs. The HMR-PIF interaction is mediated mainly by HMR's N-terminal half and PIFs' conserved active-phytochrome B binding motif. In addition, HMR possesses an acidic nine-amino-acid transcriptional activation domain (9aaTAD) and a loss-of-function mutation in this 9aaTAD impairs the expression of PIF target genes and the destruction of PIF1 and PIF3. Together, these in vivo results support a regulatory mechanism for PIFs in which HMR is a transcriptional coactivator binding directly to PIFs and the 9aaTAD of HMR couples the degradation of PIF1 and PIF3 with the transactivation of PIF target genes.

RED AND BLUE LIGHT EFFECTS DURING GROWTH ON HYDRAULIC AND STOMATAL CONDUCTANCE IN LEAVES OF YOUNG CUCUMBER PLANTS

Many horticultural crops (food and ornamental) are produced year-round in greenhouses at high latitudes, where the limited availability of natural sunlight restricts plant production during large parts of the year. To enable year-round plant production supplemental light is necessary to enhance photosynthesis, the primary process that drives growth and production. It is therefore not surprising that during the last two decades most of the research effort related to light in greenhouse horticulture has been directed towards optimizing the supplemental light use efficiency for photosynthesis, with emphasis on light intensity, duration and since recently also on light quality. For a long time, high pressure sodium (HPS) lamps were the preferred lamps for supplemental lighting. Nowadays, Light Emitting Diodes (LEDs) are gaining importance, mostly because of their potentially higher energy efficiency. Another important, less-well known attribute of LEDs is the much better possibility to control light quality. Besides the effect on photosynthesis, light quality also influences plant morphological and developmental processes, mostly mediated by a set of blue, red and far-red photoreceptors (i.e., cryptochromes, phototropins and phytochromes). Several of these processes, such as for instance internode and petiole elongation growth and leaf expansion have a direct impact on productivity via plant photosynthesis as mediated by light interception. Light quality can also induce leaf deformations and epinasty, which can negatively influence biomass production via reduced light interception. In ornamental crops, such as chrysanthemum, leaf deformations can have severe negative impact on the final ornamental value. Other important effects of light quality involve the development of stomatal density and the control of stomatal aperture, which both attribute to stomatal conductance and therefore potentially influence productivity, while also the leaf hydraulic resistance is influenced by light quality. This paper will overview some plant morphological and developmental processes that are influenced by light quality and are important for plant production in protected environments.

PLANT MORPHOLOGICAL AND DEVELOPMENTAL RESPONSES TO LIGHT QUALITY IN A HORTICULTURAL CONTEXT

Many horticultural crops (food and ornamental) are produced year-round in greenhouses at high latitudes, where the limited availability of natural sunlight restricts plant production during large parts of the year. To enable year-round plant production supplemental light is necessary to enhance photosynthesis, the primary process that drives growth and production. It is therefore not surprising that during the last two decades most of the research effort related to light in greenhouse horticulture has been directed towards optimizing the supplemental light use efficiency for photosynthesis, with emphasis on light intensity, duration and since recently also on light quality. For a long time, high pressure sodium (HPS) lamps were the preferred lamps for supplemental lighting. Nowadays, Light Emitting Diodes (LEDs) are gaining importance, mostly because of their potentially higher energy efficiency. Another important, less-well known attribute of LEDs is the much better possibility to control light quality. Besides the effect on photosynthesis, light quality also influences plant morphological and developmental processes, mostly mediated by a set of blue, red and far-red photoreceptors (i.e., cryptochromes, phototropins and phytochromes). Several of these processes, such as for instance internode and petiole elongation growth and leaf expansion have a direct impact on productivity via plant photosynthesis as mediated by light interception. Light quality can also induce leaf deformations and epinasty, which can negatively influence biomass production via reduced light interception. In ornamental crops, such as chrysanthemum, leaf deformations can have severe negative impact on the final ornamental value. Other important effects of light quality involve the development of stomatal density and the control of stomatal aperture, which both attribute to stomatal conductance and therefore potentially influence productivity, while also the leaf hydraulic resistance is influenced by light quality. This paper will overview some plant morphological and developmental processes that are influenced by light quality and are important for plant production in protected environments.

Photobodies in Light Signaling

One of the earliest light responses at the cellular level is the translocation of the red and far-red photoreceptors, phytochromes, from the cytoplasm to discrete subnuclear domains named phytochrome nuclear bodies or photobodies. In Arabidopsis, photobodies contain multiple photoreceptors including phytochromes, the ultraviolet-A/blue light sensing cryptochromes, and possibly the ultraviolet-B receptor UVR8. The localization of these photoreceptors to photobodies is triggered by a light-induced conformational switch to their active states. Accumulating evidence suggests that many light signaling molecules, including key transcriptional regulators and proteins involved in their degradation, are colocalized to photobodies and that failure to form photobodies results in defects in light responses. This suggests that photobodies are intimately involved in light signaling events. In this review, we will summarize recent developments related to photobodies and discuss the potential functions of photobodies in relation to light-dependent protein degradation and gene expression.

Regulation of Phytochrome B Nuclear Localization through Light-Dependent Unmasking of Nuclear-Localization Signals

Phytochromes are red and far-red photoreceptors that regulate plant growth and development in response to environmental light cues. Phytochromes exist in two photo-interconvertible conformational states: an inactive Pr form and an active Pfr form. The alteration of phytochromes' subcellular location functions as a major regulatory mechanism of their biological activities. Whereas phytochromes in the Pr form localize in the cytoplasm, phytochromes in the Pfr form accumulate in the nucleus, where they interact with transcription factors to regulate gene expression. The molecular details of the regulation of phytochrome translocation by light are poorly understood. Using Arabidopsis phyB as a model, we demonstrate that the C-terminal PAS-related domain (PRD) is both necessary and sufficient for phyB nuclear import and that the entire C terminus is required for nuclear-body (NB) localization. We also show that phyB's N-terminal bilin lyase domain (BLD) and PHY domain interact directly with the PRD in a light-dependent manner. In vivo localization studies indicate that BLD-PHY is sufficient to regulate phyB's nuclear accumulation. For phyB nuclear localization, our results suggest a molecular mechanism in which the nuclear-localization signal in the PRD is masked by interactions with phyB's chromophore-attachment domains and unmasked by light-dependent conformational changes.

A quadruple photoreceptor mutant still keeps track of time.

Time measurement and light detection are inextricably linked. Cryptochromes, the blue-light photoreceptors shared between plants and animals, are critical for circadian rhythms in flies and mice [1-3]. WC-1, a putative blue-light photoreceptor, is also essential for the maintenance of circadian rhythms in Neurospora [4]. In contrast, we report here that in Arabidopsis thaliana the double mutant lacking the cryptochromes cry1 and cry2, and even a quadruple mutant lacking the red/ far-red photoreceptor phytochromes phyA and phyB as well as cry1 and cry2, retain robust circadian rhythmicity. Interestingly, the quadruple mutant was nearly blind for developmental responses but perceived a light cue for entraining the circadian clock. These results indicate that cryptochromes and phytochromes are not essential components of the central oscillator in Arabidopsis and suggest that plants could possess specific photosensory mechanisms for temporal orientation, in addition to cryptochromes and phytochromes, which are used for both spatial and temporal adaptation.

Photoregulation of Nitrogen Metabolism and Protein Accumulation in the Red Alga Corallina elongata Ellis et Soland

Abstract Red and blue light pulses of 5 min applied together with 45 μM KNO3 stimulated the nitrate uptake and reduction and the assimilation of ammonium in darkness in the red alga Corallina elongata. Nitrate reductase and glutamine synthetase activities were increased in darkness after the application of both red and blue light pulses. Red light produced a dramatic increase in enzyme activities after the first hour in darkness but after 4 h the effect of blue light pulses was greater. The photostimulation of nitrogen metabolism was correlated with light-regulated accumulation of soluble proteins. Nitrogen incorporation, assimilation of ammonium, accu­mulation of total proteins and the increment in total intracellular nitrogen was greater in N-limited algae (C:N = 17.3) than in N-sufficient algae (C :N = 10.3) after the application of light pulses and nitrate. Because the stimulant effects of red and blue light on N-metabolism were partially reversed by far-red light, the possible involvement of the photoreversible red/ far-red photoreceptor, phytochrome, is proposed. In addition, the blue-light effect seems to be mediated by a specific B-light photoreceptor besides phytochrome due to the different time course of the response and the extent of the stimulation after blue compared to red light pulses.