Regulated Degradation of HFR1 Desensitizes Light Signaling in Arabidopsis

Arabidopsis seedlings undergo photomorphogenesis in the light and etiolation in the dark. HFR1, a bHLH transcription factor, is required for both phytochrome A (phyA)-mediated far-red and cryptochrome 1 (cry1)-mediated blue light signaling. We report that HFR1 is a short-lived protein in darkness and is degraded through a 26S proteasome-dependent pathway. Light, irrespective of its quality, enhances HFR1 protein accumulation via promoting its stabilization. We demonstrate that HFR1 physically interacts with COP1 and that COP1 exhibits ubiquitin ligase activity toward HFR1 in vitro. In addition, we show that COP1 is required for degradation of HFR1 in vivo. Furthermore, plants overexpressing a C-terminal 161 amino acid fragment of HFR1 (CT161) display enhanced photomorphogenesis, suggesting an autonomous function of CT161 in promoting light signaling. This truncated HFR1 gene product is more stable than the full-length HFR1 protein in darkness, indicating that the COP1-interacting N-terminal portion of HFR1 is essential for COP1-mediated destabilization of HFR1. These results suggest that light enhances HFR1 protein accumulation by abrogating COP1-mediated degradation of HFR1, which is necessary and sufficient for promoting light signaling. Additionally, our results substantiate the E3 ligase activity of COP1 and its critical role in desensitizing light signaling.

BZS1, a B-box Protein, Promotes Photomorphogenesis Downstream of Both Brassinosteroid and Light Signaling Pathways

Photomorphogenesis is controlled by multiple signaling pathways, including the light and brassinosteroid （BR） pathways. BR signaling activates the BZR1 transcription factor, which is required for suppressing photomorphogen- esis in the dark, We identified a suppressor of the BR hypersensitive mutant bzrl-lD and named it bzrl-lD suppressorl- Dominant （bzsl-D）. The bzsl-D mutation was caused by overexpression of a B-box zinc finger protein BZS1, which is transcriptionally repressed by BZR1. Overexpression of BZS1 causes de-etiolation in the dark, short hypocotyls in the light, reduced sensitivity to BR treatment, and repression of many BR-activated genes. Knockdown of BZS1 by co-suppression partly suppressed the short hypocotyl phenotypes of BR-deficient or insensitive mutants. These results support that BZSl is a negative regulator of BR response. BZS1 overexpressors are hypersensitive to different wavelengths of light and loss of function of BZS1 reduces plant sensitivity to light and partly suppresses the constitutive photomorphogenesis 1 （cop1） mutant in the dark, suggesting a positive role in light response. BZS1 protein accumulates at an increased level after light treatment of dark-grown BZSl-OXplants and in the cop1 mutants, and BZS1 interacts with COP1 in vitro, suggesting that light regulates BZS1 through COPl-mediated ubiquitination and proteasomal degradation. These results demonstrate that BZS1 mediates the crosstalk between BR and light pathways.

Coordination of Plastid and Light Signaling Pathways upon Development of Arabidopsis Leaves under Various Photoperiods

Plants synchronize their cellular and physiological functions according to the photoperiod （the length of the light period） in the cycle of 24 h. Photoperiod adjusts several traits in the plant life cycle, including flowering and senes- cence in annuals and seasonal growth cessation in perennials. Photoperiodic development is controlled by the coordinated action of photoreceptors and the circadian clock. During the past 10 years, remarkable progress has been made in under- standing the molecular mechanism of the circadian clock, especially with regard to the transition of Arabidopsis from the vegetative growth to the reproductive phase. Besides flowering photoperiod also modifies plant photosynthetic struc- tures and traits. Light signals controlling biogenesis of chloroplasts and development of leaf photosynthetic structures are perceived both by photoreceptors and in chloroplasts. In this review, we provide evidence suggesting that the photope- riodic development of Arabidopsis leaves mimics the acclimation of plant to various light intensities. Furthermore, the chloroplast-to-nucleus retrograde signals that adjust acclimation to light intensity are proposed to contribute also to the signaling pathways that control photoperiodic acclimation of leaves.

The involvement of the N-terminal PHR domain of Arabidopsis cryptochromes in mediating light signaling

Light is a key environmental cue that fundamentally regulates all aspects of plant growth and development,which is mediated by the multiple photoreceptors including the blue light photoreceptors cryptochromes(CRYs).In Arabidopsis,there are two well-characterized homologous CRYs,CRY1 and CRY2.Whereas CRYs are flavoproteins,they lack photolyase activity and are characterized by an Nterminal photolyase-homologous region(PHR)domain and a C-terminal extension domain.It has been established that the C-terminal extension domain of CRYs is involved in mediating light signaling through direct interactions with the master negative regulator of photomorphogenesis,COP1.Recent studies have revealed that the N-terminal PHR domain of CRYs is also involved in mediating light signaling.In this review,we mainly summarize and discuss the recent advances in CRYs signaling mediated by the N-terminal PHR domain,which involves the N-terminal PHR domain-mediated dimerization/oligomerization of CRYs and physical interactions with the pivotal transcription regulators in light and phytohormone signaling.

Coordinated Shoot and Root Responses to Light Signaling in Arabidopsis

Light is one of the most important environmental signals and regulates many biological processes in plants.Studies on light-regulated development have mainly focused on aspects of shoot growth,such as deetiolation,cotyledon opening,inhibition of hypocotyl elongation,flowering,and anthocyanin accumulation.However,recent studies have demonstrated that light is also involved in regulating root growth and development in Arabidopsis.In this review,we summarize the progress in understanding how shoots and roots coordinate their responses to light through different light-signaling components and pathways,including the COP1(CONSTITUTIVELY PHOTOMORPHOGENIC 1),HY5(ELONGATED HYPOCOTYL 5),and MYB73/MYB77(MYB DOMAIN PROTEIN 73/77)pathways.

Light regulation of horticultural crop nutrient uptake and utilization

Plants demonstrate dynamic changes in molecular structures under fluctuating light conditions.Accumulating evidence suggests that light plays a vital role in plant growth and morphogenesis.In particular,light has a role in the absorption and utilization of nutrients in plants.Despite significant progress in understanding the mechanism of nutrient acquisition and assimilation,how light affects and regulates ion uptake remains a question.Studies in model plants,Arabidopsis thaliana,suggest that light affects the nutrient utilization in roots through a complex regulatory network;nonetheless,the molecular mechanisms underlying the various effects of light on these processes in crop plants remain fragmentary.In this review,we discuss the light effects(light quality,light intensity,and photoperiod)on nutrient uptake and utilization in horticultural crops for optimizing crop productivity and increasing fertilizer use efficiency.

RACK1A promotes hypocotyl elongation by scaffolding light signaling components in Arabidopsis

Plants deploy versatile scaffold proteins to intricately modulate complex cell signaling.Among these,RACK1A(Receptors for Activated C Kinase 1A)stands out as a multifaceted scaffold protein functioning as a central integrative hub for diverse signaling pathways.However,the precise mechanisms by which RACK1A orchestrates signal transduction to optimize seedling development remain largely unclear.Here,we demonstrate that RACK1A facilitates hypocotyl elongation by functioning as a flexible platform that connects multiple key components of light signaling pathways.RACK1A interacts with PHYTOCHROME INTERACTING FACTOR(PIF)3,enhances PIF3 binding to the promoter of BBX11 and down-regulates its transcription.Furthermore,RACK1A associates with ELONGATED HYPOCOTYL 5(HY5)to repress HY5 biochemical activity toward target genes,ultimately contributing to hypocotyl elongation.In darkness,RACK1A is targeted by CONSTITUTIVELY PHOTOMORPHOGENIC(COP)1 upon phosphorylation and subjected to COP1-mediated degradation via the 26 S proteasome system.Our findings provide new insights into how plants utilize scaffold proteins to regulate hypocotyl elongation,ensuring proper skoto-and photo-morphogenic development.

Expression Patterns of OsPIL11,a Phytochrome-Interacting Factor in Rice,and Preliminary Analysis of Its Roles in Light Signal Transduction

The expression patterns of OsPILll, one of six putative phytochrome-interacting factors, were analyzed in different organs of transgenic tobacco （Nicotiana tabacum）. The expression of OsPIL 11 was organ-specific and was regulated by leaf development, abscisic acid （ABA）, jasmonic acid （JA） and salicylic acid （SA）. To further explore the role of OsPIL 11 in plant light signal transduction, a plant expression vector of OsPILll was constructed and introduced into tobacco. When grown under continuous red light, OsPILll-overexpressed transgenic tobacco exhibited shorter hypocotyls and larger cotyledons and leaves compared to wild-type seedlings. When grown under continuous far-red light, however, transgenic and wild-type seedlings showed similar phenotypes. These results indicate that OsPILll is involved in red light induced de-etiolation, but not in far-red light induced de-etiolation in transgenic tobacco, which lays the foundation for dissecting the function of OsPIL11 in phytochrome-mediated light signal transduction in rice.

BBX11 promotes red light-mediated photomorphogenic development by modulating phyB-PIF4 signaling

phytochrome B(phyB)acts as the red light photoreceptor and negatively regulates the growth-promoting factor PHYTOCHROME INTERACTING 4(PIF4)through a direct physical interaction,which in turn changes the expression of a large number of genes.phyB-PIF4 module regulates a variety of biological and developmental processes in plants.In this study,we demonstrate that B-BOX PROTEIN 11(BBX11)physically interacts with both phyB and PIF4.BBX11 negatively regulates PIF4 accumulation as well as its biochemical activity,consequently leading to the repression of PIF4-controlled genes’expression and promotion of photomorphogenesis in the prolonged red light.This study reveals a regulatory mechanism that mediates red light signal transduction and sheds a light on phyB-PIF4 module in promoting red light-dependent photomorphognenesis.

The DELLA-ABI4-HY5 module integrates light and gibberellin signals to regulate hypocotyl elongation

Plant growth is coordinately controlled by various environmental and hormonal signals,of which light and gibberellin(GA)signals are two critical factors with opposite effects on hypocotyl elongation.Although interactions between the light and GA signaling pathways have been studied extensively,the detailed regulatory mechanism of their direct crosstalk in hypocotyl elongation remains to be fully clarified.Previously,we reported that ABA INSENSITIVE 4(ABI4)controls hypocotyl elongation through its regulation of cellelongation-related genes,but whether it is also involved in GA signaling to promote hypocotyl elongation is unknown.In this study,we showthat promotion of hypocotyl elongation by GA is dependent on ABI4 activation.DELLAs interact directly with ABI4 and inhibit its DNA-binding activity.In turn,ABI4 combined with ELONGATED HYPOCOTYL 5(HY5),a key positive factor in light signaling,feedback regulates the expression of the GA2ox GA catabolism genes and thus modulates GA levels.Taken together,our results suggest that the DELLA-ABI4-HY5 module may serve as a molecular link that integrates GA and light signals to control hypocotyl elongation.

Role of Arabidopsis RAP2.4 in Regulating Light-and Ethylene-Mediated Developmental Processes and Drought Stress Tolerance

Light and the plant hormone ethylene regulate many aspects of plant growth and development in an overlapping and interdependent fashion. Little is known regarding how their signal transduction pathways cross-talk to regulate plant development in a coordinated manner. Here, we report functional characterization of an AP2/DREB-type transcription factor, Arabidopsis RAP2.4, in mediating light and ethylene signaling. Expression of the RAP2.4 gene is down-regulated by light but up-regulated by salt and drought stresses. RAP2.4 protein is constitutively targeted to the nucleus and it can bind to both the ethylene-responsive GCC-box and the dehydration-responsive element （DRE）. We show that RAP2.4 protein possesses an intrinsic transcriptional activation activity in yeast cells and that it can activate a reporter gene driven by the DRE cis-element in Arabidopsis protoplasts. Overexpression of RAP2.4 or mutation in RAP2.4 cause altered expression of representative light-, ethylene-, and drought-responsive genes. Although no salient phenotype was observed with a rap2.4 loss-of-function mutant, constitutive overexpression of RAP2.4 results in defects in multiple developmental processes regulated by light and ethylene, including hypocotyl elongation and gravitropism, apical hook formation and cotyledon expansion, flowering time, root elongation, root hair formation, and drought tolerance. Based on these observations, we propose that RAP2.4 acts at or downstream of a converging point of light and ethylene signaling pathways to coordinately regulate multiple developmental processes and stress responses.

Phytochrome Signaling in Green Arabidopsis Seedlings： Impact Assessment of a Mutually Negative phyB-PIF Feedback Loop

The reversibly red （R）/far-red （FR）-Iight-responsive phytochrome （phy） photosensory system initiates both the deetiolation process in dark-germinated seedlings upon first exposure to light, and the shade-avoidance process in fully deetiolated seedlings upon exposure to vegetational shade. The intracellular signaling pathway from the light-activated photoreceptor conformer （Pfr） to the transcriptional network that drives these responses involves direct, physical inter- action of Pfr with a small subfamily of bHLH transcription factors, termed Phy-lnteracting Factors （PIFs）, which induces rapid PIF proteolytic degradation. In addition, there is evidence of further complexity in light-grown seedlings, whereby phyB-PIF interaction reciprocally induces phyB degradation, in a mutually-negative, feedback-loop configuration. Here, to assess the relative contributions of these antagonistic activities to the net phenotypic readout in light-grown seedlings, we have examined the magnitude of the light- and simulated-shade-induced responses of a pentuple phyBpiflpif3pif4pif5 （phyBpifq） mutant and various multiple pif-mutant combinations. The data （1） reaffirm that phyB is the predominant, if not exclusive, photoreceptor imposing the inhibition of hypocotyl elongation in deetiolating seedlings in response to pro- longed continuous R irradiation and （2） show that the PIF quartet （PIF1, PIF3, PIF4, and PIF5） retain and exert a dual capacity to modulate hypocotyl elongation under these conditions, by concomitantly promoting cell elongation through intrinsic transcriptional-regulatory activity, and reducing phyB-inhibitory capacity through feedback-loop-induced phyB degrada- tion. In shade-exposed seedlings, immunoblot analysis shows that the shade-imposed reduction in Pfr levels induces increases in the abundance of PIF3, and mutant analysis indicates that PIF3 acts, in conjunction with PIF4 and PIF5, to promote the known shade-induced acceleration of hypocotyl elongation. Conversely, although the quadruple pifq mutant displays clearly reduced hypocotyl elongation compared to wild-type in response to prolonged shade, immunoblot analysis detects no elevation in phyB levels in the mutant seedlings compared to the wild-type during the majority of the shade-induced growth period, and phyB levels are not robustly correlated with the growth phenotype across the pif-mutant combinations compared. These results suggest that PIF feedback modulation of phyB abundance does not play a dominant role in modulating the magnitude of the PIF-promoted, shade-responsive phenotype under these conditions. In seedlings grown under diurnal light-dark cycles, the data show that FR-pulse-induced removal of Pfr at the beginning of the dark period （End-of-Day-FR （EOD-FR） treatment） results in longer hypocotyls relative to no EOD-FR treatment and that this effect is attenuated in the pif-mutant combinations tested. This result similarly indicates that the PIF quartet members are capable of intrinsically promoting hypocotyl cell elongation in light-grown plants, independently of the effects of PIF feedback modulation of photoactivated-phyB abundance.

Phytochrome Signaling： Time to Tighten up the Loose Ends

Phytochromes are red and far-red light photoreceptors that play fundamental roles in controlling many aspects of plant growth and development in response to light. The past two decades have witnessed the mechanistic elucidation of the action mode of phytochromes, including their regulation by external and endogenous factors and how they exert their function as transcriptional regulators. More importantly, recent advances have substantially deepened our understanding on the integration of the phytochromemediated signal into other cellular and developmental processes, such as elongation of hypocotyls, shoot branching, circadian clock, and flowering time, which ofteninvolves complex intercellular and interorgan signaling. Based on these advances, this review illustrates a blueprint of our current understanding of phytochrome signaling and its crosstalk with other signaling pathways, and also points out still open questions that need to be addressed in the future.

Light-Regulated Stomatal Aperture in Arabidopsis

The stomatal pores of plant leaves, situated in the epidermis and surrounded by a pair of guard cells, allow CO2 uptake for photosynthesis and water loss through transpiration. Blue light is one of the dominant environmental signals that control stomatal movements in leaves of plants in a natural environment. This blue light response is mediated by blue/UV A light-absorbing phototropins （phots） and cryptochromes （crys）. Red/far-red light-absorbing phytochromes （phys） also play a role in the control of stomatal aperture. The signaling components that link the perception of light signals to the stomatal opening response are largely unknown. This review discusses a few newly discovered nuclear genes, their function with respect to the phot-, cry-, and phy-mediated signal transduction cascades, and possible involve- ment of circadian clock.

Light Perception:A Matter of Time

Optimizing the perception of external cues and regulating physiology accordingly help plants to cope with the constantly changing environmental conditions to which they are exposed.An array of photoreceptors and intricate signaling pathways allow plants to convey the surrounding light information and synchronize an endogenous timekeeping system known as the circadian clock.This biological clock integrates multiple cues to modulate a myriad of downstream responses,timing them to occur at the best moment of the day and the year.Notably,the mechanism underlying entrainment of the light-mediated clock is not clear.This review addresses known interactions between the light-signaling and circadian-clock networks,focusing on the role of light in clock entrainment and known molecular players in this process.

A Light-Independent Allele of Phytochrome B Faithfully Recapitulates Photomorphogenic Transcriptional Networks

Dominant gain-of-function alleles of Arabidopsis phytochrome B were recently shown to confer lightindependent, constitutive photomorphogenic （cop） phenotypes to transgenic plants （Su and Lagarias, 2007）. In the present study, comparative transcription profiling experiments were performed to assess whether the pattern of gene expression regulated by these alleles accurately reflects the process of photomorphogenesis in wild-type Arabidopsis. Whole- genome transcription profiles of dark-grown phyAphyB seedlings expressing the Y^276H mutant of phyB （YHB） revealed that YHB reprograms about 13% of the Arabidopsis transcriptome in a light-independent manner. The YHB-regulated transcriptome proved qualitatively similar to but quantitatively greater than those of wild-type seedlings grown under 15 or 50 μmol m^-2 m^-1 continuous red light （Rc）. Among the 2977 genes statistically significant two-fold （SSTF） regulated by YHB in the absence of light include those encoding components of the photosynthetic apparatus, tetrapyrrole/pigment biosynthetic pathways, and early light-responsive signaling factors. Approximately 80% of genes SSTF regulated by Rc were also YHB-regulated. Expression of a notable subset of 346 YHB-regulated genes proved to be strongly attenuated by Rc, indicating compensating regulation by phyC-E and/or other Rc-dependent processes. Since the majority of these 346 genes are regulated by the circadian clock, these results suggest that phyA- and phyB-independent light signaling pathway（s） strongly influence clock output. Together with the unique plastid morphology of dark-grown YHB seedlings, these analyses indicate that the YHB mutant induces constitutive photomorphogenesis via faithful reconstruction of phyB signaling pathways in a light-independent fashion.

Arabidopsis Blue Light Receptor Phototropin 1 Undergoes Blue Light-Induced Activation in Membrane Microdomains

Phototropin （phot）-mediated signaling initiated by blue light （BL） plays a critical role in optimizing photosyn- thetic light capture at the plasma membrane （PM） in plants. However, the mechanisms underlying the regu- lation of phot activity at the PM in response to BL remain largely unclear. In this study, by single-particle tracking and stepwise photobleaching analysis of photl-GFP proteins we demonstrated that in the dark photl proteins remain in an inactive state and mostly exist as monomers. Dimerization and the diffusion rate of photl-GFP increased in a dose-dependent manner in response to BL. In contrast, BL did not affect the lateral diffusion of kinase-inactive photlD806N-GFP but did enhance its dimerization, suggesting that photl dimerization is independent of phosphorylation. Forster resonance energy transfer-fluorescence life- time imaging microscopy analysis revealed that the interaction between photl-GFP and a marker of sterol- rich lipid environments, AtRem1.3-mCherry, was enhanced with increased time of BL treatment. However, this BL-dependent interaction was not obvious in plants co-expressing phot1D806N-GFP and AtRem1.3- mCherry, indicating that BL facilitates the translocation of functional photl-GFP into AtRem1.3-1abeled microdomains to activate phot-mediated signaling. Conversely, sterol depletion attenuated photl-GFP dynamics, dimerization, and phosphorylation. Taken together, these results indicate that membrane micro- domains act as organizing platforms essential for the proper function of activated photl at the PM.

Long-distance blue light signalling regulates phosphate deficiency-induced primary root growth inhibition

Although roots are mainly embedded in the soil, recent studies revealed that light regulates mineral nutrient uptake by roots. However, it remains unclear whether the change in root system architecture in response to different rhizosphere nutrient statuses involves light signaling. Here, we report that blue light regulates primary root growth inhibition under phosphate-deficient conditions through the cryptochromes and their downstream signaling factors. We showed that the inhibition of root elongation by low phosphate requires blue light signal perception at the shoot and transduction to the root. In this process, SPA1 and COP1 play a negative role while HY5 plays a positive role. Further experiments revealed that HY5 is able to migrate from the shoot to root and that the shoot-derived HY5 autoactivates root HY5 and regulates primary root growth by directly activating the expression of LPR1, a suppressor of root growth under phosphate starvation. Taken together, our study reveals a regulatory mechanism by which blue light signaling regulates phosphate deficiency-induced primary root growth inhibition, providing new insights into the crosstalk between light and nutrient signaling.

Shedding Light on Large-Scale Chromatin Reorganization in Arabidopsis thaliana

Plants need to respond quickly and appropriately to various types of light signals from the environment to optimize growth and development. The immediate response to shading, reduced photon flux （low light）, and changes in spectral quality involves changes in gene regulation. In the case of more persistent shade, the plant shows a dramatic change in the organization of chromatin. Both plant responses are controlled via photoreceptor signaling proteins. Re- cently, several studies have revealed similar features of chromatin reorganization in response to various abiotic and biotic signals, while others have unveiled intricate molecular networks of light signaling towards gene regulation. This opinion paper briefly describes the chromatin （de）compaction response from a light-signaling perspective to provide a link be- tween chromatin and the molecular network of photoreceptors and E3 ubiquitin ligase complexes.

The Blue Light-Dependent Phosphorylation of the CCE Domain Determines the Photosensitivity of Arabidopsis CRY2

Arabidopsis cryptochrome 2 （CRY2） is a blue light receptor that mediates light inhibition of hypocotyl elongation and long-day promotion of floral initiation, CRY2 is known to undergo blue light-dependent phosphorylation, which is believed to serve regulatory roles in the function of CRY2. We report here on a biochemical and genetics study of CRY2 phosphorylation. Using mass spectrometry analysis, we identified three serine residues in the CCE domain of CRY2 （S588, S599, and S605） that undergo blue light-dependent phosphorylation in Arabidopsis seedlings. A study of serine-substitution mutations in the CCE domain of CRY2 demonstrates that CRY2 contains two types of phosphorylation in the CCE domain, one in the serine cluster that causes electrophoretic mobility upshift and the other outside the serine cluster that does not seem to cause mobility upshift. We showed that mutations in the serine residues within and outside the serine cluster diminished blue light-dependent CRY2 phosphorylation, degradation, and physiological activities. These results support the hypothesis that blue light-dependent phosphorylation of the CCE domain determines the photosensitivity of Arabidopsis CRY2.