Molecular bases for the constitutive photomorphogenic phenotypes in Arabidopsis

OsbHLH062 negatively regulates Fe homeostasis by enhancing OsHRZ1 targeting OsPRIs for degradation

Iron (Fe) is crucial for plant growth and development, and many transcription factors are involved in the maintenance of Fe homeostasis. In rice Fe signaling, the basic helix-loop-helix (bHLH) IVc proteins (OsPRI1/OsbHLH060, OsPRI2/OsbHLH058, OsPRI3/OsbHLH059, and OsPRI4/OsbHLH057) act as positive regulators, while Oryza sativa IRON-RELATED BHLH TRANSCRIPTION FACTOR 3 (OsIRO3/OsbHLH063) functions as a negative regulator. Additionally, HEMERYTHRIN MOTIF-CONTAINING REALLY INTERESTING NEW GENE AND ZINC-FINGER PROTEIN1 (OsHRZ1) plays a role in targeting OsPRIs for degradation. Here, we investigated the role of OsbHLH062 in response to Fe deficiency. We revealed that OsbHLH062 directly binds to the promoter region of Oryza sativa IRON-RELATED bHLH TRANSCRIPTION FACTOR 2 (OsIRO2), thereby repressing its activity through the recruitment of corepressors TOPLESS/TOPLESSRELATED (OsTPL/OsTPRs). When both OsbHLH062 and OsIRO3 are mutated simultaneously, it results in stunted root growth, reduced plant height, elevated Fe concentration, and the upregulation of Fe deficiency inducible genes. OsbHLH062 is found to be localized in both the cytoplasm and the nucleus. The interaction of OsbHLH062 with OsPRIs promotes its accumulation in the nucleus. Our findings also reveal that both OsbHLH062 and OsIRO3 physically interact with OsHRZ1, which in turn enhances the interaction between OsHRZ1 and OsPRI3, leading to the degradation of OsPRI3 by OsHRZ1. These findings shed light on a new function of OsbHLH062 and OsIRO3 as potential cofactors of OsHRZ1, which contribute to the reduction in OsPRI proteins and, consequently, the repression of Fe signaling pathways.

A PIF-regulated switch in cell axis growth drives cotyledon expansion through tissue-specific cell expansion and division

Despite its crucial role during seedling deetiolation, cotyledon expansion has been largely overlooked, with hypocotyl elongation favored as the primary phenotypic readout in light signaling research. Here, we investigate how cotyledon expansion is regulated during seedling establishment and reveal that light-induced cotyledon expansion involves a rapid switch in growth direction - from longitudinal in darkness to transversal upon initial light exposure. Using PIFq- and phyA/phyB-deficient Arabidopsis mutants, we demonstrate that this switch is repressed by PIFs in the dark and promoted by phytochromes under red light. Notably, expansion is antagonistically regulated in the light by GUN1-mediated plastid retrograde signaling. Cotyledon expansion involves rapid epidermis cell expansion, transitioning from rectangular in darkness to characteristic lobed cells in light. Importantly, our findings show that mesophyll extension is driven not only by cell enlargement but also by palisade cell division, consistent with an enrichment of cell cycle-related genes that are antagonistically regulated by the PIF/phy system and retrograde signaling in the cotyledon. Finally, using mutant lines expressing PIF1 and phyB specifically in the epidermis, we establish that epidermal expansion can drive palisade cell growth, while mesophyll cell division is predominantly regulated by light at the tissue-specific level. This study provides a novel framework for investigating cotyledon expansion during seedling deetiolation, incorporating tissue-level regulation. We propose that cotyledons serve as an excellent model for studying morphogenesis and organ geometry, which in plants is governed by directional cell growth.

Proteome changes during the germination and early seedling development of carnauba palm (Copernicia prunifera) under skotomorphogenic conditions

We analyze the proteome changes during the development of the carnauba palm (Copernicia prunifera) seedlings under skotomorphogenic conditions, by separating the embryo into its two components: haustorium (HA) and cotyledonary petiole (CP) and established the descriptive and quantitative proteomes of these tissues across four developmental stages. 5205 proteins were identified in HA and 6028 in CP. These proteomes are rich in proteins known to maintain the skotomorphogenic state, and in a complete set of proteins involved in cellular respiration and biosynthesis of secondary metabolites. The quantitative analysis employing a label-free approach revealed that 583 proteins in HA and 383 in CP were differentially abundant, with 251 proteins shared between the datasets. The results showed that HA participates in the digestion of food reserves present in HA itself and in the endosperm, acting as a conduit of nitrogen and carbon sources for the growing embryo axis. Among the differentially abundant proteins in the CP, we identified the presence of proteins from the cellular metabolism and proteins involved in the hydrolysis of food reserves such as starch and proteins. This indicates that the CP, in addition to the endosperm and HA, serves as a source of food reserves for the embryo axis. SIGNIFICANCE: Our results also reveal the differential regulation of specific proteins involved in reactive oxygen species scavenging, cell wall remodeling, respiratory metabolism, and protein repair in seeds and seedlings of C. prunifera. These findings have broad implications for understanding the energy metabolism that drives the transition from seed to seedling. For this study, we employed state-of-the-art proteomic techniques, including quantitative mass spectrometry and bioinformatic analysis, that allowed us to create a large dataset that will be a valuable resource for future research on the physiological and biochemical aspects of skotomorphogenesis, photomorphogenesis, and the transition between these states.

Light at the end of the tunnel: integrating signaling pathways in the coordination of lateral root development

Root system architecture (RSA) encompasses a range of physical root attributes, including the lateral roots (LRs), root hairs and adventitious roots, in addition to the primary or main root. This overall structure is a crucial trait for efficient water and mineral capture alongside providing anchorage to the plant in the soil and is vital for plant productivity and fitness. RSA dynamics are dependent upon various environmental cues such as light, soil pH, water, mineral nutrition and the belowground microbiome. Among these factors, light signaling through HY5 significantly influences the flexibility of RSA by controlling different signaling pathways that converge at photoreceptors-mediated signaling, also present in the 'hidden half'. Furthermore, several phytohormones also drive the formation and emergence of LRs and are critical to harmonize intra and extracellular stimuli in this regard. This review endeavors to elucidate the impact of these interactions on RSA, with particular emphasis on LR development and to enhance our understanding of the fundamental mechanisms governing the light-regulation of LR growth and physiology.

Light signaling as cellular integrator of multiple environmental cues in plants

Plants being sessile need to rapidly adapt to the constantly changing environment through modifications in their internal clock, metabolism, and gene expression. They have evolved an intricate system to perceive and transfer the signals from the primary environmental factors namely light, temperature and water to regulate their growth development and survival. Over past few decades rigorous research using molecular genetics approaches, especially in model plant Arabidopsis, has resulted in substantial progress in discovering various photoreceptor systems and light signaling components. In parallel several molecular pathways operating in response to other environmental cues have also been elucidated. Interestingly, the studies have shown that expression profiles of genes involved in photomorphogenesis can undergo modulation in response to other cues from the environment. Recently, the photoreceptor, PHYB, has been shown to function as a thermosensor. Downstream components of light signaling pathway like COP1 and PIF have also emerged as integrating hubs for various kinds of signals. All these findings indicate that light signaling components may act as central integrator of various environmental cues to regulate plant growth and development processes. In this review, we present a perspective on cross talk of signaling mechanisms induced in response to myriad array of signals and their integration with the light signaling components. By putting light signals on the central stage, we propose the possibilities of enhancing plant resilience to the changing environment by fine-tuning the genetic manipulation of its signaling components in the future.

Role of plastids and mitochondria in the early development of seedlings in dark growth conditions

Establishment of the seedlings is a crucial stage of the plant life cycle. The success of this process is essential for the growth of the mature plant. In Nature, when seeds germinate under the soil, seedlings follow a dark-specific program called skotomorphogenesis, which is characterized by small, non-green cotyledons, long hypocotyl, and an apical hook-protecting meristematic cells. These developmental structures are required for the seedlings to emerge quickly and safely through the soil and gain autotrophy before the complete depletion of seed resources. Due to the lack of photosynthesis during this period, the seed nutrient stocks are the primary energy source for seedling development. The energy is provided by the bioenergetic organelles, mitochondria, and etioplast (plastid in the dark), to the cell in the form of ATP through mitochondrial respiration and etio-respiration processes, respectively. Recent studies suggest that the limitation of the plastidial or mitochondrial gene expression induces a drastic reprogramming of the seedling morphology in the dark. Here, we discuss the dark signaling mechanisms involved during a regular skotomorphogenesis and how the dysfunction of the bioenergetic organelles is perceived by the nucleus leading to developmental changes. We also describe the probable involvement of several plastid retrograde pathways and the interconnection between plastid and mitochondria during seedling development. Understanding the integration mechanisms of organellar signals in the developmental program of seedlings can be utilized in the future for better emergence of crops through the soil.

MYB112 connects light and circadian clock signals to promote hypocotyl elongation in Arabidopsis

Ambient light and the endogenous circadian clock play key roles in regulating Arabidopsis (Arabidopsis thaliana) seedling photomorphogenesis. PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) acts downstream of both light and the circadian clock to promote hypocotyl elongation. Several members of the R2R3-MYB transcription factor (TF) family, the most common type of MYB TF family in Arabidopsis, have been shown to be involved in regulating photomorphogenesis. Nonetheless, whether R2R3-MYB TFs are involved in connecting the light and clock signaling pathways during seedling photomorphogenesis remains unknown. Here, we report that MYB112, a member of the R2R3-MYB family, acts as a negative regulator of seedling photomorphogenesis in Arabidopsis. The light signal promotes the transcription and protein accumulation of MYB112. myb112 mutants exhibit short hypocotyls in both constant light and diurnal cycles. MYB112 physically interacts with PIF4 to enhance the transcription of PIF4 target genes involved in the auxin pathway, including YUCCA8 (YUC8), INDOLE-3-ACETIC ACID INDUCIBLE 19 (IAA19), and IAA29. Furthermore, MYB112 directly binds to the promoter of LUX ARRHYTHMO (LUX), the central component of clock oscillators, to repress its expression mainly in the afternoon and relieve LUX-inhibited expression of PIF4. Genetic evidence confirms that LUX acts downstream of MYB112 in regulating hypocotyl elongation. Thus, the enhanced transcript accumulation and transcriptional activation activity of PIF4 by MYB112 additively promotes the expression of auxin-related genes, thereby increasing auxin synthesis and signaling and fine-tuning hypocotyl growth under diurnal cycles.

Shade avoidance in the context of climate change

When exposed to changes in the light environment caused by neighboring vegetation, shade-avoiding plants modify their growth and/or developmental patterns to access more sunlight. In Arabidopsis (Arabidopsis thaliana), neighbor cues reduce the activity of the photosensory receptors phytochrome B (phyB) and cryptochrome 1, releasing photoreceptor repression imposed on PHYTOCHROME INTERACTING FACTORs (PIFs) and leading to transcriptional reprogramming. The phyB-PIF hub is at the core of all shade-avoidance responses, whilst other photosensory receptors and transcription factors contribute in a context-specific manner. CONSTITUTIVELY PHOTOMORPHOGENIC1 is a master regulator of this hub, indirectly stabilizing PIFs and targeting negative regulators of shade avoidance for degradation. Warm temperatures reduce the activity of phyB, which operates as a temperature sensor and further increases the activities of PIF4 and PIF7 by independent temperature sensing mechanisms. The signaling network controlling shade avoidance is not buffered against climate change; rather, it integrates information about shade, temperature, salinity, drought, and likely flooding. We, therefore, predict that climate change will exacerbate shade-induced growth responses in some regions of the planet while limiting the growth potential in others.

Anterograde signaling controls plastid transcription via sigma factors separately from nuclear photosynthesis genes

Light initiates chloroplast biogenesis in Arabidopsis by eliminating PHYTOCHROME-INTERACTING transcription FACTORs (PIFs), which in turn de-represses nuclear photosynthesis genes, and synchronously, generates a nucleus-to-plastid (anterograde) signal that activates the plastid-encoded bacterial-type RNA polymerase (PEP) to transcribe plastid photosynthesis genes. However, the identity of the anterograde signal remains frustratingly elusive. The main challenge has been the difficulty to distinguish regulators from the plethora of necessary components for plastid transcription and other essential chloroplast functions, such as photosynthesis. Here, we show that the genome-wide induction of nuclear photosynthesis genes is insufficient to activate the PEP. PEP inhibition is imposed redundantly by multiple PIFs and requires PIF3's activator activity. Among the nuclear-encoded components of the PEP holoenzyme, we identify four light-inducible, PIF-repressed sigma factors as anterograde signals. Together, our results elucidate that light-dependent inhibition of PIFs activates plastid photosynthesis genes via sigma factors as anterograde signals in parallel with the induction of nuclear photosynthesis genes.

COP1 SUPPRESSOR 6 represses the PIF4 and PIF5 action to promote light-inhibited hypocotyl growth

Light signaling precisely controls photomorphogenic development in plants. PHYTOCHROME INTERACTING FACTOR 4 and 5 (PIF4 and PIF5) play critical roles in the regulation of this developmental process. In this study, we report CONSTITUTIVELY PHOTOMORPHOGENIC 1 SUPPRESSOR 6 (CSU6) functions as a key regulator of light signaling. Loss of CSU6 function largely rescues the cop1-6 constitutively photomorphogenic phenotype. CSU6 promotes hypocotyl growth in the dark, but inhibits hypocotyl elongation in the light. CSU6 not only associates with the promoter regions of PIF4 and PIF5 to inhibit their expression in the morning, but also directly interacts with both PIF4 and PIF5 to repress their transcriptional activation activity. CSU6 negatively controls a group of PIF4- and PIF5-regulated gene expressions. Mutations in PIF4 and/or PIF5 are epistatic to the loss of CSU6, suggesting that CSU6 acts upstream of PIF4 and PIF5. Taken together, CSU6 promotes light-inhibited hypocotyl elongation by negatively regulating PIF4 and PIF5 transcription and biochemical activity.

Transcriptional regulation of photomorphogenesis in seedlings of Brassica napus under different light qualities

This study displayed the transcriptional regulation network of key regulators and downstream pathway in seedling morphogenesis of Brassica napus under different light quality. Plants undergo photomorphogenesis upon the presence of light, mediated by different light (e.g., blue, red, and far-red) signaling pathways. Although the light signaling pathway has been well documented in Arabidopsis, the underlying mechanisms were studied to a less extent in other plant species including Brassica napus. In this study, we investigated the effect of different light qualities (white, blue, red, and far-red light) on the hypocotyl elongation in B. napus, and performed the transcriptomic analysis of seedlings in response to different light qualities. The results showed that hypocotyl elongation was slightly inhibited by red light, while it was strongly inhibited by blue/far-red light. Transcriptome analysis identified 9748 differentially expressed genes (DEGs) among treatments. Gene ontology (GO) enrichment analysis of DEGs showed that light-responsive and photosynthesis-related genes were highly expressed in response to blue/far-red light rather than in red light. Furthermore, the key genes in light signaling (i.e., PHYB, HY5, HYH, HFR1, and PIF3) exhibited distinct expression patterns between blue/far-red and red light treatments. In addition, subgenome dominant expression of homoeologous genes were observed for some genes, such as PHYA, PHYB, HFR1, and BBXs. The current study displayed a comprehensive dissection of light-mediated transcriptional regulation network, including light signaling, phytohormone, and cell elongation/modification, which improved the understanding on the underlying mechanism of light-regulated hypocotyl growth in B. napus.

Integration of ABA, GA, and light signaling in seed germination through the regulation of ABI5

Seed germination is precisely controlled by a variety of signals, among which light signals and the phytohormones abscisic acid (ABA) and gibberellin (GA) play crucial roles. New findings have greatly increased our understanding of the mechanisms by which these three signals regulate seed germination and the close connections between them. Although much work has been devoted to ABA, GA, and light signal interactions, there is still no systematic description of their combination, especially in seed germination. In this review, we integrate ABA, GA, and light signaling in seed germination through the direct and indirect regulation of ABSCISIC ACID INSENSITIVE5 (ABI5), the core transcription factor that represses seed germination in ABA signaling, into our current understanding of the regulatory mechanism of seed germination.

COP1 dynamics integrate conflicting seasonal light and thermal cues in the control of Arabidopsis elongation

As the summer approaches, plants experience enhanced light inputs and warm temperatures, two environmental cues with an opposite morphogenic impact. Key components of this response are PHYTOCHROME B (phyB), EARLY FLOWERING 3 (ELF3), and CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1). Here, we used single and double mutant/overexpression lines to fit a mathematical model incorporating known interactions of these regulators. The fitted model recapitulates thermal growth of all lines used and correctly predicts thermal behavior of others not used in the fit. While thermal COP1 function is accepted to be independent of diurnal timing, our model shows that it acts at temperature signaling only during daytime. Defective response of cop1-4 mutants is epistatic to phyB-9 and elf3-8, indicating that COP1 activity is essential to transduce phyB and ELF3 thermosensory function. Our thermal model provides a unique toolbox to identify best allelic combinations enhancing climate change resilience of crops adapted to different latitudes.

PEAPOD repressors modulate and coordinate developmental responses to light intensity in Arabidopsis

Higher plants adapt to different light intensities by altering hypocotyl elongation, stomatal density, seed size, and flowering time. Despite the importance of this developmental plasticity, knowledge of the underlying genetic and molecular mechanisms modulating and coordinating responses to light intensity remains incomplete. Here, I report that in Arabidopsis the PEAPOD (PPD) repressors PPD1 and PPD2 prevent exaggerated responses to light intensity. Genetic and transcriptome analyses, of a ppd deletion mutant and a PPD1 overexpression genotype, were used to identify how PPD repressors modulate the light signalling network. A ppd1/ppd2 deletion mutant has elongated hypocotyls, elevated stomatal density, enlarged seed, and delayed flowering, whereas overexpression of PPD1 results in the reverse. Transcription of both PPD1 and PPD2, upregulated in low light and downregulated in higher light, is activated by PHYTOCHROME INTERACTING FACTOR 4. I found PPDs modulate light signalling by negative regulation of SUPPRESSOR OF phyA-105 (SPA1) transcription. Whereas PPDs coordinate many of the responses to light intensity - hypocotyl elongation, flowering time, and stomatal density - by repression/de-repression of SPA1, PPD regulation of seed size occurs independent of SPA1. In conclusion PPD repressors modulate and coordinate developmental responses to light intensity by altering light signal transduction.

COP1 positively regulates ABA signaling during Arabidopsis seedling growth in darkness by mediating ABA-induced ABI5 accumulation

CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1), a well-characterized E3 ubiquitin ligase, is a central repressor of seedling photomorphogenic development in darkness. However, whether COP1 is involved in modulating abscisic acid (ABA) signaling in darkness remains largely obscure. Here, we report that COP1 is a positive regulator of ABA signaling during Arabidopsis seedling growth in the dark. COP1 mediates ABA-induced accumulation of ABI5, a transcription factor playing a key role in ABA signaling, through transcriptional and post-translational regulatory mechanisms. We further show that COP1 physically interacts with ABA-hypersensitive DCAF1 (ABD1), a substrate receptor of the CUL4-DDB1 E3 ligase targeting ABI5 for degradation. Accordingly, COP1 directly ubiquitinates ABD1 in vitro, and negatively regulates ABD1 protein abundance in vivo in the dark but not in the light. Therefore, COP1 promotes ABI5 protein stability post-translationally in darkness by destabilizing ABD1 in response to ABA. Interestingly, we reveal that ABA induces the nuclear accumulation of COP1 in darkness, thus enhancing its activity in propagating the ABA signal. Together, our study uncovers that COP1 modulates ABA signaling during seedling growth in darkness by mediating ABA-induced ABI5 accumulation, demonstrating that plants adjust their ABA signaling mechanisms according to their light environment.

BBX16 mediates the repression of seedling photomorphogenesis downstream of the GUN1/GLK1 module during retrograde signalling

Plastid-to-nucleus retrograde signalling (RS) initiated by dysfunctional chloroplasts impact photomorphogenic development. We have previously shown that the transcription factor GLK1 acts downstream of the RS regulator GUN1 in photodamaging conditions to regulate not only the well established expression of photosynthesis-associated nuclear genes (PhANGs) but also to regulate seedling morphogenesis. Specifically, the GUN1/GLK1 module inhibits the light-induced phytochrome-interacting factor (PIF)-repressed transcriptional network to suppress cotyledon development when chloroplast integrity is compromised, modulating the area exposed to potentially damaging high light. However, how the GUN1/GLK1 module inhibits photomorphogenesis upon chloroplast damage remained undefined. Here, we report the identification of BBX16 as a novel direct target of GLK1. BBX16 is induced and promotes photomorphogenesis in moderate light and is repressed via GUN1/GLK1 after chloroplast damage. Additionally, we showed that BBX16 represents a regulatory branching point downstream of GUN1/GLK1 in the regulation of PhANG expression and seedling development upon RS activation. The gun1 phenotype in lincomycin and the gun1-like phenotype of GLK1OX are markedly suppressed in gun1bbx16 and GLK1OXbbx16. This study identified BBX16 as the first member of the BBX family involved in RS, and defines a molecular bifurcation mechanism operated by GLK1/BBX16 to optimise seedling de-etiolation, and to ensure photoprotection in unfavourable light conditions.

Integration of Light and Auxin Signaling in Shade Plants: From Mechanisms to Opportunities in Urban Agriculture

With intensification of urbanization throughout the world, food security is being threatened by the population surge, frequent occurrence of extreme climate events, limited area of available cultivated land, insufficient utilization of urban space, and other factors. Determining the means by which high-yielding and high-quality crops can be produced in a limited space is an urgent priority for plant scientists. Dense planting, vertical production, and indoor cultivation are effective ways to make full use of space and improve the crop yield. The results of physiological and molecular analyses of the model plant species Arabidopsis thaliana have shown that the plant response to shade is the key to regulating the plant response to changes in light intensity and quality by integrating light and auxin signals. In this study, we have summarized the major molecular mechanisms of shade avoidance and shade tolerance in plants. In addition, the biotechnological strategies of enhancing plant shade tolerance are discussed. More importantly, cultivating crop varieties with strong shade tolerance could provide effective strategies for dense planting, vertical production, and indoor cultivation in urban agriculture in the future.

PIF4 and PIF4-Interacting Proteins: At the Nexus of Plant Light, Temperature and Hormone Signal Integrations

Basic helix-loop-helix (bHLH) family transcription factor PHYTOCHROME INTERACTING FACTOR 4 (PIF4) is necessary for plant adaption to light or high ambient temperature. PIF4 directly associates with plenty of its target genes and modulates the global transcriptome to induce or reduce gene expression levels. However, PIF4 activity is tightly controlled by its interacting proteins. Until now, twenty-five individual proteins have been reported to physically interact with PIF4. These PIF4-interacting proteins act together with PIF4 and form a unique nexus for plant adaption to light or temperature change. In this review, we will discuss the different categories of PIF4-interacting proteins, including photoreceptors, circadian clock regulators, hormone signaling components, and transcription factors. These distinct PIF4-interacting proteins either integrate light and/or temperature cues with endogenous hormone signaling, or control PIF4 abundances and transcriptional activities. Taken together, PIF4 and PIF4-interacting proteins play major roles for exogenous and endogenous signal integrations, and therefore establish a robust network for plants to cope with their surrounding environmental alterations.

Time-series transcriptomics reveals a BBX32-directed control of acclimation to high light in mature Arabidopsis leaves

The photosynthetic capacity of mature leaves increases after several days' exposure to constant or intermittent episodes of high light (HL) and is manifested primarily as changes in chloroplast physiology. How this chloroplast-level acclimation to HL is initiated and controlled is unknown. From expanded Arabidopsis leaves, we determined HL-dependent changes in transcript abundance of 3844 genes in a 0-6 h time-series transcriptomics experiment. It was hypothesized that among such genes were those that contribute to the initiation of HL acclimation. By focusing on differentially expressed transcription (co-)factor genes and applying dynamic statistical modelling to the temporal transcriptomics data, a regulatory network of 47 predominantly photoreceptor-regulated transcription (co-)factor genes was inferred. The most connected gene in this network was B-BOX DOMAIN CONTAINING PROTEIN32 (BBX32). Plants overexpressing BBX32 were strongly impaired in acclimation to HL and displayed perturbed expression of photosynthesis-associated genes under LL and after exposure to HL. These observations led to demonstrating that as well as regulation of chloroplast-level acclimation by BBX32, CRYPTOCHROME1, LONG HYPOCOTYL5, CONSTITUTIVELY PHOTOMORPHOGENIC1 and SUPPRESSOR OF PHYA-105 are important. In addition, the BBX32-centric gene regulatory network provides a view of the transcriptional control of acclimation in mature leaves distinct from other photoreceptor-regulated processes, such as seedling photomorphogenesis.

Protein Kinase Activity of Phytochrome A Positively Correlates With Photoresponses in Arabidopsis

Plant phytochromes are known as autophosphorylating serine/threonine protein kinases. However, the functional importance of their kinase activity is not fully elucidated. Previously, the kinase activity is shown to be necessary for the function of Avena sativa phytochrome A (AsphyA) using transgenic plants with mutants displaying reduced kinase activity, such as K411L and T418D. In this study, we isolated and analyzed two AsphyA mutants, K411R and T418V, that showed increased kinase activity. Transgenic phyA-201 plants with these mutants showed hypersensitive responses to far-red (FR) light, such as shorter hypocotyls and more expanded cotyledons than those of control plant (i.e., transgenic phyA-201 plant with wild-type AsphyA). Contrary to the mutants with reduced kinase activity, these mutants accelerated FR-induced phosphorylation and subsequent degradation of phytochrome-interacting factor 3 (PIF3) in Arabidopsis. Moreover, elongated hypocotyl 5 (HY5), a critical positive regulator of photoresponses in plants, accumulated in higher amounts in the transgenic plants under FR light than in the control plant. In addition, PIF1 degradation was accelerated in the transgenic plants. Consequently, the transgenic plants exhibit higher germination frequencies than the control plant. Collectively, our results demonstrate that the AsphyA mutants with increased kinase activity are hyperactive in plants, supporting a positive relationship between the kinase activity of phytochromes and photoresponses in plants.

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.

Tailoring photomorphogenic markers to organ growth dynamics

When a dark-germinated seedling reaches the soil surface and perceives sunlight for the first time, light signaling is activated to adapt the plant's development and transition to autotrophism. During this process, functional chloroplasts assemble in the cotyledons and the seedling's cell expansion pattern is rearranged to enhance light perception. Hypocotyl cells expand rapidly in the dark, while cotyledon cell expansion is suppressed. However, light reverses this pattern by activating cell expansion in cotyledons and repressing it in hypocotyls. The fact that light-regulated developmental responses, as well as the transcriptional mechanisms controlling them, are organ-specific has been largely overlooked in previous studies of seedling de-etiolation. To analyze the expansion pattern of the hypocotyl and cotyledons separately in a given Arabidopsis (Arabidopsis thaliana) seedling, we define an organ ratio, the morphogenic index (MI), which integrates either phenotypic or transcriptomic data for each tissue and provides an important resource for functional analyses. Moreover, based on this index, we identified organ-specific molecular markers to independently quantify cotyledon and hypocotyl growth dynamics in whole-seedling samples. The combination of these marker genes with those of other developmental processes occurring during de-etiolation will allow improved molecular dissection of photomorphogenesis. Along with organ growth markers, this MI contributes a key toolset to unveil and accurately characterize the molecular mechanisms controlling seedling growth.

Phytochrome B links the environment to transcription

Phytochrome B (phyB) senses the difference between darkness and light, the level of irradiance, the red/far-red ratio, and temperature. Thanks to these sensory capacities, phyB perceives whether plant organs are buried in the soil, exposed to full sunlight, in the presence of nearby vegetation, and/or under risk of heat stress. In some species, phyB perceives seasonal daylength cues. phyB affects the activity of several transcriptional regulators either by direct physical interaction or indirectly by physical interaction with proteins involved in the turnover of transcriptional regulators. Typically, interaction of a protein with phyB has either negative or positive effects on the interaction of the latter with a third party, this being another protein or DNA. Thus, phyB mediates the context-dependent modulation of the transcriptome underlying changes in plant morphology, physiology, and susceptibility to biotic and abiotic stress. phyB operates as a dynamic switch that improves carbon balance, prioritizing light interception and photosynthetic capacity in open places and the projection of the shoot towards light in the soil, under shade and in warm conditions.

COP1 mediates light-dependent regulation of flavonol biosynthesis through HY5 in Arabidopsis

Flavonols, a class of flavonoids, accumulate as protective agents in response to various stresses. Among various environmental stimuli, light is one of the factors regulating flavonol production. MYB12/11/111, members of the R2R3 MYBs family, regulates spatio-temporal flavonol accumulation in Arabidopsis. Although various studies indicate at the involvement of an E3 ubiquitin ligase CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and ELONGATED HYPOCOTYL 5 (HY5) in flavonoid biosynthesis in response to UV-B, the regulatory roles of these components under visible light are yet to be investigated. Here, we demonstrate that flavonol accumulation in Arabidopsis is light-regulated. Furthermore, our analysis suggests that MYB12 is a HY5-dependent light-inducible gene and plays a key role in the activation of the flavonol biosynthesis in response to light. Our results indicate the involvement of COP1 in the dark-dependent repression of MYB12 expression and flavonol accumulation. In addition, results also suggest that the effect of COP1 on MYB12 is indirect and is mediated through HY5, a direct transcriptional activator of the MYB12. Together these findings indicate that COP1 acts as a master negative regulator of flavonol biosynthesis in the dark.

Light and abscisic acid interplay in early seedling development

Abscisic acid (ABA) plays a crucial role in plant development, regulating germination, seedling development and stomatal movements, especially under adverse conditions. Light interacts with the ABA signalling pathway to fine tune these processes. Here, we provide an overview of the recent investigations on ABA-light interplay during early plant development after germination. We discuss the multilayered and reciprocal interactions between ABA signalling components and several light signalling modulators, including photoreceptors, transcription factors and posttranslational modifiers. ABSCISIC ACID INSENSITIVE5 acts as a central convergence point for these interactions during postgermination seedling development. ABA also regulates the adaptation of seedlings to challenging light environments. Furthermore, we enlist the role of ABA-light cross-talk in regulating seedling establishment in crops and highlight open questions for future investigations.

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

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

Basic Protein Modules Combining Abscisic Acid and Light Signaling in Arabidopsis

It is generally accepted that plants use the complex signaling system regulated by light and abscisic acid (ABA) signaling components to optimize growth and development in different situations. The role of ABA-light interactions is evident in the coupling of stress defense reactions with seed germination and root development, maintaining of stem cell identity and stem cell specification, stem elongation and leaf development, flowering and fruit formation, senescence, and shade avoidance. All these processes are regulated jointly by the ABA-light signaling system. Although a lot of work has been devoted to ABA-light signal interactions, there is still no systematic description of central signaling components and protein modules, which jointly regulate plant development. New data have emerged to promote understanding of how ABA and light signals are integrated at the molecular level, representing an extensively growing area of research. This work is intended to fill existing gaps by using literature data combined with bioinformatics analysis.

AtINO80 represses photomorphogenesis by modulating nucleosome density and H2A.Z incorporation in light-related genes

Photomorphogenesis is a critical developmental process bridging light-regulated transcriptional reprogramming with morphological changes in organisms. Strikingly, the chromatin-based transcriptional control of photomorphogenesis remains poorly understood. Here, we show that the Arabidopsis (Arabidopsis thaliana) ortholog of ATP-dependent chromatin-remodeling factor AtINO80 represses plant photomorphogenesis. Loss of AtINO80 inhibited hypocotyl cell elongation and caused anthocyanin accumulation. Both light-induced genes and dark-induced genes were affected in the atino80 mutant. Genome-wide occupancy of the H2A.Z histone variant and levels of histone H3 were reduced in atino80 In particular, AtINO80 bound the gene body of ELONGATED HYPOCOTYL 5 (HY5), resulting in lower chromatin incorporations of H2A.Z and H3 at HY5 in atino80 Genetic analysis revealed that AtINO80 acts in a phytochrome B- and HY5-dependent manner in the regulation of photomorphogenesis. Together, our study elucidates a mechanism wherein AtINO80 modulates nucleosome density and H2A.Z incorporation and represses the transcription of light-related genes, such as HY5, to fine tune plant photomorphogenesis.

COLD REGULATED 27 and 28 are targets of CONSTITUTIVELY PHOTOMORPHOGENIC 1 and negatively affect phytochrome B signalling

Phytochromes are red/far-red light receptors in plants involved in the regulation of growth and development. Phytochromes can sense the light environment and contribute to measuring day length; thereby, they allow plants to respond and adapt to changes in the ambient environment. Two well-characterized signalling pathways act downstream of phytochromes and link light perception to the regulation of gene expression. The CONSTITUTIVELY PHOTOMORPHOGENIC 1/SUPPRESSOR OF PHYA-105 (COP1/SPA) E3 ubiquitin ligase complex and the PHYTOCHROME INTERACTING FACTORs (PIFs) are key components of these pathways and repress light responses in the dark. In light-grown seedlings, phytochromes inhibit COP1/SPA and PIF activity and thereby promote light signalling. In a yeast-two-hybrid screen for proteins binding to light-activated phytochromes, we identified COLD-REGULATED GENE 27 (COR27). COR27 and its homologue COR28 bind to phyA and phyB, the two primary phytochromes in seed plants. COR27 and COR28 have been described previously with regard to a function in the regulation of freezing tolerance, flowering and the circadian clock. Here, we show that COR27 and COR28 repress early seedling development in blue, far-red and in particular red light. COR27 and COR28 contain a conserved Val-Pro (VP)-peptide motif, which mediates binding to the COP1/SPA complex. COR27 and COR28 are targeted for degradation by COP1/SPA and mutant versions with a VP to AA amino acid substitution in the VP-peptide motif are stabilized. Overall, our data suggest that COR27 and COR28 accumulate in light but act as negative regulators of light signalling during early seedling development, thereby preventing an exaggerated response to light.

A COP1-PIF-HEC regulatory module fine-tunes photomorphogenesis in Arabidopsis

Light responses mediated by the photoreceptors play crucial roles in regulating different aspects of plant growth and development. An E3 ubiquitin ligase complex CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1)1/SUPPRESSOR OF PHYA (SPA), one of the central repressors of photomorphogenesis, is critical for maintaining skotomorphogenesis. It targets several positive regulators of photomorphogenesis for degradation in darkness. Recently, we revealed that basic helix-loop-helix factors, HECATEs (HECs), function as positive regulators of photomorphogenesis by directly interacting and antagonizing the activity of another group of repressors called PHYTOCHROME-INTERACTING FACTORs (PIFs). It was also shown that HECs are partially degraded in the dark through the ubiquitin/26S proteasome pathway. However, the underlying mechanism of HEC degradation in the dark is still unclear. Here, we show that HECs also interact with both COP1 and SPA proteins in darkness, and that HEC2 is directly targeted by COP1 for degradation via the ubiquitin/26S proteasome pathway. Moreover, COP1-mediated polyubiquitylation and degradation of HEC2 are enhanced by PIF1. Therefore, the ubiquitylation and subsequent degradation of HECs are significantly reduced in both cop1 and pif mutants. Consistent with this, the hec mutants partially suppress photomorphogenic phenotypes of both cop1 and pifQ mutants. Collectively, our work reveals that the COP1/SPA-mediated ubiquitylation and degradation of HECs contributes to the coordination of skoto/photomorphogenic development in plants.

Mechanisms regulating PIF transcription factor activity at the protein level

Plant growth and development are precisely regulated by transcription factors (TFs) such as the PHYTOCHROME INTERACTING FACTORs (PIFs). PIFs regulate growth in response to various internal and external stimuli, and, accordingly, are regulated by a variety of different factors and mechanisms. Canonically, PIF activity is inhibited by light through the sequential phosphorylation, ubiquitination and degradation of these TFs in a manner dependent on their interaction with active phytochrome photoreceptors. However, work in more recent years has revealed that phytochromes also antagonize PIF activity by inhibiting their ability to bind DNA and, at least in the case of PIF7, by causing it to be retained in the cytoplasm. Recent work has also revealed specific kinases, phosphatases and E3 ubiquitin ligases which alter PIFs at the post-translational level. In a few cases, these studies have gone as far as identifying potential kinases responsible for phosphorylating PIFs in response to light. Moreover, additional factors have been identified that positively or negatively affect PIF binding to DNA or bind directly to PIF-DNA complexes and affect the transcriptional activation of target genes by these TFs. This review summarizes the variety of different mechanisms involved in PIF regulation and discusses some of the major unanswered questions in this area of research.

Genomic evidence reveals SPA-regulated developmental and metabolic pathways in dark-grown Arabidopsis seedlings

Photomorphogenesis is repressed in the dark mainly by an E3 ubiquitin ligase complex comprising CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and four homologous proteins called SUPPRESSOR OF PHYA-105 (SPA1-SPA4) in Arabidopsis. This complex induces the ubiquitination and subsequent degradation of positively acting transcription factors (TFs; e.g. ELONGATED HYPOCOTYL (HY5), LONG HYPOCOTYL IN FAR-RED 1 (HFR1), PRODUCTION OF ANTHOCYANIN PIGMENT 1 (PAP1) and others] in the dark to repress photomorphogenesis. Genomic evidence showed a large number of genes regulated by COP1 in the dark, of which many are direct targets of HY5. However, the genomic basis for the constitute photomorphogenic phenotype of spaQ remains unknown. Here, we show that >7200 genes are differentially expressed in the spaQ background compared to wild-type in the dark. Comparison of the RNA sequencing (RNA-Seq) data between cop1 and spaQ revealed a large overlapping set of genes regulated by the COP1-SPA complex. In addition, many of the genes coordinately regulated by the COP1-SPA complex are also regulated by HY5 directly and indirectly. Taken together, our data reveal that SPA proteins repress photomorphogenesis by controlling gene expression in concert with COP1, likely through regulating the abundance of downstream TFs in light signaling pathways. Moreover, SPA proteins may function both in a COP1-dependent and -independent manner in regulating many biological processes and developmental pathways in Arabidopsis.

PCH1 and PCHL Directly Interact with PIF1, Promote Its Degradation, and Inhibit Its Transcriptional Function during Photomorphogenesis

PHOTOPERIODIC CONTROL OF HYPOCOTYL 1 (PCH1) and PCH1-LIKE (PCHL) were shown to directly bind to phytochrome B (phyB) and suppress phyB thermal reversion, resulting in plants with dramatically enhanced light sensitivity. Here, we show that PCH1 and PCHL also positively regulate various light responses, including seed germination, hypocotyl gravitropism, and chlorophyll biosynthesis, by physically interacting with PHYTOCHROME INTERACTING FACTOR 1 (PIF1) and CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1). PCH1 and PCHL interact with PIF1 both in the dark and light, and regulate PIF1 abundance. Moreover, PCH1 and PCHL facilitate the physical interaction between phyB and PIF1 in vivo to promote the light-induced degradation of PIF1. PCH1 and PCHL also inhibit the DNA-binding ability of PIF1 to negatively regulate the expressions of PIF1 target genes. In addition, PCH1 and PCHL interact with COP1 and undergo degradation through the 26S proteasome pathway in the dark. Consistently, pch1 suppresses cop1 phenotype in darkness. Collectively, our study reveals a novel mechanism by which PCH1 and PCHL regulate diverse light responses not only by stabilizing phyB Pfr form but also by directly interacting with PIF1 and COP1, providing a molecular understanding of the control of hypocotyl growth by these proteins.

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.

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

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

Regulation of COP1 Function by Brassinosteroid Signaling

Small increases in temperature result in enhanced elongation of the hypocotyl and petioles and hyponastic growth, in an adaptive response directed to the cooling of the leaves and to protect the shoot meristem from the warm soil. This response, collectively termed as thermomorphogenesis, relies on the faster reversion of phyB Pfr at warmer temperatures, which leads to enhanced activity of the basic-helix-loop-helix PHYTOCHROME INTERACTING FACTOR 4 (PIF4). PIF4 acts as a molecular hub integrating light and temperature cues with endogenous hormonal signaling, and drives thermoresponsive growth by directly activating auxin synthesis and signaling genes. Growth promotion by PIF4 depends on brassinosteroid (BR) signaling, as indicated by the impaired thermoresponse of BR-defective mutants and the partial restoration of pifq thermoresponsive defects by brassinolide (BL) application. Also, phyB limits thermomorphogenic elongation through negative regulation of the E3 ubiquitin ligase COP1 that triggers nuclear degradation of multiple photomorphogenesis-promoting factors acting antagonistically to PIF4. COP1 is indeed observed to accumulate in the nucleus in darkness, or in response to warm temperatures, with constitutive photomorphogenic cop1 mutants failing to respond to temperature. Here we explored the role of BR signaling on COP1 function, by growing cop1 seedlings on BL or the inhibitor brassinazole (BRZ), under different light and temperature regimes. We show that weak cop1 alleles exhibit a hyposensitive response to BL. Furthermore, while cop1-6 mutants display as described a wild-type response to temperature in continuous darkness, this response is abolished by BRZ. Application of this inhibitor likewise suppressed temperature-induced COP1 nuclear accumulation in N. benthamiana leaves. Overall these results demonstrate that cop1-6 is not a temperature-conditional allele, but this mutation allows for a partially active protein which unveils a pivotal role of active BR signaling in the control of COP1 activity.

UVR8 disrupts stabilisation of PIF5 by COP1 to inhibit plant stem elongation in sunlight

Alterations in light quality significantly affect plant growth and development. In canopy shade, phytochrome photoreceptors perceive reduced ratios of red to far-red light (R:FR) and initiate stem elongation to enable plants to overtop competitors. This shade avoidance response is achieved via the stabilisation and activation of PHYTOCHROME INTERACTING FACTORs (PIFs) which elevate auxin biosynthesis. UV-B inhibits shade avoidance by reducing the abundance and activity of PIFs, yet the molecular mechanisms controlling PIF abundance in UV-B are unknown. Here we show that the UV-B photoreceptor UVR8 promotes rapid PIF5 degradation via the ubiquitin-proteasome system in a response requiring the N terminus of PIF5. In planta interactions between UVR8 and PIF5 are not observed. We further demonstrate that PIF5 interacts with the E3 ligase COP1, promoting PIF5 stabilisation in light-grown plants. Binding of UVR8 to COP1 in UV-B disrupts this stabilisation, providing a mechanism to rapidly lower PIF5 abundance in sunlight.

UV-B light suppresses the shade avoidance response in plants by reducing the abundance of PIF transcription factors by an undefined mechanism. Here the authors show that UV-B perceived by the UVR8 receptor inhibits the shade avoidance response by preventing stabilisation of PIF5 by COP1.

Plant photoreceptors and their signaling components compete for COP1 binding via VP peptide motifs

Plants sense different parts of the sun's light spectrum using distinct photoreceptors, which signal through the E3 ubiquitin ligase COP1. Here, we analyze why many COP1‐interacting transcription factors and photoreceptors harbor sequence‐divergent Val‐Pro (VP) motifs that bind COP1 with different binding affinities. Crystal structures of the VP motifs of the UV‐B photoreceptor UVR8 and the transcription factor HY5 in complex with COP1, quantitative binding assays, and reverse genetic experiments together suggest that UVR8 and HY5 compete for COP1. Photoactivation of UVR8 leads to high‐affinity cooperative binding of its VP motif and its photosensing core to COP1, preventing COP1 binding to its substrate HY5. UVR8–VP motif chimeras suggest that UV‐B signaling specificity resides in the UVR8 photoreceptor core. Different COP1–VP peptide motif complexes highlight sequence fingerprints required for COP1 targeting. The blue‐light photoreceptors CRY1 and CRY2 also compete with transcription factors for COP1 binding using similar VP motifs. Thus, our work reveals that different photoreceptors and their signaling components compete for COP1 via a conserved mechanism to control different light signaling cascades.

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.

Photomorphogenesis of the root system in developing sunflower seedlings: a role for sucrose

The domestic sunflower (Helianthus annuus L. cv. 'Giganteus') has been used since the 19th century as a model plant for the study of seedling development in darkness and white light (WL) (scoto- versus photomorphogenesis). However, most pertinent studies have focused on the developmental patterns of the hypocotyl and cotyledons, whereas the root system has been largely ignored. In this study, we analysed entire sunflower seedlings (root and shoot) and quantified organ development in the above- and belowground parts of the organism under natural (non-sterile) conditions. We document that seedlings, raised in moist vermiculite, are covered with methylobacteria, microbes that are known to promote root development in Arabidopsis. Quantitative data revealed that during photomorphogenesis in WL, the root system expands by 90%, whereas stem elongation is inhibited, and hook opening/cotyledon expansion occurs. Root morphogenesis may be mediated via imported sucrose provided by the green, photosynthetically active cotyledons. This hypothesis is supported by the documented effect of sucrose on the induction of lateral root initials in sunflower cuttings. Under these experimental conditions, phytohormones (auxin, cytokinin, brassinolide) exerted little effect on root and cotyledon expansion, and no hormone-induced initiation of lateral roots was observed. It is concluded that sucrose not only acts as an energy source to fuel cell metabolism but is also a shoot-derived signalling molecule that triggers root morphogenesis.

The people behind the papers - Vinh Ngoc Pham and Enamul Huq

The ability to sense and respond to light is fundamental to plant development. As seedlings move from the soil to the air, a switch in developmental program occurs to promote light capture and autotrophic growth. A paper in this issue of Development now provides a molecular analysis of the proteins that regulate this transition in Arabidopsis We caught up with first author and PhD student Vinh Ngoc Pham, and her supervisor Enamul Huq, Professor of Molecular Biosciences at The University of Texas at Austin, to find out more about the work.