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SUMMARY Tomato (Solanum lycopersicum L.) is an important model plant species in photomorphogenesis research. Ultraviolet B (UV‐B) induces the dissociation of homodimers of the photoreceptor UV RESISTANCE LOCUS8 (UVR8) into monomers, which translocate into the nucleus. Nuclear accumulation of UVR8 is a prerequisite for its signaling function. Previous studies have reported that SUPPRESSOR OF PHYTOCHROME A‐105 (SPA) family members may regulate UV‐B signaling in Arabidopsis (Arabidopsis thaliana); however, the underlying mechanism is unknown. Here, we show that the tomato genome encodes four SPA (SlSPA) orthologs. Genome‐edited Slspa3 mutants exhibited enhanced photomorphogenic responses in white light, suggesting that SlSPA3 inhibits general photomorphogenesis. By contrast, UVR8‐mediated gene expression in response to UV‐B was compromised in Slspa3 mutants, suggesting that SlSPA3 promotes UV‐B signaling. UV‐B‐induced nuclear accumulation of UVR8, which is essential for UV‐B signaling, was reduced in the Slspa3 mutants. Moreover, UV‐B‐induced nuclear accumulation of UVR8 was also reduced in the Arabidopsis spa1 spa2 spa3 and spa1 spa2 spa4 triple mutants, indicating a conserved mechanism in these two species. Notably, spa1 spa2 spa4 exhibited normal UV‐B‐induced interaction between UVR8 and the plant morphogenesis repressor CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1). This suggests that the well‐established mechanisms of UVR8 nuclear retention remained unaffected in spa1 spa2 spa4. Thus, our work uncovered a potentially unrecognized mechanism by which SPA proteins regulate UV‐B signaling through the promotion of UVR8 nuclear abundance in land plants. [ABSTRACT FROM AUTHOR]

ABSCISIC ACID‐INSENSITIVE 4 (ABI4) is a pivotal transcription factor which coordinates multiple aspects of plant growth and development as well as plant responses to environmental stresses. ABI4 has been shown to be involved in regulating seedling photomorphogenesis; however, the underlying mechanism remains elusive. Here, we show that the role of ABI4 in regulating photomorphogenesis is generally regulated by sucrose, but ABI4 promotes hypocotyl elongation of Arabidopsis seedlings under blue (B) light under all tested sucrose concentrations. We further show that ABI4 physically interacts with PHYTOCHROME INTERACTING FACTOR 4 (PIF4), a well‐characterized growth‐promoting transcription factor, and post‐translationally promotes PIF4 protein accumulation under B light. Further analyses indicate that ABI4 directly interacts with the B light photoreceptors cryptochromes (CRYs) and inhibits the interactions between CRYs and PIF4, thus relieving CRY‐mediated repression of PIF4 protein accumulation. In addition, while ABI4 could directly activate its own expression, CRYs enhance, whereas PIF4 inhibits, ABI4‐mediated activation of the ABI4 promoter. Together, our study demonstrates that the ABI4–PIF4 module plays an important role in mediating CRY‐induced B light signaling in Arabidopsis. [ABSTRACT FROM AUTHOR]

Light affects almost every aspect of plant development. It is perceived by photoreceptors, among which phytochromes (PHY) are responsible for monitoring the red and far-red spectrum. Arabidopsis thaliana possesses five phytochrome genes (phyA–phyE). Whereas functions of phyA and phyB are extensively studied, our knowledge of other phytochromes is still rudimentary. To analyze phyD function, we expressed it at high levels in different phytochrome-deficient genetic backgrounds. Overexpressed phyD-YFP can govern effective light signaling but only at low temperatures and in cooperation with functional phyC. Under these conditions, phyD-YFP accumulates to high levels, and opposite to phyB, this pool is stable in light. By comparing the photoconvertible phyD-YFP and phyB levels and their signaling in continuous and pulsed irradiation, we showed that phyD-YFP is a less efficient photoreceptor than phyB. This conclusion is supported by the facts that only a part of the phyD-YFP pool is photoconvertible and that thermal reversion of phyD-YFP is faster than that of phyB. Our data suggest that the temperature-dependent function of phyD is based on the amount of phyD protein and not on its Pfr stability, as described for phyB. We also found that phyD-YFP and phyB-GFP are associated with strongly overlapping genomic locations and are able to mediate similar changes in gene expression; however, the efficiency of phyD-YFP is lower. Based on these data, we propose that under certain conditions, synergistic interaction of phyD and phyC can substitute phyB function in seedlings and in adult plants and thus increases the ability of plants to respond more flexibly to environmental changes. [ABSTRACT FROM AUTHOR]

ELONGATED HYPOCOTOYL5 (HY5) and PHYTOCHROME INTERACTING FACTORs (PIFs) are two types of important light-related regulators of plant growth, however, their interplay remains elusive. Here, we report that the activated tomato (Solanum lycopersicum) HY5 (SlHY5) triggers the transcription of a Calcium-dependent Protein Kinase SlCPK27. SlCPK27 interacts with and phosphorylates SlPIF4 at Ser-252 and Ser-308 phosphosites to promote its degradation. SlPIF4 promotes hypocotyl elongation mainly by activating the transcription of SlDWF, a key gene in brassinosteroid (BR) biosynthesis. Such a SlHY5-SlCPK27-SlPIF4-BR cascade not only plays a crucial role in photomorphogenesis but also regulates thermomorphogenesis. Our results uncover a previously unidentified mechanism that integrates Ca2+ signaling with the light signaling pathways to regulate plant growth by modulating BR biosynthesis in response to changes in ambient light and temperature. [ABSTRACT FROM AUTHOR]

Light is one of the most essential environmental factors that tightly and precisely control various physiological and developmental processes in plants. B‐box CONTAINING PROTEINs (BBXs) play central roles in the regulation of light‐dependent development. In this study, we report that BBX9 is a positive regulator of light signaling. BBX9 interacts with the red light photoreceptor PHYTOCHROME B (phyB) and transcription factors PHYTOCHROME‐INTERACTING FACTORs (PIFs). phyB promotes the stabilization of BBX9 in light, while BBX9 inhibits the transcriptional activation activity of PIFs. In turn, PIFs directly bind to the promoter of BBX9 to repress its transcription. On the other hand, BBX9 associates with the positive regulator of light signaling, BBX21, and enhances its biochemical activity. BBX21 associates with the promoter regions of BBX9 and transcriptionally up‐regulates its expression. Collectively, this study unveiled that BBX9 forms a negative feedback loop with PIFs and a positive one with BBX21 to ensure that plants adapt to fluctuating light conditions. [ABSTRACT FROM AUTHOR]

Heat stress inhibits plant growth and productivity. Among the main regulators, B-box zinc-finger (BBX) proteins are well-known for their contribution to plant photomorphogenesis and responses to abiotic stress. Our research pinpoints that SlBBX31, a BBX protein harboring a conserved B-box domain, serves as a suppressor of plant growth and heat tolerance in tomato (Solanum lycopersicum L.). Overexpressing (OE) SlBBX31 in tomato exhibited yellowing leaves due to notable reduction in chlorophyll content and net photosynthetic rate (Pn). Furthermore, the pollen viability of OE lines obviously decreased and fruit bearing was delayed. This not only affected the fruit setting rate and the number of plump seeds but also influenced the size of the fruit. These results indicate that SlBBX31 may be involved in the growth process of tomato, specifically in terms of photosynthesis, flowering, and the fruiting process. Conversely, under heat-stress treatment, SlBBX31 knockout (KO) plants displayed superior heat tolerance, evidenced by their improved membrane stability, heightened antioxidant enzyme activities, and reduced accumulation of reactive oxygen species (ROS). Further transcriptome analysis between OE lines and KO lines under heat stress revealed the impact of SlBBX31 on the expression of genes linked to photosynthesis, heat-stress signaling, ROS scavenging, and hormone regulation. These findings underscore the essential role of SlBBX31 in regulating tomato growth and heat-stress resistance and will provide valuable insights for improving heat-tolerant tomato varieties. [ABSTRACT FROM AUTHOR]

The circadian clock is an endogenous oscillator, and its importance lies in its ability to impart rhythmicity on downstream biological processes, or outputs. Our knowledge of output regulation, however, is often limited to an understanding of transcriptional connections between the clock and outputs. For instance, the clock is linked to plant growth through the gating of photoreceptors via rhythmic transcription of the nodal growth regulators, PHYTOCHROME-INTERACTING FACTORs (PIFs), but the clock's role in PIF protein stability is less clear. Here, we identified a clock-regulated, F-box type E3 ubiquitin ligase, CLOCK-REGULATED F-BOX WITH A LONG HYPOCOTYL 1 (CFH1), that specifically interacts with and degrades PIF3 during the daytime. Additionally, genetic evidence indicates that CFH1 functions primarily in monochromatic red light, yet CFH1 confers PIF3 degradation independent of the prominent red-light photoreceptor phytochrome B (phyB). This work reveals a clock-mediated growth regulation mechanism in which circadian expression of CFH1 promotes sustained, daytime PIF3 degradation in parallel with phyB signaling. [ABSTRACT FROM AUTHOR]

Transcription factor ELONGATED HYPOCOTYL5 (HY5) is the central hub for seedling photomorphogenesis. E3 ubiquitin (Ub) ligase CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) inhibits HY5 protein accumulation through ubiquitination. However, the process of HY5 deubiquitination, which antagonizes E3 ligase-mediated ubiquitination to maintain HY5 homeostasis has never been studied. Here, we identified that Arabidopsis thaliana deubiquitinating enzyme, Ub-SPECIFIC PROTEASE 14 (UBP14) physically interacts with HY5 and enhances its protein stability by deubiquitination. The da3-1 mutant lacking UBP14 function exhibited a long hypocotyl phenotype, and UBP14 deficiency led to the failure of rapid accumulation of HY5 during dark to light. In addition, UBP14 preferred to stabilize nonphosphorylated form of HY5 which is more readily bound to downstream target genes. HY5 promoted the expression and protein accumulation of UBP14 for positive feedback to facilitate photomorphogenesis. Our findings thus established a mechanism by which UBP14 stabilizes HY5 protein by deubiquitination to promote photomorphogenesis in A. thaliana. [ABSTRACT FROM AUTHOR]

Cyanobacteria play a key role in primary production in both oceans and fresh waters and hold great potential for sustainable production of a large number of commodities. During their life, cyanobacteria cells need to acclimate to a multitude of challenges, including shifts in intensity and quality of incident light. Despite our increasing understanding of metabolic regulation under various light regimes, detailed insight into fitness advantages and limitations under shifting light quality remains underexplored. Here, we study photo-physiological acclimation in the cyanobacterium Synechocystis sp. PCC 6803 throughout the photosynthetically active radiation (PAR) range. Using light emitting diodes (LEDs) with qualitatively different narrow spectra, we describe wavelength dependence of light capture, electron transport and energy transduction to main cellular pools. In addition, we describe processes that fine-tune light capture, such as state transitions, or the efficiency of energy transfer from phycobilisomes to photosystems (PS). We show that growth was the most limited under blue light due to inefficient light harvesting, and that many cellular processes are tightly linked to the redox state of the plastoquinone (PQ) pool, which was the most reduced under red light. The PSI-to-PSII ratio was low under blue photons, however, it was not the main growth-limiting factor, since it was even more reduced under violet and near far-red lights, where Synechocystis grew faster compared to blue light. Our results provide insight into the spectral dependence of phototrophic growth and can provide the foundation for future studies of molecular mechanisms underlying light acclimation in cyanobacteria, leading to light optimization in controlled cultivations. [ABSTRACT FROM AUTHOR]

Light is one of the most important factors regulating plant gene expression patterns, metabolism, physiology, growth, and development. To explore how light may induce or alter transcript splicing, we conducted RNA-Seq-based transcriptome analyses by comparing the samples harvested as etiolated seedlings grown under continuous dark conditions vs. the light-treated green seedlings. The study aims to reveal differentially regulated protein-coding genes and novel long noncoding RNAs (lncRNAs), their light-induced alternative splicing, and their association with biological pathways. We identified 14,766 differentially expressed genes, of which 4369 genes showed alternative splicing. We observed that genes mapped to the plastid-localized methyl-erythritol-phosphate (MEP) pathway were light-upregulated compared to the cytosolic mevalonate (MVA) pathway genes. Many of these genes also undergo splicing. These pathways provide crucial metabolite precursors for the biosynthesis of secondary metabolic compounds needed for chloroplast biogenesis, the establishment of a successful photosynthetic apparatus, and photomorphogenesis. In the chromosome-wide survey of the light-induced transcriptome, we observed intron retention as the most predominant splicing event. In addition, we identified 1709 novel lncRNA transcripts in our transcriptome data. This study provides insights on light-regulated gene expression and alternative splicing in rice. [ABSTRACT FROM AUTHOR]

During the last decade, knowledge about BBX proteins has greatly increased. Genome-wide studies identified the BBX gene family in several ornamental, industry, and food crops; however, reports regarding the role of these genes as regulators of agronomically important traits are scarce. Here, by phenotyping a knockout mutant, we performed a comprehensive functional characterization of the tomato locus Solyc12g089240, hereafter called SlBBX20. The data revealed the encoded protein as a positive regulator of light signaling affecting several physiological processes during the life span of plants. Through inhibition of PHYTOCHROME INTERACTING FACTOR 4 (SlPIF4)–auxin crosstalk, SlBBX20 regulates photomorphogenesis. Later in development, it controls the balance between cell division and expansion to guarantee correct vegetative and reproductive development. In fruits, SlBBX20 is transcriptionally induced by the master transcription factor RIPENING INHIBITOR (SlRIN) and, together with ELONGATED HYPOCOTYL 5 (SlHY5), up-regulates flavonoid biosynthetic genes. Finally, SlBBX20 promotes the accumulation of steroidal glycoalkaloids and attenuates Botrytis cinerea infection. This work clearly demonstrates that BBX proteins are multilayer regulators of plant physiology because they affect not only multiple processes during plant development but they also regulate other genes at the transcriptional and post-translational levels. [ABSTRACT FROM AUTHOR]

Coordinated morphogenic adaptation of growing plants is critical for their survival and propagation under fluctuating environments. Plant morphogenic responses to light and warm temperatures, termed photomorphogenesis and thermomorphogenesis, respectively, have been extensively studied in recent decades. During photomorphogenesis, plants actively reshape their growth and developmental patterns to cope with changes in light regimes. Accordingly, photomorphogenesis is closely associated with diverse growth hormonal cues. Notably, accumulating evidence indicates that light‐directed morphogenesis is profoundly affected by two recently identified phytochemicals, karrikins (KARs) and strigolactones (SLs). KARs and SLs are structurally related butenolides acting as signaling molecules during a variety of developmental steps, including seed germination. Their receptors and signaling mediators have been identified, and associated working mechanisms have been explored using gene‐deficient mutants in various plant species. Of particular interest is that the KAR and SL signaling pathways play important roles in environmental responses, among which their linkages with photomorphogenesis are most comprehensively studied during seedling establishment. In this review, we focus on how the phytochemical and light signals converge on the optimization of morphogenic fitness. We also discuss molecular mechanisms underlying the signaling crosstalks with an aim of developing potential ways to improve crop productivity under climate changes. [ABSTRACT FROM AUTHOR]

Cr3+ doped phosphors with deep-red luminescence hold great promise as artificial lighting sources for plants growth. Among them, α-Al 2 O 3 :Cr3+ is featured with an ultra-intense pure zero phonon line (ZPL) emission with negligible sidebands. Nonetheless, further enhancements in its luminescence thermal stability are required to fully unlock its potential for practical applications. To tackle this challenge, we propose that Al 20 B 4 O 36 with a negative expansion coefficient could serve as a more favorable host materials for Cr3+ ion, thereby enhancing the luminescence thermal stability. Our first-principles calculations have unveiled similar electronic structures for α-Al 2 O 3 :Cr3+ and Al 20 B 4 O 36 :Cr3+, suggesting that the observed zero phonon R-line (2 E g) emission, arising from the 2 E g →4 A 2g transition in α-Al 2 O 3 :Cr3+, might also be present in Al 20 B 4 O 36 :Cr3+. Based on these findings, we prepared Al 20 B 4 O 36 :Cr3+ phosphors using a simple solid reaction method and confirmed that Al 20 B 4 O 36 :Cr3+ indeed exhibits a similar ultra-intense pure ZPL emission centered at 694 nm. Moreover, Al 20 B 4 O 36 :Cr3+ phosphors demonstrate remarkable properties including a high internal quantum efficiency (IQE) of 98.2 % and superior luminescence thermal stability compared to α-Al 2 O 3 :Cr3+. A phosphor converted light emitting diode (pc-LED) is developed by coating Al 20 B 4 O 36 :Cr3+ phosphor onto a near-ultraviolet LED chip. The lighting from this deep-red LED significantly impacts the photomorphogenesis of bean sprouts. Our study showcases a rational approach to design novel Cr3+ doped phosphors with enhanced luminescent properties, tailored for specific applications. [ABSTRACT FROM AUTHOR]

ICT1 is an Arabidopsis thaliana line that overexpresses the gene encoding the S30 ribosomal subunit, leading to tolerance to exogenous indole-3-carbinol. Indole-3-carbinol (I3C) is a protective chemical formed as a breakdown of I3M in cruciferous vegetables. The overexpression of S30 in ICT1 results in transcriptional changes that prime the plant for the I3C, or biotic insult. Emerging evidence suggests that ribosomal proteins play important extra-ribosomal roles in various biochemical and developmental processes, such as transcription and stress resistance. In an attempt to elucidate the mechanism leading to I3C and stress resistance in ICT1, and using a multi-pronged approach employing transcriptomics, metabolomics, phenomics, and physiological studies, we show that overexpression of S30 leads to specific transcriptional alterations, which lead to both changes in metabolites connected to biotic and oxidative stress tolerance and, surprisingly, to photomorphogenesis. [ABSTRACT FROM AUTHOR]

Summary: ELONGATED HYPOCOTYL 5 (HY5), a bZIP‐type transcription factor, is a master regulator of light‐mediated responses. ELONGATED HYPOCOTYL 5 binds to the promoter of c. 3000 genes, thereby regulating various physiological and biological processes, including photomorphogenesis, flavonoid biosynthesis, root development, response to abiotic stress and nutrient homeostasis. In recent decades, it has become clear that light signaling plays a crucial role in promoting nutrient uptake and assimilation. Recent studies have revealed the molecular mechanisms underlying such encouraging effects and the crucial function of the transcription factor HY5, whose activity is regulated by many photoreceptors. The discovery that HY5 directly activates the expression of genes involved in nutrient uptake and utilization, including several nitrogen, iron, sulphur, phosphorus and copper uptake and assimilation‐related genes, enhances our understanding of how light signaling regulates uptake and utilisation of multiple nutrients in plants. Here, we review recent advances in the role of HY5 in light‐dependent nutrient uptake and utilization. [ABSTRACT FROM AUTHOR]

Light is a crucial environmental factor that impacts various aspects of plant development. Phytochromes, as light sensors, regulate myriads of downstream genes to mediate developmental reprogramming in response to changes in environmental conditions. CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) is an E3 ligase for a number of substrates in light signaling, acting as a central repressor of photomorphogenesis. The interplay between phytochrome B (phyB) and COP1 forms an antagonistic regulatory module that triggers extensive gene expression reprogramming when exposed to light. Here, we uncover a role of COP1 in light-dependent chromatin remodeling through the regulation of VIL1 (VIN3-LIKE 1)/VERNALIZATION 5, a Polycomb protein. VIL1 directly interacts with phyB and regulates photomorphogenesis through the formation of repressive chromatin loops at downstream growth-promoting genes in response to light. Furthermore, we reveal that COP1 governs light-dependent formation of chromatin loop and limiting a repressive histone modification to fine-tune expressions of growth-promoting genes during photomorphogenesis through VIL1. [ABSTRACT FROM AUTHOR]

Plants rely upon a diverse range of metabolites to control growth and development, and to overcome stress that results from suboptimal conditions. Karrikins (KARs) are a class of butenolide compounds found in smoke that stimulate seed germination and regulate various developmental processes in plants. KARs are perceived via a plant α/β-hydrolase called KARRIKIN INSENSITIVE2 (KAI2), which also functions as a receptor for a postulated phytohormone, provisionally termed KAI2 ligand (KL). Considered natural analogues of KL, KARs have been extensively studied for their effects on plant growth and their crosstalk with plant hormones. The perception and response pathway for KAR–KL signalling is closely related to that of strigolactones, another class of butenolides with numerous functions in regulating plant growth. KAR–KL signalling influences seed germination, seedling photomorphogenesis, root system architecture, abiotic stress responses, and arbuscular mycorrhizal symbiosis. Here, we summarize current knowledge of KAR–KL signalling, focusing on its role in plant development, its effects on stress tolerance, and its interaction with other signalling mechanisms. [ABSTRACT FROM AUTHOR]

PHYTOENE SYNTHASE (PSY) is a rate-limiting enzyme catalysing the first committed step of carotenoid biosynthesis, and changes in PSY gene expression and/or protein activity alter carotenoid composition and plastid differentiation in plants. Four genetic variants of PSY (psy-4 , psy-90 , psy-130 , and psy-145) were identified using a forward genetics approach that rescued leaf virescence phenotypes and plastid abnormalities displayed by the Arabidopsis CAROTENOID ISOMERASE (CRTISO) mutant ccr2 (carotenoid and chloroplast regulation 2) when grown under a shorter photoperiod. The four non-lethal mutations affected alternative splicing, enzyme–substrate interactions, and PSY:ORANGE multi-enzyme complex binding, constituting the dynamic post-transcriptional fine-tuning of PSY levels and activity without changing localization to the stroma and protothylakoid membranes. psy genetic variants did not alter total xanthophyll or β-carotene accumulation in ccr2 , yet they reduced specific acyclic linear cis -carotenes linked to the biosynthesis of a currently unidentified apocarotenoid signal regulating plastid biogenesis, chlorophyll biosynthesis, and photomorphogenic regulation. ccr2 psy variants modulated the PHYTOCHROME-INTERACTING FACTOR 3/ELONGATED HYPOCOTYL 5 (PIF3/HY5) ratio, and displayed a normal prolamellar body formation in etioplasts and chlorophyll accumulation during seedling photomorphogenesis. Thus, suppressing PSY activity and impairing PSY:ORANGE protein interactions revealed how cis -carotene abundance can be fine-tuned through holoenzyme–metabolon interactions to control plastid development. [ABSTRACT FROM AUTHOR]

Summary: In leaves of C4 plants, the reactions of photosynthesis become restricted between two compartments. Typically, this allows accumulation of C4 acids in mesophyll (M) cells and subsequent decarboxylation in the bundle sheath (BS). In C4 grasses, proliferation of plasmodesmata between these cell types is thought to increase cell‐to‐cell connectivity to allow efficient metabolite movement. However, it is not known whether C4 dicotyledons also show this enhanced plasmodesmal connectivity and so whether this is a general requirement for C4 photosynthesis is not clear. How M and BS cells in C4 leaves become highly connected is also not known.We investigated these questions using 3D‐ and 2D‐electron microscopy on the C4 dicotyledon Gynandropsis gynandra as well as phylogenetically close C3 relatives.The M–BS interface of C4G. gynandra showed higher plasmodesmal frequency compared with closely related C3 species. Formation of these plasmodesmata was induced by light. Pharmacological agents that perturbed photosynthesis reduced the number of plasmodesmata, but this inhibitory effect could be reversed by the provision of exogenous sucrose.We conclude that enhanced formation of plasmodesmata between M and BS cells is wired to the induction of photosynthesis in C4G. gynandra. [ABSTRACT FROM AUTHOR]

In smart greenhouse farming, the impact of light qualities on plant growth and development is crucial but lacks systematic identification of optimal combinations. This study addresses this gap by analysing various light properties' effects (photoperiod, intensity, ratio, light–dark order) on Arabidopsis thaliana growth using days-to-flower (DTF) and hypocotyl length as proxies to measure plant growth and development. After establishing suitable ranges through a comprehensive literature review, these properties varied within those ranges. Compared to white light, a 16-h cycle of blue light reduces DTF and hypocotyl length by 12 % and 3 %, respectively. Interestingly, similar results can be achieved using a shorter photoperiod of 14-h light (composed of 8 h of a mixture of 66.7 μ mol m − 2 s − 1 red and 800 μ mol m − 2 s − 1 blue lights (i.e. blue:red ratio of 12:1) followed by 6 h of monochromatic red light and 10-h dark. These findings offer potential for efficient growth light recipes in smart greenhouse farming, optimizing productivity while minimizing energy consumption. [ABSTRACT FROM AUTHOR]

The article discusses the history and naming of the blue UV photoreceptor "cryptochrome." The term was coined to describe an unknown photoreceptor controlling sporulation in fungi and was initially met with resistance. However, it has since been discovered in various organisms and is now widely accepted as the name for this photoreceptor. Cryptochromes have been found to control a range of functions, including circadian rhythms, magnetoreception, and signaling in plants. The article concludes by highlighting the widespread use of the term and its significance in understanding the interactions and convergence of multiple signaling pathways. [Extracted from the article]

Summary: The development of a seedling into a photosynthetically active plant is a crucial process. Despite its importance, we do not fully understand the regulatory mechanisms behind the establishment of functional chloroplasts.We herein provide new insight into the early light response by identifying the function of three basic region/leucine zipper (bZIP) transcription factors: bZIP16, bZIP68, and GBF1. These proteins are involved in the regulation of key components required for the establishment of photosynthetically active chloroplasts. The activity of these bZIPs is dependent on the redox status of a conserved cysteine residue, which provides a mechanism to finetune light‐responsive gene expression.The blue light cryptochrome (CRY) photoreceptors provide one of the major light‐signaling pathways, and bZIP target genes overlap with one‐third of CRY‐regulated genes with an enrichment for photosynthesis/chloroplast‐associated genes. bZIP16, bZIP68, and GBF1 were demonstrated as novel interaction partners of CRY1. The interaction between CRY1 and bZIP16 was stimulated by blue light. Furthermore, we demonstrate a genetic link between the bZIP proteins and cryptochromes as the cry1cry2 mutant is epistatic to the cry1cry2bzip16bzip68gbf1 mutant.bZIP16, bZIP68, and GBF1 regulate a subset of photosynthesis associated genes in response to blue light critical for a proper greening process in Arabidopsis. [ABSTRACT FROM AUTHOR]

In Arabidopsis, the photoreceptors phytochrome B (PhyB) and UV-B resistance 8 (UVR8) mediate light responses that play a major role in regulating photomorphogenic hypocotyl growth, but how they crosstalk to coordinate this process is not well understood. Here we report map-based cloning and functional characterization of an ultraviolet (UV)-B-insensitive, long-hypocotyl mutant, lh1 , and a wild-type-like mutant, lh2 , in cucumber (Cucumis sativus), which show defective CsPhyB and GA oxidase2 (CsGA20ox-2), a key gibberellic acid (GA) biosynthesis enzyme, respectively. The lh2 mutation was epistatic to lh1 and partly suppressed the long-hypocotyl phenotype in the lh1lh2 double mutant. We identified phytochrome interacting factor (PIF) CsPIF3 as playing a critical role in integrating the red/far-red and UV-B light responses for hypocotyl growth. We show that two modules, CsPhyB–CsPIF3–CsGA20ox-2–DELLA and CsPIF3–auxin response factor 18 (CsARF18), mediate CsPhyB-regulated hypocotyl elongation through GA and auxin pathways, respectively, in which CsPIF3 binds to the G/E-box motifs in the promoters of CsGA20ox-2 and CsARF18 to regulate their expression. We also identified a new physical interaction between CsPIF3 and CsUVR8 mediating CsPhyB-dependent, UV-B-induced hypocotyl growth inhibition. Our work suggests that hypocotyl growth in cucumber involves a complex interplay of multiple photoreceptor- and phytohormone-mediated signaling pathways that show both conservation with and divergence from those in Arabidopsis. [ABSTRACT FROM AUTHOR]

Summary: In the absence of light signals, Arabidopsis plants fail to develop the rosette habit typical for this species. Instead, plants display caulescent growth due to elongation of rosette internodes. This aspect of photomorphogenic development has been paid little attention and molecular events involved, downstream of photoreceptor signaling, remain to be identified.Using a combination of genetic and molecular approaches, we show that Arabidopsis rosette habit is a photomorphogenic trait controlled by induction of ARABIDOPSIS THALIANA HOMEOBOX GENE1 (ATH1) as downstream target of multiple photoreceptors.ATH1 induction prevents rosette internode elongation by maintaining the shoot apical meristem (SAM) rib zone area inactive and requires inactivation of photomorphogenesis inhibitors, including PHYTOCHROME INTERACTING FACTOR (PIF) proteins. ATH1 activity results in tissue‐specific inhibition of PIF expression, establishing double‐negative feedback‐regulation at the SAM. Light‐requirement for ATH1 expression can be overcome by high sugar availability to the SAM. Both sugar and light signals that induce ATH1 and, subsequently, rosette habit are mediated by TOR kinase.Collectively, our data reveal a SAM‐specific, double‐negative ATH1‐PIF feedback loop at the basis of rosette habit. Upstream, TOR kinase functions as central hub integrating light and energy signals that control this for Arabidopsis quintessential trait. [ABSTRACT FROM AUTHOR]

Summary: Phytochromes are photoreceptors enabling plants to respond to various light conditions. Independent gene duplications resulted in small phytochrome families in mosses, ferns and seed plants. This phytochrome diversity is hypothesised to be critical for sensing and adapting to different light conditions, but experimental evidence for this idea is lacking for mosses and ferns.The moss model species Physcomitrium patens contains seven phytochromes grouped into three clades, PHY1/3, PHY2/4 and PHY5. Here, we used CRISPR/Cas9‐generated single and higher order mutants to investigate their role in light regulation of protonema and gametophore growth, protonema branching and induction of gametophores.We found both specific and partially overlapping roles for the three phytochrome clades in regulating these responses in different light conditions. PHY1/3 clade phytochromes act as primary far‐red light receptors, while PHY5 clade phytochromes are the primary red light receptors. PHY2/4 clade phytochromes have functions in both red and far‐red light. We also observed that PHY1/3 and PHY2/4 clade phytochromes promote gametophore growth in simulated canopy shade and also play a role in blue light.Similar to seed plants, gene duplications in the phytochrome lineage in mosses were followed by functional diversification into red and far‐red light‐sensing phytochromes. [ABSTRACT FROM AUTHOR]

Maize growth and development are regulated by light quality, intensity and photoperiod. Cryptochromes are blue/ultraviolet-A light receptors involved in stem elongation, shade avoidance, and photoperiodic flowering. To investigate the function of cryptochrome 1 (CRY1) in maize, where it is encoded by ZmCRY1, we obtained two ZmCRY1a genes (ZmCRY1a1 and ZmCRY1a2), both of which share the highest similarity with other gramineous plants, in particular rice CRY1a by phylogenetic analysis. In Arabidopsis, overexpression of ZmCRY1a genes promoted seedling de-etiolation under blue and white light, resulting in dwarfing of mature plants. In seedlings of the maize inbred line Zong 31 (ZmCRY1a-OE), overexpression of ZmCRY1a genes caused a reduction in the mesocotyl and first leaf sheath lengths due to down-regulation of genes influencing cell elongation. In mature transgenic maize plants, plant height, ear height, and internode length decreased in response to overexpression of ZmCRY1a genes. Expression of ZmCRY1a were insensitive to low blue light (LBL)-induced shade avoidance syndrome (SAS) in Arabidopsis and maize. This prompted us to investigate the regulatory role of the gibberellin and auxin metabolic pathways in the response of ZmCRY1a genes to LBL treatment. We confirmed a link between ZmCRY1a expression and hormonal influence on the growth and development of maize under LBL-induced SAS. These results reveal that ZmCRY1a has a relatively conservative function in regulating maize photomorphogenesis and may guide new strategies for breeding high density-tolerant maize cultivars. [ABSTRACT FROM AUTHOR]

The SMAX1 proteins are gradually destabilized upon exposure to warm temperatures and the thermodynamic control of SMAX1 abundance balances the phyB action, thus thermosensitizing the PIF4-dependent hypocotyl morphogenesis. The photo-induced stabilization of SMAX1 represses the nuclear accumulation of DELLA proteins in hypocotyl cells, in which SMAX1 integrates light and KAR signals into the GA-DELLA signaling pathways. The D14-mediated SL signaling pathway and the KAI2-mediated KAR signaling pathway act together to enhance plant tolerance to environmental constraints. SMAX1 lies at the crosstalks of SL and KAR signals and serves as a molecular hub that links various growth hormone signaling cascades with seedling establishment. The protein structural and functional organization and presence of predicted IDRs in the SMAX1 protein suggest that SMAX1 could incorporate multiple cellular and growth hormone signals into optimizing seedling establishment. Karrikins (KARs) are small butenolide compounds identified in the smoke of burning vegetation. Along with the stimulating effects on seed germination, KARs also regulate seedling vigor and adaptive behaviors, such as seedling morphogenesis, root hair development, and stress acclimation. The pivotal KAR signaling repressor, SUPPRESSOR OF MAX2 1 (SMAX1), plays central roles in these developmental and morphogenic processes through an extensive signaling network that governs seedling responses to endogenous and environmental cues. Here, we summarize the versatile roles of SMAX1 reported in recent years and discuss how SMAX1 integrates multiple growth hormone signals into optimizing seedling establishment. We also discuss the evolutionary relevance of the SMAX1-mediated signaling pathways during the colonization of aqueous plants to terrestrial environments. [ABSTRACT FROM AUTHOR]

The purpose of this study is to determine the effects of red and blue lights on the photomorphogenesis and photosynthetic traits of rice seedlings. The rice seedlings were cultured with red light (R), blue light (B), combined red and blue lights (R3B1/R1B1/R1B3), and white light (CK) as the control. The combined application of red and blue lights could promote the growth of rice seedlings to varying degrees; enhance photosynthesis by increasing the seedling leaf area, chlorophyll content, and chlorophyll fluorescence; improve root characteristics by increasing root number, root volume, and root activity; and thus increase the dry matter accumulation of rice seedlings. In addition, the combination of red and blue lights could regulate the expression of genes related to photosynthesis in rice leaves, affect the activity of the Rubisco enzyme, and then affect the photosynthesis of rice seedlings. These results indicate that red and blue lights have direct synergistic effects, which can regulate the growth of rice seedlings and promote the morphogenesis of rice seedlings. The combined application of red and blue lights can be used to supplement the light in rice-factory seedling raising. [ABSTRACT FROM AUTHOR]

SUMMARY: The Arabidopsis COP1/SPA ubiquitin ligase suppresses photomorphogenesis in darkness. In the light, photoreceptors inactivate COP1/SPA to allow a light response. While SPA genes are specific to the green lineage, COP1 also exists in humans. This raises the question of when in evolution plant COP1 acquired the need for SPA accessory proteins. We addressed this question by generating Physcomitrium Ppcop1 mutants and comparing their visible and molecular phenotypes with those of Physcomitrium Ppspa mutants. The phenotype of Ppcop1 nonuple mutants resembles that of Ppspa mutants. Most importantly, both mutants produce green chloroplasts in complete darkness. They also exhibit dwarfed gametophores, disturbed branching of protonemata and absent gravitropism. RNA‐sequencing analysis indicates that both mutants undergo weak constitutive light signaling in darkness. PpCOP1 and PpSPA proteins form a complex and they interact via their WD repeat domains with the VP motif of the cryptochrome CCE domain in a blue light‐dependent manner. This resembles the interaction of Arabidopsis SPA proteins with Arabidopsis CRY1, and is different from that with Arabidopsis CRY2. Taken together, the data indicate that PpCOP1 and PpSPA act together to regulate growth and development of Physcomitrium. However, in contrast to their Arabidopsis orthologs, PpCOP1 and PpSPA proteins execute only partial suppression of light signaling in darkness. Hence, additional repressors may exist that contribute to the repression of a light response in dark‐exposed Physcomitrium. Significance Statement: During the water‐to‐land transition in evolution, plants had to adapt to drastically altered light conditions. Here, we investigate the mechanisms that placed the increased plant complexity evolving during terrestrialization under the control of ambient light. Moreover, our findings address when in evolution the activity of the ubiquitin ligase COP1 became dependent on the SPA accessory proteins and cryptochrome. [ABSTRACT FROM AUTHOR]

Pyropia haitanensis, one of the most economically and ecologically important seaweed species, is often exposed to persistent or transient low irradiance (LI), resulting in limited yield and quality. However, the mechanisms mediating P. haitanensis responses to LI are largely unknown. In this study, LI-tolerant (LIT) and LI-sensitive (LIS) P. haitanensis strains were compared regarding their physiological and transcriptomic changes induced by 1 and 4 days of LI (5 μmol photons/m2·s). The results indicated that the inhibition of photomorphogenesis and decreases in photosynthesis and photosynthetic carbon fixation as the duration of LI increased are the key reasons for retarded blade growth under LI conditions. A potential self-amplifying loop involving calcium signaling, phosphatidylinositol signaling, reactive oxygen species signaling, and MAPK signaling may be triggered in blades in response to LI stress. These signaling pathways might activate various downstream responses, including improving light energy use, maintaining cell membrane stability, mitigating oxidative damage, to resist LI stress. Additionally, the LIT strain maintained transcriptional homeostasis better than the LIS strain under LI stress. Specifically, photosynthesis and energy production were relatively stable in the LIT strain, which may help to explain why the LIT strain was more tolerant to LI stress than the LIS strain. The findings of this study provide the basis for future investigations on the precise mechanisms underlying the LI stress tolerance of P. haitanensis. [ABSTRACT FROM AUTHOR]

Light-induced changes in miRNAs, morphogenesis, and photosynthetic processes in phytochrome-deficient mutant plants grown under different light qualities were studied. miRNA activity in many processes is regulated by phytochromes and phytochrome-interacting factors (PIFs). The reduced content of photoreceptors in phytochrome mutants affects the PIF-microRNA interaction. In plants grown under red light (RL) and white light (WL), the phenotype of phyb mutant was distorted; however, under blue light (BL) conditions, the phyb phenotype was normalized. The photosynthetic rates of both the mutants and wild type were higher under BL than under RL and WL. The expression of most studied miRNAs increased in phyaphyb mutants under BL conditions, which is probably one of the reasons for the normalization of the phenotype, the increase in PSII activity, and the photosynthetic rate. MicroRNAs under BL can partially improve photosynthesis and phenotype of the mutants, which indicates the conjugation of the functioning of phytochromes in miRNA formation. [ABSTRACT FROM AUTHOR]

Key message: OsiCRY2 is involved in light-regulated plant development and plays a role in regulating photomorphogenesis, plant height, flowering and most strikingly partial photomorphogenesis in dark. Cryptochrome 2 (CRY2), the blue/UV-A light photoreceptor in plants, has been reported to regulate photoperiod-dependent flowering and seedling photomorphogenesis (under low-intensity light). Among monocots, CRY2 has been reported from japonica rice, wheat, sorghum and barley. The two sub-species of rice, indica and japonica, exhibit a high degree of genetic variation and morphological and physiological differences. This article describes the characterization of CRY2 of indica rice (OsiCRY2). While the transcript levels of OsiCRY2 did not change significantly under blue light, its protein levels were found to decline with increased time duration under blue light. For phenotypic characterization, OsiCRY2 over-expression (OX) transgenics were generated in Oryza sativa Pusa Sugandh 2 (PS2) cultivar, a highly scented Basmati cultivar. The OsiCRY2OX transgenics displayed shorter coleoptiles and dwarfism than wild-type under blue light, white, and far-red light. Interestingly, even the dark-grown transgenics were shorter, concomitant with higher OsiCRY2 protein levels in transgenics than wild-type. Histological analysis revealed that the decrease in the length of the seedlings was due to a decrease in the length of the epidermal cells. The fully mature rice transgenics were shorter than the untransformed plants but flowered at the same time as wild-type. However, the OsiCRY2 Arabidopsis over-expressors exhibited early flowering by 10–15 days, indicating the potential and conservation of function of OsiCRY2. The whole-genome transcriptome profiling of rice transgenics revealed the differential up-regulation of several light-regulated genes in dark-grown coleoptiles. These data provide evidence that OsiCRY2 regulates photomorphogenesis, plant height, and flowering in indica rice. [ABSTRACT FROM AUTHOR]

Summary: 14‐3‐3s are highly conserved phosphopeptide‐binding proteins that play important roles in various developmental and signaling pathways in plants. However, although protein phosphorylation has been proven to be a key mechanism for regulating many pivotal components of the light signaling pathway, the role of 14‐3‐3 proteins in photomorphogenesis remains largely obscure. PHYTOCHROME‐INTERACTING FACTOR3 (PIF3) is an extensively studied transcription factor repressing photomorphogenesis, and it is well‐established that upon red (R) light exposure, photo‐activated phytochrome B (phyB) interacts with PIF3 and induces its rapid phosphorylation and degradation. PHOTOREGULATORY PROTEIN KINASES (PPKs), a family of nuclear protein kinases, interact with phyB and PIF3 in R light and mediate multisite phosphorylation of PIF3 in vivo.Here, we report that two members of the 14‐3‐3 protein family, 14‐3‐3λ and κ, bind to a serine residue in the bHLH domain of PIF3 that can be phosphorylated by PPKs, and act as key positive regulators of R light‐induced photomorphogenesis.Moreover, 14‐3‐3λ and κ preferentially interact with photo‐activated phyB and promote the phyB‐PIF3‐PPK complex formation, thereby facilitating phyB‐induced phosphorylation and degradation of PIF3 upon R light exposure.Together, our data demonstrate that 14‐3‐3λ and κ work in close concert with the phyB‐PIF3 module to regulate light signaling in Arabidopsis. [ABSTRACT FROM AUTHOR]

In vitro culturing can generate plants with a distorted morphology. Some distortions affect the plant's survival after transfer to an ex vitro environment, while others can affect the aesthetic value. Therefore, exogenous hormones are often applied in in vitro cultures to modulate plant architecture. In this study, it was hypothesised that regulatory effects of UV-B radiation on plant morphology can be exploited under in vitro conditions, and that UV exposure will result in sturdier, less elongated plants with more branches and smaller leaves, mediated by changes in plant hormones. Plants were grown in tissue-culture containers and exposed to ~0.22 W m−2 UV-B for 8 days. Subsequently, plants were transferred to soil and monitored for a further 7 days. Results show that UV induced a marked change in architecture with a significant increase in axillary branches, and reductions in leaf area, plant height and root weight. These changes were associated with significant alterations in concentrations of hormones, including IAA, GA7, GA3 and iP–9–G. Changes in hormone concentrations suggest a regulatory, rather than a stress response to UV-B. Therefore, it is proposed that the application of UV in in vitro culture can be an innovative approach to manipulate plant architecture. [ABSTRACT FROM AUTHOR]

[Display omitted] • The regulation mechanism of light on mycelial growth was analyzed based on transcriptomics. • Different light conditions can significantly influence the growth stages of fungi, color changes, and levels of secondary metabolites. • The study provided the basis for the optimization of mycelium culture environment. Light is a vital environmental factor that promotes the growth and development of edible fungi mycelium. Under white light, the mycelium color of Sanghuangporus vaninii shifts during its growth stages. To investigate the impact of visible light on mycelial morphogenesis, a comparative transcriptomic analysis was conducted. This analysis revealed the molecular processes that underpin mycelial growth and development in S. vaninii when cultured in both darkness and light conditions. From the analysis, 13,643 genes were aligned using Illumina raw reads. Of these, 596 genes exhibited significant expression changes under white light exposure. Specifically, 226 genes were upregulated and 370 downregulated, spanning 55 different metabolic pathways. We further classified differentially expressed genes (DEGs), these genes play roles in photomorphogenesis, signal transduction, carbohydrate metabolism, and melanin production, among other processes. Some are also implicated in cell cycle regulation and the differential expression of respiratory functions. The validation of the differentially expressed transcripts using qRT-PCR showed complete agreement with RNA-Seq data for 9 transcripts. Meanwhile, the light had an inhibitory effect on the bioactive components in S. vaninii. These findings offer valuable insights into the transcriptional shifts and molecular mechanisms driving the color change in S. vaninii under light exposure, providing a basis for further research into mechanisms of light-response regulation. [ABSTRACT FROM AUTHOR]

This article is a Commentary on Zeng et al. (2023), 239: 1253–1265. [ABSTRACT FROM AUTHOR]

Data on the energy status and activity of pro-/antioxidant metabolism during photomorphogenesis of the rhizome apex of Achillea millefolium L. were obtained. At the photophobic stage of development, etiolated rhizome apices were characterized by increased respiration intensity and energy storage rate: the share of energetically efficient cytochrome respiration was 60%, and the contribution of the alternative respiration pathway (AR) did not exceed 25% of total respiration. The etiolated apices accumulated significant amounts of prooxidants and were characterized by relatively high activity of guaiacol peroxidase and superoxide dismutase, which may be associated with the involvement of components of pro-/antioxidant metabolism in the regulation of growth and differentiation of cells and tissues in the growth cone during underground growth. A significant decrease in the rate of energy storage and an increase in the ability of an energetically low-efficient AR, the share of which was 50% of the total respiratory activity, were found in the apex of the greening sarment at the photophilic stage. The photomorphogenetic transition in the apices of greening sarments showed an increase in pro-/antioxidant metabolism: the concentration of products reacting with thiobarbituric acid (TBA-RS) and H2O2 increased by 25–30%, and the level of antioxidant enzyme activity increased by 24–86%. The photomorphogenetic transition did not lead to the emergence of new isoforms of antioxidant enzymes; however, changes in their activity depending on the phase of shoot development were revealed. The activity of the copper/zinc-containing isoform of superoxide dismutase (Cu/Zn-SOD-2) localized in chloroplasts of young leaves of sarments increased. A decrease in the content of prooxidants in the leaves and an increase in the ability of the cytochrome pathway of respiration were found, which reflects the successful adaptation of underground shoots of A. millefolium to growth in the light. [ABSTRACT FROM AUTHOR]

Summary: Light regulates the subcellular localization of plant photoreceptors, a key step in light signaling. Ultraviolet‐B radiation (UV‐B) induces the plant photoreceptor UV RESISTANCE LOCUS 8 (UVR8) nuclear accumulation, where it regulates photomorphogenesis. However, the molecular mechanism for the UV‐B‐regulated UVR8 nuclear localization dynamics is unknown.With fluorescence recovery after photobleaching (FRAP), cell fractionation followed by immunoblotting and co‐immunoprecipitation (Co‐IP) assays we tested the function of UVR8‐interacting proteins including CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1), REPRESSOR OF UV‐B PHOTOMORPHOGENESIS 1 (RUP1) and RUP2 in the regulation of UVR8 nuclear dynamics in Arabidopsis thaliana.We showed that UV‐B‐induced rapid UVR8 nuclear translocation is independent of COP1, which previously was shown to be required for UV‐B‐induced UVR8 nuclear accumulation. Instead, we provide evidence that the UV‐B‐induced UVR8 homodimer‐to‐monomer photo‐switch and the concurrent size reduction of UVR8 enables its monomer nuclear translocation, most likely via free diffusion. Nuclear COP1 interacts with UV‐B‐activated UVR8 monomer, thereby promoting UVR8 nuclear retention. Conversely, RUP1and RUP2, whose expressions are induced by UV‐B, inhibit UVR8 nuclear retention via attenuating the UVR8–COP1 interaction, allowing UVR8 to exit the nucleus.Collectively, our data suggest that UV‐B‐induced monomerization of UVR8 promotes its nuclear translocation via free diffusion. In the nucleus, COP1 binding promotes UVR8 monomer nuclear retention, which is counterbalanced by the major negative regulators RUP1 and RUP2. [ABSTRACT FROM AUTHOR]

Soybean (Glycine max) responds to ambient light variation by undergoing multiform morphological alterations, influencing its yield potential and stability in the field. Phytochromes (PHYs) are plant-specific red (R) and far-red (FR) light photoreceptors mediating photomorphogenesis and photoperiodic flowering. As an ancient tetraploid, soybean harbors four PHYA, two PHYB, and two PHYE paralogs. Except for GmPHYA2/E4 and GmPHYA3/E3, which have been identified as photoperiod-dependent flowering repressors, the functions of GmPHYs are still largely unclear. We generated a series of individual or combined mutations targeting the GmPHYA or GmPHYB genes using CRISPR/Cas9 technology. Phenotypic analysis revealed that GmPHYB1 mediates predominantly R-light induced photomorphogenesis, whereas GmPHYA2/E4 and GmPHYA3/E3, followed by GmPHYA1 and GmPHYB2, function redundantly and additively in mediating FR light responses in seedling stage. GmPHYA2/E4 and GmPHYA3/E3, with weak influence from GmPHYA1 and GmPHYA4, delay flowering time under natural long-day conditions. This study has demonstrated the diversified functions of GmPHYAs and GmPHYBs in regulating light response, and provides a core set of phytochrome mutant alleles for characterization of their functional mechanisms in regulating agronomic traits of soybean. [ABSTRACT FROM AUTHOR]

A germinating seedling incorporates environmental signals such as light into developmental outputs. Light is not only a source of energy, but also a central coordinative signal in plants. Traditionally, most research focuses on aboveground organs' response to light; therefore, our understanding of photomorphogenesis in roots is relatively scarce. However, root development underground is highly responsive to light signals from the shoot and understanding these signaling mechanisms will give a better insight into early seedling development. Here, we review the central light signaling hubs and their role in root growth promotion of Arabidopsis thaliana seedlings. The early seedling root growth is largely responsive to shoot illumination and the signaling processes leading to photomorphogenesis are functional both in shoots and roots. Developmental and nutritional tradeoffs between shoots and roots are central to organ growth. Tissue-specific responses play a prominent role in light responsive root growth. Long-distance systemic signals coordinate the seedling growth responses to light. [ABSTRACT FROM AUTHOR]

Plant seeds do not contain differentiated chloroplasts. Upon germination, the seedlings thus need to gain photoautotrophy before storage energies are depleted. This requires the coordinated expression of photosynthesis genes encoded in nuclear and plastid genomes. Chloroplast biogenesis needs to be additionally coordinated with the light regulation network that controls seedling development. This coordination is achieved by nucleus to plastid signals called anterograde and plastid to nucleus signals termed retrograde. Retrograde signals sent from plastids during initial chloroplast biogenesis are also called biogenic signals. They have been recognized as highly important for proper chloroplast biogenesis and for seedling development. The molecular nature, transport, targets, and signalling function of biogenic signals are, however, under debate. Several studies disproved the involvement of a number of key components that were at the base of initial models of retrograde signalling. New models now propose major roles for a functional feedback between plastid and cytosolic protein homeostasis in signalling plastid dysfunction as well as the action of dually localized nucleo-plastidic proteins that coordinate chloroplast biogenesis with light-dependent control of seedling development. This review provides a survey of the developments in this research field, summarizes the unsolved questions, highlights several recent advances, and discusses potential new working modes. [ABSTRACT FROM AUTHOR]

The red phytochrome and blue cryptochrome plant photoreceptors play essential roles in promoting genome-wide changes in nuclear and chloroplastic gene expression for photomorphogenesis, plastid development, and greening. While their importance in anterograde signalling has been long recognized, the molecular mechanisms involved remain under active investigation. More recently, the intertwining of the light signalling cascades with the retrograde signals for the optimization of chloroplast functions has been acknowledged. Advances in the field support the participation of phytochromes, cryptochromes, and key light-modulated transcription factors, including HY5 and the PIFs, in the regulation of chloroplastic biochemical pathways that produce retrograde signals, including the tetrapyrroles and the chloroplastic MEP-isoprenoids. Interestingly, in a feedback loop, the photoreceptors and their signalling components are targets themselves of these retrograde signals, aimed at optimizing photomorphogenesis to the status of the chloroplasts, with GUN proteins functioning at the convergence points. High light and shade are also conditions where the photoreceptors tune growth responses to chloroplast functions. Interestingly, photoreceptors and retrograde signals also converge in the modulation of dual-localized proteins (chloroplastic/nuclear) including WHIRLY and HEMERA/pTAC12, whose functions are required for the optimization of photosynthetic activities in changing environments and are proposed to act themselves as retrograde signals. [ABSTRACT FROM AUTHOR]

Light signals perceived by a group of photoreceptors have profound effects on the physiology, growth, and development of plants. The red/far-red light-absorbing phytochromes (phys) modulate these aspects by intricately regulating gene expression at multiple levels. Here, we report the identification and functional characterization of an RNA-binding splicing factor, SWAP1 (SUPPRESSOR-OF-WHITE-APRICOT/SURP RNA-BINDING DOMAIN-CONTAINING PROTEIN1). Loss-of-function swap1-1 mutant is hyposensitive to red light and exhibits a day length-independent early flowering phenotype. SWAP1 physically interacts with two other splicing factors, (SFPS) SPLICING FACTOR FOR PHYTOCHROME SIGNALING and (RRC1) REDUCED RED LIGHT RESPONSES IN CRY1CRY2 BACKGROUND 1 in a light-independent manner and forms a ternary complex. In addition, SWAP 1 physically interacts with photoactivated phyB and colocalizes with nuclear phyB photobodies. Phenotypic analyses show that the swaplsfps, swaplrrcl, and sfpsrrcl double mutants display hypocotyl lengths similar to that of the respective single mutants under red light, suggesting that they function in the same genetic pathway. The swaplsfps double and swaplsfpsrrcl triple mutants display pleiotropic phenotypes, including sterility at the adult stage. Deep RNA sequencing (RNA-seq) analyses show that SWAP1 regulates the gene expression and pre-messenger RNA (mRNA) alternative splicing of a large number of genes, including those involved in plant responses to light signaling. A comparative analysis of alternative splicing among single, double, and triple mutants showed that all three splicing factors coordinately regulate the alternative splicing of a subset of genes. Our study uncovered the function of a splicing factor that modulates light-regulated alternative splicing by interacting with photoactivated phyB and other splicing factors. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Background and Aims Elucidating how plant species respond to variable light conditions is important to understand the ecological adaptation to heterogeneous natural habitats. Plant performance and its underlying gene regulatory network have been well documented in sun-grown plants. However, the phenotypic and molecular responses of shade-grown plants under variable light conditions have remained largely unclear. Methods We assessed the differences in phenotypic performance between Panax ginseng (shade-grown) and Arabidopsis thaliana (sun-grown) under sunlight, shade and deep-shade conditions. To further address the molecular bases underpinning the phenotypic responses, we compared time-course transcriptomic expression profiling and candidate gene structures between the two species. Key Results Our results show that, compared with arabidopsis, ginseng plants not only possess a lower degree of phenotypic plasticity among the three light conditions, but also exhibit higher photosynthetic efficiency under shade and deep-shade conditions. Further comparisons of the gene expression and structure reveal that differential transcriptional regulation together with increased copy number of photosynthesis-related genes (e.g. electron transfer and carbon fixation) may improve the photosynthetic efficiency of ginseng plants under the two shade conditions. In contrast, the inactivation of phytochrome-interacting factors (i.e. absent and no upregulation of the PIF genes) are potentially associated with the observed low degree of phenotypic plasticity of ginseng plants under variable light conditions. Conclusions Our study provides new insights into how shade-grown plants respond to variable light conditions. Candidate genes related to shade adaptation in ginseng provide valuable genetic resources for future molecular breeding of high-density planting crops. [ABSTRACT FROM AUTHOR]

Summary: The plant nucleus provides a major hub for environmental signal integration at the chromatin level. Multiple light signaling pathways operate and exchange information by regulating a large repertoire of gene targets that shape plant responses to a changing environment. In addition to the established role of transcription factors in triggering photoregulated changes in gene expression, there are eminent reports on the significance of chromatin regulators and nuclear scaffold dynamics in promoting light‐induced plant responses. Here, we report and discuss recent advances in chromatin‐regulatory mechanisms modulating plant architecture and development in response to light, including the molecular and physiological roles of key modifications such as DNA, RNA and histone methylation, and/or acetylation. The significance of the formation of biomolecular condensates of key light signaling components is discussed and potential applications to agricultural practices overviewed. [ABSTRACT FROM AUTHOR]

The primary domain/leucine zipper (bZIP) transcription factor, Elongated Hypocotyl (HY5), is crucial for the photomorphogenesis of seedlings. Here, we identified BcHY5 as a regulator of hypocotyl length from the non-heading Chinese cabbage (NHCC) variety 'Suzhouqing', which encoded a protein comprised 164 amino acid residues. Ectopic expression of BcHY5 in Arabidopsis shortens the length of the hypocotyl. Additionally, we discovered a protein called BcBBX24 containing the B-BOX (BBX) domain, which is the interacting partner of BcHY5. Yeast two-hybrid (Y2H), bimolecular fluorescence complementation (BiFC) and GST pull-down assays revealed that BcHY5 interacted with BcBBX24. Additionally, by physically binding to the promoter of BcHY5, BcBBX24 inhibited the transcriptional activity of BcHY5. Therefore, our findings reveal a transcriptional mechanism through which light response occurs in NHCC seedlings, where BcHY5 can interact with BcBBX24 and BcBBX24 can prevent BcHY5 transcription. [ABSTRACT FROM AUTHOR]

The correct development of seeds is a pivotal requirement for species preservation. This process depends on the balance between sensing the environmental stimuli/stressors and hormone-mediated transduction, which results in physiological responses. The red and blue regions of the electromagnetic spectrum are known to influence seed dormancy and germination. Here, we report on the effects induced by the blue (peak at 430 nm) and red (peak at 650 nm) regions of the electromagnetic spectrum on seeds from photo- and skotomorphogenetic capsules developed under white, blue, or red light. Regardless of exposure, seeds from skotomorphogenetic capsules showed an almost absent dormancy in association with altered germination kinetics. Conversely, in seeds from photomorphogenetic capsules, the exposure to the blue region induced skotomorphogenetic-like effects, while the exposure to the whole visible range (350–750 nm), as well as to only the red region, showed a dose-related trend. The observed differences appeared to be dependent on the wavelengths in the red and to be based on transduction mechanisms taking place in fruits. While the molecular bases of this differential effect need to be clarified, the results hint at the role played by different light wavelengths and intensities in seed development and germination. These findings may be relevant for applications in crop production and species safeguarding. [ABSTRACT FROM AUTHOR]

RNA polymerases (RNAPs) are found in all living organisms. In the chloroplasts, the plastid-encoded RNA polymerase (PEP) is a prokaryotic-type multimeric RNAP involved in the selective transcription of the plastid genome. One of its active states requires the assembly of nuclear-encoded PEP-Associated Proteins (PAPs) on the catalytic core, producing a complex of more than 900 kDa, regarded as essential for chloroplast biogenesis. In this study, sequence alignments of the catalytic core subunits across various chloroplasts of the green lineage and prokaryotes combined with structural data show that variations are observed at the surface of the core, whereas internal amino acids associated with the catalytic activity are conserved. A purification procedure compatible with a structural analysis was used to enrich the native PEP from Sinapis alba chloroplasts. A mass spectrometry (MS)-based proteomic analysis revealed the core components, the PAPs and additional proteins, such as FLN2 and pTAC18. MS coupled with crosslinking (XL-MS) provided the initial structural information in the form of protein clusters, highlighting the relative position of some subunits with the surfaces of their interactions. Using negative stain electron microscopy, the PEP three-dimensional envelope was calculated. Particles classification shows that the protrusions are very well-conserved, offering a framework for the future positioning of all the PAPs. Overall, the results show that PEP-associated proteins are firmly and specifically associated with the catalytic core, giving to the plastid transcriptional complex a singular structure compared to other RNAPs. [ABSTRACT FROM AUTHOR]

Arabidopsis CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1) and PHYTOCHROME INTERACTING FACTORs (PIFs) are negative regulators, and ELONGATED HYPOCOTYL5 (HY5) is a positive regulator of seedling photomorphogenic development. Here, we report that SICKLE (SIC), a proline rich protein, acts as a novel negative regulator of photomorphogenesis. HY5 directly binds the SIC promoter and activates SIC expression in response to light. In turn, SIC physically interacts with HY5 and interferes with its transcriptional regulation of downstream target genes. Moreover, SIC interacts with PIF4 and promotes PIF4‐activated transcription of itself. Interestingly, SIC is targeted by COP1 for 26S proteasome‐mediated degradation in the dark. Collectively, our data demonstrate that light‐induced SIC functions as a brake to prevent exaggerated light response via mediating HY5 and PIF4 signaling, and its degradation by COP1 in the dark avoid too strong inhibition on photomorphogenesis at the beginning of light exposure. [ABSTRACT FROM AUTHOR]