HY5: A Pivotal Regulator of Light-Dependent Development in Higher Plants

Physiological and transcriptional analyses of Arabidopsis primary root growth in response to phosphate starvation under light and dark conditions

Plants cope with Pi deficiency by triggering an array of adaptive responses, including the remodeling of root system architecture (RSA). Arabidopsis thaliana grown on a Pi-deficient (-Pi) medium in transparent Petri dishes exhibits an inhibition of primary root (PR) growth. Previous work has shown that direct illumination on roots by blue light is both required and sufficient for the Pi deficiency-induced inhibition of PR growth. However, whether light illumination on shoots of seedlings contributes to the inhibition of PR growth under -Pi condition and whether light signaling pathway is involved in this process remain largely unknown. In addition to Pi deficiency-induced inhibition of PR growth, how light affects the transcriptomic changes under -Pi also remains elusive. Here, we found that the inhibition of PR growth under -Pi condition is determined by light illumination on roots instead of shoots. Further experiments revealed that blue light receptors CRY1/CRY2 and key regulator in blue light signaling pathway HY5 play minor roles in this process. Finally, we evaluated the light effects on the transcriptomic changes during the inhibition of PR growth under -Pi condition. We found that light promotes the expression of many genes involved in stress and phytohormones-related processes and has both upregulated and downregulated effects on the expression of typical phosphate starvation-induced (PSI) genes. Taken together, our work further demonstrates our previous hypothesis that the inhibition of PR growth under -Pi condition is caused by blue light-triggered chemical reactions, rather than blue light signaling pathways. Apart from the inhibition of PR growth under -Pi, light exposure also results in substantial alterations of transcriptome under -Pi condition, encouraging us to carefully evaluate the phenotype under illuminated, transparent Petri dishes.

MpRR-MYB2 and MpRR-MYB5: New players of chloroplast biogenesis

Photosynthesis is an essential biological process that occurs within chloroplasts. Recently, Frangedakis et al. (2024) reported that transcription factors- MpRR-MYB2 and MpRR-MYB5 work along with GLK, and also play a role in chloroplast development. The findings from this research could pave the way for engineering crops with enhanced photosynthetic efficiency.

Regulatory and retrograde signaling networks in the chlorophyll biosynthetic pathway

Plants, algae and photosynthetic bacteria convert light into chemical energy by means of photosynthesis, thus providing food and energy for most organisms on Earth. Photosynthetic pigments, including chlorophylls (Chls) and carotenoids, are essential components that absorb the light energy necessary to drive electron transport in photosynthesis. The biosynthesis of Chl shares several steps in common with the biosynthesis of other tetrapyrroles, including siroheme, heme and phycobilins. Given that many tetrapyrrole precursors possess photo-oxidative properties that are deleterious to macromolecules and can lead to cell death, tetrapyrrole biosynthesis (TBS) requires stringent regulation under various developmental and environmental conditions. Thanks to decades of research on model plants and algae, we now have a deeper understanding of the regulatory mechanisms that underlie Chl synthesis, including (i) the many factors that control the activity and stability of TBS enzymes, (ii) the transcriptional and post-translational regulation of the TBS pathway, and (iii) the complex roles of tetrapyrrole-mediated retrograde signaling from chloroplasts to the cytoplasm and the nucleus. Based on these new findings, Chls and their derivatives will find broad applications in synthetic biology and agriculture in the future.

Functional characterization of CiHY5 in salt tolerance of Chrysanthemum indicum and conserved role of HY5 under stress in chrysanthemum

Among various abiotic stresses, secondary soil salinization poses a significant threat to plant productivity and survival. Cultivated chrysanthemums (Chrysanthemum morifolium), widely grown as ornamental crops, are highly susceptible to salt stress, and their complex polyploid genome complicates the identification of stress resistance genes. In contrast, C. indicum, a native diploid species with robust stress tolerance, serves as a valuable genetic resource for uncovering stress-responsive genes and improving the resilience of ornamental chrysanthemum cultivars. In this study, we cloned, overexpressed (OE-CiHY5), and silenced (RNAi-CiHY5) the CiHY5 gene in C. indicum. OE-CiHY5 plants exhibited larger leaves, sturdier stalks, and higher chlorophyll content compared to wild-type plants, while RNAi-CiHY5 plants displayed weaker growth. Under salt stress, OE-CiHY5 plants demonstrated significantly improved growth, enhanced osmotic adjustment, and effective ROS scavenging. In contrast, RNAi-CiHY5 plants were more sensitive to salinity, showing higher electrolyte leakage and impaired osmotic regulation. Transcriptomic analyses revealed that CiHY5 regulates key hormonal pathways such as zeatin (one of cytokinins), abscisic acid and jasmonic acid, as well as metabolic pathways, including photosynthesis, carbohydrate metabolism, which collectively contribute to the enhanced stress resilience of OE-CiHY5 plants. Promoter-binding assays further confirmed that CiHY5 directly interacts with the CiABF3 promoter, highlighting its critical role in ABA signaling. Evolutionary analyses showed that HY5 is conserved across plant lineages, from early algae to advanced angiosperms, with consistent responsiveness to salt and other abiotic stresses in multiple Chrysanthemum species. These findings establish CiHY5 as a key regulator of salt tolerance in C. indicum, orchestrating a complex network of hormonal and metabolic pathways to mitigate salinity-induced damage. Given the conserved nature of HY5 and its responsiveness to various stresses, HY5 gene provides valuable insights into the molecular mechanisms underlying stress adaptation and represents a promising genetic target for enhancing salt stress resilience in chrysanthemums.

Genome-wide identification and expression analysis of the BBX gene family in Lagerstroemia indica grown under light stress

B-box proteins (BBX) play pivotal roles in the regulation of numerous growth and developmental processes in plants, particularly the light-mediated biosynthesis of pigments. To elucidate the role of BBX transcription factors in the anthocyanin biosynthetic pathway of Lagerstroemia indica leaves, this study identified 41 BBX genes in the L. indica genome. Using bioinformatics approaches, we predicted their structural and functional characteristics and examined the variations in leaf coloration under varying durations of darkness and the expression profiles of BBX genes. The LiBBX genes were categorized into five distinct subfamilies through phylogenetic analysis, with substantial gene expansion due to segmental duplication events. Promoter analysis demonstrated that the BBX family possesses an abundance of light-responsive cis-elements. Using protein interaction prediction followed by qPCR analysis, we identified 17 interacting partners. Notably, the expression levels of the majority of BBX genes in L.indica 'Ebony Embers' were significantly downregulated in the darkness compared to those in the light. Correlation analyses indicated that the expression levels of most BBX genes were positively correlated with both anthocyanin and chlorophyll contents. Ultimately, we discovered a core BBX protein, LiBBX4, which can interact with LiHY5, LiHYH, and LiCOP1, and verified its involvement in regulating anthocyanin synthesis using VIGS. This study for the first time revealed novel insights into the molecular mechanisms underlying light-induced leaf color changes in L.indica, which could provide a fundamental framework for the genetic improvement of L.indica and enhance its commercial appeal.

Ca2+-dependent H2O2 response in roots and leaves of barley - a transcriptomic investigation

BACKGROUND

Ca2+ and H2O2 are second messengers that regulate a wide range of cellular events in response to different environmental and developmental cues. In plants, stress-induced H2O2 has been shown to initiate characteristic Ca2+ signatures; however, a clear picture of the molecular connection between H2O2-induced Ca2+ signals and H2O2-induced cellular responses is missing, particularly in cereal crops such as barley. Here, we employed RNA-seq analyses to identify transcriptome changes in roots and leaves of barley after H2O2 treatment under conditions that inhibited the formation of cytosolic Ca2+ transients. To that end, plasma membrane Ca2+ channels were blocked by LaCl3 application prior to stimulation of barley tissues with H2O2.

RESULTS

We examined the expression patterns of 4246 genes that had previously been shown to be differentially expressed upon H2O2 application. Here, we further compared their expression between H2O2 and LaCl3 + H2O2 treatment. Genes showing expression patterns different to the previous study were considered to be Ca2+-dependent H2O2-responsive genes. These genes, numbering 331 in leaves and 1320 in roots, could be classified in five and four clusters, respectively. Expression patterns of several genes from each cluster were confirmed by RT-qPCR. We furthermore performed a network analysis to identify potential regulatory paths from known Ca2+-related genes to the newly identified Ca2+-dependent H2O2 responsive genes, using the recently described Stress Knowledge Map. This analysis indicated several transcription factors as key points of the responses mediated by the cross-talk between H2O2 and Ca2+.

CONCLUSION

Our study indicates that about 70% of the H2O2-responsive genes in barley roots require a transient increase in cytosolic Ca2+ concentrations for alteration in their transcript abundance, whereas in leaves, the Ca2+ dependency was much lower at about 33%. Targeted gene analysis and pathway modeling identified not only known components of the Ca2+ signaling cascade in plants but also genes that are not yet connected to stimuli-associated signaling. Potential key transcription factors identified in this study can be further analyzed in barley and other crops to ultimately disentangle the underlying mechanisms of H2O2-associated signal transduction mechanisms. This could aid breeding for improved stress resistance to optimize performance and productivity under increasing climate challenges.

Genome-wide screening of mitogen-activated protein kinase (MAPK) gene family and expression profile under heavy metal stress in Solanum lycopersicum

MAPKs are one of the essential signal transduction complexes which are responsible for the perception of abiotic stress and for the producing of related transcripts for responding to abiotic stress. For systematical analyzes of the mitogen-activated protein (MAP) kinase gene families and their expression profiles in Solanum lycopersicum L. exposed to diverse heavy metal stresses, 17 SlMAPK genes were studied in comparison with their 159 orthologs from various plant species. The result of phylogenetic analysis revealed that SlMAPKs were divided into four different subgroups (A, B, C, and D) based on their nucleic acid and protein sequence alignments. SlMAPKs including A, B and C group had lower molecular weights and more hydrophobic structures than D group SlMAPKs, while possible extra phosphorylation sites predicted in D-group SLMAPKs. 24 cis regulating elements such as Box 4, TATA-box, ABRE and CAAT-box were detected in their upstream parts of DNA sequences. Also, it was determined that SlMAPKs show interactions with important proteins such as Guanine nucleotide-binding protein beta subunit, heterotrimeric G-protein, protein phosphatase 2C and HY5. The results from our gene expression analyzes, significant increases were found in the expressions of the selected SLMAPK gene with applications of a range of increasing heavy metal concentrations (e.g., by the application of the 400 mM Ni + Pb exposure, a 16-fold increase in the expression of SlMAPK gene was noted). Overall, SlMAPK genes and proteins known were re-evaluated, and the SlMAPKs interactions with some other important proteins were observed. Also, some predictions about the extra phosphorylation sites of SlMAPKs having effects on their functions were done. In addition, the expression levels of SlMAPK genes were monitored under different levels of heavy metal stress exposures.

Photoreceptor-induced LHL4 protects the photosystem II monomer in Chlamydomonas reinhardtii

Photosynthesis, the fundamental process using light energy to convert carbon dioxide to organic matter, is vital for life on Earth. It relies on capturing light through light-harvesting complexes (LHC) in photosystem I (PSI) and PSII and on the conversion of light energy into chemical energy. Composition and organization of PSI and PSII core complexes are well conserved across evolution. PSII is particularly sensitive to photodamage but benefits from a large diversity of photoprotective mechanisms, finely tuned to handle the dynamic and ever-changing light conditions. Light Harvesting Complex protein family members (LHC and LHC-like families) have acquired a dual function during evolution. Members of the LHC antenna complexes of PS capture light energy, whereas others dissipate excess energy that cannot be harnessed for photosynthesis. This process mainly occurs through nonphotochemical quenching (NPQ). In this work, we focus on the Light Harvesting complex-Like 4 (LHL4) protein, a LHC-like protein induced by ultraviolet-B (UV-B) and blue light through UV Resistance locus 8 (UVR8) and phototropin photoreceptor-activated signaling pathways in the model green microalgae Chlamydomonas reinhardtii. We demonstrate that alongside established NPQ effectors, LHL4 plays a key role in photoprotection, preventing singlet oxygen accumulation in PSII and promoting cell survival upon light stress. LHL4 protective function is distinct from that of NPQ-related proteins, as LHL4 specifically and uniquely binds to the transient monomeric form of the core PSII complex, safeguarding its integrity. LHL4 characterization expands our understanding of the interplay between light harvesting and photoprotection mechanisms upon light stress in photosynthetic microalgae.

ELONGATED HYPOCOTYL 5 promotes root growth by maintaining redox homeostasis and repressing oxidative stress response

Oxidative stress is a major threat to plant growth and survival. To understand how plants cope with oxidative stress, we carried out a genetic screen for Arabidopsis (Arabidopsis thaliana) mutants with altered response to hydrogen peroxide (H2O2) in root growth. Herein, we report the characterization of one of the hypersensitive mutants obtained. This mutant had slightly shorter roots in normal growth medium, and this phenotype became more pronounced in H2O2-containing medium. Through genome-wide resequencing and complementation experiments, we identified the gene with the causal mutation as ELONGATED HYPOCOTYL 5 (HY5). Histochemical staining revealed that the apical meristem of hy5 roots had an elevated level of H2O2 but a lower level of superoxide. In further experiments, we showed that genes involved in redox homeostasis and oxidative response were altered in hy5 roots and that MYB DOMAIN PROTEIN 30 (MYB30), GLUTATHIONE S-TRANSFERASE PHI 2 (GSTF2), and GLUTATHIONE S-TRANSFERASE TAU 19 (GSTU19) are directly repressed by HY5. Interestingly, overexpression of MYB30, a master regulator of the oxidative stress response, exacerbated the root growth defect in hy5, whereas knocking it down by RNAi largely rescued the mutant's hypersensitivity to H2O2 without affecting the content of reactive oxygen species (ROS). Intriguingly, knocking down GSTF2 also rescued the H2O2 hypersensitivity and ROS homeostasis defects in hy5 roots. In addition to H2O2, we showed that hy5 was also hypersensitive to high salinity, Cd, and salicylic acid. Based on these results, we conclude that HY5 plays a positive role in root growth mainly under abiotic stress by modulating both redox homeostasis and oxidative stress response.

Genome-Wide Analysis of bZIP Transcription Factors and Expression Patterns in Response to Salt and Drought Stress in Vaccinium corymbosum

The basic leucine zipper (bZIP) transcription factors play essential roles in multiple stress responses and have been identified and functionally characterized in many plant species. However, the bZIP family members in blueberry are unclear. In this study, we identified 102 VcbZIP genes in Vaccinium corymbosum. VcbZIPs were divided into 10 groups based on phylogenetic analysis, and each group shared similar motifs, domains, and gene structures. Predictions of cis-regulatory elements in the upstream sequences of VcbZIP genes indicated that VcbZIP proteins are likely involved in phytohormone signaling pathways and abiotic stress responses. Analyses of RNA deep sequencing data showed that 18, 13, and 7 VcbZIP genes were differentially expressed in response to salt, drought, and ABA stress, respectively, for the blueberry cultivar Northland. Ten VcbZIP genes responded to both salt and drought stress, indicating that salt and drought have unique and overlapping signals. Of these genes, VcbZIP1-3 are responsive to salt, drought, and abscisic acid treatments, and their encoded proteins may integrate salt, drought, and ABA signaling. Furthermore, VcbZIP1-3 from group A and VcbZIP83-84 and VcbZIP75 from group S exhibited high or low expression under salt or drought stress and might be important regulators for improving drought or salt tolerance. Pearson correlation analyses revealed that VcbZIP transcription factors may regulate stress-responsive genes to improve drought or salt tolerance in a functionally redundant manner. Our study provides a useful reference for functional analyses of VcbZIP genes and for improving salt and drought stress tolerance in blueberry.

Nitrogen availability modulates carotene biosynthesis, chromoplast biogenesis, and cell wall composition in carrot callus

KEY MESSAGE

Carrot callus grown on a medium with increased nitrogen have reduced carotenoid accumulation, changed gene expression, high amount of vesicular plastids and altered cell wall composition. Carotenoid biosynthesis is vital for plant development and quality, yet its regulation under varying nutrient conditions remains unclear. To explore the effects of nitrogen (N) availability, we used carrot (Daucus carota L.) model callus cultures in vitro as a controlled system for studying nutrient-regulated metabolic processes. Two mineral media differing in N content and NO₃⁻/NH₄⁺ ratios were used. Comprehensive analyses, HPLC, transmission electron microscopy, immunochemistry, and RNA sequencing, revealed notable cellular and molecular responses to N treatments. The results demonstrated that N supplementation reduced carotenoid content by 50%, particularly β-carotene and α-carotene. The composition of chromoplast types shifted, with vesicular chromoplasts dominating (55%), followed by a globular type (23%), while in the control callus, globular and crystalline types predominated (57% and 33%, respectively). Immunohistochemistry showed increased presence of high-esterified pectins and arabinogalactan proteins in N-treated cells. Transcriptomic analysis identified 1704 differentially expressed genes (DEGs), including only two in the carotenoid biosynthesis pathway: phytoene synthase 2 (PSY2) and zeaxanthin epoxidase (ZEP). PSY2, which encodes the carotenoid rate-limiting enzyme, showed expression levels that corresponded with reduced carotene content. Other DEGs included 15 involved in nitrogen transport, 1 in nitrogen assimilation, 40 in cell wall biosynthesis and modification, and 9 in phenylpropanoid/flavonoid pathways. N-treated callus exhibited altered expression of MADS-box, NLP, bZIP, and ethylene-responsive transcription factors. These findings reveal how nitrogen availability disrupts carotenoid biosynthesis and triggers extensive chromoplast and cell wall remodeling, providing a cellular framework for understanding nutrient-regulated metabolic shifts.

Utilizing physiologies, transcriptomics, and metabolomics to unravel key genes and metabolites of Salvia miltiorrhiza Bge. seedlings in response to drought stress

Drought stress inhibits Salvia miltiorrhiza Bunge (S. miltiorrhiza) seedling growth and yield. Here, we studied the effects of drought stress on the different parts of S. miltiorrhiza seedlings through physiological, transcriptomic, and metabolomics analyses, and identified key genes and metabolites related to drought tolerance. Physiological analysis showed that drought stress increased the accumulation of hydrogen peroxide (H2O2), enhanced the activity of peroxidase (POD), decreased the activity of catalase (CAT) and the contents of chlorophyll b and total chlorophyll, reduced the degree of photosynthesis, enhanced oxidative damage in S. miltiorrhiza seedlings, and inhibited the growth of S. miltiorrhiza plants. Transcriptome analyses revealed 383 genes encoding transcription factors and 80 genes encoding plant hormones as hypothetical regulators of drought resistance in S. miltiorrhiza plants. Moreover, differentially expressed genes (DEGs) and differentially expressed metabolites (DEMs) are involved in a variety of biological processes, such as proline and glycine betaine metabolism, and biosynthesis of tanshinones and phenolic acids. Additionally, it has barely been reported that the AHL gene family may be involved in regulating the neocryptotanshinone biosynthesis. In conclusion, our results suggest that drought stress inhibits S. miltiorrhiza seedling growth by enhancing membrane lipid peroxidation, attenuating the antioxidant system, photosynthesis, and regulating proline and glycine betaine metabolism, transcription factors and plant hormones, and tanshinones and phenolic acid metabolism pathways. This study provides new insights into the complex mechanisms by which S. miltiorrhiza responds to drought stress.

MsMYB206-MsMYB450-MsHY5 complex regulates alfalfa tolerance to salt stress via regulating flavonoid biosynthesis during the day and night cycles

Flavonoids are the major secondary metabolites participating in many biological processes of plants. Although flavonoid biosynthesis has been extensively studied, its regulatory mechanisms during the day and night cycles remain poorly understood. In this study, three proteins, MsMYB206, MsMYB450, and MsHY5, were found to interact with each other, in which MsMYB206 directly transactivated two flavonoid biosynthetic genes, MsFLS and MsF3'H. The expression patterns of MsMYB206, MsMYB450, MsFLS, and MsF3'H were fully consistent at regular intervals across day/night cycles that were higher at night than in the daytime. On the contrary, both gene expression levels and protein contents of MsHY5 increased in the daytime but decreased at night, and the lower expression of MsHY5 at night led to strengthened interaction between MsMYB206 and MsMYB450. The MsMYB206-overexpression plants were more salt-tolerant and their flavonoid contents were higher than the WT during the day/night cycles. This study revealed one mechanism interpreting the fluctuating flavonoid contents during day/night cycles regulated by the MsMYB206/MsMYB450/MsHY5-MsFLS/MsF3'H module that also contributed to salt tolerance in alfalfa.

Light Spectral-Ranged Specific Metabolisms of Plant Pigments

Chlorophyll is the primary pigment responsible for capturing light energy during photosynthesis, while carotenoids assist in light absorption and provide photoprotection by dissipating excess energy. Both pigments are essential for plant growth and development, playing distinct and complementary roles in maintaining photosynthetic efficiency and protecting plants from oxidative stress. Because of their function in photosynthesis and photoprotection, chlorophyll and carotenoid accumulation are strongly associated with light conditions, especially blue and red lights, which play key roles in regulating their metabolisms. Despite advancements in understanding pigment metabolism, there remains a limited comprehensive overview of how various parts of the light spectrum influence these pathways throughout the entire process. The effects of other spectral ranges of light, such as green light, far-red light, and UV, are not yet fully understood. This review aims to synthesize recent findings about the regulatory network of chlorophyll and carotenoid pathways under different light spectral bands, emphasizing the interplay between light-regulated transcription factors and genes involved in their biosynthesis and degradation.

Cycling Dof Factor 3 mediates light-dependent ascorbate biosynthesis by activating GDP-l-galactose phosphorylase in Rosa roxburghii fruit

Light plays an important role in determining the l-ascorbate (AsA) pool size in plants, primarily through the transcriptional regulation of AsA metabolism-related genes. However, the specific mechanism of transcriptional induction responsible for light-dependent AsA biosynthesis remains unclear. In this study, we used a promoter sequence containing light-responsive motifs from GDP-L-galactose phosphorylase 2 (RrGGP2), a key gene involved in AsA overproduction in Rosa roxburghii fruits, to identify participating transcription factors. Among these factors, Cycling Dof Factor 3 (RrCDF3) was highly responsive to variations in light intensity, quality, and photoperiod, leading to alterations in RrGGP2 expression. Further yeast one-hybrid and dual-luciferase assays confirmed that RrCDF3 acts as a transcriptional activator of RrGGP2 by binding specifically to its promoter. Modulating the expression of RrCDF3 in fruits through transient overexpression and silencing resulted in significant changes in RrGGP2 expression and AsA synthesis. Additionally, the stable overexpression of RrCDF3 in R. roxburghii calli and Solanum lycopersicum plants resulted in a significant increase in AsA content. Notably, the well-known photo-signal transcription factor ELONGATED HYPOCOTYL5 (RrHY5) directly interacted with the RrCDF3 promoter, enhancing its transcription. These findings reveal a special mechanism involving the RrHY5-RrCDF3-RrGGP2 module that mediates light-induced AsA biosynthesis in R. roxburghii fruit.

Spatiotemporal bifurcation of HY5-mediated blue-light signaling regulates wood development during secondary growth

Plants have evolved photoreceptors to optimize their development during primary growth, including germination, hypocotyl elongation, cotyledon opening, and root growth, allowing them to adapt to challenging light conditions. The light signaling transduction pathway during seedling establishment has been extensively studied, but little molecular evidence is available for light-regulated secondary growth, and how light regulates cambium-derived tissue production remains largely unexplored. Here, we show that CRYPTOCHROME (CRY)-dependent blue light signaling and the subsequent attenuation of ELONGATED HYPOCOTYL 5 (HY5) movement to hypocotyls are key inducers of xylem fiber differentiation in Arabidopsis thaliana. Using grafted chimeric plants and hypocotyl-specific transcriptome sequencing of light signaling mutants under controlled light conditions, we demonstrate that the perception of blue light by CRYs in shoots drives secondary cell wall (SCW) deposition at xylem fiber cells during the secondary growth of hypocotyls. We propose that HY5 is a blue light-responsive mobile protein that inhibits xylem fiber formation via direct transcriptional repression of NAC SECONDARY WALL THICKENING PROMOTING 3 (NST3). CRYs retain HY5 in the nucleus, impede its long-distance transport from leaf to hypocotyl, and they initiate NST3-driven SCW gene expression, thereby triggering xylem fiber production. Our findings shed light on the long-range CRYs-HY5-NST3 signaling cascade that shapes xylem fiber development, highlighting the activity of HY5 as a transcriptional repressor during secondary growth.

ELONGATED HYPOCOTYL5-mediated light signaling promotes shoot regeneration in Arabidopsis thaliana

Injured plant somatic tissues regenerate themselves by establishing shoot or root meristems. In Arabidopsis (Arabidopsis thaliana), a two-step culture system ensures regeneration by first promoting the acquisition of pluripotency and subsequently specifying the fate of new meristems. Although previous studies have reported the importance of phytohormones auxin and cytokinin in determining the fate of new meristems, whether and how environmental factors influence this process remains elusive. In this study, we investigated the impact of light signals on shoot regeneration using Arabidopsis hypocotyls as explants. We found that light signals promote shoot regeneration while inhibiting root formation. ELONGATED HYPOCOTYL 5 (HY5), the pivotal transcriptional factor in light signaling, plays a central role in this process by mediating the expression of key genes controlling the fate of new meristems. Specifically, HY5 directly represses root development genes and activates shoot meristem genes, leading to the establishment of shoot progenitor from pluripotent callus. We further demonstrated that the early activation of photosynthesis is critical for shoot initiation, and this is transcriptionally regulated downstream of HY5-dependent pathways. In conclusion, we uncovered the intricate molecular mechanisms by which light signals control the establishment of new meristems through the regulatory network governed by HY5, thus highlighting the influence of light signals on plant developmental plasticity.

Involvement of epigenetic factors in flavonoid accumulation during plant cold adaptation

Plant responses to cold stress include either induction of flavonoid biosynthesis as part of defense responses or initially elevated levels of these substances to mitigate sudden temperature fluctuations. The role of chromatin modifying factors and, in general, epigenetic variability in these processes is not entirely clear. In this work, we review the literature to establish the relationship between flavonoids, cold and chromatin modifications. We demonstrate the relationship between cold acclimation and flavonoid accumulation, and then describe the cold adaptation signaling pathways and their relationship with chromatin modifying factors. Particular attention was paid to the cold signaling module OST1-HOS1-ICE1 and the novel function of the E3 ubiquitin protein ligase HOS1 (a protein involved in chromatin modification during cold stress) in flavonoid regulation.

GIBBERELLIN PERCEPTION SENSOR 2 reveals genesis and role of cellular GA dynamics in light-regulated hypocotyl growth

The phytohormone gibberellic acid (GA) is critical for environmentally sensitive plant development including germination, skotomorphogenesis, and flowering. The Förster resonance energy transfer biosensor GIBBERELLIN PERCEPTION SENSOR1, which permits single-cell GA measurements in vivo, has been used to observe a GA gradient correlated with cell length in dark-grown, but not light-grown, hypocotyls. We sought to understand how light signaling integrates into cellular GA regulation. Here, we show how the E3 ligase CONSTITUTIVE PHOTOMORPHOGENESIS1 (COP1) and transcription factor ELONGATED HYPOCOTYL 5 (HY5) play central roles in directing cellular GA distribution in skoto- and photomorphogenic hypocotyls, respectively. We demonstrate that the expression pattern of the GA biosynthetic enzyme gene GA20ox1 is the key determinant of the GA gradient in dark-grown hypocotyls and is a target of COP1 signaling. We engineered a second generation GPS2 biosensor with improved orthogonality and reversibility. GPS2 revealed a previously undetectable cellular pattern of GA depletion during the transition to growth in the light. This GA depletion partly explains the resetting of hypocotyl growth dynamics during photomorphogenesis. Achieving cell-level resolution has revealed how GA distributions link environmental conditions with morphology and morphological plasticity. The GPS2 biosensor is an ideal tool for GA studies in many conditions, organs, and plant species.

Transcriptomic and Metabolomic Analysis Reveal the Effects of Light Quality on the Growth and Lipid Biosynthesis in Chlorella pyrenoidosa

Light quality has significant effects on the growth and metabolite accumulation of algal cells. However, the related mechanism has not been fully elucidated. This study reveals that both red and blue light can promote the growth and biomass accumulation of Chlorella pyrenoidosa, with the enhancing effect of blue light being more pronounced. Cultivation under blue light reduced the content of total carbohydrate in Chlorella pyrenoidosa, while increasing the content of protein and lipid. Conversely, red light decreased the content of protein and increased the content of carbohydrate and lipid. Blue light induces a shift in carbon flux from carbohydrate to protein, while red light transfers carbon flux from protein to lipid. Transcriptomic and metabolomic analysis indicated that both red and blue light positively regulate lipid synthesis in Chlorella pyrenoidosa, but they exhibited distinct impacts on the fatty acid compositions. These findings suggest that manipulating light qualities can modulate carbon metabolic pathways, potentially converting protein into lipid in Chlorella pyrenoidosa.

Effects of UV-B and UV-C Spectrum Supplementation on the Antioxidant Properties and Photosynthetic Activity of Lettuce Cultivars

Indoor farming systems enable plant production in precisely controlled environments. However, implementing stable growth conditions and the absence of stress stimulants can weaken plants' defense responses and limit the accumulation of bioactive, health-beneficial phytochemicals. A potential solution is the controlled application of stressors, such as supplemental ultraviolet (UV) light. To this end, we analyzed the efficiency of short-term pre-harvest supplementation of the red-green-blue (RGB, LED) spectrum with ultraviolet B (UV-B) or C (UV-C) light to boost phytochemical synthesis. Additionally, given the biological harm of UV radiation due to high-energy photons, we monitored plants' photosynthetic activity during treatment and their morphology as well as sensory attributes after the treatment. Our analyses showed that UV-B radiation did not negatively impact photosynthetic activity while significantly increasing the overall antioxidant potential of lettuce through enhanced levels of secondary metabolites (total phenolics, flavonoids, anthocyanins), carotenoids, and ascorbic acid. On the contrary, UV-C radiation-induced anthocyanin accumulation in the green leaf cultivar significantly harmed the photosynthetic apparatus and limited plant growth. Taken together, we showed that short-term UV-B light supplementation is an efficient method for lettuce biofortification with healthy phytochemicals, while UV-C treatment is not recommended due to the negative impact on the quality (morphology, sensory properties) of the obtained leafy products. These results are crucial for understanding the potential of UV light supplementation for producing functional plants.

Advances in functional studies of plant MYC transcription factors

Myelocytomatosis (MYC) transcription factors (TFs) belong to the basic helix-loop-helix (bHLH) family in plants and play a central role in governing a wide range of physiological processes. These processes encompass plant growth, development, adaptation to biotic and abiotic stresses, as well as secondary metabolism. In recent decades, significant strides have been made in comprehending the multifaceted regulatory functions of MYCs. This advancement has been achieved through the cloning of MYCs and the characterization of plants with MYC deficiencies or overexpression, employing comprehensive genome-wide 'omics' and protein-protein interaction technologies. MYCs act as pivotal components in integrating signals from various phytohormones' transcriptional regulators to orchestrate genome-wide transcriptional reprogramming. In this review, we have compiled current research on the role of MYCs as molecular switches that modulate signal transduction pathways mediated by phytohormones and phytochromes. This comprehensive overview allows us to address lingering questions regarding the interplay of signals in response to environmental cues and developmental shift. It also sheds light on the potential implications for enhancing plant resistance to diverse biotic and abiotic stresses through genetic improvements achieved by plant breeding and synthetic biology efforts.

The AaBBX21-AaHY5 module mediates light-regulated artemisinin biosynthesis in Artemisia annua L

The sesquiterpene lactone artemisinin is an important anti-malarial component produced by the glandular secretory trichomes of sweet wormwood (Artemisia annua L.). Light was previously shown to promote artemisinin production, but the underlying regulatory mechanism remains elusive. In this study, we demonstrate that ELONGATED HYPOCOTYL 5 (HY5), a central transcription factor in the light signaling pathway, cannot promote artemisinin biosynthesis on its own, as the binding of AaHY5 to the promoters of artemisinin biosynthetic genes failed to activate their transcription. Transcriptome analysis and yeast two-hybrid screening revealed the B-box transcription factor AaBBX21 as a potential interactor with AaHY5. AaBBX21 showed a trichome-specific expression pattern. Additionally, the AaBBX21-AaHY5 complex cooperatively activated transcription from the promoters of the downstream genes AaGSW1, AaMYB108, and AaORA, encoding positive regulators of artemisinin biosynthesis. Moreover, AaHY5 and AaBBX21 physically interacted with the A. annua E3 ubiquitin ligase CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1). In the dark, AaCOP1 decreased the accumulation of AaHY5 and AaBBX21 and repressed the activation of genes downstream of the AaHY5-AaBBX21 complex, explaining the enhanced production of artemisinin upon light exposure. Our study provides insights into the central regulatory mechanism by which light governs terpenoid biosynthesis in the plant kingdom.

Organ-specific transcriptional regulation by HFR1 and HY5 in response to shade in Arabidopsis

Light is crucial for plants and serves as a signal for modulating their growth. Under shade, where red to far-red light ratio is low, plants exhibit shade avoidance responses (SAR). LONG HYPOCOTYL IN FAR-RED 1 (HFR1) and ELONGATED HYPOCOTYL 5 (HY5) are known to be negative regulators of SAR and physically interact with one another. However, transcriptional regulatory network underlying SAR by these two transcription factors has not been explored. Here, we performed organ-specific transcriptome analyses of Arabidopsis thaliana hfr1-5, hy5-215 and hfr1hy5 to identify genes that are co-regulated by HFR1 and HY5 in hypocotyls and cotyledons. Genes co-regulated by HFR1 and HY5 were enriched in various processes related to cell wall modification and chlorophyll biosynthesis in hypocotyls. Phytohormone (abscisic acid and jasmonic acid) and light responses were significantly regulated by HFR1 and HY5 in both organs, though it is more prominent under shade in cotyledons. HFR1 and HY5 also differentially regulate the expression of the cell wall-related genes for xyloglucan endotransglucosylase/hydrolase, expansin, arabinogalactan protein and class III peroxidase depending on the organs. Furthermore, HFR1 and HY5 cooperatively regulated hypocotyl responsiveness to shade through auxin metabolism. Together, our study illustrates the importance of the HFR1-HY5 module in regulating organ-specific shade responses in Arabidopsis.

Genomic characterization of bZIP gene family and patterns of gene regulation on Cercospora beticola Sacc resistance in sugar beet (Beta vulgaris L.)

Sugar beet (Beta vulgaris L.) is one of the most important sugar crops, accounting for nearly 30% of the world's annual sugar production. And it is mainly distributed in the northwestern, northern, and northeastern regions of China. However, Cercospora leaf spot (CLS) is the most serious and destructive foliar disease during the cultivation of sugar beet. In plants, the bZIP gene family is one of important family of transcription factors that regulate many biological processes, including cell and tissue differentiation, pathogen defense, light response, and abiotic stress signaling. Although the bZIP gene family has been mentioned in previous studies as playing a crucial role in plant defense against diseases, there has been no comprehensive study or functional analysis of the bZIP gene family in sugar beet with respect to biotic stresses. In this study, we performed a genome-wide analysis of bZIP family genes (BvbZIPs) in sugar beet to investigate their phylogenetic relationships, gene structure and chromosomal localization. At the same time, we observed the stomatal and cell ultrastructure of sugar beet leaf surface during the period of infestation by Cercospora beticola Sacc (C. beticola). And identified the genes with significant differential expression in the bZIP gene family of sugar beet by qRT-PCR. Finally we determined the concentrations of SA and JA and verified the associated genes by qRT-PCR. The results showed that 48 genes were identified and gene expression analysis indicated that 6 BvbZIPs were significantly differential expressed in C. beticola infection. It is speculated that these BvbZIPs are candidate genes for regulating the response of sugar beet to CLS infection. Meanwhile, the observation stomata of sugar beet leaves infected with C. beticola revealed that there were also differences in the surface stomata of the leaves at different periods of infection. In addition, we further confirmed that the protein encoded by the SA signaling pathway-related gene BVRB_9g222570 in high-resistant varieties was PR1, which is closely related to systemic acquired resistance. One of the protein interaction modes of JA signal transduction pathway is the response of MYC2 transcription factor caused by JAZ protein degradation, and there is a molecular interaction between JA signal transduction pathway and auxin. Despite previous reports on abiotic stresses in sugar beet, this study provides very useful information for further research on the role of the sugar beet bZIP gene family in sugar beet through experiments. The above research findings can promote the development of sugar beet disease resistance breeding.

The blue light signaling inhibitor 3-bromo-7-nitroindazole affects gene translation at the initial reception of blue light in young Arabidopsis seedlings

Initial light reception after germination is a dramatic life event when a seedling starts proper morphogenesis. Blue light contains a range of light wavelengths that plants can perceive. A previous report suggested that the chemical compound 3-bromo-7-nitroindazole (3B7N) inhibits blue light-mediated suppression of hypocotyl elongation by physically interacting with the blue light receptor Cryptochrome 1 (CRY1). We previously examined changes of genome-wide gene expression in Arabidopsis seedlings germinated in the dark and then exposed to blue light by RNA-seq and Ribo-seq analyses. The expression of ribosome-related genes was translationally upregulated in response to the initial blue light exposure, depending on signals from both the nucleus and chloroplasts. Here, we re-analyzed our previous data and examined the effect of 3B7N treatment on changes in gene expression upon blue light exposure. The results showed that 3B7N negatively affected translation of ribosome-related genes and, interestingly, the effects were similar to not only those in cry1cry2 mutants but also plants under suppression of photosynthesis. We propose an apparent crosstalk between chloroplast function and blue light signaling.

A birch ELONGATED HYPOCOTYL 5 gene enhances UV-B and drought tolerance

UV-B radiation and drought majorly restrict plant growth, particularly in summer. ELONGATED HYPOCOTYL 5 (HY5), a bZIP transcription factor (TF), has a beneficial impact on photomorphogenesis. However, the sequence of HY5 from Betula platyphylla (BpHY5) has not been identified and the gene functions remain unclarified. We cloned the sequence of BpHY5, which was targeted to the nucleus. The hypocotyl phenotypes of heterologous expression in Arabidopsis thaliana and reverse mutation showed that BpHY5 is homologous to AtHY5. The expression of BpHY5 was increased in response to UV-B radiation, drought conditions, and the presence of abscisic acid (ABA). The overexpression of BpHY5 resulted in increased tolerance to UV-B radiation and drought and decreased ABA sensitivity with higher germination and greening rate, more developmental root system, stronger reactive oxygen species scavenging ability, and lower damage degree. The lignin content under UV-B condition of BpHY5/Col was higher than that of Col. Furthermore, overexpressing BpHY5 up-regulated the expression of genes related to tolerance (NCED3/9, ABI5, DREB2A, RD20, ERF4, NDB2, and APX2). In brief, the study suggests that BpHY5 from birch serves as a beneficial modulator of plant responses to UV-B radiation and drought stress.

ELONGATED HYPOTCOTYL5 and SPINE BASE SIZE1 together mediate light-regulated spine expansion in cucumber

Plant trichome development is influenced by diverse developmental and environmental signals, but the molecular mechanisms involved are not well understood in most plant species. Fruit spines (trichomes) are an important trait in cucumber (Cucumis sativus L.), as they affect both fruit smoothness and commercial quality. Spine Base Size1 (CsSBS1) has been identified as essential for regulating fruit spine size in cucumber. Here, we discovered that CsSBS1 controls a season-dependent phenotype of spine base size in wild-type plants. Decreased light intensity led to reduced expression of CsSBS1 and smaller spine base size in wild-type plants, but not in the mutants with CsSBS1 deletion. Additionally, knockout of CsSBS1 resulted in smaller fruit spine base size and eliminated the light-induced expansion of spines. Overexpression of CsSBS1 increased spine base size and rescued the decrease in spine base size under low light conditions. Further analysis revealed that ELONGATED HYPOTCOTYL5 (HY5), a major transcription factor involved in light signaling pathways, directly binds to the promoter of CsSBS1 and activates its expression. Knockout of CsHY5 led to smaller fruit spine base size and abolished the light-induced expansion of spines. Taken together, our study findings have clarified a CsHY5-CsSBS1 regulatory module that mediates light-regulated spine expansion in cucumber. This finding offers a strategy for cucumber breeders to develop fruit with stable appearance quality under changing light conditions.

Shade responses and resistant mechanisms in Spatholobus suberectus

The medicinal plant Spatholobus suberectus Dunn is easily exposed to shade stress during growth, but its shade responses and shade stress resistant mechanisms have not been clarified. In this study, shade treatments including four attenuated sunlight intensities (100%, 60%, 40%, and 10%) and three shade durations (30 d, 45 d, and 60 d) were applied to S. suberectus. The shade-induced morphological indicators, phytohormonal regulations, metabolic flavonoids contents, transcriptomic flavonoid pathway gene expressions, and stress physiological changes of S. suberectus were analyzed. The putative promoter cis-regulatory elements (CREs) of 18 flavonoid biosynthetic pathway genes were identified. Results showed the stem growth indicators of S. suberectus were better at 40% light intensity. Phytohormones were involved in the shade-induced responses. Short-term shade (30 d) increased total flavonoids, gallated catechins and especially epigallocatechin gallate contents and favored for boosting medicinal value. Long-term shade (45 d, 60 d) tended to decrease flavonoids. The shade-induced flavonoids changes were attributed to their corresponding biosynthesizing genes expression variations. The high antioxidant capacity and the presence of phytohormone-, stress-, and development-related CREs provided the basis for stress resistance. In conclusion, the multiple responses under shade and the CREs analysis elucidated S. suberectus' shade tolerance.

The role of promoter methylation of the genes encoding the enzymes metabolizing di- and tricarboxylic acids in the regulation of plant respiration by light

We discuss the role of epigenetic changes at the level of promoter methylation of the key enzymes of carbon metabolism in the regulation of respiration by light. While the direct regulation of enzymes via modulation of their activity and post-translational modifications is fast and readily reversible, the role of cytosine methylation is important for providing a prolonged response to environmental changes. In addition, adenine methylation can play a role in the regulation of transcription of genes. The mitochondrial and extramitochondrial forms of several enzymes participating in the tricarboxylic acid cycle and associated reactions are regulated via promoter methylation in opposite ways. The mitochondrial forms of citrate synthase, aconitase, fumarase, NAD-malate dehydrogenase are inhibited while the cytosolic forms of aconitase, fumarase, NAD-malate dehydrogenase, and the peroxisomal form of citrate synthase are activated. It is concluded that promoter methylation represents a universal mechanism of the regulation of activity of respiratory enzymes in plant cells by light. The role of the regulation of the mitochondrial and cytosolic forms of respiratory enzymes in the operation of malate and citrate valves and in controlling the redox state and balancing the energy level of photosynthesizing plant cells is discussed.

Light quality-dependent roles of REVEILLE proteins in the circadian system

Several closely related Myb-like activator proteins are known to have partially redundant functions within the plant circadian clock, but their specific roles are not well understood. To clarify the function of the REVEILLE 4, REVEILLE 6, and REVEILLE 8 transcriptional activators, we characterized the growth and clock phenotypes of CRISPR-Cas9-generated single, double, and triple rve mutants. We found that these genes act synergistically to regulate flowering time, redundantly to regulate leaf growth, and antagonistically to regulate hypocotyl elongation. We previously reported that increasing intensities of monochromatic blue and red light have opposite effects on the period of triple rve468 mutants. Here, we further examined light quality-specific phenotypes of rve mutants and report that rve468 mutants lack the blue light-specific increase in expression of some circadian clock genes observed in wild type. To investigate the basis of these blue light-specific circadian phenotypes, we examined RVE protein abundances and degradation rates in blue and red light and found no significant differences between these conditions. We next examined genetic interactions between RVE genes and ZEITLUPE and ELONGATED HYPOCOTYL5, two factors with blue light-specific functions in the clock. We found that the RVEs interact additively with both ZEITLUPE and ELONGATED HYPOCOTYL5 to regulate circadian period, which suggests that neither of these factors are required for the blue light-specific differences that we observed. Overall, our results suggest that the RVEs have separable functions in plant growth and circadian regulation and that they are involved in blue light-specific circadian signaling via a novel mechanism.

Recent advances in unraveling the mystery of combined nutrient stress in plants

Efficiently regulating growth to adapt to varying resource availability is crucial for organisms, including plants. In particular, the acquisition of essential nutrients is vital for plant development, as a shortage of just one nutrient can significantly decrease crop yield. However, plants constantly experience fluctuations in the presence of multiple essential mineral nutrients, leading to combined nutrient stress conditions. Unfortunately, our understanding of how plants perceive and respond to these multiple stresses remains limited. Unlocking this mystery could provide valuable insights and help enhance plant nutrition strategies. This review focuses specifically on the regulation of phosphorous homeostasis in plants, with a primary emphasis on recent studies that have shed light on the intricate interactions between phosphorous and other essential elements, such as nitrogen, iron, and zinc, as well as non-essential elements like aluminum and sodium. By summarizing and consolidating these findings, this review aims to contribute to a better understanding of how plants respond to and cope with combined nutrient stress.

COP1 controls light-dependent chromatin remodeling

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.

Prefoldin Subunits and Its Associate Partners: Conservations and Specificities in Plants

Prefoldins (PFDs) are ubiquitous co-chaperone proteins that originated in archaea during evolution and are present in all eukaryotes, including yeast, mammals, and plants. Typically, prefoldin subunits form hexameric PFD complex (PFDc) that, together with class II chaperonins, mediate the folding of nascent proteins, such as actin and tubulin. In addition to functioning as a co-chaperone in cytoplasm, prefoldin subunits are also localized in the nucleus, which is essential for transcription and post-transcription regulation. However, the specific and critical roles of prefoldins in plants have not been well summarized. In this review, we present an overview of plant prefoldin and its related proteins, summarize the structure of prefoldin/prefoldin-like complex (PFD/PFDLc), and analyze the versatile landscape by prefoldin subunits, from cytoplasm to nucleus regulation. We also focus the specific role of prefoldin-mediated phytohormone response and global plant development. Finally, we overview the emerging prefoldin-like (PFDL) subunits in plants and the novel roles in related processes, and discuss the next direction in further studies.

Cloned genes and genetic regulation of anthocyanin biosynthesis in maize, a comparative review

Anthocyanins are plant-based pigments that are primarily present in berries, grapes, purple yam, purple corn and black rice. The research on fruit corn with a high anthocyanin content is not sufficiently extensive. Considering its crucial role in nutrition and health it is vital to conduct further studies on how anthocyanin accumulates in fruit corn and to explore its potential for edible and medicinal purposes. Anthocyanin biosynthesis plays an important role in maize stems (corn). Several beneficial compounds, particularly cyanidin-3-O-glucoside, perlagonidin-3-O-glucoside, peonidin 3-O-glucoside, and their malonylated derivatives have been identified. C1, C2, Pl1, Pl2, Sh2, ZmCOP1 and ZmHY5 harbored functional alleles that played a role in the biosynthesis of anthocyanins in maize. The Sh2 gene in maize regulates sugar-to-starch conversion, thereby influencing kernel quality and nutritional content. ZmCOP1 and ZmHY5 are key regulatory genes in maize that control light responses and photomorphogenesis. This review concludes the molecular identification of all the genes encoding structural enzymes of the anthocyanin pathway in maize by describing the cloning and characterization of these genes. Our study presents important new understandings of the molecular processes behind the manufacture of anthocyanins in maize, which will contribute to the development of genetically modified variants of the crop with increased color and possible health advantages.

Cooperative transcriptional regulation by ATAF1 and HY5 promotes light-induced cotyledon opening in Arabidopsis thaliana

The opening of the embryonic leaves (cotyledons) as seedlings emerge from the dark soil into the light is crucial to ensure the survival of the plant. Seedlings that sprout in the dark elongate rapidly to reach light but keep their cotyledons closed. During de-etiolation, the transition from dark to light growth, elongation slows and the cotyledons open. Here, we report that the transcription factor ACTIVATING FACTOR1 (ATAF1) participates in de-etiolation and facilitates light-induced cotyledon opening. The transition from dark to light rapidly induced ATAF1 expression and ATAF1 accumulation in cotyledons. Seedlings lacking or overexpressing ATAF1 exhibited reduced or enhanced cotyledon opening, respectively, and transcriptomic analysis indicated that ATAF1 repressed the expression of genes associated with growth and cotyledon closure. The activation of the photoreceptor phytochrome A (phyA) by far-red light induced its association with the ATAF1 promoter and stimulation of ATAF1 expression. The transcription factor ELONGATED HYPOCOTYL5 (HY5), which is also activated in response far-red light, cooperated with phyA to induce ATAF1 expression. ATAF1 and HY5 interacted with one another and cooperatively repressed the expression of growth-promoting and cotyledon closure genes. Together, our study reveals a mechanism through which far-red light promotes cotyledon opening.

Shoot-to-root communication via GmUVR8-GmSTF3 photosignaling and flavonoid biosynthesis fine-tunes soybean nodulation under UV-B light

Legume nodulation requires light perception by plant shoots and precise long-distance communication between shoot and root. Recent studies have revealed that TGACG-motif binding factors (GmSTFs) integrate light signals to promote root nodulation; however, the regulatory mechanisms underlying nodule formation in changing light conditions remain elusive. Here, we applied genetic engineering, metabolite measurement, and transcriptional analysis to study soybean (Glycine max) nodules. We clarify a fine-tuning mechanism in response to ultraviolet B (UV-B) irradiation and rhizobia infection, involving GmUVR8-dependent UV-B perception and GmSTF3/4-GmMYB12-GmCHS-mediated (iso)flavonoid biosynthesis for soybean nodule formation. GmUVR8 receptor-perceived UV-B signal triggered R2R3-MYB transcription factors GmMYB12-dependent flavonoid biosynthesis separately in shoot and root. In shoot, UV-B-triggered flavonoid biosynthesis relied on GmUVR8a, b, c receptor-dependent activation of GmMYB12L-GmCHS8 (chalcone synthase) module. In root, UV-B signaling distinctly promotes the accumulation of the isoflavones, daidzein, and its derivative coumestrol, via GmMYB12B2-GmCHS9 module, resulting in hypernodulation. The mobile transcription factors, GmSTF3/4, bind to cis-regulatory elements in the GmMYB12L, GmMYB12B2, and GmCHS9 promoters, to coordinate UV-B light perception in shoot and (iso)flavonoid biosynthesis in root. Our findings establish a novel shoot-to-root communication module involved in soybean nodulation and reveal an adaptive strategy employed by soybean roots in response to UV-B light.

The transcription factor SbHY5 mediates light to promote aluminum tolerance by activating SbMATE and SbSTOP1s expression

Aluminum (Al) toxicity is a major factor limiting crop yields in acid soils. Sweet sorghum (Sorghum bicolor L.) is a high-efficient energy crop widely grown in tropical and subtropical regions of the world, where acid soil is common and Al toxicity is widespread. Here, we characterized a transcription factor SbHY5 in sweet sorghum, which mediated light to promote plant Al stress adaptation. The expression of SbHY5 was induced by Al stress and increasing light intensity. The overexpression of SbHY5 improved Al tolerance in transgenic plants, which was associated with increased citrate secretion and reduced Al content in roots. Meanwhile, SbHY5 was found to localize to the nucleus and displayed transcriptional activity. SbHY5 directly activated the expression of SbMATE, indicating that a HY5-MATE-dependent citrate secretion pathway is involved in Al tolerance in plants. SbSTOP1 was reported as a key transcription factor, regulating several Al tolerance genes. Here, inspiringly, we found that SbHY5 directly promoted the transcription of SbSTOP1, implying the existence of HY5-STOP1-Al tolerance genes-mediated regulatory pathways. Besides, SbHY5 positively regulated its own transcription. Our findings revealed a novel regulatory network in which a light signaling factor, SbHY5, confers Al tolerance in plants by modulating the expression of Al stress response genes.

An LcMYB111-LcHY5 Module Differentially Activates an LcFLS Promoter in Different Litchi Cultivars

Flavonol synthase (FLS) is the crucial enzyme of the flavonol biosynthetic pathways, and its expression is tightly regulated in plants. In our previous study, two alleles of LcFLS,LcFLS-A and LcFLS-B, have been identified in litchi, with extremely early-maturing (EEM) cultivars only harboring LcFLS-A, while middle-to-late-maturing (MLM) cultivars only harbor LcFLS-B. Here, we overexpressed both LcFLS alleles in tobacco, and transgenic tobacco produced lighter-pink flowers and showed increased flavonol levels while it decreased anthocyanin levels compared to WT. Two allelic promoters of LcFLS were identified, with EEM cultivars only harboring proLcFLS-A, while MLM cultivars only harbor proLcFLS-B. One positive and three negative R2R3-MYB transcription regulators of LcFLS expression were identified, among which only positive regulator LcMYB111 showed a consistent expression pattern with LcFLS, which both have higher expression in EEM than that of MLM cultivars. LcMYB111 were further confirmed to specifically activate proLcFLS-A with MYB-binding element (MBE) while being unable to activate proLcFLS-B with mutated MBE (MBEm). LcHY5 were also identified and can interact with LcMYB111 to promote LcFLS expression. Our study elucidates the function of LcFLS and its differential regulation in different litchi cultivars for the first time.

The Adaptive Role of Carotenoids and Anthocyanins in Solanum lycopersicum Pigment Mutants under High Irradiance

The effects of high-intensity light on the pigment content, photosynthetic rate, and fluorescence parameters of photosystem II in high-pigment tomato mutants (hp 3005) and low-pigment mutants (lp 3617) were investigated. This study also evaluated the dry weight percentage of low molecular weight antioxidant capacity, expression patterns of some photoreceptor-regulated genes, and structural aspects of leaf mesophyll cells. The 3005 mutant displayed increased levels of photosynthetic pigments and anthocyanins, whereas the 3617 mutant demonstrated a heightened content of ultraviolet-absorbing pigments. The photosynthetic rate, photosystem II activity, antioxidant capacity, and carotenoid content were most pronounced in the high-pigment mutant after 72 h exposure to intense light. This mutant also exhibited an increase in leaf thickness and water content when exposed to high-intensity light, suggesting superior physiological adaptability and reduced photoinhibition. Our findings indicate that the enhanced adaptability of the high-pigment mutant might be attributed to increased flavonoid and carotenoid contents, leading to augmented expression of key genes associated with pigment synthesis and light regulation.

PSI Photoinhibition and Changing CO2 Levels Initiate Retrograde Signals to Modify Nuclear Gene Expression

Photosystem I (PSI) is a critical component of the photosynthetic machinery in plants. Under conditions of environmental stress, PSI becomes photoinhibited, leading to a redox imbalance in the chloroplast. PSI photoinhibition is caused by an increase in electron pressure within PSI, which damages the iron-sulfur clusters. In this study, we investigated the susceptibility of PSI to photoinhibition in plants at different concentrations of CO2, followed by global gene expression analyses of the differentially treated plants. PSI photoinhibition was induced using a specific illumination protocol that inhibited PSI with minimal effects on PSII. Unexpectedly, the varying CO2 levels combined with the PSI-PI treatment neither increased nor decreased the likelihood of PSI photodamage. All PSI photoinhibition treatments, independent of CO2 levels, upregulated genes generally involved in plant responses to excess iron and downregulated genes involved in iron deficiency. PSI photoinhibition also induced genes encoding photosynthetic proteins that act as electron acceptors from PSI. We propose that PSI photoinhibition causes a release of iron from damaged iron-sulfur clusters, which initiates a retrograde signal from the chloroplast to the nucleus to modify gene expression. In addition, the deprivation of CO2 from the air initiated a signal that induced flavonoid biosynthesis genes, probably via jasmonate production.

Light regulation of the biosynthesis of phenolics, terpenoids, and alkaloids in plants

Biosynthesis of specialized metabolites (SM), including phenolics, terpenoids, and alkaloids, is stimulated by many environmental factors including light. In recent years, significant progress has been made in understanding the regulatory mechanisms involved in light-stimulated SM biosynthesis at the transcriptional, posttranscriptional, and posttranslational levels of regulation. While several excellent recent reviews have primarily focused on the impacts of general environmental factors, including light, on biosynthesis of an individual class of SM, here we highlight the regulation of three major SM biosynthesis pathways by light-responsive gene expression, microRNA regulation, and posttranslational modification of regulatory proteins. In addition, we present our future perspectives on this topic.

CRISPR-Cas-mediated unfolded protein response control for enhancing plant stress resistance

Plants consistently encounter environmental stresses that negatively affect their growth and development. To mitigate these challenges, plants have developed a range of adaptive strategies, including the unfolded protein response (UPR), which enables them to manage endoplasmic reticulum (ER) stress resulting from various adverse conditions. The CRISPR-Cas system has emerged as a powerful tool for plant biotechnology, with the potential to improve plant tolerance and resistance to biotic and abiotic stresses, as well as enhance crop productivity and quality by targeting specific genes, including those related to the UPR. This review highlights recent advancements in UPR signaling pathways and CRISPR-Cas technology, with a particular focus on the use of CRISPR-Cas in studying plant UPR. We also explore prospective applications of CRISPR-Cas in engineering UPR-related genes for crop improvement. The integration of CRISPR-Cas technology into plant biotechnology holds the promise to revolutionize agriculture by producing crops with enhanced resistance to environmental stresses, increased productivity, and improved quality traits.

Integrating ATAC-seq and RNA-seq to identify differentially expressed genes with chromatin-accessible changes during photosynthetic establishment in Populus leaves

Leaves are the primary photosynthetic organs, providing essential substances for tree growth. It is important to obtain an anatomical understanding and regulatory network analysis of leaf development. Here, we studied leaf development in Populus Nanlin895 along a development gradient from the newly emerged leaf from the shoot apex to the sixth leaf (L1 to L6) using anatomical observations and RNA-seq analysis. It indicated that mesophyll cells possess obvious vascular, palisade, and spongy tissue with distinct intercellular spaces after L3. Additionally, vacuoles fuse while epidermal cells expand to form pavement cells. RNA-seq analysis indicated that genes highly expressed in L1 and L2 were related to cell division and differentiation, while those highly expressed in L3 were enriched in photosynthesis. Therefore, we selected L1 and L3 to integrate ATAC-seq and RNA-seq and identified 735 differentially expressed genes (DEGs) with changes in chromatin accessibility regions within their promoters, of which 87 were transcription factors (TFs), such as ABI3VP1, AP-EREBP, MYB, NAC, and GRF. Motif enrichment analysis revealed potential regulatory functions for the DEGs through upstream TFs including TCP, bZIP, HD-ZIP, Dof, BBR-BPC, and MYB. Overall, our research provides a potential molecular foundation for regulatory network exploration in leaf development during photosynthesis establishment.

Light-mediated anthocyanin biosynthesis in rose petals involves a balanced regulatory module comprising transcription factors RhHY5, RhMYB114a, and RhMYB3b

Roses are significant botanical species with both ornamental and economic value, displaying diverse floral traits, particularly an extensive array of petal colors. The red pigmentation of rose petals is predominantly attributed to anthocyanin accumulation. However, the underlying regulatory mechanism of anthocyanin biosynthesis in roses remains elusive. This study presents a novel light-responsive regulatory module governing anthocyanin biosynthesis in rose petals, which involves the transcription factors RhHY5, RhMYB114a, and RhMYB3b. Under light conditions (1000-1500 μmol m-2 s-1), RhHY5 represses RhMYB3b expression and induces RhMYB114a expression, positively regulating anthocyanin biosynthesis in rose petals. Notably, activation of anthocyanin structural genes probably involves an interaction and synergy between RhHY5 and the MYB114a-bHLH3-WD40 complex. Additionally, RhMYB3b is activated by RhMYB114a to prevent excessive accumulation of anthocyanin. Conversely, under low light conditions (<10 μmol m-2 s-1), the degradation of RhHY5 leads to down-regulation of RhMYB114a and up-regulation of RhMYB3b, which in turn inhibits the expression of both RhMYB114a and anthocyanin structural genes. Additionally, RhMYB3b competes with RhMYB114a for binding to RhbHLH3 and the promoters of anthocyanin-related structural genes. Overall, our study uncovers a complex light-mediated regulatory network that governs anthocyanin biosynthesis in rose petals, providing new insights into the molecular mechanisms underlying petal color formation in rose.

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

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

Light-Induced TaHY5-7A and TaBBX-3B Physically Interact to Promote PURPLE PERICARP-MYB 1 Expression in Purple-Grained Wheat

Purple-grained wheat (Triticum aestivum L.) is an important germplasm source in crop breeding. Anthocyanin biosynthesis in the pericarps of purple-grained wheat is largely light-dependent; however, the regulatory mechanisms underlying light-induced anthocyanin accumulation in the wheat pericarp remain unknown. Here we determined that anthocyanins rapidly accumulate in the pericarps of the purple-grained wheat cultivar Heixiaomai 76 (H76) at 16 days after pollination under light treatment. Using transcriptome sequencing, differential gene expression analysis, and phylogenetic analysis, we identified two key genes involved in light signaling in wheat: ELONGATED HYPOCOTYL 5-7A (TaHY5-7A) and B-BOX-3B (TaBBX-3B). TaHY5-7A and TaBBX-3B were highly expressed in purple-grained wheat pericarps. The heterologous expression of TaHY5-7A partially restored the phenotype of the Arabidopsis (Arabidopsis thaliana) hy5 mutant, resulting in increased anthocyanin accumulation and a shortened hypocotyl. The heterologous expression of TaBBX-3B in wild-type Arabidopsis had similar effects. TaHY5-7A and TaBBX-3B were nucleus-localized, consistent with a function in transcription regulation. However, TaHY5-7A, which lacks a transactivation domain, was not sufficient to activate the expression of PURPLE PERICARP-MYB 1 (TaPpm1), the key anthocyanin biosynthesis regulator in purple pericarps of wheat. TaHY5-7A physically interacted with TaBBX-3B in yeast two-hybrid and bimolecular fluorescence complementation assays. Additionally, TaHY5-7A, together with TaBBX-3B, greatly enhanced the promoter activity of TaPpm1 in a dual luciferase assay. Overall, our results suggest that TaHY5-7A and TaBBX-3B collaboratively activate TaPpm1 expression to promote light-induced anthocyanin biosynthesis in purple-pericarp wheat.

Systems-level proteomics and metabolomics reveals the diel molecular landscape of diverse kale cultivars

Kale is a group of diverse Brassicaceae species that are nutritious leafy greens consumed for their abundance of vitamins and micronutrients. Typified by their curly, serrated and/or wavy leaves, kale varieties have been primarily defined based on their leaf morphology and geographic origin, despite having complex genetic backgrounds. Kale is a very promising crop for vertical farming due to its high nutritional content; however, being a non-model organism, foundational, systems-level analyses of kale are lacking. Previous studies in kale have shown that time-of-day harvesting can affect its nutritional composition. Therefore, to gain a systems-level diel understanding of kale across its wide-ranging and diverse genetic landscape, we selected nine publicly available and commercially grown kale cultivars for growth under near-sunlight LED light conditions ideal for vertical farming. We then analyzed changes in morphology, growth and nutrition using a combination of plant phenotyping, proteomics and metabolomics. As the diel molecular activities of plants drive their daily growth and development, ultimately determining their productivity as a crop, we harvested kale leaf tissue at both end-of-day (ED) and end-of-night (EN) time-points for all molecular analyses. Our results reveal that diel proteome and metabolome signatures divide the selected kale cultivars into two groups defined by their amino acid and sugar content, along with significant proteome differences involving carbon and nitrogen metabolism, mRNA splicing, protein translation and light harvesting. Together, our multi-cultivar, multi-omic analysis provides new insights into the molecular underpinnings of the diel growth and development landscape of kale, advancing our fundamental understanding of this nutritious leafy green super-food for horticulture/vertical farming applications.

The Role of Light Quality in Regulating Early Seedling Development

It is well-established that plants are sessile and photoautotrophic organisms that rely on light throughout their entire life cycle. Light quality (spectral composition) is especially important as it provides energy for photosynthesis and influences signaling pathways that regulate plant development in the complex process of photomorphogenesis. During previous years, significant progress has been made in light quality's physiological and biochemical effects on crops. However, understanding how light quality modulates plant growth and development remains a complex challenge. In this review, we provide an overview of the role of light quality in regulating the early development of plants, encompassing processes such as seed germination, seedling de-etiolation, and seedling establishment. These insights can be harnessed to improve production planning and crop quality by producing high-quality seedlings in plant factories and improving the theoretical framework for modern agriculture.

Integrating Transcriptional, Metabolic, and Physiological Responses to Drought Stress in Ilex paraguariensis Roots

The appearance of water stress episodes triggers leaf abscission and decreases Ilex paraguariensis yield. To explore the mechanisms that allow it to overcome dehydration, we investigated how the root gene expression varied between water-stressed and non-stressed plants and how the modulation of gene expression was linked to metabolite composition and physiological status. After water deprivation, 5160 differentially expressed transcripts were obtained through RNA-seq. The functional enrichment of induced transcripts revealed significant transcriptional remodelling of stress-related perception, signalling, transcription, and metabolism. Simultaneously, the induction of the enzyme 9-cis-expoxycarotenoid dioxygenase (NCED) transcripts reflected the central role of the hormone abscisic acid in this response. Consequently, the total content of amino acids and soluble sugars increased, and that of starch decreased. Likewise, osmotic adjustment and radical growth were significantly promoted to preserve cell membranes and water uptake. This study provides a valuable resource for future research to understand the molecular adaptation of I. paraguariensis plants under drought conditions and facilitates the exploration of drought-tolerant candidate genes.