COR27 and COR28 Are Novel Regulators of the COP1-HY5 Regulatory Hub and Photomorphogenesis in Arabidopsis

Switch on and off: Phospho-events in light signaling pathways

Light is a fundamental environmental cue that dynamically orchestrates plant growth and development through spatiotemporally regulated molecular networks. Among these, phosphorylation, a key post-translational modification, plays a crucial role in controlling the function, stability, subcellular localization, and protein-protein interactions of light signaling components. This review systematically examines phosphorylation-dependent regulatory events within the Arabidopsis light signaling cascade, focusing on its regulatory mechanisms, downstream functional consequences, and crosstalk with other signaling pathways. We underscore the pivotal role of phosphorylation in light signaling transduction, elucidating how the phosphorylation-decoding framework transduces light information into growth and developmental plasticity to modulate plant-environment interactions.

GIGANTEA functions as a co-repressor of cold stress response with a histone-modifying complex

The circadian clock in plants is crucial for regulating stress responses, including cold tolerance. Cold stress induces the expression of C-REPEAT BINDING FACTOR (CBF) transcription factors, which activate COLD-REGULATED (COR) genes to mitigate cold-induced damage. Previously, we identified that HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE15 (HOS15)-HISTONE DEACETYLASE 2C (HD2C) complex regulates cold tolerance by modulating histone deacetylation on the COR genes. Our research reports that the circadian oscillator GIGANTEA (GI) regulates the association of histone deacetylase complex on the COR promoter, controlling cold tolerance. We show that GI functions downstream of HOS15, as the hos15-2 gi-2 double mutant exhibits freezing tolerance and expression of the COR gene like gi-2. Consistent with the HOS15, GI doesn't affect CBF transcription, suggesting that GI involved cold stress responses through HOS15-mediated COR gene regulation. Moreover, GI reduces histone acetylation and CBF binding at the COR15A promoter under cold stress, repressing COR15A gene expression. We further demonstrate that GI forms a co-repressor with HOS15 and HD2C, inhibiting CBF binding and preventing COR gene activation under normal conditions. These findings provide insights into molecular mechanisms by which GI, HOS15, and HD2C coordinate cold stress responses, offering potential strategies for enhancing plant cold tolerance through chromatin-mediated regulation.

The E3 ubiquitin ligase CONSTITUTIVE PHOTOMORPHOGENIC 1 and transcription factors ELONGATED HYPOCOTYL 5 and ROOT HAIR DEFECTIVE6 integrate light signaling and root hair development

Light signaling plays a substantial role in regulating plant development, including the differentiation and elongation of single-celled tissue. However, the identity of the regulatory machine that affects light signaling on root hair cell (RHC) development remains unclear. Here, we investigated how darkness inhibits differentiation and elongation of RHC in Arabidopsis (Arabidopsis thaliana). We found that light promotes the growth and development of RHC. RNA-seq analysis showed that light signaling regulates the differentiation of RHC by promoting the expression of specific genes in the root epidermis associated with cell wall remodeling, jasmonic acid, auxin, and ethylene signaling pathways. Together, these genes integrate light and phytohormone signals with root hair (RH) development. Our investigation also revealed that the core light signal factor ELONGATED HYPOCOTYL 5 (HY5) directly interacts with the key RH development factor ROOT HAIR DEFECTIVE6 (RHD6), which promotes the transcription of RSL4. However, CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) repressed the RHD6 function through the COP1-HY5 complex. Our genetic studies confirm associations between RHD6, HY5, and COP1, indicating that RHD6 largely depends on HY5 for RH development. Ultimately, our work suggests a central COP1-HY5-RHD6 regulatory module that integrates light signaling and RH development with several downstream pathways, offering perspectives to decipher single-celled RH development.

The molecular basis of CONSTITUTIVE PHOTOMORPHOGENIC1 action during photomorphogenesis

CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1), a repressor of seedling photomorphogenesis, is tightly controlled by light. In Arabidopsis, COP1 primarily acts as a part of large E3 ligase complexes and targets key light-signaling factors for ubiquitination and degradation. Upon light perception, the action of COP1 is precisely modulated by active photoreceptors. During seedling development, light plays a predominant role in modulating seedling morphogenesis, including inhibition of hypocotyl elongation, cotyledon opening and expansion, and chloroplast development. These visible morphological changes evidently result from networks of molecular action. In this review, we summarize current knowledge about the molecular role of COP1 in mediating light-controlled seedling development.

Uncovering the molecular mechanisms of Acer fabri in adjusting to low-temperature stress through integrated physiological and transcriptomic analysis

Acer fabri is an excellent color-leaf tree species, with high ornamental value. Low temperatures are known to limit the growth and geographical distribution of A. fabri. The molecular mechanism of A. fabri in response to low-temperature stress was rarely reported. To understand the molecular mechanism of A. fabri in response to low-temperature stress, relevant physiological changes were identified and the transcriptome sequencing was conducted under different stress durations. The results showed that the proline, the soluble sugar (SS) and the soluble protein (SP) content increased in A. fabri leaves under low-temperature stress, while the peroxidase (POD) and activating superoxide dismutase (SOD) activity increased first and then decreased. It was also found by the OPLS-DA analysis that SOD is the most important physiological indicator of A. fabri in response to low-temperature stress. By transcriptome sequencing, a total of 56,732 genes were identified, including 832 transcription factors (TFs). Differentially expressed genes (DEGs) were significantly enriched in metabolic pathways, phytohormone signaling, and plant mitogen-activated protein kinase (MAPK) signaling pathways. Moreover, the analysis of gene co-expression networks, specifically weighted gene co-expression network analysis (WGCNA), indicates that Af0048792 and Af0026061 could be significant in the response to stress from low temperatures. Furthermore, it was observed that NAC (Af0033429) and MIKC (Af0004917) might have interactions with Af0048792, and MIKC (Af0004917) may additionally interact with Af0026061. These findings could enhance our understanding of the molecular mechanisms of A. fabri in response to low-temperature stress.

Histone modification H3K27me3 is essential during chilling-induced flowering in Litchi chinensis

Litchi (Litchi chinensis), a prominent fruit tree in the Sapindaceae, initiates flowering in response to low autumn and winter temperatures. This study investigates the epigenetic regulation of this process, focusing on the marks histone H3 lysine 27 trimethylation (H3K27me3) and its deposition genes during the chilling-induced floral induction (FId) and initiation stages. Our genomic analysis delineated the H3K27me3 deposition landscape across the prefloral induction (PFId), FId, and floral initiation (FIn) stages. We identified 5,635 differentially H3K27me3-modified genes (DHGs) in buds and 4,801 DHGs in leaves. Integration of the RNA-seq and ChIP-seq datasets identified 1,001 differentially regulated genes (DRGs) in buds and 675 DRGs in leaves, offering insights into the genes potentially targeted by H3K27me3. To probe the functional role of H3K27me3, we employed GSK343, a histone H3 lysine methyltransferase inhibitor. Treatment with GSK343 during the chilling-induced flowering process led to reduced H3K27me3 deposition at the TREHALOSE-6-PHOSPHATE SYNTHASE 1 (LcTPS1) and FRIGIDA (LcFRI) loci, resulting in increased gene expression. This manipulation delayed flowering and reduced flowering rates, confirming the pivotal role of H3K27me3 in chilling-induced flowering in litchi. Gene coexpression network analysis identified SHORT VEGETATIVE PHASE 10 (LcSVP10) as a crucial regulator in litchi flowering. Overexpression of LcSVP10 in Arabidopsis thaliana delayed flowering, indicating a conserved function in flowering time control. Our results elucidate the molecular and epigenetic mechanisms that govern FId in litchi and highlight the potential of epigenetic modifications to regulate flowering time in horticultural plants.

The HAT1 transcription factor regulates photomorphogenesis and skotomorphogenesis via phytohormone levels

Plants dynamically modulate their growth and development to acclimate to the fluctuating light environment via a complex phytohormone network. However, the dynamic molecular regulatory mechanisms underlying how plants regulate phytohormones during skotomorphogenesis and photomorphogenesis are largely unknown. Here, we identified a HD-ZIP II transcription factor, HOMEODOMAIN ARABIDOPSIS THALIANA1 (HAT1), as a key node that modulates the dose effects of brassinosteroids (BRs) and auxin on hypocotyl growth during skotomorphogenesis and photomorphogenesis. Compared with the wild-type (Col-0), both HAT1 loss of function and its overexpression led to disrupted photomorphogenic and skotomorphogenic hypocotyl growth. HAT1 overexpression (HAT1OX) plants displayed longer hypocotyls in the light but shorter hypocotyls in darkness, whereas the triple mutant hat1hat2hat3 showed the opposite phenotype. Furthermore, we found that CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) interacted with dephosphorylated HAT1 and facilitated the degradation of HAT1 by ubiquitination in darkness, while HAT1 was phosphorylated and stabilized by BRASSINOSTEROID INSENSITIVE2 (BIN2) in the light. Interestingly, we observed distinct dose-dependent effects of BR and auxin on hypocotyl elongation under varying light conditions and that HAT1 functioned as a key node in this process. The shorter hypocotyl of HAT1OX in darkness was due to the inhibition of BR biosynthetic gene BRASSINOSTEROID-6-OXIDASE2 (BR6OX2) expression to reduce BRs content, while brassinolide (BL) treatment alleviated this growth repression. In the light, HAT1 inhibited BR biosynthesis but enhanced auxin signaling by directly repressing IAA3/SHORT HYPOCOTYL 2 (SHY2) expression. Our findings uncover a dual function of HAT1 in regulating BR biosynthesis and auxin signaling that is crucial for ensuring proper skotomorphogenic and photomorphogenic growth.

SVALKA: A Long Noncoding Cis-Natural Antisense RNA That Plays a Role in the Regulation of the Cold Response of Arabidopsis thaliana

RNA plays important roles in the regulation of gene expression in response to environmental stimuli. SVALKA, a long noncoding cis-natural antisense RNA, is a key component of regulating the response to cold temperature in Arabidopsis thaliana. There are three mechanisms through which SVALKA fine tunes the transcriptional response to cold temperatures. SVALKA regulates the expression of the CBF1 (C-Repeat Dehydration Binding Factor 1) transcription factor through a collisional transcription mechanism and a dsRNA and DICER mediated mechanism. SVALKA also interacts with Polycomb Repressor Complex 2 to regulate the histone methylation of CBF3. Both CBF1 and CBF3 are key components of the COLD REGULATED (COR) regulon that direct the plant's response to cold temperature over time, as well as plant drought adaptation, pathogen responses, and growth regulation. The different isoforms of SVALKA and its potential to form dynamic RNA conformations are important features in regulating a complex gene network in concert with several other noncoding RNA. This review will summarize the three mechanisms through which SVALKA participates in gene regulation, describe the ways that dynamic RNA structures support the function of regulatory noncoding RNA, and explore the potential for improving agricultural genetic engineering with a better understanding of the roles of noncoding RNA.

Mycorrhizal and non-mycorrhizal perennial ryegrass roots exhibit differential regulation of lipid and Ca2+ signaling pathways in response to low and high temperature stresses

Lipids and Ca2+ are involved as intermediate messengers in temperature-sensing signaling pathways. Arbuscular mycorrhizal (AM) symbiosis is a mutualistic symbiosis between fungi and terrestrial plants that helps host plants cope with adverse environmental conditions. Nonetheless, the regulatory mechanisms of lipid- and Ca2+-mediated signaling pathways in mycorrhizal plants under cold and heat stress have not been determined. The present work focused on investigating the lipid- and Ca2+-mediated signaling pathways in arbuscular mycorrhizal (AM) and non-mycorrhizal (NM) roots under temperature stress and determining the role of Ca2+ levels in AM symbiosis and temperature stress tolerance in perennial ryegrass (Lolium perenne L.) Compared with NM plants, AM symbiosis increased phosphatidic acid (PA) and Ca2+ signaling in the roots of perennial ryegrass, increasing the expression of genes associated with low temperature (LT) stress, including LpICE1, LpCBF3, LpCOR27, LpCOR47, LpIRI, and LpAFP, and high temperature (HT) stress, including LpHSFC1b, LpHSFC2b, LpsHSP17.8, LpHSP22, LpHSP70, and LpHSP90, under LT and HT conditions. These effects result in modulated antioxidant enzyme activities, reduced lipid peroxidation, and suppressed growth inhibition caused by LT and HT stresses. Furthermore, exogenous Ca2+ application enhanced AM symbiosis, leading to the upregulation of Ca2+ signaling pathway genes in roots and ultimately promoting the growth of perennial ryegrass under LT and HT stresses. These findings shed light on lipid and Ca2+ signal transduction in AM-associated plants under LT and HT stresses, emphasizing that Ca2+ enhances cold and heat tolerance in mycorrhizal plants.

GhSBI1, a CUP-SHAPED COTYLEDON 2 homologue, modulates branch internode elongation in cotton

Branch length is an important plant architecture trait in cotton (Gossypium) breeding. Development of cultivars with short branch has been proposed as a main object to enhance cotton yield potential, because they are suitable for high planting density. Here, we report the molecular cloning and characterization of a semi-dominant quantitative trait locus, Short Branch Internode 1(GhSBI1), which encodes a NAC transcription factor homologous to CUP-SHAPED COTYLEDON 2 (CUC2) and is regulated by microRNA ghr-miR164. We demonstrate that a point mutation found in sbi1 mutants perturbs ghr-miR164-directed regulation of GhSBI1, resulting in an increased expression level of GhSBI1. The sbi1 mutant was sensitive to exogenous gibberellic acid (GA) treatments. Overexpression of GhSBI1 inhibited branch internode elongation and led to the decreased levels of bioactive GAs. In addition, gene knockout analysis showed that GhSBI1 is required for the maintenance of the boundaries of multiple tissues in cotton. Transcriptome analysis revealed that overexpression of GhSBI1 affects the expression of plant hormone signalling-, axillary meristems initiation-, and abiotic stress response-related genes. GhSBI1 interacted with GAIs, the DELLA repressors of GA signalling. GhSBI1 represses expression of GA signalling- and cell elongation-related genes by directly targeting their promoters. Our work thus provides new insights into the molecular mechanisms for branch length and paves the way for the development of elite cultivars with suitable plant architecture in cotton.

Defining context-dependent m6A RNA methylomes in Arabidopsis

N6-Methyladenosine (m6A) prevalently occurs on cellular RNA across almost all kingdoms of life. It governs RNA fate and is essential for development and stress responses. However, the dynamic, context-dependent m6A methylomes across tissues and in response to various stimuli remain largely unknown in multicellular organisms. Here, we generate a comprehensive census that identifies m6A methylomes in 100 samples during development or following exposure to various external conditions in Arabidopsis thaliana. We demonstrate that m6A is a suitable biomarker to reflect the developmental lineage, and that various stimuli rapidly affect m6A methylomes that constitute the regulatory network required for an effective response to the stimuli. Integrative analyses of the census and its correlation with m6A regulators identify multiple layers of regulation on highly context-dependent m6A modification in response to diverse developmental and environmental stimuli, providing insights into m6A modification dynamics in the myriad contexts of multicellular organisms.

Comparison of four light-response models using relative curvature measures of nonlinearity

Photosynthetic light response curves serve as powerful mathematical tools for quantitatively describing the rate of photosynthesis of plants in response to changes in irradiance. However, in practical applications, the daunting task of selecting an appropriate nonlinear model to accurately fit these curves persists as a significant challenge. Thus, there arises a need for a method to systematically evaluate the efficacy of such models. In the present study, four distinct nonlinear models, namely Exponential Model (EM), Rectangular Hyperbola Model (RHM), Nonrectangular Hyperbola Model (NHM), and Modified Rectangular Hyperbola Model (MRHM), were used to fit the relationship between light intensity and the rate of photosynthesis across 42 empirical datasets. The goodness of fit for each model was assessed using the root-mean-square error, and relative curvature measures of nonlinearity were employed to assess the nonlinear behavior of the models. In terms of goodness of fit, pairwise difference tests of the root-mean-square error revealed that there was little to choose among the four models, although RHM gave a marginally poorer fit. However, in terms of nonlinear behavior, EM not only provided the most favorable linear approximation performance at the global level, but also exhibited the best close-to-linear behavior at the individual parameter level among the four models across the 42 datasets. Consequently, the results strongly advocate for EM as the most suitable mathematical framework for fitting photosynthetic light response curves. These findings provide insights into the model assessment for nonlinear regression in describing the relationship between the photosynthetic rate and light intensity.

Scaling of cotyledon and primary leaf mass versus area in Acer platanoides seedlings under different light conditions

Cotyledons play an important role in early seedling establishment. However, relative to primary leaves, cotyledons tend to have a different investment-on-return strategy. To detect the potential differences in the mass (M) versus area (A) scaling relationships between cotyledons and primary leaves in different light environments, a total of 75 Acer platanoides seedlings were sampled at an open site (n = 52; light availability: 74 ± 5 %) and a shaded site (n = 23; light availability: 4.2 ± 1.2 %). Reduced major axis regression protocols were used to fit the M versus A scaling relationships of primary leaves and cotyledons. The bootstrap percentile method was used to test the significance of the differences in the scaling exponents of M versus A between the two light environments. The scaling exponents of cotyledons at both two sites, as well as the primary leaves at the shade site, were greater than unity indicating 'diminishing returns', while the scaling exponent of primary leaves at the open site was smaller than unity indicating 'increasing returns'. The data collectively indicated light-dependent shifts in support investments and differences in the function of cotyledons and primary leaves. Average leaf structural traits displayed significant differences between the two light environments in accordance with the premium in enhancing photosynthetic capacity in high light and light interception in low light. Although the trait responses to light availability were similar for primary leaves and cotyledons, primary leaves were more responsive to light availability, indicating lower plasticity of cotyledons in response to light levels. These results advance our understanding of the roles of cotyledons and primary leaves in the life history of seedlings in different forest light environments.

Molecular Mechanisms Underlying Freezing Tolerance in Plants: Implications for Cryopreservation

Cryopreservation is a crucial technique for the long-term ex situ conservation of plant genetic resources, particularly in the context of global biodiversity decline. This process entails freezing biological material at ultra-low temperatures using liquid nitrogen, which effectively halts metabolic activities and preserves plant tissues over extended periods. Over the past seven decades, a plethora of techniques for cryopreserving plant materials have been developed. These include slow freezing, vitrification, encapsulation dehydration, encapsulation-vitrification, droplet vitrification, cryo-plates, and cryo-mesh techniques. A key challenge in the advancement of cryopreservation lies in our ability to understand the molecular processes underlying plant freezing tolerance. These mechanisms include cold acclimatization, the activation of cold-responsive genes through pathways such as the ICE-CBF-COR cascade, and the protective roles of transcription factors, non-coding RNAs, and epigenetic modifications. Furthermore, specialized proteins, such as antifreeze proteins (AFPs) and late embryogenesis abundant (LEA) proteins, play crucial roles in protecting plant cells during freezing and thawing. Despite its potential, cryopreservation faces significant challenges, particularly in standardizing protocols for a wide range of plant species, especially those from tropical and subtropical regions. This review highlights the importance of ongoing research and the integration of omics technologies to improve cryopreservation techniques, ensuring their effectiveness across diverse plant species and contributing to global efforts regarding biodiversity conservation.

HY5 and PIF antagonistically regulate HMGR expression and sterol biosynthesis in Arabidopsis thaliana

Secondary metabolites play multiple crucial roles in plants by modulating various regulatory networks. The biosynthesis of these compounds is unique to each species and is intricately controlled by a range of developmental and environmental factors. While light's role in certain secondary metabolites is evident, its impact on sterol biosynthesis remains unclear. Previous studies indicate that ELONGATED HYPOCOTYL5 (HY5), a bZIP transcription factor, is pivotal in skotomorphogenesis to photomorphogenesis transition. Additionally, PHYTOCHROME INTERACTING FACTORs (PIFs), bHLH transcription factors, act as negative regulators. To unveil the light-dependent regulation of the mevalonic acid (MVA) pathway, a precursor for sterol biosynthesis, mutants of light signaling components, specifically hy5-215 and the pifq quadruple mutant (pif 1,3,4, and 5), were analyzed in Arabidopsis thaliana. Gene expression analysis in wild-type and mutants implicates HY5 and PIFs in regulating sterol biosynthesis genes. DNA-protein interaction analysis confirms their interaction with key genes like AtHMGR2 in the rate-limiting pathway. Results strongly suggest HY5 and PIFs' pivotal role in light-dependent MVA pathway regulation, including the sterol biosynthetic branch, in Arabidopsis, highlighting a diverse array of light signaling components finely tuning crucial growth pathways.

Ubiquitin-specific protease UBP14 stabilizes HY5 by deubiquitination to promote photomorphogenesis in Arabidopsis thaliana

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.

Maize ZmSRO1e promotes mesocotyl elongation and deep sowing tolerance by inhibiting the activity of ZmbZIP61

Deep sowing is a traditional method for drought resistance in maize production, and mesocotyl elongation is strongly associated with the ability of maize to germinate from deep soil. However, little is known about the functional genes and mechanisms regulating maize mesocotyl elongation. In the present study, we identified a plant-specific SIMILAR TO RCD-ONE (SRO) protein family member, ZmSRO1e, involved in maize mesocotyl elongation. The expression of ZmSRO1e is strongly inhibited upon transfer from dark to white light. The loss-of-function zmsro1e mutant exhibited a dramatically shorter mesocotyl than the wild-type in both constant light and darkness, while overexpression of ZmSRO1e significantly promoted mesocotyl elongation, indicating that ZmSRO1e positively regulates mesocotyl elongation. We showed that ZmSRO1e physically interacted with ZmbZIP61, an ortholog of Arabidopsis ELONGATED HYPOCOTYL 5 (HY5) and showed a function similar to that of HY5 in regulating photomorphogenesis. We found that ZmSRO1e repressed the transcriptional activity of ZmbZIP61 toward target genes involved in the regulation of cell expansion, such as ZmEXPB4 and ZmEXPB6, by interfering with the binding of ZmbZIP61 to the promoters of target genes. Our results provide a new understanding of the mechanism by which SRO regulates photomorphogenesis and highlight its potential application in deep sowing-resistant breeding.

Arabidopsis thaliana MYC2 and MYC3 Are Involved in Ethylene-Regulated Hypocotyl Growth as Negative Regulators

The ethylene-regulated hypocotyl elongation of Arabidopsis thaliana involves many transcription factors. The specific role of MYC transcription factors in ethylene signal transduction is not completely understood. The results here revealed that two MYCs, MYC2 and MYC3, act as negative regulators in ethylene-suppressed hypocotyl elongation. Etiolated seedlings of the loss-of-function mutant of MYC2 or MYC3 were significantly longer than wild-type seedlings. Single- or double-null mutants of MYC2 and MYC3 displayed remarkably enhanced response to ACC(1-aminocyclopropane-1-carboxylate), the ethylene precursor, compared to wild-type seedlings. MYC2 and MYC3 directly bind to the promoter zone of ERF1, strongly suppressing its expression. Additionally, EIN3, a key component in ethylene signaling, interacts with MYC2 or MYC3 and significantly suppresses their binding to ERF1's promoter. MYC2 and MYC3 play crucial roles in the ethylene-regulated expression of functional genes. The results revealed the novel role and functional mechanism of these transcription factors in ethylene signal transduction. The findings provide valuable information for deepening our understanding of their role in regulating plant growth and responding to stress.

Flowering genes identification, network analysis, and database construction for 837 plants

Flowering is one of the most important biological phenomena in the plant kingdom, which not only has important ecological significance, but also has substantial horticultural ornamental value. In this study, we undertook an exhaustive review of the advancements in our understanding of plant flowering genes. We delved into the identification and conducted comparative analyses of flowering genes across virtually all sequenced angiosperm plant genomes. Furthermore, we established an extensive angiosperm flowering atlas, encompassing a staggering 183 720 genes across eight pathways, along with 10 155 ABCDE mode genes, which play a pivotal role in plant flowering regulation. Through the examination of expression patterns, we unveiled the specificities of these flowering genes. An interaction network between flowering genes of the ABCDE model and their corresponding upstream genes offered a blueprint for comprehending their regulatory mechanisms. Moreover, we predicted the miRNA and target genes linked to the flowering processes of each species. To culminate our efforts, we have built a user-friendly web interface, named the Plant Flowering-time Gene Database (PFGD), accessible at http://pfgd.bio2db.com/. We firmly believe that this database will serve as a cornerstone in the global research community, facilitating the in-depth exploration of flowering genes in the plant kingdom. In summation, this pioneering endeavor represents the first comprehensive collection and comparative analysis of flowering genes in plants, offering valuable resources for the study of plant flowering genetics.

Research progress on the physiological response and molecular mechanism of cold response in plants

Low temperature is a critical environmental stress factor that restricts crop growth and geographical distribution, significantly impacting crop quality and yield. When plants are exposed to low temperatures, a series of changes occur in their external morphology and internal physiological and biochemical metabolism. This article comprehensively reviews the alterations and regulatory mechanisms of physiological and biochemical indices, such as membrane system stability, redox system, fatty acid content, photosynthesis, and osmoregulatory substances, in response to low-temperature stress in plants. Furthermore, we summarize recent research on signal transduction and regulatory pathways, phytohormones, epigenetic modifications, and other molecular mechanisms mediating the response to low temperatures in higher plants. In addition, we outline cultivation practices to improve plant cold resistance and highlight the cold-related genes used in molecular breeding. Last, we discuss future research directions, potential application prospects of plant cold resistance breeding, and recent significant breakthroughs in the research and application of cold resistance mechanisms.

Co-condensation with photoexcited cryptochromes facilitates MAC3A to positively control hypocotyl growth in Arabidopsis

Cryptochromes (CRYs) are blue light receptors that mediate plant photoresponses through regulating gene expressions. We recently reported that Arabidopsis CRY2 could form light-elicited liquid condensates to control RNA methylation. However, whether CRY2 condensation is involved in other gene expression-regulatory processes remains unclear. Here, we show that MOS4-associated complex subunits 3A and 3B (MAC3A/3B) are CRY-interacting proteins and assembled into nuclear CRY condensates. mac3a3b double mutants exhibit hypersensitive photoinhibition of hypocotyl elongation, suggesting that MAC3A/3B positively control hypocotyl growth. We demonstrate the noncanonical activity of MAC3A as a DNA binding protein that modulates transcription. Genome-wide mapping of MAC3A-binding sites reveals that blue light enhances the association of MAC3A with its DNA targets, which requires CRYs. Further evidence indicates that MAC3A and ELONGATED HYPOCOTYL 5 (HY5) occupy overlapping genomic regions and compete for the same targets. These results argue that photocondensation of CRYs fine-tunes light-responsive hypocotyl growth by balancing the opposed effects of HY5 and MAC3A.

COLD REGULATED GENE 27 and 28 Antagonize the Transcriptional Activity of the RVE8/LNK1/LNK2 Circadian Complex

Many molecular and physiological processes in plants occur at a specific time of day. These daily rhythms are coordinated in part by the circadian clock, a timekeeper that uses daylength and temperature to maintain rhythms of approximately 24 hours in various clock-regulated phenotypes. The circadian MYB-like transcription factor REVEILLE 8 (RVE8) interacts with its transcriptional coactivators NIGHT LIGHT INDUCIBLE AND CLOCK REGULATED 1 (LNK1) and LNK2 to promote the expression of evening-phased clock genes and cold tolerance factors. While genetic approaches have commonly been used to discover connections within the clock and between clock elements and other pathways, here we used affinity purification coupled with mass spectrometry to identify time-of-day-specific protein interactors of the RVE8-LNK1/LNK2 complex in Arabidopsis (Arabidopsis thaliana). Among the interactors of RVE8/LNK1/LNK2 were COLD REGULATED GENE 27 (COR27) and COR28, which coprecipitated in an evening-specific manner. In addition to COR27 and COR28, we found an enrichment of temperature-related interactors that led us to establish a previously uncharacterized role for LNK1 and LNK2 in temperature entrainment of the clock. We established that RVE8, LNK1, and either COR27 or COR28 form a tripartite complex in yeast (Saccharomyces cerevisiae) and that the effect of this interaction in planta serves to antagonize transcriptional activation of RVE8 target genes, potentially through mediating RVE8 protein degradation in the evening. Together, these results illustrate how a proteomic approach can be used to identify time-of-day-specific protein interactions. Discovery of the RVE8-LNK-COR protein complex indicates a previously unknown regulatory mechanism for circadian and temperature signaling pathways.

CcNAC1 by Transcriptome Analysis Is Involved in Sudan Grass Secondary Cell Wall Formation as a Positive Regulator

Sudan grass is a high-quality forage of sorghum. The degree of lignification of Sudan grass is the main factor affecting its digestibility in ruminants such as cattle and sheep. Almost all lignocellulose in Sudan grass is stored in the secondary cell wall, but the mechanism and synthesis of the secondary cell wall in Sudan grass is still unclear. In order to study the mechanism of secondary cell wall synthesis in Sudan grass, we used an in vitro induction system of Sudan grass secondary cell wall. Through transcriptome sequencing, it was found that the NAC transcription factor CcNAC1 gene was related to the synthesis of the Sudan grass secondary cell wall. This study further generated CcNAC1 overexpression lines of Arabidopsis to study CcNAC1 gene function in secondary cell wall synthesis. It was shown that the overexpression of the CcNAC1 gene can significantly increase lignin content in Arabidopsis lines. Through subcellular localization analysis, CcNAC1 genes could be expressed in the nucleus of a plant. In addition, we used yeast two-hybrid screening to find 26 proteins interacting with CcNAC1. GO and KEGG analysis showed that CcNAC1 relates to the metabolic pathways and biosynthesis of secondary metabolites. In summary, the synthesis of secondary cell wall of Sudan grass can be regulated by CcNAC1.

Physiology and Molecular Breeding in Sustaining Wheat Grain Setting and Quality under Spring Cold Stress

Spring cold stress (SCS) compromises the reproductive growth of wheat, being a major constraint in achieving high grain yield and quality in winter wheat. To sustain wheat productivity in SCS conditions, breeding cultivars conferring cold tolerance is key. In this review, we examine how grain setting and quality traits are affected by SCS, which may occur at the pre-anthesis stage. We have investigated the physiological and molecular mechanisms involved in floret and spikelet SCS tolerance. It includes the protective enzymes scavenging reactive oxygen species (ROS), hormonal adjustment, and carbohydrate metabolism. Lastly, we explored quantitative trait loci (QTLs) that regulate SCS for identifying candidate genes for breeding. The existing cultivars for SCS tolerance were primarily bred on agronomic and morphophysiological traits and lacked in molecular investigations. Therefore, breeding novel wheat cultivars based on QTLs and associated genes underlying the fundamental resistance mechanism is urgently needed to sustain grain setting and quality under SCS.

The plant circadian clock regulates autophagy rhythm through transcription factor LUX ARRHYTHMO

Autophagy is an evolutionarily conserved degradation pathway in eukaryotes; it plays a critical role in nutritional stress tolerance. The circadian clock is an endogenous timekeeping system that generates biological rhythms to adapt to daily changes in the environment. Accumulating evidence indicates that the circadian clock and autophagy are intimately interwoven in animals. However, the role of the circadian clock in regulating autophagy has been poorly elucidated in plants. Here, we show that autophagy exhibits a robust circadian rhythm in both light/dark cycle (LD) and in constant light (LL) in Arabidopsis. However, autophagy rhythm showed a different pattern with a phase-advance shift and a lower amplitude in LL compared to LD. Moreover, mutation of the transcription factor LUX ARRHYTHMO (LUX) removed autophagy rhythm in LL and led to an enhanced amplitude in LD. LUX represses expression of the core autophagy genes ATG2, ATG8a, and ATG11 by directly binding to their promoters. Phenotypic analysis revealed that LUX is responsible for improved resistance of plants to carbon starvation, which is dependent on moderate autophagy activity. Comprehensive transcriptomic analysis revealed that the autophagy rhythm is ubiquitous in plants. Taken together, our findings demonstrate that the LUX-mediated circadian clock regulates plant autophagy rhythms.

Circadian entrainment in Arabidopsis

Circadian clocks coordinate physiology and development as an adaption to the oscillating day/night cycle caused by the rotation of Earth on its axis and the changing length of day and night away from the equator caused by orbiting the sun. Circadian clocks confer advantages by entraining to rhythmic environmental cycles to ensure that internal events within the plant occur at the correct time with respect to the cyclic external environment. Advances in determining the structure of circadian oscillators and the pathways that allow them to respond to light, temperature, and metabolic signals have begun to provide a mechanistic insight to the process of entrainment in Arabidopsis (Arabidopsis thaliana). We describe the concepts of entrainment and how it occurs. It is likely that a thorough mechanistic understanding of the genetic and physiological basis of circadian entrainment will provide opportunities for crop improvement.

Negative effects of poly(butylene adipate-co-terephthalate) microplastics on Arabidopsis and its root-associated microbiome

The degradable plastic poly(butylene adipate-co-terephthalate) (PBAT) is considered a potential replacement for low-density polyethylene (LDPE) as the main component of mulch film. However, it is not clear whether PBAT is harmful to the plant-soil system. Thus, we determined the effects of LDPE microplastics (LDPE-MPs) and PBAT microplastics (PBAT-MPs) on the growth of Arabidopsis. The inhibitory effect of PBAT-MPs was greater than that of LDPE-MPs on the growth of Arabidopsis. Transcriptome analysis showed that PBAT-MPs severely disrupted the photosynthetic system of Arabidopsis and increased the expression levels of genes in drug transport-related pathways. PBAT-MPs increased the relative abundances of Bradyrhizobium, Hydrogenophaga, and Arthrobacter in the bulk soil and rhizosphere soil. The abundances of Variovorax, Flavobacterium, and Microbacterium increased in the plant root zone only under PBAT-MPs. Functional prediction analysis suggested that microorganisms in the soil and plant root zone could degrade xenobiotics. Furthermore, the degradation products from PBAT comprising adipic acid, terephthalic acid, and butanediol were more toxic than PBAT-MPs. Our findings demonstrate that PBAT-MPs may be degraded by microorganisms to produce chemicals that are highly toxic to plants. Thus, biodegradable plastics may pose a great risk to the environment.

Transcriptional regulatory network of plant cold-stress responses

Recent studies have revealed the complex and flexible transcriptional regulatory network involved in cold-stress responses. Focusing on two major signaling pathways that respond to cold stress, we outline current knowledge of the transcriptional regulatory network and the post-translational regulation of transcription factors in the network. Cold-stress signaling pathways are closely associated with other signaling pathways such as those related to the circadian clock, and large amounts of data on their crosstalk and tradeoffs are available. However, it remains unknown how plants sense and transmit cold-stress signals to regulate gene expression. We discuss recent reports on cold-stress sensing and associated signaling pathways that regulate the network. We also emphasize future directions for developing abiotic stress-tolerant crop plants.

SICKLE represses photomorphogenic development of Arabidopsis seedlings via HY5- and PIF4-mediated signaling

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.

PIFs- and COP1-HY5-mediated temperature signaling in higher plants

Plants have to cope with the surrounding changing environmental stimuli to optimize their physiological and developmental response throughout their entire life cycle. Light and temperature are two critical environmental cues that fluctuate greatly during day-night cycles and seasonal changes. These two external signals coordinately control the plant growth and development. Distinct spectrum of light signals are perceived by a group of wavelength-specific photoreceptors in plants. PIFs and COP1-HY5 are two predominant signaling hubs that control the expression of a large number of light-responsive genes and subsequent light-mediated development in plants. In parallel, plants also transmit low or warm temperature signals to these two regulatory modules that precisely modulate the responsiveness of low or warm temperatures. The core component of circadian clock ELF3 integrates signals from light and warm temperatures to regulate physiological and developmental processes in plants. In this review, we summarize and discuss recent advances and progresses on PIFs-, COP1-HY5- and ELF3-mediated light, low or warm temperature signaling, and highlight emerging insights regarding the interactions between light and low or warm temperature signal transduction pathways in the control of plant growth.

Activation and negative feedback regulation of SlHY5 transcription by the SlBBX20/21-SlHY5 transcription factor module in UV-B signaling

In tomato (Solanum lycopersicum) and other plants, the photoreceptor UV-RESISTANCE LOCUS 8 regulates plant UV-B photomorphogenesis by modulating the transcription of many genes, the majority of which depends on the transcription factor ELONGATED HYPOCOTYL 5 (HY5). HY5 transcription is induced and then rapidly attenuated by UV-B. However, neither the transcription factors that activate HY5 transcription nor the mechanism for its attenuation during UV-B signaling is known. Here, we report that the tomato B-BOX (BBX) transcription factors SlBBX20 and SlBBX21 interact with SlHY5 and bind to the SlHY5 promoter to activate its transcription. UV-B-induced SlHY5 expression and SlHY5-controlled UV-B responses are normal in slbbx20 and slbbx21 single mutants, but strongly compromised in the slbbx20 slbbx21 double mutant. Surprisingly, UV-B responses are also compromised in lines overexpressing SlBBX20 or SlBBX21. Both SlHY5 and SlBBX20 bind to G-box1 in the SlHY5 promoter. SlHY5 outcompetes SlBBX20 for binding to the SlHY5 promoter in vitro, and inhibits the association of SlBBX20 with the SlHY5 promoter in vivo. Overexpressing 35S:SlHY5-FLAG in the WT background inhibits UV-B-induced endogenous SlHY5 expression. Together, our results reveal the critical role of the SlBBX20/21-SlHY5 module in activating the expression of SlHY5, the gene product of which inhibits its own gene transcription under UV-B, forming an autoregulatory negative feedback loop that balances SlHY5 transcription in plants.

The bud dormancy disconnect: latent buds of grapevine are dormant during summer despite a high metabolic rate

Grapevine (Vitis vinifera L.) displays wide plasticity to climate; however, the physiology of dormancy along a seasonal continuum is poorly understood. Here we investigated the apparent disconnect between dormancy and the underlying respiratory physiology and transcriptome of grapevine buds, from bud set in summer to bud burst in spring. The establishment of dormancy in summer was pronounced and reproducible; however, this was coupled with little or no change in physiology, indicated by respiration, hydration, and tissue oxygen tension. The release of dormancy was biphasic; the depth of dormancy declined substantially by mid-autumn, while the subsequent decline towards spring was moderate. Observed changes in physiology failed to explain the first phase of dormancy decline, in particular. Transcriptome data contrasting development from summer through to spring also indicated that dormancy was poorly reflected by metabolic quiescence during summer and autumn. Gene Ontology and enrichment data revealed the prevailing influence of abscisic acid (ABA)-related gene expression during the transition from summer to autumn, and promoter motif analysis suggested that photoperiod may play an important role in regulating ABA functions during the establishment of dormancy. Transcriptomic data from later transitions reinforced the importance of oxidation and hypoxia as physiological cues to regulate the maintenance of quiescence and resumption of growth. Collectively these data reveal a novel disconnect between growth and metabolic quiescence in grapevine following bud set, which requires further experimentation to explain the phenology and dormancy relationships.

How plants coordinate their development in response to light and temperature signals

Light and temperature change constantly under natural conditions and profoundly affect plant growth and development. Light and warmer temperatures promote flowering, higher light intensity inhibits hypocotyl and petiole elongation, and warmer temperatures promote hypocotyl and petiole elongation. Moreover, exogenous light and temperature signals must be integrated with endogenous signals to fine-tune phytohormone metabolism and plant morphology. Plants perceive and respond to light and ambient temperature using common sets of factors, such as photoreceptors and multiple light signal transduction components. These highly structured signaling networks are critical for plant survival and adaptation. This review discusses how plants respond to variable light and temperature conditions using common elements to coordinate their development. Future directions for research on light and temperature signaling pathways are also discussed.

ICE-CBF-COR Signaling Cascade and Its Regulation in Plants Responding to Cold Stress

Cold stress limits plant geographical distribution and influences plant growth, development, and yields. Plants as sessile organisms have evolved complex biochemical and physiological mechanisms to adapt to cold stress. These mechanisms are regulated by a series of transcription factors and proteins for efficient cold stress acclimation. It has been established that the ICE-CBF-COR signaling pathway in plants regulates how plants acclimatize to cold stress. Cold stress is perceived by receptor proteins, triggering signal transduction, and Inducer of CBF Expression (ICE) genes are activated and regulated, consequently upregulating the transcription and expression of the C-repeat Binding Factor (CBF) genes. The CBF protein binds to the C-repeat/Dehydration Responsive Element (CRT/DRE), a homeopathic element of the Cold Regulated genes (COR gene) promoter, activating their transcription. Transcriptional regulations and post-translational modifications regulate and modify these entities at different response levels by altering their expression or activities in the signaling cascade. These activities then lead to efficient cold stress tolerance. This paper contains a concise summary of the ICE-CBF-COR pathway elucidating on the cross interconnections with other repressors, inhibitors, and activators to induce cold stress acclimation in plants.

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

ELONGATED HYPOCOTYL5 (HY5), a bZIP-type transcription factor, acts as a master regulator that regulates various physiological and biological processes in plants such as photomorphogenesis, root growth, flavonoid biosynthesis and accumulation, nutrient acquisition, and response to abiotic stresses. HY5 is evolutionally conserved in function among various plant species. HY5 acts as a master regulator of light-mediated transcriptional regulatory hub that directly or indirectly controls the transcription of approximately one-third of genes at the whole genome level. The transcription, protein abundance, and activity of HY5 are tightly modulated by a variety of factors through distinct regulatory mechanisms. This review primarily summarizes recent advances on HY5-mediated molecular and physiological processes and regulatory mechanisms on HY5 in the model plant Arabidopsis as well as in crops.

Light-Response Bric-A-Brack/Tramtrack/Broad proteins mediate cryptochrome 2 degradation in response to low ambient temperature

Cryptochromes (crys) are photolyase-like blue-light receptors first discovered in Arabidopsis thaliana and later identified in all major evolutionary lineages. Crys are involved in not only blue light responses but also in temperature responses; however, whether and how cry protein stability is regulated by temperature remains unknown. Here, we show that cry2 protein abundance is modulated by ambient temperature and cry2 protein is degraded under low ambient temperature via the 26S proteasome. Consistent with this, cry2 shows high levels of ubiquitination under low ambient temperatures. Interestingly, cry2 degradation at low ambient temperatures occurs only under blue light and not under red light or dark conditions, indicating blue-light-dependent degradation of cry2 at low ambient temperature. Furthermore, low ambient temperature promotes physical interaction of Light-Response Bric-a-Brack/Tramtrack/Broad (LRB) proteins with cry2 to modulate its ubiquitination and protein stability in response to ambient temperature. LRBs promote high-temperature-induced hypocotyl elongation by modulating the protein stability of cry2 protein. These results indicate that cry2 accumulation is regulated by not only blue light but also ambient temperature, and LRBs are responsible for cry2 degradation at low ambient temperature. The stabilization of cry2 by high temperature makes cry2 a better negative regulator of temperature responses.

PIF4: Integrator of light and temperature cues in plant growth

Plants are sessile and lack behavioural responses to avoid extreme environmental changes linked to annual seasons. For survival, they have evolved elaborate sensory systems coordinating their architecture and physiology with fluctuating diurnal and seasonal temperatures. PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) was initially identified as a key component of the Arabidopsis thaliana phytochrome signalling pathway. It was then identified as playing a central role in promoting plant hypocotyl growth via the activation of auxin synthesis and signalling-related genes. Recent studies expanded its known regulatory functions to thermomorphogenesis and defined PIF4 as a central molecular hub for the integration of environmental light and temperature cues. The present review comprehensively summarizes recent progress in our understanding of PIF4 function in Arabidopsis thaliana, including PIF4-mediated photomorphogenesis and thermomorphogenesis, and the contribution of PIF4 to plant growth via the integration of environmental light and temperature cues. Remaining questions and possible directions for future research on PIF4 are also discussed.

How plants protect themselves from ultraviolet-B radiation stress

Ultraviolet-B (UV-B) radiation has a wavelength range of 280-315 nm. Plants perceive UV-B as an environmental signal and a potential abiotic stress factor that affects development and acclimation. UV-B regulates photomorphogenesis including hypocotyl elongation inhibition, cotyledon expansion, and flavonoid accumulation, but high intensity UV-B can also harm plants by damaging DNA, triggering accumulation of reactive oxygen species, and impairing photosynthesis. Plants have evolved "sunscreen" flavonoids that accumulate under UV-B stress to prevent or limit damage. The UV-B receptor UV RESISTANCE LOCUS 8 (UVR8) plays a critical role in promoting flavonoid biosynthesis to enhance UV-B stress tolerance. Recent studies have clarified several UVR8-mediated and UVR8-independent pathways that regulate UV-B stress tolerance. Here, we review these additions to our understanding of the molecular pathways involved in UV-B stress tolerance, highlighting the important roles of ELONGATED HYPOCOTYL 5, BRI1-EMS-SUPPRESSOR1, MYB DOMAIN PROTEIN 13, MAP KINASE PHOSPHATASE 1, and ATM- and RAD3-RELATED. We also summarize the known interactions with visible light receptors and the contribution of melatonin to UV-B stress responses. Finally, we update a working model of the UV-B stress tolerance pathway.

Calmodulin7: recent insights into emerging roles in plant development and stress

Analyses of the function of Arabidopsis Calmodulin7 (CAM7) in concert with multiple regulatory proteins involved in various signal transduction processes. Calmodulin (CaM) plays various regulatory roles in multiple signaling pathways in eukaryotes. Arabidopsis CALMODULIN 7 (CAM7) is a unique member of the CAM family that works as a transcription factor in light signaling pathways. CAM7 works in concert with CONSTITUTIVE PHOTOMORPHOGENIC 1 and ELONGATED HYPOCOTYL 5, and plays an important role in seedling development. Further, it is involved in the regulation of the activity of various Ca²⁺-gated channels such as cyclic nucleotide gated channel 6 (CNGC6), CNGC14 and auto-inhibited Ca²⁺ ATPase 8. Recent studies further indicate that CAM7 is also an integral part of multiple signaling pathways including hormone, immunity and stress. Here, we review the recent advances in understanding the multifaceted role of CAM7. We highlight the open-ended questions, and also discuss the diverse aspects of CAM7 characterization that need to be addressed for comprehensive understanding of its cellular functions.

HY5 regulates light-responsive transcription of microRNA163 to promote primary root elongation in Arabidopsis seedlings

MicroRNAs (miRNAs) play key roles in the post-transcriptional regulation of gene expression in plants. Many miRNAs are responsive to environmental signals. Light is the first environmental signal perceived by plants after emergence from the soil. However, less is known about the roles and regulatory mechanism of miRNAs in response to light signal. Here, using small RNA sequencing, we determined that miR163 is significantly rapidly induced by light signaling in Arabidopsis thaliana seedlings. The light-inducible response of miR163 functions genetically downstream of LONG HYPOCOTYL 5 (HY5), a central positive regulator of photomorphogenesis. HY5 directly binds to the two G/C-hybrid elements in the miR163 promoter with unequal affinity; one of these elements, which is located next to the transcription start site, plays a major role in light-induced expression of miR163. Overexpression of miR163 rescued the defective primary root elongation of hy5 seedlings without affecting lateral root growth, whereas overexpressing of miR163 target PXMT1 inhibited primary root elongation. These findings provide insight into understanding the post-transcriptional regulation of root photomorphogenesis mediated by the HY5-miR163-PXMT1 network.

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

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

Supplementary Information

The online version contains supplementary material available at 10.1007/s42994-021-00037-2.

The E3 ligase MREL57 modulates microtubule stability and stomatal closure in response to ABA

Regulation of stomatal movement is critical for plant adaptation to environmental stresses. The microtubule cytoskeleton undergoes disassembly, which is critical for stomatal closure in response to abscisic acid (ABA). However, the mechanism underlying this regulation largely remains unclear. Here we show that a ubiquitin-26S proteasome (UPS)-dependent pathway mediates microtubule disassembly and is required for ABA-induced stomatal closure. Moreover, we identify and characterize the ubiquitin E3 ligase MREL57 (MICROTUBULE-RELATED E3 LIGASE57) and the microtubule-stabilizing protein WDL7 (WAVE-DAMPENED2-LIKE7) in Arabidopsis and show that the MREL57-WDL7 module regulates microtubule disassembly to mediate stomatal closure in response to drought stress and ABA treatment. MREL57 interacts with, ubiquitinates and degrades WDL7, and this effect is clearly enhanced by ABA. ABA-induced stomatal closure and microtubule disassembly are significantly suppressed in mrel57 mutants, and these phenotypes can be restored when WDL7 expression is decreased. Our results unravel UPS-dependent mechanisms and the role of an MREL57-WDL7 module in microtubule disassembly and stomatal closure in response to drought stress and ABA.

Illuminating the COP1/SPA Ubiquitin Ligase: Fresh Insights Into Its Structure and Functions During Plant Photomorphogenesis

CONSTITUTIVE PHOTOMORPHOGENIC 1 functions as an E3 ubiquitin ligase in plants and animals. Discovered originally in Arabidopsis thaliana, COP1 acts in a complex with SPA proteins as a central repressor of light-mediated responses in plants. By ubiquitinating and promoting the degradation of several substrates, COP1/SPA regulates many aspects of plant growth, development and metabolism. In contrast to plants, human COP1 acts as a crucial regulator of tumorigenesis. In this review, we discuss the recent important findings in COP1/SPA research including a brief comparison between COP1 activity in plants and humans.