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

Jasmonate enhances cold acclimation in jojoba by promoting flavonol synthesis

Jojoba is an industrial oil crop planted in tropical arid areas, and its low-temperature sensitivity prevents its introduction into temperate areas. Studying the molecular mechanisms associated with cold acclimation in jojoba is advantageous for developing breeds with enhanced cold tolerance. In this study, metabolomic analysis revealed that various flavonols accumulate in jojoba during cold acclimation. Time-course transcriptomic analysis and weighted correlation network analysis (WGCNA) demonstrated that flavonol biosynthesis and jasmonates (JAs) signaling pathways played crucial roles in cold acclimation. Combining the biochemical and genetic analyses showed that ScMYB12 directly activated flavonol synthase gene (ScFLS). The interaction between ScMYB12 and transparent testa 8 (ScTT8) promoted the expression of ScFLS, but the negative regulator ScJAZ13 in the JA signaling pathway interacted with ScTT8 to attenuate the transcriptional activity of the ScTT8 and ScMYB12 complex, leading to the downregulation of ScFLS. Cold acclimation stimulated the production of JA in jojoba leaves, promoted the degradation of ScJAZ13, and activated the transcriptional activity of ScTT8 and ScMYB12 complexes, leading to the accumulation of flavonols. Our findings reveal the molecular mechanism of JA-mediated flavonol biosynthesis during cold acclimation in jojoba and highlight the JA pathway as a promising means for enhancing cold tolerance in breeding efforts.

What is going on inside of phytochrome B photobodies?

Plants exhibit an enormous phenotypic plasticity to adjust to changing environmental conditions. For this purpose, they have evolved mechanisms to detect and measure biotic and abiotic factors in their surroundings. Phytochrome B exhibits a dual function, since it serves as a photoreceptor for red and far-red light as well as a thermosensor. In 1999, it was first reported that phytochromes not only translocate into the nucleus but also form subnuclear foci upon irradiation by red light. It took more than 10 years until these phytochrome speckles received their name; these foci were coined photobodies to describe unique phytochrome-containing subnuclear domains that are regulated by light. Since their initial discovery, there has been much speculation about the significance and function of photobodies. Their presumed roles range from pure experimental artifacts to waste deposits or signaling hubs. In this review, we summarize the newest findings about the meaning of phyB photobodies for light and temperature signaling. Recent studies have established that phyB photobodies are formed by liquid-liquid phase separation via multivalent interactions and that they provide diverse functions as biochemical hotspots to regulate gene expression on multiple levels.

Phytochrome B photobody components

Phytochrome B (phyB) is a red and far-red photoreceptor that promotes light responses. Upon photoactivation, phyB enters the nucleus and forms a molecular condensate called a photobody through liquid-liquid phase separation. Phytochrome B photobody comprises phyB, the main scaffold molecule, and at least 37 client proteins. These clients belong to diverse functional categories enriched with transcription regulators, encompassing both positive and negative light signaling factors, with the functional bias toward the negative factors. The functionally diverse clients suggest that phyB photobody acts either as a trap to capture proteins, including negatively acting transcription regulators, for processes such as sequestration, modification, or degradation or as a hub where proteins are brought into close proximity for interaction in a light-dependent manner.

The phosphorylation of carboxyl-terminal eIF2α by SPA kinases contributes to enhanced translation efficiency during photomorphogenesis

Light triggers an enhancement of global translation during photomorphogenesis in Arabidopsis, but little is known about the underlying mechanisms. The phosphorylation of the α-subunit of eukaryotic initiation factor 2 (eIF2α) at a conserved serine residue in the N-terminus has been shown as an important mechanism for the regulation of protein synthesis in mammalian and yeast cells. However, whether the phosphorylation of this residue in plant eIF2α plays a role in regulation of translation remains elusive. Here, we show that the quadruple mutant of SUPPRESSOR OF PHYA-105 family members (SPA1-SPA4) display repressed translation efficiency after light illumination. Moreover, SPA1 directly phosphorylates the eIF2α C-terminus under light conditions. The C-term-phosphorylated eIF2α promotes translation efficiency and photomorphogenesis, whereas the C-term-unphosphorylated eIF2α results in a decreased translation efficiency. We also demonstrate that the phosphorylated eIF2α enhances ternary complex assembly by promoting its affinity to eIF2β and eIF2γ. This study reveals a unique mechanism by which light promotes translation via SPA1-mediated phosphorylation of the C-terminus of eIF2α in plants.

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.

The Characterization of R2R3-MYB Genes in Ammopiptanthus nanus Uncovers That the miR858-AnaMYB87 Module Mediates the Accumulation of Anthocyanin under Osmotic Stress

R2R3-MYB transcription factors (TFs) participate in the modulation of plant development, secondary metabolism, and responses to environmental stresses. Ammopiptanthus nanus, a leguminous dryland shrub, tolerates a high degree of environmental stress, including drought and low-temperature stress. The systematic identification, structural analysis, evolutionary analysis, and gene profiling of R2R3-MYB TFs under cold and osmotic stress in A. nanus were performed. Up to 137 R2R3-MYB TFs were identified and clustered into nine clades, with most A. nanus R2R3-MYB members belonging to clade VIII. Tandem and segmental duplication events drove the expansion of the A. nanus R2R3-MYB family. Expression profiling revealed that multiple R2R3-MYB genes significantly changed under osmotic and cold stress conditions. MiR858 and miR159 targeted 88 R2R3-MYB genes. AnaMYB87, an miR858-targeted clade VIII R2R3-MYB TF, was up-regulated under both osmotic and cold stress. A transient expression assay in apples showed that the overexpression of AnaMYB87 promoted anthocyanin accumulation. A luciferase reporter assay in tobacco demonstrated that AnaMYB87 positively affected the transactivation of the dihydroflavonol reductase gene, indicating that the miR858-MYB87 module mediates anthocyanin accumulation under osmotic stress by regulating the dihydroflavonol reductase gene in A. nanus. This study provides new data to understand the roles of R2R3-MYB in plant stress responses.

FAR-RED INSENSITIVE 219 and phytochrome B corepress shade avoidance via modulating nuclear speckle formation

Plants can sense the shade from neighboring plants by detecting a reduction of the red:far-red light (R:FR) ratio. Phytochrome B (phyB) is the primary photoreceptor that perceives shade light and regulates jasmonic acid (JA) signaling. However, the molecular mechanisms underlying phyB and JA signaling integration in shade responses remain largely unknown. Here, we show the interaction of phyB and FAR-RED INSENSITIVE 219 (FIN219)/JASMONATE RESISTANT1 (JAR1) in a functional demand manner in Arabidopsis (Arabidopsis thaliana) seedling development. Genetic evidence and interaction studies indicated that phyB and FIN219 synergistically and negatively regulate shade-induced hypocotyl elongation. Moreover, phyB interacted with various isoforms of FIN219 under high and low R:FR light. Methyl jasmonate (MeJA) treatment, FIN219 mutation, and PHYBOE digalactosyldiacylglycerol synthase1-1 (dgd1-1) plants, which show increased levels of JA, altered the patterns of phyB-associated nuclear speckles under the same conditions. Surprisingly, PHYBOE dgd1-1 showed a shorter hypocotyl phenotype than its parental mutants under shade conditions. Microarray assays using PHYBOE and PHYBOE fin219-2 indicated that PHYB overexpression substantially affects defense response-related genes under shade light and coregulates expression of auxin-responsive genes with FIN219. Thus, our findings reveal that phyB substantially crosstalks with JA signaling through FIN219 to modulate seedling development under shade light.

Phytochrome B photobodies are comprised of phytochrome B and its primary and secondary interacting proteins

Phytochrome B (phyB) is a plant photoreceptor that forms a membraneless organelle called a photobody. However, its constituents are not fully known. Here, we isolated phyB photobodies from Arabidopsis leaves using fluorescence-activated particle sorting and analyzed their components. We found that a photobody comprises ~1,500 phyB dimers along with other proteins that could be classified into two groups: The first includes proteins that directly interact with phyB and localize to the photobody when expressed in protoplasts, while the second includes proteins that interact with the first group proteins and require co-expression of a first-group protein to localize to the photobody. As an example of the second group, TOPLESS interacts with PHOTOPERIODIC CONTROL OF HYPOCOTYL 1 (PCH1) and localizes to the photobody when co-expressed with PCH1. Together, our results support that phyB photobodies include not only phyB and its primary interacting proteins but also its secondary interacting proteins.

PIL transcription factors directly interact with SPLs and repress tillering/branching in plants

Tillering is an important parameter of plant architecture in cereal crops. In this study, we identified the PHYTOCHROME-INTERACTING FACTOR-LIKE (PIL) family transcription factors as new repressors of tillering in cereal crops. Using biochemical and genetic approaches, we explore the roles of TaPIL1 in regulating wheat plant architecture. We found that the PIL protein TaPIL1 controls tiller number in wheat. Overexpression of TaPIL1 reduces wheat tiller number; additionally, overexpression of TaPIL1-SUPERMAN repression domain increases wheat tiller number. Furthermore, we show that TaPIL1 activates the transcriptional expression of wheat TEOSINTE BRANCHED1 (TaTB1); moreover, TaPIL1 physically interacts with wheat SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (TaSPL)3/17, which are activators of TaTB1 transcription. In rice, overexpression and loss-of-function mutations of OsPIL11 reduce or increase tiller number by regulating the expression of OsTB1. In Arabidopsis, we demonstrate that PHYTOCHROME-INTERACTING FACTOR 4 interacts with SPL9 to inhibit shoot branching. This study reveals that PIL family transcription factors directly interact with SPLs and play an important role in repressing tillering/branching in plants.

Identification of a delayed leaf greening gene from a mutation of pummelo

Delayed greening of young leaves is an unusual phenomenon of plants in nature. Citrus are mostly evergreen tree species. Here, a natural mutant of "Guanxi" pummelo (Citrus maxima), which shows yellow leaves at the young stage, was characterized to identify the genes underlying the trait of delayed leaf greening in plants. A segregating population with this mutant as the seed parent and a normal genotype as the pollen parent was generated. Two DNA pools respectively from the leaves of segregating seedlings with extreme phenotypes of normal leaf greening and delayed leaf greening were collected for sequencing. Bulked segregant analysis (BSA) and InDel marker analysis demonstrated that the delayed leaf greening trait is governed by a 0.3 Mb candidate region on chromosome 6. Gene expression analysis further identified a key candidate gene (Citrus Delayed Greening gene 1, CDG1) in the 0.3 Mb region, which showed significantly differential expression between the genotypes with delayed and normal leaf greening phenotypes. There was a 67 bp InDel region difference in the CDG1 promoter and the InDel region contains a TATA-box element. Confocal laser-scanning microscopy revealed that the CDG1-GFP fusion protein signals were co-localized with the chloroplast signals in the protoplasts. Overexpression of CDG1 in tobacco and Arabidopsis led to the phenotype of delayed leaf greening. These results suggest that the CDG1 gene is involved in controlling the delayed leaf greening phenotype with important functions in chloroplast development.

Phytochrome Signaling Networks

The perception of light signals by the phytochrome family of photoreceptors has a crucial influence on almost all aspects of growth and development throughout a plant's life cycle. The holistic regulatory networks orchestrated by phytochromes, including conformational switching, subcellular localization, direct protein-protein interactions, transcriptional and posttranscriptional regulations, and translational and posttranslational controls to promote photomorphogenesis, are highly coordinated and regulated at multiple levels. During the past decade, advances using innovative approaches have substantially broadened our understanding of the sophisticated mechanisms underlying the phytochrome-mediated light signaling pathways. This review discusses and summarizes these discoveries of the role of the modular structure of phytochromes, phytochrome-interacting proteins, and their functions; the reciprocal modulation of both positive and negative regulators in phytochrome signaling; the regulatory roles of phytochromes in transcriptional activities, alternative splicing, and translational regulation; and the kinases and E3 ligases that modulate PHYTOCHROME INTERACTING FACTORs to optimize photomorphogenesis.

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.

In search of function: nuclear bodies and their possible roles as plant environmental sensors

Plants must adjust their physiology, development and reproductive decisions in response to a fluctuating environment. Understanding how these adjustments are achieved is fundamental for predicting plant reactions to global environmental changes and for designing mitigation strategies. An often overlooked plant-environmental response is the formation of intranuclear membrane-less organelles known as 'nuclear bodies'. Currently, the functional role of nuclear bodies remains largely unclear. However, in recent years, they have received increased attention as possible hubs or integrators of environmental signals, and for possibly being part of the sensing machinery itself. Here, we will explore the formation of nuclear bodies under changing light, osmotic, and temperature conditions. We will then hypothesize on their potential functions in facilitating environmentally driven plant responses.

The role of light in regulating seed dormancy and germination

Seed dormancy is an adaptive trait in plants. Breaking seed dormancy determines the timing of germination and is, thereby essential for ensuring plant survival and agricultural production. Seed dormancy and the subsequent germination are controlled by both internal cues (mainly hormones) and environmental signals. In the past few years, the roles of plant hormones in regulating seed dormancy and germination have been uncovered. However, we are only beginning to understand how light signaling pathways modulate seed dormancy and interaction with endogenous hormones. In this review, we summarize current views of the molecular mechanisms by which light controls the induction, maintenance and release of seed dormancy, as well as seed germination, by regulating hormone metabolism and signaling pathways.