Phytochrome Interacting Factors: central players in phytochrome-mediated light signaling networks

Transgenic Cynodon dactylon overexpressing CdPIF4 alters plant development and cold stress tolerance

Bermudagrass [Cynodon dactylon (L.) Pers.] is widely used for soil remediation, livestock forage, and as turfgrass for sports fields, parks, and gardens due to its resilience and adaptability. However, low temperatures are critical factors limiting its geographical distribution and ornamental season, even preventing its safe overwintering. PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) acts as a hub transcription factor, not only regulating various light responses but also integrating multiple external stimuli to improve plant productivity and architectural adaptation under adverse stress conditions, which makes it potential as a target gene. In this study, we cloned and characterized the CdPIF4 genes in bermudagrass. Expression analysis revealed that it is predominantly expressed in leaves and is regulated by photoperiod and cold stress. Using Agrobacterium-mediated genetic modification, we successfully generated CdPIF4a-overexpressing bermudagrass lines. Under cold stress at 4°C, these transgenic plants demonstrated enhanced cold tolerance, as indicated by higher relative water content, reduced membrane damage, and lower levels of lipid peroxidation levels. Photosynthetic analysis revealed that CdPIF4a-overexpressing plants exhibited higher light energy capture and transfer efficiency at this low temperature, with less energy loss. Additionally, they showed higher antioxidant enzyme activity and lower levels of reactive oxygen species levels. The responsive regulation of cold stress-related genes further validated the role of the CdPIF4a gene in enhancing cold tolerance. This study elucidates that CdPIF4 enhances cold tolerance in bermudagrass through physiological and molecular mechanisms, offering new insights and valuable genetic resources for advancing cold resistance research in bermudagrass and other grass species.

The interactive effects between far-red light and temperature on lettuce growth and morphology diminish at high light intensity

Phytochromes (PHYs) play a dual role in sensing light spectral quality and temperature. PHYs can interconvert between the active Pfr form and inactive Pr form upon absorption of red (R) and far-red (FR) light (Photoconversion). In addition, active Pfr can be converted to inactive Pr in a temperature-dependent manner (Thermal Reversion). Recent studies have shown that FR light and temperature can interactively affect plant growth and morphology through co-regulating phytochrome activities. These studies were primarily conducted under relatively low light intensities. As light intensity increases, the impact of thermal reversion on phytochrome dynamics decreases. However, the light intensity dependency of the interactive effects between FR light and temperature on plant growth and morphology has not been characterized. In this study, lettuce (Lactuca sativa L.) 'Rex' was grown under two total photon flux densities (TPFD; 400-800 nm) (150 and 300 μmol m-2 s-1) x three temperatures (20, 24, and 28°C) x two light spectra (0 and 20% of FR light in TPFD). Our results showed that the effects of FR light on leaf, stem, and root elongation, leaf number, and leaf expansion were dependent on temperature at lower TPFD. However, the magnitude of the interactive effects between FR light and temperature on plant morphology decreased at higher TPFD. Particularly, at a lower TPFD, FR light stimulated leaf expansion and canopy photon capture only under a cooler temperature of 20°C. However, at a higher TPFD, FR light consistently increased total leaf area across all three temperatures. Plant biomass was more strongly correlated with the total number of photons intercepted by the leaves than with the photosynthetic activities of individual leaves. FR light decreased the contents of chlorophylls, carotenoids, flavonoids, and phenolics, as well as the total antioxidant capacity. In contrast, warmer temperatures and high light intensity increased the values of these parameters. We concluded that the interactive effects between FR light and temperature on plant growth and morphology diminished as total light intensity increased. Additionally, the combination of high light intensity, warm temperature, and FR light resulted in the highest crop yield and antioxidant capacity in lettuce.

Identification of bHLH transcription factors and screening of anthocyanin-related genes in Lagerstroemia indica

The basic helix-loop-helix (bHLH) family is one of the three major transcription factor families that play important transcriptional regulatory roles in plant growth and development. One of the most crucial elements in defining Lagerstroemia indica's decorative qualities is flower color. However, the function of the bHLH transcription factor family in L. indica anthocyanin glycoside synthesis has not been clarified. Using the transcriptome data of flower color, 79 LibHLH genes were found in this study. Phylogenetic analysis showed that the LibHLH genes can be divided into 16 subfamilies, and most of the genes in the same subfamily have similar conserved motifs. The total anthocyanin glycoside content of L. indica 'Zihua Guifei' petals was determined during three developmental stages of the petals' growth. The results showed that the total anthocyanin glycoside content grew gradually with growth and development, and that it accumulated most during the full bloom stage. By using gene expression analysis, protein interaction network analysis, and bioinformatics, it was possible to determine which member of the III f family, LibHLH29, is important for the synthesis of anthocyanin glycosides in L. indica. Its expression was confirmed by qRT-PCR, and the results were essentially compatible with the transcriptome data. It was more prominent in the light-colored bloom stage the color-transition stage of L. indica 'Zihua Guifei'. It can be further investigated as a major candidate gene for regulating anthocyanin glycoside synthesis in L. indica, thus laying the foundation for an in-depth study of the interactions among transcription factors.

Shading increases the susceptibility of alfalfa (Medicago sativa) to Pst. DC3000 by inhibiting the expression of MsIFS1

Shade is a stressful factor for most plants, leading to both morphological and physiological changes, and often resulting in increased susceptibility to diseases and pathogen attacks. Our study revealed that the isoflavonoid synthesis pathway was inhibited in alfalfa under shade, resulting in a significant reduction in disease resistance. Overexpression of MsIFS1, a switch regulator in isoflavonoid synthesis, led to a notable increase in endogenous isoflavonoids and enhanced resistance to Pseudomonas syringae pv. tomato DC3000 (Pst. DC3000). Conversely, MsIFS1-RNAi had the opposite effect. Yeast one-hybrid (Y1H) assays revealed that the shade-responsive transcription factor MsWRKY41 could directly bind to the MsIFS1 promoter. This interaction was confirmed through Dual-Luciferase Reporter (Dual-LUC) and Chromatin Immunoprecipitation coupled with quantitative PCR (ChIP-qPCR) assays, both in vitro and in vivo. Overexpression of MsWRKY41 not only enhanced alfalfa's resistance to Pst. DC3000 but also promoted the accumulation of isoflavonoids. Additionally, yeast two-hybrid (Y2H) assays showed that neither MsWRKY41 nor MsIFS1 physically interacted with the Type III effector (T3SE) HopZ1 secreted by Pst. DC3000, suggesting that the MsWRKY41-MsIFS1 module is not a direct target of HopZ1. These findings provide valuable theoretical insights and genetic resources for the development of shade-tolerant alfalfa with enhanced disease resistance.

PHOSPHATASE 2A dephosphorylates PHYTOCHROME-INTERACTING FACTOR3 to modulate photomorphogenesis in Arabidopsis

The phytochrome (phy) family of sensory photoreceptors modulates developmental programs in response to ambient light. Phys also control gene expression in part by directly interacting with the bHLH class of transcription factors, PHYTOCHROME-INTERACTING FACTORS (PIFs), and inducing their rapid phosphorylation and degradation. Several kinases have been shown to phosphorylate PIFs and promote their degradation. However, the phosphatases that dephosphorylate PIFs are less understood. In this study, we describe 4 regulatory subunits of the Arabidopsis (Arabidopsis thaliana) protein PHOSPHATASE 2A (PP2A) family (B'α, B'β, B″α, and B″β) that interact with PIF3 in yeast 2-hybrid, in vitro and in vivo assays. The pp2ab″αβ and b″αβ/b'αβ mutants display short hypocotyls, while the overexpression of the B subunits induces longer hypocotyls compared with the wild type (WT) under red light. The light-induced degradation of PIF3 is faster in the b″αβ/b'αβ quadruple mutant compared with that in the WT. Consistently, immunoprecipitated PP2A A and B subunits directly dephosphorylate PIF3-MYC in vitro. An RNA-sequencing analysis shows that B″α and B″β alter global gene expression in response to red light. PIFs (PIF1, PIF3, PIF4, and PIF5) are epistatic to these B subunits in regulating hypocotyl elongation under red light. Collectively, these data show an essential function of PP2A in dephosphorylating PIF3 to modulate photomorphogenesis in Arabidopsis.

Genome-wide identification and expression analysis of phytochrome-interacting factor genes during abiotic stress responses and secondary metabolism in the tea plant

Phytochrome-interacting factors (PIFs) are pivotal transcriptional regulators controlling photomorphogenesis, environmental responses, and development in plants. However, their specific roles in coordinating adaptation towards abiotic stress and metabolism remain underexplored in tea plants. Here, we identified seven PIF members from four distinct clades (PIF1, PIF3, PIF7, and PIF8). Promoter analysis implicated CsPIFs in integrating light, stress, hormone, and circadian signals. Most CsPIFs exhibited rapid increase in expression under shading, especially CsPIF7b/8a, which displayed significant changes in long-term shading condition. Under drought/salt stress, CsPIF3b emerged as a potential positive regulator. CsPIF3a was induced by low temperature and co-expressed with CsCBF1/3 and CsDREB2A cold response factors. Dual-luciferase assays confirmed that act as negative regulator of the CBF pathway. Expression profiling across 11 tea cultivars associated specific CsPIFs with chlorophyll biosynthesis and accumulation of anthocyanins, flavonols, and other metabolites. In summary, this study highlights the significance of CsPIFs as central coordinators in managing intricate transcriptional reactions to simultaneous abiotic stresses and metabolic adjustments in tea plants. This insight informs future strategies for enhancing this economically crucial crop through crop improvement initiatives.

Genome-Wide Identification and Characterization of MYB Transcription Factors in Sudan Grass under Drought Stress

Sudan grass (Sorghum sudanense S.) is a warm-season annual grass with high yield, rich nutritional value, good regeneration, and tolerance to biotic and abiotic stresses. However, prolonged drought affects the yield and quality of Sudan grass. As one of the largest families of multifunctional transcription factors in plants, MYB is widely involved in regulating plant growth and development, hormonal signaling, and stress responses at the gene transcription level. However, the regulatory role of MYB genes has not been well characterized in Sudan grass under abiotic stress. In this study, 113 MYB genes were identified in the Sudan grass genome and categorized into three groups by phylogenetic analysis. The promoter regions of SsMYB genes contain different cis-regulatory elements, which are involved in developmental, hormonal, and stress responses, and may be closely related to their diverse regulatory functions. In addition, collinearity analysis showed that the expansion of the SsMYB gene family occurred mainly through segmental duplications. Under drought conditions, SsMYB genes showed diverse expression patterns, which varied at different time points. Interaction networks of 74 SsMYB genes were predicted based on motif binding sites, expression correlations, and protein interactions. Heterologous expression showed that SsMYB8, SsMYB15, and SsMYB64 all significantly enhanced the drought tolerance of yeast cells. Meanwhile, the subcellular localization of all three genes is in the nucleus. Overall, this study provides new insights into the evolution and function of MYB genes and provides valuable candidate genes for breeding efforts in Sudan grass.

Genome-wide investigation of the PIF gene family in alfalfa (Medicago sativa L.) expression profiles during development and stress

BACKGROUND

Phytochrome-interacting factors (PIFs) plays an important role in plants as hubs for intracellular signaling regulation. The PIF gene family has been identified and characterized in many plants, but alfalfa (Medicago sativa L.), an important perennial high-quality legume forage, has not been reported on the PIF gene family.

RESULTS

In this study, we presented the identification and characterization of five MsPIF genes in alfalfa (Medicago sativa L.). Phylogenetic analysis indicated that PIFs from alfalfa and other four plant species could be divided into three groups supported by similar motif analysis. The collinearity analysis of the MsPIF gene family showed the presence of two gene pairs, and the collinearity analysis with AtPIFs showed three gene pairs, indicating that the evolutionary process of this family is relatively conservative. Analysis of cis-acting elements in promoter regions of MsPIF genes indicated that various elements were related to light, abiotic stress, and plant hormone responsiveness. Gene expression analyses demonstrated that MsPIFs were primarily expressed in the leaves and were induced by various abiotic stresses.

CONCLUSION

This study conducted genome-wide identification, evolution, synteny analysis, and expression analysis of the PIFs in alfalfa. Our study lays a foundation for the study of the biological functions of the PIF gene family and provides a useful reference for improving abiotic stress resistance in alfalfa.

HY5 and COP1 function antagonistically in the regulation of nicotine biosynthesis in Nicotiana tabacum

Nicotine constitutes approximately 90% of the total alkaloid content in leaves within the Nicotiana species, rendering it the most prevalent alkaloid. While the majority of genes responsible for nicotine biosynthesis express in root tissue, the influence of light on this process through shoot-to-root mobile ELONGATED HYPOCOTYL 5 (HY5) has been recognized. CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1), a key regulator of light-associated responses, known for its role in modulating HY5 accumulation, remains largely unexplored in its relationship to light-dependent nicotine accumulation. Here, we identified NtCOP1, a COP1 homolog in Nicotiana tabacum, and demonstrated its ability to complement the cop1-4 mutant in Arabidopsis thaliana at molecular, morphological, and biochemical levels. Through the development of NtCOP1 overexpression (NtCOP1OX) plants, we observed a significant reduction in nicotine and flavonol content, inversely correlated with the down-regulation of nicotine and phenylpropanoid pathway. Conversely, CRISPR/Cas9-based knockout mutant plants (NtCOP1CR) exhibited an increase in nicotine levels. Further investigations, including yeast-two hybrid assays, grafting experiments, and Western blot analyses, revealed that NtCOP1 modulates nicotine biosynthesis by targeting NtHY5, thereby impeding its transport from shoot-to-root. We conclude that the interplay between HY5 and COP1 functions antagonistically in the light-dependent regulation of nicotine biosynthesis in tobacco.

Regulation of cryptochrome-mediated blue light signaling by the ABI4-PIF4 module

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

How Histone Acetyltransferases Shape Plant Photomorphogenesis and UV Response

Higher plants have developed complex mechanisms to adapt to fluctuating environmental conditions with light playing a vital role in photosynthesis and influencing various developmental processes, including photomorphogenesis. Exposure to ultraviolet (UV) radiation can cause cellular damage, necessitating effective DNA repair mechanisms. Histone acetyltransferases (HATs) play a crucial role in regulating chromatin structure and gene expression, thereby contributing to the repair mechanisms. HATs facilitate chromatin relaxation, enabling transcriptional activation necessary for plant development and stress responses. The intricate relationship between HATs, light signaling pathways and chromatin dynamics has been increasingly understood, providing valuable insights into plant adaptability. This review explores the role of HATs in plant photomorphogenesis, chromatin remodeling and gene regulation, highlighting the importance of chromatin modifications in plant responses to light and various stressors. It emphasizes the need for further research on individual HAT family members and their interactions with other epigenetic factors. Advanced genomic approaches and genome-editing technologies offer promising avenues for enhancing crop resilience and productivity through targeted manipulation of HAT activities. Understanding these mechanisms is essential for developing strategies to improve plant growth and stress tolerance, contributing to sustainable agriculture in the face of a changing climate.

Light signaling in plants-a selective history

In addition to providing the radiant energy that drives photosynthesis, sunlight carries signals that enable plants to grow, develop and adapt optimally to the prevailing environment. Here we trace the path of research that has led to our current understanding of the cellular and molecular mechanisms underlying the plant's capacity to perceive and transduce these signals into appropriate growth and developmental responses. Because a fully comprehensive review was not possible, we have restricted our coverage to the phytochrome and cryptochrome classes of photosensory receptors, while recognizing that the phototropin and UV classes also contribute importantly to the full scope of light-signal monitoring by the plant.

Assessing the Function of CBF1 in Modulating the Interaction Between Phytochrome B and PIF4

Phytochromes are red (R) and far-red (FR) light photoreceptors in plants. Upon light exposure, photoactivated phytochromes translocate into the nucleus, where they interact with their partner proteins to transduce light signals. The yeast two-hybrid (Y2H) system is a powerful technique for rapidly identifying and verifying protein-protein interactions, and PHYTOCHROME-INTERACTING FACTOR3 (PIF3), the founding member of the PIF proteins, was initially identified in a Y2H screen for phytochrome B (phyB)-interacting proteins. Recently, we developed a yeast three-hybrid (Y3H) system by introducing an additional vector into this Y2H system, and thus a new regulator could be co-expressed and its role in modulating the interactions between phytochromes and their signaling partners could be examined. By employing this Y3H system, we recently showed that both MYB30 and CBF1, two negative regulators of seedlings photomorphogenesis, act to inhibit the interactions between phyB and PIF4/PIF5. In this chapter, we will use the CBF1-phyB-PIF4 module as an example and describe the detailed procedure for performing this Y3H assay. It will be intriguing and exciting to explore the potential usage of this Y3H system in future research.

Glucose status within dark-grown etiolated cotyledons determines seedling de-etiolation upon light irradiation

Exposure of dark-grown etiolated seedlings to light triggers the transition from skotomorphogenesis/etiolation to photomorphogenesis/de-etiolation. In the life cycle of plants, de-etiolation is essential for seedling development and plant survival. The mobilization of soluble sugars (glucose [Glc], sucrose, and fructose) derived from stored carbohydrates and lipids to target organs, including cotyledons, hypocotyls, and radicles, underpins de-etiolation. Therefore, dynamic carbohydrate biochemistry is a key feature of this phase transition. However, the molecular mechanisms coordinating carbohydrate status with the cellular machinery orchestrating de-etiolation remain largely opaque. Here, we show that the Glc sensor HEXOKINASE 1 (HXK1) interacts with GROWTH REGULATOR FACTOR5 (GRF5), a transcriptional activator and key plant growth regulator, in Arabidopsis (Arabidopsis thaliana). Subsequently, GRF5 directly binds to the promoter of phytochrome A (phyA), encoding a far-red light (FR) sensor/cotyledon greening inhibitor. We demonstrate that the status of Glc within dark-grown etiolated cotyledons determines the de-etiolation of seedlings when exposed to light irradiation by the HXK1-GRF5-phyA molecular module. Thus, following seed germination, accumulating Glc within dark-grown etiolated cotyledons stimulates a HXK1-dependent increase of GRF5 and an associated decrease of phyA, triggering the perception, amplification, and relay of HXK1-dependent Glc signaling, thereby facilitating the de-etiolation of seedlings following light irradiation. Our findings, therefore, establish how cotyledon carbohydrate signaling under subterranean darkness is sensed, amplified, and relayed, determining the phase transition from skotomorphogenesis to photomorphogenesis on exposure to light irradiation.

Phytochrome-Interacting Proteins

Phytochromes are photoreceptors of plants, fungi, slime molds bacteria and heterokonts. These biliproteins sense red and far-red light and undergo light-induced changes between the two spectral forms, Pr and Pfr. Photoconversion triggered by light induces conformational changes in the bilin chromophore around the ring C-D-connecting methine bridge and is followed by conformational changes in the protein. For plant phytochromes, multiple phytochrome interacting proteins that mediate signal transduction, nuclear translocation or protein degradation have been identified. Few interacting proteins are known as bacterial or fungal phytochromes. Here, we describe how the interacting partners were identified, what is known about the different interactions and in which context of signal transduction these interactions are to be seen. The three-dimensional arrangement of these interacting partners is not known. Using an artificial intelligence system-based modeling software, a few predicted and modulated examples of interactions of bacterial phytochromes with their interaction partners are interpreted.

PIFs interact with SWI2/SNF2-related 1 complex subunit 6 to regulate H2A.Z deposition and photomorphogenesis in Arabidopsis

Light is an essential environmental signal perceived by a broad range of photoreceptors in plants. Among them, the red/far-red light receptor phytochromes function to promote photomorphogenesis, which is critical to the survival of seedlings after seeds germination. The basic-helix-loop-helix transcription factors phytochrome-interacting factors (PIFs) are the pivotal direct downstream components of phytochromes. H2A.Z is a highly conserved histone variant regulating gene transcription, and its incorporation into nucleosomes is catalyzed by SWI2/SNF2-related 1 complex, in which SWI2/SNF2-related 1 complex subunit 6 (SWC6) and actin-related protein 6 (ARP6) serve as core subunits. Here, we show that PIFs physically interact with SWC6 in vitro and in vivo, leading to the disassociation of HY5 from SWC6. SWC6 and ARP6 regulate hypocotyl elongation partly through PIFs in red light. PIFs and SWC6 coregulate the expression of auxin-responsive genes such as IAA6, IAA19, IAA20, and IAA29 and repress H2A.Z deposition at IAA6 and IAA19 in red light. Based on previous studies and our findings, we propose that PIFs inhibit photomorphogenesis, at least in part, through repression of H2A.Z deposition at auxin-responsive genes mediated by the interactions of PIFs with SWC6 and promotion of their expression in red light.

Suppression of a hexokinase gene SlHXK1 in tomato affects fruit setting and seed quality

Hexokinase is considered to be the key molecule in sugar signaling and metabolism. Here, we reported that silencing SlHXK1 resulted in a decrease in flower number, increased rate of flower dropping, abnormal thickening of the anther wall, and reduced pollen and seed viability. An anatomical analysis revealed the loss of small cells and abnormal thickening of anther walls in SlHXK1-RNAi lines. Treatment with auxin and 1-methylcyclopropene inhibited flower dropping from the pedicel abscission zone. qRT-PCR analysis revealed that the effect of SlHXK1 on abscission was associated with the expression levels of genes related to key meristem, auxin, ethylene, cell wall metabolism and programmed cell death. Pollen germination and pollen staining experiments showed that pollen viability was significantly reduced in the SlHXK1-RNAi lines. Physiological and biochemical analyses showed that hexokinase activity and starch content were markedly decreased in the transgenic lines. The expression of genes related to tomato pollen development was also suppressed in the transgenic lines. Although the RNAi lines eventually produced some viable seeds, the yield and quality of the seeds was lower than that of wild-type plants. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that SlHXK1 interacted with SlKINγ. Furthermore, SlPIF4 inhibited the transcriptional expression of SlHXK1. In conclusion, our results demonstrate that SlHXK1 may play important roles in pollen, anther, seed and the pedicel abscission zone by affecting starch accumulation or cell wall synthesis, as well as by regulating the number of the transcripts of genes that are involved in auxin, ethylene and cell wall degradation.

Light signaling as cellular integrator of multiple environmental cues in plants

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

PIF1, a phytochrome-interacting factor negatively regulates drought tolerance and carotenoids biosynthesis in tobacco

The phytochrome-interacting factors (PIFs) function crucially in multiple physiological processes, but the biological functions of some PIFs remain elusive in some species. Here, a PIF transcription factor NtPIF1 was cloned and characterized in tobacco (Nicotiana tabacum L.). The transcript of NtPIF1 was significantly induced by drought stress treatments, and it localized in the nuclear. Knockout of NtPIF1 by CRISPR/Cas9 system led to the improved drought tolerance of tobacco with increased osmotic adjustment, antioxidant activity, photosynthetic efficiency and decreased water loss rate. On the contrary, NtPIF1-overexpression plants displays drought-sensitive phenotypes. In addition, NtPIF1 reduced the biosynthesis of abscisic acid (ABA) and its upstream carotenoids by regulating the expression of genes involved in ABA and carotenoids biosynthetic pathway upon drought stress. Electrophoretic mobility shift and dual-luciferase assays illustrated that, NtPIF1 directly bind to the E-box elements within the promoters of NtNCED3, NtABI5, NtZDS and Ntβ-LCY to repress their transcription. Overall, these data suggested that NtPIF1 negatively regulate tobacco adaptive response to drought stress and carotenoids biosynthesis; moreover, NtPIF1 has the potential to develop drought-tolerant tobacco plants using CRISPR/Cas9 system.

Genome-Wide Identification and Expression Analysis of the bHLH Transcription Factor Family in Wintersweet (Chimonanthus praecox)

Wintersweet (Chimonanthus praecox (L.) Link, Calycanthaceae) is an esteemed ornamental flowering shrub known for its distinct blooming period in winter, vibrant color petals, and captivating floral fragrance. Basic helix-loop-helix (bHLH) transcription factors (TFs) play pivotal roles as key regulators in secondary metabolites biosynthesis, growth, and development in plants. However, the systematic analysis of the bHLH family members and their role in the regulation of floral traits in Wintersweet remains insufficiently understood. To bridge this knowledge gap, we conducted a comprehensive genome-wide analysis of the C. praecox bHLH (CpbHLH) gene family, identifying a total of 131 CpbHLH genes across 11 chromosomes. Phylogenetic analysis classified these CpbHLH genes into 23 subfamilies, wherein most members within the same subfamily exhibited analogous intron/exon patterns and motif composition. Moreover, the expansion of the CpbHLH gene family was primarily driven by segmental duplication, with duplicated gene pairs experiencing purifying selection during evolution. Transcriptomic analysis revealed diverse expression patterns of CpbHLH genes in various tissues and distinct stages of Wintersweet flower development, thereby suggesting their involvement in a diverse array of physiological processes. Furthermore, yeast 2-hybrid assay demonstrated interaction between CpbHLH25 and CpbHLH59 (regulators of floral scent and color) as well as with CpbHLH112 and CpMYB2, suggesting potential coordinately regulation of secondary metabolites biosynthesis in Wintersweet flowers. Collectively, our comprehensive analysis provides valuable insights into the structural attributes, evolutionary dynamics, and expression profiles of the CpbHLH gene family, laying a solid foundation for further explorations of the multifaceted physiological and molecular roles of bHLH TFs in Wintersweet.

Functions of Plant Phytochrome Signaling Pathways in Adaptation to Diverse Stresses

Phytochromes are receptors for red light (R)/far-red light (FR), which are not only involved in regulating the growth and development of plants but also in mediated resistance to various stresses. Studies have revealed that phytochrome signaling pathways play a crucial role in enabling plants to cope with abiotic stresses such as high/low temperatures, drought, high-intensity light, and salinity. Phytochromes and their components in light signaling pathways can also respond to biotic stresses caused by insect pests and microbial pathogens, thereby inducing plant resistance against them. Given that, this paper reviews recent advances in understanding the mechanisms of action of phytochromes in plant resistance to adversity and discusses the importance of modulating the genes involved in phytochrome signaling pathways to coordinate plant growth, development, and stress responses.

Phytochrome-interacting factor PIF3 integrates phytochrome B and UV-B signaling pathways to regulate gibberellin- and auxin-dependent growth in cucumber hypocotyls

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

Phytochromes enhance SOS2-mediated PIF1 and PIF3 phosphorylation and degradation to promote Arabidopsis salt tolerance

Soil salinity is one of the most detrimental abiotic stresses affecting plant survival, and light is a core environmental signal regulating plant growth and responses to abiotic stress. However, how light modulates the plant's response to salt stress remains largely obscure. Here, we show that Arabidopsis (Arabidopsis thaliana) seedlings are more tolerant to salt stress in the light than in the dark, and that the photoreceptors phytochrome A (phyA) and phyB are involved in this tolerance mechanism. We further show that phyA and phyB physically interact with the salt tolerance regulator SALT OVERLY SENSITIVE2 (SOS2) in the cytosol and nucleus, and enhance salt-activated SOS2 kinase activity in the light. Moreover, SOS2 directly interacts with and phosphorylates PHYTOCHROME-INTERACTING FACTORS PIF1 and PIF3 in the nucleus. Accordingly, PIFs act as negative regulators of plant salt tolerance, and SOS2 phosphorylation of PIF1 and PIF3 decreases their stability and relieves their repressive effect on plant salt tolerance in both light and dark conditions. Together, our study demonstrates that photoactivated phyA and phyB promote plant salt tolerance by increasing SOS2-mediated phosphorylation and degradation of PIF1 and PIF3, thus broadening our understanding of how plants adapt to salt stress according to their dynamic light environment.

The FLOWERING LOCUS T gene expression is controlled by high-irradiance response and external coincidence mechanism in long days in Arabidopsis

In natural long days, the florigen gene FLOWERING LOCUS T (FT) shows a bimodal expression pattern with morning and dusk peaks in Arabidopsis. This pattern differs from the one observed in the laboratory, and little is known about underlying mechanisms. A red : far-red (R : FR) ratio difference between sunlight and fluorescent light causes this FT pattern mismatch. We showed that bimodal FT expression patterns were induced in a day longer than 14 h with sunlight R : FR (= c. 1) conditions. By circadian gating experiments, we found that cumulative exposure of R : FR-adjusted light (R : FR ratio was adjusted to 1 with FR supplement) spanning from the afternoon to the next morning required full induction of FT in the morning. Conversely, only 2 h of R : FR adjustment in the late afternoon was sufficient for FT induction at dusk. We identified that phytochrome A (phyA) is required for the morning FT expression in response to the R : FR adjustment on the previous day. As a part of this mechanism, we showed that PHYTOCHROME-INTERACTING FACTOR 7 contributes to FT regulation. Our results suggest that phyA-mediated high-irradiance response and the external coincidence mechanism contribute to morning FT induction under natural long-day conditions.

Functions of Phytochrome-Interacting Factors (PIFs) in the regulation of plant growth and development: A comprehensive review

Transcription factors play important roles in governing plant responses upon changes in their ambient conditions. Any fluctuation in the supply of critical requirements for plants, such as optimum light, temperature, and water leads to the reprogramming of gene-signaling pathways. At the same time, plants also evaluate and shift their metabolism according to the various stages of development. Phytochrome-Interacting Factors are one of the most important classes of transcription factors that regulate both developmental and external stimuli-based growth of plants. This review focuses on the identification of PIFs in various organisms, regulation of PIFs by various proteins, functions of PIFs of Arabidopsis in diverse developmental pathways such as seed germination, photomorphogenesis, flowering, senescence, seed and fruit development, and external stimuli-induced plant responses such as shade avoidance response, thermomorphogenesis, and various abiotic stress responses. Recent advances related to the functional characterization of PIFs of crops such as rice, maize, and tomato have also been incorporated in this review, to ascertain the potential of PIFs as key regulators to enhance the agronomic traits of these crops. Thus, an attempt has been made to provide a holistic view of the function of PIFs in various processes in plants.

Arabidopsis FIN219/JAR1 interacts with phytochrome a under far-red light and jasmonates in regulating hypocotyl elongation via a functional demand manner

Integration of light and phytohormones is essential for plant growth and development. FAR-RED INSENSITIVE 219 (FIN219)/JASMONATE RESISTANT 1 (JAR1) participates in phytochrome A (phyA)-mediated far-red (FR) light signaling in Arabidopsis and is a jasmonate (JA)-conjugating enzyme for the generation of an active JA-isoleucine. Accumulating evidence indicates that FR and JA signaling integrate with each other. However, the molecular mechanisms underlying their interaction remain largely unknown. Here, the phyA mutant was hypersensitive to JA. The double mutant fin219-2phyA-211 showed a synergistic effect on seedling development under FR light. Further evidence revealed that FIN219 and phyA antagonized with each other in a mutually functional demand to modulate hypocotyl elongation and expression of light- and JA-responsive genes. Moreover, FIN219 interacted with phyA under prolonged FR light, and MeJA could enhance their interaction with CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) in the dark and FR light. FIN219 and phyA interaction occurred mainly in the cytoplasm, and they regulated their mutual subcellular localization under FR light. Surprisingly, the fin219-2 mutant abolished the formation of phyA nuclear bodies under FR light. Overall, these data identified a vital mechanism of phyA-FIN219-COP1 association in response to FR light, and MeJA may allow the photoactivated phyA to trigger photomorphogenic responses.

Maize WRKY28 interacts with the DELLA protein D8 to affect skotomorphogenesis and participates in the regulation of shade avoidance and plant architecture

Competition for light from neighboring vegetation can trigger the shade-avoidance response (SAR) in plants, which is detrimental to their yield. The molecular mechanisms regulating SAR are well established in Arabidopsis, and some regulators of skotomorphogenesis have been found to be involved in the regulation of the SAR and plant architecture. However, the role of WRKY transcription factors in this process has rarely been reported, especially in maize (Zea mays). Here, we report that maize Zmwrky28 mutants exhibit shorter mesocotyls in etiolated seedlings. Molecular and biochemical analyses demonstrate that ZmWRKY28 directly binds to the promoter regions of the Small Auxin Up RNA (SAUR) gene ZmSAUR54 and the Phytochrome-Interacting Factor (PIF) gene ZmPIF4.1 to activate their expression. In addition, the maize DELLA protein Dwarf Plant8 (D8) interacts with ZmWRKY28 in the nucleus to inhibit its transcriptional activation activity. We also show that ZmWRKY28 participates in the regulation of the SAR, plant height, and leaf rolling and erectness in maize. Taken together, our results reveal that ZmWRKY28 is involved in GA-mediated skotomorphogenic development and can be used as a potential target to regulate SAR for breeding of high-density-tolerant cultivars.

Functional Characterization of a (E)-β-Ocimene Synthase Gene Contributing to the Defense against Spodoptera litura

Soybean is a worldwide crop that offers valuable proteins, fatty acids, and phytonutrients to humans but is always damaged by insect pests or pathogens. Plants have captured sophisticated defense mechanisms in resisting the attack of insects and pathogens. How to protect soybean in an environment- or human-friendly way or how to develop plant-based pest control is a hotpot. Herbivore-induced plant volatiles that are released by multiple plant species have been assessed in multi-systems against various insects, of which (E)-β-ocimene has been reported to show anti-insect function in a variety of plants, including soybean. However, the responsible gene in soybean is unknown, and its mechanism of synthesis and anti-insect properties lacks comprehensive assessment. In this study, (E)-β-ocimene was confirmed to be induced by Spodoptera litura treatment. A plastidic localized monoterpene synthase gene, designated as GmOCS, was identified to be responsible for the biosynthesis of (E)-β-ocimene through genome-wide gene family screening and in vitro and in vivo assays. Results from transgenic soybean and tobacco confirmed that (E)-β-ocimene catalyzed by GmOCS had pivotal roles in repelling a S. litura attack. This study advances the understanding of (E)-β-ocimene synthesis and its function in crops, as well as provides a good candidate for further anti-insect soybean improvement.

PHYTOCHROME-INTERACTING FACTORS are involved in starch degradation adjustment via inhibition of the carbon metabolic regulator QUA-QUINE STARCH in Arabidopsis

As sessile organisms, plants encounter dynamic and challenging environments daily, including abiotic/biotic stresses. The regulation of carbon and nitrogen allocations for the synthesis of plant proteins, carbohydrates, and lipids is fundamental for plant growth and adaption to its surroundings. Light, one of the essential environmental signals, exerts a substantial impact on plant metabolism and resource partitioning (i.e., starch). However, it is not fully understood how light signaling affects carbohydrate production and allocation in plant growth and development. An orphan gene unique to Arabidopsis thaliana, named QUA-QUINE STARCH (QQS) is involved in the metabolic processes for partitioning of carbon and nitrogen among proteins and carbohydrates, thus influencing leaf, seed composition, and plant defense in Arabidopsis. In this study, we show that PHYTOCHROME-INTERACTING bHLH TRANSCRIPTION FACTORS (PIFs), including PIF4, are required to suppress QQS during the period at dawn, thus preventing overconsumption of starch reserves. QQS expression is significantly de-repressed in pif4 and pifQ, while repressed by overexpression of PIF4, suggesting that PIF4 and its close homologs (PIF1, PIF3, and PIF5) act as negative regulators of QQS expression. In addition, we show that the evening complex, including ELF3 is required for active expression of QQS, thus playing a positive role in starch catabolism during night-time. Furthermore, QQS is epigenetically suppressed by DNA methylation machinery, whereas histone H3 K4 methyltransferases (e.g., ATX1, ATX2, and ATXR7) and H3 acetyltransferases (e.g., HAC1 and HAC5) are involved in the expression of QQS. This study demonstrates that PIF light signaling factors help plants utilize optimal amounts of starch during the night and prevent overconsumption of starch before its biosynthesis during the upcoming day.

The Arabidopsis Phytoglobin 2 mediates phytochrome B (phyB) light signaling responses during somatic embryogenesis

During the light induction of somatic embryogenesis, phyB-Pfr suppresses Phytoglobin 2, known to elevate nitric oxide (NO). NO depresses Phytochrome Interacting Factor 4 (PIF4) relieving its inhibition on embryogenesis through auxin. An obligatory step of many in vitro embryogenic systems is the somatic-embryogenic transition culminating with the formation of the embryogenic tissue. In Arabidopsis, this transition requires light and is facilitated by high levels of nitric oxide (NO) generated by either suppression of the NO scavenger Phytoglobin 2 (Pgb2), or its removal from the nucleus. Using a previously characterized induction system regulating the cellular localization of Pgb2, we demonstrated the interplay between phytochrome B (phyB) and Pgb2 during the formation of embryogenic tissue. The deactivation of phyB in the dark coincides with the induction of Pgb2 known to reduce the level of NO; consequently, embryogenesis is inhibited. Under light conditions, the active form of phyB depresses the levels of Pgb2 transcripts, thus expecting an increase in cellular NO. Induction of Pgb2 increases Phytochrome Interacting Factor 4 (PIF4) suggesting that high levels of NO repress PIF4. The PIF4 inhibition is sufficient to induce several auxin biosynthetic (CYP79B2, AMI1, and YUCCA 1, 2, and 6) and response (ARF5, 8, and 16) genes, conducive to the formation of the embryonic tissue and production of somatic embryos. Auxin responses mediated by ARF10 and 17 appear to be regulated by Pgb2, possibly through NO, in a PIF4-independent fashion. Overall, this work provides a new and preliminary model integrating Pgb2 (and NO) with phyB in the light regulation of in vitro embryogenesis.

Generation of High-Value Genomic Resource in Rice: A “Subgenomic Library” of Low-Light Tolerant Rice Cultivar Swarnaprabha

Rice is the major staple food crop for more than 50% of the world’s total population, and its production is of immense importance for global food security. As a photophilic plant, its yield is governed by the quality and duration of light. Like all photosynthesizing plants, rice perceives the changes in the intensity of environmental light using phytochromes as photoreceptors, and it initiates a morphological response that is termed as the shade-avoidance response (SAR). Phytochromes (PHYs) are the most important photoreceptor family, and they are primarily responsible for the absorption of the red (R) and far-red (FR) spectra of light. In our endeavor, we identified the morphological differences between two contrasting cultivars of rice: IR-64 (low-light susceptible) and Swarnaprabha (low-light tolerant), and we observed the phenological differences in their growth in response to the reduced light conditions. In order to create genomic resources for low-light tolerant rice, we constructed a subgenomic library of Swarnaprabha that expedited our efforts to isolate light-responsive photoreceptors. The titer of the library was found to be 3.22 × 105 cfu/mL, and the constructed library comprised clones of 4–9 kb in length. The library was found to be highly efficient as per the number of recombinant clones. The subgenomic library will serve as a genomic resource for the Gramineae community to isolate photoreceptors and other genes from rice.

Guard cell activity of PIF4 and HY5 control transpiration

Whole-plant transpiration, controlled by plant hydraulics and stomatal movement, is regulated by endogenous and environmental signals, with the light playing a dominant role. Stomatal pore size continuously adjusts to changes in light intensity and quality to ensure optimal CO₂ intake for photosynthesis on the one hand, together with minimal water loss on the other. The link between light and transpiration is well established, but the genetic knowledge of how guard cells perceive those signals to affect stomatal conductance is still somewhat limited. In the current study, we evaluated the role of two central light-responsive transcription factors; a bZIP-family transcription factor ELONGATED HYPOCOTYL5 (HY5) and the basic helix-loop-helix (BHLH) transcription factor PHYTOCHROME INTERACTING FACTOR4 (PIF4), in the regulation of steady-state transpiration. We show that overexpression of PIF4 exclusively in guard cells (GCPIF4) decreases transpiration, and can restrain the high transpiration of the pif4 mutant. Expression of HY5 specifically in guard cells (GCHY5) had the opposite effect of enhancing transpiration rates of WT- Arabidopsis and tobacco plants and of the hy5 mutant in Arabidopsis. In addition, we show that GCHY5 can reverse the low transpiration caused by guard cell overexpression of the sugar sensor HEXOKINASE1 (HXK1, GCHXK), an established low transpiring genotype. Finally, we suggest that the GCHY5 reversion of low transpiration by GCHXK requires the auto-activation of the endogenous HY5 in other tissues. These findings support the existence of an ongoing diurnal regulation of transpiration by the light-responsive transcription factors HY5 and PIF4 in the stomata, which ultimately determine the whole-plant water use efficiency.

Effect of the biosynthesis of the volatile compound phenylacetaldehyde on chloroplast modifications in tea (Camellia sinensis) plants

Plant volatile compounds have important physiological and ecological functions. Phenylacetaldehyde (PAld), a volatile phenylpropanoid/benzenoid, accumulates in the leaves of tea (Camellia sinensis) plants grown under continuous shading. This study was conducted to determine whether PAld production is correlated with light and to elucidate the physiological functions of PAld in tea plants. Specifically, the upstream mechanism modulating PAld biosynthesis in tea plants under different light conditions as well as the effects of PAld on chloroplast/chlorophyll were investigated. The biosynthesis of PAld was inhibited under light, whereas it was induced in darkness. The structural gene encoding aromatic amino acid aminotransferase 1 (CsAAAT1) was expressed at a high level in darkness, consistent with its importance for PAld accumulation. Additionally, the results of a transcriptional activation assay and an electrophoretic mobility shift assay indicated CsAAAT1 expression was slightly activated by phytochrome-interacting factor 3-2 (CsPIF3-2), which is a light-responsive transcription factor. Furthermore, PAld might promote the excitation of chlorophyll in dark-treated chloroplasts and mediate electron energy transfer in cells. However, the accumulated PAld can degrade chloroplasts and chlorophyll, with potentially detrimental effects on photosynthesis. Moreover, PAld biosynthesis is inhibited in tea leaves by red and blue light, thereby decreasing the adverse effects of PAld on chloroplasts during daytime. In conclusion, the regulated biosynthesis of PAld in tea plants under light and in darkness leads to chloroplast modifications. The results of this study have expanded our understanding of the biosynthesis and functions of volatile phenylpropanoids/benzenoids in tea leaves.

Brachypodium distachyon Seedlings Display Accession-Specific Morphological and Transcriptomic Responses to the Microgravity Environment of the International Space Station

Plants have been recognized as key components of bioregenerative life support systems for space exploration, and many experiments have been carried out to evaluate their adaptability to spaceflight. Unfortunately, few of these experiments have involved monocot plants, which constitute most of the crops used on Earth as sources of food, feed, and fiber. To better understand the ability of monocot plants to adapt to spaceflight, we germinated and grew Brachypodium distachyon seedlings of the Bd21, Bd21-3, and Gaz8 accessions in a customized growth unit on the International Space Station, along with 1-g ground controls. At the end of a 4-day growth period, seedling organ’s growth and morphologies were quantified, and root and shoot transcriptomic profiles were investigated using RNA-seq. The roots of all three accessions grew more slowly and displayed longer root hairs under microgravity conditions relative to ground control. On the other hand, the shoots of Bd21-3 and Gaz-8 grew at similar rates between conditions, whereas those of Bd21 grew more slowly under microgravity. The three Brachypodium accessions displayed dramatically different transcriptomic responses to microgravity relative to ground controls, with the largest numbers of differentially expressed genes (DEGs) found in Gaz8 (4527), followed by Bd21 (1353) and Bd21-3 (570). Only 47 and six DEGs were shared between accessions for shoots and roots, respectively, including DEGs encoding wall-associated proteins and photosynthesis-related DEGs. Furthermore, DEGs associated with the “Oxidative Stress Response” GO group were up-regulated in the shoots and down-regulated in the roots of Bd21 and Gaz8, indicating that Brachypodium roots and shoots deploy distinct biological strategies to adapt to the microgravity environment. A comparative analysis of the Brachypodium oxidative-stress response DEGs with the Arabidopsis ROS wheel suggests a connection between retrograde signaling, light response, and decreased expression of photosynthesis-related genes in microgravity-exposed shoots. In Gaz8, DEGs were also found to preferentially associate with the “Plant Hormonal Signaling” and “MAP Kinase Signaling” KEGG pathways. Overall, these data indicate that Brachypodium distachyon seedlings exposed to the microgravity environment of ISS display accession- and organ-specific responses that involve oxidative stress response, wall remodeling, photosynthesis inhibition, expression regulation, ribosome biogenesis, and post-translational modifications. The general characteristics of these responses are similar to those displayed by microgravity-exposed Arabidopsis thaliana seedlings. However, organ- and accession-specific components of the response dramatically differ both within and between species. These results suggest a need to directly evaluate candidate-crop responses to microgravity to better understand their specific adaptability to this novel environment and develop cultivation strategies allowing them to strive during spaceflight.

The Histone H3K27 Demethylase REF6 Is a Positive Regulator of Light-Initiated Seed Germination in Arabidopsis

Seed germination is the first step in initiating a new life cycle in seed plants. Light is a major environmental factor affecting seed germination. Phytochrome B (phyB) is the primary photoreceptor promoting germination during the initial phase of imbibition. Post-translational histone methylation occurring at both lysine and arginine residues plays a crucial role in transcriptional regulation in plants. However, the role of histone lysine demethylation in light-initiated seed germination is not yet reported. Here, we identified that Relative of Early Flowering 6 (REF6)/Jumonji Domain-containing Protein 12 (JMJ12), a histone H3 lysine 27 (H3K27) demethylase, acts as a positive regulator of light-initiated seed germination. The loss of function of REF6 in Arabidopsis inhibits phyB-dependent seed germination. Genome-wide RNA-sequencing analysis revealed that REF6 regulates about half of the light-responsive transcriptome in imbibed seeds, including genes related to multiple hormonal signaling pathways and cellular processes. Phenotypic analyses indicated that REF6 not only regulates seed germination through GA (gibberellin) and ABA (abscisic acid) processes but also depends on the auxin signaling pathway. Furthermore, REF6 directly binds to and decreases the histone H3K27me3 levels of auxin-signaling- and cell-wall-loosening-related genes, leading to the activated expression of these genes in imbibed seeds. Taken together, our study identifies REF6 as the first histone lysine demethylase required for light-initiated seed germination. Our work also reveals the important role of REF6-mediated histone H3K27 demethylation in transcriptional reprogramming in the light-initiated seed germination process.

Basic Helix-Loop-Helix Transcription Factors: Regulators for Plant Growth Development and Abiotic Stress Responses

Plant basic helix-loop-helix (bHLH) transcription factors are involved in many physiological processes, and they play important roles in the abiotic stress responses. The literature related to genome sequences has increased, with genome-wide studies on the bHLH transcription factors in plants. Researchers have detailed the functionally characterized bHLH transcription factors from different aspects in the model plant Arabidopsis thaliana, such as iron homeostasis and abiotic stresses; however, other important economic crops, such as rice, have not been summarized and highlighted. The bHLH members in the same subfamily have similar functions; therefore, unraveling their regulatory mechanisms will help us to identify and understand the roles of some of the unknown bHLH transcription factors in the same subfamily. In this review, we summarize the available knowledge on functionally characterized bHLH transcription factors according to four categories: plant growth and development; metabolism synthesis; plant signaling, and abiotic stress responses. We also highlight the roles of the bHLH transcription factors in some economic crops, especially in rice, and discuss future research directions for possible genetic applications in crop breeding.

Transcriptome-wide characterization of bHLH transcription factor genes in Lycoris radiata and functional analysis of their response to MeJA

As one of the biggest plant specific transcription factor (TF) families, basic helix-loop-helix (bHLH) protein, plays significant roles in plant growth, development, and abiotic stress responses. However, there has been minimal research about the effects of methyl jasmonate (MeJA) treatment on the bHLH gene family in Lycoris radiata (L'Her.) Herb. In this study, based on transcriptome sequencing data, 50 putative L. radiata bHLH (LrbHLH) genes with complete open reading frames (ORFs), which were divided into 20 bHLH subfamilies, were identified. The protein motif analyses showed that a total of 10 conserved motifs were found in LrbHLH proteins and motif 1 and motif 2 were the most highly conserved motifs. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of LrbHLH genes revealed their involvement in regulation of plant growth, jasmonic acid (JA) mediated signaling pathway, photoperiodism, and flowering. Furthermore, subcellular localization revealed that most LrbHLHs were located in the nucleus. Expression pattern analysis of LrbHLH genes in different tissues and at flower developmental stages suggested that their expression differed across lineages and might be important for plant growth and organ development in Lycoris. In addition, all LrbHLH genes exhibited specific spatial and temporal expression patterns under MeJA treatment. Moreover, protein-protein interaction (PPI) network analysis and yeast two-hybrid assay showed that numerous LrbHLHs could interact with jasmonate ZIM (zinc-finger inflorescence meristem) domain (JAZ) proteins. This research provides a theoretical basis for further investigation of LrbHLHs to find their functions and insights for their regulatory mechanisms involved in JA signaling pathway.

14-3-3 proteins regulate photomorphogenesis by facilitating light-induced degradation of PIF3

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

Regulatory Mechanisms of Heat Stress Response and Thermomorphogenesis in Plants

As worldwide warming intensifies, the average temperature of the earth continues to increase. Temperature is a key factor for the growth and development of all organisms and governs the distribution and seasonal behavior of plants. High temperatures lead to various biochemical, physiological, and morphological changes in plants and threaten plant productivity. As sessile organisms, plants are subjected to various hostile environmental factors and forced to change their cellular state and morphological architecture to successfully deal with the damage they suffer. Therefore, plants have evolved multiple strategies to cope with an abnormal rise in temperature. There are two main mechanisms by which plants respond to elevated environmental temperatures. One is the heat stress response, which is activated under extremely high temperatures; the other is the thermomorphogenesis response, which is activated under moderately elevated temperatures, below the heat-stress range. In this review, we summarize recent progress in the study of these two important heat-responsive molecular regulatory pathways mediated, respectively, by the Heat Shock Transcription Factor (HSF)-Heat Shock Protein (HSP) pathway and PHYTOCHROME INTER-ACTING FACTOR 4 (PIF4) pathways in plants and elucidate the regulatory mechanisms of the genes involved in these pathways to provide comprehensive data for researchers studying the heat response. We also discuss future perspectives in this field.

Phytochrome interacting factor regulates stomatal aperture by coordinating red light and abscisic acid

Stomata are crucial valves coordinating the fixation of carbon dioxide by photosynthesis and water loss through leaf transpiration. Phytochrome interacting factors (PIFs) are negative regulators of red light responses that belong to the basic helix-loop-helix family of transcription factors. Here, we show that the rice (Oryza sativa) PIF family gene OsPIL15 acts as a negative regulator of stomatal aperture to control transpiration in rice. OsPIL15 reduces stomatal aperture by activating rice ABSCISIC ACID INSENSITIVE 5 (OsABI5), which encodes a critical positive regulator of ABSCISIC ACID (ABA) signaling in rice. Moreover, OsPIL15 interacts with the NIGT1/HRS1/HHO family transcription factor rice HRS1 HOMOLOG 3 (OsHHO3) to possibly enhance the regulation of stomatal aperture. Notably, we discovered that the maize (Zea mays) PIF family genes ZmPIF1 and ZmPIF3, which are homologous to OsPIL15, are also involved in the regulation of stomatal aperture in maize, indicating that PIF-mediated regulation of stomatal aperture may be conserved in the plant lineage. Our findings explain the molecular mechanism by which PIFs play a role in red-light-mediated stomatal opening, and demonstrate that PIFs regulate stomatal aperture by coordinating the red light and ABA signaling pathways.

Phytochrome B enhances seed germination tolerance to high temperature by reducing S-nitrosylation of HFR1

Light and ambient high temperature (HT) have opposite effects on seed germination. Light induces seed germination through activating the photoreceptor phytochrome B (phyB), resulting in the stabilization of the transcription factor HFR1, which in turn sequesters the suppressor PIF1. HT suppresses seed germination and triggers protein S-nitrosylation. Here, we find that HT suppresses seed germination by inducing the S-nitrosylation of HFR1 at C164, resulting in its degradation, the release of PIF1, and the activation of PIF1-targeted SOMNUS (SOM) expression to alter gibberellin (GA) and abscisic acid (ABA) metabolism. Active phyB (phyBY276H ) antagonizes HFR1 S-nitrosylation and degradation by increasing S-nitrosoglutathione reductase (GSNOR) activity. In line with this, substituting cysteine-164 of HFR1 with serine (HFR1C164S ) abolishes the S-nitrosylation of HFR1 and decreases the HT-induced degradation of HFR1. Taken together, our study suggests that HT and phyB antagonistically modulate the S-nitrosylation level of HFR1 to coordinate seed germination, and provides the possibility to enhance seed thermotolerance through gene-editing of HFR1.

Transcriptome Analysis of Early Senescence in the Post-Anthesis Flag Leaf of Wheat (Triticum aestivum L.)

Flag leaf senescence is an important determinant of wheat yield, as leaf senescence occurs in a coordinated manner during grain filling. However, the biological process of early senescence of flag leaves post-anthesis is not clear. In this study, early senescence in wheat was investigated using a high-throughput RNA sequencing technique. A total of 4887 differentially expressed genes (DEGs) were identified, and any showing drastic expression changes were then linked to particular biological processes. A hierarchical cluster analysis implied potential relationships between NAC genes and post-anthesis senescence in the flag leaf. In addition, a large set of genes associated with the synthesis; transport; and signaling of multiple phytohormones (JA, ABA, IAA, ET, SA, BR, and CTK) were expressed differentially, and many DEGs related to ABA and IAA were identified. Our results provide insight into the molecular processes taking place during the early senescence of flag leaves, which may provide useful information in improving wheat yield in the future.

Casein kinase CK2 structure and activities in plants

Casein kinase CK2 is a highly conserved serine/threonine protein kinase and exists in all eukaryotes. It has been demonstrated to be widely involved in the biological processes of plants. The CK2 holoenzyme is a heterotetramer consisting of two catalytic subunits (α and/or α') and two regulatory subunits (β). CK2 in plants is generally encoded by multiple genes, with monomeric and oligomeric forms present in the tissue. Various subunit genes of CK2 have been cloned and characterized from Arabidopsis thaliana, tobacco, maize, wheat, tomato, and other plants. This paper reviews the structural features of CK2, provides a clear classification of its physiological functions and mechanisms of action, and elaborates on the regulation of CK2 activity to provide a knowledge base for subsequent studies of CK2 in plants.

Genome-wide analysis of basic helix-loop-helix genes in Dendrobium catenatum and functional characterization of DcMYC2 in jasmonate-mediated immunity to Sclerotium delphinii

Dendrobium catenatum, belonging to the Orchidaceae, is a precious Chinese herbal medicine. Sclerotium delphinii (P1) is a broad-spectrum fungal disease, which causes widespread loss in the near-wild cultivation of D. catenatum. Thus, resistance breeding of D. catenatum has become the key to solve this problem. The basic helix-loop-helix (bHLH) gene family is closely related to plant resistance to external stresses, but the related research in D. catenatum is not deep enough yet. Phylogenetic analysis showed that 108 DcbHLH genes could be divided into 23 subgroups. Promoter cis-acting elements revealed that DcbHLHs contain a large number of stress-related cis-acting elements. Transcriptome analysis of MeJA and P1 treatment manifested that exogenous MeJA can change the expression pattern of most bHLH genes, especially the IIIe subgroup, including inhibiting the expression of DcbHLH026 (MYC2a) and promoting the expression of DcbHLH027 (MYC2b). Subcellular localization indicated that they were located in the nucleus. Furthermore, exogenous MeJA treatment significantly delayed disease time and reduced lesion size after infection with P1. DcMYC2b-overexpression Arabidopsis lines showed significantly smaller lesions after being infected with P1 than the wild type, indicating that DcMYC2b functions as an important positive regulator in D. catenatum defense against P1. Our findings shed more insights into the critical role of the DcbHLH family in plants and the resistance breeding of D. catenatum.

Comparative transcriptomics identifies candidate genes involved in the evolutionary transition from dehiscent to indehiscent fruits in Lepidium (Brassicaceae)

BACKGROUND

Fruits are the seed-bearing structures of flowering plants and are highly diverse in terms of morphology, texture and maturation. Dehiscent fruits split open upon maturation to discharge their seeds while indehiscent fruits are dispersed as a whole. Indehiscent fruits evolved from dehiscent fruits several times independently in the crucifer family (Brassicaceae). The fruits of Lepidium appelianum, for example, are indehiscent while the fruits of the closely related L. campestre are dehiscent. Here, we investigate the molecular and genetic mechanisms underlying the evolutionary transition from dehiscent to indehiscent fruits using these two Lepidium species as model system.

RESULTS

We have sequenced the transcriptomes and small RNAs of floral buds, flowers and fruits of L. appelianum and L. campestre and analyzed differentially expressed genes (DEGs) and differently differentially expressed genes (DDEGs). DEGs are genes that show significantly different transcript levels in the same structures (buds, flowers and fruits) in different species, or in different structures in the same species. DDEGs are genes for which the change in expression level between two structures is significantly different in one species than in the other. Comparing the two species, the highest number of DEGs was found in flowers, followed by fruits and floral buds while the highest number of DDEGs was found in fruits versus flowers followed by flowers versus floral buds. Several gene ontology terms related to cell wall synthesis and degradation were overrepresented in different sets of DEGs highlighting the importance of these processes for fruit opening. Furthermore, the fruit valve identity genes FRUITFULL and YABBY3 were among the DEGs identified. Finally, the microRNA miR166 as well as the TCP transcription factors BRANCHED1 (BRC1) and TCP FAMILY TRANSCRIPTION FACTOR 4 (TCP4) were found to be DDEGs.

CONCLUSIONS

Our study reveals differences in gene expression between dehiscent and indehiscent fruits and uncovers miR166, BRC1 and TCP4 as candidate genes for the evolutionary transition from dehiscent to indehiscent fruits in Lepidium.

Shade Delayed Flowering Phenology and Decreased Reproductive Growth of Medicago sativa L

Alfalfa (Medicago sativa L.) is an important forage in intercropping or rotation ecosystem, and shading is the principal limiting factor for its growth under the crop or forest. Agronomic studies showed that shading would systematically reduce the biomass of alfalfa. However, little is known about the reproduction of alfalfa under shading conditions. In order to study the effect of shading on the reproductive characteristics of alfalfa, two alfalfa cultivars ("Victoria" and "Eureka") were used to study the effect of shading levels (full light, 56.4% shade, and 78.7% shade) on alfalfa flowering phenology, pollen viability, stigma receptivity, and seed quality. Results showed that shading delayed flowering phenology, shortened the flowering stage, faded the flower colors, and significantly reduced pollen viability, stigma receptivity, the number of flowers, quantity, and quality of seeds. Under shading conditions, seed yield per plant was obviously positively correlated with germination potential, germination rate, pollen viability, and 1,000-seed weight. The number of flower buds, pollen viability, 1,000-seed weight, and germination rate had the greatest positive direct impact on seed yield per plant. Our findings suggested that delayed flowering and reducing reproduction growth were important strategies for alfalfa to cope with shading and pollen viability was the key bottleneck for the success of alfalfa reproduction under shading. However, given that alfalfa is a perennial vegetative-harvest forage, delaying flowering in a weak light environment was beneficial to maintain the high aboveground biomass of alfalfa. Therefore, this should be taken into account when breeding alfalfa cultivars suitable for intercropping. Future research should further reveal the genetic and molecular mechanism of delayed flowering regulating the accumulation and distribution of assimilates between vegetative and reproductive organs of alfalfa under shading, so as to provide a theoretical basis for breeding of shade-tolerant alfalfa cultivars.

Comprehensive analysis of cucumber C-repeat/dehydration-responsive element binding factor family genes and their potential roles in cold tolerance of cucumber

BACKGROUND

Cold stress is one of the main abiotic stresses limiting cucumber (Cucumis sativus L.) growth and production. C-repeat binding factor/Dehydration responsive element-binding 1 protein (CBF/DREB1), containing conserved APETALA2 (AP2) DNA binding domains and two characteristic sequences, are key signaling genes that can be rapidly induced and play vital roles in plant response to low temperature. However, the CBF family has not been systematically elucidated in cucumber, and the expression pattern of this family genes under cold stress remains unclear.

RESULTS

In this study, three CsCBF family genes were identified in cucumber genome and their protein conserved domain, protein physicochemical properties, gene structure and phylogenetic analysis were further comprehensively analyzed. Subcellular localization showed that all three CsCBFs were localized in the nucleus. Cis-element analysis of the promoters indicated that CsCBFs might be involved in plant hormone response and abiotic stress response. Expression analysis showed that the three CsCBFs could be significantly induced by cold stress, salt and ABA. The overexpression of CsCBFs in cucumber seedlings enhanced the tolerance to cold stress, and importantly, the transcript levels of CsCOR genes were significantly upregulated in 35S:CsCBFs transgenic plants after cold stress treatment. Biochemical analyses ascertained that CsCBFs directly activated CsCOR genes expression by binding to its promoter, thereby enhancing plant resistance to cold stress.

CONCLUSION

This study provided a foundation for further research on the function of CsCBF genes in cold stress resistance and elucidating its mechanism.

Phytochrome-interacting factors orchestrate hypocotyl adventitious root initiation in Arabidopsis

Adventitious roots (ARs) are an important type of plant root and display high phenotypic plasticity in response to different environmental stimuli. It is known that photoreceptors inhibit darkness-induced hypocotyl adventitious root (HAR) formation by directly stabilizing Aux/IAA proteins. In this study, we further report that phytochrome-interacting factors (PIFs) plays a central role in HAR initiation by simultaneously inducing the expression of genes involved in auxin biosynthesis, auxin transport and the transcriptional control of root primordium initiation. We found that, on the basis of their activity downstream of phytochrome, PIFs are required for darkness-induced HAR formation. Specifically, PIFs directly bind to the promoters of some genes involved in root formation, including auxin biosynthesis genes YUCCA2 (YUC2) and YUC6, the auxin influx carrier genes AUX1 and LAX3, and the transcription factors WOX5/7 and LBD16/29, to activate their expression. These findings reveal a previously uncharacterized transcriptional regulatory network underlying HAR formation.

Genetic Dissection of Light-Regulated Adventitious Root Induction in Arabidopsis thaliana Hypocotyls

Photomorphogenic responses of etiolated seedlings include the inhibition of hypocotyl elongation and opening of the apical hook. In addition, dark-grown seedlings respond to light by the formation of adventitious roots (AR) on the hypocotyl. How light signaling controls adventitious rooting is less well understood. Hereto, we analyzed adventitious rooting under different light conditions in wild type and photomorphogenesis mutants in Arabidopsis thaliana. Etiolation was not essential for AR formation but raised the competence to form AR under white and blue light. The blue light receptors CRY1 and PHOT1/PHOT2 are key elements contributing to the induction of AR formation in response to light. Furthermore, etiolation-controlled competence for AR formation depended on the COP9 signalosome, E3 ubiquitin ligase CONSTITUTIVELY PHOTOMORPHOGENIC (COP1), the COP1 interacting SUPPRESSOR OF PHYA-105 (SPA) kinase family members (SPA1,2 and 3) and Phytochrome-Interacting Factors (PIF). In contrast, ELONGATED HYPOCOTYL5 (HY5), suppressed AR formation. These findings provide a genetic framework that explains the high and low AR competence of Arabidopsis thaliana hypocotyls that were treated with dark, and light, respectively. We propose that light-induced auxin signal dissipation generates a transient auxin maximum that explains AR induction by a dark to light switch.

RNA-Seq Analysis Identifies Transcription Factors Involved in Anthocyanin Biosynthesis of 'Red Zaosu' Pear Peel and Functional Study of PpPIF8

Red-skinned pears are favored by people for their attractive appearance and abundance of anthocyanins. However, the molecular basis of anthocyanin biosynthesis in red pears remains elusive. Here, a comprehensive transcriptome analysis was conducted to explore the potential regulatory mechanism of anthocyanin biosynthesis in 'Red Zaosu' pear (Pyrus pyrifolia × Pyrus communis). Gene co-expression analysis and transcription factor mining identified 263 transcription factors, which accounted for 6.59% of the total number of transcription factors in the pear genome in two gene modules that are highly correlated with anthocyanin biosynthesis. Clustering, gene network modeling with STRING-DB, and local motif enrichment analysis (CentriMo) analysis suggested that PpPIF8 may play a role in anthocyanin biosynthesis. Furthermore, eight PIFs were identified in the pear genome, of which only PpPIF8 was rapidly induced by light. Functional studies showed that PpPIF8 localizes in the nucleus and is preferentially expressed in the tissue of higher levels of anthocyanin. The overexpression of PpPIF8 in pear peel and pear calli promotes anthocyanin biosynthesis and upregulates the expression of anthocyanin biosynthesis genes. Yeast-one hybrid and transgenic analyses indicated that PpPIF8 binds to the PpCHS promoter to induce PpCHS expression. The positive effect of PpPIF8 on anthocyanin biosynthesis is different from previously identified negative regulators of PyPIF5 and MdPIF7 in pear and apple. Taken together, our data not only provide a comprehensive view of transcription events during the coloration of pear peel, but also resolved the regulatory role of PpPIF8 in the anthocyanin biosynthesis pathway.