Gibberellin signaling modulates flowering via the DELLA-BRAHMA-NF-YC module in Arabidopsis.

Gibberellin (GA) plays a key role in floral induction by activating the expression of floral integrator genes in plants, but the epigenetic regulatory mechanisms underlying this process remain unclear. Here, we show that BRAHMA (BRM), a core subunit of the chromatin-remodeling SWItch/sucrose nonfermentable (SWI/SNF) complex that functions in various biological processes by regulating gene expression, is involved in GA-signaling-mediated flowering via the formation of the DELLA-BRM-NF-YC module in Arabidopsis (Arabidopsis thaliana). DELLA, BRM, and NF-YC transcription factors interact with one another, and DELLA proteins promote the physical interaction between BRM and NF-YC proteins. This impairs the binding of NF-YCs to SOC1, a major floral integrator gene, to inhibit flowering. On the other hand, DELLA proteins also facilitate the binding of BRM to SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1). The GA-induced degradation of DELLA proteins disturbs the DELLA-BRM-NF-YC module, prevents BRM from inhibiting NF-YCs, and decreases the DNA-binding ability of BRM, which promote the deposition of H3K4me3 on SOC1 chromatin, leading to early flowering. Collectively, our findings show that BRM is a key epigenetic partner of DELLA proteins during the floral transition. Moreover, they provide molecular insights into how GA signaling coordinates an epigenetic factor with a transcription factor to regulate the expression of a flowering gene and flowering in plants.

Arabidopsis NF-YCs play dual roles in repressing brassinosteroid biosynthesis and signaling during light-regulated hypocotyl elongation.

Light functions as the primary environmental stimulus and brassinosteroids (BRs) as important endogenous growth regulators throughout the plant lifecycle. Photomorphogenesis involves a series of vital developmental processes that require the suppression of BR-mediated seedling growth, but the mechanism underlying the light-controlled regulation of the BR pathway remains unclear. Here, we reveal that nuclear factor YC proteins (NF-YCs) function as essential repressors of the BR pathway during light-controlled hypocotyl growth in Arabidopsis thaliana. In the light, NF-YCs inhibit BR biosynthesis by directly targeting the promoter of the BR biosynthesis gene BR6ox2 and repressing its transcription. NF-YCs also interact with BIN2, a critical repressor of BR signaling, and facilitate its stabilization by promoting its Tyr200 autophosphorylation, thus inhibiting the BR signaling pathway. Consistently, loss-of-function mutants of NF-YCs show etiolated growth and constitutive BR responses, even in the light. Our findings uncover a dual role of NF-YCs in repressing BR biosynthesis and signaling, providing mechanistic insights into how light antagonizes the BR pathway to ensure photomorphogenic growth in Arabidopsis.

EDS1-interacting J protein 1 is an essential negative regulator of plant innate immunity in Arabidopsis.

Plants have evolved precise mechanisms to optimize immune responses against pathogens. ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1) plays a vital role in plant innate immunity by regulating basal resistance and effector-triggered immunity. Nucleocytoplasmic trafficking of EDS1 is required for resistance reinforcement, but the molecular mechanism remains elusive. Here, we show that EDS1-INTERACTING J PROTEIN1 (EIJ1), which acts as a DnaJ protein-like chaperone in response to pathogen infection, functions as an essential negative regulator of plant immunity by interacting with EDS1. The loss-of-function mutation of EIJ1 did not affect plant growth but significantly enhanced pathogen resistance. Upon pathogen infection, EIJ1 relocalized from the chloroplast to the cytoplasm, where it interacted with EDS1, thereby restricting pathogen-triggered trafficking of EDS1 to the nucleus and compromising resistance at an early infection stage. During disease development, EIJ1 was gradually degraded, allowing the nuclear accumulation of EDS1 for transcriptional resistance reinforcement. The avirulent strain Pst DC3000 (AvrRps4) abolished the repressive action of EIJ1 by rapidly inducing its degradation in the effector-triggered immunity response. Thus, our findings show that EIJ1 is an essential EDS1-dependent negative regulator of innate plant immunity and provide a mechanistic understanding of how the nuclear versus cytoplasmic distribution of EDS1 is regulated during the immune response.

Genetic mapping and functional genomics of soybean seed protein.

Soybean is an utterly important crop for high-quality meal protein and vegetative oil. Soybean seed protein content has become a key factor in nutrients for livestock feed as well as human dietary consumption. Genetic improvement of soybean seed protein is highly desired to meet the demands of rapidly growing world population. Molecular mapping and genomic analysis in soybean have identified many quantitative trait loci (QTL) underlying seed protein content control. Exploring the mechanisms of seed storage protein regulation will be helpful to achieve the improvement of protein content. However, the practice of breeding higher protein soybean is challenging because soybean seed protein is negatively correlated with seed oil content and yield. To overcome the limitation of such inverse relationship, deeper insights into the property and genetic control of seed protein are required. Recent advances of soybean genomics have strongly enhanced the understandings for molecular mechanisms of soybean with better seed quality. Here, we review the research progress in the genetic characteristics of soybean storage protein, and up-to-date advances of molecular mappings and genomics of soybean protein. The key factors underlying the mechanisms of the negative correlation between protein and oil in soybean seeds are elaborated. We also briefly discuss the future prospects of breaking the bottleneck of the negative correlation to develop high protein soybean without penalty of oil and yield. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-023-01373-5.

Stress response proteins NRP1 and NRP2 are pro-survival factors that inhibit cell death during ER stress.

Environmental stresses cause an increased number of unfolded or misfolded proteins to accumulate in the endoplasmic reticulum (ER), resulting in ER stress. To restore ER homeostasis and survive, plants initiate an orchestrated signaling pathway known as the unfolded protein response (UPR). Asparagine-rich protein (NRP) 1 and NRP2, two homologous proteins harboring a Development and Cell Death domain, are associated with various stress responses in Arabidopsis (Arabidopsis thaliana), but the relevant molecular mechanism remains obscure. Here, we show that NRP1 and NRP2 act as key pro-survival factors during the ER stress response and that they inhibit cell death. Loss-of-function of NRP1 and NRP2 results in decreased tolerance to the ER stress inducer tunicamycin (TM), accelerating cell death. NRP2 is constitutively expressed while NRP1 is induced in plants under ER stress. In Arabidopsis, basic leucine zipper protein (bZIP) 28 and bZIP60 are important transcription factors in the UPR that activates the expression of many ER stress-related genes. Notably, under ER stress, bZIP60 activates NRP1 by directly binding to the UPRE-I element in the NRP1 promoter. These findings reveal a pro-survival strategy in plants wherein the bZIP60-NRPs cascade suppresses cell death signal transmission, improving survival under adverse conditions.

The gibberellin signaling negative regulator RGA-LIKE3 promotes seed storage protein accumulation.

Seed storage protein (SSP) acts as one of the main components of seed storage reserves, of which accumulation is tightly mediated by a sophisticated regulatory network. However, whether and how gibberellin (GA) signaling is involved in this important biological event is not fully understood. Here, we show that SSP content in Arabidopsis (Arabidopsis thaliana) is significantly reduced by GA and increased in the GA biosynthesis triple mutant ga3ox1/3/4. Further investigation shows that the DELLA protein RGA-LIKE3 (RGL3), a negative regulator of GA signaling, is important for SSP accumulation. In rgl3 and 35S:RGL3-HA, the expression of SSP genes is down- and upregulated, respectively, compared with that in the wild-type. RGL3 interacts with ABSCISIC ACID INSENSITIVE3 (ABI3), a critical transcription factor for seed developmental processes governing SSP accumulation, both in vivo and in vitro, thus greatly promoting the transcriptional activating ability of ABI3 on SSP genes. In addition, genetic evidence shows that RGL3 and ABI3 regulate SSP accumulation in an interdependent manner. Therefore, we reveal a function of RGL3, a little studied DELLA member, as a coactivator of ABI3 to promote SSP biosynthesis during seed maturation stage. This finding advances the understanding of mechanisms in GA-mediated seed storage reserve accumulation.

A novel Arabidopsis gene RGAT1 is required for GA-mediated tapetum and pollen development.

The phytohormone gibberellin (GA) is critical for anther development. RGA, a member of the DELLA family of proteins that are central GA signalling repressors, is a key regulator of male fertility in plants. However, the downstream genes in GA-RGA-mediated anther development remain to be characterised. We identified RGA Target 1 (RGAT1), a novel Arabidopsis gene, that functions as an important RGA-regulated target in pollen development. RGAT1 is predominantly expressed in the tapetum and microspores during anther stages 8-11, and can be directly activated by RGA and suppressed by GA in inflorescence apices. Both loss of function and gain of function of RGAT1 led to abnormal tapetum development, resulting in abortive pollen and short siliques. In RGAT1-knockdown and overexpression lines, pollen abortion occurred at stage 10. Loss of RGAT1 function induced the premature degeneration of tapetal cells with defective ER-derived tapetosomes, while RGAT1 overexpression delayed tapetum degeneration. TUNEL assay confirmed that RGAT1 participates in timely tapetal programmed cell death. Moreover, reducing RGAT1 expression partially rescued the tapetal developmental defects in GA-deficient ga1-3 mutant. Our findings revealed that RGAT1 is a direct target of RGA and plays an essential role in GA-mediated tapetum and pollen development.

NF-YCs modulate histone variant H2A.Z deposition to regulate photomorphogenic growth in Arabidopsis.

In plants, light signals trigger a photomorphogenic program involving transcriptome changes, epigenetic regulation, and inhibited hypocotyl elongation. The evolutionarily conserved histone variant H2A.Z, which functions in transcriptional regulation, is deposited in chromatin by the SWI2/SNF2-RELATED 1 complex (SWR1c). However, the role of H2A.Z in photomorphogenesis and its deposition mechanism remain unclear. Here, we show that in Arabidopsis thaliana, H2A.Z deposition at its target loci is induced by light irradiation via NUCLEAR FACTOR-Y, subunit C (NF-YC) proteins, thereby inhibiting photomorphogenic growth. NF-YCs physically interact with ACTIN-RELATED PROTEIN6 (ARP6), a key component of the SWR1c that is essential for depositing H2A.Z, in a light-dependent manner. NF-YCs and ARP6 function together as negative regulators of hypocotyl growth by depositing H2A.Z at their target genes during photomorphogenesis. Our findings reveal an important role for the histone variant H2A.Z in photomorphogenic growth and provide insights into a novel transcription regulatory node that mediates H2A.Z deposition to control plant growth in response to changing light conditions.

FT5a interferes with the Dt1-AP1 feedback loop to control flowering time and shoot determinacy in soybean.

Flowering time and stem growth habit determine inflorescence architecture in soybean, which in turn influences seed yield. Dt1, a homolog of Arabidopsis TERMINAL FLOWER 1 (TFL1), is a major controller of stem growth habit, but its underlying molecular mechanisms remain unclear. Here, we demonstrate that Dt1 affects node number and plant height, as well as flowering time, in soybean under long-day conditions. The bZIP transcription factor FDc1 physically interacts with Dt1, and the FDc1-Dt1 complex directly represses the expression of APETALA1 (AP1). We propose that FT5a inhibits Dt1 activity via a competitive interaction with FDc1 and directly upregulates AP1. Moreover, AP1 represses Dt1 expression by directly binding to the Dt1 promoter, suggesting that AP1 and Dt1 form a suppressive regulatory feedback loop to determine the fate of the shoot apical meristem. These findings provide novel insights into the roles of Dt1 and FT5a in controlling the stem growth habit and flowering time in soybean, which determine the adaptability and grain yield of this important crop.

Low temperature synergistically promotes wounding-induced indole accumulation by INDUCER OF CBF EXPRESSION-mediated alterations of jasmonic acid signaling in Camellia sinensis.

Plants have to cope with various environmental stress factors which significantly impact plant physiology and secondary metabolism. Individual stresses, such as low temperature, are known to activate plant volatile compounds as a defense. However, less is known about the effect of multiple stresses on plant volatile formation. Here, the effect of dual stresses (wounding and low temperature) on volatile compounds in tea (Camellia sinensis) plants and the underlying signalling mechanisms were investigated. Indole, an insect resistance volatile, was maintained at a higher content and for a longer time under dual stresses compared with wounding alone. CsMYC2a, a jasmonate (JA)-responsive transcription factor, was the major regulator of CsTSB2, a gene encoding a tryptophan synthase ß-subunit essential for indole synthesis. During the recovery phase after tea wounding, low temperature helped to maintain a higher JA level. Further study showed that CsICE2 interacted directly with CsJAZ2 to relieve inhibition of CsMYC2a, thereby promoting JA biosynthesis and downstream expression of the responsive gene CsTSB2 ultimately enhancing indole biosynthesis. These findings shed light on the role of low temperature in promoting plant damage responses and advance knowledge of the molecular mechanisms by which multiple stresses coordinately regulate plant responses to the biotic and abiotic environment.

Temporal-Specific Interaction of NF-YC and CURLY LEAF during the Floral Transition Regulates Flowering.

The flowering time of higher plants is controlled by environmental cues and intrinsic signals. In Arabidopsis (Arabidopsis thaliana), flowering is accelerated by exposure to long-day conditions via the key photoperiod-induced factor FLOWERING LOCUS T (FT). Nuclear Factor-Y subunit C (NF-YC) proteins function as important mediators of epigenetic marks in different plant developmental stages and play an important role in the regulation of FT transcription, but the mechanistic details of this remain unknown. In this study, we show that Arabidopsis NF-YC homologs temporally interact with the histone methyltransferase CURLY LEAF (CLF) during the flowering transition. The binding of NF-YC antagonizes the association of CLF with chromatin and the CLF-dependent deposition of H3 lysine-27 trimethylation, thus relieving the repression of FT transcription and facilitating flowering under long-day conditions. Our findings reveal a novel mechanism of NF-YC/CLF-mediated epigenetic regulation of FT activation in photoperiod-induced flowering and, consequently, contribute to our understanding of how plants control developmental events in a temporal-specific regulatory manner.

Arabidopsis LEAFY COTYLEDON1 Mediates Postembryonic Development via Interacting with PHYTOCHROME-INTERACTING FACTOR4.

Plants undergo postembryonic growth during the developmental transition from germinating seeds to seedlings. Recent studies suggest LEAFY COTYLEDON1 (LEC1), initially identified as a central regulator in embryogenesis and seed maturation in Arabidopsis thaliana, plays a distinct role in postembryonic development. However, the mechanism by which LEC1 regulates nonembryonic development still remains elusive. In this study, we observed etiolation-related phenotypes in early seedlings of lec1 mutants and inducible LEC1 overexpression transgenic lines. Consistent with this, LEC1 promotes the expression of hypocotyl elongation-related genes in a darkness-dependent manner in spite of the comparable LEC1 transcript levels in the light- and dark-grown seedlings. Furthermore, we show that LEC1 interacts with PHYTOCHROME-INTERACTING FACTOR4 (PIF4), a major transcription modulator in postgermination development, to interdependently regulate hypocotyl elongation-related genes via direct binding to G-box element in the dark. Moreover, loss of LEC1 function suppresses the elongated hypocotyl phenotype of PIF-overaccumulating plants; conversely, inducible overexpression of LEC1 does not rescue the short hypocotyl in pif4 mutants. Our findings reveal that LEC1 acts as a coactivator of PIFs in transcriptional regulation during postembryonic growth, providing a possible mechanism by which plants fine-tune morphological development for their survival during the transition from the embryonic phase to seedling establishment.

STUNTED mediates the control of cell proliferation by GA in Arabidopsis.

Gibberellins (GA) are an important family of plant growth regulators, which are essential for many aspects of plant growth and development. In the GA signaling pathway, the action of GA is opposed by a group of DELLA family repressors, such as RGA. Although the mechanisms of action of the DELLA proteins have been studied in great detail, the effectors that act downstream of DELLA proteins and bring about GA-responsive growth and development remain largely unknown. In this study, we have characterized STUNTED (STU), a receptor-like cytoplasmic kinase (RLCK) VI family gene, which is ubiquitously detectable in all the tissues examined. RGA activity and GA signaling specifically mediate the levels of STU transcripts in shoot apices that contain actively dividing cells. stu-1 loss-of-function mutants exhibit retarded growth in many aspects of plant development. During the vegetative phase, stu-1 seedlings develop smaller leaves and shorter roots than wild-type seedlings, while during the reproductive phase, stu-1 exhibits delayed floral transition and lower fertility. The reduced stature of stu-1 partly results from a reduction in cell proliferation. Furthermore, we present evidence that STU serves as an important regulator mediating the control of cell proliferation by GA possibly through two cyclin-dependent kinase inhibitors, SIM and SMR1. Taken together, our results suggest that STU acts downstream of RGA and promotes cell proliferation in the GA pathway.

FTIP1 is an essential regulator required for florigen transport.

The capacity to respond to day length, photoperiodism, is crucial for flowering plants to adapt to seasonal change. The photoperiodic control of flowering in plants is mediated by a long-distance mobile floral stimulus called florigen that moves from leaves to the shoot apex. Although the proteins encoded by FLOWERING LOCUS T (FT) in Arabidopsis and its orthologs in other plants are identified as the long-sought florigen, whether their transport is a simple diffusion process or under regulation remains elusive. Here we show that an endoplasmic reticulum (ER) membrane protein, FT-INTERACTING PROTEIN 1 (FTIP1), is an essential regulator required for FT protein transport in Arabidopsis. Loss of function of FTIP1 exhibits late flowering under long days, which is partly due to the compromised FT movement to the shoot apex. FTIP1 and FT share similar mRNA expression patterns and subcellular localization, and they interact specifically in phloem companion cells. FTIP1 is required for FT export from companion cells to sieve elements, thus affecting FT transport through the phloem to the SAM. Our results provide a mechanistic understanding of florigen transport, demonstrating that FT moves in a regulated manner and that FTIP1 mediates FT transport to induce flowering.

A simple and efficient in planta transformation method based on the active regeneration capacity of plants.

Plant genetic transformation strategies serve as essential tools for the genetic engineering and advanced molecular breeding of plants. However, the complicated operational protocols and low efficiency of current transformation strategies restrict the genetic modification of most plant species. This paper describes the development of the regenerative activity-dependent in planta injection delivery (RAPID) method based on the active regeneration capacity of plants. In this method, Agrobacterium tumefaciens is delivered to plant meristems via injection to induce transfected nascent tissues. Stable transgenic plants can be obtained by subsequent vegetative propagation of the positive nascent tissues. The method was successfully used for transformation of plants with strong regeneration capacity, including different genotypes of sweet potato (Ipomoea batatas), potato (Solanum tuberosum), and bayhops (Ipomoea pes-caprae). Compared with traditional transformation methods, RAPID has a much higher transformation efficiency and shorter duration, and it does not require tissue culture procedures. The RAPID method therefore overcomes the limitations of traditional methods to enable rapid in planta transformation and can be potentially applied to a wide range of plant species that are capable of active regeneration.

Dt1 inhibits SWEET-mediated sucrose transport to regulate photoperiod-dependent seed weight in soybean.

Soybean is a photoperiod-sensitive short-day crop whose reproductive period and yield are markedly affected by day-length changes. Seed weight is one of the key traits determining the soybean yield; however, the prominent genes that control the final seed weight of soybean and the mechanisms underlying the photoperiod's effect on this trait remain poorly understood. In this study, we identify SW19 as a major locus controlling soybean seed weight by QTL mapping and determine Dt1, an orthologous gene of Arabidopsis TFL1 that is known to govern the soybean growth habit, as the causal gene of the SW19 locus. We showed that Dt1 is highly expressed in developing seeds and regulates photoperiod-dependent seed weight in soybean. Further analyses revealed that the Dt1 protein physically interacts with the sucrose transporter GmSWEET10a to negatively regulate the import of sucrose from seed coat to the embryo, thus modulating seed weight under long days. However, Dt1 does not function in seed development under short days due to its very low expression. Importantly, we discovered a novel natural allelic variant of Dt1 (H4 haplotype) that decouples its pleiotropic effects on seed size and growth habit; i.e., this variant remains functional in seed development but fails to regulate the stem growth habit of soybean. Collectively, our findings provide new insights into how soybean seed development responds to photoperiod at different latitudes, offering an ideal genetic component for improving soybean's yield by manipulating its seed weight and growth habit.

MOTHER OF FT AND TFL1 regulates seed germination through a negative feedback loop modulating ABA signaling in Arabidopsis.

Abscisic acid (ABA) and gibberellin (GA) are two antagonistic phytohormones that regulate seed germination in response to biotic and abiotic environmental stresses. We demonstrate here that MOTHER OF FT AND TFL1 (MFT), which encodes a phosphatidylethanolamine-binding protein, regulates seed germination via the ABA and GA signaling pathways in Arabidopsis thaliana. MFT is specifically induced in the radical-hypocotyl transition zone of the embryo in response to ABA, and mft loss-of-function mutants show hypersensitivity to ABA in seed germination. In germinating seeds, MFT expression is directly regulated by ABA-INSENSITIVE3 (ABI3) and ABI5, two key transcription factors in ABA signaling pathway. MFT is also upregulated by DELLA proteins in the GA signaling pathway. MFT in turn provides negative feedback regulation of ABA signaling by directly repressing ABI5. We conclude that during seed germination, MFT promotes embryo growth by constituting a negative feedback loop in the ABA signaling pathway.

Crosstalk between GA and JA signaling mediates plant growth and defense.

Gibberellins (GAs) and jasmonates (JAs) are two types of essential phytohormones that control many aspects of plant growth and development in response to environmental and endogenous signals. GA regulates many essential plant developmental processes, while JA plays a dominant role in mediating plant response to stress. Recent studies have revealed that intensive crosstalk between GA and JA signaling is involved in both plant development and defense to biotic or abiotic stress. In particular, interaction between DELLAs and JA ZIM-domain (JAZ) proteins, which are key repressors in GA- and JA-signaling pathways, respectively, plays a key role in mediating the balance between plant growth and defense through modulating the activity of their interacting transcriptional factors in response to GA and JA signals. Here, we briefly review the recent progress in understanding the antagonistic and synergistic crosstalk between GA and JA signaling with a focus on the central role of DELLA-JAZ interaction in addressing the plant dilemma between "to grow" and "to defend" in response to various stimuli.

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.