FERONIA coordinates plant growth and salt tolerance via the phosphorylation of phyB

Phytochrome B-mediated light signalling enhances rice resistance to saline-alkaline and sheath blight by regulating multiple downstream transcription factors

Light signalling regulates plant growth and stress resistance, whereas its mechanism in controlling saline-alkaline tolerance (SAT) remains largely unknown. This study identified that light signalling, primarily mediated by Phytochrome B (PhyB), inhibited ammonium transporter 1 (AMT1) to negatively regulate SAT. Our previous findings have shown that PhyB can impede the transcription factors indeterminate domain 10 (IDD10) and brassinazole resistant 1 (BZR1) to reduce NH4 + uptake, thereby modulating SAT and sheath blight (ShB) resistance in rice. However, inhibition of IDD10 and BZR1 in the phyB background did not fully suppress NH4 + uptake, suggesting that other signalling pathways regulated AMT1 downstream of PhyB. Further analysis revealed that PhyB interacted with Calcineurin B-like protein-interacting protein kinase 31 (CIPK31), which positively regulated AMT1 expression. CIPK31 also interacted with Teosinte Branched1/Cycloidea/PCF19 (TCP19), a key regulator of nitrogen use efficiency (NUE). However, PhyB neither degraded CIPK31 nor directly interacted with TCP19. Instead, PhyB inhibited the CIPK31-TCP19 interaction, releasing TCP19, which repressed AMT1;2 directly and AMT1;1 and AMT1;3 indirectly, thereby inhibiting NH4 + uptake and SAT while reducing ShB resistance. Additionally, Phytochrome Interacting Factor-Like 15 (PIL15) interacted with TCP19. Different from TCP19, PIL15 directly activated AMT1;2 to promote SAT, suggesting a balancing mechanism for NH4 + uptake downstream of PhyB. Furthermore, PIL15 interacted with IDD10 and BZR1 to form a transcriptional complex that collaboratively activated AMT1;2 expression. Overall, this study provides novel insights into how PhyB signalling regulates NH4 + uptake and coordinates SAT and ShB resistance in rice.

Phosphorylation of the strawberry MADS-box CMB1 regulates ripening via the catabolism of abscisic acid

Research on the ripening of fleshy fruits has relied on techniques that measure transcriptional changes. How ripening is linked to posttranslational modifications such as protein phosphorylation remains less studied. Here, we characterize the MADS-box SEPALLATA 4 (SEP4) subfamily transcription factor FaCMB1, a key negative regulator controlling strawberry ripening, whose transcript and protein abundance decrease progressively with fruit development and are repressed by abscisic acid (ABA). Transient RNAi or overexpression of FaCMB1 significantly altered the fruit ripening process and affected the content of endogenous ABA and ripening-related quality. Transcriptome sequencing (RNA-seq) analysis suggested that manipulation of FaCMB1 expression levels affected the transcription of FaASR (ABA-, stress-, ripening-induced), while FaCMB1 can repress the gene expression of FaASR by directly binding to its promoter. Furthermore, FaASR inhibited the transcriptional activity of FaCYP707A4, a key ABA 8'-hydroxylase enzyme involved in ABA catabolism. We show that FaCMB1 can be phosphorylated by the kinase FaSTPK, and Phos-tag assays indicated that the phosphorylation level of FaCMB1 increases during fruit ripening. This phosphorylation of FaCMB1 affects the binding ability of FaCMB1 to the FaASR promoter and alleviates its transcriptional repression. In conclusion, we elucidated a feedback regulatory path involving FaCMB1-FaASR-FaCYP707A4-ABA. During the fruit ripening process, an increase in ABA content led to a decrease in FaCMB1 transcript and protein levels, which, combined with increased phosphorylation levels, collectively impaired the transcriptional repression of FaASR by FaCMB1. Meanwhile, the increased transcriptional level of FaASR further repressed the expression level of FaCYP707A4, leading to ABA accumulation and fruit ripening.

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

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

Coenzyme Q GhCoQ9 enhanced the salt resistance by preserving the homeostasis of mitochondrial in upland cotton

Coenzyme Q (CoQ) was an electron carrier within the mitochondrial respiratory chain, serves as a cofactor for various mitochondrial dehydrogenases thereby playing a significant role in plant growth and development. In this study, GhCoQ9 was identified through transcriptomic analysis of cotton under salt stress. GhCoQ9 participates in the synthesis of coenzyme Q. Under salt stress condition, cotton plants with GhCoQ9 silenced exhibited more pronounced growth inhibition compared to the control group. Additionally, the catalase (CAT) and superoxide dismutase (SOD) levels were significantly increased, while the level of malondialdehyde (MDA) showed an upward trend. Microscopic analysis of cotton leaves revealed that under salt stress conditions GhCoQ9 -silenced plants exhibited reduced stomatal aperture, cellular destruction, cell shrinkage and deformation, and increased intercellular space compared to the control plants. The ultrastructure of GhCoQ9-silenced plants exhibited increased susceptibility to salt stress, primarily manifested as damage to the chloroplast and mitochondrial structures. We also investigated the function of CoQ9 in Arabidopsis, the results showed that coq9 mutant exhibited reduced germination rate and significant inhibited growth under salt stress. These findings suggest that GhCoQ9 plays a crucial role in the adaptation of cotton to salt stress by preserving the integrity of chloroplast and mitochondrial structures.

Genomic Signatures of Environmental Adaptation in Castanopsis hainanensis (Fagaceae)

As an endemic Castanopsis species on Hainan Island, Castanopsis hainanensis Merr. is uniquely adapted to tropical climatic conditions and occupies a relatively narrow habitat range. Given its long generation times, limited dispersal capacity, and ecological and economic importance, understanding the genomic processes shaping this dominant tree species is critical for conservation. Its adaptation to specialized habitats and distinct geographical distribution provide valuable insights into biodiversity challenges in island ecosystems. This study employs genome-wide single-nucleotide polymorphism (SNP) markers to investigate genetic structure, population dynamics, and adaptive variation. Analyses revealed weak genetic divergence among populations, suggesting high gene flow. Demographic reconstruction indicated a historical population bottleneck, consistent with MaxEnt modeling projections of future range contraction under climate change. Selective sweep and genotype-environment association (GEA) analyses identified SNPs strongly correlated with environmental variables, particularly moisture and temperature. Using these SNPs, we quantified the risk of non-adaptedness (RONA) across climate scenarios, pinpointing regions at heightened vulnerability. Gene Ontology (GO) enrichment highlighted the key genes involved in plant growth and stress adaptation. By integrating genomic and environmental data, this study establishes a framework for deciphering adaptive mechanisms of C. hainanensis and offers actionable insights for informed conservation strategies to mitigate climate-driven biodiversity loss.

Salt stress activates the CDK8-AHL10-SUVH2/9 module to dynamically regulate salt tolerance in Arabidopsis

Salt stress has devastating effects on agriculture, yet the key regulators modulating the transcriptional dynamics of salt-responsive genes remain largely elusive in plants. Here, we discover that salt stress substantially induces the kinase activity of Mediator cyclin-dependent kinase 8 (CDK8), which is essential for its positive role in regulating salt tolerance. CDK8 is identified to phosphorylate AT-hook motif nuclear-localized protein 10 (AHL10) at serine 314, leading to its degradation under salt stress. Consistently, AHL10 is found to negatively regulate salt tolerance. Transcriptome analysis further indicates that CDK8 regulates over 20% of salt-responsive genes, half of which are co-regulated by AHL10. Moreover, AHL10 is revealed to recruit SU(VAR)3-9 homologs (SUVH2/9) to AT-rich DNA sequences in the nuclear matrix-attachment regions (MARs) of salt-responsive gene promoters, facilitating H3K9me2 deposition and repressing salt-responsive genes. Our study thereby has identified the CDK8-AHL10-SUVH2/9 module as a key molecular switch controlling transcriptional dynamics in response to salt stress.

Signalling and regulation of plant development by carbon/nitrogen balance

The two most abundant macronutrients in plant cells are carbon (C) and nitrogen (N). Coordination of their cellular metabolism is a fundamental factor in guaranteeing the optimal growth and development of plants. N availability and assimilation profoundly affect plant gene expression and modulate root and stem architecture, thus affecting whole plant growth and crop yield. N status also affects C fixation, as it is an important component of the photosynthetic machinery in leaves. Reciprocally, increasing C supply promotes N uptake and assimilation. There is extensive knowledge of the different mechanisms that plants use for sensing and signalling their nutritional status to regulate the assimilation, metabolism and transport of C and N. However, the crosstalk between C and N pathways has received much less attention. Plant growth and development are greatly affected by suboptimal C/N balance, which can arise from nutrient deficiencies or/and environmental cues. Mechanisms that integrate and respond to changes in this specific nutritional balance have started to arise. This review will examine the specific responses to C/N imbalance in plants by focusing on the main inorganic and organic metabolites involved, how they are sensed and transported, and the interconnection between the early signalling components and hormonal networks that underlies plants' adaptive responses.

A comprehensive proteomic map revealing the regulation of the development of long-duration, red butterfly-shaped fruit in Euscaphis japonica

Fruit features are crucial for plant propagation, population growth, biodiversity preservation, and evolutionary survival. However, the synergistic regulatory mechanisms underlying the development of fruit traits such as color, shape and duration are unclear. Euscaphis japonica, whose fruits have a red-winged pericarp and persist for a long period of time, is an important ornamental plant in eastern Asia. In this study, we present a complete proteome spanning multiple time points and the phosphoproteome landscape of E. japonica fruit during the maturation and ripening phases. Quantitative evaluation via proteome and phosphoproteome analysis revealed three distinct phases that are consistent with the fruit maturation and ripening stages on a longitudinal time scale. The two-way proteomics analysis revealed functionally important biological events, including anthocyanin accumulation and phytohormone and light signal transduction. Importantly, our integrated analysis, along with experimental validation and phytohormone treatments, suggested that alterations in EjPHYBS21/S37 and EjPHOT1S394/S429 phosphorylation may lead to auxin accumulation and the inhibition of ethylene biosynthesis, thereby initiating the development of long-duration, red butterfly-shaped E. japonica fruit. Our study reveals a mechanism of E. japonica fruit formation that highlights plant adaptive strategies that potentially evolved through interactions with frugivores.

Phosphorylation of cellulose synthases in plant responses to environmental changes

Cellulose, synthesized by cellulose synthase (CESA) complexes, is an essential component of plant cell walls; defects in cellulose synthesis compromise cell wall integrity. The maintenance of this integrity is vital for plant growth, development, and stress responses. Consequently, plants must continuously synthesize and remodel their cell walls, a process intricately linked to cellulose biosynthesis. Phosphorylation modifications at specific sites on cellulose synthase represent a critical regulatory mechanism governing the dynamics of CESA complexes. In this minireview, we summarize the phosphorylation sites responsive to environmental factors in CESAs and discuss how alterations in phosphorylation status influence plant adaptation to environmental conditions as well as the dynamics of CESA complexes. Additionally, we propose potential upstream kinases targeting CESAs along with their respective target sites. Our efforts aim to enhance understanding of CESA phosphorylation's role in facilitating plant adaptation to environmental challenges.

Stress sensing and response through biomolecular condensates in plants

Plants have developed intricate mechanisms for rapid and efficient stress perception and adaptation in response to environmental stressors. Recent research highlights the emerging role of biomolecular condensates in modulating plant stress perception and response. These condensates function through numerous mechanisms to regulate cellular processes such as transcription, translation, RNA metabolism, and signaling pathways under stress conditions. In this review, we provide an overview of current knowledge on stress-responsive biomolecular condensates in plants, including well-defined condensates such as stress granules, processing bodies, and the nucleolus, as well as more recently discovered plant-specific condensates. By briefly referring to findings from yeast and animal studies, we discuss mechanisms by which plant condensates perceive stress signals and elicit cellular responses. Finally, we provide insights for future investigations on stress-responsive condensates in plants. Understanding how condensates act as stress sensors and regulators will pave the way for potential applications in improving plant resilience through targeted genetic or biotechnological interventions.

GSK3s promote the phyB-ELF3-HMR complex formation to regulate plant thermomorphogenesis

Although elevated ambient temperature causes many effects on plant growth and development, the mechanisms of plant high-ambient temperature sensing remain unknown. In this study, we show that GLYCOGEN SYNTHASE KINASE 3s (GSK3s) negatively regulate high-ambient temperature response and oligomerize upon high-temperature treatment. We demonstrate that GSK3 kinase BIN2 specifically interacts with the high-temperature sensor phytochrome B (phyB) but not the high-temperature sensor EARLY FLOWER 3 (ELF3) to phosphorylate and promote phyB photobody formation. Furthermore, we show that phosphorylation of phyB by GSK3s promotes its interaction with ELF3. Subsequently, we find that ELF3 recruits the phyB photobody facilitator HEMERA (HMR) to promote its association with phyB. Taken together, our data reveal a mechanism that GSK3s promote the phyB-ELF3-HMR complex formation in regulating plant thermomorphogenesis.

Current progress in deciphering the molecular mechanisms underlying plant salt tolerance

Enhancing crop salt tolerance through genetics and genomics is important for food security. It is environmentally friendly and cost-effective in maintaining crop production in farmlands affected by soil salinization and can also facilitate the utilization of marginal saline land. Despite the limited success achieved so far, it is becoming possible to bridge the gap between fundamental research and crop breeding owing to a deeper understanding of plant salt tolerance at both physiological and molecular levels. Therefore, we review the recent key progress in identifying the molecular mechanisms contributing to plant salt tolerance with a focus on balancing growth and salt resilience. With the accruing knowledge and the rapidly evolving tools (e.g. genome editing and artificial intelligence), it is reasonable to expect the future salt-tolerant crops in a few decades.

Phosphorylation of phyB by GSK3s, a key mechanism that brings temperature sensors together

This article is a Commentary on Yang et al. (2025), 245: 1577–1588.

TANDEM ZINC-FINGER/PLUS3: a multifaceted integrator of light signaling

TANDEM ZINC-FINGER/PLUS3 (TZP) is a nuclear-localized protein with multifaceted roles in modulating plant growth and development under diverse light conditions. The unique combination of two intrinsically disordered regions (IDRs), two zinc-fingers (ZFs), and a PLUS3 domain provide a platform for interactions with the photoreceptors phytochrome A (phyA) and phyB, light signaling components, and nucleic acids. TZP controls flowering and hypocotyl elongation by regulating gene expression and protein abundance in a blue, red, or far-red light-specific context. Recently, TZP was shown to undergo liquid-liquid phase separation through its IDRs, thus promoting phyA phosphorylation. Collectively, TZP is an emerging regulator of diverse light signaling pathways; therefore, understanding its biochemical function in integrating environmental signaling networks is key for optimizing plant adaptation.

An mRNA methylase and demethylase regulate sorghum salt tolerance by mediating N6-methyladenosine modification

N 6-methyladenosine (m6A) modification is a crucial and widespread molecular mechanism governing plant development and stress tolerance. The specific impact of m6A regulation on plants with inherently high salt tolerance remains unclear. Existing research primarily focuses on the overexpression or knockout of individual writer or eraser components to alter m6A levels. However, a comprehensive study simultaneously altering overall m6A modification levels within the same experiment is lacking. Such an investigation is essential to determine whether opposing changes in m6A modification levels exert entirely different effects on plant salt tolerance. In this study, we identified the major writer member mRNA adenosine methylase A (SbMTA) in sorghum (Sorghum bicolor) as critical for sorghum survival. The sbmta mutant exhibits a phenotype characterized by reduced overall m6A, developmental arrest, and, ultimately, lethality. Overexpression of SbMTA increased m6A levels and salt tolerance, while overexpression of the m6A eraser alkylated DNA repair protein AlkB homolog 10B (SbALKBH10B) in sorghum showed the opposite phenotype. Comparative analyses between sorghum with different m6A levels reveal that SbMTA- and SbALKBH10B-mediated m6A alterations significantly impact the stability and expression levels of genes related to the abscisic acid signaling pathway and growth under salt stress. In summary, this study unveils the intricate relationship between m6A modifications and salt tolerance in sorghum, providing valuable insights into how m6A modification levels on specific transcripts influence responses to salt stress.

RAPID ALKALINIZATION FACTOR 22 is a key modulator of the root hair growth responses to fungal ethylene emissions in Arabidopsis

In Arabidopsis (Arabidopsis thaliana (L.) Heynh), exposure to volatile compounds (VCs) emitted by Penicillium aurantiogriseum promotes root hair (RH) proliferation and hyper-elongation through mechanisms involving ethylene, auxin, and photosynthesis signaling. In addition, this treatment enhances the levels of the small signaling peptide RAPID ALKALINIZATION FACTOR 22 (RALF22). Here, we used genetics to address the role of RALF22 in fungal VC-promoted RH growth and to identify the bioactive fungal VC. We found that RHs of ralf22 and feronia (fer-4) plants impaired in the expression of RALF22 and its receptor FERONIA, respectively, responded weakly to fungal VCs. Unlike in wild-type roots, fungal VC exposure did not enhance RALF22 transcript levels in roots of fer-4 and ethylene- and auxin-insensitive mutants. In ralf22 and fer-4 roots, this treatment did not enhance the levels of ERS2 transcripts encoding one member of the ethylene receptor family and those of some RH-related genes. RHs of ers2-1 and the rsl2rsl4 double mutants impaired in the expression of ERS2 and the ethylene- and auxin-responsive ROOT HAIR DEFECTIVE 6-LIKE 2 and 4 transcription factors, respectively, weakly responded to fungal VCs. Moreover, roots of plants defective in photosynthetic responsiveness to VCs exhibited weak RALF22 expression and RH growth responses to fungal VCs. VCs of ΔefeA strains of P. aurantiogriseum cultures impaired in ethylene synthesis weakly promoted RH proliferation and elongation in exposed plants. We conclude that RALF22 simultaneously functions as a transcriptionally regulated signaling molecule that participates in the ethylene, auxin, and photosynthesis signaling-mediated RH growth response to fungal ethylene emissions and regulation of ethylene perception in RHs.

FERONIA adjusts CC1 phosphorylation to control microtubule array behavior in response to salt stress

Cell wall remodeling is important for plants to adapt to environmental stress. Under salt stress, cortical microtubules undergo a depolymerization-reassembly process to promote the biosynthesis of stress-adaptive cellulose, but the regulatory mechanisms underlying this process are still largely unknown. In this study, we reveal that FERONIA (FER), a potential cell wall sensor, interacts with COMPANION OF CELLULOSE SYNTHASE1 (CC1) and its closest homolog, CC2, two proteins that are required for cortical microtubule reassembly under salt stress. Biochemical data indicate that FER phosphorylates CC1 on multiple residues in its second and third hydrophobic microtubule-binding regions and that these phosphorylations modulate CC1 trafficking and affect the ability of CC1 to engage with microtubules. Furthermore, CC1 phosphorylation level is altered upon exposure to salt stress, which coincides with the changes of microtubule organization. Together, our study outlines an important intracellular mechanism that maintains microtubule arrays during salt exposure in plant cells.

FERONIA controls ABA-mediated seed germination via the regulation of CARK1 kinase activity

Seed germination is the initial step of the whole life cycle for an individual plant, and thus it needs to be tightly controlled to avoid plant growth under unfavorable conditions. Here, we report that FERONIA (FER), a receptor-like kinase, controls early seed germination under ABA conditions. FER interacts with and phosphorylates cytosolic ABA receptor kinase 1 (CARK1) protein, a receptor-like cytoplasmic kinase (RLCK) that modulates ABA signaling. In both the fer-4 and cark1 mutants, ABA-triggered SNF1-related protein kinase 2 (SnRK2) activation and ABI5 protein accumulation are attenuated. FER phosphorylates the Ser233 and Thr234 residues of CARK1, and the CARK1 protein with the substitutions of these two residues with Ala exhibits a reduced kinase activity and fails to rescue the increased seed germination rate of the cark1 mutant under ABA conditions. Collectively, our study not only uncovers an RLCK protein that functions downstream of FER but also provides a mechanistic insight into ABA-mediated early seed germination regulation by the FER-CARK1 module.

FERONIA regulates salt tolerance in Arabidopsis by controlling photorespiratory flux

Photorespiration is an energetically costly metabolic pathway in plants that responds to environmental stresses. The molecular basis of the regulation of the photorespiratory cycle under stress conditions remains unclear. Here, we discovered that FERONIA (FER) regulates photorespiratory flow under salt stress in Arabidopsis (Arabidopsis thaliana). FER mutation results in hypersensitivity to salt stress, but disruption of ferredoxin-dependent glutamate synthase 1 (GLU1), an enzyme that participates in the photorespiratory pathway by producing glutamate, greatly suppresses fer-4 hypersensitivity to salt stress primarily due to reduced glycine yield. In contrast, disrupting mitochondrial serine hydroxymethyltransferase1 (SHM1), which is supposed to increase glycine levels by hampering the conversion of glycine to serine in the photorespiratory cycle, aggravates fer-4 hypersensitivity to salt stress. Biochemical data show that FER interacts with and phosphorylates SHM1, and this phosphorylation modulates SHM1 stability. Additionally, the production of proline and its intermediate △1-pyrroline-5-carboxylate (P5C), which are both synthesized from glutamate, also contributes to fer-4 hypersensitivity to salt stress. In conclusion, this study elucidates the functional mechanism of FER in regulating salt tolerance by modulating photorespiratory flux, which greatly broadens our understanding of how plants adapt to high salinity.

Regulatory Networks Underlying Plant Responses and Adaptation to Cold Stress

Cold is an important environmental factor limiting plant growth and development. Recent studies have revealed the complex regulatory networks associated with plant responses to cold and identified their interconnections with signaling pathways related to light, the circadian clock, plant hormones, and pathogen defense. In this article, we review recent advances in understanding the molecular basis of cold perception and signal transduction pathways. We also summarize recent developments in the study of cold-responsive growth and flowering. Finally, we propose future directions for the study of long-term cold sensing, RNA secondary structures in response to cold, and the development of cold-tolerant and high-yield crops.

NF-YC15 transcription factor activates ethylene biosynthesis and improves cassava disease resistance

The nuclear factor Y (NF-Y) transcription factors play important roles in plant development and physiological responses. However, the relationship between NF-Y, plant hormone and plant stress resistance in tropical crops remains unclear. In this study, we identified MeNF-YC15 gene in the NF-Y family that significantly responded to Xanthomonas axonopodis pv. manihotis (Xam) treatment. Using MeNF-YC15-silenced and -overexpressed cassava plants, we elucidated that MeNF-YC15 positively regulated disease resistance to cassava bacterial blight (CBB). Notably, we illustrated MeNF-YC15 downstream genes and revealed the direct genetic relationship between MeNF-YC15 and 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase (MeACO1)-ethylene module in disease resistance, as evidenced by the rescued disease susceptibility of MeNF-YC15 silenced cassava plants with ethylene treatment or overexpressing MeACO1. In addition, the physical interaction between 2C-type protein phosphatase 1 (MePP2C1) and MeNF-YC15 inhibited the transcriptional activation of MeACO1 by MeNF-YC15. In summary, MePP2C1-MeNF-YC15 interaction modulates ethylene biosynthesis and cassava disease resistance, providing gene network for cassava genetic improvement.

The RALF2-FERONIA-MYB63 module orchestrates growth and defense in tomato roots

Plant secreted peptides RAPID ALKALINISATION FACTORs (RALFs), which act through the receptor FERONIA (FER), play important roles in plant growth. However, it remains unclear whether and how RALF-FER contributes to the trade-off of plant growth-defense. Here, we used a variety of techniques such as CRISPR/Cas9, protein-protein interaction and transcriptional regulation methods to investigate the role of RALF2 and its receptor FER in regulating lignin deposition, root growth, and defense against Fusarium oxysporum f. sp. lycopersici (Fol) in tomato (Solanum lycopersicum). The ralf2 and fer mutants show reduced primary root length, elevated lignin accumulation, and enhanced resistance against Fol than the wild-type. FER interacts with and phosphorylates MYB63 to promote its degradation. MYB63 serves as an activator of lignin deposition by regulating the transcription of dirigent protein gene DIR19. Mutation of DIR19 suppresses lignin accumulation, and reverses the short root phenotype and Fol resistance in ralf2 or fer mutant. Collectively, our results demonstrate that the RALF2-FER-MYB63 module fine-tunes root growth and resistance against Fol through regulating the deposition of lignin in tomato roots. The study sheds new light on how plants maintain the growth-defense balance via RALF-FER.

FERONIA: A Receptor Kinase at the Core of a Global Signaling Network

Initially identified as a key regulator of female fertility in Arabidopsis, the FERONIA (FER) receptor kinase is now recognized as crucial for almost all aspects of plant growth and survival. FER partners with a glycosylphosphatidylinositol-anchored protein of the LLG family to act as coreceptors on the cell surface. The FER-LLG coreceptor interacts with different RAPID ALKALINIZATION FACTOR (RALF) peptide ligands to function in various growth and developmental processes and to respond to challenges from the environment. The RALF-FER-LLG signaling modules interact with molecules in the cell wall, cell membrane, cytoplasm, and nucleus and mediate an interwoven signaling network. Multiple FER-LLG modules, each anchored by FER or a FER-related receptor kinase, have been studied, illustrating the functional diversity and the mechanistic complexity of the FER family signaling modules. The challenges going forward are to distill from this complexity the unifying schemes where possible and attain precision and refinement in the knowledge of critical details upon which future investigations can be built. By focusing on the extensively characterized FER, this review provides foundational information to guide the next phase of research on FER in model as well as crop species and potential applications for improving plant growth and resilience.

Environmental Control of Hypocotyl Elongation

The hypocotyl is the embryonic stem connecting the primary root to the cotyledons. Hypocotyl length varies tremendously depending on the conditions. This developmental plasticity and the simplicity of the organ explain its success as a model for growth regulation. Light and temperature are prominent growth-controlling cues, using shared signaling elements. Mechanisms controlling hypocotyl elongation in etiolated seedlings reaching the light differ from those in photoautotrophic seedlings. However, many common growth regulators intervene in both situations. Multiple photoreceptors including phytochromes, which also respond to temperature, control the activity of several transcription factors, thereby eliciting rapid transcriptional reprogramming. Hypocotyl growth often depends on sensing in green tissues and interorgan communication comprising auxin. Hypocotyl auxin, in conjunction with other hormones, determines epidermal cell elongation. Plants facing cues with opposite effects on growth control hypocotyl elongation through intricate mechanisms. We discuss the status of the field and end by highlighting open questions.

A cytosol-tethered YHB variant of phytochrome B retains photomorphogenic signaling activity

The red and far-red light photoreceptor phytochrome B (phyB) transmits light signals following cytosol-to-nuclear translocation to regulate transcriptional networks therein. This necessitates changes in protein-protein interactions of phyB in the cytosol, about which little is presently known. Via introduction of a nucleus-excluding G767R mutation into the dominant, constitutively active phyBY276H (YHB) allele, we explore the functional consequences of expressing a cytosol-localized YHBG767R variant in transgenic Arabidopsis seedlings. We show that YHBG767R elicits selective constitutive photomorphogenic phenotypes in dark-grown phyABCDE null mutants, wild type and other phy-deficient genotypes. These responses include light-independent apical hook opening, cotyledon unfolding, seed germination and agravitropic hypocotyl growth with minimal suppression of hypocotyl elongation. Such phenotypes correlate with reduced PIF3 levels, which implicates cytosolic targeting of PIF3 turnover or PIF3 translational inhibition by YHBG767R. However, as expected for a cytoplasm-tethered phyB, YHBG767R elicits reduced light-mediated signaling activity compared with similarly expressed wild-type phyB in phyABCDE mutant backgrounds. YHBG767R also interferes with wild-type phyB light signaling, presumably by formation of cytosol-retained and/or otherwise inactivated heterodimers. Our results suggest that cytosolic interactions with PIFs play an important role in phyB signaling even under physiological conditions.

FERONIA homologs in stress responses of horticultural plants: current knowledge and missing links

Owing to its versatile roles in almost all aspects of plants, FERONIA (FER), a receptor-like kinase of the Catharanthus roseus receptor-like kinase 1-like (CrRLK1L) subfamily, has received extensive research interests during the past decades. Accumulating evidence has been emerged that FER homologs in horticultural crops also play crucial roles in reproductive biology and responses to environmental stimuli (abiotic and biotic stress factors). Here, we provide a review for the latest advances in the studies on FER homologs in modulating stress responses in horticultural crops, and further analyze the underlying mechanisms maintained by FER. Moreover, we also envisage the missing links in current work and provide a perspective for future studies on this star protein.

What is going on inside of phytochrome B photobodies?

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

Overexpression of GhGSTF9 Enhances Salt Stress Tolerance in Transgenic Arabidopsis

Soil salinization is a major abiotic stress factor that negatively impacts plant growth, development, and crop yield, severely limiting agricultural production and economic development. Cotton, a key cash crop, is commonly cultivated as a pioneer crop in regions with saline-alkali soil due to its relatively strong tolerance to salt. This characteristic renders it a valuable subject for investigating the molecular mechanisms underlying plant salt tolerance and for identifying genes that confer salt tolerance. In this study, focus was placed on examining a salt-tolerant variety, E991, and a salt-sensitive variety, ZM24. A combined analysis of transcriptomic data from these cotton varieties led to the identification of potential salt stress-responsive genes within the glutathione S-transferase (GST) family. These versatile enzyme proteins, prevalent in animals, plants, and microorganisms, were demonstrated to be involved in various abiotic stress responses. Our findings indicate that suppressing GhGSTF9 in cotton led to a notably salt-sensitive phenotype, whereas heterologous overexpression in Arabidopsis plants decreases the accumulation of reactive oxygen species under salt stress, thereby enhancing salt stress tolerance. This suggests that GhGSTF9 serves as a positive regulator in cotton's response to salt stress. These results offer new target genes for developing salt-tolerant cotton varieties.

Liquid-liquid phase separation of TZP promotes PPK-mediated phosphorylation of the phytochrome A photoreceptor

Phytochrome A (phyA) is the plant far-red (FR) light photoreceptor and plays an essential role in regulating photomorphogenic development in FR-rich conditions, such as canopy shade. It has long been observed that phyA is a phosphoprotein in vivo; however, the protein kinases that could phosphorylate phyA remain largely unknown. Here we show that a small protein kinase family, consisting of four members named PHOTOREGULATORY PROTEIN KINASES (PPKs) (also known as MUT9-LIKE KINASES), directly phosphorylate phyA in vitro and in vivo. In addition, TANDEM ZINC-FINGER/PLUS3 (TZP), a recently characterized phyA-interacting protein required for in vivo phosphorylation of phyA, is also directly phosphorylated by PPKs. We reveal that TZP contains two intrinsically disordered regions in its amino-terminal domain that undergo liquid-liquid phase separation (LLPS) upon light exposure. The LLPS of TZP promotes colocalization and interaction between PPKs and phyA, thus facilitating PPK-mediated phosphorylation of phyA in FR light. Our study identifies PPKs as a class of protein kinases mediating the phosphorylation of phyA and demonstrates that the LLPS of TZP contributes significantly to more production of the phosphorylated phyA form in FR light.

Phytochrome B photobody components

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

The zinc finger protein DHHC09 S-acylates the kinase STRK1 to regulate H2O2 homeostasis and promote salt tolerance in rice

Soil salinity results in oxidative stress and heavy losses to crop production. The S-acylated protein SALT TOLERANCE RECEPTOR-LIKE CYTOPLASMIC KINASE 1 (STRK1) phosphorylates and activates CATALASE C (CatC) to improve rice (Oryza sativa L.) salt tolerance, but the molecular mechanism underlying its S-acylation involved in salt signal transduction awaits elucidation. Here, we show that the DHHC-type zinc finger protein DHHC09 S-acylates STRK1 at Cys5, Cys10, and Cys14 and promotes salt and oxidative stress tolerance by enhancing rice H2O2-scavenging capacity. This modification determines STRK1 targeting to the plasma membrane or lipid nanodomains and is required for its function. DHHC09 promotes salt signaling from STRK1 to CatC via transphosphorylation, and its deficiency impairs salt signal transduction. Our findings demonstrate that DHHC09 S-acylates and anchors STRK1 to the plasma membrane to promote salt signaling from STRK1 to CatC, thereby regulating H2O2 homeostasis and improving salt stress tolerance in rice. Moreover, overexpression of DHHC09 in rice mitigates grain yield loss under salt stress. Together, these results shed light on the mechanism underlying the role of S-acylation in RLK/RLCK-mediated salt signal transduction and provide a strategy for breeding highly salt-tolerant rice.

Rice kinase OsMRLK63 contributes to drought tolerance by regulating reactive oxygen species production

Drought is a major adverse environmental factor that plants face in nature but the molecular mechanism by which plants transduce stress signals and further endow themselves with tolerance remains unclear. Malectin/malectin-like domains containing receptor-like kinases (MRLKs) have been proposed to act as receptors in multiple biological signaling pathways, but limited studies show their roles in drought-stress signaling and tolerance. In this study, we demonstrate OsMRLK63 in rice (Oryza sativa L.) functions in drought tolerance by acting as the receptor of 2 rapid alkalization factors, OsRALF45 and OsRALF46. We show OsMRLK63 is a typical receptor-like kinase that positively regulates drought tolerance and reactive oxygen species (ROS) production. OsMRLK63 interacts with and phosphorylates several nicotinamide adenine dinucleotide phosphate (NADPH) oxidases with the primarily phosphorylated site at Ser26 in the N-terminal of RESPIRATORY BURST OXIDASE HOMOLOGUE A (OsRbohA). The application of the 2 small signal peptides (OsRALF45/46) on rice can greatly alleviate the dehydration of plants induced by mimic drought. This function depends on the existence of OsMRLK63 and the NADPH oxidase-dependent ROS production. The 2 RALFs interact with OsMRLK63 by binding to its extracellular domain, suggesting they may act as drought/dehydration signal sensors for the OsMRLK63-mediated process. Our study reveals a OsRALF45/46-OsMRLK63-OsRbohs module which contributes to drought-stress signaling and tolerance in rice.

Designing salt stress-resilient crops: Current progress and future challenges

Excess soil salinity affects large regions of land and is a major hindrance to crop production worldwide. Therefore, understanding the molecular mechanisms of plant salt tolerance has scientific importance and practical significance. In recent decades, studies have characterized hundreds of genes associated with plant responses to salt stress in different plant species. These studies have substantially advanced our molecular and genetic understanding of salt tolerance in plants and have introduced an era of molecular design breeding of salt-tolerant crops. This review summarizes our current knowledge of plant salt tolerance, emphasizing advances in elucidating the molecular mechanisms of osmotic stress tolerance, salt-ion transport and compartmentalization, oxidative stress tolerance, alkaline stress tolerance, and the trade-off between growth and salt tolerance. We also examine recent advances in understanding natural variation in the salt tolerance of crops and discuss possible strategies and challenges for designing salt stress-resilient crops. We focus on the model plant Arabidopsis (Arabidopsis thaliana) and the four most-studied crops: rice (Oryza sativa), wheat (Triticum aestivum), maize (Zea mays), and soybean (Glycine max).

Extracellular pectin-RALF phase separation mediates FERONIA global signaling function

The FERONIA (FER)-LLG1 co-receptor and its peptide ligand RALF regulate myriad processes for plant growth and survival. Focusing on signal-induced cell surface responses, we discovered that intrinsically disordered RALF triggers clustering and endocytosis of its cognate receptors and FER- and LLG1-dependent endocytosis of non-cognate regulators of diverse processes, thus capable of broadly impacting downstream responses. RALF, however, remains extracellular. We demonstrate that RALF binds the cell wall polysaccharide pectin. They phase separate and recruit FER and LLG1 into pectin-RALF-FER-LLG1 condensates to initiate RALF-triggered cell surface responses. We show further that two frequently encountered environmental challenges, elevated salt and temperature, trigger RALF-pectin phase separation, promiscuous receptor clustering and massive endocytosis, and that this process is crucial for recovery from stress-induced growth attenuation. Our results support that RALF-pectin phase separation mediates an exoskeletal mechanism to broadly activate FER-LLG1-dependent cell surface responses to mediate the global role of FER in plant growth and survival.

Insights into plant salt stress signaling and tolerance

Soil salinization is an essential environmental stressor, threatening agricultural yield and ecological security worldwide. Saline soils accumulate excessive soluble salts which are detrimental to most plants by limiting plant growth and productivity. It is of great necessity for plants to efficiently deal with the adverse effects caused by salt stress for survival and successful reproduction. Multiple determinants of salt tolerance have been identified in plants, and the cellular and physiological mechanisms of plant salt response and adaption have been intensely characterized. Plants respond to salt stress signals and rapidly initiate signaling pathways to re-establish cellular homeostasis with adjusted growth and cellular metabolism. This review summarizes the advances in salt stress perception, signaling, and response in plants. A better understanding of plant salt resistance will contribute to improving crop performance under saline conditions using multiple engineering approaches. The rhizosphere microbiome-mediated plant salt tolerance as well as chemical priming for enhanced plant salt resistance are also discussed in this review.

Phytochrome B phosphorylation expanded: site-specific kinases are identified

The phytochrome B (phyB) photoreceptor is a key participant in red and far-red light sensing, playing a dominant role in many developmental and growth responses throughout the whole life of plants. Accordingly, phyB governs diverse signaling pathways, and although our knowledge about these pathways is constantly expanding, our view about their fine-tuning is still rudimentary. Phosphorylation of phyB is one of the relevant regulatory mechanisms, and - despite the expansion of the available methodology - it is still not easy to examine. Phosphorylated phytochromes have been detected using various techniques for decades, but the first phosphorylated phyB residues were only identified in 2013. Since then, concentrated attention has been turned toward the functional role of post-translational modifications in phyB signaling. Very recently in 2023, the first kinases that phosphorylate phyB were identified. These discoveries opened up new research avenues, especially by connecting diverse environmental impacts to light signaling and helping to explain some long-term unsolved problems such as the co-action of Ca2+ and phyB signaling. This review summarizes our recent views about the roles of the identified phosphorylated phyB residues, what we know about the enzymes that modulate the phospho-state of phyB, and how these recent discoveries impact future investigations.

Main Habitat Factors Driving the Phenotypic Diversity of Litsea cubeba in China

Litsea cubeba (Lour.) Pers. is an important woody spice tree in southern China, and its fruit is a rich source of valuable essential oil. We surveyed and sampled L. cubeba germplasm resources from 36 provenances in nine Chinese provinces, and detected rich phenotypic diversity. The survey results showed that plants of SC-KJ, SC-HJ, and SC-LS provenance presented higher leaf area (LA); YN-SM and YN-XC plants had larger thousand-grain fresh weight (TFW); and HN-DX plants had the highest essential oil content (EOC). To explain the large differences in the phenotypes of L. cubeba among different habitats, we used Pearson's correlation analysis, multiple stepwise regression path analysis, and redundancy analysis to evaluate the phenotypic diversity of L. cubeba. It was found that compared to other traits, leaf and fruit traits had more significant geographical distributions, and that leaf phenotypes were correlated to fruit phenotypes. The results showed that elevation, latitude, longitude, total soil porosity (SP), soil bulk density (SBD), and average annual rainfall (AAR, mm) contributed significantly to the phenotypic diversity of L. cubeba. Geographical factors explained a higher percentage of variation in phenotypic diversity than did soil factors and climate factors. Plants of SC-KJ and HN-DX provenances could be important resources for domestication and breeding to develop new high-yielding varieties of this woody aromatic plant. This study describes significant phenotypic differences in L. cubeba related to adaptation to different environments, and provides a theoretical basis for the development of a breeding strategy and for optimizing L. cubeba cultivation.

How do plants maintain pH and ion homeostasis under saline-alkali stress?

Salt and alkaline stresses often occur together, severely threatening plant growth and crop yields. Salt stress induces osmotic stress, ionic stress, and secondary stresses, such as oxidative stress. Plants under saline-alkali stress must develop suitable mechanisms for adapting to the combined stress. Sustained plant growth requires maintenance of ion and pH homeostasis. In this review, we focus on the mechanisms of ion and pH homeostasis in plant cells under saline-alkali stress, including regulation of ion sensing, ion uptake, ion exclusion, ion sequestration, and ion redistribution among organs by long-distance transport. We also discuss outstanding questions in this field.

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.

FERONIA, the kinase that phosphorylates PhyB

The phosphorylation status of phyB changes dynamically in response to environmental conditions and critically governs the corresponding plant's responses. However, the kinase(s) that phosphorylates phyB is/are still unknown. Liu et al. have not only identified the kinase that phosphorylates phyB but also revealed its biological implications during salt stress.

Integrated Analysis of Transcriptome and Metabolome Reveals Molecular Mechanisms of Rice with Different Salinity Tolerances

Rice is a crucial global food crop, but it lacks a natural tolerance to high salt levels, resulting in significant yield reductions. To gain a comprehensive understanding of the molecular mechanisms underlying rice's salt tolerance, further research is required. In this study, the transcriptomic and metabolomic differences between the salt-tolerant rice variety Lianjian5 (TLJIAN) and the salt-sensitive rice variety Huajing5 (HJING) were examined. Transcriptome analysis revealed 1518 differentially expressed genes (DEGs), including 46 previously reported salt-tolerance-related genes. Notably, most of the differentially expressed transcription factors, such as NAC, WRKY, MYB, and EREBP, were upregulated in the salt-tolerant rice. Metabolome analysis identified 42 differentially accumulated metabolites (DAMs) that were upregulated in TLJIAN, including flavonoids, pyrocatechol, lignans, lipids, and trehalose-6-phosphate, whereas the majority of organic acids were downregulated in TLJIAN. The interaction network of 29 differentially expressed transporter genes and 19 upregulated metabolites showed a positive correlation between the upregulated calcium/cation exchange protein genes (OsCCX2 and CCX5_Ath) and ABC transporter gene AB2E_Ath with multiple upregulated DAMs in the salt-tolerant rice variety. Similarly, in the interaction network of differentially expressed transcription factors and 19 upregulated metabolites in TLJIAN, 6 NACs, 13 AP2/ERFs, and the upregulated WRKY transcription factors were positively correlated with 3 flavonoids, 3 lignans, and the lipid oleamide. These results suggested that the combined effects of differentially expressed transcription factors, transporter genes, and DAMs contribute to the enhancement of salt tolerance in TLJIAN. Moreover, this study provides a valuable gene-metabolite network reference for understanding the salt tolerance mechanism in rice.

Secreted Peptide SpPIP1 Modulates Disease Resistance and Salt Tolerance in Tomato

Tomato is a globally important horticultural and economic crop, but its productivity is severely affected by various stresses. Plant small secretory peptides have been identified as crucial mediators in plant resistance. Here, we conducted a comparative transcriptome analysis and identified the prePIP1 gene from Solanum pimpinellifolium (SpprePIP1), as an ortholog of Arabidopsis prePIP1 encoding the precursor protein of PAMP-induced SSP 1. The expression level of SpprePIP1 is transcriptionally induced in tomato upon infection with Phytophthora infestans (P. infestans), the pathogen responsible for late blight. Overexpression of SpprePIP1 resulted in enhanced tomato resistance to P. infestans. In addition, exogenous application of SpPIP1, whether through spraying or irrigation, improved tomato resistance by enhancing the transcript accumulations of pathogenesis-related proteins, as well as reactive oxygen species and the jasmonic acid (JA) levels. Integrated analysis of transcriptomics and metabolomics revealed the potential contributions of JA and phenylpropanoid biosynthesis to SpPIP1-induced tomato immunity. Additionally, SpPIP1 may strengthen tomato resistance to salt stress through the ABA signaling pathway. Overall, our findings demonstrate that SpPIP1 positively regulates tomato tolerance to P. infestans and salt stress, making it a potential plant elicitor for crop protection in an environmentally friendly way.

Genome-Wide Identification and Functional Characterization of FAR1-RELATED SEQUENCE (FRS) Family Members in Potato (Solanum tuberosum)

FAR1-RELATED SEQUENCE (FRS) transcription factors are generated by transposases and play vital roles in plant growth and development, light signaling transduction, phytohormone response, and stress resistance. FRSs have been described in various plant species. However, FRS family members and their functions remain poorly understood in vegetative crops such as potato (Solanum tuberosum, St). In the present study, 20 putative StFRS proteins were identified in potato via genome-wide analysis. They were non-randomly localized to eight chromosomes and phylogenetic analysis classified them into six subgroups along with FRS proteins from Arabidopsis and tomato. Conserved protein motif, protein domain, and gene structure analyses supported the evolutionary relationships among the FRS proteins. Analysis of the cis-acting elements in the promoters and the expression profiles of StFRSs in various plant tissues and under different stress treatments revealed the spatiotemporal expression patterns and the potential roles of StFRSs in phytohormonal and stress responses. StFRSs were differentially expressed in the cultivar "Xisen 6", which is exposed to a variety of stresses. Hence, these genes may be critical in regulating abiotic stress. Elucidating the StFRS functions will lay theoretical and empirical foundations for the molecular breeding of potato varieties with high light use efficiency and stress resistance.