LYSINE-SPECIFIC DEMETHYLASE 1-like (LDL) proteins are conserved FAD-dependent amine oxidases that serve as pivotal regulators in plants. While animal systems typically rely on a single LSD1/KDM1A enzyme, the Arabidopsis thaliana genome encodes an expanded family of LDL homologues (FLD, LDL1, LDL2, and LDL3), resulting in substantial subfunctionalization and specialized recruitment mechanisms. This review explores the diverse developmental roles of plant LDLs, ranging from flowering time and circadian clock regulation to heterochromatin maintenance and epigenetic regulation. We discuss the redundant roles of FLD, LDL1, and LDL2 in repressing the floral repressor FLC and their nonredundant specialized function within the CCA1/LHY-TOC1 circadian feedback loop. A central focus of our review is the emerging mechanism of transcription-coupled demethylation, in which LDLs associate with the phosphorylated C-terminal domain of RNA polymerase II to modify chromatin cotranscriptionally within gene bodies. By integrating findings from Arabidopsis thaliana and crops such as tomato and soybean, we illustrate how the diversified LDL-mediated regulatory toolkit facilitates precise, gene-specific regulation. Ultimately, the LDL family represents a cornerstone of the sophisticated epigenetic strategies that regulate plant phenotypic plasticity in response to developmental and environmental cues.
The desert moss Syntrichia caninervis is one of the most desiccation-tolerant land plants known and provides a powerful system for dissecting the molecular foundations of extreme stress adaptation in early-diverging land lineages. The MYB transcription factor superfamily orchestrates secondary metabolism and stress signaling across plants, yet its lineage-specific evolution and mechanistic deployment in bryophytes remain poorly understood. Here, we identified 65 ScMYB genes in the S. caninervis genome and showed that the family expanded predominantly through dispersed duplication, with no detectable synteny to vascular-plant MYBs, indicating bryophyte-specific neo-functionalization. Integrating phylogenetic clustering, cis-element architecture and stress-responsive expression profiling, we pinpointed ScMYB20, a nuclear-localized, S13-subgroup R2R3-MYB that is rapidly and strongly induced by dehydration and salinity. Heterologous overexpression in Arabidopsis, together with overexpression and RNAi in S. caninervis, demonstrated that ScMYB20 negatively regulates drought and salt tolerance by suppressing antioxidant capacity, osmotic adjustment and photosynthetic performance, while concomitantly elevating ROS and MDA accumulation. Mechanistically, ScMYB20 directly binds a TAACCA motif in the ScCHS1 promoter to repress its transcription, and simultaneously sequesters the WD40 protein ScTTG1, a positive transcriptional activator of ScCHS1, thereby antagonising ScTTG1-mediated activation. Transient ScCHS1 overexpression restored flavonoid accumulation, antioxidant capacity and stress tolerance. Together, our findings define a dual-repression module (ScMYB20-ScTTG1-ScCHS1) that fine-tunes flavonoid flux under abiotic stress, and provide evolutionary and mechanistic insights into how R2R3-MYB repressors evolved to balance metabolic investment and stress survival in land plants.
To evaluate whether root-supplied ABA affects tomato leaf and whole-plant water use efficiency (WUE) and tissue ABA status, wild-type (WT) and ABA-deficient flacca (flc) genotypes were self- and reciprocally-grafted. Root xylem ABA concentration was rootstock-dependent irrespective of sap flow rate, thus ABA delivery to the scion of reciprocal grafts was substantially altered compared to self-grafted plants. However, a flc rootstock had minimal effects on WT leaf and whole plant photosynthesis or stomatal and canopy conductance, as it didn't affect leaf ABA concentration (ABAleaf) and water potential (Ψleaf) of WT scions. A WT rootstock had variable effects on a flc scion. At ambient vapour pressure deficits (VPD) exceeding 1.5 kPa (but not at lower VPDs) or with deficit irrigation (supplying 30% less water), it increased WUE of a flc scion by diminishing stomatal and canopy conductance while increasing ABAleaf and Ψleaf. Across all graft combinations, WUE and ABAleaf were positively correlated independent of variation in Ψleaf or soil moisture. While WT scions regulated their WUE and ABA status independently of the root system, acropetal root-to shoot ABA signalling regulated flc scion ABA status (and thus WUE) under high evaporative demand or soil drying, independently of changing Ψleaf.
Flooding-induced hypoxia severely limits crop productivity, and Group VII Ethylene Response Factors (ERFVIIs) function as central transcriptional regulators of physiological and transcriptional acclimation to hypoxia. In rice, the ERFVII transcription factor SUB1A-1 confers strong submergence tolerance. It displays unusually high steady-state protein levels and reduced sensitivity to oxygen-dependent turnover despite retaining a canonical N-terminal degron motif that promotes rapid turnover of other ERFVIIs under normoxia. The basis of this property remains incompletely resolved. Here, we investigate structural and regulatory features associated with SUB1A-1 accumulation using ex vivo protein accumulation assays, domain-truncation analyses, biophysical characterization, and promoter-activity assays. We show that the C-terminal region, especially Gly256 to Ala281, of SUB1A-1 is associated with increased steady-state protein levels, and that its removal is associated with reduced accumulation and effects consistent with increased turnover in this assay. Full-length SUB1A-1 forms higher-order assemblies, and removal of the C-terminal region yields a smaller species by size-exclusion chromatography. In addition, SUB1A-1-dependent transcriptional activation requires clustered GCC-box motifs within target promoters, indicating that promoter context strongly influences regulatory output. Notably, the GCC1-box motifs most relevant to SUB1A-1 activity coincide with HRPE-like sequence motifs, suggesting that the local promoter sequence context may further shape SUB1A-1-dependent activation. Together, these observations indicate that elevated accumulation of SUB1A-1 correlates with C-terminal-associated assembly behavior and promoter-associated regulatory features. We propose that these properties may reduce functional accessibility to N-degron pathway components, providing a framework for understanding how SUB1A-1 is structurally and functionally configured to support transcriptional regulation under submergence and other energy-limiting conditions.
Autophagy is a conserved degradation and recycling pathway that sustains cellular homeostasis and provides energy and building blocks under adverse conditions. Despite detailed core machinery knowledge, transcriptional regulation of autophagy initiation in response to carbon status remains incompletely understood. Here, we combine scalable phenotyping of natural variation with molecular and functional analyses to dissect genotype-dependent autophagy responses to fixed-carbon deprivation in Arabidopsis thaliana. We show that transcription of genes encoding the autophagy initiation complex (ATG1, ATG11, ATG13, and ATG101) is repressed by soluble sugars, and that ATG101 displays the strongest enrichment of sugar-related cis-regulatory elements. Guided by this sugar-regulation framework, we phenotyped 181 accessions under prolonged darkness-induced carbon deprivation and quantified responses using chlorophyll retention (dark/light chlorophyll ratio) as a proxy trait, revealing natural variation in tolerance. ATG101 is induced more strongly upon deprivation in carbon starvation-resistant accessions. Association analysis identifies three SNPs in the ATG101 locus linked to the proxy phenotype, and we demonstrate that these polymorphisms differentially affect ATG101 sugar responsiveness and expression during carbon deprivation. Together, our results link natural variation in carbon-deprivation tolerance to regulatory polymorphisms at ATG101, supporting a model in which sugar-responsive control of autophagy initiation shapes genotype-specific sensitivity to carbon starvation in Arabidopsis.
The marine red alga Pyropia yezoensis employs two heat-stress signaling pathways, one dependent and one independent of membrane fluidity, each targeting distinct sets of heat stress-inducible genes, but the underlying factors are unclear. Here, to assess the importance of Ca2+ in the heat-stress response of P. yezoensis, we treated all three stages of its life cycle with Ca2+ chelators, which blocked the upregulation of both membrane fluidity-dependent and -independent genes. This repression was rescued by adding CaCl2. In addition, treatment with the calcium ionophore A23187 induced the expression of these genes at 15°C and 25°C. Thus, extracellular Ca2+ influx is a shared factor of both signaling pathways. Moreover, H2O2 contents increased upon exposure to 25°C and when membrane fluidity increased due to treatment with benzyl alcohol, which induced the expression of only membrane fluidity-dependent genes. Thus, H2O2 production is specifically involved in the membrane fluidity-dependent pathway. Furthermore, the heat stress-dependent production of H2O2 was inhibited by treatment with Ca2+ chelators, placing extracellular Ca2+ influx upstream of H2O2 production in the membrane fluidity-dependent pathway. Therefore, Ca2+ contributes to both pathways, whereas H2O2 is only involved in the membrane fluidity-dependent pathway in P. yezoensis.
Maize (Zea mays) produces terpenoid-based chemical defenses through a large family of terpene synthases, but the contributions of individual enzymes to specific compounds and stress resistance remain difficult to predict. Maize terpene synthase 8 (ZmTPS8) produces multiple sesquiterpenes in heterologous systems, but its in planta function remains unknown. We integrated a metabolite genome-wide association study (mGWAS), CRISPR/Cas9 generated tps8 loss-of-function mutants, metabolite profiling, and biotic stress assays to define ZmTPS8's role in terpene synthesis and biotic stress responses. The mGWAS identified ZmTPS8 as the primary locus associated with herbivore-induced emission of the sesquiterpene volatile germacrene D. Consistently, ZmTPS8 expression was induced by foliar and root herbivory, and tps8 mutants exhibited reduced emission of germacrene D, α-copaene, and δ-cadinene during Spodoptera frugiperda feeding. Loss of ZmTPS8 increased S. frugiperda larval growth but did not affect the belowground herbivore Diabrotica virgifera virgifera. ZmTPS8 also contributed to resistance against sugarcane mosaic virus, and the fungal pathogen Fusarium verticillioides, affecting terpenoid profiles, global metabolism, and fungal toxin production, but had no impact on Cochliobolus heterostrophus or Pythium spp. susceptibility. Together, these results demonstrate that ZmTPS8 contributes to maize defense in a threat-dependent manner, shaping volatile emissions and defense outcomes.
Developing breakthrough products that deliver at least 25% improvements in productivity in farmers' fields requires that breeding pipelines more closely align with farmers' and end-user needs and the target population of environments (TPEs). In the case of maize, climate change is accelerating climatic shifts within the TPE, potentially limiting future realised genetic gain. On-farm breeding approaches can play a valuable role in supporting breeding programs transitioning towards breakthrough products. Increased sampling of the TPE by moving selection into farmers' fields can overcome the challenges of climatic changes within the TPE and extensive farmer diversity, whilst providing information to refine managed environment trials designed to sample the TPE. This review highlights advances in inclusive host farmer sampling, sparse testing strategies and phenotyping to facilitate scaling of on-farm testing within breeding pipelines.
Abstract Chromatin remodeling plays a central role in regulating plant development and physiology by shaping the gene expression patterns that drive biological processes. Among epigenetic modifications, histone acetylation is particularly relevant as it alters chromatin structure and influences transcriptional activity. MYST-type histone acetyltransferases (HAT) are evolutionarily conserved components of the Nucleosome Acetyltransferase of Histone H4 complex (NuA4-C), a key regulator that acetylates histones H4, H2A, and the histone variant H2A.Z. Growing evidence supports the presence of a canonical NuA4-C in plants, similar to that described in yeast. In this review, we summarize recent studies that have begun to uncover its broad role in plant biology, highlighting its involvement in diverse processes such as the skoto- to photomorphogenesis switch, chloroplast development, shade avoidance responses, thermomorphogenesis, the vegetative-to-reproductive transition, plant growth, reproduction, and hormonal signaling. In addition, we discuss recent advances in understanding the crosstalk of NuA4-C-mediated H4 acetylation and H2A.Z deposition with other chromatin remodeling complexes in plants. Although significant progress has been made, a full understanding of the complex functions remains unavailable. Current evidence indicates that NuA4-C in yeast and TIP60 in humans are central regulators of transcription, acting not only through histone acetylation but also by influencing transcription elongation and RNA splicing, although direct evidence for similar functions in plant NuA4-C still remains limited. This regulatory role might be critical for integrating developmental programs with environmental signaling pathways. While initial insights into the recruitment of NuA4-C to target genes have emerged, further research is needed to clarify how its activity is controlled and modulated in different biological contexts.
Abstract Photorespiration is connected to other aspects of plant metabolism, including one-carbon (C1) metabolism. While a major contributor of C1 units in leaves is serine, formate production through non-enzymatic decarboxylation of glyoxylate by H2O2 has been hypothesized to also contribute under some conditions. To determine if flux to C1 metabolism via formate can be increased through metabolic engineering, we developed a high-throughput 13CO2 labeling system and used it to investigate wild-type (WT), catalase (cat) knockout, formate dehydrogenase (fdh) knockout, and fdh×cat double knockout Arabidopsis thaliana leaves. When fdh plants were labeled with 13C, there were no significant differences between fdh and WT plants in labeling kinetics of their C1 metabolites. Additionally, the 13C labeling kinetics revealed that C1 metabolites were labeled more slowly in the cat and fdh×cat double mutant plants compared with WT plants, suggesting that formate production from glyoxylate is not a major contributor to C1 metabolism, nor can it be engineered to be so.
Under global climate warming, plants evolve unique growth and developmental strategies to cope with frequent abiotic stresses. The plant-specific DNA-BINDING WITH ONE FINGER (DOF) transcription factors (TFs) originated in green algae and are phylogenetically divided into four subfamilies (A, B, C, D), governing plant growth development and stress adaptation. Subfamily B mainly regulates vegetative growth, subfamily C is predominantly involved in seed development and vegetative growth, and subfamily D1 (CYCLING DOF FACTOR, CDF) participates extensively in vegetative growth, flowering, and stress responses. Given emerging studies on DOF functions, a comprehensive review integrating recent advances, especially in seed dormancy, reproductive development and stress tolerance remains lacking. This review integrates current advances in the multifaceted roles of the DOF family, including regulating seed germination, vegetative growth, reproductive development and leaf senescence, as well as coordinating adaptive responses to various abiotic stresses.
Tea plants are typical aluminum hyperaccumulators, characterized by high aluminum accumulation in roots and old leaves. However, the systematic mechanisms underlying aluminum uptake and translocation in tea plants remain largely unclear. Here, we characterized the functions of the transporter CsALS3s and their transcription factor CsART1 in the process of aluminum tolerance in tea plants. Two ABC transporter genes, CsALS3.1 and CsALS3.2, were identified via bioinformatic and expression analyses. Transcriptomic and qRT-PCR assays showed that CsALS3.1 and CsALS3.2 were highly expressed in mature leaves and roots, respectively, and specifically induced by aluminum but not by other metal ions. Subcellular localization revealed that CsALS3.1 was targeted to the tonoplast, whereas CsALS3.2 was localized to the plasma membrane. Heterologous overexpression of CsALS3s significantly enhanced aluminum tolerance of Arabidopsis. Transient overexpression in tea leaves elevated aluminum concentration in the symplast but reduced it in the apoplast. When CsALS3s was stably overexpressed into the roots of tea seedlings, the content of aluminum in the transgenic roots was significantly increased, proved that CsALS3s mediate aluminum uptake and transport. Promoter analysis identified aluminum-responsive cis-elements in CsALS3s promoters, and Dual-luciferase and yeast one-hybrid assays confirmed that CsALS3s are transcriptionally activated by CsART1. Overexpression of CsART1 in Arabidopsis and tea plants improved aluminum tolerance and root aluminum accumulation, respectively. This study reveals that the transcription factor CsART1 activates CsALS3s to promote aluminum uptake and transport in tea plants, providing a basis for elucidating the molecular mechanisms of aluminum tolerance and hyperaccumulation in tea plants.
The biological complexity of plants arises from highly coordinated cellular activities. We propose that a "cellular spatiotemporal dogma" governs the zygote's programmed development into a complete plant and its adaptation to various environmental stresses, representing the set of principles describing how gene expression, cell identity, and function are coordinated across physical spatial contexts and temporal developmental progressions. Historically, our understanding of this dogma remains limited because traditional bulk tissue sequencing provides only a homogenized average of gene expression, making it challenging to isolate and resolve functionally significant but rare cell populations, such as the root quiescent center. However, the "resolution revolution" driven by single-cell and spatially resolved omics has dismantled these barriers to reveal cellular niches: local microenvironments where neighboring cells interact and coordinate function. Here, we firstly synthesize the current landscape of single-cell and spatial multi-omics technologies, highlighting how they bypass botanical barriers like the cell wall. Next, we detail how these technologies decode plant cellular characteristics, from defining novel cell subtypes to reconstructing dynamic trajectories and identifying pan-cell populations that remain ultra-conserved across hundreds of millions of years of evolution. Finally, we discuss the paradigm shift toward Large Foundation Models (FMs), which are computational paradigms that conceptualize biological data as a structured language to enable predictive modeling. Despite challenges such as data scarcity and phylogenetic bias, the integration of high-resolution omics with AI-driven intelligence is paving the way for a "Virtual Plant Cell, " a comprehensive digital model capable of simulating and predicting cellular responses to genetic and environmental perturbations, offering a transformative foundation for smart breeding and climate-resilient agriculture.
Despite extreme heat and limited water availability, invasive plant species are rapidly expanding in arid ecosystems, threatening native biodiversity. To understand the physiological mechanisms underlying invasive success in water-limited ecosystems, we analyzed photosynthetic, hydraulic and morphological traits of the invasive African grass Cenchrus ciliaris and three native North American dryland grasses (Bouteloua gracilis, Schizachyrium scoparium, and Sporobolus cryptandrus) in a full factorial growth chamber experiment combining two vapor pressure deficit (VPD) levels and three soil moisture levels. We hypothesized that C. ciliaris would exhibit greater physiological acclimation and morphological plasticity than native grasses, enabling superior tolerance to atmospheric and soil drought. Our results showed that rather than a simple invasive vs. native dichotomy, species grouped into functional strategies: a risk-prone, anisohydric group (C. ciliaris and S. scoparium) and a conservative, drought-avoidant group (B. gracilis and S. cryptandrus). The invasive C. ciliaris distinguished itself not through superior photosynthetic capacity, but through a unique ability to proactively allocate carbon to roots under high VPD combined with high soil moisture, differing from all native species. Contrary to our hypothesis, none of the species showed stomatal acclimation to sudden increases in VPD; instead, stomatal sensitivity to instantaneous VPD spikes operated as an intrinsic, species-level trait inflexible to prior environmental conditioning. Together, these findings suggest that the dominance of C. ciliaris in water-limited conditions is explained by allocation plasticity and anisohydric tolerance rather than superior carbon gain or stomatal acclimation.
Buried seeds avoid predation ensuring their survival until conditions are suitable for germination. The ability of seedlings to emerge from the soil depends on soil characteristics, burial depth, and the skotomorphogenic program of each species. This process is of interest to agriculture, as deep planting is practiced in wheat, sorghum, oats, and maize crops in certain arid and semi-arid regions of the world. In maize, deep planting can range from 10 to 40 cm, and only certain landraces are competent for this practice. It is known that deep-planting resistant varieties exhibit exaggerated mesocotyl elongation, but it is unclear whether resistance to deep planting has selected positively or negatively the growth capacity and/or development of other seedling organs and whether deep-planting resistance is an ancestral trait in Zea or evolved after maize domestication. To determine the skotomorphogenic patterns in the subtribe Tripsacinae, deep planting trials were conducted with representatives belonging to the genera Zea and Tripsacum and the length or number of seedling organs measured. The majority of maize seedlings grown in darkness exhibited features that we refer to as quasi-photomorphogenic (i.e., rupture of the coleoptile tip by the first plumular leaf and development of adventitious roots at the coleoptilar node [ARCN]), unlike teosintes that displayed a small proportion of individuals with the quasi-photomorphogenic phenotype or species of Tripsacum that maintained a strict skotomorphogenic phenotype prior to emergence. Moreover, ARCN were absent in Tripsacum and rare in teosintes, while seminal roots were uncommon in both Tripsacum and teosintes. In Tripsacinae, relative deep sowing depth (RDSD) for seedling emergence correlated positively with mesocotyl and stem lengths. Moreover, RDSD correlated negatively with the number of ARCN and SR and the length of the primary root and, to a lesser extent, of the coleoptile. In maize, SR development primordia ensued both embryonically and post-embryonically. These findings indicate that emergence from deeper soil depths has influenced the growth and development of all seedling organs, not just the mesocotyl, and that deep planting resistance is a characteristic that appeared within the Zea genus prior to maize domestication. Further, we report that Tripsacum caryopses are dispersed by myrmecochory and teosinte caryopses by seed-caching rodents. The ecological significance of skotomorphogenic development programs that aid in the escaping of wild Tripsacinae seedlings, from underground caches made by their animal dispersers, is discussed.
