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.
Plants perceive diverse extracellular molecules derived from microbes and insects and activate immune responses. While significant progress has been made in understanding plant recognition of microbial proteins and carbohydrates such as chitin, the mechanisms underlying lipid recognition have remained largely elusive. Lipids are essential components of cells, and various microbe- and insect-derived lipid molecules have been reported to induce or modulate immune responses in plants. Recent findings have revealed that lipid perception involves not only canonical receptor-mediated recognition but also the sensing of changes in membrane-associated properties, highlighting the diverse mechanisms underlying lipid-mediated immune regulation. This review focuses on naturally occurring microbial and insect lipids that trigger plant defense responses upon exogenous application. Particular emphasis is placed on plasma membrane-localized lipid receptors identified to date, as well as receptor-independent mechanisms whereby changes in plasma membrane biophysical properties are directly perceived and translated into immune activation. This review provides an overview of recent findings on plant lipid perception and discusses unresolved issues and future directions in this field.
Seasonal fluctuations strongly shape the physiology of long-lived trees by coordinating growth, dormancy, and stress responses. Increasing evidence points to epigenetic mechanisms, particularly DNA methylation, as regulators of these processes, yet their role in long-lived trees across seasons, developmental stages and generations remains poorly understood. We generated single-base resolution maps of cytosine methylation exploring the epigenetic landscape of 180 year-old mature oak (Quercus robur) trees (genetically homogeneous) along spring, summer and autumn, and in their progeny. Genome-wide DNA-methylation revealed a progressive increase in the CHH context (H = A, T or C) from Spring to Summer and Autumn, suggesting epigenetic reprogramming is happening over season and growing cycle. Differentially Methylated Regions (DMRs) were concentrated in promoter regions and terminal inverted repeat (TIR) transposons. Observed differentially methylated transposable elements (TEs) and genes were majorly involved in leaf development and hormonal signalling. By contrast, generational differences (parents versus offspring) were most prominent in CG and CHG contexts and were concentrated in genic regions. Oaks exhibit distinct seasonal and generational DNA methylation signatures, highlighting the plasticity and developmental specificity of epigenetic regulation. These findings provide a genomic foundation for understanding how epigenetic memory contributes to phenology, developmental programming and long-term adaptation in long-lived plants.
A major strength of forward genetic screens is their unbiased nature: the plant reveals which genes underlie a physiological process. Yet this strength often presents a new challenge: determining the biochemical basis of the mutant phenotype. BIG/DARK OVEREXPRESSION OF CAB1/TRANSPORT INHIBITOR RESPONSE3 encodes an exceptionally large (∼0.5 MDa) protein identified in diverse genetic screens. big mutants have smaller stature, reduced elongation growth and apical dominance, and defects in lateral root formation, phenotypes consistent with disrupted auxin gradients. However, they also display altered stomatal behaviour, circadian regulation, pathogen responses, and changes in other hormone pathways. This broad pleiotropy points to wide-ranging roles in signalling and development, yet the biochemical function of BIG remained unresolved for more than three decades. Recently, we showed that BIG participates in the Arg/N-degron pathways, a specialised form of proteostasis in which the half-lives of proteins are influenced by their N-terminal (Nt) residues. However, this does not explain the pleiotropic phenotypes of big mutants. New structural and functional clues from the mammalian homologue ubiquitin amino-end recognising protein 4 (UBR4) point to wider proteostatic roles for BIG, providing a potential explanation for the impacts of BIG on plant physiology and a rich source of hypotheses for future studies.
Cyanogenic glycosides function as defense compounds and nitrogen reservoirs in sorghum, but their roles during seed germination under salt stress remain unclear. Here, two sorghum cultivars differing in salt tolerance were compared using physiological, biochemical, pharmacological and transcriptomic analyses to investigate the relationship between dhurrin metabolism and germination performance under salinity. Salt stress inhibited germination and early seedling growth in both cultivars, whereas the tolerant genotype SB19 maintained higher germination rates, earlier radicle emergence and stronger antioxidant capacity than the sensitive genotype SB08. SB19 exhibited lower dhurrin accumulation but more stable hydrogen cyanide potential (HCNp) and higher β-glucosidase activity during germination. HCNp stability was positively associated with germination performance and antioxidant enzyme activities, and negatively associated with reactive oxygen species accumulation. Pharmacological inhibition of alternative oxidase or cyanide detoxification reduced the salt tolerance advantage of SB19, while sodium thiosulfate partially alleviated the inhibitory effects of cyanide detoxification blockage. Transcriptomic and co-expression analyses further associated dhurrin turnover with redox regulation, membrane-related processes and stress-responsive regulatory networks. Collectively, these findings indicate that coordinated dhurrin turnover and HCNp homeostasis are associated with improved germination performance under salt stress in sorghum.
Hydrogen sulfide (H2S) is a gasotransmitter molecule that regulates essential plant biological processes. In the context of climate change and increasing flooding events, its role in plant responses to oxygen (O2) deficiency has gained significant attention. Accumulating evidence indicates that H2S exerts beneficial effects under hypoxia by modulating antioxidant defenses, mitochondrial function and hormonal signaling, mainly through its ability to refine protein activity via the post-translational modification (PTM) of persulfidation. Here, we discuss how this PTM is linked to the gasotransmitter molecule nitric oxide (NO) and reactive oxygen species (ROS) and how they can act synergistically or antagonistically, influencing the cell redox state and survival. Additionally, we examine how H2S turnover is intrinsically linked to O2 availability, acting as conserved mediator of low O2 responses in different domains of life. By integrating biochemical insights with molecular signaling, we underscore the potential of H2S in enhancing crop resilience to low O2 related stresses, such as submergence and waterlogging.
