The Plant Journal最新文献

Apple is a globally significant fruit tree with considerable economic value. However, it is severely affected by soil salinization, which leads to a reduction in both yield and quality. Since salt tolerance in grafted apple trees largely depends on the rootstock, this study compared transcriptomic responses between salt-tolerant (R5-5) and salt-sensitive (M9T337) rootstocks under salt stress. A key salt-responsive gene, MdWRKY33d, was identified. Overexpressing MdWRKY33d in apple improved salt tolerance, while silencing it had the opposite effect. Additionally, under salt stress, compared with the control, chlorophyll fluorescence values, superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) levels were elevated in MdWRKY33d transgenic apple and poplar materials. Functional analyses demonstrated that MdWRKY33d directly activates the expression of Peroxidase55 (MdPER55) and Dehydration-Responsive Element-Binding protein1D (MdDREB1D), thereby enhancing reactive oxygen species (ROS) scavenging and salt tolerance in transgenic plants. Yeast two-hybrid screening identified MdVQ22 as an interacting partner of MdWRKY33d, which was confirmed by pull-down, bimolecular fluorescence complementation (BiFC), and luciferase complementation imaging (LCI) assays. MdVQ22 negatively regulated apple salt tolerance by suppressing MdWRKY33d-mediated transcriptional activation of MdPER55 and MdDREB1D. Collectively, this study explores a putative regulatory module MdVQ22-MdWRKY33d-MdPER55/MdDREB1D to coordinate the responses to apple salt stress and provides potential targets for engineering salt-tolerant varieties.

Plants constantly face adverse environmental conditions, with temperature drops posing major threats to growth and productivity. To adapt, plants have evolved complex mechanisms of transcriptional reprogramming. While various cold-responsive pathways have been described, the contribution of chromatin-level regulation, particularly histone modifications, remains poorly understood. Here, we identify the histone methyltransferase SET DOMAIN GROUP 26 (SDG26) as a positive regulator of cold stress responses in Arabidopsis thaliana. We show that SDG26 is transcriptionally induced and posttranscriptionally stabilized by cold, and that its loss of function compromises several abscisic acid (ABA)-related phenotypes. At the molecular level, SDG26 promotes the expression of cold-responsive genes, including members of the CBF-COR regulon, through direct chromatin binding and deposition of histone H3 lysine 36 trimethylation (H3K36me3). Additionally, SDG26 modulates ABA biosynthesis, catabolism, and transport, thereby promoting ABA accumulation, stomatal closure, and drought tolerance. Collectively, our results reveal that SDG26 integrates ABA-dependent and ABA-independent pathways to fine-tune Arabidopsis responses to abiotic stresses. We further establish SDG26 as a chromatin modifier contributing to stress-responsive H3K36me3 enrichment at specific loci. Together, our findings position SDG26 as a chromatin-based hub that coordinates cold acclimation and water conservation to enhance plant resilience.

Annexins (ANNs) are Ca²⁺-dependent phospholipid-binding proteins that play important roles in plant responses to environmental stress. However, the apple ANN gene family and the regulatory mechanisms by which ANNs participate in cold-stress responses remain poorly understood. In this study, 15 MdANN family members were identified in the apple genome and divided into three subfamilies. Among them, MdANN2 expression was strongly induced by low temperature. Functional analyses showed that MdANN2 overexpression markedly enhanced cold tolerance in apple, whereas virus-induced gene silencing (VIGS) of MdANN2 compromised cold tolerance. Subcellular localization assays revealed that MdANN2 localized to the plasma membrane, cytoplasm, and nucleus. Non-invasive micro-test technology (NMT) further showed that MdANN2 is associated with Ca²⁺-permeable channel activity: cold stimulation significantly enhanced cytosolic Ca²⁺ influx in MdANN2-overexpressing plants, whereas exogenous application of the Ca²⁺ channel blocker LaCl₃ or the Ca²⁺ chelator EGTA substantially inhibited this influx. The kinases MdMPK6a and MdMPK6b physically interacted with and phosphorylated MdANN2 both in vitro and in vivo. Silencing MdMPK6a/b significantly increased apple cold tolerance, whereas overexpression of MdMPK6a/b reduced apple cold tolerance. Moreover, transient overexpression of MdMPK6a/b in the MdANN2-overexpression background attenuated MdANN2-mediated cold tolerance and Ca²⁺ influx. In addition, co-localization assays showed that MdMPK6a/b decreased the accumulation of MdANN2 at the plasma membrane. Together, these findings demonstrate that MdANN2 positively regulates apple cold tolerance by promoting cold-induced Ca²⁺ influx, a process inhibited by MdMPK6a/b-mediated phosphorylation. This study identifies a novel MdMPK6a/b-MdANN2 module that governs Ca²⁺ signaling in apple under cold stress, thereby providing promising molecular targets for improving cold tolerance in apple and other crop species.

Allantoin, a central intermediate of purine catabolism, plays key roles in nitrogen remobilization and is also implicated in stress protection in plants. As in other eukaryotes, allantoin biosynthesis in land plants has long been considered restricted to peroxisomes, where this process is catalyzed by ALLANTOIN SYNTHASE (ALNS). However, angiosperms produce not only the canonical peroxisomal isoform but also a shorter splice variant lacking a type 2 peroxisomal targeting signal (PTS2), raising the question of whether allantoin biosynthesis can occur outside peroxisomes. Through comparative sequence analyses across Archaeplastida, we show that PTS2-lacking ALNS exhibits a patchy distribution within Viridiplantae, including species without identifiable PTS2-containing ALNS homologs, suggesting the evolutionary significance of non-peroxisomal allantoin biosynthesis. Fluorescent protein fusion analysis showed that PTS2-lacking ALNS proteins from the angiosperm Arabidopsis thaliana, the monilophyte Dryopteris erythrosora, and the bryophyte Marchantia polymorpha localize outside peroxisomes, consistent with cytosolic localization. Furthermore, recombinant proteins from all three species catalyzed stereospecific (S)-allantoin formation. Arabidopsis alns knockout mutants accumulated racemic allantoin, indicating that ALNS ensures the stereospecific formation of (S)-allantoin while preventing the generation of poorly metabolizable (R)-allantoin, which likely arises through spontaneous decomposition of the unstable ALNS substrate 5-hydroxyisourate. Importantly, expression of either ALNS isoform restored normal allantoin metabolism and largely rescued the growth and physiological defects of the alns mutants. These findings demonstrate the functional equivalence of cytosolic and peroxisomal ALNS in Arabidopsis and reveal previously unrecognized flexibility in the subcellular organization of purine catabolism in plants.

Concerted evolution is the model by which multicopy gene families are homogenized across genomes, with ribosomal DNA (rDNA) as its textbook example. However, the extent and efficiency of this process may vary depending on genomic factors. The plant family Asteraceae provides a natural comparative system to address the evolutionary dynamics of rDNA, as it is uniquely characterized by the coexistence of two contrasting genomic arrangements: a separate (S-type) and a linked (L-type) organization of 5S and 35S rRNA genes. Here we analyzed rDNA arrangements in 71 representative Asteraceae species (50 S-type and 21 L-type) and, using WGS data and repeatome analyses, we have reconstructed full rDNA units and quantified the intragenomic variability across coding (genic) and non-coding (spacer) regions. No intermediate (coexisting L-type+S-type) genotypes were found. Our results reveal contrasting patterns of 5S rDNA variation depending on its genomic context. S-type species exhibit high levels of 5S polymorphism in both genic and spacer regions, while L-type species show near-complete sequence homogeneity, consistent with variation in homogenization efficiency and selective constraints related to copy number and chromosomal position of 5S rRNA genes. In contrast, 35S rDNA shows a low polymorphism level overall. The findings support a context-dependent view of concerted evolution across rDNA and highlight the influence of genome architecture on rDNA evolution. In particular, the contrasting behavior of 5S (highly conserved when linked but highly variable when separate) emerges as a key example of how structural genomic context shapes the evolution of even the most conserved housekeeping genes.

Specialised metabolism is an important factor in how plants cope with biotic and, to a lesser extent, abiotic stress. Current approaches to identify and study the genes involved in such metabolic pathways mainly leverage genomic and transcriptomic datasets of plants, in order to improve our understanding of plant resilience. Even though modern sequencing techniques have provided access to high-quality reference genome or transcriptome datasets, sequencing costs have for a long time forced a restriction to a selected reference accession. However, individual plants within a population often exhibit substantial differences in metabolic profiles, sometimes even leading to completely different chemotypes. This generated an urgent need to transition from single-reference accessions to the wider diversity of plant populations or even beyond the species level. Thanks to decreasing costs and improved reliability of sequencing techniques, this is now possible through pangenomic or pantranscriptomic approaches. In this review, we provide an introduction into the current state of the fields of pangenomics and pantranscriptomics and highlight recent examples on how these approaches have been used to elucidate and investigate specialised metabolic pathways in plants. We also provide an overview of database resources that might be useful for researchers in the field. Lastly, we present a critical summary and discussion of limitations and trends that are important for future innovations. With these developments in mind, we anticipate that pangenomics and pantranscriptomics will play a crucial role in exploring and harnessing the diversity of plant specialised metabolism beyond single individuals.

The wound healing process in postharvest citrus fruit represents a crucial physiological mechanism that effectively resists external stress and minimizes quality deterioration. Nevertheless, the molecular mechanisms involved in wound healing by GATA transcription factors in citrus remain largely unexplored. In this research, CsGATA5 was characterized as a newly identified transcriptional activator promoting wound healing in citrus fruit. Transient overexpression of CsGATA5 in tobacco also confirmed its role in promoting suberin accumulation. Gene expression and metabolite profiling analyses following CsGATA5 overexpression revealed that CsGATA5 activated pathways associated with amino acid metabolism during wound healing. DLR, EMSA, ChIP-qPCR, and Y1H assays demonstrated that CsGATA5 bound to the promoter regions of target genes in tryptophan metabolism (CsTRYS and CsTDC2), thereby activating their expression. Notably, the activation of CsTRYS and CsTDC2 genes during citrus wound healing contributed to the subsequent induction of downstream suberin biosynthesis. Moreover, the exogenous treatment of key metabolites of the amino acid pathway, including tryptophan, 5-hydroxytryptamine, and phenylalanine, significantly promoted wound healing and further supported a potential regulatory cascade of tryptophan metabolism– tricarboxylic acid cycle– suberin biosynthesis. This study sheds light on the molecular regulatory network by which GATA transcription factors modulate wound healing in fruit.

Perennial plants rely on two key ecological strategies to supply nitrogen (N) for photosynthetic tissue construction: root N remobilization (internal cycling) and soil N uptake. How plants trade-off these strategies determines the economy of N use and is likely context-dependent. Yet, it is rarely quantified in situ across growth stages and under varying management, limiting the mechanistic understanding of how plants rebalance N-use trade-offs to adapt to grazing disturbance. To address this gap, we conducted an in situ experiment using ¹⁵N isotope labelling techniques in a semiarid grassland to quantify the contributions of these two strategies at two plant growth stages under nil, summer or autumn grazing. We found that the plant relied more on soil N uptake (58%) during the regreen stage, but more on N remobilization (57%) during the rapid-growth stage. Grazing, especially in autumn, significantly leaned N use trade-off toward conservative N remobilization. The shift in plant N use strategies was driven primarily by plant growth demand and soil N supply, but not root N stock. Plant N use trade-off leaned toward internal cycling when source traits were below or sink traits were above the thresholds, for example, soil N availability <9.0 mg kg⁻¹ or shoot carbon content >41.88%. Our study highlights the importance of the N resource-sink relations in mediating the trade-off in plant N use strategies, buffering grazing stress to grassland plants. These findings provide a mechanistic basis for improving ecosystem N cycling modeling and adaptive grazing management.