Plant Physiology[JOURNAL]
Sun
200 papers
Toward scalable wood anatomy: a toolkit for automated xylem cell identification and quantification in woody angiosperms.
Mei L, Qi C, Pei Z … +12 more , Zhao B, Fu Q, Jiang Z, Li C, Jin Z, Zhao R, Cheng J, Wang Y, Li Q, Bao M, Zheng B, Shi X
Plant Physiol · 2026 Jun · PMID 42335874 · Publisher ↗
Xylem is essential for water and nutrient transport, mechanical support, and carbohydrate storage. Identification and quantification of vascular cell types remain manual, time-consuming, and prone to observer bias, limit...
Xylem is essential for water and nutrient transport, mechanical support, and carbohydrate storage. Identification and quantification of vascular cell types remain manual, time-consuming, and prone to observer bias, limiting throughput and reproducibility. Automated, integrated tools are critical for scaling wood anatomical studies and enabling comparative analyses across taxa. We assembled a poplar xylem dataset of 1,790 microscopy images with 173,434 annotated instances. Using this dataset, we evaluated seven semantic segmentation models and five YOLOv8 detection models across section types for xylem cell recognition and morphometric attribute extraction and adopted a "Segmentation-then-Detection" pipeline to reduce misidentifications in complex backgrounds. Mask2Former achieved the best segmentation performance, covering transverse sections (whole xylem, vessels, fibers, rays) and tangential sections (rays and four ray cell image types). YOLOv8x and YOLOv8m performed consistently for object detection and morphometrics, and the PLXY-AI toolkit was accordingly developed based on YOLOv8 architecture. The combined pipeline markedly improved fiber identification in challenging images. In a generalization test, 34 of 42 woody angiosperms (81.0%) met >90% accuracy for identifying all cell types. The workflow and PLXY-AI toolkit enable automated identification and quantification of vessels, fibers, and rays, extracting size and area while substantially reducing manual workload and observer bias. Per-image processing time averages <1 s. Designed for batch analysis, the pipeline minimizes operational complexity and integrates easily into existing laboratory and computational environments. With a user-friendly graphical interface, this framework supports high-throughput analysis of vascular tissue structure and function across multiple tree species.
FveMYB1-FveTPR2-FveHDA6 complex prevents anthocyanin overaccumulation during strawberry fruit ripening.
Zhang Z, Yao J, Wang B … +5 more , Guan Y, Jiao H, Zhang Z, Zhang J, Li H
Plant Physiol · 2026 Jun · PMID 42335873 · Publisher ↗
Anthocyanins serve as critical secondary metabolites in plants. However, the molecular mechanisms underlying plant regulation to prevent anthocyanin overaccumulation remain largely elusive. This study reveals that both t...
Anthocyanins serve as critical secondary metabolites in plants. However, the molecular mechanisms underlying plant regulation to prevent anthocyanin overaccumulation remain largely elusive. This study reveals that both transcript and protein levels of the anthocyanin repressor FveMYB1 in woodland strawberry progressively increase during fruit development, peaking at the ripening stage. Stable transformation confirmed that FveMYB1 suppressed anthocyanin biosynthesis. To investigate how FveMYB1 suppresses anthocyanin biosynthesis, we performed yeast two-hybrid screening of a strawberry fruit cDNA library using FveMYB1 as bait. FveMYB1 was found to interact with two types of regulators: the transcriptional co-repressor FveTPR2 and histone deacetylases FveHDA6, respectively. Both FveTPR2 and FveHDA6 exhibited the highest expression levels in ripening fruits, and these genes were found to repress anthocyanin biosynthesis during fruit maturation. Interestingly, three members (FveMYB1, FveTPR2 and FveHDA6) interact with each other to form a ternary complex to repress anthocyanin biosynthesis. Furthermore, TSA treatment and Chip-qPCR demonstrated that FveMYB1-FveTPR2-FveHDA6 complex mediate histone deacetylation at key anthocyanin biosynthetic genes (FveF3H, FveCHS, and FveANS). This epigenetic modification represses the expression of these genes, ultimately reducing anthocyanin accumulation to prevent overproduction in strawberry fruits and this regulatory mechanism is conserved in various plants. These findings elucidate a novel regulatory pathway that fine-tunes anthocyanin biosynthesis during fruit ripening.
Resistance to embolism is critical for post-drought recovery in resprouting Ceratonia siliqua.
Wagner Y, Müllers Y, Volkov M … +3 more , Delzon S, Hochberg U, Klein T
Plant Physiol · 2026 Jun · PMID 42335871 · Publisher ↗
Xylem embolism persists long after drought has ended and should thus have a lasting effect on plants' ability to recover from severe drought. This assumption has rarely been tested, as quantifying the amount of embolism...
Xylem embolism persists long after drought has ended and should thus have a lasting effect on plants' ability to recover from severe drought. This assumption has rarely been tested, as quantifying the amount of embolism in individual intact trees is difficult, and following recovery would require long-term monitoring, specifically when studying trees. Our goal was to test the effect of embolism on recovery from drought in a broad population. We exposed 210 carob seedlings (Ceratonia siliqua), a species with high resistance to embolism, to a gradient of drought durations and monitored their ability to recover over five months with respect to their embolism level (assessed using micro-computed tomography). Seedlings that suffered 38% embolism had a 50% chance of dying. In the surviving seedlings, stomatal conductance was still inhibited a month after rehydration (i.e., 82% lower than in the irrigated control, even in plants that sustained only 10% embolism) but recovered to pre-drought levels after five months, regardless of the embolism levels. The hydraulic limitations were mostly noticed in the canopy size, as five months after rehydration, canopy area and the ability to resprout were strongly correlated with embolism level sustained during drought (but not with water potential). Our results suggest that embolism can be fatal even at levels below 50% and that maintaining the integrity of the hydraulic system is critical for rapid drought recovery.
Molecular Insights into Trx System Genes Identified Role of miR6427-5p-PagCDPS32 module in Poplar under Drought Stress.
Yang Y, Zhu Y, Wang Z … +3 more , Fu T, Liu J, Wang Y
Plant Physiol · 2026 Jun · PMID 42335870 · Publisher ↗
Thioredoxins (TRXs), a class of ubiquitous oxidoreductases, are essential for thiol redox regulation in plants. So far, the Trx system has been established in herbaceous plants. However, studies of the Trx system and its...
Thioredoxins (TRXs), a class of ubiquitous oxidoreductases, are essential for thiol redox regulation in plants. So far, the Trx system has been established in herbaceous plants. However, studies of the Trx system and its post-transcriptional regulation mediated by miRNAs in woody plants are scarce, and especially the functions of the regulatory mode in poplar responding to drought remain unclear. In this investigation, antioxidant enzyme activities and osmotic adjustment responses suggested that the chloroplast-specific antioxidants were indispensable for regulating the drought tolerance of poplar. The Trx system genes were comprehensively identified and classified, and the miRNA-mediated post-transcriptional regulation of Trx system genes was investigated in poplar, revealing the high number of atypical TRXs and their special functions. PagCDSP32, an atypical TRX located in the chloroplast, was identified as a drought tolerance candidate. Transgenic poplars overexpressing PagCDSP32 exhibited stronger ROS scavenging ability and drought tolerance, while those with suppressed PagCDSP32 expression showed the opposite. Transcriptomic analysis indicated that differentially expressed genes affected by PagCDSP32 were mainly enriched in maintaining cell homeostasis. PagCDSP32 could interact with two peroxiredoxins, and inhibition of miR6427-5p expression increased the ROS scavenging ability of poplar under drought stress by liberating the cleavage of PagCDSP32. Intriguingly, the expression of the miR6427-5p-PagCDSP32 module determined the drought tolerance of poplar varieties. Overall, a potential module regulating poplar drought tolerance was proposed, which would provide a valuable resource of Trx system genes in poplars and facilitate future efforts to decipher the role of TRXs in regulating plant tolerance to abiotic stresses.
Upregulation of PpHsfB2b at high temperature represses light-induced anthocyanin biosynthesis in pear.
Wang X, Wang L, Zheng Y … +4 more , Li H, Ni J, Teng Y, Bai S
Plant Physiol · 2026 Jun · PMID 42335869 · Publisher ↗
In recent years, escalating global temperatures have adversely affected the yield and quality of horticultural crops. Red pears (Pyrus spp.), prized for their vibrant pigmentation, derive their characteristic coloration...
In recent years, escalating global temperatures have adversely affected the yield and quality of horticultural crops. Red pears (Pyrus spp.), prized for their vibrant pigmentation, derive their characteristic coloration primarily from anthocyanin accumulation. Light and temperature are important environmental factors regulating anthocyanin biosynthesis. Light induces the accumulation of anthocyanins in red pear; however, the specific molecular mechanism by which elevated temperatures inhibit anthocyanin biosynthesis in red pear remains unclear. The integration nodes of the light and temperature signals also remain to be discovered. In this study, we identified a high-temperature-responsive repressor, pear HEAT SHOCK FACTOR B2b (PpHsfB2b), which exhibits rapid upregulation under high-temperature treatment. A stable transformation system using pear calli demonstrated that PpHsfB2b functions as a repressor of anthocyanin biosynthesis. PpHsfB2b directly bound to the promoters of anthocyanin biosynthesis-promoting factors MYB transcription factor 10 (PpMYB10) and ELONGATED HYPOCOTYL 5-LIKE (PpHY5L), inhibiting their expression. Additionally, we identified a key light-temperature signaling node gene, B-box transcription factor 16 (PpBBX16), through which PpHsfB2b exerts a dual inhibitory effect on anthocyanin biosynthesis. PpHsfB2b not only interacted with PpBBX16 to attenuate transcriptional activation of downstream genes PpMYB10 and UDP-glucose: flavonoid 3-O-glucosyltransferase (PpUFGT), but also suppressed anthocyanin accumulation by competitively weakening the PpHY5L-PpBBX16 interaction. These insights deepen our understanding of high-temperature-regulated fruit pigmentation and identify PpBBX16, a critical light-temperature signaling node, providing a molecular framework for the color change of pear fruits under increasing temperatures.
Alternative splicing of WRKY55 orchestrates ABA signaling to enhance plant stress resistance.
Quan S, Wang Q, Liu M … +11 more , Wang K, Li N, An Y, Xu D, Wang G, Wang X, Shi Q, Ma L, Kong F, Zhang H, Li G
Plant Physiol · 2026 Jun · PMID 42334883 · Publisher ↗
Plant abiotic stress critically threatens plant survival and agricultural productivity. The phytohormone abscisic acid (ABA) plays a key role in regulating plant acclimation to abiotic stress. Although the perception and...
Plant abiotic stress critically threatens plant survival and agricultural productivity. The phytohormone abscisic acid (ABA) plays a key role in regulating plant acclimation to abiotic stress. Although the perception and activation of ABA signaling have been extensively studied, the molecular regulatory mechanisms that terminate ABA signaling remain largely unknown. Here, we identified WRKY55 as a key regulator of ABA signaling. Disrupting WRKY55 function significantly reduced ABA sensitivity, leading to increased seed germination rates, cotyledon greening rates, and primary root length. Notably, WRKY55 undergoes alternative splicing (AS) to generate two protein isoforms, WRKY55.1 and WRKY55.2, which play opposite roles in ABA-mediated plant development. WRKY55.1 transcript levels gradually increased in response to short-term ABA treatment, followed by a rapid decrease during prolonged ABA treatment. WRKY55.2 transcript levels gradually increased under prolonged ABA treatment. We demonstrated that WRKY55.1 directly promotes the expression of ABSCISIC ACID INSENSITIVE5 (ABI5) to activate ABA responses. Notably, WRKY55.2 interacts with WRKY55.1 to suppress the direct activation of ABI5 expression. Moreover, WRKY46 interacts with WRKY55.1 to antagonistically regulate ABI5 expression. Collectively, our study reveals that WRKY55 acts as a master regulator that orchestrates both the activation and desensitization of ABA signaling, thereby enhancing plant resistance and acclimation under stress conditions.
Chitinase 38 confers cadmium tolerance via reduced cadmium uptake and metabolic reprogramming in barley.
Shi SH, Chen Q, Qiu CW … +6 more , Zhang S, Sreesaeng J, Cao F, Wang Y, Chen ZH, Wu F
Plant Physiol · 2026 Jun · PMID 42334431 · Publisher ↗
Soil cadmium (Cd) contamination threatens crop productivity and food safety. Chitinase genes (Chit) are well-characterized for their roles in plant defense against biotic stresses, but their functions in Cd stress respon...
Soil cadmium (Cd) contamination threatens crop productivity and food safety. Chitinase genes (Chit) are well-characterized for their roles in plant defense against biotic stresses, but their functions in Cd stress responses remain elusive. Here, we functionally characterize HvChit38, a novel Cd-induced Class I chitinase gene from a Cd-tolerant barley genotype. Chit38 sequences are highly conserved during green plant evolution, with a likely origin from streptophyte algae. HvChit38-overexpression significantly improves plant growth and yield, substantially reduces Cd concentrations in roots, shoots and grains under Cd stress, whereas HvChit38-silencing results in the opposite phenotypes. Integrated transcriptomic and metabolomic analyses indicate that HvChit38 activates the shikimate pathway mediated by upregulating HvDHQD, which in turn promotes the biosynthesis of downstream phenylpropanoid and terpenoid compounds. This metabolic shift enhances antioxidant capacity and promotes cell wall remodeling with increased lignin and hemicellulose contents and reduced pectin content, thereby restricting Cd uptake and translocation. Virus-induced gene silencing of HvDHQD in HvChit38-overexpressing plants reduced lignin and flavonoid contents while increasing Cd accumulation, confirming that HvChit38 enhances Cd tolerance in barley through HvDHQD upregulation. Collectively, our findings provide the first evidence for a potential link between HvChit38, HvDHQD-mediated shikimate pathway, and Cd tolerance, highlighting HvChit38 as a promising target for breeding Cd-tolerant and low-Cd-accumulation cereal crops.
Molecular basis underlying the isoprene emission diversity in Fagaceae.
Koita S, Munakata R, Kamata Y … +9 more , Shinya N, Fukushima K, Nagano AJ, Ikezaki Y, Satake A, Saito T, Miura K, Sugiyama A, Yazaki K
Plant Physiol · 2026 Jun · PMID 42320526 · Publisher ↗
Plants emit volatile organic compounds (VOCs) into the atmosphere, reaching approximately 109 tons of carbon per year. These biogenic VOCs exhibit significant chemical diversity, with terpenoids being the dominant group,...
Plants emit volatile organic compounds (VOCs) into the atmosphere, reaching approximately 109 tons of carbon per year. These biogenic VOCs exhibit significant chemical diversity, with terpenoids being the dominant group, and isoprene accounting for nearly half of the total biogenic VOCs. Due to its high chemical reactivity, isoprene has a strong impact on atmospheric quality and climate. Quercus (Fagaceae) species are the main isoprene emitters in the Northern Hemisphere. However, isoprene synthase has not been identified in the entire Fagaceae family. Even within a single genus such as Quercus, both isoprene-emitting and non-emitting species coexist, yet the molecular basis of this dichotomy remains unclear. Here, we report the identification of the IspS gene from the isoprene-emitting species Quercus serrata (QsIspS1) through seasonal transcriptome analysis and detailed biochemical characterization of the gene product. We also identified two genes with high sequence similarity to QsIspS1 in the genomes of non-emitting species: Q. glauca (QgIspS1-like) and Lithocarpus edulis (LeIspS1-like). We discovered mutations in these sequences that likely impair their function. Biochemical analysis revealed that QgIspS1-like is a monoterpene synthase, whereas LeIspS1-like is a pseudogene incapable of isoprene synthesis, explaining these plants' inability to emit isoprene. Furthermore, site-directed mutagenesis revealed an amino acid that plays a pivotal role in the substrate and product specificities of isoprene synthase. Our findings provide insight into the molecular mechanisms underlying isoprene emission diversity in Fagaceae.
GH3 phylogenetic subgroups define divergent routes of auxin inactivation via aspartate and glutamine conjugation.
Helusová L, Ušák D, Havránková Z … +7 more , Dobrev PI, Svobodová B, Talpová J, Brunoni F, Moravec T, Müller K, Petrášek J
Plant Physiol · 2026 Jun · PMID 42320524 · Publisher ↗
Auxin conjugation represents a key metabolic mechanism in regulating auxin activity within plant cells. GRETCHEN HAGEN3 (GH3) enzymes conjugate the major naturally occurring auxin indole-3-acetic acid (IAA) with amino ac...
Auxin conjugation represents a key metabolic mechanism in regulating auxin activity within plant cells. GRETCHEN HAGEN3 (GH3) enzymes conjugate the major naturally occurring auxin indole-3-acetic acid (IAA) with amino acids, thereby contributing to the maintenance of auxin homeostasis. Although the transcription of GH3 genes is auxin-regulated, the complexity of this regulation is still not fully understood. Therefore, in this study, we employed β-estradiol-inducible and CRISPR/Cas9-mediated knock-out transgenic tobacco (Nicotiana tabacum) cell lines with modified expression of representative genes from two GH3 subgroups with contrasting response to auxin, NtGH3.1a and NtGH3.6e. Using IAA metabolite profiling and bacterial enzyme assays, we show that NtGH3.1a preferentially catalyzes the formation of indole-3-acetyl-aspartate (IAA-Asp), while NtGH3.6e facilitates the production of the less-characterized conjugates indole-3-acetyl-glutamine (IAA-Gln) and 2-oxindole-3-acetyl-glutamine (oxIAA-Gln). We further validated these results by testing the Arabidopsis thaliana homologs of both GH3 subgroups, showing that AtGH3.1 favors aspartate, while both AtGH3.5/6 preferentially utilize glutamine. Finally, subcellular localization analyses using GFP-tagged NtGH3.1aT and NtGH3.6eT expressed under inducible promoters demonstrated that both enzymes localized to the nucleus and cytoplasm, independently of the presence of auxin. Moreover, we provide evidence of GH3 localization under native promoters, confirming their presence in both compartments. Collectively, our results suggest the evolutionary conservation of amino acid type-preferential IAA conjugation and underscore the functional divergence of GH3 isoforms in IAA metabolism.
Multilayered regulation of chloroplast development by single B-BOX CONSTANS-LIKE and GOLDEN2-LIKE proteins in Arabidopsis.
Kakuda K, Abumi M, Kinoshita H … +11 more , Higashi M, Shiiba H, Shimizu S, Kuramoto S, Nishida F, Kawajiri K, Sakugawa K, Sato M, Toyooka K, Ito-Inaba Y, Inaba T
Plant Physiol · 2026 Jun · PMID 42320513 · Publisher ↗
Chloroplast development is primarily regulated by transcription factors, including those belonging to the GOLDEN2-LIKE (GLK) family, that alter the expression of genes encoding chloroplast proteins. However, the mechanis...
Chloroplast development is primarily regulated by transcription factors, including those belonging to the GOLDEN2-LIKE (GLK) family, that alter the expression of genes encoding chloroplast proteins. However, the mechanisms by which multiple transcription factors coordinate to optimize chloroplast development remain unclear. In this study, we identified the single B-BOX (BBX) CONSTANS-LIKE (COL) proteins COL6 (also known as BBX14), COL7 (BBX16), COL8 (BBX17), and COL16 (BBX15) as novel regulators of chloroplast development in Arabidopsis thaliana. Notably, the col6 col16 (col-d) double mutant exhibited a chlorophyll-excess phenotype, which was further enhanced in the quadruple col6 col7 col8 col16 (col-q) mutant. Introduction of col-d and col-q mutations in the glk1 glk2 (glk-d) mutant partially restored the pale-green phenotype of the original glk-d mutant. COL proteins negatively and redundantly regulated a class of genes encoding chloroplast proteins, acting directly on their promoters. Moreover, COL6 and COL7 expression exhibited a diurnal cycle, with their expression patterns contrasting with those of GLK1 and GLK2, which are positive regulators of chloroplast development. Furthermore, GLK expression was markedly higher in the col-q mutants than in wild-type plants. Co-immunoprecipitation assays revealed that COL proteins interacted with the GARP DNA-binding domain in the N-terminus of GLK1, likely affecting its function. Moreover, COL proteins associate with each other to form homomeric and heteromeric complexes, suggesting functional redundancies at the protein level. In conclusion, these results suggest that the multilayered regulatory mechanisms of single BBX COL and GLK proteins optimize chloroplast development in Arabidopsis thaliana in fluctuating environments.
Regulatory plasticity balances photosynthetic electron flow with enhanced pH-dependent cytochrome b6f control.
Kobayashi R, Shimatani Z, Nishida K … +1 more , Shikanai T
Plant Physiol · 2026 Jun · PMID 42319120 · Publisher ↗
To avoid photodamage of photosystem I (PSI) under fluctuating light, plants have evolved multiple photoprotective mechanisms. One key mechanism is photosynthetic control, in which acidification of the thylakoid lumen dow...
To avoid photodamage of photosystem I (PSI) under fluctuating light, plants have evolved multiple photoprotective mechanisms. One key mechanism is photosynthetic control, in which acidification of the thylakoid lumen downregulates electron transport through the cytochrome b6f (Cyt b6f) complex, thereby preventing over-reduction of PSI. The Arabidopsis proton gradient regulation 5 (pgr5) mutant, which is defective in cyclic electron transport around PSI, fails to induce photosynthetic control and consequently suffers severe PSI photodamage under fluctuating light. Previously, we showed that introduction of the pgr1 mutation, which enhances the pH sensitivity of the Cyt b6f complex, partially restored PSI oxidation and alleviated PSI photodamage in the pgr5 background. However, excessively strong photosynthetic control limits electron transport at relatively low light intensities. To investigate whether a milder enhancement of photosynthetic control can protect PSI without compromising photosynthetic performance, we introduced a series of amino acid substitutions into the Rieske subunit of the cytochrome b6f complex using Target-AID-mediated base editing. Among these, the E143K mutation partially oxidized PSI and improved photosynthetic induction in the pgr5-2 background more effectively than the pgr1 mutation. Although the E143K mutation had little effect on electron transport parameters in the wild-type background, it significantly reduced the proton motive force. The unexpected reduction in proton motive force suggests that moderately enhanced photosynthetic control can be accommodated without major impairment of photosynthetic electron transport.
Conserved and Lineage-Specific Roles of KEA-Mediated Ion Homeostasis in Chlamydomonas.
Wunder T, Eulitz L, Kramer L … +19 more , Ali ZM, Ostermeier M, Leu C, Szulc B, Holzner LJ, Fechter J, Padovani F, Brandt B, Girr P, Teh JT, Mühlbauer S, Sotos C, Angstenberger M, Mackinder LCM, Schmoller KM, Rädler JO, Nickelsen J, de Vries J, Kunz HH
Plant Physiol · 2026 Jun · PMID 42319078 · Publisher ↗
In Arabidopsis thaliana, seamless plastid gene expression and development depend on finely balanced ion homeostasis across the inner envelope (IE) membrane, maintained by the K+/H+ antiporters AtKEA1/2. To assess whether...
In Arabidopsis thaliana, seamless plastid gene expression and development depend on finely balanced ion homeostasis across the inner envelope (IE) membrane, maintained by the K+/H+ antiporters AtKEA1/2. To assess whether these functions are retained across mono- and polyplastidic representatives of the green lineage, we studied CrKEA1, the sole IE KEA homolog in the unicellular alga Chlamydomonas reinhardtii. Using CRISPR/Cas9, we generated a Cr-kea1 knockout mutant that exhibits impaired photoautotrophic growth, chloroplast deformation, and photoinhibition. Transcriptomics revealed strong induction of ribosome biogenesis genes and reduced abundance of transcripts associated with cell and plastid division. Further RNA analyses confirmed defects in stromal rRNA maturation of Cr-kea1, paralleling observations from Arabidopsis kea1kea2 mutants. Expression of CrKEA1 in Arabidopsis rescued growth and rRNA maturation in At-kea1kea2, demonstrating functional continuity after the ancient divergence between the two lineages. Cross-species transcriptomic comparisons further revealed that IE KEA loss elicits both shared and species-specific transcriptional responses: PhANG repression was conserved between algae and plants, whereas activation of the chloroplast unfolded protein response (cpUPR) and reduced expression of genes tied to cell-cycle and plastid fission occurred only in Chlamydomonas. Single-cell time-lapse imaging confirmed that Cr-kea1 exhibits an increased frequency of aberrant cytokinesis, unequal division, and division failure. Our findings demonstrate that while IE KEA transporters fulfill conserved roles in maintaining the conditions for plastid gene expression, their integration into broader cellular networks has diverged between unicellular chlorophytes and embryophytes (land plants). This underscores a lineage-dependent tuning of plastid-nucleus communication shaped by organismal complexity and plastid number.
Lignin structural changes and high p-coumaroylation in incipient lignification in moso bamboo.
Munekata N, Karlen SD, Yoshinaga A … +6 more , Tsuyama T, Smith RA, Guillon F, Awano T, Ralph J, Sugiyama J
Plant Physiol · 2026 Jun · PMID 42315133 · Publisher ↗
Lignification is a crucial process for strengthening plant tissues, facilitating water transport, and providing defense against pathogens. In the Poaceae family, p-hydroxycinnamic acids are commonly incorporated into lig...
Lignification is a crucial process for strengthening plant tissues, facilitating water transport, and providing defense against pathogens. In the Poaceae family, p-hydroxycinnamic acids are commonly incorporated into lignin, with acylation by p-coumarate (pCA) occurring during lignification. In this study, we performed DFRC and 2D HSQC-NMR analyses to investigate changes in lignin substructures and the degree of lignin pCA-acylation throughout bamboo stem development. Furthermore, immunohistochemical analysis was conducted to elucidate the spatial distribution of lignin substructures within different cell types. Our results revealed that, in young tissues, β-O-4-linked lignin units are predominantly derived from monolignol-pCA conjugates, specifically coniferyl- and sinapyl-pCA. Both lignin structure and the pattern of pCA acylation varied depending on the stage of cell wall formation and the cell type, particularly between vascular fiber cells and parenchyma cells. Based on our results, moso bamboo culms exhibit a distinctive feature during incipient lignification, in which monolignols are predominantly acylated with pCA. This feature has not been reported in other grasses, suggesting that extensive p-coumaroylation of monolignols plays an important role in the rapid elongation of bamboo culms.
A non-coding SNP in ELF3 alters ELF3β expression and confers adaptation of Arabidopsis to a continental climate.
Buckley CR, Philippova A, Fournier-Level A … +1 more , Haydon MJ
Plant Physiol · 2026 Jun · PMID 42315129 · Publisher ↗
Plant circadian clocks govern the timing of physiological and developmental processes that determine growth, reproduction, and seasonal phenology. As a result, natural variation in clock genes can directly influence loca...
Plant circadian clocks govern the timing of physiological and developmental processes that determine growth, reproduction, and seasonal phenology. As a result, natural variation in clock genes can directly influence local adaptation, but the components of the clock that have already been targeted by selection are unclear. We found that naturally occurring variation in the core clock gene EARLY FLOWERING 3 (ELF3) determines circadian period length and has been selected for in hot, seasonal climates. We measured the circadian rhythms of 287 global Arabidopsis (Arabidopsis thaliana) accessions using a seedling transformation protocol with a circadian luciferase reporter. Genome-wide association studies identified multiple single nucleotide polymorphisms (SNPs) in ELF3, and their identities were used to define three haplogroups associated with seasonal variability in temperature. We found strong evidence of a selective sweep in haplogroups from continental climates, which is estimated to coincide with the most recent de-glaciation period in Europe. One of the SNPs is located within intron 2 of ELF3 in the region upstream of an alternative transcription start site affecting the expression of a shorter ELF3β transcript. Our results indicate the important role of subtle variation in a core circadian clock gene in adaptation to a changing climate.
OsMAPK20-1 and OsMAPK20-4 phosphorylate OsCK2β3 to regulate its stability in response to phosphate starvation in rice.
Xie M, Yan M, Kuang H … +5 more , Chen W, Wang Z, Zhu Y, Lin H, Yang J
Plant Physiol · 2026 Jun · PMID 42315126 · Publisher ↗
Phosphorus is crucial for plant growth. Rice (Oryza sativa) OsCK2, composed of the catalytic subunit OsCK2α3 and the regulatory subunit OsCK2β3, plays a role in regulating phosphate (Pi) homeostasis. The function of OsCK...
Phosphorus is crucial for plant growth. Rice (Oryza sativa) OsCK2, composed of the catalytic subunit OsCK2α3 and the regulatory subunit OsCK2β3, plays a role in regulating phosphate (Pi) homeostasis. The function of OsCK2 activity depends on phosphorylation of OsCK2β3. We show that the plant-specific N-terminal domain in OsCK2β3, rather than the conserved β subunit domain, is responsible for its stability. Both OsMAPK20-1 and OsMAPK20-4 interact with OsCK2β3 and phosphorylate it at Ser-45 in the plant-specific N-terminal domain. Mutation of either OsMAPK20-1 or OsMAPK20-4 leads to more Pi accumulation in rice, while overexpression of the constitutively active MAPKK1 variant, OsMEK1DD, decreases the rice Pi concentration. Moreover, phospho-mimicry in OsCK2β3 increases its stability and enhances its interaction with OsCK2α3 to form the OsCK2α3/β3 holoenzyme. Overexpression of phosphorylatable-mimicking forms of OsCK2β3 reduces Pi levels even under Pi-deficient conditions. Finally, we verify that overexpression of OsMEK1DD inhibits the trafficking of the Pi transporter targeting to the plasma membrane, similar to the effect of OsCK2β3. Collectively, our results suggest that OsMAPK20-1 and OsMAPK20-4 phosphorylate OsCK2β3 at Ser-45 in the plant-specific N-terminal domain to maintain Pi homeostasis in response to the Pi supply in rice.
NOD-like immune receptor Prf prevents ubiquitin-proteasome-mediated degradation of the defense-related transcription factor SlNAC1.
Niu X, Kud J, Yuan Y … +11 more , Lu H, Wang W, Fan Y, Huang L, Du X, Miao M, Eckels M, Zhang N, Martin GB, Liu Y, Xiao F
Plant Physiol · 2026 Jun · PMID 42315123 · Publisher ↗
In tomato, resistance to the bacterial pathogen Pseudomonas syringae pv. tomato (Pst) is determined by the intracellular nucleotide-binding oligomerization domain (NOD)-like immune receptor (NLR) Pseudomonas resistance a...
In tomato, resistance to the bacterial pathogen Pseudomonas syringae pv. tomato (Pst) is determined by the intracellular nucleotide-binding oligomerization domain (NOD)-like immune receptor (NLR) Pseudomonas resistance and fenthion sensitivity (Prf). The activation of Prf depends on perception of Pst-secreted effectors AvrPto or AvrPtoB by the Pto kinase that is physically associated with Prf. Recent studies have shown that the Pto/Prf receptor complex interacts with helper NLRs, NLR-Required for Cell death 2 (Nrc2) and Nrc3, as well as 14-3-3 proteins, tomato 14-3-3 protein 1 (Tft1) and Tft3, to activate the MAPK pathway and trigger hypersensitive response (HR) cell death. However, the direct role for Prf in transcriptional reprogramming remains largely unknown. We found that activated Prf interacts with and stabilizes the defense-related transcription factor NAM, ATAF1/2, and CUC2 (SlNAC1), which otherwise is highly unstable due to ubiquitin ligase Seven in absentia (SlSINA3)-dependent ubiquitin-proteasome-mediated degradation. Importantly, binding of activated Prf to SlNAC1 sequesters SlNAC1 from SlSINA3, thereby preventing SlNAC1 ubiquitination, which leads to enhanced transcriptional potential of SlNAC1. Moreover, SlNAC1 directly regulates the expression of pathogenesis-related (PR) genes and acts as a positive regulator in immune signaling in tomato, as shown by enhanced resistance to Pst in transgenic tomato plants overexpressing SlNAC1. Our findings reveal a mechanism utilized by an NLR protein to activate immune signaling via manipulation of a defense-related transcription factor.
Fungal effector CgCAP1 suppresses the MdMVQ4-MdWRKY100-MdChi5 immune module during Colletotrichum gloeosporioides infection.
Shi J, Zhang F, Wang F … +8 more , Nie X, Yan J, Zhang X, Zhang S, Chen J, He P, Dai H, Ma Y
Plant Physiol · 2026 Jun · PMID 42315118 · Publisher ↗
Apple bitter rot, caused by Colletotrichum gloeosporioides, leads to widespread yield loss and quality decline. Fungal virulence effectors are essential determinants of pathogenicity. However, the molecular mechanisms un...
Apple bitter rot, caused by Colletotrichum gloeosporioides, leads to widespread yield loss and quality decline. Fungal virulence effectors are essential determinants of pathogenicity. However, the molecular mechanisms underlying C. gloeosporioides effector-mediated pathogenesis in apple remain largely elusive. Here, we found that the transcription factor MdWRKY100 binds to the promoter of the chitinase gene MdChi5, directly promoting its transcription and thereby improving apple bitter rot resistance. Meanwhile, a VQ-motif containing protein 4-like in apple, MdMVQ4, interacts with MdWRKY100, enhancing apple resistance to C. gloeosporioides. We identified the effector CgCAP1 in C. gloeosporioides via yeast two-hybrid (Y2H) and confirmed its interaction with MdMVQ4 using luciferase complementation imaging, bimolecular fluorescence complementation, and co-immunoprecipitation assays. In addition, knockout and complementation assays in C. gloeosporioides demonstrated that CgCAP1 functions as a critical virulence effector. Furthermore, the interaction of CgCAP1 with MdMVQ4 weakened the interaction between MdMVQ4 and MdWRKY100, leading to a reduction in chitinase activity during C. gloeosporioides infection and reduced apple bitter rot resistance. Together, these findings show how C. gloeosporioides utilizes CgCAP1 to suppress chitinase activity in apple, revealing the molecular interaction between the pathogen and its host.
MYB73 modulates apple flesh browning by repressing the expression of three polyphenol oxidase genes.
Zhang M, Wang N, Borejsza-Wysocka E … +1 more , Cheng L
Plant Physiol · 2026 Jun · PMID 42315108 · Publisher ↗
Apple flesh browning results from the oxidation of phenolic compounds to quinones by polyphenol oxidases (PPOs), affecting the quality of fresh-cut apple products. Both the activity of PPOs and the concentration of their...
Apple flesh browning results from the oxidation of phenolic compounds to quinones by polyphenol oxidases (PPOs), affecting the quality of fresh-cut apple products. Both the activity of PPOs and the concentration of their substrates contribute to browning; however, how the MdPPO genes are transcriptionally regulated remains largely unclear. Here, we show that overexpression of the coding sequence of Ma1 (cMa1-OE), a major gene controlling apple fruit acidity, leads to a significant increase in flesh browning in 'Royal Gala' apple. By measuring PPO activities and phenolic concentrations, we found that while slightly elevated concentrations of chlorogenic acid and catechin may contribute to enhanced flesh browning in cMa1-OE fruit at the early stages of fruit development, increased flesh browning at harvest is primarily caused by up-regulated PPO activities. Gene expression analysis throughout fruit development identified MdPPO3 as the gene primarily responsible for the enhanced PPO activity in cMa1-OE fruits at the early stages of fruit development, whereas both MdPPO15 and MdPPO16 are responsible at fruit harvest. An R2R3-MYB transcription factor, MdMYB73, repressed the expression of MdPPO3, MdPPO15, and MdPPO16 by binding to their promoters. RNAi suppression of MdMYB73 increased MdPPO3, MdPPO15, and MdPPO16 expression and total PPO activity, leading to enhanced flesh browning; however, this effect was blocked by RNAi of MdPPO3/MdPPO15/MdPPO16. These results indicate that MdMYB73 regulates apple flesh browning via suppressing MdPPO3, MdPPO15, and MdPPO16 expression; overexpression of Ma1 decreases MdMYB73 expression in fruit, which releases the suppression of the MdPPO genes, leading to enhanced flesh browning.
GRAIN SIZE AND WEIGHT 3 affects rice grain size and weight through interaction with SR45a and its transcriptional efficiency.
Chen W, Ma H, Li X … +7 more , Zhan J, Yang L, Feng X, Chen Z, Wu J, Liu X, Wang L
Plant Physiol · 2026 Jun · PMID 42315101 · Publisher ↗
Grain size is a critical factor determining rice yield. We previously identified the gene GSW3, derived from Oryza rufipogon, which negatively regulates rice grain size and weight; however, the regulatory mechanism remai...
Grain size is a critical factor determining rice yield. We previously identified the gene GSW3, derived from Oryza rufipogon, which negatively regulates rice grain size and weight; however, the regulatory mechanism remained unclear. GSW3 encodes two polypeptides of different lengths: a 147-aa peptide GSW3HY3 and a 166-aa peptide GSW3KJ01. In this study, we characterized the functional differences between the two peptides and investigated the mechanism by which GSW3 regulates grain size. The two polypeptides were colocalized in the nucleus. The function of the GSW3KJ01 allele was similar to that of the GSW3HY3 allele, and the gsw3KJ01 line showed an increase in grain length and width, although the degree of increase was significantly lower than that of the gsw3HY3 line. GSW3HY3 and GSW3KJ01 physically and genetically interacted with SR45a, but their interaction sites with SR45a were different. SR45a positively regulated grain size in rice and acted upstream of GSW3. The promoter activity of GSW3KJ01 was 0.62 times that of GSW3HY3, and the overexpression of GSW3HY3 and haplotype analysis indicated that the transcriptional efficiency affected grain size and weight. Core promoter element analysis revealed that GSW3 might play a role in plant hormone signaling pathways. Compared with the wild-type HY3, the gsw3HY3 line was more sensitive to exogenous IAA and ABA. GSW3 influences grain size and weight through its interaction with SR45a and the transcription efficiency of its promoter. Our studies elucidate a pathway for regulating rice grain size and weight.
The ABRE-BINDING FACTOR 4-eukaryotic translation initiation factor 2B β module mediates drought-potentiated Turnip mosaic virus susceptibility in Brassica juncea.
Jin X, Sha T, Yu Y … +5 more , Liu C, Li Z, Hu Z, Zhang M, Yang J
Plant Physiol · 2026 Jun · PMID 42314206 · Publisher ↗
Turnip mosaic virus (TuMV), an important member of the Potyvirus genus, exhibits broad host adaptability with increased prevalence under moderate drought and elevated temperature conditions. While our previous research i...
Turnip mosaic virus (TuMV), an important member of the Potyvirus genus, exhibits broad host adaptability with increased prevalence under moderate drought and elevated temperature conditions. While our previous research identified eukaryotic translation initiation factor 2Bβ (eIF2Bβ) as a critical resistance determinant against TuMV in mustard (Brassica juncea), the mechanistic interplay between environmental factors and viral pathogenesis remains poorly understood. Here, we demonstrated that drought facilitates TuMV infection in an abscisic acid (ABA)-dependent manner in B. juncea. Integrated coexpression analysis revealed the functional relevance between ABA signaling and eukaryotic translation initiation pathways. We showed that ABA-responsive element-binding factor 4 (ABF4) directly binds to the eIF2Bβ promoter and activates its expression and that ABF4 overexpression significantly enhances TuMV accumulation in wild-type plants. Notably, eIF2Bβ knockout lines exhibited significantly reduced viral accumulation even when ABF4 was overexpressed, establishing that functional eIF2Bβ is required to mediate ABF4-dependent viral infection. These findings elucidate a new ABA-eIF2Bβ regulatory module that links drought responses with plant-virus interactions, providing mechanistic insights into the role of environmental factors in modulating pathogen susceptibility.
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