Plant and Cell Physiology最新文献

{"title":"Not whether, but when: contextual rules for defense-induced plant-soil feedbacks.","authors":"Huei-Hsuan Merissa Tsai","doi":"10.1093/pcp/pcag116","DOIUrl":"10.1093/pcp/pcag116","url":null,"abstract":"","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":" ","pages":"1458-1460"},"PeriodicalIF":4.7,"publicationDate":"2026-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148697942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Conserved trans-regulatory logic and evolving cis-modules drive the diversification of inducible diterpenoid biosynthetic gene clusters across the Oryzoideae.","authors":"Youming Liu, Shiho Tomiyama, Ikuya Motegi, Naoki Yamamoto, Aiping Zheng, Masaki Mori, Ryoka Kawahara-Miki, Yoshimasa Tsujii, Koji Miyamoto, Hiroyasu Furuumi, Yutaka Sato, Hideaki Nojiri, Kazunori Okada","doi":"10.1093/pcp/pcag086","DOIUrl":"10.1093/pcp/pcag086","url":null,"abstract":"<p><p>Diterpenoid phytoalexins are major inducible defense metabolites in rice, whose biosynthetic genes are organized into biosynthetic gene clusters (BGCs). While BGC architecture varies across the Oryzoideae, their shared inducibility is known; however, the regulatory logic and evolutionary trajectory governing this response remains poorly understood. Here, we investigate the evolution of clustered gene regulation by examining the interplay between conserved trans-acting factors and progressively diverged cis-regulatory elements. We demonstrate that diterpenoid BGC induction is governed by a stable trans-acting framework built upon rapidly evolving cis-regulatory landscapes. Comparative genomics reveals that the basic helix-loop-helix (bHLH)-type diterpenoid phytoalexin factor (DPF) is deeply conserved across the Oryzoideae and broader grass lineages. By contrast, the promoters of diterpenoid biosynthetic genes exhibit extensive sequence divergence, particularly between AA and non-AA genome lineages of Oryza, which represent distinct genome groups defined by cytogenetic and phylogenetic relationships. Despite this overall divergence, we identified discrete, gene-specific regulatory modules (evolutionary 'islands') that recur across species. These modules are enriched in canonical DPF-recognizable N-boxes and newly defined N-box-like elements (NLEs). Functional assays demonstrate that variation in the number and arrangement of these cis-elements quantitatively calibrates DPF-mediated activation, providing a mechanistic basis for species-specific differences in metabolic inducibility. Together, our findings elucidate how BGC regulatory systems diversify through a synergy of 'trans stability and cis plasticity', offering a framework for understanding the evolution of inducible specialized metabolism in plants.</p>","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":" ","pages":"1613-1627"},"PeriodicalIF":4.7,"publicationDate":"2026-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13621222/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148339811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Remodeling of leaf lipidome during cold acclimation, de-acclimation, and re-acclimation influences frost tolerance of Festuca arundinacea.","authors":"Julia Górna, Dawid Perlikowski, Saleh Alseekh, Marcin Rapacz, Alisdair R Fernie, Magdalena Wójcik-Jagła, Arkadiusz Kosmala","doi":"10.1093/pcp/pcag073","DOIUrl":"10.1093/pcp/pcag073","url":null,"abstract":"<p><p>Seasonal temperature increases in autumn and winter can significantly disrupt frost tolerance in plants. This inducible trait is acquired during cold acclimation (CA), reduced or lost during de-acclimation (DA), and potentially restored during re-acclimation (RA). The functionality of cellular membranes, closely associated with lipid composition, plays a crucial adaptive role in enabling plants to withstand low-temperature stress. However, studies focusing on effects of DA and RA on frost tolerance, particularly in forage grasses, remain limited. Here, we assessed frost tolerance in high frost tolerant (HFT) and low frost tolerant (LFT) genotypes of Festuca arundinacea following CA, DA, and RA, based on the assessment of their cellular membrane integrity as reflected by the parameter describing the temperature causing a 50% level of electrolyte leakage from cells. Analyses of membrane integrity and lipid composition during CA revealed that the HFT genotype maintained greater membrane stability through extensive remodeling of glycerolipids, including increased lipid unsaturation, particularly in phosphatidylethanolamine, preserved a balanced monogalactosyldiacylglycerol/digalactosyldiacylglycerol ratio, and enhanced triacylglycerol (TAG) accumulation, compared to the LFT genotype. DA reversed rearrangements in structural lipids and reduced frost tolerance, whereas RA induced strong genotype-dependent responses, especially in phosphoglycerolipid profiles. Analysis of mRNA accumulation profiles indicated key enzymes potentially involved in lipid remodeling. Major transcriptional changes were observed in phytyl ester synthase 1 (PES1), digalactosyldiacylglycerol synthase 1 (DGD1), and lipoxygenase family genes, indicating their importance during CA, DA, and RA. Collectively, these findings demonstrate, for the first time, that genotype-dependent lipid remodeling underlies the capacity of F. arundinacea to maintain and recover frost tolerance. We further suggest that stress-induced TAG accumulation may function as a protective metabolic buffer, sequestering excess free fatty acids, limiting lipid oxidation, and supporting membrane stability under low-temperature stress.</p>","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":" ","pages":"1533-1556"},"PeriodicalIF":4.7,"publicationDate":"2026-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13621223/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148043184","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Jasmonic and salicylic acid pathways shape the rhizosphere microbiome, affecting aphid herbivory and soil-mediated insect-plant interactions in a density-dependent manner.","authors":"Marcela Aragón, Haris Spyridis, Pieter Mostard, Michael Reichelt, Jonathan Gershenzon, Marcel Dicke, Karen J Kloth","doi":"10.1093/pcp/pcag048","DOIUrl":"10.1093/pcp/pcag048","url":null,"abstract":"<p><p>Aboveground induction of plant defense pathways can shape root-associated microbial communities. However, whether these changes are pathway-specific and how they affect plant growth and resistance remain unclear. We evaluated how induction of the jasmonic acid (JA) and salicylic acid (SA) defense pathways shapes the root microbiome of Brassica oleracea and whether these soil-mediated shifts affect plant growth and resistance to herbivory in a subsequent generation using a plant-soil feedback approach. In the conditioning phase, defense pathways were induced either through foliar application of methyl jasmonate and SA solutions or through herbivory by caterpillars (JA) and aphids (SA). Both pathways led to distinct shifts in microbial communities, with the bacterial and fungal composition varying by pathway identity and induction method. JA induction resulted in more differentially abundant amplicon sequence variants than SA induction, particularly with Proteobacteria depletion. Conversely, Planctomycetota (bacteria) and Mortierellomycota (fungi) were enriched under both pathways, suggesting that these represent general stress-responsive groups. In the feedback phase, JA- and SA-conditioned soils had no effect on resistance under high aphid pressure, whereas under low aphid density, plants grown in SA-conditioned soil exhibited reduced phloem feeding and lower aphid population development. Together, our results indicate that the benefits provided by the defense-shaped root microbiome depend on pest pressure intensity and arise from overall community shifts rather than specific taxa enrichment. Our findings underscore the complex interactions between plant defense pathways, rhizosphere microbes, and herbivores.</p>","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":" ","pages":"1473-1488"},"PeriodicalIF":4.7,"publicationDate":"2026-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13621220/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147691818","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PUB4 activates chitin signaling by ubiquitination-linked degradation of the immune suppressor FERONIA.","authors":"Shingo Maruyama, Abdelaziz Ramadan, Wendi Jiang, Akira Nozawa, Ryou Takaoka, Sayuki Nakazawa, Tatsuya Sawasaki, Kana Miyata, Gen-Ichiro Arimura, Keiji Kito, Hanae Kaku, Yoshitake Desaki","doi":"10.1093/pcp/pcag085","DOIUrl":"10.1093/pcp/pcag085","url":null,"abstract":"<p><p>Ubiquitination regulates pattern-triggered immune responses in plants, but the underlying mechanisms remain incompletely understood. In Arabidopsis, the E3 ubiquitin ligase plant U-box protein 4 (PUB4) has been implicated in growth, development, and stress responses, and is known to interact with and be phosphorylated by chitin elicitor receptor kinase 1 (CERK1), resulting in the positive regulation of chitin-triggered immunity. In this study, we identified ubiquitinated proteins enriched from chitin-treated microsomal fractions and discovered that the receptor kinase FERONIA (FER) as a potential target of PUB4. FER interacted with PUB4 both in vivo and in vitro, as evidenced by yeast two-hybrid, bimolecular fluorescence complementation, and co-immunoprecipitation assays. An in vitro ubiquitination assay demonstrated that PUB4 ubiquitinates the cytoplasmic domain of FER. Moreover, transient expression assays in wild-type and pub4-2 mutant protoplasts revealed that PUB4 mediates chitin-induced FER degradation. Unlike PUB4, which positively regulates chitin-induced defense responses, FER negatively regulates them. For example, fer4 mutants exhibited elevated basal and chitin-induced reactive oxygen species and callose levels. This suggests that FER suppresses immune signaling under steady-state conditions, and that PUB4-mediated degradation of FER relieves this inhibition. These findings clearly reveal a novel mechanism by which PUB4 regulates chitin-induced immunity, driven by CERK1, through the targeted degradation of FER. This highlights the balance between positive and negative regulators of plant immune signaling.</p>","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":" ","pages":"1603-1612"},"PeriodicalIF":4.7,"publicationDate":"2026-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148309114","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Disrupted FLOWERING LOCUS C alleles from weedy radish enhance the florigenic potential of rootstocks for graft-mediated floral induction in Brassicaceae.","authors":"Ko Motoki, Saki Kobayashi, Kazusa Nishimura, Yu Kinoshita, Makoto Kashima, Koichiro Ushijima, Tanjuro Goto, Ken-Ichiro Yasuba, Munetaka Hosokawa","doi":"10.1093/pcp/pcag119","DOIUrl":"https://doi.org/10.1093/pcp/pcag119","url":null,"abstract":"<p><p>Graft-mediated floral induction is a classical yet promising breeding technique that accelerates seed production and shortens generation time in crops. However, its application remains limited to a few species because floral induction is often unstable. Even among florally induced rootstocks, grafted scions can differ in their flowering response depending on rootstock genotype, but the genetic basis of this variation remains unclear. Here, using a Brassicaceae grafting model, we investigated two early-bolting radish (Raphanus sativus) accessions differing in their ability to induce flowering. We focused on a significant difference in FLOWERING LOCUS T (FT) expression between these accessions and identified two quantitative trait loci (QTLs) associated with FT levels. Transcriptomic and genomic analyses revealed that both QTLs harbored previously unreported disrupted alleles of FLOWERING LOCUS C (FLC) homologs, key floral repressors involved in vernalization, which showed reduced expression and produced defective transcripts. Grafting experiments demonstrated that these disrupted FLC alleles enhanced floral induction, with RsFLC1 having a major effect. Our results indicate that the FT expression threshold required for graft-mediated floral induction is higher than that for rootstock flowering itself and that this threshold is reached when FLC-mediated repression is substantially reduced. These alleles were inferred to have originated from weedy radish (Raphanus raphanistrum), likely contributing to early flowering in disturbed environments. This study suggests that exploring genetic variations in FT expression is an effective strategy to develop highly florigenic rootstocks, thereby broadening the application of graft-mediated floral induction in crop breeding.</p>","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":" ","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149070006","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ROS function during the early phase of vascular regeneration in Arabidopsis.","authors":"Yusuke Ohba, Jiuyi Li, Ryosuke Sato, Keita Matsuoka, Yuki Kondo, Kazuyuki Kuchitsu, Shinobu Satoh, Hiroaki Iwai, Masashi Asahina","doi":"10.1093/pcp/pcag120","DOIUrl":"https://doi.org/10.1093/pcp/pcag120","url":null,"abstract":"<p><p>When vascular tissues are damaged, plants induce site-specific formation of vascular stem cells that proliferate and differentiate into xylem and phloem, restoring vascular continuity. In addition, reactive oxygen species (ROS) are rapidly generated at wound sites in response to damage. However, the role of ROS during vascular regeneration remains largely unknown. Here, we investigated the role of ROS using an Arabidopsis inflorescence stem incision model and the vascular cell induction culture system (VISUAL). During tissue reunion of incised inflorescence stems, scavenging ROS with potassium iodide (KI) suppressed the proliferation of cambial cell layers. Consistently, the expression of cambium- and xylem-related genes, including TDR/PXY and VND7, was significantly reduced by KI treatment. Furthermore, mutation in respiratory burst oxidase homolog D (RBOHD), which encodes an ROS-producing enzyme, suppressed the proliferation of cambial cell layers. In VISUAL, KI treatment inhibited ectopic xylem formation and reduced the expression of vascular stem cell-related genes. Temporal analyses further indicated that ROS functions during the early phase of induction, as the expression of dedifferentiation-related genes such as WAK1 and ACS6 decreased under KI treatment. Notably, the expression of Arabidopsis NAC domain-containing protein 071 (ANAC071) and ANAC096 was not suppressed by KI in incised stems, and estradiol-induced expression of ANAC071 failed to rescue vascular differentiation in VISUAL under KI treatment. These findings demonstrated that ROS act prior to ANAC function during the early phase of vascular regeneration.</p>","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":" ","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149031235","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unveiling The Origin of Sacred Red Rice Preserved in Japanese Shrines.","authors":"Manaki Mimura, Nanase Aikawa, Tsuyoshi Mashiko, Takeshi Izawa","doi":"10.1093/pcp/pcag132","DOIUrl":"https://doi.org/10.1093/pcp/pcag132","url":null,"abstract":"<p><p>Pericarp color is a key trait selected during rice domestication. Although most modern cultivars have a white pericarp, ancestral rice likely had a red pericarp, as extant wild rice retains this trait and the 14-bp deletion in the Rc gene, which confers white pericarp, is prevalent among modern cultivars. In Japan, several red rice accessions have been preserved in geographically separated shrines for ritual use. Here, we investigated the genomic origin and evolutionary history of the sacred red rice accessions preserved in four shrines across three regions of Japan, together with a red rice landrace from Kokubunji, Tokyo. Genome-wide analyses showed that all the shrine accessions belong to temperate japonica, whereas the Kokubunji landrace is tropical japonica. In addition, we found that the Rc region among all the GJ accessions belongs to a major haplotype cluster regardless of the Rc function, consistent with the reduced genetic diversity surrounding the Rc locus in GJ. Further analyses of the Rc region revealed that three shrine accessions belong to a haplogroup derived from the lineage associated with white pericarp origin, while one accession belong to another haplogroup in the haplotype cluster. The Kokubunji landrace showed introgression in the Rc flanking region. In addition, analyses of heading date-related genes suggest that shrine-preserved red rice retains ancient genetic features and has been minimally influenced by modern breeding. Overall, sacred red rice preserved in Japanese shrines represents a valuable genetic resource that has maintained ancient diversity in temperate japonica over a long period.</p>","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":" ","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149012763","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Keeping time with nutrients: integrating circadian rhythms and mineral nutrition in plants.","authors":"Andrea Garcia Hernandez, Run Qi, Christian Hermans","doi":"10.1093/pcp/pcag130","DOIUrl":"https://doi.org/10.1093/pcp/pcag130","url":null,"abstract":"<p><p>Plants grow in environments structured by predictable daily cycles of light, temperature and nutrient supply. To anticipate these fluctuations, they rely on the circadian clock, an endogenous timekeeping system that coordinates metabolic and physiological processes in time. This review synthesizes current knowledge on the role of the circadian system in mineral nutrition in plants. Core clock components rhythmically regulate the expression of nutrient transporters and homeostatic pathways. In turn, nutrient status feeds back on circadian timing, revealing tight bidirectional coupling between the clock and nutrient signalling networks. Beyond mineral homeostasis, circadian regulation extends to root system architecture, coordinating developmental rhythms that determine how plants explore and exploit the soil environment to take up mineral elements. Although many clock-nutrient interactions are supported by transcriptomic evidence, functional validation at the level of nutrient fluxes and whole-plant performance remains limited. The emerging framework of chronoculture further emphasizes that aligning crop fertilization regimes with plant biological timing may enhance soil resource use. Integrating circadian biology into crop management thus offers a promising avenue to optimize crop productivity in variable environments.</p>","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":" ","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148991024","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Precision-Based Filtering Facilitates Cross-Referencing of Conventional and Single-Nucleus Transcriptomes to Identify Time- and Temperature-Sensitive Cell Populations.","authors":"Adam Seluzicki, Travis A Lee, Nolan T Hartwick, Todd P Michael, Joseph R Ecker","doi":"10.1093/pcp/pcag126","DOIUrl":"https://doi.org/10.1093/pcp/pcag126","url":null,"abstract":"<p><p>Transcriptome analysis via RNA sequencing (RNAseq) has become a ubiquitous method of molecular characterization from whole organisms, dissected tissues, and single cells. These experiments continue to provide an extraordinary volume of data describing molecular states and responses to many conditions. However, standard approaches to RNAseq analysis commonly use expression level filters that eliminate potentially useful data in the service of decreasing noise. Here we describe the implementation of a coefficient of variation-based filter for RNAseq gene expression data. This filter prioritizes consistent data across replicates, allowing lowly-expressed genes with low-variation measurements to be retained for downstream analysis. We show, using two independent Arabidopsis RNAseq datasets, that this filter allows for the inclusion of many more transcription factors than even a low-stringency expression level filter. This effect is independent of sequencing depth. We find that these lowly-expressed genes mark specific cell clusters in our single-nucleus (sn)RNAseq dataset and may facilitate future characterization of currently unknown cell types or states. We further characterize communities of co-expressed genes, sampled across the day at two growth temperatures, in relation to snRNAseq cell clusters, finding evidence for a highly photosynthetic cell population, and a cell state marked by high cell division and translation. These methods can be expanded to RNAseq analysis in many systems, facilitating the construction of more detailed models of tissue-specific gene regulatory networks.</p>","PeriodicalId":20575,"journal":{"name":"Plant and Cell Physiology","volume":" ","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148970869","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}