The Plant Cell最新文献

{"title":"From stress perception to metabolite disposition: dynamic regulation of stilbene biosynthesis in plants","authors":"Yang Li, Lingchao Kong, Yanshen Ren, Guotian Liu, Jochen Bogs, Alessandro Vannozzi, Yuejin Wang, Zhenchang Liang, Ling Yuan, Lijun Wang","doi":"10.1093/plcell/koag315","DOIUrl":"https://doi.org/10.1093/plcell/koag315","url":null,"abstract":"Stilbenes are inducible plant specialized metabolites, best exemplified by resveratrol, a phytoalexin that links environmental perception, defense responses, and phenylpropanoid resource allocation. Stilbene accumulation may be controlled at three mechanistically distinct levels: signaling cascades that connect environmental and hormonal cues to kinase-dependent activation; combinatorial transcriptional control, which governs the response amplitude and specificity of stilbene synthase (STS) genes; and branch selection together with product disposition, which shapes the final metabolic output. Within this framework, MYB and WRKY proteins serve as major transcriptional nodes as activators or repressors, yet their regulatory effects depend on combinatorial interactions, phosphorylation events, competitive promoter occupancy, and metabolic context. We explicitly distinguish strongly supported mechanisms, defined by genetic perturbation, direct target validation, and metabolite quantification from emerging models built primarily on transient expression assays or co-expression correlations. This distinction avoids equating regulators supported by disparate levels of experimental evidence, identifies the most robust principles governing pathway control, and highlights experiments required to turn descriptive associations into causal mechanistic models. We further highlight conceptual insights extending beyond stilbene metabolism to inducible specialized metabolism in general, and outline research priorities for comparative genetics, cell-resolved analysis, and predictive pathway engineering.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"150 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149187912","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The energy sensor SnRK1 promotes starvation-induced autophagosome formation by modulating ATG13a phosphorylation in Arabidopsis","authors":"Lin-Na Wang, Weicheng Wang, Hui-Min Zhang, Xin-Yu Lu, Zhong-Rong Yan, Tian-Yi Zhang, Yao Wang, Qiao-Ling Zhong, Ke Liao, Shan Yu, Liwen Jiang, Daoxin Xie, Shi Xiao","doi":"10.1093/plcell/koag314","DOIUrl":"https://doi.org/10.1093/plcell/koag314","url":null,"abstract":"In eukaryotes, autophagy is an evolutionarily conserved cellular degradation and recycling process that is tightly associated with cellular nutrient status. The energy sensor SNF1-RELATED KINASE 1 (SnRK1) is thought to sense nutrient starvation and induce autophagy, but how it regulates autophagosome formation in plant cells remains largely unknown. Here, we show that the SnRK1 α-catalytic subunit KIN10 regulates autophagosome formation in Arabidopsis (Arabidopsis thaliana) by interacting with and phosphorylating AUTOPHAGY-RELATED PROTEIN 13a (ATG13a), a key component of the ATG1a–ATG13a protein kinase complex involved in autophagy initiation. KIN10 directly phosphorylates ATG13a in vitro and in vivo, inhibiting its ubiquitination and increasing its abundance. Moreover, we identified ten serine residues in ATG13a that are important for KIN10-mediated phosphorylation. Transgenic plants accumulating a nonphosphorylatable ATG13a variant with mutations of these ten residues were less tolerant of starvation than ATG13a-overexpressing plants and displayed accelerated leaf senescence and lower autophagic flux. The KIN10-mediated phosphorylation of ATG13a did not affect ATG1a–ATG13a complex formation; instead, it facilitated ATG1a phosphorylation, thereby promoting autophagosome formation. Therefore, our findings suggest that the KIN10–ATG13a module modulates SnRK1-mediated autophagosome formation, likely representing a key step in integrating energy sensing and autophagy initiation in plant cells.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149187906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Arsenic-sensing domain controls ACR3 transporter trafficking in\u0000 Marchantia polymorpha","authors":"Ignacy Bonter,Katarzyna Mizio,Alicja Dolzblasz,Paulina Tomaszewska,Kacper Zbieralski,Jacek Staszewski,Donata Wawrzycka,Anna Reymer,Wojciech Bialek,Verena Kriechbaumer,Jim Haseloff,Robert Wysocki,Ewa Maciaszczyk-Dziubinska","doi":"10.1093/plcell/koag306","DOIUrl":"https://doi.org/10.1093/plcell/koag306","url":null,"abstract":"Abstract Arsenic is a toxic, carcinogenic metalloid that threatens human health through contaminated water and food. Arsenite [As(III)] efflux mediated by ACR3 transporters is an ancient detoxification mechanism conserved across prokaryotes, fungi, algae, and non-angiosperm land plants, yet plant ACR3 proteins remain poorly characterized. Here, we show that MpACR3, the ACR3 ortholog from the model liverwort Marchantia polymorpha, contains an arsenic-responsive N-terminal domain that regulates intracellular trafficking. Under non-stress conditions, MpACR3 is detected in Golgi bodies as well as at the plasma membrane in plant cells, whereas As(III) promotes its relocalization to the plasma membrane. As(III) interacts with a cysteine-rich N-terminal region and stabilizes this domain, as shown by arsenite-biotin competition and increased protease resistance. Together with molecular dynamics simulations, which predicts As(III)-dependent changes in secondary structure and surface properties, these findings support a model in which ligand-induced remodeling of the N terminus modulates MpACR3 retention and trafficking. We further identify a di-arginine-containing LRCRF motif in which leucine and arginine residues are required for intracellular retention, whereas cysteine and phenylalanine residues are required for As(III)-induced relocalization to the plasma membrane. The broad conservation of related N-terminal domains in plant ACR3 transporters suggests that arsenic-regulated trafficking is a conserved plant adaptation to arsenic toxicity.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149090391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A kinesin motor complex localizes microtubule-severing proteins to direct gravitropism in\u0000 Physcomitrium patens","authors":"Zhaoguo Deng,Zhiren Chen,Tongda Xu,Haodong Chen","doi":"10.1093/plcell/koag307","DOIUrl":"https://doi.org/10.1093/plcell/koag307","url":null,"abstract":"Abstract Gravitropism enables plants to adjust growth direction and architecture in response to gravity. The classical Cholodny–Went theory posits that asymmetric auxin redistribution drives differential growth during gravitropism in seed plants, but the nature of the equivalent asymmetric process in moss protonemata is still unclear. Here, through forward genetic screening, we identified GTRD, which encodes a coiled-coil protein whose loss reverses the direction of protonemal gravitropism. We further demonstrated that GTRD forms a complex with the kinesin-14 motor GTRC, and that GTRC drives the minus-end-directed movement of GTRD along microtubules. This GTRC-GTRD complex transports a microtubule anchoring module MSD1-WDR8 that positions katanin. Under gravistimulation, katanin-dependent microtubule severing facilitates the asymmetric formation of a microtubule focus on the upper flank of the tip cell, where it spatially constrains the apical actin cluster. This cytoskeletal reorganization guides the upward growth of the protonemata. Together, the GTRC-GTRD motor complex spatially organizes katanin-mediated microtubule remodeling to establish cytoskeletal polarity, which serves as a key asymmetric cue that directs gravitropic growth in protonemal tip cells.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"18 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149090429","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Successful predictive modeling of pollen fitness phenotypes is enabled by measures of expression specificity","authors":"Sebastian A F Mueller,Zuzana Vejlupkova,Molly Megraw,John E Fowler","doi":"10.1093/plcell/koag272","DOIUrl":"https://doi.org/10.1093/plcell/koag272","url":null,"abstract":"Abstract The ability to predict phenotypes from genotypes in multicellular organisms remains limited despite rapid advances in genotyping and phenotyping methods. Machine learning offers a promising way to model phenotype from genotype but requires sizable datasets that quantitatively link phenotype to specific genes. Such datasets remain limited; however, maize pollen provides a unique biological system that is especially well suited for this challenge. Because maize pollen is haploid, mutations that affect its function can result in a quantitative phenotypic effect on pollen fitness, measurable as deviations in transmission rate from the expected Mendelian ratio. We leveraged a large set of fluorescently-marked insertional mutations, the Ds-GFP lines, to link fitness effects to specific genes. We then developed a machine learning framework that integrates expression profiling and genomic data to predict genes contributing to pollen fitness in maize. Well performing models that distinguish genes with strong fitness effects from those with little or no fitness effect could be generated using features, such as codon usage, derived solely from genome sequence (area under receiver operating characteristic curve 85%). Using expression data enabled even more successful models, achieving area under receiver operating characteristic curve values above 90%. Because we used interpretable machine learning methods, we were able to identify expression specificity as a critical feature for strongest model performance. The best-performing model was achieved when specificity measures were complemented with certain genomic sequence features. Models that include expression specificity generalize well across the maize genome, as predictions meet expectations of mutational frequencies for thousands of genes in a well characterized mutagenized population.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149090454","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nuclear localization controls BED-NLR Xa1–mediated immunity in rice","authors":"Xiameng Xu, Bo Liu, Longfei Wang, Chenhao Li, Yong Wang, Jiali Yan, Qi Wang, Ajay Gupta, Zhengyin Xu, Lifang Zou, Gongyou Chen, Bing Yang","doi":"10.1093/plcell/koag305","DOIUrl":"https://doi.org/10.1093/plcell/koag305","url":null,"abstract":"Transcription activator-like effectors (TALEs) are major virulence factors of Xanthomonas oryzae, the causal agent of bacterial blight in rice. The BED-domain nucleotide-binding leucine-rich repeat receptor Xa1 confers resistance by recognizing TALEs, but the mechanisms underlying Xa1 activation remain unclear. Here we show that structurally conserved canonical TALEs differ in their ability to activate Xa1, revealing unexpected specificity in effector recognition. Using transient expression assays, endogenous epitope tagging, and prime editing of the native Xa1 locus, we demonstrate that nuclear localization is essential for Xa1-mediated immunity. We identified three functional nuclear localization signals (NLSs) within the Xa1 N-terminal region. Prime-edited rice lines carrying mutations in these motifs exhibited compromised resistance, with mutation of the first NLS causing the strongest susceptibility phenotype. Disruption of the NLS motifs in either Xa1 or TALEs did not prevent their physical interaction, indicating that effector binding can occur independently of nuclear localization. However, only nuclear-localized Xa1 triggered cytosolic Ca2+ influx, a hallmark of immune activation. Together, our results establish nuclear localization as a prerequisite for Xa1 immune function and reveal a nuclear surveillance mechanism for BED-NLR–mediated immunity in plants.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"138 2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149086552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Making precision breeding bloom: APL is a promising target to engineer flowering time","authors":"Vanessica Jawahir","doi":"10.1093/plcell/koag299","DOIUrl":"https://doi.org/10.1093/plcell/koag299","url":null,"abstract":"","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"37 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149090457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DDM1 Safeguards the Stability of a Complex Plant Genome","authors":"Leonardo I Pereyra-Bistraín","doi":"10.1093/plcell/koag304","DOIUrl":"https://doi.org/10.1093/plcell/koag304","url":null,"abstract":"","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"4 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149090458","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Arabidopsis thaliana triggers Phelipanche ramosa germination via isothiocyanates under negative strigolactone regulation","authors":"Ahmed Choukri, Léo Andruszkow, Nathalie Marnet, Solenne Berardocco, Philippe Lebris, Alexandre de Saint Germain, Antoine Gravot, Alain Bouchereau, Jean-Bernard Pouvreau, Philippe Simier, Lucie Poulin","doi":"10.1093/plcell/koag302","DOIUrl":"https://doi.org/10.1093/plcell/koag302","url":null,"abstract":"Parasitic weeds are major agricultural threats through fine-tuned chemical interactions with their hosts. We investigated the germination-stimulating metabolites released by Arabidopsis thaliana germinating seeds into the spermosphere, the zone surrounding the seeds and showed that host–parasite chemical recognition can be initiated at the earliest stages of host seed germination. Through co-germination assays, biochemical fractionation of host germinating seed exudates and a mutant approach targeting the glucosinolate (GSL) and strigolactone (SL) pathways, we demonstrated that germinating A. thaliana Col-0 seeds specifically stimulated P. ramosa germination via GSL-derived isothiocyanates (ITCs), not SLs. This activity was MYB28, MYB29-dependent (aliphatic GSLs) and MYB34, MYB51, MYB122-independent (indolic GSLs). These results were confirmed throughout developmental stages of A. thaliana GSL-deficient lines using minirhizotron assays. The primary detected bio-active compound was 4-methylsulfinylbutyl isothiocyanate (4MSOB-NCS, sulforaphane). Additionally, 7-methylsulfinylheptyl isothiocyanate (7MSOH-NCS) was detected as another significant bio-active compound, although it was released in its GSL form and required myrosinase-mediated hydrolysis for activation. By contrast, SL-dependent inhibition of GSLs accumulation in seeds and P. ramosa germination stimulation operated through SLs AtD14 and KARs HTL-3 receptors partially independent on MAX2 integrator. These findings reinforce and complement our views on the major role played by A. thaliana exudated ITC and GSLs in triggering P. ramosa seed germination notably early in the spermosphere of the germinating host seeds. It also reveals a novel regulatory network where SLs indirectly modulate plant-plant interaction chemistry, representing an evolutionary trade-off between pathways. Understanding host–parasite chemical communication offers new avenues for controlling parasitic plants in Brassica crops.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"167 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149083837","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The multiomics landscape of small peptides encoded by long noncoding RNA-derived small open reading frames in rice","authors":"Zhipeng Chen, Haocheng Lin, Lirong Wei, Xinhe Wang, Wei Song, Gencheng Xu, Shunxi Wang, Lu Peng, Ting Peng, Dacheng Wang, Yufeng Wu, Chao Li, Liuji Wu, Jingni Wu, Yiming Wang","doi":"10.1093/plcell/koag273","DOIUrl":"https://doi.org/10.1093/plcell/koag273","url":null,"abstract":"Long noncoding RNAs (lncRNAs), as a major class of noncoding transcripts, constitute a large proportion of the genomes in complex organisms. Accumulating evidence has revealed that a subset of lncRNAs harbors peptide-encoding potential. Nevertheless, the existence and biological functions of lncRNA-derived small open reading frames-encoded polypeptides (LSEPs) in plants remain largely elusive. In this study, we established an integrated multiomics pipeline combining transcriptomics, translatomics (Ribo-seq), and proteomics to systematically identify LSEPs in rice. Among the 2,764 lncRNAs detected in our transcriptomic profiling, 42.69% were shown to be associated with ribosomes, implying their potential to be translated into polypeptides. To further validate LSEP expression at the protein level, we optimized an extraction protocol for small peptides. Using this optimized method, low-molecular-weight peptides were isolated from rice leaves and subjected to LC-MS/MS analysis. Across 4 custom-constructed search databases, a total of 376 LSEPs were confidently identified. Our work provides direct experimental evidence supporting the peptide-encoding capacity of rice lncRNAs. Collectively, this study establishes a robust and efficient multiomics workflow for identifying lncRNA-encoded small peptides, which will facilitate the large-scale discovery and functional characterization of LSEPs across diverse plant species.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"101 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149033083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}