Plant Communications最新文献

{"title":"Wheat Yr6 locus allelic to Pm5 harboring an NLR gene pair confers stripe rust resistance.","authors":"Weihang Sun, Haitao Dong, Shengjie Liu, Shengwei Ma, Qingdong Zeng, Jihu Li, Ke Ke, Wenjie Yue, Wenjing Zhang, Xinrui Fang, Jinyu Han, Xinying Zhou, Jiwen Zhao, Guanghao Guo, Genying Li, Xinyou Cao, Weijun Zheng, Chunlian Li, Zhensheng Kang, Dejun Han, Zhiyong Liu, Gang Li, Xiaojie Wang, Jianhui Wu","doi":"10.1016/j.xplc.2025.101541","DOIUrl":"https://doi.org/10.1016/j.xplc.2025.101541","url":null,"abstract":"","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101541"},"PeriodicalIF":11.6,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145208195","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PTF-Vāc: An explainable and generative deep co-learning encoders-decoders system for ab-initio discovery of plant transcription factor binding sites.","authors":"Sagar Gupta, Jyoti, Umesh Bhati, Veerbhan Kesarwani, Akanksha Sharma, Ravi Shankar","doi":"10.1016/j.xplc.2025.101543","DOIUrl":"https://doi.org/10.1016/j.xplc.2025.101543","url":null,"abstract":"<p><p>Discovery of transcription factors (TFs) binding sites (TFBS) and their motifs in plants pose significant challenges due to high cross-species variability. The interaction between TFs and their binding sites is highly specific and context dependent. Most of the existing TFBS finding tools are not accurate enough to discover these binding sites in plants. They fail to capture the cross-species variability, interdependence between TF structure and its TFBS, and context specificity of binding. Since they are coupled to predefined TF specific model/matrix, they are highly vulnerable towards the volume and quality of data provided to build the motifs. All these software make a presumption that the user input would be specific to any particular TF which renders them of very limited use for practical applications like genomic annotations of newly sequenced species. Here, we report an explainable Deep Encoders-Decoders generative system, PTF-Vāc, founded on a universal model of deep co-learning on variability in binding sites and TF structure, PTFSpot, making it completely free from the bottlenecks mentioned above. It has successfully decoupled the process of TFBS discovery from the prior step of motif finding and requirement of TF specific motif models. Due to the universal model for TF:DNA interactions as its guide, it can discover the binding motifs in total independence from data volume, species and TF specific models. In a comprehensive benchmarking study across a huge volume of experimental data, it has outperformed most advanced motif finding deep learning (DL) algorithms. With this all, PTF-Vāc brings a completely new chapter in ab-initio TFBS discovery through generative AI.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101543"},"PeriodicalIF":11.6,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145208140","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-based mutant RNA mapping (GMRM) identifies an NLR pair underlying Yr6-mediated stripe rust resistance in wheat.","authors":"Shuo Huang, Lu Zhang, Jiabao Liang, Yi Ouyang, Yurong Yan, Huike Ju, Yaxin Wang, Hao Zhang, Taiguo Liu, Chunlei Tang, Xiaojie Wang, Yajun Wang","doi":"10.1016/j.xplc.2025.101542","DOIUrl":"https://doi.org/10.1016/j.xplc.2025.101542","url":null,"abstract":"","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101542"},"PeriodicalIF":11.6,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145208149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantitative glycoproteomics identifies target N-glycoproteins of the Golgi-class I α-mannosidase SlMNSI1 that is important for tomato fruit development.","authors":"Xiao-Yong Zhao, Ruo-Han Ou, Tong-Hao Cui, Jian-Cong Liao, Yu-Yang Mei, Yu-Di Wu, Qian-Yu Wang, Yi Yang, Yi-Long Liu, Ya-Qin Liu, Chang-Jie Xu, Yuan-Jiang Pan, Qing-Qiu Gong, Zhi-Ping Deng, Bo Zhang, Xian Li, Kun-Song Chen","doi":"10.1016/j.xplc.2025.101537","DOIUrl":"https://doi.org/10.1016/j.xplc.2025.101537","url":null,"abstract":"<p><p>Protein N-glycosylation is a fundamental post-translational modification, yet its role in regulating fleshy fruit development is poorly understood. Here we combined chemical genetics, CRISPR/Cas9-mediated gene editing, quantitative site-specific glycoproteomics, and genetic complementation analyses to investigate the function of the class I α-mannosidase SlMNSI1 in tomato (Solanum lycopersicum). Kifunensine (Kif) inhibition or knockout of SlMNSI1 caused severe pleiotropic defects, including impaired fruit development, and led to the accumulation of Man₉GlcNAc₂ and Man₈GlcNAc₂ respectively on its expected glycoprotein substrates. To identify its targets, we generated the most comprehensive site-specific N-glycoproteome of tomato fruit to date and identified 3,091 intact N-glycopeptides containing 873 N-glycosites and 158 N-glycans within 573 N-glycoproteins. By comparing the Kif-injected tomatoes against Mock and slmnsl1 against WT, 97 N-glycoproteins with 127 high-confidence N-glycosites were identified as candidate target N-glycoproteins of SlMNSI1. Strikingly, we discovered that the Golgi-localized SlMNSI1 is itself an N-glycoprotein. Mutagenesis of N-glycosites demonstrated that N-glycosylation at Asn288 and Asn334 in SlMNSI1 is essential for its proper Golgi localization and protein stability. Genetic complementation assays confirmed this in vivo: while overexpression of the wild-type SlMNSI1 rescued the fruit development defects of the mutant, overexpression of a non-glycosylatable version of SlMNSI1 only partially complemented these phenotypes. Collectively, our findings reveal the critical role of SlMNSI1 and the processing of mannosidic N-glycans in fruit development. Identifying the SlMNSI1 N-glycoprotein substrates could help to further investigate the role of N-glycans in this process.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101537"},"PeriodicalIF":11.6,"publicationDate":"2025-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145187425","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-dimensional epigenomic dynamics converge on H3K4 regulation of low CO2 adaptation in Nannochloropsis oceanica.","authors":"Yanhai Gong, Qintao Wang, Li Wei, Lianhong Wang, Nana Lv, Xuefeng Du, Chen Shen, Yi Xin, Luyang Sun, Jian Xu","doi":"10.1016/j.xplc.2025.101534","DOIUrl":"https://doi.org/10.1016/j.xplc.2025.101534","url":null,"abstract":"<p><p>Despite their ecological and biotechnological importance, whether and how microalgae are regulated by epigenetics have remained poorly understood. In the model industrial microalga of Nannochloropsis oceanica, by comprehensive, multi-dimensional epigenomic analyses, we uncovered an epigenetic regulatory mechanism in response to CO2 level that involves the complex interplays among DNA methylation, histone modifications, dynamic nucleosome positioning, and 3D chromatin structure during low CO2 adaptation. Despite minimal DNA methylation, histone modifications including lysine acetylation, crotonylation, and methylation were associated with active chromatin states, and linked to 43.1% of the differentially expressed genes. Notably, histone H3K4 di-methylation (H3K4me2) exhibited a distinct dual-peak profile around the transcription start site, and is linked to dynamics of chromatin compartmentation. Knockout of NO24G02310, a candidate H3K4 methyltransferase, resulted in genome-wide H3K4me2 peak shifts and a decrease in H3K4me1 levels, accompanied by direct or indirect downregulation of NoHINT and NoPMA2 expression, slower microalgal growth and reduced photosynthesis (indicated by Fv/Fm), specifically under low CO2 conditions. Deletion and overexpression of the histidine triad nucleotide-binding protein of NoHINT and the plasma membrane H+-ATPase of NoPMA2 revealed the two enzymes' roles on growth and photosynthetic efficiency under low CO2, with NoHINT regulating growth and NoPMA2 influencing photosynthesis. Thereby, as a previously unappreciated strategy of low CO2 adaptation, NO24G02310 may coordinate the regulation of NoHINT and NoPMA2 through the participation of H3K4 modifications. These findings lay the foundation for enhancing microalgal productivity through epigenetic engineering.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101534"},"PeriodicalIF":11.6,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145180169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural insights into the catalytic mechanism of the phenylethanoid glycoside rhamnosyltransferase UGT79G15 from Rehmannia glutinosa.","authors":"Ruolong Ma, Hongli Wei, Yibin Zhuang, Yanan Wu, Zhishuai Li, Yangyang Chen, Jing Huang, Xiaohui Yan, Weidong Liu, Tao Liu","doi":"10.1016/j.xplc.2025.101539","DOIUrl":"https://doi.org/10.1016/j.xplc.2025.101539","url":null,"abstract":"<p><p>Phenylethanoid glycosides (PhGs) are a group of important natural products found in a wide variety of medicinal plants, and are known to possess outstanding pharmacological properties. Uridine diphosphate (UDP) glycosyltransferase 79G15 (UGT79G15) from Rehmannia glutinosa‌ catalyzes the conversion of osmanthuside A to osmanthuside B, a key intermediate in the PhG biosynthetic pathway, via the formation of a (1→3) glycosidic bond. In this study, we report the crystal structure of UGT79G15 in its apo form, UDP-bound form and, most importantly, its ternary complex form containing UDP and a mimic acceptor, forsythiaside A, in its active site. Structural and comparative analyses revealed that UGT79G15 has a unique 'funnel-shaped' acceptor-binding pocket with a small accessory cave sufficient to accommodate the 4'-hydroxycinnamoyl group of PhG, explaining the enzyme's regiospecificity for the 3'-OH of PhG. Further structural analysis and site-directed mutagenesis explored a number of variants of the enzyme and identified key residues that recognize and stabilize UDP-rhamnose and the sugar acceptor. Meanwhile, I204W, a point variant obtained in the process, was found to possess increased catalytic efficiency for osmanthuside A conversion, up to 2.2 times the efficiency of the wild type. This study provides mechanistic insights into the donor specificity and acceptor regioselectivity of PhG 1,3-rhamnosyltransferase and enriches structural information on plant UGTs.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101539"},"PeriodicalIF":11.6,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145180137","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Domestication of CSA1, the homolog of rice Tiller Angle Control 1, improves shoot compactness and increases seed yield in soybean.","authors":"Zhandong Cai, Yuanyuan Huang, Huan Du, Junjie Liu, Mingming Duan, Xianyi Hu, Kaifeng Lu, Qibing Ma, Yanbo Cheng, Hai Nian, Liangfa Ge","doi":"10.1016/j.xplc.2025.101538","DOIUrl":"https://doi.org/10.1016/j.xplc.2025.101538","url":null,"abstract":"","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101538"},"PeriodicalIF":11.6,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145180086","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transport of secondary metabolites in plants: Mechanistic insights and transporter engineering for crop improvement.","authors":"Chunsheng Xiao, Gaofeng Zhou, Tianhua He, Chengdao Li","doi":"10.1016/j.xplc.2025.101536","DOIUrl":"https://doi.org/10.1016/j.xplc.2025.101536","url":null,"abstract":"<p><p>Secondary metabolites (SMs) are crucial for plant survival and adaptation and play multiple roles in mediating ecological interactions, such as defense and stress tolerance. Specialized transporters relocate SMs from synthesis sites to defense tissues or storage organs. The spatiotemporal distribution of defense-related SMs is a key determinant of plant fitness. However, the accumulation of anti-nutritional SMs in crop seeds or fruits may pose health risks to humans and livestock. Recent advances have highlighted the significant role of SM transporters in optimizing the allocation of metabolites. This review explores the transport mechanisms for both defense and anti-nutritional SMs, focusing on long-distance transporters that regulate source-sink dynamics and their potential implications in agricultural biotechnology. We highlight innovative approaches to manipulating transporter activities, ranging from multi-omics integration to precision engineering, and discuss how these tools can be used to design crops with enhanced defense capacity, increased levels of beneficial compounds, and more palatable seeds and fruits. We explore the technologies and frameworks for the discovery and characterization of long-distance transporters of SMs for crop improvement. Transporter-focused frameworks offer a promising solution to global agricultural challenges and present exciting opportunities for advancing crop improvement in the context of global food supply.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101536"},"PeriodicalIF":11.6,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145180074","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Spatio-temporal dynamics of AHA2 reveals that RAFL1 induces its endocytosis and vacuolar degradation.","authors":"Yuqing Lu, Yuan Zhang, Mingyang Li, Lijuan Yao, Xueping Zhang, Xiaoyan Yuan, Xiao Su, Jinxing Lin, Yaning Cui, Xiaojuan Li","doi":"10.1016/j.xplc.2025.101535","DOIUrl":"https://doi.org/10.1016/j.xplc.2025.101535","url":null,"abstract":"<p><p>Plasma membrane H⁺-ATPases (AHAs) are master enzymes of plant biology, driving the absorption of cellular nutrients and ion transport across the cell membrane. Here, we analyzed the diffusion dynamics of GFP-AHA2 in Arabidopsis thaliana by combining single-particle tracking with variable-angle total internal reflection fluorescence microscopy. Treatment with RALF1, which caused extracellular alkalinization, markedly inhibited AHA2 activity and decreased the velocity of GFP-AHA2. RALF1 promoted the internalization and degradation of GFP-AHA2 via both clathrin-mediated endocytosis (CME) and clathrin-independent endocytosis (CIE). Moreover, Single-particle tracking revealed that phosphorylation affected AHA2 spatiotemporal dynamics. Our findings identify a previously unreported role for RALF1 in promoting AHA2 internalization and degradation by synergistic endocytosis under RALF1 treatment, providing insights that can broadly impact research into plant signaling, environmental responses, and protein endocytosis.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101535"},"PeriodicalIF":11.6,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145151977","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nuclear factor-Y transcription factors in crops: Biological roles, regulation, and breeding applications.","authors":"Huan Wu, Xingliang Hou, Chunyu Zhang","doi":"10.1016/j.xplc.2025.101530","DOIUrl":"https://doi.org/10.1016/j.xplc.2025.101530","url":null,"abstract":"<p><p>Given the global challenges such as climate change and food security, crop species must develop sophisticated strategies to enhance phenotypic plasticity and stress resilience, thereby ensuring yield stability and environmental adaptability in agricultural practices. NF-Y transcription factors, which exist multiple paralogs and function as a trimeric complex, enable a vast number of combinations that likely serve pivotal regulatory functions in these processes. Over the past decade, research on NF-Y has notably shifted focus from the model plant Arabidopsis to crop species, yielding significant advances in our genetic and molecular understanding. However, comprehensive reviews on crop NF-Y remain absent. Here, we provide a systematic summary of the current knowledge of NF-Y in crops across multiple regulatory layers, emphasize the mechanisms underlying the assembly and disassembly of the NF-Y complex, and discuss the mechanistic functions of NF-Y in the epigenetic regulation of target genes. These mechanistic insights, combined with the diverse biological roles of NF-Y, establish a theoretical foundation for exploiting NF-Y in crop molecular breeding. Notably, we also discuss practical implementation strategies and potential challenges in translating NF-Y research into field applications. Collectively, this review provides significant insights into the function and regulation of crop NF-Y, offering valuable guidance for further research and the development of innovative strategies for crop improvement in the future molecular design breeding process.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101530"},"PeriodicalIF":11.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145139528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}