Root metabolites are essential for plant development and environmental stress adaptation. However, the genetic basis controlling root metabolome variation in crops and its role in stress resilience remain largely uncharacterized. In this study, we employed a comprehensive multi-omics approach, integrating root metabolome and transcriptome profiles of 273 maize (Zea mays L.) inbred lines at the seedling stage. Our analysis annotated 407 metabolites, of which 155 exhibited significant correlations with root traits. Using a variome-transcriptome-metabolome association (VTM) network, we identified the glutamate decarboxylase (GAD) gene ZmGAD as a crucial regulator that enhances root growth and stress tolerance by modulating gamma-aminobutyric acid (GABA) biosynthesis. ZmGAD-derived GABA confers stress tolerance by regulating stomatal aperture and scavenging reactive oxygen species. A transcription factor, ZmZIM2, acts as a negative regulator of ZmGAD expression and GABA accumulation. Moreover, a 2-bp insertion in ZmGAD causes a premature translation termination, resulting in reduced GABA content, shorter roots, and decreased stress tolerance in maize. The reduced frequency of a 2-bp deletion suggests it may have been inadvertently lost during maize domestication and modern breeding. This study elucidates the genetic and molecular framework underlying root metabolite regulation in maize and provides a valuable resource for enhancing root traits and stress tolerance in maize breeding.
{"title":"A variome-transcriptome-metabolome network links GABA biosynthesis to stress resilience in maize","authors":"Yunyun Wang, Dan Sun, Yamin Duan, Aiqing Yang, Xiaoyi Yang, Tianze Zhu, Yuxing Yan, Wei Li, Wenye Rui, Shuai Fang, Baoqing Wang, Yimei Tian, Houmiao Wang, Fanjun Chen, Zhongtao Jia, Qingchun Pan, Zefeng Yang, Lixing Yuan, Chenwu Xu, Pengcheng Li","doi":"10.1093/plcell/koaf221","DOIUrl":"https://doi.org/10.1093/plcell/koaf221","url":null,"abstract":"Root metabolites are essential for plant development and environmental stress adaptation. However, the genetic basis controlling root metabolome variation in crops and its role in stress resilience remain largely uncharacterized. In this study, we employed a comprehensive multi-omics approach, integrating root metabolome and transcriptome profiles of 273 maize (Zea mays L.) inbred lines at the seedling stage. Our analysis annotated 407 metabolites, of which 155 exhibited significant correlations with root traits. Using a variome-transcriptome-metabolome association (VTM) network, we identified the glutamate decarboxylase (GAD) gene ZmGAD as a crucial regulator that enhances root growth and stress tolerance by modulating gamma-aminobutyric acid (GABA) biosynthesis. ZmGAD-derived GABA confers stress tolerance by regulating stomatal aperture and scavenging reactive oxygen species. A transcription factor, ZmZIM2, acts as a negative regulator of ZmGAD expression and GABA accumulation. Moreover, a 2-bp insertion in ZmGAD causes a premature translation termination, resulting in reduced GABA content, shorter roots, and decreased stress tolerance in maize. The reduced frequency of a 2-bp deletion suggests it may have been inadvertently lost during maize domestication and modern breeding. This study elucidates the genetic and molecular framework underlying root metabolite regulation in maize and provides a valuable resource for enhancing root traits and stress tolerance in maize breeding.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"18 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145116551","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}
Tracie A Hennen-Bierwagen, Martha G James, Carter J Newton, Emily M Juhl, Ugo Cenci, Steven Ball, Christophe Colleoni, Stacie L Shuler, William F Tracy, Alan T Culbertson, Alan M Myers
Starch arose in chloroplast-containing species from a combination of prokaryotic and eukaryotic genes involved in the metabolism of soluble branched α-polyglucan, i.e., glycogen. Non-mutant plants entirely lack such soluble polymers and instead contain amylopectin in insoluble starch granules. The transition between soluble and insoluble branched α-polyglucans during plant evolution is not well understood. This study generated maize (Zea mays L.) lines exhibiting a gradually varying distribution between soluble α-polyglucan and starch in the endosperm. These chemotypes were determined by complexes of conserved α-(1→6)-glucosidases of the isoamylase class (ISA). Four independent spontaneous missense substitutions in the ISA1 subunit of these complexes each cause a distinct soluble/insoluble α-polyglucan ratio, even though all four ISA1 variants lack detectable catalytic activity. These substitutions are located near each other in a domain distant from the active site. A separate region of ISA1 binds its non-catalytic paralog ISA2. Removal of ISA2 from the ISA1 mutant lines conditions further variability in the proportions of soluble α-polyglucan and starch. Thus, the extent of precursor α-polyglucan crystallization is determined by aspects of the ISA complexes beyond enzymatic activity. Various arrangements of multiple glucan-binding sites in different forms of the ISA1/ISA2 assemblies are proposed to determine how those complexes interact with precursor polymers. In turn, structural organization of the polymers is proposed to influence their crystallization, independent of α-1,6-glucosidase activity. Gradual change from soluble α-polyglucan metabolism to starch metabolism is proposed as a selective advantage leading to ISA2 conservation despite its lack of a functional catalytic site.
{"title":"Non-catalytic functions of ISOAMYLASE 1 and 2 affect the proportion of insoluble and soluble α-polyglucans in maize","authors":"Tracie A Hennen-Bierwagen, Martha G James, Carter J Newton, Emily M Juhl, Ugo Cenci, Steven Ball, Christophe Colleoni, Stacie L Shuler, William F Tracy, Alan T Culbertson, Alan M Myers","doi":"10.1093/plcell/koaf220","DOIUrl":"https://doi.org/10.1093/plcell/koaf220","url":null,"abstract":"Starch arose in chloroplast-containing species from a combination of prokaryotic and eukaryotic genes involved in the metabolism of soluble branched α-polyglucan, i.e., glycogen. Non-mutant plants entirely lack such soluble polymers and instead contain amylopectin in insoluble starch granules. The transition between soluble and insoluble branched α-polyglucans during plant evolution is not well understood. This study generated maize (Zea mays L.) lines exhibiting a gradually varying distribution between soluble α-polyglucan and starch in the endosperm. These chemotypes were determined by complexes of conserved α-(1→6)-glucosidases of the isoamylase class (ISA). Four independent spontaneous missense substitutions in the ISA1 subunit of these complexes each cause a distinct soluble/insoluble α-polyglucan ratio, even though all four ISA1 variants lack detectable catalytic activity. These substitutions are located near each other in a domain distant from the active site. A separate region of ISA1 binds its non-catalytic paralog ISA2. Removal of ISA2 from the ISA1 mutant lines conditions further variability in the proportions of soluble α-polyglucan and starch. Thus, the extent of precursor α-polyglucan crystallization is determined by aspects of the ISA complexes beyond enzymatic activity. Various arrangements of multiple glucan-binding sites in different forms of the ISA1/ISA2 assemblies are proposed to determine how those complexes interact with precursor polymers. In turn, structural organization of the polymers is proposed to influence their crystallization, independent of α-1,6-glucosidase activity. Gradual change from soluble α-polyglucan metabolism to starch metabolism is proposed as a selective advantage leading to ISA2 conservation despite its lack of a functional catalytic site.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"79 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145116498","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}
RNA trafficking is crucial in almost every phase of plant development. Fibrillarin (FIB), a highly conserved nucleolar protein with methyltransferase (MTase) activity, functions in methylation and rRNA processing and facilitates the transport of several RNA viruses in plants. Previously, we demonstrated that bamboo mosaic virus satellite RNA (satBaMV) traffics autonomously and systemically in a helper virus-independent but FIB-dependent manner by forming a mobile ribonucleoprotein (RNP) complex comprising satBaMV, FIB, and satBaMV-encoded P20 movement protein. Here, we show that FIB methylates the arginine-rich motif (ARM) of P20 and relies on its MTase activity for the systemic movement of satBaMV. FIB MTase-defective mutants failed to complement long-distance satBaMV transport in FIBi plants, despite still binding to satBaMV in vivo. We also demonstrate that the ARM of P20 guides its nucleolar localization for FIB-mediated methylation. P20 methylation not only contributes to its plasmodesmata (PD) targeting but also triggers nucleocytoplasmic shuttling of FIB with P20 as the RNP complex to PD. A satBaMV mutant harboring a non-methylated P20, but not a methylation-mimic P20, exhibited disrupted PD targeting and impaired P20-assisted satBaMV trafficking. Our findings provide mechanistic insights into how FIB-mediated P20 methylation positively regulates systemic trafficking of a subviral agent in plants.
{"title":"Nucleolar fibrillarin methyltransferase regulates systemic trafficking of a plant virus satellite RNA","authors":"Chih-Hao Chang, Jiun-Da Wang, Shu-Chuan Lee, Yau-Heiu Hsu, Chung-Chi Hu, Na-Sheng Lin","doi":"10.1093/plcell/koaf224","DOIUrl":"https://doi.org/10.1093/plcell/koaf224","url":null,"abstract":"RNA trafficking is crucial in almost every phase of plant development. Fibrillarin (FIB), a highly conserved nucleolar protein with methyltransferase (MTase) activity, functions in methylation and rRNA processing and facilitates the transport of several RNA viruses in plants. Previously, we demonstrated that bamboo mosaic virus satellite RNA (satBaMV) traffics autonomously and systemically in a helper virus-independent but FIB-dependent manner by forming a mobile ribonucleoprotein (RNP) complex comprising satBaMV, FIB, and satBaMV-encoded P20 movement protein. Here, we show that FIB methylates the arginine-rich motif (ARM) of P20 and relies on its MTase activity for the systemic movement of satBaMV. FIB MTase-defective mutants failed to complement long-distance satBaMV transport in FIBi plants, despite still binding to satBaMV in vivo. We also demonstrate that the ARM of P20 guides its nucleolar localization for FIB-mediated methylation. P20 methylation not only contributes to its plasmodesmata (PD) targeting but also triggers nucleocytoplasmic shuttling of FIB with P20 as the RNP complex to PD. A satBaMV mutant harboring a non-methylated P20, but not a methylation-mimic P20, exhibited disrupted PD targeting and impaired P20-assisted satBaMV trafficking. Our findings provide mechanistic insights into how FIB-mediated P20 methylation positively regulates systemic trafficking of a subviral agent in plants.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145116500","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}
The anatomy or the arrangement of cells often determines the organization and function of plant tissues. However, current methods in large-scale imaging and accurate quantification of anatomical traits face major limitations. To address these challenges, we introduce the AnatomyArray system, an integrated platform for multiplexed tissue sectioning and anatomical phenotyping in plants. This system includes a highly adaptable device for high-throughput paraffin sectioning and multi-channel slide imaging of various plant tissues, along with AnatomyNet, a deep learning tool for analyzing tissue-scale patterns of cell arrangement and morphology. AnatomyNet delivers accurate, automated quantification of anatomical traits at both the tissue and cellular levels, outperforming existing tools in image analysis. Using the AnatomyArray system, we dissected the genetic basis of root anatomy in a diverse wheat (Triticum aestivum L.) population through anatomcis-based genome-wide association studies (GWAS). Among the candidate genes identified, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 14 (TaSPL14) was associated with stele and pericycle size in roots. Analysis of Taspl14 mutants confirmed that TaSPL14 plays a critical role in regulating root growth and tissue size by influencing phytohormone pathways. The AnatomyArray platform enables high-throughput characterization of cellular-level features and provides insights into the mechanisms shaping anatomical structure in plants.
{"title":"AnatomyArray: a high-throughput platform for anatomical phenotyping in plants.","authors":"Yikeng Cheng,Jiawei Shi,Zhanghan Pang,Nuo Xu,Kejie Chai,Jie Gao,Zhen Jia,Bingqian Hao,Huanran Yin,Ruiling Fang,Shangyuan Xie,Wei Chen,Daoquan Xiang,Zhuqing Zhou,Wanneng Yang,Qiang Li","doi":"10.1093/plcell/koaf223","DOIUrl":"https://doi.org/10.1093/plcell/koaf223","url":null,"abstract":"The anatomy or the arrangement of cells often determines the organization and function of plant tissues. However, current methods in large-scale imaging and accurate quantification of anatomical traits face major limitations. To address these challenges, we introduce the AnatomyArray system, an integrated platform for multiplexed tissue sectioning and anatomical phenotyping in plants. This system includes a highly adaptable device for high-throughput paraffin sectioning and multi-channel slide imaging of various plant tissues, along with AnatomyNet, a deep learning tool for analyzing tissue-scale patterns of cell arrangement and morphology. AnatomyNet delivers accurate, automated quantification of anatomical traits at both the tissue and cellular levels, outperforming existing tools in image analysis. Using the AnatomyArray system, we dissected the genetic basis of root anatomy in a diverse wheat (Triticum aestivum L.) population through anatomcis-based genome-wide association studies (GWAS). Among the candidate genes identified, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 14 (TaSPL14) was associated with stele and pericycle size in roots. Analysis of Taspl14 mutants confirmed that TaSPL14 plays a critical role in regulating root growth and tissue size by influencing phytohormone pathways. The AnatomyArray platform enables high-throughput characterization of cellular-level features and provides insights into the mechanisms shaping anatomical structure in plants.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145103530","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}
Anna van Weringh,Paul J Gamueda,Hasna Khan,Asher Pasha,Eddi Esteban,Nicholas J Provart
Drought is an important environmental stress that limits crop production. Guard cells (GCs) act to control the rate of water loss. To better understand how gene expression in GCs changes during progressive drought, we generated GC-specific RNA-seq transcriptomes during mild, moderate, and severe drought stress. Additionally, we sampled re-watered plants after severe drought. These transcriptomes were generated using the INTACT (isolation of nuclei tagged in specific cell types) system to capture the RNA from GC nuclei. We optimized the INTACT protocol for Arabidopsis thaliana leaf tissue, incorporating fixation to preserve RNA during nuclear isolation. To identify gene expression changes unique to GCs, we also generated INTACT transcriptomes from all leaf cell types, using the 35S viral promoter. These data sets highlight shared and unique gene expression changes between GCs and the bulk leaf tissue. Only GCs have detectable gene expression changes at the earliest drought time point and a high percentage of moderate drought GC DEGs are not observed in severe drought, unlike the bulk leaf tissue, showing that GCs tailor their gene expression changes to drought severity. A thermal imaging screen of mutants of 80 candidate early drought-responsive genes revealed that ten of these exhibit a cooler-than-wild-type phenotype under moderate drought conditions. The drought-responsive GC and leaf RNA-seq transcriptomes are available in the Arabidopsis ePlant at the Bio-Analytic Resource for Plant Biology website. These findings provide valuable insights into GC-specific drought responses and identify targets for enhancing drought tolerance in crops.
{"title":"INTACT-based guard cell transcriptomes from a progressive drought time course reveal targets for modifying stomatal responses.","authors":"Anna van Weringh,Paul J Gamueda,Hasna Khan,Asher Pasha,Eddi Esteban,Nicholas J Provart","doi":"10.1093/plcell/koaf218","DOIUrl":"https://doi.org/10.1093/plcell/koaf218","url":null,"abstract":"Drought is an important environmental stress that limits crop production. Guard cells (GCs) act to control the rate of water loss. To better understand how gene expression in GCs changes during progressive drought, we generated GC-specific RNA-seq transcriptomes during mild, moderate, and severe drought stress. Additionally, we sampled re-watered plants after severe drought. These transcriptomes were generated using the INTACT (isolation of nuclei tagged in specific cell types) system to capture the RNA from GC nuclei. We optimized the INTACT protocol for Arabidopsis thaliana leaf tissue, incorporating fixation to preserve RNA during nuclear isolation. To identify gene expression changes unique to GCs, we also generated INTACT transcriptomes from all leaf cell types, using the 35S viral promoter. These data sets highlight shared and unique gene expression changes between GCs and the bulk leaf tissue. Only GCs have detectable gene expression changes at the earliest drought time point and a high percentage of moderate drought GC DEGs are not observed in severe drought, unlike the bulk leaf tissue, showing that GCs tailor their gene expression changes to drought severity. A thermal imaging screen of mutants of 80 candidate early drought-responsive genes revealed that ten of these exhibit a cooler-than-wild-type phenotype under moderate drought conditions. The drought-responsive GC and leaf RNA-seq transcriptomes are available in the Arabidopsis ePlant at the Bio-Analytic Resource for Plant Biology website. These findings provide valuable insights into GC-specific drought responses and identify targets for enhancing drought tolerance in crops.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"89 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145089913","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}
Betula species exhibit exceptional cold tolerance, yet the evolutionary drivers of their cold adaptation remain unclear. Betula fujianensis, a subtropical member of this genus, is an ideal model to investigate the evolution of cold adaptation. Here, we present a nearly telomere-to-telomere genome assembly and identify a ten-fold reduction in nucleotide diversity in the extant B. fujianensis population compared to its temperate relatives (B. pendula and B. platyphylla). This decrease in nucleotide diversity was driven by two historical population declines during global cooling periods. B. fujianensis exhibits heightened sensitivity to low temperatures, associated with a contracted C-repeat binding factor (CBF) gene family and a 185-bp insertion in the DREB and EAR motif protein 1 (DEAR1) promoter, which enhances its expression. We demonstrate that DEAR1 is a negative regulator of CBF expression in a negative feedback loop. Collectively, our results identify the DEAR1–CBF interplay as an important regulatory module for cold adaptation. Our findings shed light on plant cold adaptation mechanisms and provide critical genomic resources to guide conservation strategies for this climate-vulnerable species under global climate change.
桦树物种表现出特殊的耐寒性，但其冷适应的进化驱动因素尚不清楚。福建桦树（Betula fujianensis）是亚热带桦树属植物，是研究其冷适应进化的理想模式。在这里，我们展示了一个近端粒到端粒的基因组组装，并发现与温带近亲（B. pendula和B. platyphylla）相比，现存福建白檀种群的核苷酸多样性减少了10倍。这种核苷酸多样性的减少是由全球变冷期间的两次历史种群下降造成的。福建B.对低温的敏感性增强，与C-repeat binding factor （CBF）基因家族的收缩和DREB and EAR motif protein 1 （DEAR1）启动子中185 bp的插入有关，从而增强了其表达。我们证明了DEAR1在负反馈回路中是CBF表达的负调节因子。总的来说，我们的研究结果确定了DEAR1-CBF的相互作用是冷适应的一个重要调节模块。我们的研究结果揭示了植物的冷适应机制，并为指导全球气候变化下这种气候脆弱物种的保护策略提供了重要的基因组资源。
{"title":"InDel variation and contraction of the C-repeat binding factor family contribute to cold sensitivity in Betula fujianensis","authors":"Hebi Zhuang, Erpei Lin, Jianbo Xie, Mei Jiang, Fei Ni, Shuaibin Shi, Meng Liu, Siyu Miao, Ming Wei, Chenghao Li, Jiming Liu, Xiaojuan Liu, Xian-Ge Hu, Wenwu Wu, Jarkko Salojärvi, Huahong Huang","doi":"10.1093/plcell/koaf216","DOIUrl":"https://doi.org/10.1093/plcell/koaf216","url":null,"abstract":"Betula species exhibit exceptional cold tolerance, yet the evolutionary drivers of their cold adaptation remain unclear. Betula fujianensis, a subtropical member of this genus, is an ideal model to investigate the evolution of cold adaptation. Here, we present a nearly telomere-to-telomere genome assembly and identify a ten-fold reduction in nucleotide diversity in the extant B. fujianensis population compared to its temperate relatives (B. pendula and B. platyphylla). This decrease in nucleotide diversity was driven by two historical population declines during global cooling periods. B. fujianensis exhibits heightened sensitivity to low temperatures, associated with a contracted C-repeat binding factor (CBF) gene family and a 185-bp insertion in the DREB and EAR motif protein 1 (DEAR1) promoter, which enhances its expression. We demonstrate that DEAR1 is a negative regulator of CBF expression in a negative feedback loop. Collectively, our results identify the DEAR1–CBF interplay as an important regulatory module for cold adaptation. Our findings shed light on plant cold adaptation mechanisms and provide critical genomic resources to guide conservation strategies for this climate-vulnerable species under global climate change.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"73 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145089416","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}
Yumin Zhang, Lynnette M A Dirk, Jingliang Zheng, Jiahao Chai, Xianbo Song, Jie Cao, Hao Wang, Yan Liu, Yunjun Liu, Sihan Zhen, Junjie Fu, Guoji Wang, Shixiao Li, Arthur G Hunt, A Bruce Downie, Tianyong Zhao
PROTEIN L-ISOASPARTYL O-METHYLTRANSFERASE (PIMT) promotes seed vigor by repairing damaged proteins. However, whether PIMT variants have arisen during maize (Zea mays) domestication remains unknown. Here, we found two variants in the ZmPIMT1 promoter. The ZmPIMT1 Hap C7-2 promoter exhibited stronger activity than the ZmPIMT1 Hap Z58 promoter. Maize inbred lines carrying the ZmPIMT1 Hap C7-2 promoter had greater seed vigor than ZmPIMT1 Hap Z58 lines in a population of Zhengdan 958 recombinant inbred lines (RILs) and a maize inbred population. By characterizing the maize zmpimt1 knockdown mutant, ZmPIMT1-overexpressing maize and Arabidopsis thaliana heterologous ZmPIMT1 overexpression lines, we demonstrated that ZmPIMT1 positively regulates seed vigor. Co-IP and LC-MS/MS assays showed that ZmPIMT1 interacts with and repairs damaged POLY(A) BINDING PROTEIN2 (PABP2). ZmPIMT1 stabilizes PABP2 RNA-binding activity and regulates the stability and translation efficiency of the mRNA during maize seed germination. Disruption of PABP2 decreases seed vigor in Arabidopsis thaliana. Furthermore, the F-statistics (Fixation index; FST) and nucleotide diversity (θπ) ratio between teosinte and maize lines showed that ZmPIMT1 likely has not undergone selection during maize domestication. Our findings unveil a molecular mechanism in which ZmPIMT1 regulates seed vigor in maize and highlight a potential application of the advantageous ZmPIMT1 haplotype for breeding new varieties with increased seed vigor.
{"title":"Natural variation in the ZmPIMT1 promoter enhances seed aging tolerance by regulating PABP2 repair in maize","authors":"Yumin Zhang, Lynnette M A Dirk, Jingliang Zheng, Jiahao Chai, Xianbo Song, Jie Cao, Hao Wang, Yan Liu, Yunjun Liu, Sihan Zhen, Junjie Fu, Guoji Wang, Shixiao Li, Arthur G Hunt, A Bruce Downie, Tianyong Zhao","doi":"10.1093/plcell/koaf217","DOIUrl":"https://doi.org/10.1093/plcell/koaf217","url":null,"abstract":"PROTEIN L-ISOASPARTYL O-METHYLTRANSFERASE (PIMT) promotes seed vigor by repairing damaged proteins. However, whether PIMT variants have arisen during maize (Zea mays) domestication remains unknown. Here, we found two variants in the ZmPIMT1 promoter. The ZmPIMT1 Hap C7-2 promoter exhibited stronger activity than the ZmPIMT1 Hap Z58 promoter. Maize inbred lines carrying the ZmPIMT1 Hap C7-2 promoter had greater seed vigor than ZmPIMT1 Hap Z58 lines in a population of Zhengdan 958 recombinant inbred lines (RILs) and a maize inbred population. By characterizing the maize zmpimt1 knockdown mutant, ZmPIMT1-overexpressing maize and Arabidopsis thaliana heterologous ZmPIMT1 overexpression lines, we demonstrated that ZmPIMT1 positively regulates seed vigor. Co-IP and LC-MS/MS assays showed that ZmPIMT1 interacts with and repairs damaged POLY(A) BINDING PROTEIN2 (PABP2). ZmPIMT1 stabilizes PABP2 RNA-binding activity and regulates the stability and translation efficiency of the mRNA during maize seed germination. Disruption of PABP2 decreases seed vigor in Arabidopsis thaliana. Furthermore, the F-statistics (Fixation index; FST) and nucleotide diversity (θπ) ratio between teosinte and maize lines showed that ZmPIMT1 likely has not undergone selection during maize domestication. Our findings unveil a molecular mechanism in which ZmPIMT1 regulates seed vigor in maize and highlight a potential application of the advantageous ZmPIMT1 haplotype for breeding new varieties with increased seed vigor.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"90 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145089419","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}
Marianne C Kramer, Thivanka Sandaruwan Ratnayake, Seth A Edwards, Harper L Lowrey, Gerald Klaas, Lyudmila Sidorenko, Beth A Rowan, Richard Michelmore, Blake C Meyers, R Keith Slotkin
The success of many engineered crop traits depends on the stable expression of transgenes, but their effectiveness is frequently at risk due to transgene silencing. The reason why certain transgenes are targeted by silencing pathways while others remain highly expressed and durable has remained a major question for decades due to the lack of technologies to study the initiation of transgene silencing. We developed two technologies to identify the trigger of transgene silencing in Arabidopsis (Arabidopsis thaliana) and in lettuce (Latuca sativa): one using the RUBY transgene to visualize the precise developmental time point of transgene silencing and the second to identify all transcripts produced from a transgene. By combining these two methods with Machine Learning, we identified an aberrant transgene-derived RNA that accumulates to high levels and closely correlates with the onset of transgene silencing. Our data suggest that a ribosome stalled at an unusual three-consecutive-histidine peptide sequence on the RUBY transcript triggers No-Go RNA Decay and cleavage of the RUBY mRNA. The production of this cleaved aberrant RNA precedes RNA interference during the triggering of transgene silencing; it is innate to the transgene coding sequence, independent of the promoter used or whether it is transformed into a model plant or crop.
{"title":"Identification of a cleaved aberrant RNA associated with the initiation of transgene silencing","authors":"Marianne C Kramer, Thivanka Sandaruwan Ratnayake, Seth A Edwards, Harper L Lowrey, Gerald Klaas, Lyudmila Sidorenko, Beth A Rowan, Richard Michelmore, Blake C Meyers, R Keith Slotkin","doi":"10.1093/plcell/koaf219","DOIUrl":"https://doi.org/10.1093/plcell/koaf219","url":null,"abstract":"The success of many engineered crop traits depends on the stable expression of transgenes, but their effectiveness is frequently at risk due to transgene silencing. The reason why certain transgenes are targeted by silencing pathways while others remain highly expressed and durable has remained a major question for decades due to the lack of technologies to study the initiation of transgene silencing. We developed two technologies to identify the trigger of transgene silencing in Arabidopsis (Arabidopsis thaliana) and in lettuce (Latuca sativa): one using the RUBY transgene to visualize the precise developmental time point of transgene silencing and the second to identify all transcripts produced from a transgene. By combining these two methods with Machine Learning, we identified an aberrant transgene-derived RNA that accumulates to high levels and closely correlates with the onset of transgene silencing. Our data suggest that a ribosome stalled at an unusual three-consecutive-histidine peptide sequence on the RUBY transcript triggers No-Go RNA Decay and cleavage of the RUBY mRNA. The production of this cleaved aberrant RNA precedes RNA interference during the triggering of transgene silencing; it is innate to the transgene coding sequence, independent of the promoter used or whether it is transformed into a model plant or crop.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"38 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145089420","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}
Baolei Li,Panpan Wang,Fan Sun,Jing Qin,Xiaojing Zhao,Xinyue Yu,Zhen Su,Tonglin Mao,Xiangfeng Wang
Plant thermomorphogenesis is a critical adaptive response to elevated ambient temperatures. The transcription factor PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) integrates diverse environmental and phytohormone signals to coordinate thermoresponsive growth. However, the cellular mechanisms underlying plant thermomorphogenic growth remain poorly understood. In this study, we show that elevated ambient temperature activates autophagy in a PIF4-dependent manner. The autophagy-deficient mutants autophagy-related 5 (atg5)-1 and autophagy-related 7 (atg7)-2 exhibit shorter hypocotyls compared with the wild type at 28 °C, highlighting the important role of autophagy in regulating thermomorphogenic growth in Arabidopsis (Arabidopsis thaliana). Moreover, we identified TIMING OF CAB EXPRESSION 1 (TOC1), a negative regulator of PIF4, as a target of selective autophagy. TOC1 directly interacts with AUTOPHAGY-RELATED 8 (ATG8) via the conserved ATG8-interacting motif-LIR/AIM docking site interface and is degraded through the autophagy pathway in response to elevated temperature. TOC1 accumulates in the autophagy-deficient mutant atg5-1 at 28 °C, where it inhibits PIF4 function and reduces thermosensitivity. Conversely, the reduced TOC1 level in atg5-1 toc1-21 rescues the short-hypocotyl phenotype of atg5-1 at 28 °C. Our study demonstrates that warm temperature-induced autophagy promotes plant thermomorphogenic growth by mediating the selective degradation of TOC1. This study reveals the reciprocal regulation between autophagy and thermomorphogenic signaling and identifies a molecular mechanism underlying this crosstalk.
{"title":"Warm temperature-induced autophagy mediates selective degradation of TIMING OF CAB EXPRESSION 1 thus promoting plant thermomorphogenesis.","authors":"Baolei Li,Panpan Wang,Fan Sun,Jing Qin,Xiaojing Zhao,Xinyue Yu,Zhen Su,Tonglin Mao,Xiangfeng Wang","doi":"10.1093/plcell/koaf211","DOIUrl":"https://doi.org/10.1093/plcell/koaf211","url":null,"abstract":"Plant thermomorphogenesis is a critical adaptive response to elevated ambient temperatures. The transcription factor PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) integrates diverse environmental and phytohormone signals to coordinate thermoresponsive growth. However, the cellular mechanisms underlying plant thermomorphogenic growth remain poorly understood. In this study, we show that elevated ambient temperature activates autophagy in a PIF4-dependent manner. The autophagy-deficient mutants autophagy-related 5 (atg5)-1 and autophagy-related 7 (atg7)-2 exhibit shorter hypocotyls compared with the wild type at 28 °C, highlighting the important role of autophagy in regulating thermomorphogenic growth in Arabidopsis (Arabidopsis thaliana). Moreover, we identified TIMING OF CAB EXPRESSION 1 (TOC1), a negative regulator of PIF4, as a target of selective autophagy. TOC1 directly interacts with AUTOPHAGY-RELATED 8 (ATG8) via the conserved ATG8-interacting motif-LIR/AIM docking site interface and is degraded through the autophagy pathway in response to elevated temperature. TOC1 accumulates in the autophagy-deficient mutant atg5-1 at 28 °C, where it inhibits PIF4 function and reduces thermosensitivity. Conversely, the reduced TOC1 level in atg5-1 toc1-21 rescues the short-hypocotyl phenotype of atg5-1 at 28 °C. Our study demonstrates that warm temperature-induced autophagy promotes plant thermomorphogenic growth by mediating the selective degradation of TOC1. This study reveals the reciprocal regulation between autophagy and thermomorphogenic signaling and identifies a molecular mechanism underlying this crosstalk.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"35 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145025551","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}
Enoch Lok Him Yuen, Zachary Savage, Vojtěch Pražák, Zhongyuan Liu, Vanda Adamkova, Freddie King, Cristina Vuolo, Tarhan Ibrahim, Yijun Wang, Saskia Jenkins, Yuanyang Zhou, Yasin Tumtas, Jessica Lee Erickson, Jennifer Prautsch, Andrada I Balmez, Johannes Stuttmann, Cian Duggan, Francesco Rivetti, Camilla Molinari, David C A Gaboriau, Philip Carella, Xiaohong Zhuang, Martin Schattat, Tolga O Bozkurt
Communication between cellular organelles is essential for mounting effective innate immune responses. The transport of organelles to pathogen penetration sites and their assembly around the host membrane, which delineates the plant-pathogen interface, are well-documented. However, whether organelles associate with these specialized interfaces, and the extent to which this process contributes to immunity, remain unknown. Here, we discovered defense-related membrane contact sites (MCS) comprising a membrane tethering complex between chloroplasts and the extrahaustorial membrane (EHM) surrounding the haustorium of the pathogen Phytophthora infestans in Nicotiana benthamiana. The assembly of this complex involves association between the chloroplast outer envelope protein CHLOROPLAST UNUSUAL POSITIONING 1 (CHUP1) and its plasma membrane-associated partner KINESIN-LIKE PROTEIN FOR ACTIN-BASED CHLOROPLAST MOVEMENT 1 (KAC1). Our biochemical assays revealed that CHUP1 and KAC1 interact, and infection cell biology assays demonstrated their co-accumulation in foci where chloroplasts contact the EHM. Genetic depletion of CHUP1 or KAC1 reduces the focal deposition of callose around the haustorium without affecting other core immune processes. Our findings suggest that the chloroplast-EHM attachment complex promotes plant focal immunity, revealing key components and their potential roles in the deposition of defense materials at the pathogen interface. These results advance our understanding of organelle-mediated immunity and highlight the significance of MCS in plant-pathogen interactions.
{"title":"Membrane contact sites between chloroplasts and the pathogen interface underpin plant focal immune responses","authors":"Enoch Lok Him Yuen, Zachary Savage, Vojtěch Pražák, Zhongyuan Liu, Vanda Adamkova, Freddie King, Cristina Vuolo, Tarhan Ibrahim, Yijun Wang, Saskia Jenkins, Yuanyang Zhou, Yasin Tumtas, Jessica Lee Erickson, Jennifer Prautsch, Andrada I Balmez, Johannes Stuttmann, Cian Duggan, Francesco Rivetti, Camilla Molinari, David C A Gaboriau, Philip Carella, Xiaohong Zhuang, Martin Schattat, Tolga O Bozkurt","doi":"10.1093/plcell/koaf214","DOIUrl":"https://doi.org/10.1093/plcell/koaf214","url":null,"abstract":"Communication between cellular organelles is essential for mounting effective innate immune responses. The transport of organelles to pathogen penetration sites and their assembly around the host membrane, which delineates the plant-pathogen interface, are well-documented. However, whether organelles associate with these specialized interfaces, and the extent to which this process contributes to immunity, remain unknown. Here, we discovered defense-related membrane contact sites (MCS) comprising a membrane tethering complex between chloroplasts and the extrahaustorial membrane (EHM) surrounding the haustorium of the pathogen Phytophthora infestans in Nicotiana benthamiana. The assembly of this complex involves association between the chloroplast outer envelope protein CHLOROPLAST UNUSUAL POSITIONING 1 (CHUP1) and its plasma membrane-associated partner KINESIN-LIKE PROTEIN FOR ACTIN-BASED CHLOROPLAST MOVEMENT 1 (KAC1). Our biochemical assays revealed that CHUP1 and KAC1 interact, and infection cell biology assays demonstrated their co-accumulation in foci where chloroplasts contact the EHM. Genetic depletion of CHUP1 or KAC1 reduces the focal deposition of callose around the haustorium without affecting other core immune processes. Our findings suggest that the chloroplast-EHM attachment complex promotes plant focal immunity, revealing key components and their potential roles in the deposition of defense materials at the pathogen interface. These results advance our understanding of organelle-mediated immunity and highlight the significance of MCS in plant-pathogen interactions.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"163 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145002877","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}
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