Extreme heat constrains global rice production. Polyploidy, a central driver of flowering plant evolution, is frequently associated with enhanced resilience to adverse environments. However, the epigenomic and transcriptomic programs that support heat tolerance in autotetraploid rice remain largely unexplored. In this study, we compared a diploid japonica rice line (GFD 2X) and its isogenic autotetraploid counterpart (GFD 4X) under short-term heat stress and subsequent recovery using physiological measurements, transcriptome profiling, and whole-genome DNA methylation analysis. Both cytotypes showed elevated physiological and biochemical indicators after heat treatment, with GFD 4X displaying consistently stronger responses. Transcriptome analysis revealed that heat adaptation relies mainly on hormone-related signaling pathways, heat shock proteins, and antioxidant enzyme systems. Genome-wide DNA methylation profiling revealed a contrasting pattern in which polyploidization promotes widespread DNA hypermethylation, while acute heat stress triggers broad DNA hypomethylation. This bidirectional regulatory shift suggests a dynamic feedback mechanism that contributes to environmental adaptability. Integrated analysis of methylation and gene expression further showed that heat stress reshapes the methylation patterns of stress-responsive genes, thereby altering their transcriptional regulation. Together, these results support a model in which polyploidy-associated epigenomic features and heat-induced methylation dynamics are linked to enhanced physiological and molecular responsiveness under elevated temperature. This study provides a systems-level view of how polyploid rice responds to heat stress and offers insight into the potential epigenetic basis of heat tolerance in a warming climate.
{"title":"Transcriptomic and DNA methylation insights into polyploidy-enhanced heat tolerance in rice (Oryza sativa L.).","authors":"Changjiang Zhang,Yu Wang,Weilong Meng,Xinfang Yu,Minghong Xu,Yingkai Wang,Lingxi Xiong,Xin Qi,Xintong Ma,Jian Ma,Ningning Wang","doi":"10.1093/plphys/kiag135","DOIUrl":"https://doi.org/10.1093/plphys/kiag135","url":null,"abstract":"Extreme heat constrains global rice production. Polyploidy, a central driver of flowering plant evolution, is frequently associated with enhanced resilience to adverse environments. However, the epigenomic and transcriptomic programs that support heat tolerance in autotetraploid rice remain largely unexplored. In this study, we compared a diploid japonica rice line (GFD 2X) and its isogenic autotetraploid counterpart (GFD 4X) under short-term heat stress and subsequent recovery using physiological measurements, transcriptome profiling, and whole-genome DNA methylation analysis. Both cytotypes showed elevated physiological and biochemical indicators after heat treatment, with GFD 4X displaying consistently stronger responses. Transcriptome analysis revealed that heat adaptation relies mainly on hormone-related signaling pathways, heat shock proteins, and antioxidant enzyme systems. Genome-wide DNA methylation profiling revealed a contrasting pattern in which polyploidization promotes widespread DNA hypermethylation, while acute heat stress triggers broad DNA hypomethylation. This bidirectional regulatory shift suggests a dynamic feedback mechanism that contributes to environmental adaptability. Integrated analysis of methylation and gene expression further showed that heat stress reshapes the methylation patterns of stress-responsive genes, thereby altering their transcriptional regulation. Together, these results support a model in which polyploidy-associated epigenomic features and heat-induced methylation dynamics are linked to enhanced physiological and molecular responsiveness under elevated temperature. This study provides a systems-level view of how polyploid rice responds to heat stress and offers insight into the potential epigenetic basis of heat tolerance in a warming climate.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"16 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2026-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147471754","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}
Hai Shi,Michaela McGinn,Nathaphon Yu King Hing,Brice A Jarvis,Barsanti Gautam,Cathleen Kuczynski,Alexander Hilo,Hardy Rolletschek,John C Sedbrook,Jorg Schwender
Overexpression of WRINKLED1 (WRI1), a master regulator of glycolysis and fatty acid biosynthesis, together with DIACYLGLYCEROL ACYLTRANSFERASE1 (DGAT1), which catalyzes the final step of triacylglycerol assembly, is a promising strategy for enhancing seed oil content. However, how these regulators coordinate system-wide metabolic reprogramming at the levels of gene expression, metabolite pools, and fluxes remains poorly understood. To address this, we performed 13C-metabolic flux analysis, metabolomics, and transcriptomics on in vitro cultured pennycress (Thlaspi arvense L.) embryos overexpressing the native WRI1 and DGAT1 homologs. In cultured embryos, WRI1/DGAT1 overexpression increased triacylglycerol accumulation by 28% while reducing protein content by 34%, relative to the wild type. Embryos showed ∼20-fold and 50-fold upregulation of WRI1 and DGAT1 along with induction of WRI1 target genes in glycolysis and fatty acid biosynthesis. Genes associated with photosynthesis and Calvin cycle functions were also upregulated, whereas genes encoding ribosomal proteins and seed storage proteins were strongly repressed, consistent with the observed lipid-protein tradeoff. Flux analysis revealed that enhanced triacylglycerol biosynthesis is supported by increased flux through the Rubisco shunt and cytosolic pyruvate kinase, while the oxidative pentose phosphate pathway and malic enzyme contributed little to NADPH or pyruvate supply. Metabolomic profiling revealed extensive perturbations in glycolytic intermediates, tricarboxylic acid cycle metabolites, and amino acids. In plant grown seeds, WRI1/DGAT1 lines also showed a modest but significant increase in total lipid content. Collectively, these findings reveal how WRI1 and DGAT1 reprogram central metabolism to enhance oil accumulation, with relevance to mature seeds.
{"title":"Metabolic flux, metabolite, and transcript analysis uncover reprogramming of metabolism toward higher seed oil.","authors":"Hai Shi,Michaela McGinn,Nathaphon Yu King Hing,Brice A Jarvis,Barsanti Gautam,Cathleen Kuczynski,Alexander Hilo,Hardy Rolletschek,John C Sedbrook,Jorg Schwender","doi":"10.1093/plphys/kiag148","DOIUrl":"https://doi.org/10.1093/plphys/kiag148","url":null,"abstract":"Overexpression of WRINKLED1 (WRI1), a master regulator of glycolysis and fatty acid biosynthesis, together with DIACYLGLYCEROL ACYLTRANSFERASE1 (DGAT1), which catalyzes the final step of triacylglycerol assembly, is a promising strategy for enhancing seed oil content. However, how these regulators coordinate system-wide metabolic reprogramming at the levels of gene expression, metabolite pools, and fluxes remains poorly understood. To address this, we performed 13C-metabolic flux analysis, metabolomics, and transcriptomics on in vitro cultured pennycress (Thlaspi arvense L.) embryos overexpressing the native WRI1 and DGAT1 homologs. In cultured embryos, WRI1/DGAT1 overexpression increased triacylglycerol accumulation by 28% while reducing protein content by 34%, relative to the wild type. Embryos showed ∼20-fold and 50-fold upregulation of WRI1 and DGAT1 along with induction of WRI1 target genes in glycolysis and fatty acid biosynthesis. Genes associated with photosynthesis and Calvin cycle functions were also upregulated, whereas genes encoding ribosomal proteins and seed storage proteins were strongly repressed, consistent with the observed lipid-protein tradeoff. Flux analysis revealed that enhanced triacylglycerol biosynthesis is supported by increased flux through the Rubisco shunt and cytosolic pyruvate kinase, while the oxidative pentose phosphate pathway and malic enzyme contributed little to NADPH or pyruvate supply. Metabolomic profiling revealed extensive perturbations in glycolytic intermediates, tricarboxylic acid cycle metabolites, and amino acids. In plant grown seeds, WRI1/DGAT1 lines also showed a modest but significant increase in total lipid content. Collectively, these findings reveal how WRI1 and DGAT1 reprogram central metabolism to enhance oil accumulation, with relevance to mature seeds.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"27 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2026-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147471805","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}
Ha Eun Jeh,Isaac Dopp,Zizhang Li,Shunyuan Xiao,Devidutta Samantaray,John M Howard,Seth T McMahon,Annapurna Devi Allu,Sally A Mackenzie
Plants adapt to environmental changes by adjusting growth and defense, and the role of epigenetic modifications in this process remains unclear. Sensing and adjusting to environmental changes are more pronounced in certain tissues such as epidermis, vasculature, meristem, and reproductive tissues. These tissues possess sensory plastids that are enriched in stress response proteins. We investigated the effects of perturbation of four sensory plastid-localized proteins, MutS HOMOLOG 1 (MSH1), PsbP DOMAIN-CONTAINING PROTEIN 3 (PPD3), CAB UNDEREXPRESSED 1 (CUE1), and 3'(2'),5'-BISPHOSPHATE NUCLEOTIDASE 1 (SAL1), on the Arabidopsis (Arabidopsis thaliana) epigenome, detecting gene expression and DNA methylation changes within gene networks associated with environmental sensing. These effects significantly overlapped with a set of CHG hypermethylated genes identified within the chromatin remodeler mutant histone deacetylase 6 (hda6) at 12-hr daylength. At 16-hr daylength, hda6 lost this CHG hypermethylation in gene bodies, and the sensory plastid mutants showed milder adjustments in phenotype and methylation- and gene expression- associated gene networks. We detected daylength-responsive epistatic interaction between sensory plastid mutants with hda6. We also found that the hda6 mutation conferred daylength memory and, with msh1, enhanced tolerance to heat and biotic stresses. These results support a model of epigenetically programmed adjustments in plant phenotype triggered by sensory plastid-to-nucleus retrograde signaling in direct response to daylength and environmental cues.
{"title":"Plastid perturbations trigger epigenetic programs during environmental sensing in plants.","authors":"Ha Eun Jeh,Isaac Dopp,Zizhang Li,Shunyuan Xiao,Devidutta Samantaray,John M Howard,Seth T McMahon,Annapurna Devi Allu,Sally A Mackenzie","doi":"10.1093/plphys/kiag136","DOIUrl":"https://doi.org/10.1093/plphys/kiag136","url":null,"abstract":"Plants adapt to environmental changes by adjusting growth and defense, and the role of epigenetic modifications in this process remains unclear. Sensing and adjusting to environmental changes are more pronounced in certain tissues such as epidermis, vasculature, meristem, and reproductive tissues. These tissues possess sensory plastids that are enriched in stress response proteins. We investigated the effects of perturbation of four sensory plastid-localized proteins, MutS HOMOLOG 1 (MSH1), PsbP DOMAIN-CONTAINING PROTEIN 3 (PPD3), CAB UNDEREXPRESSED 1 (CUE1), and 3'(2'),5'-BISPHOSPHATE NUCLEOTIDASE 1 (SAL1), on the Arabidopsis (Arabidopsis thaliana) epigenome, detecting gene expression and DNA methylation changes within gene networks associated with environmental sensing. These effects significantly overlapped with a set of CHG hypermethylated genes identified within the chromatin remodeler mutant histone deacetylase 6 (hda6) at 12-hr daylength. At 16-hr daylength, hda6 lost this CHG hypermethylation in gene bodies, and the sensory plastid mutants showed milder adjustments in phenotype and methylation- and gene expression- associated gene networks. We detected daylength-responsive epistatic interaction between sensory plastid mutants with hda6. We also found that the hda6 mutation conferred daylength memory and, with msh1, enhanced tolerance to heat and biotic stresses. These results support a model of epigenetically programmed adjustments in plant phenotype triggered by sensory plastid-to-nucleus retrograde signaling in direct response to daylength and environmental cues.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"17 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2026-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147471752","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":"Trees follow rhythms: Diel dynamics of non-structural carbohydrates are influenced by environment, taxonomy and functional traits.","authors":"Yuzhen Fan,Laura Fernández de Uña","doi":"10.1093/plphys/kiag153","DOIUrl":"https://doi.org/10.1093/plphys/kiag153","url":null,"abstract":"","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"52 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2026-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147465661","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":"Ordered sacrifice for survival - insights from drought-stressed fine roots in soybean.","authors":"Guannan Wang","doi":"10.1093/plphys/kiag152","DOIUrl":"https://doi.org/10.1093/plphys/kiag152","url":null,"abstract":"","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"38 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2026-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147465662","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}
Keke Yu, Danyang Guo, Xiaoyan Tang, Wenkai Du, Yi Wei, Jieyang Jin, Chenru Wei, Qiang Wang, Yutong Hu, Yuting Pan, Jingming Wang, Mingyue Zhao, Bo Li, Mengting Zhang, Tingting Jing, Chuankui Song
Low temperature imposes a significant threat to plant development. Plants counteract cold stress through UDP-glycosyltransferase (UGT)-mediated glycosylation. Although nerolidol, a widely distributed phytohormone-like compound, participates in cold acclimation and interplant signaling, its regulation remains elusive. Here, we demonstrated that ATBS1-Interacting Factor 3 (CsAIF3), an atypical basic helix-loop-helix (bHLH) transcription factor lacking DNA-binding activity, activates CsUGT91Q2 expression to promote nerolidol glucoside accumulation and cold tolerance in tea plants (Camellia sinensis). Furthermore, we determined that C-repeat Binding Factor 4 (CsCBF4), a cold-responsive transcription factor, binds to the CsAIF3 promoter. In vitro and in vivo experiments confirmed that CsCBF4–CsAIF3–CsUGT91Q2 form a cascade pathway and positively regulate the cold tolerance of tea plants. Under ambient conditions, CsWRKY4 suppressed CsUGT91Q2 expression by interacting with CsAIF3, whereas under cold stress, the cold-inducible CsCBF5 competitively displaced CsWRKY4 from the CsAIF3 complex, thereby relieving transcriptional repression on CsUGT91Q2, leading to increased nerolidol glycoside accumulation and cold tolerance in tea plants. These results not only unveil non-canonical functions for DNA-binding-deficient bHLHs but also provide critical insight into how plants precisely control specialized metabolism to cope with temperature changes.
{"title":"Precise control of volatile glucosylation in tea plants by CBF4, WRKY4, and an atypical bHLH transcription factor","authors":"Keke Yu, Danyang Guo, Xiaoyan Tang, Wenkai Du, Yi Wei, Jieyang Jin, Chenru Wei, Qiang Wang, Yutong Hu, Yuting Pan, Jingming Wang, Mingyue Zhao, Bo Li, Mengting Zhang, Tingting Jing, Chuankui Song","doi":"10.1093/plphys/kiag145","DOIUrl":"https://doi.org/10.1093/plphys/kiag145","url":null,"abstract":"Low temperature imposes a significant threat to plant development. Plants counteract cold stress through UDP-glycosyltransferase (UGT)-mediated glycosylation. Although nerolidol, a widely distributed phytohormone-like compound, participates in cold acclimation and interplant signaling, its regulation remains elusive. Here, we demonstrated that ATBS1-Interacting Factor 3 (CsAIF3), an atypical basic helix-loop-helix (bHLH) transcription factor lacking DNA-binding activity, activates CsUGT91Q2 expression to promote nerolidol glucoside accumulation and cold tolerance in tea plants (Camellia sinensis). Furthermore, we determined that C-repeat Binding Factor 4 (CsCBF4), a cold-responsive transcription factor, binds to the CsAIF3 promoter. In vitro and in vivo experiments confirmed that CsCBF4–CsAIF3–CsUGT91Q2 form a cascade pathway and positively regulate the cold tolerance of tea plants. Under ambient conditions, CsWRKY4 suppressed CsUGT91Q2 expression by interacting with CsAIF3, whereas under cold stress, the cold-inducible CsCBF5 competitively displaced CsWRKY4 from the CsAIF3 complex, thereby relieving transcriptional repression on CsUGT91Q2, leading to increased nerolidol glycoside accumulation and cold tolerance in tea plants. These results not only unveil non-canonical functions for DNA-binding-deficient bHLHs but also provide critical insight into how plants precisely control specialized metabolism to cope with temperature changes.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"31 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2026-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147465663","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}
C4 photosynthesis requires more ATP than C3 photosynthesis to drive the C4 cycle, which concentrates CO2 in the bundle sheath cells. This ATP demand is expected to be met by cyclic electron transport around photosystem I. Of the two cyclic electron transport pathways, PROTON GRADIENT REGULATION 5 (PGR5)/PGR5-like photosynthetic phenotype 1 (PGRL1)-dependent and chloroplast NADH dehydrogenase-like (NDH)-dependent, ATP is supplied primarily by the NDH-dependent pathway in NADP-malic enzyme-type C4 plants. However, the roles of these pathways in photoprotection of photosystem I have not been fully evaluated in C4 plants. In this study, we used Flaveria bidentis knockdown lines targeting PGRL1 or NdhO and their double-knockdown lines to investigate the redox state of the electron transport chain and high light sensitivity of photosystems. The double-knockdown line exhibited poorer growth than the FbNdhO-RNAi line, indicating that both pathways were essential for ATP production. The acceptor side of P700 was limited under high light conditions in the FbNdhO-RNAi line, while it was limited under lower to high light conditions in the FbPGRL1-RNAi and double-knockdown lines. Ferredoxin was reduced more in the FbPGRL1-RNAi line than in the wild type, and it was even more reduced in the double-knockdown line. Photoinhibition caused by high light exposure was more pronounced in photosystem I than in photosystem II in these lines. These results demonstrate that both cyclic electron transport pathways are essential not only for ATP production required for growth but also for protecting photosystem I from photoinhibition by alleviating the acceptor-side limitations of P700 in C4 plants.
{"title":"Cyclic electron flow around photosystem I provides energy production and photoprotection in C4 plants","authors":"Asuka Nakamura, Takako Ogawa, Ginga Shimakawa, Ryouhei Kobayashi, Toshiharu Shikanai, Yuri N Munekage","doi":"10.1093/plphys/kiag146","DOIUrl":"https://doi.org/10.1093/plphys/kiag146","url":null,"abstract":"C4 photosynthesis requires more ATP than C3 photosynthesis to drive the C4 cycle, which concentrates CO2 in the bundle sheath cells. This ATP demand is expected to be met by cyclic electron transport around photosystem I. Of the two cyclic electron transport pathways, PROTON GRADIENT REGULATION 5 (PGR5)/PGR5-like photosynthetic phenotype 1 (PGRL1)-dependent and chloroplast NADH dehydrogenase-like (NDH)-dependent, ATP is supplied primarily by the NDH-dependent pathway in NADP-malic enzyme-type C4 plants. However, the roles of these pathways in photoprotection of photosystem I have not been fully evaluated in C4 plants. In this study, we used Flaveria bidentis knockdown lines targeting PGRL1 or NdhO and their double-knockdown lines to investigate the redox state of the electron transport chain and high light sensitivity of photosystems. The double-knockdown line exhibited poorer growth than the FbNdhO-RNAi line, indicating that both pathways were essential for ATP production. The acceptor side of P700 was limited under high light conditions in the FbNdhO-RNAi line, while it was limited under lower to high light conditions in the FbPGRL1-RNAi and double-knockdown lines. Ferredoxin was reduced more in the FbPGRL1-RNAi line than in the wild type, and it was even more reduced in the double-knockdown line. Photoinhibition caused by high light exposure was more pronounced in photosystem I than in photosystem II in these lines. These results demonstrate that both cyclic electron transport pathways are essential not only for ATP production required for growth but also for protecting photosystem I from photoinhibition by alleviating the acceptor-side limitations of P700 in C4 plants.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"5 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2026-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147465666","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}
Low-temperature stress significantly affects plant growth and development. NAM, ATAF, and CUC transcription factors (NAC TFs) play a crucial role in enhancing plant tolerance to low-temperature, drought, and salinity stresses by promoting the initiation of stress responses and signal transduction. In this study, we found that the NAC transcription factor gene NON RIPENING (SlNOR) is significantly induced by low-temperature and jasmonic acid (JA), and it promotes JA biosynthesis by directly targeting and regulating LIPOXYGENASE 10/LIPOXYGENASE 11 (SlLOX10/SlLOX11), thereby positively regulating low-temperature tolerance of tomato (Solanum lycopersicum). Both SlNOR- and SlLOX11-overexpressing lines exhibited a significant increase in JA accumulation under low-temperature stress, reducing excessive reactive oxygen species (ROS) accumulation. SlNOR interacted with V-MYB AVIAN MYELOBLASTOSIS VIRAL ONCOGENE HOMOLOG 60 (SlMYB60) at the protein level, and SlMYB60 directly targeted and regulated SlLOX10/SlLOX11. The phenotype of SlMYB60 overexpression was consistent with SlNOR overexpression. Additionally, MYELOCYTOMATOSIS 2 (SlMYC2), a key transcription factor in the JA signaling pathway, directly bound to SlNOR and promoted SlNOR expression. This study reveals the core function of the SlMYC2-SlNOR-SlMYB60-SlLOX10/11 module in regulating JA synthesis and clarifies the molecular mechanism through which this module regulates JA accumulation to participate in the low-temperature stress response in tomato.
{"title":"SlNOR interacts with SlMYB60 to regulate the jasmonic acid-mediated low-temperature stress response in tomato","authors":"Xiangguang Meng, Zhen Kang, Guo Chen, Zhimei Chen, Songshen Hu, Guobin Li, Tianlai Li, Xiaohui Hu, Changan Zhu","doi":"10.1093/plphys/kiag144","DOIUrl":"https://doi.org/10.1093/plphys/kiag144","url":null,"abstract":"Low-temperature stress significantly affects plant growth and development. NAM, ATAF, and CUC transcription factors (NAC TFs) play a crucial role in enhancing plant tolerance to low-temperature, drought, and salinity stresses by promoting the initiation of stress responses and signal transduction. In this study, we found that the NAC transcription factor gene NON RIPENING (SlNOR) is significantly induced by low-temperature and jasmonic acid (JA), and it promotes JA biosynthesis by directly targeting and regulating LIPOXYGENASE 10/LIPOXYGENASE 11 (SlLOX10/SlLOX11), thereby positively regulating low-temperature tolerance of tomato (Solanum lycopersicum). Both SlNOR- and SlLOX11-overexpressing lines exhibited a significant increase in JA accumulation under low-temperature stress, reducing excessive reactive oxygen species (ROS) accumulation. SlNOR interacted with V-MYB AVIAN MYELOBLASTOSIS VIRAL ONCOGENE HOMOLOG 60 (SlMYB60) at the protein level, and SlMYB60 directly targeted and regulated SlLOX10/SlLOX11. The phenotype of SlMYB60 overexpression was consistent with SlNOR overexpression. Additionally, MYELOCYTOMATOSIS 2 (SlMYC2), a key transcription factor in the JA signaling pathway, directly bound to SlNOR and promoted SlNOR expression. This study reveals the core function of the SlMYC2-SlNOR-SlMYB60-SlLOX10/11 module in regulating JA synthesis and clarifies the molecular mechanism through which this module regulates JA accumulation to participate in the low-temperature stress response in tomato.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"26 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2026-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147465667","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}
Lysine acetylation represents a pivotal regulatory layer in plant stress responses, yet its functional significance in desiccation-tolerant (DT) species remains uncharacterized. Here, we report a comprehensive lysine acetylome of the extremophyte Syntrichia caninervis (S. caninervis) through dehydration-rehydration cycles, identifying 11,474 acetylation sites on 4,171 proteins and representing a large dataset of lysine acetylome in plants. Acetylation dynamics coordinated a metabolic reprogramming crucial for survival: during dehydration, acetylated proteins were enriched in carbon fixation, glutathione metabolism, and nucleotide sugar biosynthesis, facilitating structural reinforcement and redox homeostasis. Upon rehydration, acetylation rapidly targeted core metabolic pathways, including glycolysis and the proteasome, to power recovery. Notably, the extensive acetylation of glycolytic enzymes likely facilitates the rapid recovery of S. caninervis from dehydration. Functional validation established that acetylation at lysine 513 (K513) of pyruvate kinase (cPK5) is essential for its catalytic activity and required for desiccation tolerance. Our study provides an in vivo acetylome landscape of a DT plant, delineating the dynamic regulatory network that coordinates metabolic adaptation to water stress and offering a key resource for engineering drought resilience.
{"title":"Lysine acetylation drives metabolic reprogramming for desiccation tolerance in the desert moss Syntrichia caninervis","authors":"Amangul Hawar, Fangliu Yin, Xuncheng Liu, Qilin Yang, Jiahui Liu, Yakupjan Haxim, Xiaoshuang Li, Daoyuan Zhang","doi":"10.1093/plphys/kiag139","DOIUrl":"https://doi.org/10.1093/plphys/kiag139","url":null,"abstract":"Lysine acetylation represents a pivotal regulatory layer in plant stress responses, yet its functional significance in desiccation-tolerant (DT) species remains uncharacterized. Here, we report a comprehensive lysine acetylome of the extremophyte Syntrichia caninervis (S. caninervis) through dehydration-rehydration cycles, identifying 11,474 acetylation sites on 4,171 proteins and representing a large dataset of lysine acetylome in plants. Acetylation dynamics coordinated a metabolic reprogramming crucial for survival: during dehydration, acetylated proteins were enriched in carbon fixation, glutathione metabolism, and nucleotide sugar biosynthesis, facilitating structural reinforcement and redox homeostasis. Upon rehydration, acetylation rapidly targeted core metabolic pathways, including glycolysis and the proteasome, to power recovery. Notably, the extensive acetylation of glycolytic enzymes likely facilitates the rapid recovery of S. caninervis from dehydration. Functional validation established that acetylation at lysine 513 (K513) of pyruvate kinase (cPK5) is essential for its catalytic activity and required for desiccation tolerance. Our study provides an in vivo acetylome landscape of a DT plant, delineating the dynamic regulatory network that coordinates metabolic adaptation to water stress and offering a key resource for engineering drought resilience.","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"13 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2026-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147465665","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}
Auxin plays a central regulatory role in plant development and secondary metabolism. Crocins are key compounds responsible for the pharmacological effects of saffron, and their content is reduced by exogenous IAA. However, the mechanism underlying this regulation remains unclear. In this study, we identified an auxin response factor, ARF18, whose gene expression is induced by IAA and negatively correlates with crocin biosynthesis. Silencing of CsARF18 resulted in increased crocin content, whereas overexpression of CsARF18 led to a decrease in crocin content. CsARF18 was shown to bind to AuxREs within the promoters of CsPSY1 and CsALDH5, consequently inhibiting their transcription. Furthermore, the microRNA Csa-miR160 was identified as a regulator of CsARF18, promoting its degradation. Co-overexpression of Csa-miR160 and CsARF18 in Crocus sativus L. alleviated the inhibitory effect of CsARF18 on crocin biosynthesis, whereas silencing Csa-miR160 failed to alleviate this inhibition. Our results demonstrate that Csa-miR160 targets and degrades CsARF18, thereby weakening its inhibitory regulation on CsPSY1 and CsALDH5. Based on these findings, we propose the “CsARF18–CsPSY/CsALDH–crocin” regulatory model, in which Csa-miR160 modulates auxin signaling during crocin biosynthesis in C. sativus. This study lays the foundation for further research on the secondary metabolites of saffron..
{"title":"Csa-miR160 targets transcriptional repressor CsARF18 and modulates auxin-mediated crocin biosynthesis in Crocus sativus L","authors":"Bingcong Xing, Shiyu Wang, Aiwen Zhang, Xiaolei Zhu, Ying Zheng, Lei Zhang, Lanying Pan, Qingsong Shao","doi":"10.1093/plphys/kiag142","DOIUrl":"https://doi.org/10.1093/plphys/kiag142","url":null,"abstract":"Auxin plays a central regulatory role in plant development and secondary metabolism. Crocins are key compounds responsible for the pharmacological effects of saffron, and their content is reduced by exogenous IAA. However, the mechanism underlying this regulation remains unclear. In this study, we identified an auxin response factor, ARF18, whose gene expression is induced by IAA and negatively correlates with crocin biosynthesis. Silencing of CsARF18 resulted in increased crocin content, whereas overexpression of CsARF18 led to a decrease in crocin content. CsARF18 was shown to bind to AuxREs within the promoters of CsPSY1 and CsALDH5, consequently inhibiting their transcription. Furthermore, the microRNA Csa-miR160 was identified as a regulator of CsARF18, promoting its degradation. Co-overexpression of Csa-miR160 and CsARF18 in Crocus sativus L. alleviated the inhibitory effect of CsARF18 on crocin biosynthesis, whereas silencing Csa-miR160 failed to alleviate this inhibition. Our results demonstrate that Csa-miR160 targets and degrades CsARF18, thereby weakening its inhibitory regulation on CsPSY1 and CsALDH5. Based on these findings, we propose the “CsARF18–CsPSY/CsALDH–crocin” regulatory model, in which Csa-miR160 modulates auxin signaling during crocin biosynthesis in C. sativus. This study lays the foundation for further research on the secondary metabolites of saffron..","PeriodicalId":20101,"journal":{"name":"Plant Physiology","volume":"44 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2026-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147465668","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}
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