Ana B Romero-Losada, Christina Arvanitidou, M Elena García-Gómez, María Morales-Pineda, M José Castro-Pérez, Yen Peng Chew, Gerben van Ooijen, Mercedes García-González, Francisco J Romero-Campero
Earth's tilted rotation and translation around the Sun produce pervasive rhythms on our planet, giving rise to photoperiodic changes in diel cycles. Although marine phytoplankton plays a key role in ecosystems, multiomics analysis of its responses to these periodic environmental signals remains largely unexplored. The marine picoalga Ostreococcus tauri was chosen as a model organism due to its cellular and genomic simplicity. Ostreococcus was subjected to different light regimes to investigate its responses to periodic environmental signals: long summer days, short winter days, constant light, and constant dark conditions. Although less than 5% of the transcriptome maintained oscillations under both constant conditions, 80% presented diel rhythmicity. A drastic reduction in diel rhythmicity was observed at the proteome level, with 39% of the detected proteins oscillating. Photoperiod-specific rhythms were identified for key physiological processes such as the cell cycle, photosynthesis, carotenoid biosynthesis, starch accumulation, and nitrate assimilation. In this study, a photoperiodic plastic global orchestration among transcriptome, proteome, and physiological dynamics was characterized to identify photoperiod-specific temporal offsets between the timing of transcripts, proteins, and physiological responses.
{"title":"Multiomics integration unveils photoperiodic plasticity in the molecular rhythms of marine phytoplankton","authors":"Ana B Romero-Losada, Christina Arvanitidou, M Elena García-Gómez, María Morales-Pineda, M José Castro-Pérez, Yen Peng Chew, Gerben van Ooijen, Mercedes García-González, Francisco J Romero-Campero","doi":"10.1093/plcell/koaf033","DOIUrl":"https://doi.org/10.1093/plcell/koaf033","url":null,"abstract":"Earth's tilted rotation and translation around the Sun produce pervasive rhythms on our planet, giving rise to photoperiodic changes in diel cycles. Although marine phytoplankton plays a key role in ecosystems, multiomics analysis of its responses to these periodic environmental signals remains largely unexplored. The marine picoalga Ostreococcus tauri was chosen as a model organism due to its cellular and genomic simplicity. Ostreococcus was subjected to different light regimes to investigate its responses to periodic environmental signals: long summer days, short winter days, constant light, and constant dark conditions. Although less than 5% of the transcriptome maintained oscillations under both constant conditions, 80% presented diel rhythmicity. A drastic reduction in diel rhythmicity was observed at the proteome level, with 39% of the detected proteins oscillating. Photoperiod-specific rhythms were identified for key physiological processes such as the cell cycle, photosynthesis, carotenoid biosynthesis, starch accumulation, and nitrate assimilation. In this study, a photoperiodic plastic global orchestration among transcriptome, proteome, and physiological dynamics was characterized to identify photoperiod-specific temporal offsets between the timing of transcripts, proteins, and physiological responses.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"55 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143393297","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}
Jinwei Wei, Minghui Liu, Dan Zhao, Pengmeng Du, Lu Yan, Derui Liu, Qinghua Shi, Changxian Yang, Guochen Qin, Biao Gong
Soil salinization and alkalization disrupt redox homeostasis, impairing plant survival and crop production. Disruption of redox homeostasis can cause accumulation of reactive nitrogen species, such as nitric oxide (NO), which causes nitrosative damage in which the properties of biomacromolecules are altered. It is unclear whether melatonin regulates NO homeostasis, thereby affecting plant saline-alkali tolerance. In tomato (Solanum lycopersicum), excess NO caused by saline-alkali stress resulted in nitrosative damage, which was alleviated by S-nitrosoglutathione reductase (GSNOR). Moreover, saline-alkali stress-triggered NO stimulated caffeic acid O-methyltransferase (COMT) transcription and melatonin biosynthesis to scavenge excess NO and alleviate nitrosative damage at the proteome level. Under saline-alkali stress, plasma membrane-localized H+-ATPase 2 (HA2) was S-nitrosylated at Cys206, impairing its interaction with 14-3-3 protein 1 (TFT1). HA2 S-nitrosylation resulted in reduced HA activity, H+ efflux, and saline-alkali tolerance. Conversely, COMT-generated melatonin alleviated HA2 S-nitrosylation, recovering its function and tomato saline-alkali tolerance. Therefore, we propose that melatonin and NO are redox switches of HA2 S-nitrosylation for saline-alkali tolerance. Under natural saline-alkali conditions, tomato productivity was improved by grafting with COMT-, GSNOR-, or HA2-overexpressing rootstocks, or by generating non-nitrosylated HA2C206S mutants. By establishing the melatonin–NO–HA2 module, this study illuminates a molecular function of melatonin and suggests possible genetic engineering strategies to improve agriculture.
{"title":"Melatonin confers saline-alkali tolerance in tomato by alleviating nitrosative damage and S-nitrosylation of H+-ATPase 2","authors":"Jinwei Wei, Minghui Liu, Dan Zhao, Pengmeng Du, Lu Yan, Derui Liu, Qinghua Shi, Changxian Yang, Guochen Qin, Biao Gong","doi":"10.1093/plcell/koaf035","DOIUrl":"https://doi.org/10.1093/plcell/koaf035","url":null,"abstract":"Soil salinization and alkalization disrupt redox homeostasis, impairing plant survival and crop production. Disruption of redox homeostasis can cause accumulation of reactive nitrogen species, such as nitric oxide (NO), which causes nitrosative damage in which the properties of biomacromolecules are altered. It is unclear whether melatonin regulates NO homeostasis, thereby affecting plant saline-alkali tolerance. In tomato (Solanum lycopersicum), excess NO caused by saline-alkali stress resulted in nitrosative damage, which was alleviated by S-nitrosoglutathione reductase (GSNOR). Moreover, saline-alkali stress-triggered NO stimulated caffeic acid O-methyltransferase (COMT) transcription and melatonin biosynthesis to scavenge excess NO and alleviate nitrosative damage at the proteome level. Under saline-alkali stress, plasma membrane-localized H+-ATPase 2 (HA2) was S-nitrosylated at Cys206, impairing its interaction with 14-3-3 protein 1 (TFT1). HA2 S-nitrosylation resulted in reduced HA activity, H+ efflux, and saline-alkali tolerance. Conversely, COMT-generated melatonin alleviated HA2 S-nitrosylation, recovering its function and tomato saline-alkali tolerance. Therefore, we propose that melatonin and NO are redox switches of HA2 S-nitrosylation for saline-alkali tolerance. Under natural saline-alkali conditions, tomato productivity was improved by grafting with COMT-, GSNOR-, or HA2-overexpressing rootstocks, or by generating non-nitrosylated HA2C206S mutants. By establishing the melatonin–NO–HA2 module, this study illuminates a molecular function of melatonin and suggests possible genetic engineering strategies to improve agriculture.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"167 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143385359","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}
Huangjun Sheng, Han Zhang, Hua Deng, Zuxin Zhang, Fazhan Qiu, Fang Yang
Compact plant architecture allows more efficient light capture under higher planting density. Thus, it is a crucial strategy for improving crop yield, particularly in maize (Zea mays L.) Here, we isolated a maize gene, COMPACT PLANT 3 (CT3), regulating plant architecture, using map-based cloning. CT3, encoding a GRAS protein, interacts with an AP2 transcription factor (TF), DWARF AND IRREGULAR LEAF 1 (DIL1). The genetic analysis showed that CT3 and DIL1 regulate leaf angle and plant height via the same pathway, supporting the biological role of their interaction by forming a complex. Transcriptome and DNA profiling analyses revealed that these two TFs share many common target genes. We further observed that CT3 functions as a co-regulator to enhance the DNA affinity and transcriptional activity of DIL1. This finding was further supported by the direct binding of DIL1 to two cell wall-related genes, ZmEXO1 and ZmXTH14, which were downregulated in the ct3 mutant. Furthermore, ZmEXO1 regulated plant architecture in a manner similar to CT3- and DIL1-mediated regulation. Zmexo1, ct3, and dil1 mutants showed defective cell wall integrity and had reduced cell wall-related components. The introduction of the ct3 or dil1 mutant allele into elite maize hybrids led to a more compact architecture and increased yield under high planting density. Our findings reveal a regulatory pathway of maize plant architecture and provided targets to increase yield under high planting density.
{"title":"Maize COMPACT PLANT 3 regulates plant architecture and facilitates high-density planting","authors":"Huangjun Sheng, Han Zhang, Hua Deng, Zuxin Zhang, Fazhan Qiu, Fang Yang","doi":"10.1093/plcell/koaf029","DOIUrl":"https://doi.org/10.1093/plcell/koaf029","url":null,"abstract":"Compact plant architecture allows more efficient light capture under higher planting density. Thus, it is a crucial strategy for improving crop yield, particularly in maize (Zea mays L.) Here, we isolated a maize gene, COMPACT PLANT 3 (CT3), regulating plant architecture, using map-based cloning. CT3, encoding a GRAS protein, interacts with an AP2 transcription factor (TF), DWARF AND IRREGULAR LEAF 1 (DIL1). The genetic analysis showed that CT3 and DIL1 regulate leaf angle and plant height via the same pathway, supporting the biological role of their interaction by forming a complex. Transcriptome and DNA profiling analyses revealed that these two TFs share many common target genes. We further observed that CT3 functions as a co-regulator to enhance the DNA affinity and transcriptional activity of DIL1. This finding was further supported by the direct binding of DIL1 to two cell wall-related genes, ZmEXO1 and ZmXTH14, which were downregulated in the ct3 mutant. Furthermore, ZmEXO1 regulated plant architecture in a manner similar to CT3- and DIL1-mediated regulation. Zmexo1, ct3, and dil1 mutants showed defective cell wall integrity and had reduced cell wall-related components. The introduction of the ct3 or dil1 mutant allele into elite maize hybrids led to a more compact architecture and increased yield under high planting density. Our findings reveal a regulatory pathway of maize plant architecture and provided targets to increase yield under high planting density.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143385361","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}
Glycogen synthase kinase 3 (GSK3)-like kinases play important roles in stress responses in plants. However, the mechanism of GSK3-like kinases in drought-induced antioxidant defense is not clear. In this study, we discovered that the GSK3-like kinase SHAGGY-like kinase 1 (ZmSK1) negatively regulates drought tolerance by inhibiting antioxidant defense in maize (Zea mays). Then, we determined that Cysteine-rich Polycomb-like protein 2 (ZmCPP2) interacts with ZmSK1 and enhances maize drought tolerance by inducing antioxidant defense. ZmCPP2 is phosphorylated at Ser-250 by ZmSK1, which is dependent on ZmSK1 kinase activity and attenuates maize drought tolerance. Furthermore, ZmCPP2 directly binds to the promoter of the superoxide dismutase (SOD) gene ZmSOD4, encoding an antioxidant defense enzyme, and activates its expression. ZmSK1 phosphorylating ZmCPP2 at Ser-250 represses the binding of ZmCPP2 to the ZmSOD4 promoter. Taken together, our results indicate that the phosphorylation of ZmCPP2 by ZmSK1 results in decreased SOD activity, and thus reduces drought tolerance in maize. These findings reveal a mechanism of GSK3-like kinases regulating antioxidant defense in the drought stress response.
{"title":"The maize GSK3-like kinase ZmSK1 negatively regulates drought tolerance by phosphorylating the transcription factor ZmCPP2","authors":"Yang Xiang, Weijuan Liu, Yingxue Niu, Qian Li, Chongyang Zhao, Yitian Pan, Guangdong Li, Xiangli Bian, Yadan Miao, Aying Zhang","doi":"10.1093/plcell/koaf032","DOIUrl":"https://doi.org/10.1093/plcell/koaf032","url":null,"abstract":"Glycogen synthase kinase 3 (GSK3)-like kinases play important roles in stress responses in plants. However, the mechanism of GSK3-like kinases in drought-induced antioxidant defense is not clear. In this study, we discovered that the GSK3-like kinase SHAGGY-like kinase 1 (ZmSK1) negatively regulates drought tolerance by inhibiting antioxidant defense in maize (Zea mays). Then, we determined that Cysteine-rich Polycomb-like protein 2 (ZmCPP2) interacts with ZmSK1 and enhances maize drought tolerance by inducing antioxidant defense. ZmCPP2 is phosphorylated at Ser-250 by ZmSK1, which is dependent on ZmSK1 kinase activity and attenuates maize drought tolerance. Furthermore, ZmCPP2 directly binds to the promoter of the superoxide dismutase (SOD) gene ZmSOD4, encoding an antioxidant defense enzyme, and activates its expression. ZmSK1 phosphorylating ZmCPP2 at Ser-250 represses the binding of ZmCPP2 to the ZmSOD4 promoter. Taken together, our results indicate that the phosphorylation of ZmCPP2 by ZmSK1 results in decreased SOD activity, and thus reduces drought tolerance in maize. These findings reveal a mechanism of GSK3-like kinases regulating antioxidant defense in the drought stress response.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"49 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143385416","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}
Dominika Bednarczyk, Oded Skaliter, Shane Kerzner, Tania Masci, Elena Shklarman, Ekaterina Shor, Alexander Vainstein
In petunia (Petunia x hybrida), MADS-box homeotic genes dictate floral organ identity. For instance, DEFICIENS (PhDEF), GLOBOSA1, and GLOBOSA2 (PhGLO1/2) are responsible for petal and stamen identity. However, whether homeotic genes, particularly PhDEF, have a function at the later stages of flower development, remains elusive. In petunia flowers, scent production initiates at anthesis, when the flower is ready for pollination, and is triggered by activation of EMISSION OF BENZENOIDS I (EOBI) and EOBII, MYB transcriptional regulators of scent-related genes. Here, we revealed the role of PhDEF in mature flowers, showing that it activates scent production. PhDEF suppression using a transient viral system in petunia flowers led to a significant reduction in volatile emission and pool levels, and in the transcript levels of scent-related transcriptional regulators and enzymes. Promoter activity assays demonstrated that PhDEF activates EOBI, EOBII and the phenylpropanoid biosynthesis genes L-PHENYLALANINE AMMONIA LYASE and PHENYLACETALDEHYDE SYNTHASE. Our findings underscore the importance of PhDEF in petunia flower development from initiation to maturation and in coordinating petal specification and the establishment of showy pollination-related traits.
{"title":"The homeotic gene PhDEF regulates production of volatiles in petunia flowers by activating EOBI and EOBII","authors":"Dominika Bednarczyk, Oded Skaliter, Shane Kerzner, Tania Masci, Elena Shklarman, Ekaterina Shor, Alexander Vainstein","doi":"10.1093/plcell/koaf027","DOIUrl":"https://doi.org/10.1093/plcell/koaf027","url":null,"abstract":"In petunia (Petunia x hybrida), MADS-box homeotic genes dictate floral organ identity. For instance, DEFICIENS (PhDEF), GLOBOSA1, and GLOBOSA2 (PhGLO1/2) are responsible for petal and stamen identity. However, whether homeotic genes, particularly PhDEF, have a function at the later stages of flower development, remains elusive. In petunia flowers, scent production initiates at anthesis, when the flower is ready for pollination, and is triggered by activation of EMISSION OF BENZENOIDS I (EOBI) and EOBII, MYB transcriptional regulators of scent-related genes. Here, we revealed the role of PhDEF in mature flowers, showing that it activates scent production. PhDEF suppression using a transient viral system in petunia flowers led to a significant reduction in volatile emission and pool levels, and in the transcript levels of scent-related transcriptional regulators and enzymes. Promoter activity assays demonstrated that PhDEF activates EOBI, EOBII and the phenylpropanoid biosynthesis genes L-PHENYLALANINE AMMONIA LYASE and PHENYLACETALDEHYDE SYNTHASE. Our findings underscore the importance of PhDEF in petunia flower development from initiation to maturation and in coordinating petal specification and the establishment of showy pollination-related traits.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"140 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143258310","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}
Ting Jiang, Lei Li, Qianqian Hu, Xianyu Kuang, Lei Zhang, Wenjie Zeng, Daisuke Miki, Binglian Zheng
Female gametophyte development initiates from the megaspore mother cell (MMC), and only one somatic cell develops into an MMC. Here, we report that the balance between DNA methylation and demethylation ensures the maintenance of a single MMC in Arabidopsis (Arabidopsis thaliana). Surprisingly, a decrease or an increase of all three DNA methylation types (mCG, mCHG, and mCHH) caused abnormal enlargement of MMC-like cells and re-balancing DNA methylation rescued the enlarged MMC-like cellsin the mutants of regulators for DNA methylation and demethylation.. Systematic quantification of DNA methylation at the single-cell level demonstrated that mCHH levels begin to decrease from the central precursor MMC, preceding expression of the MMC marker KNUCKLES(KNU). Disrupting the regulation of DNA methylation caused the mCHH levels to become similar in the MMC and its neighboring cells, and these neighbors usually developed into MMC-like cells. Levels of the de novo DNA methyltransferase DOMAINS REARRANGED METHYLTRANSFERASE2 (DRM2) in the precursor MMC decreased before KNU expression, but the levels of the DNA glycosylase DEMETER decreased after KNU expression. Re-introduction of DRM2 or knockdown of DEMETER specifically in neighboring cells rescued the defects in drm1 drm2 double mutants. Collectively, our findings demonstrate that the balance of DNA methylation, rather than total methylation levels, facilitates maintenance of a single MMC.
{"title":"The DNA methylation–demethylation balance prevents development of multiple megaspore mother cells in Arabidopsis","authors":"Ting Jiang, Lei Li, Qianqian Hu, Xianyu Kuang, Lei Zhang, Wenjie Zeng, Daisuke Miki, Binglian Zheng","doi":"10.1093/plcell/koaf023","DOIUrl":"https://doi.org/10.1093/plcell/koaf023","url":null,"abstract":"Female gametophyte development initiates from the megaspore mother cell (MMC), and only one somatic cell develops into an MMC. Here, we report that the balance between DNA methylation and demethylation ensures the maintenance of a single MMC in Arabidopsis (Arabidopsis thaliana). Surprisingly, a decrease or an increase of all three DNA methylation types (mCG, mCHG, and mCHH) caused abnormal enlargement of MMC-like cells and re-balancing DNA methylation rescued the enlarged MMC-like cellsin the mutants of regulators for DNA methylation and demethylation.. Systematic quantification of DNA methylation at the single-cell level demonstrated that mCHH levels begin to decrease from the central precursor MMC, preceding expression of the MMC marker KNUCKLES(KNU). Disrupting the regulation of DNA methylation caused the mCHH levels to become similar in the MMC and its neighboring cells, and these neighbors usually developed into MMC-like cells. Levels of the de novo DNA methyltransferase DOMAINS REARRANGED METHYLTRANSFERASE2 (DRM2) in the precursor MMC decreased before KNU expression, but the levels of the DNA glycosylase DEMETER decreased after KNU expression. Re-introduction of DRM2 or knockdown of DEMETER specifically in neighboring cells rescued the defects in drm1 drm2 double mutants. Collectively, our findings demonstrate that the balance of DNA methylation, rather than total methylation levels, facilitates maintenance of a single MMC.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"85 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143084094","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}
Jia Dong, Seth W Croslow, Stephan T Lane, Daniel C Castro, Jantana Blanford, Shuaizhen Zhou, Kiyoul Park, Steven Burgess, Mike Root, Edgar Cahoon, John Shanklin, Jonathan V Sweedler, Huimin Zhao, Matthew E Hudson
Plant bioengineering is a time-consuming and labor-intensive process with no guarantee of achieving desired traits. Here, we present a fast, automated, scalable, high-throughput pipeline for plant bioengineering (FAST-PB) in maize (Zea mays) and Nicotiana benthamiana. FAST-PB enables genome editing and product characterization by integrating automated biofoundry engineering of callus and protoplast cells with single-cell matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). We first demonstrated that FAST-PB could streamline Golden Gate cloning, with the capacity to construct 96 vectors in parallel. Using FAST-PB in protoplasts, we found that PEG2050 increased transfection efficiency by over 45%. For proof-of-concept, we established a reporter-gene-free method for CRISPR editing and phenotyping via mutation of high chlorophyl fluorescence 136 (HCF136). We show that diverse lipids were enhanced up to sixfold using CRISPR activation of lipid controlling genes. In callus cells, an automated transformation platform was employed to regenerate plants with enhanced lipid traits through introducing multi-gene cassettes. Lastly, FAST-PB enabled high-throughput single-cell lipid profiling by integrating MALDI-MS with the biofoundry, protoplast, and callus cells, differentiating engineered and unengineered cells using single-cell lipidomics. These innovations massively increase the throughput of synthetic biology, genome editing, and metabolic engineering and change what is possible using single-cell metabolomics in plants.
{"title":"Enhancing lipid production in plant cells through automated high-throughput genome editing and phenotyping","authors":"Jia Dong, Seth W Croslow, Stephan T Lane, Daniel C Castro, Jantana Blanford, Shuaizhen Zhou, Kiyoul Park, Steven Burgess, Mike Root, Edgar Cahoon, John Shanklin, Jonathan V Sweedler, Huimin Zhao, Matthew E Hudson","doi":"10.1093/plcell/koaf026","DOIUrl":"https://doi.org/10.1093/plcell/koaf026","url":null,"abstract":"Plant bioengineering is a time-consuming and labor-intensive process with no guarantee of achieving desired traits. Here, we present a fast, automated, scalable, high-throughput pipeline for plant bioengineering (FAST-PB) in maize (Zea mays) and Nicotiana benthamiana. FAST-PB enables genome editing and product characterization by integrating automated biofoundry engineering of callus and protoplast cells with single-cell matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). We first demonstrated that FAST-PB could streamline Golden Gate cloning, with the capacity to construct 96 vectors in parallel. Using FAST-PB in protoplasts, we found that PEG2050 increased transfection efficiency by over 45%. For proof-of-concept, we established a reporter-gene-free method for CRISPR editing and phenotyping via mutation of high chlorophyl fluorescence 136 (HCF136). We show that diverse lipids were enhanced up to sixfold using CRISPR activation of lipid controlling genes. In callus cells, an automated transformation platform was employed to regenerate plants with enhanced lipid traits through introducing multi-gene cassettes. Lastly, FAST-PB enabled high-throughput single-cell lipid profiling by integrating MALDI-MS with the biofoundry, protoplast, and callus cells, differentiating engineered and unengineered cells using single-cell lipidomics. These innovations massively increase the throughput of synthetic biology, genome editing, and metabolic engineering and change what is possible using single-cell metabolomics in plants.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"82 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143083546","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}
Yun Huang, Jiahui Gao, Guiming Ji, Wenjing Li, Jiaxue Wang, Qinghua Wang, Yuanyue Shen, Jiaxuan Guo, Fan Gao
Polyamines (PAs), such as putrescine, spermidine, and spermine, are essential for plant growth and development. However, the post-translational regulation of PA metabolism remains unknown. Here, we report the COP9 SIGNALOSOME SUBUNIT 5A (FvCSN5A) mediates the degradation of the POLYAMINE OXIDASE 5 (FvPAO5), which catalyzes the conversion of spermidine/spermine to produce H2O2 in strawberry (Fragaria vesca). FvCSN5A is localized in the cytoplasm and nucleus, is ubiquitously expressed in strawberry plants, and is rapidly induced during fruit ripening. FvCSN5A RNA interference (RNAi) transgenic strawberry lines exhibit pleiotropic effects on plant development, fertility, and fruit ripening due to altered PA and H2O2 homeostasis, similar to FvPAO5 transgenic overexpression lines. Moreover, FvCSN5A interacts with FvPAO5 in vitro and in vivo, and the ubiquitination and degradation of FvPAO5 are impaired in FvCSN5A RNAi lines. Additionally, FvCSN5A interacts with cullin 1 (FvCUL1), a core component of the E3 ubiquitin-protein ligase complex. Transient genetic analysis in cultivated strawberry (Fragaria × ananassa) fruits showed that inhibiting FaPAO5 expression could partially rescue the ripening phenotype of FaCSN5A RNAi fruits. Taken together, our results suggest that the CSN5A-CUL1-PAO5 signaling pathway responsible for PA and H2O2 homeostasis is crucial for strawberry vegetative and reproductive growth in particular fruit ripening. Our findings present a promising strategy for improving crop yield and quality.
{"title":"COP9 SIGNALOSOME SUBUNIT 5A facilitates POLYAMINE OXIDASE 5 degradation to regulate strawberry plant growth and fruit ripening","authors":"Yun Huang, Jiahui Gao, Guiming Ji, Wenjing Li, Jiaxue Wang, Qinghua Wang, Yuanyue Shen, Jiaxuan Guo, Fan Gao","doi":"10.1093/plcell/koaf022","DOIUrl":"https://doi.org/10.1093/plcell/koaf022","url":null,"abstract":"Polyamines (PAs), such as putrescine, spermidine, and spermine, are essential for plant growth and development. However, the post-translational regulation of PA metabolism remains unknown. Here, we report the COP9 SIGNALOSOME SUBUNIT 5A (FvCSN5A) mediates the degradation of the POLYAMINE OXIDASE 5 (FvPAO5), which catalyzes the conversion of spermidine/spermine to produce H2O2 in strawberry (Fragaria vesca). FvCSN5A is localized in the cytoplasm and nucleus, is ubiquitously expressed in strawberry plants, and is rapidly induced during fruit ripening. FvCSN5A RNA interference (RNAi) transgenic strawberry lines exhibit pleiotropic effects on plant development, fertility, and fruit ripening due to altered PA and H2O2 homeostasis, similar to FvPAO5 transgenic overexpression lines. Moreover, FvCSN5A interacts with FvPAO5 in vitro and in vivo, and the ubiquitination and degradation of FvPAO5 are impaired in FvCSN5A RNAi lines. Additionally, FvCSN5A interacts with cullin 1 (FvCUL1), a core component of the E3 ubiquitin-protein ligase complex. Transient genetic analysis in cultivated strawberry (Fragaria × ananassa) fruits showed that inhibiting FaPAO5 expression could partially rescue the ripening phenotype of FaCSN5A RNAi fruits. Taken together, our results suggest that the CSN5A-CUL1-PAO5 signaling pathway responsible for PA and H2O2 homeostasis is crucial for strawberry vegetative and reproductive growth in particular fruit ripening. Our findings present a promising strategy for improving crop yield and quality.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143083563","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}
Shiyu Tian, Shen Zhang, Fan Xu, Qingbin Sun, Gang Xu, Min Ni
In Arabidopsis (Arabidopsis thaliana), light and circadian clock signaling converge on PHYTOCHROME-INTERACTING FACTORS (PIFs) 4 and 5 to produce a daily rhythm of hypocotyl elongation. PIF4 and PIF5 expression is repressed at dusk by the evening complex (EC), consisting of EARLY FLOWERING3 (ELF3), ELF4, and LUX ARRHYTHMO (LUX). Here, we report that ELF3 recruits the JUMONJI (JMJ) H3K4me3 demethylases JMJ17 and JMJ18 to the PIF4 and PIF5 loci in the evening to remove their H3K4me3 marks. The association of JMJ17 and JMJ18 with the 2 genomic loci depends on the EC, and the H3K4me3 marks are enriched in the elf3 and jmj17 jmj18 mutants. Half of the globally differentially expressed genes are overlapping in elf3 and jmj17 jmj18. Cleavage Under Targets and Tagmentation sequencing analysis identified 976 H3K4me3-enriched loci in elf3. Aligning the H3K4me3-enriched loci in elf3 to genes with increased expression in elf3 and jmj17 jmj18 identified 179 and 176 target loci, respectively. Half of the loci are targeted by both ELF3 and JMJ17/JMJ18. This suggests a strong connection between the 2 JMJ proteins and EC function. Our studies reveal that an array of key genes in addition to PIF4 and PIF5 are repressed by the EC through the H3K4me3 demethylation pathway.
{"title":"The evening complex component ELF3 recruits H3K4me3 demethylases to repress PHYTOCHROME INTERACTING FACTOR4 and 5 in Arabidopsis","authors":"Shiyu Tian, Shen Zhang, Fan Xu, Qingbin Sun, Gang Xu, Min Ni","doi":"10.1093/plcell/koaf014","DOIUrl":"https://doi.org/10.1093/plcell/koaf014","url":null,"abstract":"In Arabidopsis (Arabidopsis thaliana), light and circadian clock signaling converge on PHYTOCHROME-INTERACTING FACTORS (PIFs) 4 and 5 to produce a daily rhythm of hypocotyl elongation. PIF4 and PIF5 expression is repressed at dusk by the evening complex (EC), consisting of EARLY FLOWERING3 (ELF3), ELF4, and LUX ARRHYTHMO (LUX). Here, we report that ELF3 recruits the JUMONJI (JMJ) H3K4me3 demethylases JMJ17 and JMJ18 to the PIF4 and PIF5 loci in the evening to remove their H3K4me3 marks. The association of JMJ17 and JMJ18 with the 2 genomic loci depends on the EC, and the H3K4me3 marks are enriched in the elf3 and jmj17 jmj18 mutants. Half of the globally differentially expressed genes are overlapping in elf3 and jmj17 jmj18. Cleavage Under Targets and Tagmentation sequencing analysis identified 976 H3K4me3-enriched loci in elf3. Aligning the H3K4me3-enriched loci in elf3 to genes with increased expression in elf3 and jmj17 jmj18 identified 179 and 176 target loci, respectively. Half of the loci are targeted by both ELF3 and JMJ17/JMJ18. This suggests a strong connection between the 2 JMJ proteins and EC function. Our studies reveal that an array of key genes in addition to PIF4 and PIF5 are repressed by the EC through the H3K4me3 demethylation pathway.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"84 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143057036","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}
C4 photosynthesis is a highly efficient form of photosynthesis that utilises a biochemical pump to concentrate CO2 around rubisco. Although variation in the implementation of this biochemical pump exists between species, each variant of the C4 pathway is critically dependent on metabolite transport between organelles and between cells. Here we review our understanding of metabolite transport in C4 photosynthesis. We discuss how the majority of our knowledge of the metabolite transporters co-opted for use in C4 photosynthesis has been obtained from studying C3 plants, and how there is a pressing need for in planta validation of transporter function in C4 species. We further explore the diversity of transport pathways present in disparate C4 lineages and highlight the important gaps in our understanding of metabolite transport in C4 plants. Finally, through integration of functional and transcriptional data from multiple C3 and C4 plants we propose a molecular blueprint for metabolite transport for NAD-ME photosynthesis.
{"title":"The metabolite transporters of C4 photosynthesis.","authors":"Oliver Mattinson, Steven Kelly","doi":"10.1093/plcell/koaf019","DOIUrl":"https://doi.org/10.1093/plcell/koaf019","url":null,"abstract":"C4 photosynthesis is a highly efficient form of photosynthesis that utilises a biochemical pump to concentrate CO2 around rubisco. Although variation in the implementation of this biochemical pump exists between species, each variant of the C4 pathway is critically dependent on metabolite transport between organelles and between cells. Here we review our understanding of metabolite transport in C4 photosynthesis. We discuss how the majority of our knowledge of the metabolite transporters co-opted for use in C4 photosynthesis has been obtained from studying C3 plants, and how there is a pressing need for in planta validation of transporter function in C4 species. We further explore the diversity of transport pathways present in disparate C4 lineages and highlight the important gaps in our understanding of metabolite transport in C4 plants. Finally, through integration of functional and transcriptional data from multiple C3 and C4 plants we propose a molecular blueprint for metabolite transport for NAD-ME photosynthesis.","PeriodicalId":501012,"journal":{"name":"The Plant Cell","volume":"111 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143049915","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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