Pub Date : 2025-02-14DOI: 10.1038/s41477-025-01906-0
Huazhen Liu, Lakshminarayan M. Iyer, Paul Norris, Ruiying Liu, Keshun Yu, Murray Grant, L. Aravind, Aardra Kachroo, Pradeep Kachroo
Dietary consumption of lysine in humans leads to the biosynthesis of Δ1-piperideine-6-carboxylic acid (P6C), with elevated levels linked to the neurological disorder epilepsy. Here we demonstrate that P6C biosynthesis is also a critical component of lysine catabolism in Arabidopsis thaliana. P6C regulates vitamin B6 homeostasis, and increased P6C levels deplete B6 vitamers, resulting in compromised plant immunity. We further establish a key role for pyridoxal and pyridoxal-5-phosphate biosynthesis in plant immunity. Our analysis indicates that P6C metabolism probably evolved through combining select lysine and proline metabolic enzymes horizontally acquired from diverse bacterial sources at different points during evolution. More generally, certain enzymes from the lysine and proline metabolic pathways were probably recruited in evolution as potential guardians of B6 vitamers and for semialdehyde detoxification. This study identifies the conversion of lysine to Δ1-piperideine-6-carboxylic acid (P6C) via pipecolate oxidase as a conserved pathway in plants and humans. P6C interacts with vitamin B6, affecting its homeostasis. Imbalances in vitamin B6 homeostasis disrupt defence in plants and cause neuropathology in humans.
{"title":"Piperideine-6-carboxylic acid regulates vitamin B6 homeostasis and modulates systemic immunity in plants","authors":"Huazhen Liu, Lakshminarayan M. Iyer, Paul Norris, Ruiying Liu, Keshun Yu, Murray Grant, L. Aravind, Aardra Kachroo, Pradeep Kachroo","doi":"10.1038/s41477-025-01906-0","DOIUrl":"10.1038/s41477-025-01906-0","url":null,"abstract":"Dietary consumption of lysine in humans leads to the biosynthesis of Δ1-piperideine-6-carboxylic acid (P6C), with elevated levels linked to the neurological disorder epilepsy. Here we demonstrate that P6C biosynthesis is also a critical component of lysine catabolism in Arabidopsis thaliana. P6C regulates vitamin B6 homeostasis, and increased P6C levels deplete B6 vitamers, resulting in compromised plant immunity. We further establish a key role for pyridoxal and pyridoxal-5-phosphate biosynthesis in plant immunity. Our analysis indicates that P6C metabolism probably evolved through combining select lysine and proline metabolic enzymes horizontally acquired from diverse bacterial sources at different points during evolution. More generally, certain enzymes from the lysine and proline metabolic pathways were probably recruited in evolution as potential guardians of B6 vitamers and for semialdehyde detoxification. This study identifies the conversion of lysine to Δ1-piperideine-6-carboxylic acid (P6C) via pipecolate oxidase as a conserved pathway in plants and humans. P6C interacts with vitamin B6, affecting its homeostasis. Imbalances in vitamin B6 homeostasis disrupt defence in plants and cause neuropathology in humans.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 2","pages":"263-278"},"PeriodicalIF":15.8,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143417549","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}
Pub Date : 2025-02-14DOI: 10.1038/s41477-025-01919-9
Pavel Krupař, Matyáš Fendrych
The acid growth theory states that the auxin-induced acidification of plant cell walls causes their expansion. A model now suggests that excessive acidification leads to growth inhibition, which explains the biphasic response of hypocotyl to auxin.
{"title":"When more becomes too much in acid growth","authors":"Pavel Krupař, Matyáš Fendrych","doi":"10.1038/s41477-025-01919-9","DOIUrl":"10.1038/s41477-025-01919-9","url":null,"abstract":"The acid growth theory states that the auxin-induced acidification of plant cell walls causes their expansion. A model now suggests that excessive acidification leads to growth inhibition, which explains the biphasic response of hypocotyl to auxin.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 2","pages":"155-156"},"PeriodicalIF":15.8,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143417547","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}
Pub Date : 2025-02-11DOI: 10.1038/s41477-025-01924-y
Ming Wang, Yan He, Zhenhui Zhong, Ashot Papikian, Shuya Wang, Jason Gardiner, Basudev Ghoshal, Suhua Feng, Yasaman Jami-Alahmadi, James A. Wohlschlegel, Steven E. Jacobsen
Patterning of DNA methylation in eukaryotic genomes is controlled by de novo methylation, maintenance mechanisms and demethylation pathways. In Arabidopsis thaliana, DNA demethylation enzymes are clearly important for shaping methylation patterns, but how they are regulated is poorly understood. Here we show that the targeting of histone H3 lysine four trimethylation (H3K4me3) with the catalytic domain of the SDG2 histone methyltransferase potently erased DNA methylation and gene silencing at FWA and also erased CG DNA methylation in many other regions of the Arabidopsis genome. This methylation erasure was completely blocked in the ros1 dml2 dml3 triple mutant lacking DNA demethylation enzymes, showing that H3K4me3 promotes the active removal of DNA methylation. Conversely, we found that the targeted removal of H3K4me3 increased the efficiency of targeted DNA methylation. These results highlight H3K4me3 as a potent anti-DNA methylation mark and also pave the way for development of more powerful epigenome engineering tools. This study revealed that targeting H3K4me3 via the H3K4 methyltransferase SDG2 activates gene expression and removes DNA methylation by recruiting DNA demethylases. Conversely, the removal of H3K4me3 synergistically enhances targeted DNA methylation.
{"title":"Histone H3 lysine 4 methylation recruits DNA demethylases to enforce gene expression in Arabidopsis","authors":"Ming Wang, Yan He, Zhenhui Zhong, Ashot Papikian, Shuya Wang, Jason Gardiner, Basudev Ghoshal, Suhua Feng, Yasaman Jami-Alahmadi, James A. Wohlschlegel, Steven E. Jacobsen","doi":"10.1038/s41477-025-01924-y","DOIUrl":"10.1038/s41477-025-01924-y","url":null,"abstract":"Patterning of DNA methylation in eukaryotic genomes is controlled by de novo methylation, maintenance mechanisms and demethylation pathways. In Arabidopsis thaliana, DNA demethylation enzymes are clearly important for shaping methylation patterns, but how they are regulated is poorly understood. Here we show that the targeting of histone H3 lysine four trimethylation (H3K4me3) with the catalytic domain of the SDG2 histone methyltransferase potently erased DNA methylation and gene silencing at FWA and also erased CG DNA methylation in many other regions of the Arabidopsis genome. This methylation erasure was completely blocked in the ros1 dml2 dml3 triple mutant lacking DNA demethylation enzymes, showing that H3K4me3 promotes the active removal of DNA methylation. Conversely, we found that the targeted removal of H3K4me3 increased the efficiency of targeted DNA methylation. These results highlight H3K4me3 as a potent anti-DNA methylation mark and also pave the way for development of more powerful epigenome engineering tools. This study revealed that targeting H3K4me3 via the H3K4 methyltransferase SDG2 activates gene expression and removes DNA methylation by recruiting DNA demethylases. Conversely, the removal of H3K4me3 synergistically enhances targeted DNA methylation.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 2","pages":"206-217"},"PeriodicalIF":15.8,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41477-025-01924-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143385357","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-07DOI: 10.1038/s41477-025-01907-z
Jose Julian, Peng Gao, Alessia Del Chiaro, Juan Carlos De La Concepcion, Laia Armengot, Marc Somssich, Heloise Duverge, Marion Clavel, Nenad Grujic, Roksolana Kobylinska, Ingo Polivka, Maarten Besten, Tonni Grube Andersen, Christian Dank, Barbara Korbei, Andreas Bachmair, Nuria S. Coll, Elena A. Minina, Joris Sprakel, Yasin Dagdas
Vacuoles are essential for cellular metabolism and growth and the maintenance of internal turgor pressure. They sequester lytic enzymes, ions and secondary metabolites that, if leaked into the cytosol, could lead to cell death. Despite their pivotal roles, quality control pathways that safeguard vacuolar integrity have remained elusive in plants. Here we describe a conserved vacuolar quality control pathway that is activated upon cell wall damage in a turgor-pressure-dependent manner. Cell wall perturbations induce a distinct modification—ATG8ylation—on the vacuolar membrane (tonoplast) that is regulated by the V-ATPase and ATG8 conjugation machinery. Genetic disruption of tonoplast ATG8ylation impairs vacuolar integrity, leading to cell death. Together, our findings reveal a homeostatic pathway that preserves vacuolar integrity upon cell wall damage. ATG8ylation of the tonoplast, triggered by cell wall damage, acts as a vital vacuolar quality control mechanism that safeguards vacuolar integrity and ensures cell survival under stress.
{"title":"ATG8ylation of vacuolar membrane protects plants against cell wall damage","authors":"Jose Julian, Peng Gao, Alessia Del Chiaro, Juan Carlos De La Concepcion, Laia Armengot, Marc Somssich, Heloise Duverge, Marion Clavel, Nenad Grujic, Roksolana Kobylinska, Ingo Polivka, Maarten Besten, Tonni Grube Andersen, Christian Dank, Barbara Korbei, Andreas Bachmair, Nuria S. Coll, Elena A. Minina, Joris Sprakel, Yasin Dagdas","doi":"10.1038/s41477-025-01907-z","DOIUrl":"10.1038/s41477-025-01907-z","url":null,"abstract":"Vacuoles are essential for cellular metabolism and growth and the maintenance of internal turgor pressure. They sequester lytic enzymes, ions and secondary metabolites that, if leaked into the cytosol, could lead to cell death. Despite their pivotal roles, quality control pathways that safeguard vacuolar integrity have remained elusive in plants. Here we describe a conserved vacuolar quality control pathway that is activated upon cell wall damage in a turgor-pressure-dependent manner. Cell wall perturbations induce a distinct modification—ATG8ylation—on the vacuolar membrane (tonoplast) that is regulated by the V-ATPase and ATG8 conjugation machinery. Genetic disruption of tonoplast ATG8ylation impairs vacuolar integrity, leading to cell death. Together, our findings reveal a homeostatic pathway that preserves vacuolar integrity upon cell wall damage. ATG8ylation of the tonoplast, triggered by cell wall damage, acts as a vital vacuolar quality control mechanism that safeguards vacuolar integrity and ensures cell survival under stress.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 2","pages":"321-339"},"PeriodicalIF":15.8,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41477-025-01907-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143258459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cell plate formation in plants is a complex process orchestrated by the targeted delivery of Golgi-derived and endosomal vesicles containing cell plate components to the phragmoplast midzone. It has long been hypothesized that vesicles are directionally transported along phragmoplast microtubules by motor proteins. However, the mechanisms governing the accumulation and immobilization of vesicles at the phragmoplast midzone remain elusive, and the motor protein responsible has yet to be identified. Here we show that the plant-specific class II kinesin-12 (kinesin12-II) functions as a motor protein that drives vesicle transport towards the phragmoplast midzone in the moss Physcomitrium patens. In the kinesin12-II mutant, the directional movement of cell plate materials towards the midzone and their retention were abolished, resulting in delayed cell plate formation and phragmoplast disassembly. A macroscopic phenotype arising from kinesin12-II disruption was the impediment to gametophore development. We showed that this defect was attributable to the production of aneuploid and polyploid cells in the early gametophore, where chromosome missegregation and cytokinesis failure occurred. These findings suggest that plant kinesin-12 has evolved to acquire a unique and critical function that facilitates cell plate formation in the presence of phragmoplasts. Class II kinesin-12 is responsible for transporting vesicles containing cell plate materials along phragmoplast microtubules towards the midzone, facilitating efficient cell plate formation during cytokinesis and enabling sequential cell division during multicellular organ development.
{"title":"Class II kinesin-12 facilitates cell plate formation by transporting cell plate materials in the phragmoplast","authors":"Moé Yamada, Hironori J. Matsuyama, Noriko Takeda-Kamiya, Mayuko Sato, Kiminori Toyooka","doi":"10.1038/s41477-025-01909-x","DOIUrl":"10.1038/s41477-025-01909-x","url":null,"abstract":"Cell plate formation in plants is a complex process orchestrated by the targeted delivery of Golgi-derived and endosomal vesicles containing cell plate components to the phragmoplast midzone. It has long been hypothesized that vesicles are directionally transported along phragmoplast microtubules by motor proteins. However, the mechanisms governing the accumulation and immobilization of vesicles at the phragmoplast midzone remain elusive, and the motor protein responsible has yet to be identified. Here we show that the plant-specific class II kinesin-12 (kinesin12-II) functions as a motor protein that drives vesicle transport towards the phragmoplast midzone in the moss Physcomitrium patens. In the kinesin12-II mutant, the directional movement of cell plate materials towards the midzone and their retention were abolished, resulting in delayed cell plate formation and phragmoplast disassembly. A macroscopic phenotype arising from kinesin12-II disruption was the impediment to gametophore development. We showed that this defect was attributable to the production of aneuploid and polyploid cells in the early gametophore, where chromosome missegregation and cytokinesis failure occurred. These findings suggest that plant kinesin-12 has evolved to acquire a unique and critical function that facilitates cell plate formation in the presence of phragmoplasts. Class II kinesin-12 is responsible for transporting vesicles containing cell plate materials along phragmoplast microtubules towards the midzone, facilitating efficient cell plate formation during cytokinesis and enabling sequential cell division during multicellular organ development.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 2","pages":"340-358"},"PeriodicalIF":15.8,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143083417","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}
Pub Date : 2025-02-03DOI: 10.1038/s41477-025-01926-w
Patricia Baldrich
A groundbreaking study reveals how pseudouridine modifications across plant RNA species orchestrate translation dynamics, and provides a comprehensive atlas of these modifications in four major crop species. This discovery illuminates a crucial mechanism that controls translation and tissue development in plants.
{"title":"Pseudouridine is the hidden language of plant RNA translation","authors":"Patricia Baldrich","doi":"10.1038/s41477-025-01926-w","DOIUrl":"10.1038/s41477-025-01926-w","url":null,"abstract":"A groundbreaking study reveals how pseudouridine modifications across plant RNA species orchestrate translation dynamics, and provides a comprehensive atlas of these modifications in four major crop species. This discovery illuminates a crucial mechanism that controls translation and tissue development in plants.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 2","pages":"151-152"},"PeriodicalIF":15.8,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143077617","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}
Legumes form root nodules with symbiotic nitrogen-fixing rhizobacteria, which require ample iron to ensure symbiosis establishment and efficient nitrogen fixation. The functions and mechanisms of iron in nitrogen-fixing nodules are well established. However, the role of iron and the mechanisms by which legumes sense iron and incorporate this cue into nodulation signalling pathways remain unclear. Here we show that iron is a key driver of nodulation because symbiotic nodules cannot form without iron, even under conditions of sufficient light and low nitrogen. We further identify an iron optimum for soybean nodulation and the iron sensor BRUTUS A (BTSa) which acts as a hub for integrating iron and nodulation cues. BTSa is induced by rhizobia, binds to and is stabilized by iron. In turn, BTSa stabilizes and enhances the transcriptional activation activity of pro-nodulation transcription factor NSP1a by monoubiquitination from its RING domain and consequently activates nodulation signalling. Monoubiquitination of NSP1 by BTS is conserved in legumes to trigger nodulation under iron sufficiency. Thus, iron status is an essential cue to trigger nodulation and BTSa integrates cues from rhizobial infection and iron status to orchestrate host responses towards establishing symbiotic nitrogen fixation. The authors report that iron binds to and stabilizes the iron sensor BRUTUS A (BTSa), which monoubiquitinates the pro-nodulation transcription factor NSP1a to increase its stability and transcriptional activity, thereby regulating nodulation in legumes.
{"title":"The BRUTUS iron sensor and E3 ligase facilitates soybean root nodulation by monoubiquitination of NSP1","authors":"Ziyin Ren, Ling Zhang, Haizhen Li, Mi Yang, Xuesong Wu, Runxu Hu, Jingjing Lu, Hui Wang, Xinying Wu, Zhijuan Wang, Xia Li","doi":"10.1038/s41477-024-01896-5","DOIUrl":"10.1038/s41477-024-01896-5","url":null,"abstract":"Legumes form root nodules with symbiotic nitrogen-fixing rhizobacteria, which require ample iron to ensure symbiosis establishment and efficient nitrogen fixation. The functions and mechanisms of iron in nitrogen-fixing nodules are well established. However, the role of iron and the mechanisms by which legumes sense iron and incorporate this cue into nodulation signalling pathways remain unclear. Here we show that iron is a key driver of nodulation because symbiotic nodules cannot form without iron, even under conditions of sufficient light and low nitrogen. We further identify an iron optimum for soybean nodulation and the iron sensor BRUTUS A (BTSa) which acts as a hub for integrating iron and nodulation cues. BTSa is induced by rhizobia, binds to and is stabilized by iron. In turn, BTSa stabilizes and enhances the transcriptional activation activity of pro-nodulation transcription factor NSP1a by monoubiquitination from its RING domain and consequently activates nodulation signalling. Monoubiquitination of NSP1 by BTS is conserved in legumes to trigger nodulation under iron sufficiency. Thus, iron status is an essential cue to trigger nodulation and BTSa integrates cues from rhizobial infection and iron status to orchestrate host responses towards establishing symbiotic nitrogen fixation. The authors report that iron binds to and stabilizes the iron sensor BRUTUS A (BTSa), which monoubiquitinates the pro-nodulation transcription factor NSP1a to increase its stability and transcriptional activity, thereby regulating nodulation in legumes.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 3","pages":"595-611"},"PeriodicalIF":15.8,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143077618","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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