Pub Date : 2025-11-14DOI: 10.1038/s41477-025-02151-1
Lingling Ye, Xin Wang, Juan José Valle-Delgado, Julia P. Vainonen, Isaac Wopereis, Kavindra Kumar Kesari, Junko Takahashi, Maija Sierla, Ari Pekka Mähönen
Plant growth originates from the interlinked action of cell division and cell growth. During radial growth of secondary tissues, bifacial cambial stem cells grow and divide to produce xylem and phloem precursors, which subsequently undergo expansion characteristic of their respective differentiation processes. In Arabidopsis roots, cytokinins and four downstream LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factors are key players in promoting radial growth, though the underlying mechanisms remain unknown. Here our results indicate that these LBD genes primarily regulate cell growth rather than proliferation. Through a large-scale CRISPR–Cas9-aided reverse genetic screen, we identified a set of PECTATE LYASE-LIKE (PLL) genes that function downstream of cytokinin and the LBDs in the regulation of radial growth. We show that at least one of these PLLs, PLL18, possesses pectate lyase activity. In accordance with this activity, PLLs and LBDs promote radial growth by modifying the pectin composition and mechanical properties of the primary cell wall. Our findings thus connect the central role of cytokinins in radial growth with cell wall remodelling and pave a way for further research on hormone-mediated plant growth regulation and cell wall metabolism. This study reveals that LBD transcription factors in the cambium drive radial plant growth by regulating PECTATE LYASE-LIKE (PLL) enzymes that remodel cell wall pectin, promoting cell expansion.
{"title":"Cambium LBDs promote radial growth by regulating PLL-mediated pectin metabolism","authors":"Lingling Ye, Xin Wang, Juan José Valle-Delgado, Julia P. Vainonen, Isaac Wopereis, Kavindra Kumar Kesari, Junko Takahashi, Maija Sierla, Ari Pekka Mähönen","doi":"10.1038/s41477-025-02151-1","DOIUrl":"10.1038/s41477-025-02151-1","url":null,"abstract":"Plant growth originates from the interlinked action of cell division and cell growth. During radial growth of secondary tissues, bifacial cambial stem cells grow and divide to produce xylem and phloem precursors, which subsequently undergo expansion characteristic of their respective differentiation processes. In Arabidopsis roots, cytokinins and four downstream LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factors are key players in promoting radial growth, though the underlying mechanisms remain unknown. Here our results indicate that these LBD genes primarily regulate cell growth rather than proliferation. Through a large-scale CRISPR–Cas9-aided reverse genetic screen, we identified a set of PECTATE LYASE-LIKE (PLL) genes that function downstream of cytokinin and the LBDs in the regulation of radial growth. We show that at least one of these PLLs, PLL18, possesses pectate lyase activity. In accordance with this activity, PLLs and LBDs promote radial growth by modifying the pectin composition and mechanical properties of the primary cell wall. Our findings thus connect the central role of cytokinins in radial growth with cell wall remodelling and pave a way for further research on hormone-mediated plant growth regulation and cell wall metabolism. This study reveals that LBD transcription factors in the cambium drive radial plant growth by regulating PECTATE LYASE-LIKE (PLL) enzymes that remodel cell wall pectin, promoting cell expansion.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 12","pages":"2565-2580"},"PeriodicalIF":13.6,"publicationDate":"2025-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41477-025-02151-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145509226","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 : 2025-11-13DOI: 10.1038/s41477-025-02145-z
Frej Tulin, Yalikunjiang Aizezi, Andres V. Reyes, Yuji Fujieda, Arthur Grossman, Shou-ling Xu, Masayuki Onishi, Farhah F. Assaad, Zhi-Yong Wang
Cell cycle regulation is well understood in opisthokonts (fungi and metazoans) but not in plants or Apicomplexa, as some cell cycle regulators are not conserved. In opisthokonts, cell cycle progression requires the dephosphorylation of cyclin-dependent kinase (CDK) by the CDC25 phosphatase. Plants have no CDC25, and thus their mechanisms of cell cycle regulation remain elusive. Here we show that the BSL1 phosphatase dephosphorylates CDKB1 to promote mitotic entry in Chlamydomonas. Alterations of BSL1 or CDKB1 block mitotic entry after DNA replication. BSL1 shows dynamic localization through the cell cycle at the basal bodies, spindle poles and cleavage furrow. CDKB1 is hyperphosphorylated at the Thr14 and Tyr15 residues in the bsl1 mutant and in wild-type cells treated with DNA replication inhibitors. BSL1 binds to CDKB1 and dephosphorylates CDKB1 pThr14/pTyr15 in vitro. Phospho-mimicking alterations of Thr14/Tyr15 inactivate CDKB1 function, whereas phospho-blocking alterations cause sensitivity to DNA replication inhibitors, which delay cytokinesis in wild-type cells more than in cells expressing unphosphorylatable mutant CDKB1. These results indicate that CDKB1 Thr14 and Tyr15 are phosphorylated to block mitotic entry before DNA replication is complete, and BSL1 dephosphorylates CDKB1 to promote mitosis. Our study demonstrates that BSL1, a phosphatase conserved in plants and Apicomplexa but absent in fungi and animals, is a CDKB1-activating mitosis-promoting factor that has evolved additional signalling functions in receptor kinase pathways in higher plants. The mechanism controlling mitosis is not understood in plants. Tulin et al. show that mitosis is prevented by CDKB phosphorylation and promoted by BSL1-mediated dephosphorylation, revealing the mechanism of mitotic control in the plant kingdom.
{"title":"Mitotic entry is controlled by the plant-specific phosphatase BSL1 and cyclin-dependent kinase B","authors":"Frej Tulin, Yalikunjiang Aizezi, Andres V. Reyes, Yuji Fujieda, Arthur Grossman, Shou-ling Xu, Masayuki Onishi, Farhah F. Assaad, Zhi-Yong Wang","doi":"10.1038/s41477-025-02145-z","DOIUrl":"10.1038/s41477-025-02145-z","url":null,"abstract":"Cell cycle regulation is well understood in opisthokonts (fungi and metazoans) but not in plants or Apicomplexa, as some cell cycle regulators are not conserved. In opisthokonts, cell cycle progression requires the dephosphorylation of cyclin-dependent kinase (CDK) by the CDC25 phosphatase. Plants have no CDC25, and thus their mechanisms of cell cycle regulation remain elusive. Here we show that the BSL1 phosphatase dephosphorylates CDKB1 to promote mitotic entry in Chlamydomonas. Alterations of BSL1 or CDKB1 block mitotic entry after DNA replication. BSL1 shows dynamic localization through the cell cycle at the basal bodies, spindle poles and cleavage furrow. CDKB1 is hyperphosphorylated at the Thr14 and Tyr15 residues in the bsl1 mutant and in wild-type cells treated with DNA replication inhibitors. BSL1 binds to CDKB1 and dephosphorylates CDKB1 pThr14/pTyr15 in vitro. Phospho-mimicking alterations of Thr14/Tyr15 inactivate CDKB1 function, whereas phospho-blocking alterations cause sensitivity to DNA replication inhibitors, which delay cytokinesis in wild-type cells more than in cells expressing unphosphorylatable mutant CDKB1. These results indicate that CDKB1 Thr14 and Tyr15 are phosphorylated to block mitotic entry before DNA replication is complete, and BSL1 dephosphorylates CDKB1 to promote mitosis. Our study demonstrates that BSL1, a phosphatase conserved in plants and Apicomplexa but absent in fungi and animals, is a CDKB1-activating mitosis-promoting factor that has evolved additional signalling functions in receptor kinase pathways in higher plants. The mechanism controlling mitosis is not understood in plants. Tulin et al. show that mitosis is prevented by CDKB phosphorylation and promoted by BSL1-mediated dephosphorylation, revealing the mechanism of mitotic control in the plant kingdom.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 11","pages":"2395-2408"},"PeriodicalIF":13.6,"publicationDate":"2025-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41477-025-02145-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145498267","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}
Plant guard cells perceive pathogens and close stomata to prevent their invasion. Biomolecular condensates are membraneless organelles essential for life processes. However, guard cell biomolecular condensates mediating stomatal immunity remain unknown. Here we identify a guard-cell-preferential RNA-recognition-motif-type RNA-BINDING PROTEIN, STOMATAL IMMUNE RNA-BINDING PROTEIN 1 (SAIR1), that forms pathogen-responsive guard cell condensates via phase separation. Upon perception of the pathogen molecular pattern flg22, the activated kinases MPK3 and MPK6 phosphorylate SAIR1 and trigger its condensation in guard cells for stomatal immunity. SAIR1 condensates recruit translational regulators such as POLYADENYLATE-BINDING PROTEINs and eIFiso4G, and sequester defence-related mRNAs, including key components of the salicylic acid pathway. Through these interactions, SAIR1 condensates enhance the translation of defence mRNAs, ultimately promoting stomatal closure. Our findings reveal phosphorylation-regulated SAIR1 condensates as a critical hub that links flg22–MPK3/6 signalling to stomatal immunity. The RNA-binding protein SAIR1 forms phosphorylation-regulated condensates in guard cells, which link PAMP–MPK3/6 signalling to stomatal immunity. This finding reveals how biomolecular condensates regulate spatially specific immune responses in plants.
{"title":"Pathogen-induced condensation of the guard cell RNA-binding protein SAIR1 fine-tunes translation for immunity","authors":"Qiangsheng Yu, Jie Wu, Yunfan Jin, Tianxue Song, Wenrui Wang, Yuejuan Zeng, Huang Huang, Haiteng Deng, Wei Wang, Jianghui Xie, Zhi John Lu, Xiaofeng Fang, Susheng Song, Tiancong Qi","doi":"10.1038/s41477-025-02154-y","DOIUrl":"10.1038/s41477-025-02154-y","url":null,"abstract":"Plant guard cells perceive pathogens and close stomata to prevent their invasion. Biomolecular condensates are membraneless organelles essential for life processes. However, guard cell biomolecular condensates mediating stomatal immunity remain unknown. Here we identify a guard-cell-preferential RNA-recognition-motif-type RNA-BINDING PROTEIN, STOMATAL IMMUNE RNA-BINDING PROTEIN 1 (SAIR1), that forms pathogen-responsive guard cell condensates via phase separation. Upon perception of the pathogen molecular pattern flg22, the activated kinases MPK3 and MPK6 phosphorylate SAIR1 and trigger its condensation in guard cells for stomatal immunity. SAIR1 condensates recruit translational regulators such as POLYADENYLATE-BINDING PROTEINs and eIFiso4G, and sequester defence-related mRNAs, including key components of the salicylic acid pathway. Through these interactions, SAIR1 condensates enhance the translation of defence mRNAs, ultimately promoting stomatal closure. Our findings reveal phosphorylation-regulated SAIR1 condensates as a critical hub that links flg22–MPK3/6 signalling to stomatal immunity. The RNA-binding protein SAIR1 forms phosphorylation-regulated condensates in guard cells, which link PAMP–MPK3/6 signalling to stomatal immunity. This finding reveals how biomolecular condensates regulate spatially specific immune responses in plants.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 12","pages":"2548-2564"},"PeriodicalIF":13.6,"publicationDate":"2025-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145498266","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 : 2025-11-12DOI: 10.1038/s41477-025-02146-y
Julia M. Kraus, Michaela Neubergerová, Alvaro Furones Cuadrado, Neeltje Schilling, Dominique Eeckhout, Nancy De Winne, Eveline Van De Slijke, Michaël Vandorpe, Klaas Yperman, Evelien Mylle, Marcus Fislage, Geert De Jaeger, Roman Pleskot, Daniël Van Damme
Eukaryotic cells maintain homeostasis of their outer membrane by controlled internalization of lipid and protein constituents via endocytosis. Endocytosis is evolutionary conserved and uses similarly folded domains. How these structural folds are combined into proteins and protein complexes, however, differs between eukaryotic kingdoms. The TPLATE complex (TPC) in plants is an evolutionary ancient protein module that combines several protein domains with a conserved role in endocytosis into a single octameric protein complex. Its molecular architecture, lipid-nucleated condensate formation and requirement for clathrin cage curvature revealed its function in endocytosis initiation in plants. Mechanistic understanding of how this complex drives membrane deformation during plant endocytosis is, however, lacking. Here we used an integrative structural approach to obtain a precise molecular structure of the TPC of Arabidopsis thaliana. In addition, our approach allowed visualizing the structural flexibility that hallmarks this enigmatic complex. We prove that the intrinsic structural flexibility is required for its functionality and membrane recruitment. The membrane-binding interface consists of several domains with differential lipid preferences. Finally, we demonstrate via molecular dynamics simulations that the crescent shape of the structured part of the complex is sufficient for membrane curvature generation. Our mechanistic insight, obtained by a combined biochemical and computational approach, shows that the structured part of the TPC likely contributes to the execution of plant endocytosis, which does not depend on cytoskeletal-based force generation. The manuscript uses an integrative approach to generate a comprehensive structure of the multisubunit endocytic TPLATE complex and to study its membrane targeting and its role in membrane deformation during the initial phase of plant endocytosis.
{"title":"A combined biochemical and computational approach provides evidence for membrane remodelling by the structural scaffold of the endocytic TPLATE complex","authors":"Julia M. Kraus, Michaela Neubergerová, Alvaro Furones Cuadrado, Neeltje Schilling, Dominique Eeckhout, Nancy De Winne, Eveline Van De Slijke, Michaël Vandorpe, Klaas Yperman, Evelien Mylle, Marcus Fislage, Geert De Jaeger, Roman Pleskot, Daniël Van Damme","doi":"10.1038/s41477-025-02146-y","DOIUrl":"10.1038/s41477-025-02146-y","url":null,"abstract":"Eukaryotic cells maintain homeostasis of their outer membrane by controlled internalization of lipid and protein constituents via endocytosis. Endocytosis is evolutionary conserved and uses similarly folded domains. How these structural folds are combined into proteins and protein complexes, however, differs between eukaryotic kingdoms. The TPLATE complex (TPC) in plants is an evolutionary ancient protein module that combines several protein domains with a conserved role in endocytosis into a single octameric protein complex. Its molecular architecture, lipid-nucleated condensate formation and requirement for clathrin cage curvature revealed its function in endocytosis initiation in plants. Mechanistic understanding of how this complex drives membrane deformation during plant endocytosis is, however, lacking. Here we used an integrative structural approach to obtain a precise molecular structure of the TPC of Arabidopsis thaliana. In addition, our approach allowed visualizing the structural flexibility that hallmarks this enigmatic complex. We prove that the intrinsic structural flexibility is required for its functionality and membrane recruitment. The membrane-binding interface consists of several domains with differential lipid preferences. Finally, we demonstrate via molecular dynamics simulations that the crescent shape of the structured part of the complex is sufficient for membrane curvature generation. Our mechanistic insight, obtained by a combined biochemical and computational approach, shows that the structured part of the TPC likely contributes to the execution of plant endocytosis, which does not depend on cytoskeletal-based force generation. The manuscript uses an integrative approach to generate a comprehensive structure of the multisubunit endocytic TPLATE complex and to study its membrane targeting and its role in membrane deformation during the initial phase of plant endocytosis.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 11","pages":"2423-2436"},"PeriodicalIF":13.6,"publicationDate":"2025-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145492617","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 : 2025-11-10DOI: 10.1038/s41477-025-02147-x
Xiaoxia Gao, Dianye Zhang, Yunfeng Peng, Josep Peñuelas, Yann Hautier, Michel Loreau, Yaping Niu, Shiting Yao, Zan Wu, Qinlu Li, Lina Zhou, Yang Liu, Xuning Liu, Bin Wei, Shuqi Qin, Yutong Song, Luyao Kang, Lin Jiang, Shaopeng Wang, Yuanhe Yang
Biodiversity is known to promote ecosystem multifunctionality (EMF), but how grassland degradation influences the relationship between biodiversity and EMF remains unclear. Here, using paired observations at 44 sites (a total of 792 sampling quadrats) along a 2,600 km transect, we test how moderate grassland degradation influences 20 surrogates of ecosystem functions, EMF, plant richness, soil bacterial, fungal and protist richness, and biodiversity–EMF relationships in Tibetan alpine grasslands. Our results reveal significant declines in individual ecosystem functions and EMF with moderate grassland degradation. By contrast, both plant richness and integrated soil biodiversity exhibit significant increases. The structural equation models analyses show that following degradation, the effect of soil biodiversity on EMF strengthens, whereas that of plant richness weakens. These findings offer large-scale empirical evidence that moderate grassland degradation can amplify both soil biodiversity and its functional importance, emphasizing the key role of below-ground biodiversity in supporting ecosystem functioning in degraded grasslands. This study reports that grassland degradation reduces ecosystem functionality while promoting soil biodiversity, highlighting the role of this diversity in sustaining degraded grasslands.
{"title":"Grassland degradation alters plant and soil biodiversity–multifunctionality relationships","authors":"Xiaoxia Gao, Dianye Zhang, Yunfeng Peng, Josep Peñuelas, Yann Hautier, Michel Loreau, Yaping Niu, Shiting Yao, Zan Wu, Qinlu Li, Lina Zhou, Yang Liu, Xuning Liu, Bin Wei, Shuqi Qin, Yutong Song, Luyao Kang, Lin Jiang, Shaopeng Wang, Yuanhe Yang","doi":"10.1038/s41477-025-02147-x","DOIUrl":"10.1038/s41477-025-02147-x","url":null,"abstract":"Biodiversity is known to promote ecosystem multifunctionality (EMF), but how grassland degradation influences the relationship between biodiversity and EMF remains unclear. Here, using paired observations at 44 sites (a total of 792 sampling quadrats) along a 2,600 km transect, we test how moderate grassland degradation influences 20 surrogates of ecosystem functions, EMF, plant richness, soil bacterial, fungal and protist richness, and biodiversity–EMF relationships in Tibetan alpine grasslands. Our results reveal significant declines in individual ecosystem functions and EMF with moderate grassland degradation. By contrast, both plant richness and integrated soil biodiversity exhibit significant increases. The structural equation models analyses show that following degradation, the effect of soil biodiversity on EMF strengthens, whereas that of plant richness weakens. These findings offer large-scale empirical evidence that moderate grassland degradation can amplify both soil biodiversity and its functional importance, emphasizing the key role of below-ground biodiversity in supporting ecosystem functioning in degraded grasslands. This study reports that grassland degradation reduces ecosystem functionality while promoting soil biodiversity, highlighting the role of this diversity in sustaining degraded grasslands.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 12","pages":"2487-2497"},"PeriodicalIF":13.6,"publicationDate":"2025-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145478095","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 : 2025-11-10DOI: 10.1038/s41477-025-02164-w
Guillaume Tena
{"title":"Engineering RLP receptors from the C side","authors":"Guillaume Tena","doi":"10.1038/s41477-025-02164-w","DOIUrl":"10.1038/s41477-025-02164-w","url":null,"abstract":"","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 11","pages":"2188-2188"},"PeriodicalIF":13.6,"publicationDate":"2025-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145478130","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 : 2025-11-07DOI: 10.1038/s41477-025-02148-w
Pierre Bourguet, Zdravko J. Lorković, Darya Kripkiy Casado, Valentin Bapteste, Chung Hyun Cho, Anna A. Igolkina, Cheng-Ruei Lee, Magnus Nordborg, Frédéric Berger, Eriko Sasaki
DNA methylation is a key epigenetic mark that impacts gene expression and represses transposable elements in eukaryotes. Numerous examples of cis elements targeted by DNA methylation, particularly at CG sites (mCG), have been reported to be under selective pressure in animals and plants. By contrast, there is limited knowledge of trans regulators of mCG leading to adaptation. Here, a genome-wide association study identifies CELL DIVISION CYCLE-ASSOCIATED PROTEIN 7 (CDCA7) as a major trans determinant of mCG in natural populations of Arabidopsis thaliana. CDCA7 or its paralogue physically binds the chromatin remodeller DECREASE IN DNA METHYLATION 1 (DDM1), which facilitates access of methyltransferases to DNA. Epigenomic analysis shows that while CDCA7 proteins control all DDM1-dependent processes, their predominant function is the maintenance of mCG. We identify a 26-bp promoter indel modulating CDCA7 expression in natural populations and determining the degree of mCG and transposable element silencing. The geographic distribution of CDCA7 alleles suggests that new alleles have repeatedly expanded to novel ecological niches, indicating a potential role in local adaptation. Our findings establish CDCA7 proteins as dedicated regulators of mCG and imply that DDM1 relies on alternative partners to regulate other chromatin features. Broadly, they illustrate how changes in global DNA methylation levels through transcriptional regulation of the epigenetic machinery have the capacity to facilitate local adaptation. This genome-wide association study identifies CELL DIVISION CYCLE-ASSOCIATED PROTEIN 7 (CDCA7) as a regulator of DNA methylation in natural Arabidopsis thaliana populations. CDCA7 binds the chromatin remodeller DDM1 and modulates the control of CG methylation.
{"title":"Major alleles of CDCA7 shape CG methylation in Arabidopsis thaliana","authors":"Pierre Bourguet, Zdravko J. Lorković, Darya Kripkiy Casado, Valentin Bapteste, Chung Hyun Cho, Anna A. Igolkina, Cheng-Ruei Lee, Magnus Nordborg, Frédéric Berger, Eriko Sasaki","doi":"10.1038/s41477-025-02148-w","DOIUrl":"10.1038/s41477-025-02148-w","url":null,"abstract":"DNA methylation is a key epigenetic mark that impacts gene expression and represses transposable elements in eukaryotes. Numerous examples of cis elements targeted by DNA methylation, particularly at CG sites (mCG), have been reported to be under selective pressure in animals and plants. By contrast, there is limited knowledge of trans regulators of mCG leading to adaptation. Here, a genome-wide association study identifies CELL DIVISION CYCLE-ASSOCIATED PROTEIN 7 (CDCA7) as a major trans determinant of mCG in natural populations of Arabidopsis thaliana. CDCA7 or its paralogue physically binds the chromatin remodeller DECREASE IN DNA METHYLATION 1 (DDM1), which facilitates access of methyltransferases to DNA. Epigenomic analysis shows that while CDCA7 proteins control all DDM1-dependent processes, their predominant function is the maintenance of mCG. We identify a 26-bp promoter indel modulating CDCA7 expression in natural populations and determining the degree of mCG and transposable element silencing. The geographic distribution of CDCA7 alleles suggests that new alleles have repeatedly expanded to novel ecological niches, indicating a potential role in local adaptation. Our findings establish CDCA7 proteins as dedicated regulators of mCG and imply that DDM1 relies on alternative partners to regulate other chromatin features. Broadly, they illustrate how changes in global DNA methylation levels through transcriptional regulation of the epigenetic machinery have the capacity to facilitate local adaptation. This genome-wide association study identifies CELL DIVISION CYCLE-ASSOCIATED PROTEIN 7 (CDCA7) as a regulator of DNA methylation in natural Arabidopsis thaliana populations. CDCA7 binds the chromatin remodeller DDM1 and modulates the control of CG methylation.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 12","pages":"2511-2530"},"PeriodicalIF":13.6,"publicationDate":"2025-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41477-025-02148-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145455694","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 : 2025-11-06DOI: 10.1038/s41477-025-02139-x
Despite the extensive use of Arabidopsis thaliana as a model system, parts of its biology remain unknown, including the architecture of its largest cellular protein assembly, the nuclear pore complex (NPC). Using cryo-electron tomography, we have obtained the three-dimensional architecture of the A. thaliana NPC, which suggests it has both conserved and distinct features.
{"title":"The Arabidopsis thaliana nuclear pore complex structure reveals conserved and distinct features","authors":"","doi":"10.1038/s41477-025-02139-x","DOIUrl":"10.1038/s41477-025-02139-x","url":null,"abstract":"Despite the extensive use of Arabidopsis thaliana as a model system, parts of its biology remain unknown, including the architecture of its largest cellular protein assembly, the nuclear pore complex (NPC). Using cryo-electron tomography, we have obtained the three-dimensional architecture of the A. thaliana NPC, which suggests it has both conserved and distinct features.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 11","pages":"2198-2199"},"PeriodicalIF":13.6,"publicationDate":"2025-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145447268","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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