Nature PlantsPub Date : 2025-07-22DOI: 10.1038/s41477-025-02053-2
Ping Xu, Sophia Fundneider, Birgit Lange, Rafał Maksym, Johannes Stuttmann, Anton R. Schäffner
{"title":"A root-based N-hydroxypipecolic acid standby circuit to direct immunity and growth of Arabidopsis shoots","authors":"Ping Xu, Sophia Fundneider, Birgit Lange, Rafał Maksym, Johannes Stuttmann, Anton R. Schäffner","doi":"10.1038/s41477-025-02053-2","DOIUrl":"https://doi.org/10.1038/s41477-025-02053-2","url":null,"abstract":"<p>Soil-borne microorganisms can systemically affect shoot resistance to pathogens relying on jasmonic acid and/or salicylic acid. However, the emanating root triggers in these scenarios remain elusive. Here we identify an <i>N</i>-hydroxypipecolic-acid-(NHP-)directed, salicylic-acid-related mechanism of root-triggered systemic resistance in <i>Arabidopsis</i>, which uses components of systemic acquired resistance known in leaves. However, in contrast to the inductive nature of systemic acquired resistance, FLAVIN-DEPENDENT MONOOXYGENASE 1 (FMO1) continuously synthesizes NHP in roots, while the glucosyltransferase UGT76B1 concomitantly conjugates and immobilizes NHP. Physical grafting experiments and tissue-specific knockouts revealed that the loss of UGT76B1 in roots leads to enhanced NHP release, initiating shoot responses. This counteracting standby FMO1/UGT76B1 circuit is specifically and sensitively modulated by root-associated microorganisms. Endophytic and (hemi)biotrophic fungi induce UGT76B1 degradation and FMO1 expression, resulting in varying levels of NHP being released to the shoot, where this root signal differently modulates defence and growth.</p>","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"98 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144677302","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}
Nature PlantsPub Date : 2025-07-21DOI: 10.1038/s41477-025-02075-w
{"title":"The human factor","authors":"","doi":"10.1038/s41477-025-02075-w","DOIUrl":"https://doi.org/10.1038/s41477-025-02075-w","url":null,"abstract":"Plant science is, as yet, conducted not by large language models or artificial intelligence, but by people. From this month, Nature Plants will be publishing pieces specifically focused on the personal side of research and researchers.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"102 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144677679","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}
Nature PlantsPub Date : 2025-07-21DOI: 10.1038/s41477-025-02063-0
Catherine Walker
{"title":"Creating resilience through agroforestry","authors":"Catherine Walker","doi":"10.1038/s41477-025-02063-0","DOIUrl":"https://doi.org/10.1038/s41477-025-02063-0","url":null,"abstract":"Aster Gebrekirstos is a senior scientist at the Center for International Forestry Research and World Agroforestry (CIFOR-ICRAF). Her multidisciplinary work in agroforestry, dendrochronology and forest ecology examines how trees respond to climate change. Aster talks to Nature Plants about the importance of putting people at the heart of her research.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"10 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144677689","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}
Nature PlantsPub Date : 2025-07-21DOI: 10.1038/s41477-025-02071-0
John J. Ross
{"title":"Beyond the identification of Mendel’s genes","authors":"John J. Ross","doi":"10.1038/s41477-025-02071-0","DOIUrl":"https://doi.org/10.1038/s41477-025-02071-0","url":null,"abstract":"After a long hiatus, a recent paper identifies the molecular basis of Mendel’s remaining three traits and demonstrates that the genes concerned are major contributors to phenotypic variation in pea.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"33 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144669623","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}
Nature PlantsPub Date : 2025-07-17DOI: 10.1038/s41477-025-02069-8
Guillaume Tena
{"title":"Edible second-hand solar panels","authors":"Guillaume Tena","doi":"10.1038/s41477-025-02069-8","DOIUrl":"https://doi.org/10.1038/s41477-025-02069-8","url":null,"abstract":"<p>This transient endosymbiotic process, reminiscent of the primary incorporation of organelles that gave birth to eukaryotic cells, is called kleptoplasty. While it has been known for a long time, a recent study in <i>Cell</i> reveals intricate new details of the molecular mechanisms behind this association, which can last for a year and increase survival in case of starvation.</p><p>In the sea slug <i>Elysia crispata</i>, the stolen chloroplasts are highly concentrated in regulated specialized cells named plastid cells, localized around the body surface to better catch the light. The thylakoid stack ultrastructure is conserved and functional, despite the lack of the algal nuclear genome to provide needed maintenance proteins. Each chloroplast is individually wrapped in a membrane containing ATP-sensitive ion channels, forming organelles named kleptosomes, and actively kept in a functional state to produce energy in response to light. In case of prolonged starvation, a different program is activated: chloroplasts are degraded and digested. The sea slugs lose their green colour but are provided with an internal source of nutrients that can double their survival time.</p>","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"676 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144645629","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}
Nature PlantsPub Date : 2025-07-16DOI: 10.1038/s41477-025-02059-w
Patricia Caballero-Carretero, Joaquin Medina
{"title":"A mobile transcription factor coordinates systemic responses to nitrogen deficiency","authors":"Patricia Caballero-Carretero, Joaquin Medina","doi":"10.1038/s41477-025-02059-w","DOIUrl":"https://doi.org/10.1038/s41477-025-02059-w","url":null,"abstract":"Long-distance signalling helps plants to coordinate responses to environmental stress, but identification of these signals can be technically challenging. A recent study presented a new method for mobile transcription factor identification based on trans-organ gene co-expression, enabling characterization of the shoot-derived transcription factor TGA7 and providing insights into how plants coordinate regulatory processes across different tissues.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"7 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144640367","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":"Trans-organ analysis of gene co-expression networks reveals a mobile long-distance regulator that balances shoot and root development in Arabidopsis","authors":"Jia Yuan Ye, Yasuhito Sakuraba, Meng Na Zhuo, Yousuke Torii, Namie Ohtsuki, Wen Hao Tian, Chong Wei Jin, Shao Jian Zheng, Keiichi Mochida, Shuichi Yanagisawa","doi":"10.1038/s41477-025-02052-3","DOIUrl":"https://doi.org/10.1038/s41477-025-02052-3","url":null,"abstract":"<p>Long-distance regulation between individual organs is a fundamental process for the optimized adaptation of the plant body to diverse environments. However, systematic methods for identifying key genes for long-distance regulation are currently unavailable. Here we present a new approach, trans-organ analysis of gene co-expression networks, which offers a unique way of identifying candidates for such genes. This approach revealed that TGA7 functions as a shoot-to-root mobile bZIP transcription factor in <i>Arabidopsis</i> to activate photosynthetic genes directly in shoots and nitrate-uptake-related genes, both directly and via a transcriptional cascade, in roots. Analysis of grafted chimeras showed that nitrogen-deficiency-induced enhanced <i>TGA7</i> expression in shoot vascular tissue promotes TGA7 protein accumulation in roots, boosting root growth and nitrate uptake. Furthermore, the loss of TGA7-mediated long-distance regulation perturbed the balance between shoot and root development under nitrogen deficiency. These findings underscore the utility of our approach for uncovering long-distance regulation in plants.</p>","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144640382","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}
Nature PlantsPub Date : 2025-07-16DOI: 10.1038/s41477-025-02065-y
Raphael Trösch
{"title":"ARC3 required for constriction","authors":"Raphael Trösch","doi":"10.1038/s41477-025-02065-y","DOIUrl":"https://doi.org/10.1038/s41477-025-02065-y","url":null,"abstract":"<p>Chloroplast division requires the formation of a stromal Z ring composed of two tubulin-like FtsZ homologues, FtsZ1 and FtsZ2. This ring is linked to the inner envelope membrane through ARC6 and further connected to the outer envelope membranes through PLASTID DIVISION proteins and to a cytosolic plastid division ring containing dynamin-like ARC5. The correct positioning of the Z ring depends on a chloroplast version of the Min system in which ARC3 has a key role as a negative regulator of Z ring formation. ARC3 displays a diffuse localization at non-division sites where it probably prevents Z ring formation. However, ARC3 also localizes to the Z ring itself, but the function of this subpopulation was unclear.</p><p>The researchers show that ARC3 physically interacts with ARC6, and that this interaction depends on its membrane occupation and recognition nexus (MORN) domain with which it was known to bind to the paralogue of ARC6 (PARC6). Indeed, localization of ARC3 in <i>arc6 parc6</i> and <i>arc6</i> mutant background suggests that there is some functional overlap between ARC6 and PARC6 in recruiting ARC3 to the Z ring. Expression of ARC3 with a deleted MORN domain abolishes filament assembly of FtsZ1 in a heterologous yeast system, providing evidence for the autoinhibitory function of this domain. Co-expression of ARC6 with ARC3 inhibited FtsZ1 filament formation, presumably due to interaction with the MORN domain, which may release the autoinhibitory function similar to PARC6. However, in contrast to PARC6, ARC6 has a J-like domain that prevents interaction with ARC3 in planta. Indeed, deletion of the J-like domain of ARC6 led to reduced FtsZ1 assembly and chloroplast division defects, similar to plants overexpressing ARC3. This is not the case in the <i>arc3</i> mutant background, suggesting that inhibition of FtsZ1 assembly depends on ARC3. Intriguingly, co-expression of ARC3 and ARC6 in the heterologous system <i>Pichia pastoris</i> led to enhanced Z ring constriction dynamics, suggesting that ARC3 function is not only negatively controlled by ARC6 within the Z ring but is also beneficial for constriction dynamics.</p>","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"44 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144640366","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}
Nature PlantsPub Date : 2025-07-15DOI: 10.1038/s41477-025-02061-2
Mary Galli, Andrea Gallavotti
{"title":"A binding agreement","authors":"Mary Galli, Andrea Gallavotti","doi":"10.1038/s41477-025-02061-2","DOIUrl":"https://doi.org/10.1038/s41477-025-02061-2","url":null,"abstract":"Transcription factors are proteins that recognize and bind short, specific DNA sequences and regulate when, where and how genes are expressed in a cell. A recent large-scale study of transcription factor binding across multiple flowering plant species reveals conservation of cell-type-specific regulatory pathways as well as rewiring of ancient regulatory networks for lineage-specific phenotypes, including tolerance to stresses.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"48 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144629730","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}
Nature PlantsPub Date : 2025-07-15DOI: 10.1038/s41477-025-02047-0
Leo A. Baumgart, Sharon I. Greenblum, Abraham Morales-Cruz, Peng Wang, Yu Zhang, Lin Yang, Cindy Chen, David J. Dilworth, Alexis C. Garretson, Nicolas Grosjean, Guifen He, Emily Savage, Yuko Yoshinaga, Ian K. Blaby, Chris G. Daum, Ronan C. O’Malley
{"title":"Recruitment, rewiring and deep conservation in flowering plant gene regulation","authors":"Leo A. Baumgart, Sharon I. Greenblum, Abraham Morales-Cruz, Peng Wang, Yu Zhang, Lin Yang, Cindy Chen, David J. Dilworth, Alexis C. Garretson, Nicolas Grosjean, Guifen He, Emily Savage, Yuko Yoshinaga, Ian K. Blaby, Chris G. Daum, Ronan C. O’Malley","doi":"10.1038/s41477-025-02047-0","DOIUrl":"https://doi.org/10.1038/s41477-025-02047-0","url":null,"abstract":"<p>Transcription factors (TFs) are proteins that bind DNA to control where and when genes are expressed. In plants, dozens of TF families interact with distinct sets of binding sites (TFBSs) that reflect each TF’s role in organismal function and species-specific adaptations. However, defining these roles and understanding broader patterns of regulatory evolution remain challenging, as predicted TFBSs may lack a clear impact on transcription, and experimentally derived TF binding maps to date are modest in scale or restricted to model organisms. Here we present a scalable TFBS assay that we leveraged to create an atlas of nearly 3,000 genome-wide binding site maps for 360 TFs in ten species spanning 150 million years of flowering plant evolution. We found that TF orthologues from distant species retain nearly identical binding preferences, while on the same timescales the gain and loss of TFBSs are widespread. Within lineages, however, conserved TFBSs are over-represented and found in regions harbouring signatures of functional regulatory elements. Moreover, genes with conserved TFBSs showed striking enrichment for cell-type-specific expression in 14 single-nucleus RNA atlases, providing a robust marker of each TF’s activity and developmental role. Finally, we compare distant lineages, illustrating how ancient regulatory modules were recruited and rewired to enable adaptations underlying the evolutionary success of grasses.</p>","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"3 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144629619","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}