Nature Plants最新文献

{"title":"Suppression of plastid-to-nucleus gene transfer by DNA double-strand break repair","authors":"Enrique Gonzalez-Duran, Xenia Kroop, Anne Schadach, Ralph Bock","doi":"10.1038/s41477-025-02005-w","DOIUrl":"https://doi.org/10.1038/s41477-025-02005-w","url":null,"abstract":"<p>Plant nuclear genomes contain thousands of genes of mitochondrial and plastid origin as the result of endosymbiotic gene transfer (EGT). EGT is a still-ongoing process, but the molecular mechanisms determining its frequency remain largely unknown. Here we demonstrate that nuclear double-strand break (DSB) repair is a strong suppressor of EGT. Through large-scale genetic screens in tobacco plants, we found that EGT from plastids to the nucleus occurs more frequently in somatic cells when individual DSB repair pathways are inactive. This effect is explained by the expected increase in the number and residence time of DSBs available as integration sites for organellar DNA. We also show that impaired DSB repair causes EGT to increase 5- to 20-fold in the male gametophyte. Together, our data (1) uncover DSB levels as a key determinant of EGT frequency, (2) reveal the strong mutagenic potential of organellar DNA and (3) suggest that changes in DNA repair capacity can impact EGT across evolutionary timescales.</p>","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"4 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144066046","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":"A gatekeeper for gene transfers","authors":"Eva C. M. Nowack","doi":"10.1038/s41477-025-02004-x","DOIUrl":"https://doi.org/10.1038/s41477-025-02004-x","url":null,"abstract":"Large-scale genetic screening for plastid-to-nucleus gene transfers identifies that fast double-strand break repair functions as a key barrier for nuclear integration of organellar DNA and provides initial insights into the genetic control of this process.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"23 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144066036","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":"SCREAM to stop SPEECHLESS","authors":"Raphael Trösch","doi":"10.1038/s41477-025-02014-9","DOIUrl":"https://doi.org/10.1038/s41477-025-02014-9","url":null,"abstract":"<p>During stomatal development, protodermal cells differentiate into meristemoid mother cells, which undergo a limited number of asymmetric cell divisions that each produce a smaller meristemoid and a larger stomatal-lineage ground cell. The final meristemoid further differentiates into a guard mother cell, which divides symmetrically to produce two guard cells. The asymmetric divisions of the meristemoid mother cell are initiated by SPCH, whereas MUTE is required for termination of asymmetric divisions and further differentiation of the meristemoid into the guard mother cell. Finally, FAMA is required for symmetric division of the guard mother cell. SPCH, MUTE and FAMA can all form heterodimers with SCREAM; however, the specific role of SCREAM in stomatal development is less clear.</p><p>The researchers investigate stomatal development in <i>scrm</i> mutants and find that differentiation of stomatal-lineage cells into guard cells is inhibited. Although the number of asymmetric cell divisions in <i>scrm</i> mutants differs between developmental stages compared with the wild type, lack of SCRM generally leads to excessive asymmetric cell divisions of meristemoids. As overexpression of <i>SCRM</i> leads to increased stomatal-lineage density but not stomatal density, it seems that SCRM is required both for the initiation and termination of asymmetric cell division at different stages. Transcription of SPCH and known SPCH targets is enhanced in <i>scrm</i> mutants, and indeed SCRM can directly bind and repress the <i>SPCH</i> promoter. It is further shown that <i>SPCH</i> is epistatic to <i>SCRM</i> and that downregulation of <i>SPCH</i> expression in the <i>scrm</i> background can partially suppress the excessive asymmetric cell divisions, suggesting that this phenotype can be at least partially attributed to upregulation of <i>SPCH</i> in the <i>scrm</i> mutant. Overexpression of <i>SCRM</i> in the <i>mute</i> background leads to fewer asymmetric cell divisions than in <i>mute</i> alone, and MUTE does not bind to the <i>SPCH</i> promoter in vivo, pointing to a role for SCRM in the termination of asymmetric cell divisions that is independent of MUTE. As it was shown before that SPCH can also be inhibited by non-cell autonomous patterning signals, it is tempting to speculate that relative quantities of SPCH and SCRM may determine the initiation or termination of asymmetric cell division.</p>","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"5 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144066043","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":"E3 ubiquitin ligases at the frontline of antiviral defence","authors":"Zeyun Hao, Xiao Xu, Guo-Liang Wang, Ruyi Wang, Yuese Ning","doi":"10.1038/s41477-025-02008-7","DOIUrl":"https://doi.org/10.1038/s41477-025-02008-7","url":null,"abstract":"The mechanisms underlying virus perception and immune activation in plants remain poorly understood. Recent work shows that in rice, an E3 ubiquitin ligase senses viral coat proteins to activate the jasmonate signalling pathway by degrading NINJA3, and triggers downstream antiviral defence responses.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"121 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143945699","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":"The regulatory potential of transposable elements in maize","authors":"Kerry L. Bubb, Morgan O. Hamm, Thomas W. Tullius, Joseph K. Min, Bryan Ramirez-Corona, Nicholas A. Mueth, Jane Ranchalis, Yizi Mao, Erik J. Bergstrom, Mitchell R. Vollger, Cole Trapnell, Josh T. Cuperus, Andrew B. Stergachis, Christine Queitsch","doi":"10.1038/s41477-025-02002-z","DOIUrl":"https://doi.org/10.1038/s41477-025-02002-z","url":null,"abstract":"<p>The genomes of flowering plants consist largely of transposable elements (TEs), some of which modulate gene regulation and function. However, the repetitive nature of TEs and difficulty of mapping individual TEs by short-read sequencing have hindered our understanding of their regulatory potential. Here we show that long-read chromatin fibre sequencing (Fiber-seq) comprehensively identifies accessible chromatin regions (ACRs) and CpG methylation across the maize genome. We uncover stereotypical ACR patterns at young TEs that degenerate with evolutionary age, resulting in TE enhancers preferentially marked by a novel plant-specific epigenetic feature: simultaneous hyper-CpG methylation and chromatin accessibility. We show that TE ACRs are co-opted as gene promoters and that ACR-containing TEs can facilitate gene amplification. Lastly, we uncover a pervasive epigenetic signature—hypo-5mCpG methylation and diffuse chromatin accessibility—directing TEs to specific loci, including the loci that sparked McClintock’s discovery of TEs.</p>","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"20 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143940094","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":"Mycorrhizal CLE mimicry","authors":"Guillaume Tena","doi":"10.1038/s41477-025-02015-8","DOIUrl":"https://doi.org/10.1038/s41477-025-02015-8","url":null,"abstract":"<p>Since the discovery of systemin in tomato in the past century, small peptides have become ubiquitous in plant signalling pathways. Various families with increasingly funny names each contain dozens of individual peptides: PEP, RALF, CEP, IDA, PSK, PSY, SCOOP, SCREW and so on. The CLE family (named after CLV3 and ESR) consists of secreted peptides that are 12–14 amino acids in length, which are perceived locally or systemically by leucine-rich repeat receptor-like kinases. They are broadly involved in many biological processes: maintenance of the shoot and root meristems, vascular development, senescence, nutrition, stomatal patterning, flower and fruit development, and stress responses — the list continues to increase.</p><p>CLE peptides also have a role in plant–microbe interactions, including during symbioses. A recent study in the <i>Proceedings of the National Academy of Sciences USA</i>, which comes from the Salk Institute and is led by Lena Maria Müller, identifies a positive role for CLE16 from <i>Medicago truncatula</i> during arbuscular mycorrhizal (AM) symbiosis, with an interesting twist: the AM fungus itself produces a CLE16 mimic to facilitate colonization.</p>","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"27 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143940093","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":"Quantitative dissection of Agrobacterium T-DNA expression in single plant cells reveals density-dependent synergy and antagonism","authors":"Simon Alamos, Matthew J. Szarzanowicz, Mitchell G. Thompson, Danielle M. Stevens, Liam D. Kirkpatrick, Amanda Dee, Hamreet Pannu, Ruoming Cui, Shuying Liu, Monikaben Nimavat, Ksenia Krasileva, Edward E. K. Baidoo, Patrick M. Shih","doi":"10.1038/s41477-025-01996-w","DOIUrl":"https://doi.org/10.1038/s41477-025-01996-w","url":null,"abstract":"<p><i>Agrobacterium</i> pathogenesis, which involves transferring T-DNA into plant cells, is the cornerstone of plant genetic engineering. As the applications that rely on <i>Agrobacterium</i> increase in sophistication, it becomes critical to achieve a quantitative and predictive understanding of T-DNA expression at the level of single plant cells. Here we examine if a classic Poisson model of interactions between pathogens and host cells holds true for <i>Agrobacterium</i> infecting <i>Nicotiana benthamiana</i>. Systematically challenging this model revealed antagonistic and synergistic density-dependent interactions between bacteria that do not require quorum sensing. Using various approaches, we studied the molecular basis of these interactions. To overcome the engineering constraints imposed by antagonism, we created a dual binary vector system termed ‘BiBi’, which can improve the efficiency of a reconstituted complex metabolic pathway in a predictive fashion. Our findings illustrate how combining theoretical models with quantitative experiments can reveal new principles of bacterial pathogenesis, impacting both fundamental and applied plant biology.</p>","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"34 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143933502","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":"Cooperation and antagonism in Agrobacterium-mediated transformation","authors":"Teng-Kuei Huang, Erh-Min Lai","doi":"10.1038/s41477-025-01998-8","DOIUrl":"https://doi.org/10.1038/s41477-025-01998-8","url":null,"abstract":"By integrating theoretical modelling and single-cell analysis of Agrobacterium-mediated transformation in Nicotiana plants, a recent study reveals how agrobacterial density governs synergistic and antagonistic effects on transformation outcomes. These insights led to the development of a dual binary vector system that mitigates immune-triggered antagonism, enabling more efficient engineering of complex metabolic pathways in plants.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"26 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143933499","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":"Herbivory-induced green leaf volatiles increase plant performance through jasmonate-dependent plant–soil feedbacks","authors":"Lingfei Hu, Kaidi Zhang, Yachun Xu, Xiaoxuan Zheng, Jamie M. Waterman, Xiao Ouyang, Zhenwei Wu, Zhicheng Shen, Yan He, Bin Ma, Christelle A. M. Robert, Jos M. Raaijmakers, Meng Ye, Matthias Erb, Jianming Xu","doi":"10.1038/s41477-025-01987-x","DOIUrl":"https://doi.org/10.1038/s41477-025-01987-x","url":null,"abstract":"<p>Plants influence each other chemically by releasing leaf volatiles and root exudates, but whether and how these two phenomena interact remains unknown. Here we demonstrate that volatiles that are released by herbivore-attacked leaves trigger plant–soil feedbacks, resulting in increased performance of different plant species. We show that this phenomenon is due to green leaf volatiles that induce jasmonate-dependent systemic defence signalling in receiver plants, which results in the accumulation of beneficial soil bacteria in the rhizosphere. These soil bacteria then increase plant growth and enhance plant defences. In maize, a cysteine-rich receptor-like protein kinase, ZmCRK25, is required for this effect. In four successive year-field experiments, we demonstrate that this phenomenon can suppress leaf herbivore abundance and enhance maize growth and yield. Thus, volatile-mediated plant–plant interactions trigger plant–soil feedbacks that shape plant performance across different plant species through broadly conserved defence signalling mechanisms and changes in soil microbiota. This phenomenon expands the repertoire of biologically relevant plant–plant interactions in space and time and holds promise for the sustainable intensification of agriculture.</p>","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"104 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143893444","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":"Airborne cues shape soil legacies","authors":"Christopher J. Frost, Sophia L. Shomper","doi":"10.1038/s41477-025-01988-w","DOIUrl":"https://doi.org/10.1038/s41477-025-01988-w","url":null,"abstract":"Plants are known to respond to odour cues emitted by other plants that may indicate impending environmental stress. These responses are now understood to extend belowground, where root exudates condition rhizosphere soil bacteria communities in ways that enhance future plant growth and defence.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"49 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143893443","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}