Nature Plants最新文献_第8页

A mobile transcription factor coordinates systemic responses to nitrogen deficiency 一个可移动的转录因子协调对氮缺乏的全身反应

IF 13.6 1区生物学

Nature Plants Pub Date : 2025-07-16 DOI: 10.1038/s41477-025-02059-w

Patricia Caballero-Carretero, Joaquin Medina

引用次数: 0

Trans-organ analysis of gene co-expression networks reveals a mobile long-distance regulator that balances shoot and root development in Arabidopsis 基因共表达网络的跨器官分析揭示了一个平衡拟南芥茎和根发育的移动远程调节因子

IF 13.6 1区生物学

Nature Plants Pub Date : 2025-07-16 DOI: 10.1038/s41477-025-02052-3

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

{"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":"10.1038/s41477-025-02052-3","url":null,"abstract":"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 Arabidopsis 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 TGA7 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. Trans-organ analysis of gene co-expression networks in different tissues provides a unique method for uncovering long-distance regulation.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 8","pages":"1544-1557"},"PeriodicalIF":13.6,"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}

引用次数: 0

ARC3 required for constriction 收缩需要ARC3

IF 13.6 1区生物学

Nature Plants Pub Date : 2025-07-16 DOI: 10.1038/s41477-025-02065-y

Raphael Trösch

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A binding agreement 有约束力的协议

IF 13.6 1区生物学

Nature Plants Pub Date : 2025-07-15 DOI: 10.1038/s41477-025-02061-2

Mary Galli, Andrea Gallavotti

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Recruitment, rewiring and deep conservation in flowering plant gene regulation 开花植物基因调控中的招募、重组和深度保护

IF 13.6 1区生物学

Nature Plants Pub Date : 2025-07-15 DOI: 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":"10.1038/s41477-025-02047-0","url":null,"abstract":"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. A highly scalable approach is used to generate 3,000 genome-wide maps of transcription factor binding in ten flowering plants, along with multi-species single-nucleus RNA-seq atlases. Together, the results reveal both ancient regulation and key regulatory adaptations.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 8","pages":"1514-1527"},"PeriodicalIF":13.6,"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}

引用次数: 0

Warming risks Tibetan meadow collapse 气候变暖可能导致西藏草甸崩溃

IF 13.6 1区生物学

Nature Plants Pub Date : 2025-07-15 DOI: 10.1038/s41477-025-02068-9

Jun Lyu

引用次数: 0

Wounding induces multilayered barrier formation in mature leaves via phytohormone signalling and ATML1-mediated epidermal specification 损伤通过植物激素信号和atml1介导的表皮规范诱导成熟叶片形成多层屏障

IF 13.6 1区生物学

Nature Plants Pub Date : 2025-07-14 DOI: 10.1038/s41477-025-02028-3

Jung-Min Lee, Woo-Taek Jeon, Minsoo Han, Min-Soo Choi, Myung Kwon, Kyungyoon Kim, Sujeong Je, Hoon Jung, Geon Heo, Youngsung Joo, Yasuyo Yamaoka, Yuree Lee

{"title":"Wounding induces multilayered barrier formation in mature leaves via phytohormone signalling and ATML1-mediated epidermal specification","authors":"Jung-Min Lee, Woo-Taek Jeon, Minsoo Han, Min-Soo Choi, Myung Kwon, Kyungyoon Kim, Sujeong Je, Hoon Jung, Geon Heo, Youngsung Joo, Yasuyo Yamaoka, Yuree Lee","doi":"10.1038/s41477-025-02028-3","DOIUrl":"10.1038/s41477-025-02028-3","url":null,"abstract":"The epidermis of plants forms a protective barrier against biotic and abiotic stress. Little is known about how breaches in the epidermis are repaired, especially in mature leaves. Here we investigated wound healing in the mature leaves of Arabidopsis. We discovered a wound protection mechanism comprising a multilayered ligno-suberized barrier covered with cuticular wax. This barrier is formed by mesophyll cells that adopt an epidermal fate. This cell fate transition is regulated in two steps by ATML1, a key transcription factor in epidermal specification. First, mesophyll cells of protective layer 1, just beneath the wound, transition into epidermal cells and seal the wound by depositing cuticle, a mechanism that involves signalling through ethylene and reactive oxygen species produced by RbohE. This signalling also promotes cell death in protective layer 1, ensuring wax accumulation on the surface. Second, the underlying protective layer 2 undergoes ligno-suberization, driven by jasmonic acid and RbohD, forming a cork-like layer on the leaf surface. ATML1 regulates this process in protective layer 2 as well. Wound healing in mature leaves thus involves the integration of ethylene and jasmonic acid signalling with ATML1-mediated epidermal cell specification to coordinate cell-layer-specific functions, including cuticular wax formation and ligno-suberization. This protective mechanism also occurs in the leaves of tobacco and Capsella, suggesting it is widespread. Arabidopsis repairs leaf wounds by reprogramming mesophyll cells into epidermal-like cells that build a ligno-suberized barrier topped with cuticle. ATML1 directs this process via ethylene–RbohE and jasmonic acid–RbohD signalling across cell layers in space and time.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"11 7","pages":"1298-1315"},"PeriodicalIF":13.6,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144622474","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}

引用次数: 0

Heal the wound to make a better seal 愈合伤口，使伤口愈合

IF 13.6 1区生物学

Nature Plants Pub Date : 2025-07-14 DOI: 10.1038/s41477-025-02035-4

Shinobu Takada

引用次数: 0

Author Correction: Leaf venation network evolution across clades and scales 作者更正：叶脉网络在枝和尺度上的进化。

IF 13.6 1区生物学

Nature Plants Pub Date : 2025-07-11 DOI: 10.1038/s41477-025-02070-1

Ilaine Silveira Matos, Bradley Vu, Joseph Mann, Emily Xie, Srinivasan Madhavan, Satvik Sharma, Izzi Niewiadomski, Andrea Echevarria, Connor Tomaka, Sonoma Carlos, Monica Antonio, Ashley Chu, Meg Scudder, Nicole Yokota, Hailey J. Park, Natalie Vuong, Mickey Boakye, Miguel A. Duarte, Caroline Pechuzal, Luiza Maria T. Aparecido, Mia B. Franco, Ryan Jen Wong, Jocelyn Liu, Emily Guevara Heredia, Brad Boyle, Martha Ryan, Rafael E. Cárdenas, Brian J. Enquist, Diane M. Erwin, Holly Forbes, Kyle Dexter, Mark Fricker, Benjamin W. Blonder

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Greater tree species richness results in increased ecosystem photosynthesis in forests globally 树种丰富度的增加导致全球森林生态系统光合作用的增加

IF 13.6 1区生物学

Nature Plants Pub Date : 2025-07-10 DOI: 10.1038/s41477-025-02055-0

引用次数: 0