Nature Plants最新文献_第2页

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 18 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":"https://doi.org/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.","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}

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 18 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 18 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":"https://doi.org/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.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"668 1","pages":""},"PeriodicalIF":18.0,"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 18 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 18 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

引用次数: 0

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 18 1区生物学

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

引用次数: 0

Bromodomain-containing proteins interact with a non-canonical RNA polymerase II kinase to maintain gene expression upon heat stress 含溴结构域的蛋白与非规范RNA聚合酶II激酶相互作用，在热应激下维持基因表达

IF 18 1区生物学

Nature Plants Pub Date : 2025-07-09 DOI: 10.1038/s41477-025-02044-3

Xinjing Zheng, Zhihao Zuo, Peng Yao, Xiaojing Li, Qingche Zhang, Xiangsong Chen

{"title":"Bromodomain-containing proteins interact with a non-canonical RNA polymerase II kinase to maintain gene expression upon heat stress","authors":"Xinjing Zheng, Zhihao Zuo, Peng Yao, Xiaojing Li, Qingche Zhang, Xiangsong Chen","doi":"10.1038/s41477-025-02044-3","DOIUrl":"https://doi.org/10.1038/s41477-025-02044-3","url":null,"abstract":"Phosphorylation at the carboxy-terminal domain of the largest subunit of RNA polymerase II plays a critical role in transcription, and histone acetylation is correlated with active transcription. However, the regulatory mechanisms by which histone acetylation modulates RNA polymerase II phosphorylation in plants remain unclear. Here we show that two functionally redundant bromodomain-containing proteins, global transcription factor group E2 (GTE2) and GTE7, can bind to acetylated histone H4. Both GTE2 and GTE7 interact with cyclin-dependent kinase-like 9 (CDKL9), which belongs to a plant-specific CDKL group. Unlike canonical CDKs, CDKL9 functions in a cyclin- and CDK-activating-kinase-independent manner and can phosphorylate at least the serine 2 and serine 5 residues of the carboxy-terminal domain in vitro. The GTE2/GTE7–CDKL9 complex is required to maintain serine 2 and serine 5 phosphorylation under heat stress. Consistently, loss-of-function gte2/gte7 and cdkl9 mutants show similar heat-sensitive phenotypes. We also demonstrate that the acetylated-histone-binding activity of GTE7 is essential for the association of CDKL9 with chromatin and for plant heat tolerance. Together, these findings provide mechanistic insight into transcriptional regulation via histone acetylation in response to heat stress and suggest that plants might have evolved a unique group of carboxy-terminal domain kinases for stress tolerance.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"1 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144586949","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

Guard cells on the adaxial and abaxial leaf surfaces use different compositions of potassium ion channels to drive light-induced stomatal opening 叶片正面和背面的保护细胞利用不同组成的钾离子通道来驱动光诱导的气孔打开

IF 18 1区生物学

Nature Plants Pub Date : 2025-07-09 DOI: 10.1038/s41477-025-02026-5

Jian Wei, Kunshen Hu, Menglong Liu, Yali Liu, Wang Tian, Yue Zhou, Liu-Min Fan, Yizhou Wang, Yin Wang

{"title":"Guard cells on the adaxial and abaxial leaf surfaces use different compositions of potassium ion channels to drive light-induced stomatal opening","authors":"Jian Wei, Kunshen Hu, Menglong Liu, Yali Liu, Wang Tian, Yue Zhou, Liu-Min Fan, Yizhou Wang, Yin Wang","doi":"10.1038/s41477-025-02026-5","DOIUrl":"https://doi.org/10.1038/s41477-025-02026-5","url":null,"abstract":"In the leaves of most herbaceous plants, stomata exist in both the adaxial (upper) and abaxial (lower) surfaces1,2. Many previous studies have reported that stomata on the abaxial surface are more responsive to light than those on the adaxial surface3,4,5,6,7,8,9. However, the underlying molecular mechanism is still unclear. Here, by examining the model plants Arabidopsis and tobacco, we confirmed that the distinct feature occurred at the guard cell level. Next, with both single-cell RNA sequencing and transcriptome sequencing, we compared gene expression patterns of adaxial and abaxial guard cells and highlighted the possibility of different utilization of potassium ion (K+) channels. Via in silico OnGuard simulation and genetic modifications, we found that adaxial and abaxial guard cells rely on different K+in channels, which control K+ influx for stomatal opening. The present study provides insights into understanding the distinct stomatal light response of different leaf surfaces.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"37 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144586948","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

Structural snapshots show the roles of TEF30 in repairing the broken photosystem II 结构快照显示TEF30在修复受损光系统II中的作用

IF 18 1区生物学

Nature Plants Pub Date : 2025-07-08 DOI: 10.1038/s41477-025-02062-1

引用次数: 0

When and where soil dryness matters to ecosystem photosynthesis 何时何地土壤干燥对生态系统光合作用有影响

IF 18 1区生物学

Nature Plants Pub Date : 2025-07-07 DOI: 10.1038/s41477-025-02024-7

Jiangong Liu, Qiren Wang, Weiwei Zhan, Xu Lian, Pierre Gentine

{"title":"When and where soil dryness matters to ecosystem photosynthesis","authors":"Jiangong Liu, Qiren Wang, Weiwei Zhan, Xu Lian, Pierre Gentine","doi":"10.1038/s41477-025-02024-7","DOIUrl":"https://doi.org/10.1038/s41477-025-02024-7","url":null,"abstract":"Projected increases in the intensity and frequency of droughts in the twenty-first century are expected to cause a substantial negative impact on terrestrial gross primary productivity (GPP). Yet, the relative role of soil water supply (indicated by soil moisture) and atmospheric water demand (indicated by vapour pressure deficit, VPD) on GPP remains debated, primarily due to their strong covariations, the presence of confounding factors and unresolved causal relationships among the interconnected hydrometeorological drivers of GPP. Here using a causality-guided explainable artificial intelligence framework, we show that soil moisture is the dominant regulator of water stress, surpassing the role of VPD, when and where soil water supply limits ecosystem functions. Temporally, we use in situ flux tower data to demonstrate that soil moisture dominates the GPP response during periods of insufficient soil water supply. Spatially, we assess the global spatial patterns of satellite sun-induced chlorophyll fluorescence (a proxy for GPP) in water-limited regions and demonstrate that they are mostly dominated by soil moisture. Conversely, VPD plays a greater role in controlling the temporal and spatial variations in GPP than soil moisture when and where soil water supply is not limited. The relative role of soil moisture and VPD is modulated by plant adaptation to long-term climatological aridity. Our findings advance the understanding of the impacts of soil and atmospheric dryness on ecosystem photosynthesis. They provide crucial insights into how terrestrial ecosystems respond to increasing aridity and more frequent droughts, particularly given the potential ecosystem shifts from energy to water limitation.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"72 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144568773","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