Pub Date : 2024-05-21DOI: 10.1038/s41477-024-01698-9
Yu Tang, Xiangyun Yang, Aobo Huang, Kyungyong Seong, Mao Ye, Mengting Li, Qiao Zhao, Ksenia Krasileva, Yangnan Gu
The nuclear pore complex (NPC) is vital for nucleocytoplasmic communication. Recent evidence emphasizes its extensive association with proteins of diverse functions, suggesting roles beyond cargo transport. Yet, our understanding of NPC’s composition and functionality at this extended level remains limited. Here, through proximity-labelling proteomics, we uncover both local and global NPC-associated proteome in Arabidopsis, comprising over 500 unique proteins, predominantly associated with NPC’s peripheral extension structures. Compositional analysis of these proteins revealed that the NPC concentrates chromatin remodellers, transcriptional regulators and mRNA processing machineries in the nucleoplasmic region while recruiting translation regulatory machinery on the cytoplasmic side, achieving a remarkable orchestration of the genetic information flow by coupling RNA transcription, maturation, transport and translation regulation. Further biochemical and structural modelling analyses reveal that extensive interactions with nucleoporins, along with phase separation mediated by substantial intrinsically disordered proteins, may drive the formation of the unexpectedly large nuclear pore proteome assembly. Tang et al. utilized proximity labelling to assemble the Arabidopsis nuclear pore-associated proteome and revealed the nuclear pore as an integrated platform coupling multiple steps in gene expression regulation, beyond its conventional transport role.
{"title":"Proxiome assembly of the plant nuclear pore reveals an essential hub for gene expression regulation","authors":"Yu Tang, Xiangyun Yang, Aobo Huang, Kyungyong Seong, Mao Ye, Mengting Li, Qiao Zhao, Ksenia Krasileva, Yangnan Gu","doi":"10.1038/s41477-024-01698-9","DOIUrl":"10.1038/s41477-024-01698-9","url":null,"abstract":"The nuclear pore complex (NPC) is vital for nucleocytoplasmic communication. Recent evidence emphasizes its extensive association with proteins of diverse functions, suggesting roles beyond cargo transport. Yet, our understanding of NPC’s composition and functionality at this extended level remains limited. Here, through proximity-labelling proteomics, we uncover both local and global NPC-associated proteome in Arabidopsis, comprising over 500 unique proteins, predominantly associated with NPC’s peripheral extension structures. Compositional analysis of these proteins revealed that the NPC concentrates chromatin remodellers, transcriptional regulators and mRNA processing machineries in the nucleoplasmic region while recruiting translation regulatory machinery on the cytoplasmic side, achieving a remarkable orchestration of the genetic information flow by coupling RNA transcription, maturation, transport and translation regulation. Further biochemical and structural modelling analyses reveal that extensive interactions with nucleoporins, along with phase separation mediated by substantial intrinsically disordered proteins, may drive the formation of the unexpectedly large nuclear pore proteome assembly. Tang et al. utilized proximity labelling to assemble the Arabidopsis nuclear pore-associated proteome and revealed the nuclear pore as an integrated platform coupling multiple steps in gene expression regulation, beyond its conventional transport role.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141073871","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 : 2024-05-20DOI: 10.1038/s41477-024-01714-y
Jun Lyu
{"title":"Coffee history under the genomic lens","authors":"Jun Lyu","doi":"10.1038/s41477-024-01714-y","DOIUrl":"10.1038/s41477-024-01714-y","url":null,"abstract":"","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":18.0,"publicationDate":"2024-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141069451","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 : 2024-05-20DOI: 10.1038/s41477-024-01689-w
Paavo A. Penttilä, Antti Paajanen
{"title":"Critical comment on the assumptions leading to 24-chain microfibrils in wood","authors":"Paavo A. Penttilä, Antti Paajanen","doi":"10.1038/s41477-024-01689-w","DOIUrl":"10.1038/s41477-024-01689-w","url":null,"abstract":"","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141069473","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 : 2024-05-17DOI: 10.1038/s41477-024-01681-4
Sarah M. Venter, Ed T. F. Witkowski
{"title":"Baobabs as symbols of resilience","authors":"Sarah M. Venter, Ed T. F. Witkowski","doi":"10.1038/s41477-024-01681-4","DOIUrl":"10.1038/s41477-024-01681-4","url":null,"abstract":"","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":18.0,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140953552","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}
Growing evidence indicates that plant community structure and traits have changed under climate warming, especially in cold or high-elevation regions. However, the impact of these warming-induced changes on ecosystem carbon sequestration remains unclear. Using a warming experiment on the high-elevation Qinghai-Tibetan Plateau, we found that warming not only increased plant species height but also altered species composition, collectively resulting in a taller plant community associated with increased net ecosystem productivity (NEP). Along a 1,500 km transect on the Plateau, taller plant community promoted NEP and soil carbon through associated chlorophyll content and other photosynthetic traits at the community level. Overall, plant community height as a dominant trait is associated with species composition and regulates ecosystem C sequestration in the high-elevation biome. This trait-based association provides new insights into predicting the direction, magnitude and sensitivity of ecosystem C fluxes in response to climate warming. Quan et al. show that warming-induced changes in plant community height in a cold, high-elevation region enhance ecosystem carbon sequestration, emphasizing the importance of plant traits in shaping the carbon cycle under climate change.
{"title":"Plant height as an indicator for alpine carbon sequestration and ecosystem response to warming","authors":"Quan Quan, Nianpeng He, Ruiyang Zhang, Jinsong Wang, Yiqi Luo, Fangfang Ma, Junxiao Pan, Ruomeng Wang, Congcong Liu, Jiahui Zhang, Yiheng Wang, Bing Song, Zhaolei Li, Qingping Zhou, Guirui Yu, Shuli Niu","doi":"10.1038/s41477-024-01705-z","DOIUrl":"10.1038/s41477-024-01705-z","url":null,"abstract":"Growing evidence indicates that plant community structure and traits have changed under climate warming, especially in cold or high-elevation regions. However, the impact of these warming-induced changes on ecosystem carbon sequestration remains unclear. Using a warming experiment on the high-elevation Qinghai-Tibetan Plateau, we found that warming not only increased plant species height but also altered species composition, collectively resulting in a taller plant community associated with increased net ecosystem productivity (NEP). Along a 1,500 km transect on the Plateau, taller plant community promoted NEP and soil carbon through associated chlorophyll content and other photosynthetic traits at the community level. Overall, plant community height as a dominant trait is associated with species composition and regulates ecosystem C sequestration in the high-elevation biome. This trait-based association provides new insights into predicting the direction, magnitude and sensitivity of ecosystem C fluxes in response to climate warming. Quan et al. show that warming-induced changes in plant community height in a cold, high-elevation region enhance ecosystem carbon sequestration, emphasizing the importance of plant traits in shaping the carbon cycle under climate change.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41477-024-01705-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140949366","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 : 2024-05-14DOI: 10.1038/s41477-024-01683-2
Yuebin Wang, Yun Luo, Xing Guo, Yunfu Li, Jiali Yan, Wenwen Shao, Wenjie Wei, Xiaofeng Wei, Tao Yang, Jing Chen, Lihua Chen, Qian Ding, Minji Bai, Lin Zhuo, Li Li, David Jackson, Zuxin Zhang, Xun Xu, Jianbing Yan, Huan Liu, Lei Liu, Ning Yang
A comprehensive understanding of inflorescence development is crucial for crop genetic improvement, as inflorescence meristems give rise to reproductive organs and determine grain yield. However, dissecting inflorescence development at the cellular level has been challenging owing to a lack of specific marker genes to distinguish among cell types, particularly in different types of meristems that are vital for organ formation. In this study, we used spatial enhanced resolution omics-sequencing (Stereo-seq) to construct a precise spatial transcriptome map of the developing maize ear primordium, identifying 12 cell types, including 4 newly defined cell types found mainly in the inflorescence meristem. By extracting the meristem components for detailed clustering, we identified three subtypes of meristem and validated two MADS-box genes that were specifically expressed at the apex of determinate meristems and involved in stem cell determinacy. Furthermore, by integrating single-cell RNA transcriptomes, we identified a series of spatially specific networks and hub genes that may provide new insights into the formation of different tissues. In summary, this study provides a valuable resource for research on cereal inflorescence development, offering new clues for yield improvement. The authors integrate spatial (Stereo-seq) and single-cell transcriptomes of the developing maize ear to produce an atlas of maize ear cells and their developmental trajectories. They also identify a pair of transcription factors involved in inflorescence development.
{"title":"A spatial transcriptome map of the developing maize ear","authors":"Yuebin Wang, Yun Luo, Xing Guo, Yunfu Li, Jiali Yan, Wenwen Shao, Wenjie Wei, Xiaofeng Wei, Tao Yang, Jing Chen, Lihua Chen, Qian Ding, Minji Bai, Lin Zhuo, Li Li, David Jackson, Zuxin Zhang, Xun Xu, Jianbing Yan, Huan Liu, Lei Liu, Ning Yang","doi":"10.1038/s41477-024-01683-2","DOIUrl":"10.1038/s41477-024-01683-2","url":null,"abstract":"A comprehensive understanding of inflorescence development is crucial for crop genetic improvement, as inflorescence meristems give rise to reproductive organs and determine grain yield. However, dissecting inflorescence development at the cellular level has been challenging owing to a lack of specific marker genes to distinguish among cell types, particularly in different types of meristems that are vital for organ formation. In this study, we used spatial enhanced resolution omics-sequencing (Stereo-seq) to construct a precise spatial transcriptome map of the developing maize ear primordium, identifying 12 cell types, including 4 newly defined cell types found mainly in the inflorescence meristem. By extracting the meristem components for detailed clustering, we identified three subtypes of meristem and validated two MADS-box genes that were specifically expressed at the apex of determinate meristems and involved in stem cell determinacy. Furthermore, by integrating single-cell RNA transcriptomes, we identified a series of spatially specific networks and hub genes that may provide new insights into the formation of different tissues. In summary, this study provides a valuable resource for research on cereal inflorescence development, offering new clues for yield improvement. The authors integrate spatial (Stereo-seq) and single-cell transcriptomes of the developing maize ear to produce an atlas of maize ear cells and their developmental trajectories. They also identify a pair of transcription factors involved in inflorescence development.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":18.0,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140919637","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 : 2024-05-13DOI: 10.1038/s41477-024-01700-4
Mengke Wang, Deliang Kong, Xiaohan Mo, Yinghui Wang, Qingpei Yang, Paul Kardol, Oscar J. Valverde-Barrantes, Myrna J. Simpson, Hui Zeng, Peter B. Reich, Joana Bergmann, Nishanth Tharayil, Junjian Wang
Carbon influences the evolution and functioning of plants and their roots. Previous work examining a small number of commonly measured root traits has revealed a global multidimensionality of the resource economics traits in fine roots considering carbon as primary currency but without considering the diversity of carbon-related traits. To address this knowledge gap, we use data from 66 tree species from a tropical forest to illustrate that root economics space co-varies with a novel molecular-level traits space based on nuclear magnetic resonance. Thinner fine roots exhibit higher proportions of carbohydrates and lower diversity of molecular carbon than thicker roots. Mass-denser fine roots have more lignin and aromatic carbon compounds but less bioactive carbon compounds than lighter roots. Thus, the transition from thin to thick fine roots implies a shift in the root carbon economy from ‘do-it-yourself’ soil exploration to collaboration with mycorrhizal fungi, while the shift from light to dense fine roots emphasizes a shift from acquisitive to conservative root strategy. We reveal a previously undocumented role of molecular-level carbon traits that potentially undergird the multidimensional root economics space. This finding offers new molecular insight into the diversity of root form and function, which is fundamental to our understanding of plant evolution, species coexistence and adaptations to heterogeneous environments. Wang and colleagues report a two-dimensional root carbon trait space coupled with the root economics space, offering molecular insights into the great diversity of root form and function.
{"title":"Molecular-level carbon traits underlie the multidimensional fine root economics space","authors":"Mengke Wang, Deliang Kong, Xiaohan Mo, Yinghui Wang, Qingpei Yang, Paul Kardol, Oscar J. Valverde-Barrantes, Myrna J. Simpson, Hui Zeng, Peter B. Reich, Joana Bergmann, Nishanth Tharayil, Junjian Wang","doi":"10.1038/s41477-024-01700-4","DOIUrl":"10.1038/s41477-024-01700-4","url":null,"abstract":"Carbon influences the evolution and functioning of plants and their roots. Previous work examining a small number of commonly measured root traits has revealed a global multidimensionality of the resource economics traits in fine roots considering carbon as primary currency but without considering the diversity of carbon-related traits. To address this knowledge gap, we use data from 66 tree species from a tropical forest to illustrate that root economics space co-varies with a novel molecular-level traits space based on nuclear magnetic resonance. Thinner fine roots exhibit higher proportions of carbohydrates and lower diversity of molecular carbon than thicker roots. Mass-denser fine roots have more lignin and aromatic carbon compounds but less bioactive carbon compounds than lighter roots. Thus, the transition from thin to thick fine roots implies a shift in the root carbon economy from ‘do-it-yourself’ soil exploration to collaboration with mycorrhizal fungi, while the shift from light to dense fine roots emphasizes a shift from acquisitive to conservative root strategy. We reveal a previously undocumented role of molecular-level carbon traits that potentially undergird the multidimensional root economics space. This finding offers new molecular insight into the diversity of root form and function, which is fundamental to our understanding of plant evolution, species coexistence and adaptations to heterogeneous environments. Wang and colleagues report a two-dimensional root carbon trait space coupled with the root economics space, offering molecular insights into the great diversity of root form and function.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8,"publicationDate":"2024-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140914901","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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