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Annual review of plant biology最新文献

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Molecular Mechanisms Underlying the Establishment, Maintenance, and Removal of DNA Methylation in Plants. 植物DNA甲基化的建立、维持和去除的分子机制。
IF 21.3 1区 生物学
Annual review of plant biology Pub Date : 2025-05-01 Epub Date: 2025-03-03 DOI: 10.1146/annurev-arplant-083123-054357
Guohui Xie, Xuan Du, Hongmiao Hu, Jiamu Du
{"title":"Molecular Mechanisms Underlying the Establishment, Maintenance, and Removal of DNA Methylation in Plants.","authors":"Guohui Xie, Xuan Du, Hongmiao Hu, Jiamu Du","doi":"10.1146/annurev-arplant-083123-054357","DOIUrl":"10.1146/annurev-arplant-083123-054357","url":null,"abstract":"<p><p>Methylation at the fifth position of the cytosine base (5mC) is a critical DNA modification with important functions in gene silencing, genome imprinting, and suppression of transposable elements in eukaryotes. Biochemically, DNA methylation is dynamically regulated by three critical processes: the de novo establishment of DNA methylation, the maintenance of DNA methylation by preexisting methylation patterns, and the removal of DNA methylation. In plants, DNA methylation is very complex with unique features. In past decades, a series of biochemical and structural studies, especially empowered by the recent breakthroughs of high-resolution cryogenic electron microscopy, have helped uncover the molecular mechanisms underlying the establishment, maintenance, and removal of DNA methylation in plants. This review summarizes recent research advances in these three aspects of DNA methylation and lays out a molecular view of plant DNA methylation from biochemical and structural perspectives.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":" ","pages":"143-170"},"PeriodicalIF":21.3,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143603718","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
Between Host and Invaders: The Subcellular Cell Wall Dynamics at the Plant-Pathogen Interface. 寄主与入侵者之间：植物-病原体界面的亚细胞细胞壁动力学。
IF 21.3 1区 生物学
Annual review of plant biology Pub Date : 2025-05-01 DOI: 10.1146/annurev-arplant-061824-115733
Lucrezia Pinto, Luis Soler-López, Antonio Serrano, Clara Sánchez-Rodríguez
{"title":"Between Host and Invaders: The Subcellular Cell Wall Dynamics at the Plant-Pathogen Interface.","authors":"Lucrezia Pinto, Luis Soler-López, Antonio Serrano, Clara Sánchez-Rodríguez","doi":"10.1146/annurev-arplant-061824-115733","DOIUrl":"10.1146/annurev-arplant-061824-115733","url":null,"abstract":"<p><p>Plant-pathogen interactions have profound ecological implications and are crucial for food security. Usually studied at the two extreme scales of plant organ symptomatology and host-microbe molecules, they are a cell-cell event mainly occurring at the subcellular level of the plant apoplast. Here, the cell walls of both organisms suffer an intense alteration as a consequence of active degradation by the opponent and self-protection mechanisms to survive and continue growing. The plant cell wall modifications and their role in defense as danger signals and activators of signaling cascades have been studied for a few decades, mainly at the organ plane. Still, much remains unknown about this process, including cellular and subcellular minority decorations, proteins, and mechanical cues. Comparatively, the microbial cell wall changes in planta are virtually unexplored. By investigating the interface between plant and microbial cell walls biochemically, structurally, and mechanically, we aim to highlight the dynamic interplay in these subcellular areas and its significance for the host-invader interaction.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":"76 1","pages":"255-284"},"PeriodicalIF":21.3,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144109292","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
Root Growth and Development in "Real Life": Advances and Challenges in Studying Root-Environment Interactions. 现实生活中的根系生长和发育：研究根系与环境相互作用的进展与挑战》。
IF 21.3 1区 生物学
Annual review of plant biology Pub Date : 2025-05-01 Epub Date: 2025-03-14 DOI: 10.1146/annurev-arplant-083123-074506
Poonam Mehra, Jason Banda, Lucas León Peralta Ogorek, Riccardo Fusi, Gabriel Castrillo, Tino Colombi, Bipin K Pandey, Craig J Sturrock, Darren M Wells, Malcolm J Bennett
{"title":"Root Growth and Development in \"Real Life\": Advances and Challenges in Studying Root-Environment Interactions.","authors":"Poonam Mehra, Jason Banda, Lucas León Peralta Ogorek, Riccardo Fusi, Gabriel Castrillo, Tino Colombi, Bipin K Pandey, Craig J Sturrock, Darren M Wells, Malcolm J Bennett","doi":"10.1146/annurev-arplant-083123-074506","DOIUrl":"10.1146/annurev-arplant-083123-074506","url":null,"abstract":"<p><p>Plant roots play myriad roles that include foraging for resources in complex soil environments. Within this highly dynamic soil environment roots must sense, interact with, and acclimate to factors such as water availability, microbiota, and heterogeneous distribution of nutrients. To aid their acclimation, roots alter their growth and development to optimize their architecture and actively regulate the physical, chemical, and biological properties of their rhizosphere. Understanding the complex interactions between roots and rhizosphere is critical for designing future crops with improved root traits better adapted to diverse and challenging soil conditions. However, studying roots and their interactions with soil under real-world conditions presents significant challenges. Addressing these challenges demands developing realistic laboratory-based model systems and innovative field-based root imaging techniques. Our review surveys the current knowledge and recent advances in understanding root-environment interactions while proposing future solutions to study roots under more \"real-life\" soil conditions.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":" ","pages":"467-492"},"PeriodicalIF":21.3,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143630124","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
Target of Rapamycin (TOR): A Master Regulator in Plant Growth, Development, and Stress Responses. 雷帕霉素靶点（TOR）：植物生长、发育和胁迫反应的主要调控因子。
IF 21.3 1区 生物学
Annual review of plant biology Pub Date : 2025-05-01 Epub Date: 2025-02-14 DOI: 10.1146/annurev-arplant-083123-050311
Yanlin Liu, Jun Hu, Xiaoli Duan, Wenlong Ding, Menglan Xu, Yan Xiong
{"title":"Target of Rapamycin (TOR): A Master Regulator in Plant Growth, Development, and Stress Responses.","authors":"Yanlin Liu, Jun Hu, Xiaoli Duan, Wenlong Ding, Menglan Xu, Yan Xiong","doi":"10.1146/annurev-arplant-083123-050311","DOIUrl":"10.1146/annurev-arplant-083123-050311","url":null,"abstract":"<p><p>The target of rapamycin (TOR) is a central regulator of growth, development, and stress adaptation in plants. This review delves into the molecular intricacies of TOR signaling, highlighting its conservation and specificity across eukaryotic lineages. We explore the molecular architecture of TOR complexes, their regulation by a myriad of upstream signals, and their consequential impacts on plant physiology. The roles of TOR in orchestrating nutrient sensing, hormonal cues, and environmental signals are highlighted, illustrating its pivotal function in modulating plant growth and development. Furthermore, we examine the impact of TOR on plant responses to various biotic and abiotic stresses, underscoring its potential as a target for agricultural improvements. This synthesis of current knowledge on plant TOR signaling sheds light on the complex interplay between growth promotion and stress adaptation, offering a foundation for future research and applications in plant biology.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":" ","pages":"341-371"},"PeriodicalIF":21.3,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143424515","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
RNA Structure: Function and Application in Plant Biology. RNA 结构：植物生物学中的功能和应用
IF 21.3 1区 生物学
Annual review of plant biology Pub Date : 2025-05-01 Epub Date: 2025-03-18 DOI: 10.1146/annurev-arplant-083123-055521
Huakun Zhang, Yiliang Ding
{"title":"RNA Structure: Function and Application in Plant Biology.","authors":"Huakun Zhang, Yiliang Ding","doi":"10.1146/annurev-arplant-083123-055521","DOIUrl":"10.1146/annurev-arplant-083123-055521","url":null,"abstract":"<p><p>RNA orchestrates intricate structures that influence gene expression and protein production in all living organisms, with implications for fundamental biology, medicine, and agriculture. Although extensive research has been conducted on RNA biology, many regulatory mechanisms remain elusive due to the complex and dynamic nature of RNA structures and past technological limitations. Recent advancements in RNA structure technology have revolutionized plant RNA biology research. Here, we review cutting-edge technologies for studying RNA structures in plants and their functional significance in diverse biological processes. Additionally, we highlight the pivotal role of RNA structure in influencing plant growth, development, and responses to environmental stresses. We also discuss the potential evolutionary significance of RNA structure in natural adaptation and crop domestication. Finally, we propose leveraging RNA structure-mediated gene regulation as an innovative strategy to bolster plant resilience against climate change.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":" ","pages":"115-141"},"PeriodicalIF":21.3,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143656162","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
Nitrate Sensing and Signaling in Plants: Comparative Insights and Nutritional Interactions. 植物的硝酸盐感知和信号传导：比较见解和营养相互作用。
IF 21.3 1区 生物学
Annual review of plant biology Pub Date : 2025-05-01 DOI: 10.1146/annurev-arplant-083123-053039
Sandrine Ruffel, Jorge Del Rosario, Benoît Lacombe, Hatem Rouached, Rodrigo A Gutiérrez, Gloria M Coruzzi, Gabriel Krouk
{"title":"Nitrate Sensing and Signaling in Plants: Comparative Insights and Nutritional Interactions.","authors":"Sandrine Ruffel, Jorge Del Rosario, Benoît Lacombe, Hatem Rouached, Rodrigo A Gutiérrez, Gloria M Coruzzi, Gabriel Krouk","doi":"10.1146/annurev-arplant-083123-053039","DOIUrl":"10.1146/annurev-arplant-083123-053039","url":null,"abstract":"<p><p>Plant nitrogen nutrition is an essential and energy-costly component of terrestrial food chains. Understanding nitrate sensing in plants can lead to improved crop yields and nutrient use efficiency, directly impacting food security and agricultural sustainability. Herein, we review and present a comprehensive framework for understanding nitrate sensing in plants, integrating molecular, genetic, and physiological aspects. We begin by detailing the primary nitrate response and nitrate starvation response, which are central to the plant's ability to sense and respond to nitrate availability. We then explore the intricate interactions between nitrate signaling and other nutritional pathways such as those for carbon, phosphorus, potassium, and sulfur assimilation and reactive oxygen species (ROS) handling, and how it unfolds in long-distance systemic communication between roots and shoots. Finally, evolutionary insights are provided by comparing nitrate-sensing mechanisms across different plant species as well as Bacteria, Archaea, Chlorophyta, Charophyta (algae), and Fungi, revealing how these mechanisms may have evolved in diverse ecological niches. This review not only provides a framework to project our present and future understanding of plant nitrate and nitrogen nutrition but also offers potential strategies for improving nutrient use efficiency in crops through genetic and biotechnological interventions.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":"76 1","pages":"25-52"},"PeriodicalIF":21.3,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144109364","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
Centrophilic Retrotransposons of Plant Genomes. 植物基因组的亲中心反转录转座子。
IF 21.3 1区 生物学
Annual review of plant biology Pub Date : 2025-05-01 Epub Date: 2025-02-14 DOI: 10.1146/annurev-arplant-083123-082220
Alexandros Bousios, Tetsuji Kakutani, Ian R Henderson
{"title":"Centrophilic Retrotransposons of Plant Genomes.","authors":"Alexandros Bousios, Tetsuji Kakutani, Ian R Henderson","doi":"10.1146/annurev-arplant-083123-082220","DOIUrl":"10.1146/annurev-arplant-083123-082220","url":null,"abstract":"<p><p>The centromeres of eukaryotic chromosomes are required to load CENH3/CENP-A variant nucleosomes and the kinetochore complex, which connects to spindle microtubules during cell division. Despite their conserved function, plant centromeres show rapid sequence evolution within and between species and a range of monocentric, holocentric, and polymetacentric architectures, which vary in kinetochore numbers and spacing. Plant centromeres are commonly composed of tandem satellite repeat arrays, which are invaded by specific families of centrophilic retrotransposons, whereas in some species the entire centromere is composed of such retrotransposons. We review the diversity of plant centrophilic retrotransposons and their mechanisms of integration, together with how epigenetic information and small RNAs control their proliferation. We discuss models for rapid centromere sequence evolution and speculate on the roles that centrophilic retrotransposons may play in centromere dynamics. We focus on plants but draw comparisons with animal and fungal centromeric transposons to highlight conserved and divergent themes across the eukaryotes.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":" ","pages":"579-604"},"PeriodicalIF":21.3,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143424572","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
Planting Genomes in the Wild: Arabidopsis from Genetics History to the Ecology and Evolutionary Genomics Era. 野生种植基因组：拟南芥从遗传学历史到生态学和进化基因组学时代。
IF 21.3 1区 生物学
Annual review of plant biology Pub Date : 2025-05-01 Epub Date: 2025-02-19 DOI: 10.1146/annurev-arplant-071123-095146
Laura Leventhal, Megan Ruffley, Moises Exposito-Alonso
{"title":"Planting Genomes in the Wild: <i>Arabidopsis</i> from Genetics History to the Ecology and Evolutionary Genomics Era.","authors":"Laura Leventhal, Megan Ruffley, Moises Exposito-Alonso","doi":"10.1146/annurev-arplant-071123-095146","DOIUrl":"10.1146/annurev-arplant-071123-095146","url":null,"abstract":"<p><p>The genetics model system <i>Arabidopsis thaliana</i> (L.) Heynh. lives across a vast geographic range with contrasting climates, in response to which it has evolved diverse life histories and phenotypic adaptations. In the last decade, the cataloging of worldwide populations, DNA sequencing of whole genomes, and conducting of outdoor field experiments have transformed it into a powerful evolutionary ecology system to understand the genomic basis of adaptation. Here, we summarize new insights on <i>Arabidopsis</i> following the coordinated efforts of the 1001 Genomes Project, the latest reconstruction of biogeographic and demographic history, and the systematic genomic mapping of trait natural variation through 15 years of genome-wide association studies. We then put this in the context of local adaptation across climates by summarizing insights from 73 <i>Arabidopsis</i> outdoor common garden experiments conducted to date. We conclude by highlighting how molecular and genomic knowledge of adaptation can help us to understand species' (mal)adaptation under ongoing climate change.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":" ","pages":"605-635"},"PeriodicalIF":21.3,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143456620","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
Systems Biology of Streptophyte Cell Evolution. 链藻细胞进化的系统生物学。
IF 21.3 1区 生物学
Annual review of plant biology Pub Date : 2025-05-01 Epub Date: 2025-01-16 DOI: 10.1146/annurev-arplant-083123-060254
Elisa S Goldbecker, Jan de Vries
{"title":"Systems Biology of Streptophyte Cell Evolution.","authors":"Elisa S Goldbecker, Jan de Vries","doi":"10.1146/annurev-arplant-083123-060254","DOIUrl":"10.1146/annurev-arplant-083123-060254","url":null,"abstract":"<p><p>More than 500 million years ago, a streptophyte algal population established a foothold on land and started terraforming Earth through an unprecedented radiation. This event is called plant terrestrialization and yielded the Embryophyta. Recent advancements in the field of plant evolutionary developmental biology (evo-devo) have propelled our knowledge of the closest algal relatives of land plants, the zygnematophytes, highlighting that several aspects of plant cell biology are shared between embryophytes and their sister lineage. High-throughput exploration determined that routes of signaling cascades, biosynthetic pathways, and molecular physiology predate plant terrestrialization. But how do they assemble into biological programs, and what do these programs tell us about the principal functions of the streptophyte cell? Here, we make the case that streptophyte algae are unique organisms for understanding the systems biology of the streptophyte cell, informing on not only the origin of embryophytes but also their fundamental biology.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":" ","pages":"493-522"},"PeriodicalIF":21.3,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998892","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
Autophagy in Plant Health and Disease. 植物健康与疾病中的自噬
IF 21.3 1区 生物学
Annual review of plant biology Pub Date : 2025-05-01 Epub Date: 2025-01-22 DOI: 10.1146/annurev-arplant-060324-094912
Angelina S Gross, Margot Raffeiner, Yonglun Zeng, Suayib Üstün, Yasin Dagdas
{"title":"Autophagy in Plant Health and Disease.","authors":"Angelina S Gross, Margot Raffeiner, Yonglun Zeng, Suayib Üstün, Yasin Dagdas","doi":"10.1146/annurev-arplant-060324-094912","DOIUrl":"10.1146/annurev-arplant-060324-094912","url":null,"abstract":"<p><p>Autophagy has emerged as an essential quality control pathway in plants that selectively and rapidly removes damaged or unwanted cellular components to maintain cellular homeostasis. It can recycle a broad range of cargoes, including entire organelles, protein aggregates, and even invading microbes. It involves the de novo biogenesis of a new cellular compartment, making it intimately linked to endomembrane trafficking pathways. Autophagy is induced by a wide range of biotic and abiotic stress factors, and autophagy mutant plants are highly sensitive to stress, making it an attractive target for improving plant stress resilience. Here, we critically discuss recent discoveries related to plant autophagy and highlight open questions and future research areas.</p>","PeriodicalId":8335,"journal":{"name":"Annual review of plant biology","volume":" ","pages":"197-227"},"PeriodicalIF":21.3,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143021623","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
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