Current opinion in plant biology最新文献

英文中文

The functions of long noncoding RNAs in plants. 长链非编码rna在植物中的功能。

IF 7.5 2区生物学 Q1 PLANT SCIENCES

Current opinion in plant biology

Pub Date : 2025-12-09 DOI: 10.1016/j.pbi.2025.102830

Jeky Chanwala, Isabell Rosenkranz, Peter Kindgren

Noncoding RNAs are emerging as major regulators in plant development and environmental response. MicroRNAs, small RNAs, and ribosomal RNAs have established mechanisms for generation, maturation, and function. However, long noncoding RNAs (lncRNAs) currently lack a robust classification according to their function. lncRNAs are here defined as noncoding RNAs that are longer than 200 nucleotides and generally transcribed by RNA polymerase II. They often exhibit low expression and limited sequence conservation yet display tissue or stress-specific regulation. Furthermore, lncRNAs are categorized based on their location relative to nearby genes, including sense (overlapping a gene on the same strand), antisense (overlapping on the opposite strand), intronic (located within intron), intergenic (found between genes), and bidirectional (transcribed in the opposite direction from a nearby gene). Here, we summarized the last years of work in the field of lncRNA, but instead of grouping them into the biological processes they are involved in, we attempt to group them into general functions in plants. This will not be an exhaustive grouping of known functions for lncRNA, rather a list of established functions with several characterized cases.

非编码rna正在成为植物发育和环境反应的主要调控因子。MicroRNAs、小rna和核糖体rna已经建立了产生、成熟和功能的机制。然而，长链非编码rna （lncrna）目前缺乏一个根据其功能的可靠分类。lncrna在这里被定义为长度超过200个核苷酸的非编码RNA，通常由RNA聚合酶II转录。它们通常表现出低表达和有限的序列保守，但显示组织或应力特异性调节。此外，lncrna根据其相对于附近基因的位置进行分类，包括正义（在同一条链上重叠一个基因）、反义（在相反的一条链上重叠）、内含子（位于内含子内）、基因间（发现于基因之间）和双向（与附近基因相反方向转录）。在这里，我们总结了近年来lncRNA领域的工作，但我们没有将它们归类到它们所参与的生物过程中，而是试图将它们归类到植物中的一般功能中。这将不是lncRNA已知功能的详尽分组，而是具有几个特征案例的已建立功能列表。

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引用次数: 0

Histone variants: Distinct building blocks of the chromatin acting at the core 组蛋白变体：核心染色质的不同组成部分

IF 7.5 2区生物学 Q1 PLANT SCIENCES

Current opinion in plant biology

Pub Date : 2025-12-04 DOI: 10.1016/j.pbi.2025.102829

Vivek Hari-Sundar Gandhivel , P.V. Shivaprasad

Histone variants alter the core properties of the nucleosomes they decorate and hence constitute a significant epigenetic layer to control cellular processes. Historically, histone variants have been studied using classical genetics to implicate the functions associated with them. However, over the last few years, advanced (epi)genomics and structural investigations have revealed the fine molecular steps involved in histone variant-specific genome regulation. This review outlines the key mechanistic findings that uncovered both structural and functional aspects of plant histone variants in unprecedented resolution. We also highlight the key avenues that might hold potential for future studies, including chromatin engineering using histone variants.

组蛋白变异改变了它们修饰的核小体的核心特性，因此构成了一个重要的表观遗传层来控制细胞过程。从历史上看，组蛋白变异已经使用经典遗传学来研究与它们相关的功能。然而，在过去的几年里，先进的基因组学和结构研究揭示了组蛋白变异特异性基因组调控的精细分子步骤。这篇综述概述了以前所未有的分辨率揭示植物组蛋白变异的结构和功能方面的关键机制发现。我们还强调了可能具有未来研究潜力的关键途径，包括使用组蛋白变体的染色质工程。

引用次数: 0

Architects of plant immunity: Structure-informed strategies for engineering plant nucleotide-binding leucine-rich repeat receptors 植物免疫的建筑师：工程植物核苷酸结合的富含亮氨酸重复序列受体的结构通知策略。

IF 7.5 2区生物学 Q1 PLANT SCIENCES

Current opinion in plant biology

Pub Date : 2025-11-30 DOI: 10.1016/j.pbi.2025.102828

Daniel S. Yu, Mark J. Banfield

Diseases caused by plant pathogens are a major factor decreasing crop yields that lead to food insecurity. To protect against pathogen threats, plants possess a multifaceted immune system that perceive threats derived from plant pathogens, resulting in the activation of immune responses. Evolutionary pressures allow plant pathogens to evolve rapidly and evade recognition by nucleotide-binding leucine-rich repeat (NLR) receptors. In recent years, advancements in our understanding of the molecular and structural basis of effector recognition by NLRs have enabled targeted strategies for engineered receptors that contain novel or expanded recognition profiles. In conjunction with advancements in structural modeling and synthetic biology tools, this has transformed our ability to manipulate plant receptors with precision. Here, we highlight structure-based approaches toward engineering plant NLRs, including integrated domain (ID) engineering and leucine-rich repeat resurfacing, discuss challenges associated with NLR engineering, and highlight future engineering approaches to enhance the plant immune system against pathogen threats.

由植物病原体引起的疾病是导致粮食不安全的作物产量下降的一个主要因素。为了保护植物免受病原体的威胁，植物拥有一个多方面的免疫系统，可以感知来自植物病原体的威胁，从而激活免疫反应。进化压力允许植物病原体快速进化并逃避核苷酸结合富亮氨酸重复（NLR）受体的识别。近年来，我们对nlr效应识别的分子和结构基础的理解取得了进展，这使得针对含有新的或扩展的识别谱的工程受体的靶向策略成为可能。结合结构建模和合成生物学工具的进步，这已经改变了我们精确操纵植物受体的能力。在这里，我们重点介绍了基于结构的植物NLR工程方法，包括集成结构域（ID）工程和富含亮氨酸的重复重表面，讨论了NLR工程相关的挑战，并强调了未来的工程方法，以增强植物免疫系统抵御病原体的威胁。

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引用次数: 0

Conserved, yet distinct: revisiting the roles of C core vacuole/endosome tethering (CORVET) and homotypic fusion and vacuole protein sorting (HOPS) complexes in plants 保守，但独特：重新审视C核液泡/核内体系聚（CORVET）和同型融合和液泡蛋白分选（HOPS）复合物在植物中的作用

IF 7.5 2区生物学 Q1 PLANT SCIENCES

Current opinion in plant biology

Pub Date : 2025-11-27 DOI: 10.1016/j.pbi.2025.102827

Graciela Veronica Castro, Cecilia Rodriguez-Furlan

The spatially constrained nature of plant cells makes them highly reliant on targeted membrane vesicle trafficking, which sustains proper cellular function, tissue organization, and overall plant growth and development. These mechanisms are regulated by small GTPases, which function assembling tethering complexes and later serve as their effectors. Tethering factors facilitate the initial contact between the target membrane and incoming vesicles, thereby playing a pivotal role in vesicle targeting and fusion. This review focuses on two tethering complexes, the class C core vacuole/endosome tethering (CORVET) and the homotypic fusion and vacuole protein sorting (HOPS) tethering complex, which have been best studied in the model plant Arabidopsis thaliana. The activity of these complexes has been linked to the regulation of multivesicular endosomes with the vacuole membrane. However, recent reports propose additional functions for specific HOPS subunits regulating other fusion events. Despite these advances, our understanding of HOPS/CORVET function and regulation, including the input of small GTPases, remains incomplete. Thus, in this review, we emphasize the essential role of the HOPS/CORVET tethering complex in plant growth and development while identifying key gaps for future research.

植物细胞的空间有限性使得它们高度依赖于靶向膜泡运输，这维持了正常的细胞功能、组织组织和整体植物的生长发育。这些机制是由小的gtp酶调节的，它的功能是组装系缚复合物，然后作为它们的效应器。系泊因子促进了靶膜与传入囊泡的初始接触，在囊泡靶向融合中起着关键作用。本文综述了在模式植物拟南芥中研究最多的两种系留复合物，即C类核心液泡/核内体系留复合物（CORVET）和同型融合与液泡蛋白分选复合物（HOPS）。这些复合物的活性与液泡膜对多泡内体的调节有关。然而，最近的报道提出了特定的HOPS亚基调节其他融合事件的附加功能。尽管取得了这些进展，但我们对HOPS/CORVET功能和调控（包括小GTPases的输入）的了解仍然不完整。因此，在这篇综述中，我们强调了啤酒花/CORVET系结复合物在植物生长发育中的重要作用，同时指出了未来研究的关键空白。

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引用次数: 0

Every step you take: How pathogens hijack host proteostasis from transcription, through translation, to degradation 你走的每一步：病原体如何劫持宿主的蛋白质平衡，从转录，到翻译，再到降解

IF 7.5 2区生物学 Q1 PLANT SCIENCES

Current opinion in plant biology

Pub Date : 2025-11-22 DOI: 10.1016/j.pbi.2025.102826

Manuel González-Fuente, Margot Raffeiner, Suayib Üstün

Proteostasis, the regulated balance between protein synthesis and degradation, is crucial for the cellular function and survival. Disruptions in this balance caused by different internal cues and environmental stresses, including pathogen infection, lead to proteotoxicity, which can be highly detrimental or even lethal to the organisms. Pathogens, in their efforts to modulate the host physiology to accommodate their own needs, target and manipulate host proteostasis processes. The extent of pathogen-mediated manipulation of host proteostasis spans every step in the life cycle of a protein: from the transcription and maturation of its coding mRNA, to the protein turnover via the ubiquitin-proteasome system or vacuolar degradation. These diverse sophisticated strategies to manipulate the host proteostasis ultimately lead to the overaccumulation of unfunctional and misfolded proteins, causing proteotoxic stress and facilitating in most cases the pathogen colonization. In turn, plants try to cope with this pathogen-induced proteotoxicity by attenuating translation, promoting chaperon-assisted protein folding and increasing the activity of different proteolytic pathways. Here, we discuss recent advances in understanding the global picture of how pathogens modulate plant proteostasis as well as how plants counter this, which will be crucial for the future development of more tolerant crops to mitigate emerging food security threats.

蛋白质平衡是调节蛋白质合成和降解之间的平衡，对细胞功能和生存至关重要。不同的内部信号和环境压力（包括病原体感染）导致这种平衡被破坏，导致蛋白质毒性，这对生物体可能是非常有害的，甚至是致命的。病原体在努力调节宿主生理以适应自身需要的过程中，瞄准并操纵宿主的蛋白酶平衡过程。病原体介导的对宿主蛋白质稳态的调控范围涵盖了蛋白质生命周期的每一步：从编码mRNA的转录和成熟，到通过泛素-蛋白酶体系统或空泡降解的蛋白质周转。这些复杂多样的控制宿主蛋白质稳态的策略最终导致无功能和错误折叠蛋白质的过度积累，导致蛋白质毒性应激，并在大多数情况下促进病原体定植。反过来，植物试图通过减弱翻译，促进伴侣辅助蛋白质折叠和增加不同蛋白质水解途径的活性来应对这种病原体诱导的蛋白质毒性。在这里，我们讨论了在了解病原体如何调节植物蛋白酶抑制以及植物如何对抗这种情况的全球情况方面的最新进展，这将对未来开发更具耐受性的作物以减轻新出现的粮食安全威胁至关重要。

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引用次数: 0

Pangenomics combined with artificial intelligence and precision breeding can accelerate crop improvement 泛基因组学与人工智能和精准育种相结合，可以加速作物改良。

IF 7.5 2区生物学 Q1 PLANT SCIENCES

Current opinion in plant biology

Pub Date : 2025-11-16 DOI: 10.1016/j.pbi.2025.102825

Teng Li , Shameela Mohamedikbal , Mitchell Bestry , Jacqueline Batley , David Edwards

Pangenomics significantly expands our understanding of genetic diversity in plants beyond single reference genomes by capturing extensive genomic variations. In this review, we discuss recent methodological breakthroughs in pangenomics, including advances in long-read sequencing, graph-based pangenome tools, artificial intelligence, and multiomics approaches that have collectively enabled pangenomes to become more accurate and prevalent. We review the broad applications of pangenomics in plant science, particularly focusing on crop breeding, including haplotype-based selection, improved prediction for genomic selection, multiomics guided marker discovery, precise identification of genome-editing targets, association of genes with agronomic traits, understanding transposable element dynamics, and providing valuable insights to guide crop improvement. Furthermore, we discuss current challenges and future directions for pangenomics studies.

泛基因组学通过捕获广泛的基因组变异，大大扩展了我们对植物遗传多样性的理解，超越了单一参考基因组。在这篇综述中，我们讨论了泛基因组学最近在方法上的突破，包括长读测序、基于图的泛基因组工具、人工智能和多组学方法的进展，这些方法共同使泛基因组学变得更加准确和普遍。综述了泛基因组学在植物科学中的广泛应用，特别是在作物育种方面的应用，包括基于单倍型的选择、基因组选择的改进预测、多组学指导下的标记发现、基因组编辑靶点的精确鉴定、基因与农艺性状的关联、转座因子动力学的理解，以及为指导作物改良提供有价值的见解。最后，讨论了泛基因组学研究面临的挑战和未来发展方向。

引用次数: 0

Monoubiquitination of histone H2A and H2B: News and views 组蛋白H2A和H2B的单泛素化：新闻和观点。

IF 7.5 2区生物学 Q1 PLANT SCIENCES

Current opinion in plant biology

Pub Date : 2025-11-06 DOI: 10.1016/j.pbi.2025.102824

Sara Farrona , Fredy Barneche

Fine-tuning eukaryotic gene expression heavily relies on chromatin regulatory mechanisms involving dynamic exchanges and modifications of histones. Here, we review the main pathways that mediate histone H2A and H2B monoubiquitination and deubiquitination in Arabidopsis thaliana. These histone post-translational modifications are linked to multiple chromatin regulatory layers, enabling distinct functional outcomes across the genome and in response to developmental and environmental signals. Indeed, while H2A deubiquitination primarily attenuates transcription either independently or together with PRC2-mediated H3K27 trimethylation, H2B monoubiquitination facilitates nucleosome dynamics and RNA polymerase II progression during gene activation. Given the widespread role of histone deubiquitination mechanisms in plant development, we also discuss how H2Aub and H2Bub homeostasis influences genome regulation. Finally, by referencing yeast and metazoans, we highlight examples of distinctive plant molecular mechanisms and epigenetic interplays involving histone ubiquitination.

真核生物基因表达的微调很大程度上依赖于染色质调控机制，包括组蛋白的动态交换和修饰。本文综述了拟南芥中介导组蛋白H2A和H2B单泛素化和去泛素化的主要途径。这些组蛋白翻译后修饰与多个染色质调控层相关，从而在整个基因组中实现不同的功能结果，并响应发育和环境信号。事实上，虽然H2A去泛素化主要是单独或与prc2介导的H3K27三甲基化一起减弱转录，但H2B单泛素化促进了基因激活过程中核小体动力学和RNA聚合酶II的进展。鉴于组蛋白去泛素化机制在植物发育中的广泛作用，我们还讨论了H2Aub和H2Bub稳态如何影响基因组调控。最后，通过引用酵母和后生动物，我们强调了独特的植物分子机制和涉及组蛋白泛素化的表观遗传相互作用的例子。

引用次数: 0

Telomeres: The EPI-Ending 端粒：epi的终结。

IF 7.5 2区生物学 Q1 PLANT SCIENCES

Current opinion in plant biology

Pub Date : 2025-11-05 DOI: 10.1016/j.pbi.2025.102823

Petra Procházková Schrumpfová , Miloslava Fojtová , Martina Dvořáčková

Telomeres are essential chromosomal structures that protect genome integrity and play a central role in aging and cell proliferation. In plants, the epigenetic landscape of telomeres and their adjacent subtelomeric regions has emerged as a critical component regulating telomere function and genome organization. This review summarizes current knowledge of chromatin modifications at plant telomeres, and the impact of chromatin-associated factors on telomere stability. We also discuss experimental tools for studying telomere epigenetics, and identify key open questions in the field.

端粒是保护基因组完整性的基本染色体结构，在衰老和细胞增殖中发挥核心作用。在植物中，端粒及其邻近的亚端粒区域的表观遗传景观已成为调节端粒功能和基因组组织的关键组成部分。本文综述了目前对植物端粒染色质修饰的研究进展，以及染色质相关因子对端粒稳定性的影响。我们还讨论了研究端粒表观遗传学的实验工具，并确定了该领域的关键开放问题。

引用次数: 0

Piecing the puzzle together: Analyses in plants at the single-cell resolution 拼凑拼图：单细胞分辨率的植物分析。

IF 7.5 2区生物学 Q1 PLANT SCIENCES

Current opinion in plant biology

Pub Date : 2025-11-05 DOI: 10.1016/j.pbi.2025.102821

Nora Damaris Pasquali Medici de Biron , Sara Farrona

In recent years, single-cell and single-nuclei-omic technologies have advanced rapidly in plant research, with RNA sequencing being widely adopted, and chromatin accessibility profiling through assay for transposase-accessible chromatin with sequencing steadily expanding. These approaches have provided unprecedented insight into plant development, cell identity, and stress responses. Integrating transcriptomic and chromatin accessibility data has made it possible to link regulatory elements with gene expression across diverse plant tissues. The goal of this review is to provide a practical guide synthetizing current methods, bioinformatic tools, and applications for a clear perspective on the opportunities and challenges of implementing these technologies in plants. We place particular emphasis on the technical aspects of single-cell/single-nuclei methods, with the aim of enabling informed decisions regarding the choice of protocol. We also highlight emerging multi-omic strategies, the bioinformatic frameworks that enable their analysis, and applications across diverse plant species. In light of the current progress, we discuss that expanding the use of these technologies in plants will advance fundamental biology and generate actionable insights for crop improvement, driving the translation of single-cell discoveries into agricultural innovation.

近年来，单细胞和单核组学技术在植物研究中迅速发展，RNA测序被广泛采用，通过转座酶可及染色质分析的染色质可及性分析随着测序的不断扩大。这些方法为植物发育、细胞身份和胁迫反应提供了前所未有的见解。整合转录组学和染色质可及性数据使得将调控元件与不同植物组织中的基因表达联系起来成为可能。本文综述的目的是综合现有的方法、生物信息学工具和应用，为在植物中实施这些技术的机遇和挑战提供一个清晰的视角。我们特别强调单细胞/单核方法的技术方面，目的是使有关方案选择的知情决定成为可能。我们还重点介绍了新兴的多组学策略，使其能够分析的生物信息学框架，以及在不同植物物种中的应用。鉴于目前的进展，我们讨论了扩大这些技术在植物中的应用将推进基础生物学，并为作物改良产生可操作的见解，推动单细胞发现转化为农业创新。

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引用次数: 0

Hydathodes at the forefront of plant immunity against vascular pathogens 水蛭在植物免疫对抗血管病原体方面处于领先地位。

IF 7.5 2区生物学 Q1 PLANT SCIENCES

Current opinion in plant biology

Pub Date : 2025-11-03 DOI: 10.1016/j.pbi.2025.102822

Sebastian Pfeilmeier , Misha Paauw , Nanne W. Taks , Harrold A. van den Burg

Hydathodes are tiny plant organs that form an interface between the leaf surface and xylem vasculature. They facilitate excretion of xylem fluid under conditions when leaf transpiration is low and root pressure high—a process known as guttation. Guttation fluid facilitates the entry of (opportunistic) bacterial pathogens into hydathodes. The notorious vascular pathogens of the bacterial genera Xanthomonas and Clavibacter have evolved unique mechanisms to colonize hydathodes and gain access to xylem and then spread systemically throughout the plant causing disease. For a long time, hydathodes were overlooked as plant immune barrier. Recent studies found that plants mount a defense response in hydathodes via known plant immune signaling hubs indicating that hydathode immunity involves both cell surface and intracellular immune receptors to restrict bacterial colonization. In hydathode-adapted Xanthomonas pathovars, the type III secretion system (T3SS) is critical for hydathode colonization. Through the T3SS, bacteria inject effector proteins into plant cells, indicating a role for type III-secreted effectors of Xanthomonas in promoting hydathode colonization. In addition, the type II secretion system (T2SS) and plant cell wall degrading enzymes secreted by Xanthomonas are required for bacterial translocation from the hydathode to the xylem, which indicates the presence of a physical barrier between these tissues. Future research using advanced molecular techniques give now the opportunity to deepen our understanding of hydathode colonization and hydathode immunity in order to develop novel breeding strategies against these devastating vascular bacterial pathogens.

水合器是微小的植物器官，在叶表面和木质部维管系统之间形成一个界面。在叶片蒸腾作用低而根压高的情况下，它们促进木质部液体的排泄，这一过程被称为谷化。唾液有助于（机会性的）细菌病原体进入水罐。黄单胞菌（Xanthomonas）和锁骨杆菌（Clavibacter）这两种臭名昭著的维管束病原体已经进化出独特的机制来定殖水合管并进入木质部，然后在整个植物中系统地传播引起疾病。长期以来，水蛭作为植物的免疫屏障被忽视。最近的研究发现，植物通过已知的植物免疫信号中枢在水蛭体内产生防御反应，表明水蛭免疫涉及细胞表面和细胞内免疫受体，以限制细菌定植。在适应水蛭的黄单胞菌病原菌中，III型分泌系统（T3SS）对水蛭定植至关重要。细菌通过T3SS将效应蛋白注入植物细胞，表明黄单胞菌iii型分泌效应蛋白促进水合菌定植。此外，由黄单胞菌分泌的II型分泌系统（T2SS）和植物细胞壁降解酶是细菌从水合质转移到木质部所必需的，这表明这些组织之间存在物理屏障。利用先进的分子技术进行未来的研究，现在有机会加深我们对水蛭定殖和水蛭免疫的理解，以便开发新的育种策略来对抗这些破坏性的血管细菌病原体。

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