RNA interference (RNAi) has emerged as a promising approach to sustainable crop protection. Extensive proof-of-concept studies have led to the approval of the first sprayable plant protection products in the United States and China, with Europe currently evaluating them. Although gene silencing mechanisms are among the most extensively studied processes in molecular biology, with two Nobel Prizes recognizing their discovery, the optimization of delivery systems and field performance remains an area currently undergoing extensive development. The uptake, stability, and efficacy of double-stranded RNA (dsRNA) are influenced by species-specific and environmental factors, introducing variability that must be understood in order to select robust targets, design effective dsRNA, and assess risk. Although these knowledge gaps remain, they are increasingly addressed through systematic experimental and technological advances. This review summarizes the current knowledge on RNAi mechanisms in plants, fungi, and insects, emphasizing the differences in dsRNA uptake and processing between species. We highlight advances in formulations and delivery technologies, discuss how regulatory and ecological questions are being systematically investigated, and present examples of approved products that demonstrate the approach's feasibility and safety. Finally, we outline how remaining uncertainties can be addressed through targeted research and risk-mitigation strategies and how RNAi technologies can be incorporated into comprehensive pest and disease management systems.
Biomolecular condensates have emerged as versatile regulators of plant cellular processes, offering a dynamic and reversible mechanism to coordinate development, stress response, and spatial organization. Through phase separation, these condensates spatially and temporally modulate biochemical reactions, sequester or activate specific proteins and RNAs, and reshape cellular architecture. This review presents a comprehensive and multidimensional framework for understanding biomolecular condensates in plant biology, from their biophysical properties and ensemble dynamics to their roles across diverse cellular compartments, including plasma membranes, cytoskeleton, intracellular compartments, and chromatin. We highlight their functions in growth, environmental sensing, and defense and discuss current challenges in studying their composition, material properties, and context-dependent behaviors. Understanding plant condensates not only deepens our knowledge of plant cell organization and adaptability but also opens new avenues for biotechnological innovation in agriculture.
This article traces more than four decades of Eva Kondorosi's personal life and scientific journey in symbiotic nitrogen fixation, from early insights into nitrogenase structure to the molecular mechanisms governing root nodule development and symbiotic cell differentiation in the Medicago-Sinorhizobium meliloti symbiosis. Effective symbiosis depends on precise molecular communication between the partners, beginning in the soil and continuing through a highly coordinated, progressive differentiation program. A defining feature of symbiotic cell development is endoreduplication in both host plant cells and their Rhizobium partners. Host-induced bacterial endoreduplication results in the formation of large, polyploid, noncultivable nitrogen-fixing bacteroids. This terminal differentiation is orchestrated by plant-derived effector peptides, notably nodule-specific cysteine-rich (NCR) and nodulin glycine-rich (nodGRP) peptides, which act sequentially to reprogram bacterial physiology. Together, these findings establish symbiotic nitrogen fixation as a model for cross-kingdom cellular differentiation and highlight NCR and nodGRP peptides as a vast, largely unexplored resource with promising applications in agriculture and medicine.
Chloroplasts, the photosynthetic organelles of plants and algae, rely on the import of thousands of nuclear-encoded proteins to sustain their diverse physiological roles. This process is mediated by the coordinated action of the translocon at the outer chloroplast membrane (TOC), the translocon at the inner chloroplast membrane (TIC), and an ATP-driven import motor. However, research on these key machineries has long been intensely debated in the field. Recent advances in structural characterization have now resolved long-standing controversies regarding the composition and architecture of these complexes. This review summarizes the most recent structural, functional, and evolutionary insights into the chloroplast protein import apparatus, emphasizing the transformative role of high-resolution structural biology in redefining long-held paradigms.
Photosynthesis is the fundamental biological process that introduced oxygen into Earth's atmosphere and continues to power life, from the earliest single-celled organisms to entire global ecosystems. Yet, measuring photosynthesis across scales has been challenging because traditional techniques have not transcended scales. The emergence of remote-sensing techniques to measure solar-induced chlorophyll fluorescence (SIF) provides a unique approach to estimate photosynthesis across spatiotemporal scales, representing a new age for optical remote sensing to study photosynthesis and shaping the decades of satellite SIF research. Here, focusing on spatiotemporal scales, we review the mechanisms that drive the relationship between SIF and photosynthesis. Remotely sensed SIF is modulated by biological drivers, environmental drivers, the interaction between biological and environmental drivers, and the viewing geometry. Studying fluorescence at small scales provides the ecophysiological understanding needed to disentangle the biological and environmental drivers of SIF at larger scales. Leveraging progress in satellite SIF, future research should focus on cross-scale mechanistic understanding of the drivers of SIF and using SIF as a metric for plant function beyond photosynthesis.
Plants generate long-range signals via complex mechanisms that integrate electrical, calcium, and chemical signals. While animals employ synaptic/neural connections for cell-cell and organ-organ signal transduction, plants depend on specialized structures, such as plasmodesmata and vascular bundles. This review examines recent advances in elucidating these plant-specific long-range signal mechanisms, emphasizing the initiation, propagation, and integration of diverse signals throughout the plant body. We highlight how the combination of traditional electrical potential measurements and modern bioimaging techniques, particularly genetically encoded fluorescent indicators, has improved our understanding of long-range signals in various plant species, including Arabidopsis thaliana, Mimosa pudica, and Dionaea muscipula. These technological advancements have enabled the development of integrated models that encompass biological components (e.g., ion channel activities), chemical mechanisms (e.g., compound diffusion), and physical processes (e.g., hydraulic signals). This integration offers new insights into how plants coordinate systemic responses across spatially distant organs.
The plant circadian clock enables the precise timing of physiological processes across the day-night cycle by generating endogenous 24-h rhythms in gene expression. In Arabidopsis, an iteration between experiments and modeling has uncovered a core oscillator comprising interlocked transcriptional feedback loops. However, emerging techniques now reveal that circadian dynamics vary across organs, tissues, and even individual cells, highlighting the need for spatially resolved clock models. In this review, we explore evidence for spatial variation in clock regulation, including differences in sensitivity to environmental cues, the timing of clock components, and the nature of downstream outputs. We discuss how local cellular rhythms are coordinated to achieve robust organism-level timing and consider how spatial regulation of the clock may contribute to the control of diverse developmental processes.
The advent of spatial and quantitative biology has led to immense advances in understanding the complex inner workings of plants, down to the molecular scale. Functional imaging of live plants, which enables the spatial and quantitative mapping of biochemical cues, physicochemical properties of cellular structures, and the dynamics of physical and chemical signals with unprecedented resolution, has become a key technology for advancing the mechanistic understanding of plant cell biology. In this review, we highlight progress in live functional imaging in plants through the use and development of chemical fluorescent probes, which enable plant functional imaging without requiring genetic manipulation of the study object. We explain how probes sense, target, and report on functional features within the plant cell; discuss their limitations, including toxicity; and provide case studies to exemplify how these tools can complement biological studies to unravel the complex machinery that makes plants work. We conclude by outlining the expected future development of this field and identifying key challenges that lie ahead.
Plant hormones are essential small molecules that regulate plant growth, development, and systemic responses to environmental stimuli. These processes are mediated by complex signaling networks involving structurally diverse receptors, regulatory proteins, and dynamic protein-protein interactions. Advances in structural and functional biology over the past two decades have revealed how hormone receptors recognize their ligands and how they mediate responses from perception to signaling through transduction pathways and feedback regulation. In this review, we summarize the current knowledge of plant hormone receptors with experimentally determined structures and highlight their central roles in shaping plant biology. Finally, we discuss outstanding questions in the field and how emerging computational tools may help address these gaps.
Nicotinamide adenine dinucleotide (NAD) is an essential coenzyme in cellular metabolism with a long-established role in energy production, biosynthesis, and oxidative stress responses. Recent research demonstrates that NAD hydrolysis is a key step in immune signaling, beyond its primary metabolic functions. Here, we review how NAD and NAD-derived small molecules influence defense-related processes including reactive oxygen species production, calcium dynamics, and immune activation. We introduce diverse NAD-modifying enzymes in plants and discuss how they regulate immunity, with a special emphasis on Toll/interleukin 1 receptor (TIR) domain proteins, which hydrolyze NAD+ to produce immune-activating molecules. We also discuss how pathogens use NAD-modifying enzymes as virulence factors to manipulate host defenses, highlighting NAD metabolism as a newly emerged, critical battleground in the plant-pathogen arms race. Recent developments in this aspect of pathogenesis offer new opportunities to enhance disease resistance.
Grasses (Poaceae) dominate many natural and agricultural ecosystems. Grasses form longitudinal leaves with parallel venation and highly specialized, graminoid stomatal complexes. Theoretical concepts and experimental studies highlight that these anatomical features contribute to physiologically innovative properties, including enhanced capacity and dynamics of water transport and gas exchange. The genetic and molecular regulators underlying vein and epidermal patterning in grasses continue to be elucidated in model species, though integration of these processes is lacking. This review summarizes our current understanding of leaf vein and leaf epidermal development, describes the morphological and physiological characteristics of grass leaves, and highlights those related to water transport pathways and gas exchange. We conclude that an integrative anatomical and physiological framework linking water transport supply and demand must be considered for developmental research and novel crop design. This will enable an understanding of the causes and consequences of anatomical patterns of diverse grass leaves and their translational potential for agriculture in a changing climate.
Epitranscriptomics, the study of dynamic and site-specific RNA modifications, has emerged as a crucial layer of gene regulation in plants, paralleling the role of classical epigenetic mechanisms such as DNA and histone modifications. Among these, N 6 -methyladenosine (m 6 A) has been identified as a central mark involved in the control of the delicate gene expression patterns during plant development and stress responses. This review highlights recent advances in characterizing m 6 A distribution, identifying its regulatory components, and deciphering its molecular functions, with an emphasis on insights from Arabidopsis . We further explore its roles in developmental transitions, environmental adaptation, and epigenetic plasticity. By elucidating the multilayered functions of m 6 A, we underscore its application as a target for crop improvement with epitranscriptome-based yield enhancement and programmable gene editing, offering new frontiers for precision agriculture.
γ-Aminobutyric acid (GABA), a nonproteinogenic amino acid first identified in biological systems over 70 years ago, has long been recognized as a metabolic intermediate. More recently, GABA has also been acknowledged as a signaling molecule that couples physiological responses to metabolic status. This review presents a conceptual framework for how metabolism sets GABA concentration and localization, which then modulate ion transport and membrane potential dynamics to influence plant growth, development, and adaptation to stress. We explore the emerging network of GABA's interactions with other signaling pathways, highlighting its involvement in environmental sensing and internal regulatory mechanisms via hormones and reactive oxygen species. These interactions influence key physiological processes including stomatal regulation, pathogen and herbivore defense, root growth, and even the modulation of flavor. Collectively, these findings position GABA as a metabolic signal integrator of plant physiological status and responses, with broad implications for enhancing crop stress resilience and food quality.
Cryo-electron tomography (cryo-ET) is a transformative technique in cell biology that enables three-dimensional visualization of cellular structures in near-native states and at nanometer and even subnanometer resolution. Unlike traditional imaging methods, cryo-ET preserves the ultrastructure of cells without chemical fixation or staining, allowing researchers to observe macromolecular complexes in situ. Cryo-focused ion beam milling has overcome sample thickness limitations, enabling high-resolution imaging of complex and large specimens. When combined with correlative light microscopy and subtomogram averaging, cryo-ET can localize and resolve macromolecular assemblies within the cell. We discuss how cryo-ET has provided unprecedented insights into cellular architecture by bridging the gap between molecular and cellular scales and highlight examples in photosynthetic organisms. We also discuss new efforts to increase automation, throughput, and validation that make cryo-ET accessible to a larger community of scientists, including plant biologists.
Membrane lipid composition underpins the structural and functional identity of all plant membranes. This review examines membrane lipid metabolism and trafficking, with an emphasis on how lipid diversity and interorganelle movement support plant cell function. We explore the biophysical and biochemical specialization of subcellular membranes, with discussion of the endoplasmic reticulum, plasma membrane, apoplastic vesicles and barriers, tonoplast, peroxisomes, mitochondria, plastids, and thylakoids. We review both vesicular and nonvesicular lipid transport pathways, including membrane contact sites. Particular attention is given to glycerolipids, including phospholipids and galactolipids, sphingolipids, sterols, and, to a lesser extent, fatty acid exchange. By focusing on mechanisms of lipid transfer and remodeling, this review synthesizes our understanding of subcellular membrane lipid composition in the context of dynamic cellular processes including cell plate expansion, environmental stress responses, and photosynthetic membrane assembly.
Phenotypic plasticity (PP) is a fundamental property of plants, enabling a single genotype to produce different phenotypes in response to environmental variation. This ability is crucial for survival and reproduction in heterogeneous habitats, allowing plants to optimize their physiology, development, and growth under changing conditions. Widespread natural genetic variation for plasticity enables selection to shape environmental responses. This review synthesizes the current knowledge on the genetic and molecular mechanisms underlying PP in plants, highlighting its importance for crop breeding and for enhancing resilience to climate change. We discuss experimental approaches to quantify plasticity and identify its genetic basis and consider factors that may constrain the evolution of plasticity. We also explore how advances in the analysis of multisite field trials and genomic prediction have propelled the study of PP in agriculture. Ultimately, a deeper understanding and targeted use of PP hold promise for developing crop varieties that can maintain stable yields in increasingly variable environments.
Inositol phosphates and pyrophosphates are small, water-soluble molecules involved in a range of physiological processes across eukaryotic organisms, including plants. Over the past two decades, significant advancements in inositol (pyro)phosphate detection and chemical synthesis, coupled with the characterization of plant mutants and the structural analysis of receptors and associated proteins, have greatly enhanced our understanding of their production, degradation, and perception in plants. This growing knowledge base demonstrates that inositol (pyro)phosphates are crucial for regulating key processes, such as phosphorus homeostasis, hormone signaling, and plant-microbe interactions. We provide a global perspective on these processes, highlighting recent discoveries, new possibilities, and unresolved questions.
Plants and microbes exchange macromolecules such as RNA and proteins. How this exchange is accomplished is poorly understood, but extracellular vesicles (EVs) have been proposed as likely vehicles. Here, we review recent work on the biogenesis and functions of plant EVs and the current evidence in support of and against their role in cross-kingdom RNA interference. Plant EVs, like EVs from other kingdoms of life, are released in part by the fusion of multivesicular bodies with the plasma membrane, a complex and conserved mechanism involving lipid-modifying proteins, the exocyst complex, and Rab GTPases. Though some plant EV subpopulations are involved in immunity, it appears unlikely that plant EVs contribute to cross-kingdom RNA interference. Recent work has shown that plants secrete extravesicular RNA, including small RNAs and long noncoding RNAs, into the leaf apoplast and onto leaf surfaces, while very little RNA is found inside of EVs. We propose that these free extracellular RNAs play a central role in maintaining a healthy leaf microbiome.
The transition from one pollination syndrome to another should be difficult as it requires coordinated changes of multiple component traits, with each involving multiple genes, yet these transitions occur frequently in nature. Here, we explore the genetic and genomic properties that facilitate such rapid pollination syndrome switches. We begin this review by recognizing the important role of relaxed pollinator specificity and delayed selfing in providing adaptive continuity during pollinator shifts. We then compare theoretical predictions with empirical studies on the genetic architecture and molecular basis underlying pollination syndrome divergence. We find that dominance, pleiotropy, tight genetic linkage, and standing genetic variation are important contributors and highlight the novel insights provided by detailed molecular characterizations. We conclude by suggesting where future efforts can help us bridge the genetic basis of individual trait divergence, the fitness effect of each variant, and the genome-wide recombination landscape into a coherent, predictive framework.
Developmental patterning—such as longitudinal zonation of roots in growth domains, the transversal subdivision into layers of distinct cell types, and asymmetric growth during tropisms—is inherently multiscale and multiprocess. Consequently, computational models integrating these processes and scales are powerful tools to test whether our current understanding of involved players is both necessary and sufficient. Additionally, models help identify missing factors and reveal how the whole exceeds the sum of its parts. In this review, we discuss influential models that have advanced our understanding of root development and its adaptation to environmental conditions. We also highlight the potential for further integration of growth, mechanics, physiology, and physicochemical processes in these models. Such expansions are critical to advance the explanatory power of current models beyond genetic causes and identify the importance of cell size, nutrients, forces, pH, and ionic charge for developmental processes.
