Selenate and sulfate are structurally similar anions that compete for uptake in plants via sulfate transporters (SULTRs). Consistent with previous reports that selenate alters SULTR transcription, we observed that increasing selenate concentrations under a constant sulfate background induced several SULTR genes, including SULTR1.1, SULTR1.2, SULTR2.1, SULTR2.2, SULTR3.1, SULTR4.1, and SULTR4.2, whereas SULTR1.3 and SULTR3.3 were repressed. To extend these transcriptional observations, we compared root-growth responses and sulfur/selenium accumulation in Arabidopsis sultr mutants under controlled sulfate-selenate conditions. The sultr3.1 mutant maintained longer primary roots under selenate stress without a significant change in total sulfur or selenium content, suggesting that SULTR3.1 contributes to selenate-associated root-growth sensitivity through internal anion distribution or downstream stress responses rather than by simply altering total elemental accumulation. In contrast, sultr4.1 and sultr4.2 mutants showed impaired root growth and altered sulfur and selenium contents, supporting roles for vacuolar sulfate transporters in internal anion distribution during selenate stress. Elemental analysis further indicated that SULTR3.5, SULTR4.1, and SULTR4.2 contribute to sulfur/selenium homeostasis, whereas SULTR2.2 is important for maintaining sulfur content under selenate exposure and for selenium accumulation. These findings refine the functional framework of Arabidopsis SULTRs in sulfate-selenate interactions and identify transporters that may be useful targets for improving plant performance in selenium-rich environments.
In low-phosphate (Pi) environments, plants remodel their root system architecture primarily through the inhibition of primary root growth to promote phosphate uptake at top soil. However, the molecular mechanism by which primary root growth is inhibited in response to phosphate deficiency remains unclear. Here, we show that the auxin signaling repressor IAA12 acts as a positive regulator of the Pi deficiency-induced inhibition of primary root growth. As a molecular mechanism, we found that IAA12 restricts primary root elongation by increasing reactive oxygen species (ROS) accumulation, which subsequently suppresses cell division in the root apical meristem. This developmental role of IAA12 depends on blue light signaling. Notably, ectopic expression of IAA12 completely rescues the insensitive primary root phenotypes of cry1cry2 and hy5 mutants in response to phosphate deficiency, indicating that IAA12 functions genetically downstream of the blue light signaling machinery. Taken together, our study provides a signaling framework in which IAA12 mediates blue light-dependent inhibition of primary root elongation in response to phosphate deficiency.
ABA-HYPERSENSITIVE BTB/POZ PROTEIN 1 (AHT1) has been known as a repressor of ABA-mediated inhibition of seed germination in Arabidopsis. Abscisic acid (ABA) is an important phytohormone that regulates seed germination and mediates plant responses to environmental stress. To investigate whether AHT1-mediated ABA signaling is functionally conserved between Arabidopsis and rice, we identified a rice homolog of Arabidopsis AHT1 (AtAHT1) in Oryza sativa L. and designated it OsAHT1. OsAHT1 shares 63.8
ROC5, an HD-ZIP IV transcription factor, negatively regulates bulliform cell development and leaf rolling in rice (Oryza sativa L.). Its molecular partners in epidermal cell fate are well characterised, but its broader effects on agronomic performance and gene expression remain largely unexplored. We evaluated a CRISPR/Cas9-generated roc5 loss-of-function line in the Korean elite japonica cultivar 'Samkwang' over two field seasons, with comparative RNA-seq analysis of flag leaf and panicle tissues at the heading stage. The roc5 line exhibited abaxial leaf rolling; reductions in culm and panicle length, grain number per panicle, and spikelet fertility, resulted in a 32.9
Molecular ecology links the smallest units of genetic variation to the largest patterns of ecological organization, encompassing the phenotypes, interactions, and fitness outcomes on which natural selection acts. Here we review plant molecular ecology as a series of transitions. Molecular markers first made natural variation visible and reconstructed the histories shaping plant distributions. A genomic era followed, in which reference genomes and population-scale sequencing identified the genetic basis of adaptation, though association alone could not reveal gene function in nature. Attention then shifted from correlation to function, testing the ecological roles of genes in native habitats. Advances in single-cell analysis have made it possible to link genes to function with far greater precision. Other technological advances have simultaneously pushed the field’s questions outward, toward communities and ecosystems increasingly reshaped by climate change. We discuss emerging approaches that seek to bridge this widening gap, and argue that a discipline born from the molecule must ultimately account for the ecosystem.
Our previous study of the sugar-regulated expression of OsHXK7 uncovered a functional link between sugar and methyl jasmonate (MJ) signaling in rice. Further examination of additional sugar-responsive genes, including Amy3D and CIPK15, indicated that MJ interferes with sugar-mediated repression. To access global transcriptomic overlap, we performed RNA-seq analysis on rice embryos treated with or without glucose and MJ. About 70
Phospholipase D (PLD)–mediated lipid signaling has been implicated in plant development and stress responses; however, its direct genetic role in plant reproduction remains poorly understood. In this study, we investigated the function of OsPLDα2, a rice homolog of maize ZmPLD3, in pollen tube growth and fertilization. Phylogenetic and domain analyses revealed that OsPLDα2 belongs to the C2-PLD subfamily and contains a conserved C2 domain and two HKD catalytic motifs. Expression analyses showed that OsPLDα2 is highly expressed in mature pollen. Subcellular localization showed its association with cytoskeletal and membrane systems. Using CRISPR/Cas9-mediated gene editing, we generated ospldα2 knockout mutants and found that they exhibited normal vegetative growth but significantly reduced fertility. Cytological analyses revealed that ospldα2 pollen displayed reduced germination rates, abnormal pollen tube elongation both in in vitro and in vivo. In addition, phalloidin staining showed altered F-actin labeling patterns in mutant pollen tubes, suggesting an association between OsPLDα2 function and cytoskeletal organization during pollen tube growth. Our study provides direct genetic evidence linking PLD-mediated lipid signaling to pollen function in a monocot species and highlights the importance of PLD in reproductive development beyond its established roles in stress responses.
Messenger RNA (mRNA) stability is a key determinant of gene expression in plants, linking transcriptional outputs to developmental programs and environmental responses. Epitranscriptomic modifications have emerged as an additional regulatory layer that fine-tunes mRNA fate. Among these, N6-methyladenosine (m6A), 5-methylcytosine (m5C), and pseudouridine (Ψ) are increasingly recognized as major contributors to mRNA stability control. Here, we synthesize current knowledge on how these modifications regulate transcript turnover in plants. We first summarize advances in profiling technologies, including antibody-based approaches, single-base resolution methods, and nanopore direct RNA sequencing. We then discuss the mechanistic roles of m6A as a dynamic and context-dependent signal that can either promote mRNA decay through reader-mediated pathways or stabilize transcripts depending on cellular conditions. In contrast, m5C is generally associated with transcript stabilization via structural reinforcement and regulation of mRNA export, whereas Ψ appears to modulate a trade-off between translation efficiency and mRNA stability. We further highlight how positional effects, developmental stage, and environmental stress influence modification outcomes. Finally, we discuss emerging evidence for crosstalk among epitranscriptomic modifications and outline key challenges, including identifying missing regulatory components and establishing causal relationships. Together, these findings support a model in which mRNA modifications act combinatorially to regulate mRNA homeostasis in plants.
The nuclear pore complex (NPC) is an essential component of the nuclear envelope in all eukaryotic organisms, serving as the unique channel for transport between the nucleus and the cytoplasm. Consistent with NPCs’ macromolecular transport functions, NPCs are highly conserved across diverse lineages, including animals, yeast, and plants. Recent studies have revealed that NPCs have variant functions not only in traditional transport roles but also in direct and indirect gene regulation. Despite many researchers’ efforts, our understanding of NPC function remains fragmentary because NPCs have high structural levels of complexity consisting of many constituent proteins called nucleoporins (NUPs) and their interconnected interaction networks. Furthermore, plant NPCs contain plant-specific NUPs that are absent in other organisms. Given that plants are sessile organisms, these plant-specific NUPs likely evolved to precisely regulate a variety of developmental processes and environmental changes. In this review, we integrate the current knowledge regarding plant NPCs, suggesting that they act intricate and active regulatory hubs integrating a variety of endogenous and exogenous signals.
Chloroplast RNA post-transcriptional regulation, including RNA editing, splicing, and stabilization, is essential for chloroplast biogenesis. Although numerous factors involved in plastid RNA metabolism have been identified, the regulatory networks and functional relationships among them remain largely elusive. Here, we characterized a rice mutant, young seedling stripe3 (yss3), which exhibits a distinct white stripe phenotype at the seedling stage accompanied by severe defects in chloroplast development. Map-based cloning and transgenic complementation assays revealed that the yss3 phenotype is caused by a mutation in the Multiple Organellar RNA Editing Factor 9 (OsMORF9) gene. Further analysis demonstrated that the yss3 mutant displays widespread defects in chloroplast RNA editing and in the splicing of multiple chloroplast group II introns. Moreover, yeast two-hybrid and bimolecular fluorescence complementation assays suggested that OsMORF9 interacts with OsDYW2 and OsCLB19, whose Arabidopsis homologs are core components of the chloroplast RNA editosome. Additionally, OsMORF9 interacts with OsSLA4, OsTHA8, and OsYSA; notably, OsTHA8 is a small P-type PPR protein implicated in both RNA editing and splicing. Collectively, these results establish that OsMORF9 acts as a central hub in chloroplast RNA processing.
Trans-acting small interfering RNAs (tasiRNAs) produced from TAS1/2 loci regulate HEAT-INDUCED TAS1 TARGET transcripts and mRNAs encoding pentatricopeptide repeat proteins in Arabidopsis thaliana (A. thaliana). However, their genomic organization in polyploid crops is unknown. Here, we identified and characterized TAS1/2-like loci (TAS1L/2L) in 12 cultivars of the allohexaploid crop Camelina sativa (C. sativa) using conserved miR173/TAS1c 3′D6(–) trigger sites with TAS1/2-derived tasiRNAs. Through phasing analysis with publicly available sRNA-Seq dataset from one of 12 cultivars, we confirmed that these loci tend to produce small RNAs in a phased manner. We also identified that TAS2–TAS1 arrangement in A. thaliana is also conserved in all identified TAS1L/2L loci across the genome of 12 C. sativa’s cultivars. Furthermore, for C. sativa cv. Ames1043, identified TAS2L–TAS1L loci showed a distinct miR173-triggered 21-nucleotide-length phasing, whereas one TAS2L–TAS1L with a disrupted miR173-binding site exhibited weak aberrant phasing. Our findings suggest that the copy number variations in TAS1L-derived tasiR255-like and TAS1c 3′D6(–)-like elements may contribute to cultivar-specific differences in the potential regulation of their target genes. Together, our results suggest a significant conservation of TAS1L/2L and their relative genomic organization of TAS1/2 loci across C. sativa cultivars and provide functioning of miR173-triggered phasing mechanism on TAS1L/2Ls, offering a concise framework for dissecting small-RNA regulatory networks in polyploid crops.
As sessile, plants are continuously threatened by a number of potential pathogens. To survive in nature, plants have evolved sophisticated immune systems to effectively disarm pathogens. Plant immune responses are triggered by the recognition of pathogen-derived molecules by immune receptors, and are often accompanied by the extracellular secretion of immune molecules. Plants generally utilize two distinct mechanisms to discharge immune molecules out of cells: plasma membrane (PM)-localized transporter-associated secretion and secretory vesicle-related exocytosis. For exocytosis, plants, as eukaryotes, require the complex formation of soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) to facilitate membrane fusion between a vesicle and the PM. In this review, we discuss relevant SNARE complexes involved in plant immune exocytosis. Furthermore, we discuss how plants control the complex formation of a specific set of SNAREs involved in immune responses.
DNAJ E1 proteins constitute a structurally distinct subgroup of DNAJ-related proteins that retain DnaJ-like zinc-finger motifs but lack the J-domain required for canonical HSP70 co-chaperone activity. By classifying plant DNAJ and DNAJ-related proteins according to domain composition and surveying their subcellular localization, we reveal a strong enrichment of E1-type proteins in chloroplast localization. Across plant species, DNAJ E1 proteins have been implicated in plastid development, chloroplast function, photosynthetic pigment regulation, stress adaptation, and reproductive output, collectively underpinning plant survival. Sequence and structural predictions indicate that rice homologs retain conserved CxxC-containing motifs shared with functionally characterized Arabidopsis DNAJ E1 proteins. Rice expression profiles further support this framework by showing green tissue-enriched and stress-responsive expression patterns together with seed-associated expression of several homologs. By integrating comparative functional studies, conserved structural features, and rice expression profiles, we propose a stage- and trait-centered framework for interpreting DNAJ E1 function in rice. This perspective highlights DNAJ E1 proteins as promising genetic resources for investigating plastid biogenesis, chloroplast maintenance, stress responsiveness, and developmental performance in cereal crops.
Protein–protein interactions (PPIs) are central to cellular processes, and their interpretation increasingly relies on structure-based analyses enabled by advances in protein structure prediction. Although three-dimensional (3D) molecular visualization tools provide detailed spatial information, two-dimensional (2D) interaction diagrams remain valuable for summarizing amino acid residue-level contacts in a compact and interpretable format. Among available tools, DIMPLOT is widely used to generate residue-level 2D PPI diagrams; however, the resulting diagrams are typically static, limiting their reuse, inspection, and sharing across analytical contexts. To address this limitation, we developed 2DPPI-Viewer, a Python-based tool that converts DIMPLOT outputs into standalone interactive HTML visualizations. 2DPPI-Viewer embeds inspection capabilities directly within the exported diagrams, enabling exploration of residue-level interactions without reliance on the original software environment. By decoupling diagram generation from downstream inspection, 2DPPI-Viewer preserves original interaction detection results while improving accessibility for collaborative and multi-device workflows. In addition, chain-separated layout stabilization and clear visual separation of interaction classes enhance interpretation of complex PPI interfaces. Together, these features extend the usability of 2D PPI diagrams in modern structure-based studies.
Nonexpressor of pathogenesis-related gene 1 (NPR1) is a pivotal regulator coordinating salicylic acid (SA)-mediated immunity with physiological adaptation to environmental stress. NPR1 has been primarily described as a redox-responsive transcriptional coactivator in the nucleus. In confocal analysis, we previously observed that NPR1 tended to transiently accumulate in the chloroplasts of Nicotiana tabacum mesophyll and guard cells under abiotic and biotic stress, suggesting a potential signaling role at the organelle level. To address this question, we conducted RNA sequencing of Nicotiana tabacum lines expressing the chloroplast-targeted NPR1 (cTP–NPR1) and compared their transcriptomes with those of wild-type plants 48h after Phytophthora parasitica infection. The analysis identified distinct clusters of differentially expressed genes involved in SA and ethylene–jasmonic acid cross-talk, redox response, calcium signaling, and transcriptional regulation. Interestingly, functional enrichment revealed that several genes participated in membrane trafficking pathways, notably those involved in vesicle-mediated transport, phospholipid metabolism, and Golgi-to-ER retrograde trafficking. Collectively, our results support a model in which chloroplast-targeted NPR1 functions within a chloroplast-originated signaling network that integrates redox, metabolic, and hormonal cues to reprogram nuclear transcription during immune activation.
The phytocystatins (PhyCYSs) of plants are members of the cystatin superfamily of proteins, which function as potent inhibitors of cysteine proteases. Arabidopsis PhyCYS2 (AtCYS2) is involved in various biological processes, including protein turnover, development and stress responses. However, the molecular mechanisms of AtCYS2 expression under abiotic stresses remain obscure. Here, we demonstrate that AtCYS2 transcript levels and AtCYS2 promoter-driven β-glucuronidase (PAtCYS2::GUS) activity are significantly induced by exogenous abscisic acid (ABA) as well as by drought, osmotic, and salt stress. Histochemical analysis of PAtCYS2::GUS plants confirmed strong induction in leaves, particularly in guard cells, and in root tips following ABA and abiotic stress treatments. We further identified that the transcription factor ELONGATED HYPOCOTYL 5 (HY5) regulates AtCYS2 expression by directly binding to its promoter. Transient overexpression of HY5 with the PAtCYS2::GUS reporter in Arabidopsis protoplasts revealed that HY5 suppresses AtCYS2 expression under ABA treatment. Consistent with its regulation through ABA signaling, AtCYS2 expression was severely compromised in ABA-insensitive (abi) mutants but was markedly upregulated in the hy5 null mutant. Collectively, these results indicate that while ABA signaling triggers AtCYS2 induction, HY5 acts as a transcriptional repressor to fine-tune this response. This negative feedback loop likely prevents excessive protease inhibition, ensuring optimal adaptation to adverse environments.
Soil salinity imposes a complex combination of ionic, osmotic, and oxidative stresses that disrupt plant cellular homeostasis and significantly limit crop productivity. Over the past decades, major signaling components of salinity responses, including Ca2+ and reactive oxygen species (ROS) signaling, abscisic acid (ABA) pathways, kinase networks and transcription factor (TF)-mediated gene regulation have been extensively characterized. However, existing models remain largely pathway-centric and do not adequately explain how these components are hierarchically organized and dynamically integrated into coherent adaptive responses. Here, we synthesize current knowledge across multiple regulatory layers, spanning early stress perception and Ca2+-ROS amplification, kinase-mediated signal integration, transcriptional regulation, post-translational control and emerging mechanisms such as miRNAs and epigenetic modifications. We highlight that while core modules, including CBL-CIPK-SOS signaling, PYR/PYL-PP2C-SnRK2 ABA pathways and MAPK/CDPK-mediated phosphorylation are strongly supported by biochemical and genetic evidence, many higher-order interactions remain partially validated or inferred. To address these limitations, we propose a Hierarchical Signal Integration Model (HSIM) that organizes salinity signaling into three functional layers: input (ionic and osmotic sensing), integration (ABA signaling, kinase networks, and Ca2+-ROS feedback modules) and output (transcriptional and post-translational regulation). Within this framework, kinase hubs emerge as central nodes of signal convergence and amplification, whereas ABA functions as a context-dependent regulator rather than a universally dominant pathway. By emphasizing hierarchical organization, feedback dynamics, and context-dependent interactions, HSIM provides a testable framework for understanding signal prioritization, robustness and growth-stress trade-offs, and offers a foundation for predictive modeling and rational engineering of salinity tolerance in crops.
Abscission is the process through which plants shed organs, including petals, leaves, fruits, and seeds. Quantitative measurement of organ detachment force is crucial for characterizing abscission phenotypes; however, most studies still depend on qualitative assessments, such as visual scoring of attached versus detached organs at specific developmental stages. Although a method for constructing a petal break strength meter has been reported, the reliance of this method on microcontrollers and manual petal pulling has limited accessibility and consistency. Thus, this study presents the Plant Organ Detachment Force Analyzer (PODFA), a Raspberry Pi-based device that improves accessibility and measurement precision. A PODFA incorporates an automated vertical stage to minimize operator-dependent error and provides a user‑friendly interface to facilitate using this analyzer in abscission research. While optimized for Arabidopsis petals, a PODFA can be readily adapted to measure detachment forces in other plant organs by modifying the gripping components, making this analyzer a versatile and cost‑effective tool for studying organ abscission.
Drought stress limits plant growth, development and crop yield. As chromatin-associated proteins, high mobility groups B (HMGBs) play key roles in abiotic stress response regulatory networks. However, the roles of HMGB proteins in tolerance to drought remain largely unclear. In this study, the function of the MdHMGB15 gene in response to drought and abscisic acid (ABA) in apple (Malus × domestica) was identified. Promoter analysis revealed multiple stress-related response elements in MdHMGB15 promoter, while protein sequence analysis confirmed its classification within the HMGB subfamily, containing typical ARID and HMG domains. MdHMGB15 overexpression enhanced apple drought tolerance, shown by higher fresh weight, increased endogenous ABA accumulation, reduced hydrogen peroxide (H2O2) and superoxide anion (O2−) production and decreased relative electrical conductivity under drought stress. The heterologous expression of MdHMGB15 promoted stomatal closure and enhanced the tolerance of tomato and Arabidopsis to drought stress. MdHMGB15-overexpressing calli reduced sensitivity to drought treatment. However, MdHMGB15-overexpressing plants increased the sensitivity to ABA in apple and tomato. Under ABA treatment conditions, the heterologous expression of MdHMGB15 in Arabidopsis showed an inhibitory effect on seed germination and seedling growth rates. In conclusion, this work identifies the chromatin associated protein MdHMGB15 as a key positive regulator of plant drought tolerance and ABA sensitivity, providing a theoretical basis for further research into its chromatin mediated molecular mechanisms.
Sand dunes are important barriers to the coastal interior and provide habitat for numerous organisms. Species composition influences the shape and size of dunes, yet recent studies have documented changes in range of native species and increased abundance of invasive species. Warming temperatures are attributed to changes in plant species distributions, yet the effects of varying temperature on the physiology of dominant dune grasses in the southeast US are largely unknown. We characterized how the temperature and light environments affected the physiology of dominant species differing in photosynthetic pathways and compared to field values. Species physiological responses were not fully explained by differences in photosynthetic pathways. Carex kobomugi (invasive C3) exhibited the highest rates of photosynthesis, stomatal conductance (GSW), and electron transport rate (ETR) at 20 to 40 °C compared to native species. Physiology of Ammophila breviligulata (native C3) was negatively impacted at high temperatures, potentially impacting future range distributions, whereas physiological performance was reduced at 25 °C and below in Panicum amarum (native C4). In contrast, Uniola paniculata (native C4) exhibited similar photosynthetic rates to A. breviligulata at most temperatures. These results demonstrate that temperature differentially impacts species physiology and may impact future range distributions with climate warming.
