Small G proteins, functioning as monomeric GTPases, are critical molecular switches that regulate diverse processes in plants. However, little is known about their protein homeostasis during immune responses. Here, we demonstrate that OsRab11C1, encoding a Rab-type GTPase, is transcriptionally upregulated upon Magnaporthe oryzae infection. Strikingly, loss of OsRab11C1 enhances rice blast resistance, concomitant with increased defense gene expression, MAPK activation, and ROS burst. Mechanistically, we identify the E3 ubiquitin ligase EL5 as an interactor that ubiquitinates and targets OsRab11C1 for degradation via the 26S proteasome. Consistently, EL5 acts upstream of OsRab11C1 and positively regulates rice immunity. Further analysis reveals that OsRab11C1 interacts with and stabilizes mitogen-activated protein kinase kinase OsMKK6, thereby facilitating its autophosphorylation activity. In return, OsMKK6 acts as a negative regulator of rice programmed cell death and immunity. Collectively, our findings unveil a dynamic EL5-OsRab11C1-OsMKK6 signaling module that orchestrates rice immunity against pathogen invasion.

Jasmonic acid (JA), a key phytohormone in plant defense, plays essential roles in regulating plant stress responses and growth. However, how JA signaling and nitrate signaling regulate nitrate uptake in maize (Zea mays L.) remains elusive. Here, we report that low-nitrate stress promotes JA accumulation in maize roots, and JA treatment leads to a low-nitrate phenotype. JA triggers ZmbHLH99 expression, encoding a transcription factor that binds to ZmNLP3.2 promoter and inhibits ZmNLP3.2 expression, thereby regulating nitrate uptake. In addition, the JA ZIM-domain (JAZ) transcriptional repressor ZmZIM13 interacts with ZmbHLH99 to release its inhibitory effect on the ZmNLP3.2-ZmNRT cascade and promotes ZmNLP3.2 expression. Furthermore, loss of ZmbHLH99 or overexpression of ZmZIM13 promotes plant growth and nitrate uptake, leading to higher grain yield. These findings reveal the transcriptional regulatory landscape of how JA signaling regulates nitrate uptake via the ZmZIM13-ZmbHLH99-ZmNLP3.2 module and integrates with nitrate signaling to coordinate plant growth and stress responses.

CRISPR-Cas9 is a widely used platform for plant genome editing, but its outcomes are typically dominated by small insertions and deletions (indels). Such limited mutation profiles restrict its utility in functional studies of non-coding RNAs and regulatory elements, such as microRNAs (miRNAs), untranslated regions (UTRs), and promoter sequences, where larger sequence disruptions are often required. Here, we developed enhanced exonuclease-Cas9 platforms, termed multiple nucleotide deletion Cas9 (MND-Cas9) systems, for efficient generation of large deletions in rice. By screening four exonucleases (RecJ, T5, TREX2, and SbcB), we established MND-Cas9v1 systems based on TREX2 or SbcB that produced substantially larger deletions without reducing editing efficiency. Further optimization with an inserted DNA-binding domain (DBD) between Cas9 and exonuclease yielded MND-Cas9v2, which simultaneously enhanced efficiency and deletion size. To expand PAM compatibility, we introduced PAM-relaxed Cas9-NG and SpG variants, generating MND-Cas9-NG/SpGv2 systems with broader targeting scope and superior performance compared to their parental nucleases. Finally, we demonstrated the utility of these systems in two applications: MND-Cas9v2 efficiently knocked out the miRNA gene OsMIR530, producing larger seeds, and generated extended deletions in the 3'UTR of OsGhd2, which upregulated its expression and increased grain size. These results demonstrate that MND-Cas9 systems enable high-efficiency generation of extended deletions and facilitate functional analyses of non-coding RNAs and regulatory sequences. Overall, this work establishes a versatile and expandable exonuclease-Cas9 platform that substantially broadens the mutational spectrum and application potential of CRISPR-Cas9 for plant genome engineering.

Understanding cellular events in three dimensions (3D) is of great importance for the annotation and illustration of biological processes in a contextual way. Imaging techniques based on electron microscopy (EM), such as those derived from scanning electron microscopy (SEM) and transmission electron microscopy (TEM), provide various options to visualize biological samples at scales ranging from cells to macromolecules in situ. Recently, a series of cryogenic techniques has brought EM-based imaging to a new level, enabling specimens to retain their hydrated state throughout the sample preparation and imaging steps, thereby offering a near-native visualization of cellular events. The application of dual-beam focused ion beam (FIB)-SEM to biological samples has enabled high-resolution reconstructions in 3D and streamlined sample preparation workflows for downstream cryo-electron tomography (cryo-ET) imaging. However, applications of these technologies to plant materials are limited due to intrinsic characteristics of plant cells (e.g., non-adhesive growth, large size with a central vacuole, and the presence of cell walls). For the timely application of dual-beam FIB-SEM in three-dimensional subcellular imaging of plant materials, we have recently tested and developed three major workflows with proof-of-concept evidence using developing anthers and in vitro-cultured pollen tubes based on Aquilos 2 Cryo-FIB, including (1) room-temperature FIB-SEM volume imaging, (2) cryo-lamellae preparation from cell suspension culture or high-pressure-frozen organs for cryo-ET imaging, and (3) cryo-FIB-SEM volume imaging, which will facilitate structural studies of plant materials and provide technical guidance for the broader plant cell biology research community.

Beyond their traditional roles as biological building blocks and energy sources, metabolites also influence gene expression, exerting direct effects on the epigenetic landscape. For example, core metabolites such as acetyl coenzyme A (acetyl-CoA) and S-adenosylmethionine (SAM) serve as substrates or cofactors for chromatin-modifying enzymes, thereby modulating transcription through the chemical modification of histones and DNA. In addition, metabolites regulate the transcription of the genes encoding these chromatin modifiers, as well as the post-translational modifications and enzymatic activities of these proteins. Therefore, we propose that the metabolic state of a cell or organism is a dynamic and active driver of epigenomic reprogramming, adjusting gene expression in response to fluctuations in the environment.

Supplementation of Driver and Kuniyuki Walnut Medium with phloroglucinol enhanced regeneration efficiency in tomato tissue culture. Heterologous expression of an Arabidopsis growth-regulating factor gene, GROWTH-REGULATING FACTOR5 (GRF5), in tomato improved regeneration and transformation efficiency, suggesting a synergistic effect between phloroglucinol treatment and GRF-mediated pathways.

A haplotype-resolved telomere-to-telomere genome reveals that the bird-shaped turquoise flowers of Strongylodon macrobotrys (jade vine) arise from co-pigmentation between the anthocyanin malvin and the flavonoid saponarin, shaped by genome dynamics and geological event-associated expansions of long terminal repeat retrotransposons.

Ongoing climate warming has altered precipitation patterns and increased the frequency and intensity of climate extremes such as droughts, heatwaves, floods, and frosts. These changes have significantly influenced tree growth and development processes, including canopy phenology, intra-annual wood formation dynamics, and annual stem growth. However, these processes are affected by various climatic factors, and their responses are highly species-specific and vary across temporal and spatial scales. Beyond these rapid growth responses, trees may also undergo long-term genetic adaptation to climate change. This review synthesizes how canopy phenology, intra-annual wood formation dynamics, and annual stem growth respond to climate change and climate extremes. We summarize the response and adaptation of these growth processes to various climatic drivers and highlight the interactions among them in determining tree growth. Concepts and mechanisms of rapid response and heritable genetic adaptation in trees under climate change are also reviewed. We identify the key knowledge gaps in tree growth response and adaptation, such as integrative multiple organ and growth process monitoring and genetic-level studies, which are critical to further improve our understanding of tree growth to support sustainable forest management and enhance forest carbon storage under ongoing climate warming.

Cold damage during the seedling and reproductive stages has a pronounced impact on rice development and yield. Although significant progress has been achieved in understanding the physiological and molecular mechanisms underlying rice responses to cold stress, the mechanisms of cold stress perception and adaptation in rice remain mostly unclear. Here, we report the functional study of a cold-responsive gene named LENG, which encodes a plasma membrane-localized leucine-rich repeat (LRR) receptor-like pseudokinase. Gene knockout and overexpression analyses indicated that LENG positively regulates chilling tolerance in rice seedlings. LENG interacts with the plasma membrane-localized cytoplasmic protein kinase, cold-responsive protein kinase 1 (OsCRPK1). Knockout of OsCRPK1 in wild-type and leng mutants elevates rice chilling tolerance, indicating that OsCRPK1 plays a negative role and acts downstream of LENG. In vitro kinase assays revealed that OsCRPK1 is an active protein kinase, but it does not phosphorylate LENG, whereas LENG does not have a kinase activity, but it suppresses the kinase activity of OsCRPK1. In addition, LENG interferes with the interaction between OsCRPK1 and the rice 14-3-3 protein OsGF14d (G-box factor 14-3-3 homolog d), which is known to be a positive regulator of chilling tolerance. The polymorphisms in the promoter and coding region of LENG in japonica and indica rice were correlated with the differential gene expression patterns and chilling tolerance in response to chilling treatment. Taken together, these findings suggest that LENG regulates rice chilling tolerance by modulating the kinase activity of OsCRPK1 and eventually the phosphorylation status of OsGF14d protein. The polymorphisms in LENG provide a selection marker for molecular breeding of rice with improved chilling tolerance.

Saline-alkali stress is one of the major abiotic factors limiting crop production and affecting the ecological environment. The plasma membrane (PM) H+-ATPases are involved in modulating the membrane potential in response to alkaline stress. The central loop (cytoplasmic domain) of the PM H+-ATPase AHA2, in contrast to its well-studied C-terminal regulatory domain, remains poorly understood in terms of its regulatory function. In this study, we found that CARK1 and CARK3 (cytosolic ABA receptor kinase 1 and 3) positively modulate saline-alkali stress tolerance in Arabidopsis. Using molecular biology and biochemistry approaches, we reveal that CARK1 and CARK3 interact with and phosphorylate AHA2 at Thr469 in the central loop domain. Molecular mechanism indicates that CARK1/3-mediated phosphorylation elevates AHA2 activity through two key actions: First, by increasing Thr947 phosphorylation and promoting binding to 14-3-3 protein, and second, by releasing autoinhibitory interaction between the C-terminus and the central loop of AHA2. Functional and genetic analyses reveal that the phosphorylation-mimicking mutation AHA2T469D dramatically rescues hypersensitivity to alkali tolerance, H+ efflux, and cytosolic ROS accumulation in aha2 and cark1/3aha2 triple mutants. Collectively, our work reveals the central regulatory loop of AHA2 in response to alkali stress and reports that its activity is enhanced through Thr469 phosphorylation by CARK1/3.