Plant Communications最新文献

CRISPR/Cas-based genome editing has revolutionized plant biotechnology, enabling precise genomic modifications for crop improvement and functional genomics. The success of these applications hinges on designing single guide RNAs (sgRNAs) that maximize on-target efficiency while minimizing off-target effects. Current resources for sgRNA design and performance evaluation in plants are fragmented and lack integration with genomic and epigenomic context, which influences both editing efficacy and specificity. Here, we present PCdb (Plant CRISPR Database; https://gmo.sjtu.edu.cn/pcdb), a comprehensive plant-focused database by integrating experimentally validated sgRNAs, their annotated genomic contexts, genome-wide off-target predictions, and multi-layered epigenomic annotations. PCdb encompasses 6,172 manually curated editing records from 2,132 publications, covering 4,320 unique sgRNAs and 6,117,424 predicted off-target sites across nine major plant species. Uniquely, PCdb contextualizes potential editing outcomes-both on-target and off-target-within the chromatin landscape by incorporating DNA methylation profiles, chromatin accessibility data, and histone modification patterns. The database features an intuitive web interface supporting flexible queries, interactive visualization tools, and comprehensive analytical modules for both sgRNA efficiency assessment and off-target analysis. A case study reanalysis of Oryza sativa yield-related genes demonstrates PCdb's capability to provide a comprehensive performance profile, evaluating both on-target characteristics and off-target risks within their native epigenomic context. Through systematic analysis of the database, we reveal critical sequence and chromatin features influencing editing outcomes, providing novel insights for improved gene editing efficacy and specificity.

Methylation of histone H3 at lysine 4 (H3K4me) marks transcribed elements of the eukaryotic genome, and its distribution dynamically changes through developmental stages and in response to environmental factors. These dynamic regulatory changes are achieved by the combinatorial action of H3K4me methyltransferases, with multi-cellular organisms carrying multiple copies of these enzymes. The model plant Arabidopsis has at least seven H3K4 methyltransferase genes. Here, we comparatively analyze the seven H3K4 methyltransferases using epigenomics and biochemical approaches to better understand the mechanisms underlying their target specificity. Our findings, in combination with previous work, show that ATX1 to ATX5 (Trx/Trr-type methyltransferases) localize to loci with distinct sets of chromatin modifications and DNA motifs, which differ among the various ATX proteins. Notably, ATX3 localizes to the binding motifs of ASR3 and RAP2.11 transcriptional factors and directly interacts with these TFs. ATXR7 (Set1-type) and ATXR3 (non-canonical H3K4 methyltransferase) co-localize with the transcriptional machinery, suggesting co-transcriptional mechanisms of action for these enzymes. Interestingly, ATXR3, the major H3K4me3 methyltransferase in Arabidopsis, appears to form a protein complex independent of COMPASS, indicating that the regulatory mechanisms of H3K4me3 have diverged between plants and animals. Our work provides a foundation for understanding the chromatin targeting of H3K4 methyltransferases in plants and highlights significant differences in H3K4me3 regulation between plants and other eukaryotes.

Fruit secondary metabolites play pivotal roles in plant evolution by deterring herbivores and attracting seed dispersers. However, the mechanisms by which these compounds evolve and drive diversification in citrus remain poorly understood. In this study, we demonstrate that the emergence of the bitter compound neohesperidoside (Neo) has contributed to citrus dissemination by enhancing defense against biotic stresses. Targeted metabolomic analyses revealed that Neo accumulation emerged in early-diverging citrus, whereas the presence of its non-bitter counterpart rutinoside (Rut) can be traced back to Citrus-related species. Comparative genomics and enzyme functional assays revealed that Neo biosynthesis arose from duplication of two di-glucosyltransferase genes, CmdGlcT-1 and UGT79B203, in early-diverging citrus, followed by neofunctionalization into enzymes of Cm1,2RhaT and UGT79B202, capable of synthesizing Neo. A structurally conserved amino acid residue, corresponding to Phe195 in Cm1,2RhaT and Leu201 in UGT79B203, was identified as essential for this functional shift. Compared to Rut, Neo exhibited stronger antifungal and anti-feeding effects, suggesting its potential role in enhancing biotic defense, which may have contributed to the broader geographical distribution of early-diverging citrus species. These findings provide new insights into the evolutionary origin of citrus bitterness and highlight the adaptive role of specialized metabolites in mediating plant-environment interactions.

The formation of symbiotic associations with rhizospheric microbes is an important strategy for sessile plants to acquire nitrogen and phosphorus from the soil. Root exudate plays a key role in shaping the rhizosphere microbiome. Depending on their needs for nitrogen or phosphorus, plants can adjust the composition of root exudate to attract the appropriate microbes. Flavonoids, a group of secondary metabolites, have been well studied for their role in shaping the root microbiome, particularly in mediating root nodule symbiosis in legumes. However, the mechanism by which plants regulate the absorption of microbe-mediated nitrogen and phosphorus remains unclear. Here, we show that the Medicago truncatula phosphate starvation response regulatory network SPX1/3-PHR2 controls flavonoid biosynthesis to recruit nitrogen-fixing microbes for nitrogen acquisition. Nitrogen-fixing microbes, including rhizobia, were fewer recruited in the rhizosphere of the spx1spx3 double mutant. This was caused by lower flavonoid levels in the root exudate compared to wild-type plants R108. Further results indicate that the control of flavonoid biosynthesis is exerted via PHR2, the interacting transcription factor of SPX1/3. Under phosphate-limiting conditions, PHR2 suppresses the expression of flavonoid biosynthetic genes to reduce root nodule symbiosis levels. Under phosphate-sufficient conditions, the interaction between SPX1/3 and PHR2 releases this suppression, thereby promoting root nodule symbiosis. We further showed that PHR2 can bind to the promoter regions of flavonoid biosynthetic genes in yeast. We propose that the SPX1/3-PHR2 network can modulate root nodule-dependent nitrogen acquisition in response to phosphate levels. Thus, the SPX1/3-PHR2 module contributes to maintaining a balance in microbe-mediated nitrogen and phosphorus acquisition for optimal plant growth.

RNA splicing removes non-coding introns from pre-mRNA to generate mature mRNA in eukaryotes, and accurate identification of splice sites is essential for understanding gene structure and regulation. Traditional gene annotation and splice-site prediction rely heavily on high-quality genome assemblies, extensive functional characterization, and substantial computational and experimental resources, limiting their applicability to many non-model species. Here, we present UniSplicer, a deep-learning-based training framework capable of generating accurate intron splice-site prediction models for diverse species using relatively limited transcriptomic data. UniSplicer-based models (http://www.unisplicer.com) consistently outperform existing prediction tools across a wide range of taxa, including plants, fungi, and metazoans. UniSplicer prediction scores serve as reliable indicators of mutational effects across multiple types of splice mutants. Moreover, application of the UniSplicer Arabidopsis thaliana model identified genes in natural ecotypes that exhibit aberrant splicing due to sequence variation near splice sites, suggesting potential roles in environmental adaptation. Collectively, UniSplicer-based models achieve high predictive accuracy and provide insight into how sequence variation drives splicing alterations across large genomic datasets.

Excessive cadmium (Cd) in rice grains seriously threatens food security. Cd uptake by roots and transport to grains are mediated by the transporters for mineral elements in rice. Therefore, the reduction of Cd accumulation is often accompanied by the decrease of mineral elements. How to substantially reduce grain Cd concentrations and maintain proper concentrations of mineral elements is the bottleneck in low-Cd rice breeding. Here, we report that the combination of elite alleles of OsNRAMP5 and OsHMA3, two key Cd transporter-encoding genes, conferred low-Cd accumulation in grains without causing sensitivity to Mn-deficiency in Layandabu (LAA), a tropical japonica rice cultivar. The amino acid substitution at position 313 from serine (S) to phenylalanine (F) in OsNRAMP5^LAA weakens its binding to OsVAP1-3, which is a vesicle-associated membrane protein (VAMP)-associated protein and facilitates OsNRAMP5 export from the endoplasmic reticulum (ER) to the plasma membrane. This results in partial retention of OsNRAMP5^LAA in the ER, consequently diminishing Cd and Mn uptake in rice. Introgression of the linked OsNRAMP5^LAA and OsHMA3^LAA into a commercial rice cultivar WSSM dramatically reduced brown rice Cd concentrations in Cd-contaminated fields without yield penalty, even when exposed to heat and low-Mn stress. Thus, our findings provide mechanistic insights into the balance between low-Cd accumulation and stress resilience and a novel strategy for developing rice cultivars with low-Cd grains and broad adaptability.