Plant Communications最新文献

Peanut (Arachis hypogaea) is an economically important legume crop, but a comprehensive understanding of its gene expression dynamics across developmental stages remains limited. To address this gap, we constructed an integrative multi-omics atlas spanning transcriptomic, proteomic, and metabolomic profiles across 22 primary vegetative and reproductive tissues. We identified 53 030 expressed genes at the transcript level, 12 826 with protein evidence, and 2035 metabolites. Among these, 2147 genes encode novel proteins, and 274 produce microproteins. Functional analyses identified WDR13, TANGO, RPP13, DEF3, SLR1-BP, and SLE2 as key genes involved in development and stress responses. Co-expression analysis grouped genes into 24 modules, many of which exhibited tissue-specific expression patterns. Pathway enrichment and correlation network analyses further highlighted the critical roles of the IAA and ARF gene families in hormone signaling and cell growth, particularly in peg development. To facilitate data accessibility and downstream research, we developed PeanutOmics (https://cgm.sjtu.edu.cn/PeanutOmics), a user-friendly web platform that integrates multi-omics datasets with advanced analytical tools. This atlas offers a valuable resource for understanding gene and metabolite regulation in peanut and lays the groundwork for advanced molecular breeding to improve crop productivity.

Olive (Olea europaea) is one of the most important crop trees, with olive oil being a key ingredient of the Mediterranean diet. Oleuropein, an oleoside-type secoiridoid, is the major determinant of olive oil flavor and quality. Iridoid biosynthesis has been elucidated in Catharanthus roseus, which produces secologanin-type secoiridoids, but iridoid biosynthesis in other species remains unresolved. In this work, we sequenced RNA from the fruit mesocarp of six commercial olive cultivars with various oleuropein contents during maturation and ripening. Using these data, we discovered three polyphenol oxidases with oleuropein synthase (OS) activity, a novel oleoside-11-methyl ester glucosyltransferase (OMEGT) that synthesizes a potential intermediate in the pathway, and a 7-epi-loganic acid O-methyltransferase (7eLAMT). Interestingly, the use of transcriptome assemblies for 15 plant species from three iridoid-producing plant orders (Lamiales, Gentianales, and Cornales) for orthogroup inference, and integration of two tissue expression panels from Jasminum sambac and Fraxinus excelsior, enabled the discovery of two 2-oxoglutarate-dependent dioxygenases (named 7eLAS) that synthesize 7-epi-loganic acid; by contrast, C. roseus 7-deoxy-loganic acid hydroxylase (7DLH), a known bottleneck in MIA production, is a cytochrome P450. This comparative co-expression method, which combines guilt-by-association and comparative transcriptomics approaches, can successfully leverage large datasets for untargeted discovery of enzymes. Given the increasing availability of expression data from species across the plant kingdom, the methods for gene discovery used in the present work can be readily applied to other untraced pathways.

Early postgermination growth is critical for uniform seedling emergence in direct-seeded rice; however, the underlying regulatory mechanisms remain unclear. Here, we identified DS1, which encodes the shikimate pathway entry enzyme DAHPS2, from a dwarf and sterile mutant (ds1) in 'Huazhan' (HZ). Loss of DS1 disrupted the shikimate pathway, reduced indole-3-acetic acid (IAA) levels through the downstream tryptophan-dependent IAA biosynthesis pathway, and induced excessive jasmonic acid (JA) accumulation, resulting in severely impaired postgermination growth. Exogenous application of the auxin analog 1-naphthaleneacetic acid or the JA biosynthesis inhibitor diethyldithiocarbamic acid partially rescued the mutant phenotype. Conversely, DS1 overexpression elevated IAA levels, reduced JA accumulation, and promoted postgermination growth, facilitating rapid seedling emergence under submergence conditions. This effect was further validated in the 'Zhongjia 3' cultivar. We demonstrate that DS1 is transcriptionally activated by RR26, a type-B cytokinin (CK) response regulator, through direct binding to the DS1-7 cis element. Using prime editing, we precisely modified DS1-7 in HZ to generate transgene-free germplasm with improved DS1 expression and enhanced submergence tolerance. Collectively, our findings establish an RR26-DS1 module that regulates IAA-JA homeostasis through the shikimate pathway, providing mechanistic insights into postgermination growth and valuable genetic resources for breeding direct-seeded rice cultivars.

Sustainable bioenergy is pivotal to the global transition from fossil fuels to a circular bioeconomy. However, conventional biomass conversion remains hindered by limitations in efficiency, cost, and versatility. This review examines how recent interdisciplinary advances are overcoming these challenges. We survey the convergence of synthetic biology, genomics, artificial intelligence (AI), and chemistry, which together are revitalizing bioenergy production through the engineering of optimized biomass. Key strategies for bioenergy production range from enhancing nutrient efficiency and tailoring lignin content by genomic editing of energy crops to the development of AI-informed smart biorefineries. As an example of this synergy, we present an in-depth case study on autoluminescent plants. This frontier application harnesses the fungal bioluminescence pathway (FBP) to convert photosynthetic energy into visible light emission. The FBP's unique reliance on the endogenous metabolite caffeic acid establishes a transformative platform for sustainable and autonomous biological illumination. An interdisciplinary approach integrating omics, engineering, and agronomy is critical for solving such complex bioengineering challenges and making high-brightness plants a reality. We propose that the next paradigm shift will be driven by generative AI, transitioning research, and development from subject-specific inquiries to a holistic model of multidisciplinary convergence, thereby accelerating the realization of advanced, sustainable plant-based energy production.

Photosystem II (PSII) is highly susceptible to photodamage under high-light stress, necessitating an efficient repair cycle involving degradation of the damaged D1 protein, primarily mediated by FtsH proteases. Although the role of FtsH in D1 turnover is well established, the regulatory mechanisms that ensure precise and controlled degradation remain unclear. Here, we characterize TEF6, a conserved thylakoid membrane protein containing two transmembrane domains in Chlamydomonas reinhardtii. The tef6 mutant exhibits severe growth inhibition, reduced PSII activity, impaired accumulation of PSII supercomplexes, and disorganized thylakoid membranes specifically under high-light conditions. Physiological, cellular, biochemical, and genetic analyses demonstrate that loss of TEF6 compromises PSII stability and repair. Multiple approaches-including co-immunoprecipitation coupled with mass spectrometry, yeast two-hybrid assays, and bimolecular fluorescence complementation (BiFC)-further reveal that TEF6 directly interacts with both the D1 protein and the FtsH proteases (FtsH1/FtsH2). Loss of TEF6 leads to misregulated and excessive accumulation of FtsH under high light, correlating with accelerated and uncontrolled degradation of D1 and ultimately disrupting PSII repair and homeostasis. Collectively, our findings identify TEF6 as a crucial scaffold-like factor in the PSII repair machinery. TEF6 stabilizes the proper accumulation of the FtsH protease complex in the thylakoid membrane, thereby ensuring accurate and regulated turnover of photodamaged D1. This study reveals a novel regulatory mechanism mediated by a GreenCut protein that maintains PSII quality control and photosynthetic efficiency under light stress.

CRISPR-Cas-based genome editing has transformed plant biotechnology by enabling precise genomic modifications for crop improvement and functional genomics. The success of these applications hinges on the design of single guide RNAs (sgRNAs) that maximize on-target efficiency while minimizing off-target effects. However, existing resources for sgRNA design and performance evaluation in plants remain fragmented and lack integration with genomic and epigenomic contexts that influence both editing efficacy and specificity. Here, we present PCdb (Plant CRISPR Database; https://gmo.sjtu.edu.cn/pcdb), a comprehensive plant-focused database that integrates experimentally validated sgRNAs, annotated genomic contexts, genome-wide off-target predictions, and multilayer epigenomic annotations. PCdb encompasses 6172 manually curated editing records from 2132 publications, covering 4320 unique sgRNAs and 6 117 424 predicted off-target sites across nine major plant species. Notably, 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 that supports flexible queries, interactive visualization tools, and comprehensive analytical modules for sgRNA efficiency assessment and off-target analysis. A case study reanalysis of Oryza sativa yield-related genes demonstrates PCdb's ability to generate a detailed performance profile by evaluating both on-target characteristics and off-target risks within their native epigenomic context. Systematic analysis of the database further identifies key sequence and chromatin features that influence editing outcomes, providing novel insights to improve gene-editing efficacy and specificity.

Methylation of histone H3 at lysine 4 (H3K4me) marks transcribed elements of the eukaryotic genome, and its distribution changes dynamically across developmental stages and in response to environmental factors. These dynamic regulatory changes are mediated by the combinatorial action of H3K4me methyltransferases, and multicellular organisms carry multiple copies of these enzymes. The model plant Arabidopsis has at least seven H3K4 methyltransferase genes. Here, we comparatively analyze these seven enzymes using epigenomic and biochemical approaches to better understand the mechanisms underlying their target specificity. Our findings, in combination with previous work, show that ATX1-ATX5 (Trx/Trr-type methyltransferases) localize to genomic regions with distinct sets of chromatin modifications and DNA motifs, which vary among the ATX proteins. Notably, ATX3 localizes to the binding motifs of the ASR3 and RAP2.11 transcription factors (TFs) and directly interacts with these TFs. ATXR7 (a Set1-type H3K4 methyltransferase) and ATXR3 (a non-canonical H3K4 methyltransferase) co-localize with the transcriptional machinery, suggesting co-transcriptional mechanisms of action for these enzymes. Interestingly, ATXR3, the primary H3K4 trimethylation (H3K4me3) methyltransferase in Arabidopsis, appears to form a protein complex independent of the Complex Proteins Associated with Set1 (COMPASS), which indicates that the regulatory mechanisms governing 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.