Plant Communications最新文献

Targeted protein degradation through the CDC48 unfoldase enables the maintenance and rapid adaptation of proteomes across eukaryotes. However, the substantial differences among animals, fungi, and plants presumably drove extensive adaptation of CDC48-mediated degradation. Although animal and fungal CDC48 systems have shown structural and functional preservation, comparable analysis has been lacking for plants. We determined the structural and functional characteristics of Arabidopsis thaliana CDC48A in multiple states and in complex with the target-identifying cofactors UFD1 and NPL4. Our analysis revealed several features that distinguish AtCDC48A from its animal and yeast counterparts despite 80% sequence identity. Key findings include that AtCDC48A exhibits distinct domain dynamics and engages AtNPL4 in a unique manner. Moreover, AtNPL4 and AtUFD1 do not form an obligate heterodimer; instead, AtNPL4 can independently bind to AtCDC48A and mediate target degradation, although their combined action is synergistic. An evolutionary analysis indicates that these Arabidopsis features are conserved across plants and represent the ancestral state of eukaryotic CDC48 systems. Collectively, our findings suggest that plant CDC48 retains a more modular and combinatorial mode of cofactor usage, highlighting a specific adaptation of targeted protein degradation in plants.

In the current context of climate change, there is a need to develop more sustainable agrifood strategies. As an alternative to the intensive use of chemically synthesized fertilizers and pesticides that pollute water and impact biodiversity, there is a growing interest in using beneficial microbes as biostimulants and/or bioprotection agents. However, their implementation in agriculture remains a challenge due to highly variable outcomes and benefits. Furthermore, there are major knowledge gaps about the molecular mechanisms that regulate different plant-microbe interactions. In the present review, we summarize current knowledge on the molecular mechanisms that control different beneficial plant root-microbe interactions; namely, arbuscular mycorrhiza, the rhizobium-legume symbiosis, ectomycorrhiza, and fungal and bacterial endophytic associations. This includes the signaling pathways required for recognition of microbes as beneficial, the metabolic pathways that provide nutritional benefits to the plant, and the regulatory pathways that modulate the extent of symbiosis establishment depending on soil nutrient availability and plant needs. Our aim is to highlight the main common mechanisms, as well as knowledge gaps, in order to promote the use of microbes, either individually or in consortia, within the framework of a sustainable agriculture that is less dependent on chemicals and more protective of biodiversity and water resources.

An unprecedented number of studies have explored hormone levels in plants; however, only a small fraction includes comprehensive metabolite analyses spanning multiple hormone classes. Here, we aim to establish a unique and detailed resource integrating the absolute concentrations of diverse hormone classes and their metabolites in tomato floral organs and early fruit tissues across developmental stages. We quantified 58 hormone metabolites from six chemical classes in whole flower buds, individual floral organs at five developmental stages, mature pollen, and early fruit tissues up to 15 days after anthesis. Hormone profiling was complemented by matched transcriptomic and shotgun proteomic analyses. This integrated dataset revealed distinct spatial and temporal hormone signatures, including a gradual decline in active auxin levels-especially in stamens-contrasting with the accumulation of oxidized and conjugated auxin forms toward anthesis. Multi-omics analyses identified three GRETCHEN HAGEN 3(GH3) genes (GH3-2, GH3-7, and GH3-15) likely involved in auxin inactivation within reproductive organs. In vitro enzyme assays and transient overexpression in Nicotiana benthamiana confirmed their capacity to conjugate indole-3-acetic acid (IAA) to various amino acids. CRISPR/Cas9-generated single, double, and triple gh3 mutants showed increased levels of free IAA in mature stamens. Proteomic profiling of gh3-2 stamens revealed upregulation of stress-related proteins under normal conditions, whereas under heat stress, gh3-2 stamens exhibited fewer proteomic changes than the wild type. Moreover, pollen from gh3-2 and gh3-7 mutants maintained higher viability after prolonged heat stress. This study offers the most comprehensive hormone-focused multi-omics resource for tomato reproductive development to date. It provides a detailed map of hormone distribution across floral and early fruit tissues, and demonstrates its utility by uncovering a stamen-specific auxin conjugation mechanism that contributes to pollen thermotolerance.

Global climate change poses increasing threats to seed production and thus food security. The seed microbiome plays an essential role in regulating the whole seed life cycle. Specific seed endophytes and spermosphere microorganisms orchestrate the maintenance and termination of dormancy towards the synchronization of germination plasticity to meet agricultural demands. In this review, we summarize recent advances by linking seed-microbiome interactions with seed processes. We review the sources of seed microbiomes and their physiological regulation on dormancy and germination in response to environmental changes with a focus on phytohormone crosstalk. We also discuss the molecular mechanisms by which seed-microbe interactions affect seed destiny. Finally, we explore emerging precision applications of microbiomes in the seed industry by integrating cutting-edge technologies such as microbial seed coatings and artificial intelligence (AI) in seed science and technology. In conclusion, harnessing microbiome-based strategies to manipulate seed life cycle holds immense promise for sustainable food production in a changing global climate.

In Arabidopsis thaliana, METHYL-CpG-BINDING DOMAIN 7 (MBD7) and its associated α-crystallin domain (ACD) proteins form a complex that interprets DNA methylation to prevent the silencing of methylated luciferase (LUC) reporter transgenes. However, the mechanism by which the MBD7 complex effectively targets methylated transgenes remains largely unclear. Here, we identify a novel role for SAWADEE HOMEODOMAIN HOMOLOG 1 (SHH1), extending its function beyond the canonical RNA-directed DNA methylation (RdDM) pathway. We demonstrate that SHH1 prevents the transcriptional silencing of methylated LUC transgenes and a subset of endogenous genes by acting in concert with MBD7 within the same regulatory pathway. SHH1 co-localizes with MBD7 at nuclear foci and physically interacts with it to enhance its stability. Furthermore, SHH1 binds to methylated loci via its SAWADEE domain, which recognizes the H3K9me2 histone mark. This interaction promotes the reciprocal recruitment of SHH1 and MBD7 to methylated loci, revealing a cooperative mechanism that maintains transcriptional activity at promoter-methylated genes. Collectively, our findings unveil a dynamic, mutually reinforcing SHH1-MBD7 module that enhances the expression of promoter-methylated genes, likely by facilitating effective binding to chromatin marked by repressive epigenetic modifications. This work provides important insights into how DNA methylation fine-tunes gene expression in plants by balancing between transcriptional repression and activation.

Long non-coding RNAs (lncRNAs) regulate numerous biological processes in plants, including development and stress responses. Although previous studies have mainly examined their sequences and transcriptional activity, other essential aspects, such as in vivo RNA secondary structure and post-transcriptional regulation, remain poorly understood in plants. Here, we comprehensively characterized lncRNA features, including length, sequence composition, conservation, and in vivo secondary structure, in two representative species: Arabidopsis thaliana (dicot) and durum wheat (monocot). While lncRNAs show limited conservation across the plant kingdom, their sequences display moderate conservation within evolutionary clades. We further identified conserved RNA structural motifs that form stable folds in vivo. Comparative genome-wide analyses of post-transcriptional regulation revealed that plant lncRNAs vary widely in translation efficiency and RNA stability, with RNA structure emerging as a major determinant of both processes. Moreover, transcriptome-wide analyses uncovered structural motifs associated with translation and stability, predominantly enriched at the 3' ends of plant lncRNAs. Together, these findings provide a comprehensive framework for understanding plant lncRNA features and reveal a central role of RNA structure in shaping their post-transcriptional regulation.

Bulked segregant analysis (BSA) is a widely used method for identifying genomic loci associated with traits of interest in crops. However, conventional BSA is limited by its reliance on phenotype-driven bulk sampling, which restricts its scalability and confines its applicability to single-trait analysis. This study introduces a novel method, reverse BSA-QTLseq, which uses genotype-driven bulk reconstruction through bioinformatics, enabling the simultaneous mapping of multiple traits from the same genotypic dataset. Reverse BSA-QTLseq uses a two-step strategy-low-resolution genotyping of the entire population followed by high-resolution sequencing of selected bulks-enabling cost-effective identification of genetically divergent lines to enhance the discovery of quantitative trait loci (QTLs). Using a bread wheat recombinant inbred line (RIL) population as a case study, we mapped loci associated with heading date and plant height , confirming approximately 95% of known QTLs, including both dwarfing genes (e.g., Rht-B1 and Rht-5) and flowering-time regulators (e.g., Vrn-A1), and identified novel QTLs and candidate loci with strong phenotypic effects. The phased genotyping strategy maximized genetic distance in the initial sampling, facilitating the in silico reconstruction of trait-specific contrasting bulks. Integration of transcriptional profiles from the parental lines of the RIL population, from which the bulks were derived, aided in identifying candidate genes and regulatory networks underlying the variation of traits such as photoperiod response, nutrient transport, and stress adaptation. The versatility and potential for data reuse offered by the proposed method represent a significant advancement in QTL mapping, with broad implications for marker-assisted breeding and selection programs. Future integration of transcriptomic and epigenomic data is expected to further enhance the power of reverse BSA-QTLseq, accelerating genetic improvement in crops.