Plant Communications最新文献

Anthocyanins are plant pigments that play diverse roles in plant growth, adaptation, and stress tolerance. Anthocyanin biosynthesis is tightly regulated, but the underlying regulatory mechanisms remain unclear. Here, we identify a regulatory module composed of the DNA-binding protein VAL1 (VIVIPAROUS1/ABI3-LIKE 1) and a SIN3 (SWI-INDEPENDENT 3)-like histone deacetylase complex that dynamically regulates anthocyanin biosynthesis in Arabidopsis thaliana. Under normal growth conditions, VAL1 recruits the SNL (SIN3-Like)-HDA19 (HISTONE DEACETYLASE 19) complex (SNL-HDA19c) to the PRODUCTION OF ANTHOCYANIN PIGMENT 1 (PAP1) locus for histone deacetylation. Moreover, the negative regulators of jasmonic acid (JA) signaling, JASMONATE-ZIM DOMAIN (JAZ) proteins, interact with VAL1 and further stabilize the binding of VAL1 and SNL-HDA19c to PAP1 chromatin. These molecular interactions transcriptionally repress PAP1 and inhibit anthocyanin biosynthesis. Upon JA accumulation, JAZs are degraded, resulting in the release of both VAL1 and SNL-HDA19c from the PAP1 chromatin. This release leads to an immediate increase in histone acetylation, promoting transcriptional activation of PAP1 and anthocyanin production. These findings elucidate a regulatory module (VAL1-JAZ-SNL-HDA19c) that represses anthocyanin biosynthesis under normal growth conditions and further reveal how the stress hormone JA rapidly induces anthocyanin production, enabling plants to adapt to their growth conditions.

Early postgermination growth is critical for uniform seedling emergence in direct-seeded rice, yet its regulatory mechanism remains unclear. Here, we identified DS1, encoding the shikimate pathway initial enzyme DAHPS2, from a dwarf and sterile mutant (ds1) in Huazhan (HZ). Loss of DS1 disrupted the shikimate pathway, thereby reducing indole-3-acetic acid (IAA) levels via the downstream tryptophan-dependent IAA biosynthesis pathway and inducing excessive jasmonic acid (JA) production, resulting in severely inhibited postgermination growth. Exogenous auxin analog NAA or the JA biosynthesis inhibitor DIECA partially rescued the mutant phenotype. Conversely, DS1 overexpression elevated IAA levels, reduced JA accumulation, and enhanced postgermination growth, thereby facilitating rapid seedling emergence in rice under submergence. This result was subsequently confirmed in the Zhongjia3 (ZJ3) cultivar. We further demonstrated that DS1 is transcriptionally activated by RR26, a type-B cytokinin response regulator, through binding to the DS1-7 cis-element. Using prime editing, we precisely modified DS1-7 in HZ, generating transgene-free germplasm with improved DS1 expression and enhanced submergence tolerance. Our findings establish an RR26-DS1 module that regulates IAA-JA homeostasis through the shikimate pathway, providing mechanistic insights into postgermination growth and valuable germplasm for breeding direct-seeded rice.

Olive (Olea europaea L.) 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 flavor and quality of olive oil. 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 olive fruit mesocarp of six commercial olive cultivars with varying oleuropein content, during maturation and ripening. Using this data we discovered three polyphenol oxidases with oleuropein synthase (OS) activity, a novel oleoside-11-methyl ester glucosyl transferase (OMEGT) synthesizing a potential intermediate in the route, and a 7-epi-loganic acid O-methyltransferase (7eLAMT). Interestingly, using transcriptome assemblies of 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, allowed the discovery of two 2-oxoglutarate dependent dioxygenases (named 7eLAS) that synthesize 7-epi-loganic acid; in 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 big datasets for untargeted discovery of enzymes. Given the increasing availability of expression data from species across the plant kingdom, the methods used for gene discovery used in this work can be readily applied to other untraced pathways.

Sustainable bioenergy is pivotal for the global transition from fossil fuels to a circular bioeconomy, yet conventional biomass conversion is hindered by limitations in efficiency, cost, and versatility. This review examines how contemporary interdisciplinary advances are overcoming these challenges. We survey the convergence of synthetic biology, genomics, artificial intelligence (AI), and chemistry, which is revitalizing bioenergy production through the engineering of optimized biomass. Key strategies range from genomic editing of energy crops for enhanced nutrient efficiency and tailored lignin content to the development of AI-informed smart biorefineries. As a prime exemplar of this synergy, we present an in-depth case study on autoluminescent plants. This frontier application harnesses the fungal bioluminescence pathway (FBP) to directly convert photosynthetic energy into sustainable visible light. The FBP's unique reliance on the endogenous metabolite caffeic acid establishes a transformative platform for autonomous biological illumination. Our analysis underscores that an integrated approach, spanning omics, engineering, and agronomy, is critical for solving complex bioengineering problems and realizing the vision of high-brightness plants. We conclude by proposing 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.

Photosystem II (PSII) is susceptible to photodamage under high light stress, necessitating an efficient repair cycle that involves the degradation of the damaged D1 protein, primarily by FtsH proteases. While the involvement of FtsH in D1 turnover is established, the regulatory mechanisms ensuring precise degradation remain unclear. In this study, we characterize the function of TEF6, a conserved thylakoid membrane protein with two transmembrane domains in Chlamydomonas reinhardtii. The tef6 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 genetics assays confirmed that loss of TEF6 specifically impairs PSII stability and repair. Furthermore, multiple approaches including co-immunoprecipitation coupled with mass spectrometry, yeast two-hybrid assays, and bimolecular fluorescence complementation (BiFC) experiments demonstrated that TEF6 directly interacts with both the D1 protein and the FtsH proteases (FtsH1/FtsH2). Loss of TEF6 leads to misregulated, excessive accumulation of FtsH under high light, which correlates with accelerated and uncontrolled degradation of the D1 protein, ultimately disrupting the PSII repair cycle and homeostasis. Our findings identify TEF6 functioning 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 the correct and regulated turnover of photo-damaged D1. This study reveals a novel regulatory mechanism, mediated by a GreenCut protein, for maintaining PSII quality control and photosynthetic efficiency under light stress.

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.