Plant Communications最新文献

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.

Phospholipases are major regulators of lipid-dependent signaling and play crucial roles in plant immunity. Rice (Oryza sativa) phospholipase C4 (OsPLC4) is a major functional enzyme in the rice phospholipase family that regulates intracellular Ca²⁺ levels. Here we show that OsPLC4 translocates primarily to the plasma membrane in a Ca²⁺-dependent manner, with its C2 domain functioning as a membrane trafficker. Transient expression of OsPLC4 and its truncated variants triggers cell death and immune responses in plants. During effector-triggered immunity (ETI) in rice, OsPLC4 expression and Ca²⁺ influx are specifically and strongly induced in response to avirulent Magnaporthe oryzae. Upon infection, the rice Osplc4 knockout mutant (ΔOsplc4) exhibits substantially reduced Ca²⁺, reactive oxygen species (ROS), and Fe³⁺ accumulation, as well as diminished lipid peroxidation and hypersensitive response (HR) cell death. Complementation of ΔOsplc4 can fully restore Ca²⁺-mediated ferroptotic cell death. OsPLC4 expression also activates HR cell death and the expression of defense-related genes such as OsRbohB, OsMEK2, OsMPK1, and OsPAL1 during avirulent M. oryzae infection. The Ca²⁺ chelator ethylene glycol-bis(2-aminoethyl ether)-N,N,N',N'-tetraacetic acid (EGTA) substantially inhibits Ca²⁺, ROS, and Fe³⁺ accumulation and HR-related cell death in rice, whereas the Ca²⁺ influx enhancers trifluoperazine hydrochloride (TFP) and acibenzolar-S-methyl (ASM) strongly induce Ca²⁺-mediated ferroptotic cell death. Additionally, OsPLC4 overexpression triggers cell death and immune responses in Arabidopsis. Collectively, our findings demonstrate that OsPLC4 acts as a downstream target of resistosome activation and sustains the co-elevation of Ca²⁺ and ROS levels during rice ETI, thereby promoting Ca²⁺-mediated, lipid ROS-dependent ferroptotic cell death. These results establish OsPLC4 as a key regulator of Ca²⁺-dependent plant immunity.

Seagrasses are marine flowering plants that perform oxygenic photosynthesis both under high, white sunlight and under low, blue-green light, conditions fundamentally different from those experienced by land plants. Thus far, the adaptation of seagrass photosynthetic machinery to this underwater light gradient remains poorly understood. Here, we investigate the Mediterranean seagrass Posidonia oceanica, an ecosystem engineer thriving from the surface down to 40 m depth, to uncover how it maintains efficient photosynthesis across this gradient. Combining spectroscopy with pigment and blue native-PAGE analysis, we show that P. oceanica maintains a high but stable photosystem I (PSI)/PSII ratio and constant antenna size at all depths, in conjunction with a high abundance of light-harvesting complex II (LHCII). Electron microscopy observation indicated that adjustment of photosynthetic efficiency along the depth gradient is primarily achieved through structural remodeling of thylakoid architecture, rather than major changes in photosystem composition. We also identify a previously undescribed large PSI supercomplex (L-PSI-LHCII) that binds an additional Lhca1-Lhca4 dimer and a phosphorylated LHCII trimer. This complex, expressed at all tested depths, is enriched in chlorophyll b, lacks the far-red-absorbing chlorophylls (red forms) typical of land plants, and exhibits distinct energy-transfer dynamics optimized for blue-light harvesting. The presence of similar PSI supercomplex in other marine seagrasses, such as Zostera marina, suggests a conserved strategy among deep-growing species. Collectively, these results reveal how seagrasses combine structural adaptation at the level of PSI with thylakoid architecture reorganization to sustain efficient photosynthesis and long-term carbon fixation under blue-dominated marine light.

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.

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.

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 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.