Plant Communications最新文献

{"title":"Three cytochrome P450 enzymes consecutively catalyze the biosynthesis of furanoclerodane precursors in Salvia species.","authors":"Ruoxi Lin, Haixiu Li, Yiren Xiao, Zhuo Wang, Licheng Liu, Gerhard Saalbach, Carlo Martins, Matthew Furry, Christopher D Vanderwal, Cathie Martin, Evangelos C Tatsis","doi":"10.1016/j.xplc.2025.101286","DOIUrl":"10.1016/j.xplc.2025.101286","url":null,"abstract":"<p><p>Salvia species native to the Americas are rich in valuable bioactive furanoclerodanes like the psychoactive salvinorin A found in Salvia divinorum, which is used in the treatment of opioid addiction. However, relatively little is known about their biosynthesis. To address this, we investigated the biosynthesis of salviarin, the most abundant furanoclerodane structure in the ornamental sage Salvia splendens. Using a self-organizing map and mutual rank analysis of RNA-seq co-expression data, we identified three cytochrome P450 enzymes responsible for the consecutive conversion of kolavenol into the salviarin precursors: annonene, hardwickiic acid, and hautriwaic acid. Annonene and hardwickiic acid have been proposed as intermediates in the biosynthesis of salvinorin A, and we therefore tested for a common evolutionary origin of the furanoclerodane pathway in these Salvia species by searching for homologous genes in available data for S. divinorum. The enzymes encoded by orthologous genes from S. divinorum displayed kolavenol synthase, annonene synthase, and hardwickiic acid synthase activity, respectively, supporting the view that these are intermediate steps in the biosynthesis of salvinorin A. We further investigated the origin of annonene synthase and the role of gene duplication in the evolution of this specific activity. Our work shows how S. splendens can serve as a model species for the study of furanoclerodane biosynthesis in Salvia species, contributes to understanding the evolution of specialized metabolism in plants, and provides new tools for the production of salvinorin A in biotechnological chassis.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101286"},"PeriodicalIF":9.4,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143158/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143460594","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"AtKC1 inhibits AKT1 activation via its amino-terminal inhibitory domain.","authors":"Zijie Zheng, Yannan Qu, Jiexin Chen, Yuyue Tang, Dongliang Liu, Zhuo Huang, Huaizong Shen","doi":"10.1016/j.xplc.2025.101288","DOIUrl":"10.1016/j.xplc.2025.101288","url":null,"abstract":"","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101288"},"PeriodicalIF":9.4,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143135/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143469948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"EasyOmics: A graphical interface for population-scale omics data association, integration, and visualization.","authors":"Yu Han, Qiao Du, Yifei Dai, Shaobo Gu, Mengyu Lei, Wei Liu, Wenjia Zhang, Mingjia Zhu, Landi Feng, Huan Si, Jianquan Liu, Yanjun Zan","doi":"10.1016/j.xplc.2025.101293","DOIUrl":"10.1016/j.xplc.2025.101293","url":null,"abstract":"<p><p>The rapid growth of population-scale whole-genome resequencing, RNA sequencing, bisulfite sequencing, and metabolomic and proteomic profiling has led quantitative genetics into the era of big omics data. Association analyses of omics data, such as genome-, transcriptome-, proteome-, and methylome-wide association studies, along with integrative analyses of multiple omics datasets, require various bioinformatics tools, which rely on advanced programming skills and command-line interfaces and thus pose challenges for wet-lab biologists. Here, we present EasyOmics, a stand-alone R Shiny application with a user-friendly interface that enables wet-lab biologists to perform population-scale omics data association, integration, and visualization. The toolkit incorporates multiple functions designed to meet the increasing demand for population-scale omics data analyses, including data quality control, heritability estimation, genome-wide association analysis, conditional association analysis, omics quantitative trait locus mapping, omics-wide association analysis, omics data integration, and visualization. A wide range of publication-quality graphs can be prepared in EasyOmics by pointing and clicking. EasyOmics is a platform-independent software that can be run under all operating systems, with a docker container for quick installation. It is freely available to non-commercial users at Docker Hub https://hub.docker.com/r/yuhan2000/easyomics.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101293"},"PeriodicalIF":9.4,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143152/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143525230","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Striga hermonthica induces lignin deposition at the root tip to facilitate prehaustorium formation and obligate parasitism.","authors":"Songkui Cui, Yuri Takeda-Kimura, Takanori Wakatake, Jun Luo, Yuki Tobimatsu, Satoko Yoshida","doi":"10.1016/j.xplc.2025.101294","DOIUrl":"10.1016/j.xplc.2025.101294","url":null,"abstract":"<p><p>Striga hermonthica, an obligate parasitic plant that causes severe agricultural damage, recognizes its hosts by sensing haustorium-inducing factors (HIFs). Perception of HIFs induces the rapid transformation of S. hermonthica radicles into prehaustoria, structures that enable host invasion and mature into haustoria. HIFs consist of various aromatic compounds, including quinones, lignin monomers, and flavonoids. However, the downstream molecular pathways that orchestrate these developmental events are largely unknown. Here, we report that S. hermonthica root-tip cells rapidly deposit lignin, a major cell wall component, in response to HIFs. In addition to enhancing lignin levels, HIFs strongly induce genes involved in lignin monomer biosynthesis and polymerization, including several respiratory burst oxidase homologs (RBOHs) and class III peroxidases. Disruption of lignin monomer biosynthesis compromises prehaustorium formation, whereas HIF-induced class III peroxidases facilitate the process by promoting lignification. Our study demonstrates that cell wall lignification is a converged cellular process downstream of various HIFs that guides root meristematic cells in prehaustorium development.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101294"},"PeriodicalIF":9.4,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143140/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143544407","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of a key peptide cyclase for novel cyclic peptide discovery in Pseudostellaria heterophylla.","authors":"Xianjin Qin, Fengjiao Wang, Dejin Xie, Qi Zhou, Sheng Lin, Wenxiong Lin, Wei Li","doi":"10.1016/j.xplc.2025.101315","DOIUrl":"10.1016/j.xplc.2025.101315","url":null,"abstract":"<p><p>Orbitides, also known as Caryophyllaceae-type cyclic peptides, from the Traditional Chinese Medicine plant Pseudostellaria heterophylla (Miq.) Pax, exhibit great potential for improving memory and treating diabetes. Orbitides are ribosomally encoded and post-translationally modified peptides; however, the key biosynthetic enzyme mediating this process remains unknown in P. heterophylla. In this study, we investigated the distribution of orbitides in P. heterophylla and mined novel precursor peptide genes and peptide cyclases from multiple omics datasets. The function of PhPCY3, a gene encoding a key tailoring enzyme, was elucidated using transient heterologous expression and virus-induced gene silencing systems. Our findings suggest that PhPCY3 specifically cyclizes linear precursor peptides in planta. Molecular docking and multiple sequence alignment, followed by site-directed mutagenesis, identified N500 and S502 as critical amino acid residues for PhPCY3 function. We identified gene sequences for over 100 precursor peptides and successfully biosynthesized known active orbitides, such as heterophyllin B and pseudostellarin E/F/G. Additionally, four novel orbitides, cyclo-[LDGPPPYF], cyclo-[WGSSTPHT], cyclo-[GLPIGAPWG], and cyclo-[FGDVGPVI], were synthesized using a heterologous expression platform. This study introduces a gene-guided approach for elucidating the biosynthesis pathway and discovering novel orbitides, providing a strategy for mining and biosynthesizing novel orbitides in P. heterophylla and other plants to further investigate their activities.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101315"},"PeriodicalIF":9.4,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143145/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143626794","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of maize genes that condition early systemic infection of sugarcane mosaic virus through single-cell transcriptomics.","authors":"Xi Chen, Ru Yao, Xia Hua, Kaitong Du, Boxin Liu, Yongxian Yuan, Pei Wang, Qin Yan, Laihua Dong, Simon C Groen, Sanjie Jiang, Tao Zhou","doi":"10.1016/j.xplc.2025.101297","DOIUrl":"10.1016/j.xplc.2025.101297","url":null,"abstract":"<p><p>During the early systemic infection of plant pathogens, individual cells can harbor pathogens at various stages of infection, ranging from absent to abundant. Consequently, gene expression levels within these cells in response to the pathogens exhibit significant variability. These variations are pivotal in determining pathogenicity or susceptibility, yet they remain largely unexplored and poorly understood. Sugarcane mosaic virus (SCMV) is a representative member of the monocot-infecting potyviruses with a polyadenylated RNA genome, which can be captured by single-cell RNA sequencing (scRNA-seq). Here, we performed scRNA-seq on SCMV-infected maize leaves during early systemic infection (prior to symptom manifestation) to investigate the co-variation patterns between viral accumulation and intracellular gene expression alterations. We identified five cell types and found that mesophyll-4 (MS4) cells exhibited the highest levels of viral accumulation in most cells. Early systemic infection of SCMV resulted in a greater upregulation of differentially expressed genes, which were mainly enriched in biological processes related to translation, peptide biosynthesis, and metabolism. Co-variation analysis of the altered maize gene expression and viral accumulation levels in MS1, 2, and 4 revealed several patterns, and the co-expression relationships between them were mainly positive. Furthermore, functional studies identified several potential anti- or pro-viral factors that may play crucial roles during the early stage of SCMV systemic infection. These results not only provide new insights into plant gene regulation during viral infection but also offer a foundation for future investigations of host-virus interactions across molecular, cellular, and physiological scales.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101297"},"PeriodicalIF":9.4,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143147/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143568805","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PlantRing: A high-throughput wearable sensor system for decoding plant growth, water relations, and innovating irrigation.","authors":"Ting Sun, Chenze Lu, Zheng Shi, Mei Zou, Peng Bi, Xiaodong Xu, Qiguang Xie, Rujia Jiang, Yunxiu Liu, Rui Cheng, Wenzhao Xu, Huasen Wang, Yingying Zhang, Pei Xu","doi":"10.1016/j.xplc.2025.101322","DOIUrl":"10.1016/j.xplc.2025.101322","url":null,"abstract":"<p><p>The integration of flexible electronics with plant science has generated various plant-wearable sensors, yet challenges persist in their application to real-world agriculture, particularly in high-throughput settings. Overcoming the trade-off between sensing sensitivity and range, adapting sensors to a wide range of crop types, and bridging the gap between sensor measurements and biological understandings remain primary obstacles. Here, we introduce PlantRing, an innovative, nano-flexible sensing system designed to address these challenges. PlantRing employs bio-sourced carbonized silk georgette as the strain-sensing material, offering an exceptional detection limit (0.03%-0.17% strain, depending on sensor model), high stretchability (tensile strain up to 100%), and remarkable durability (season-long use). PlantRing effectively monitors plant growth and water status by measuring organ circumference dynamics, performing reliably under harsh conditions, and adapting to a wide range of plant species. Applying PlantRing to study fruit cracking in tomato and watermelon has revealed a novel hydraulic mechanism characterized by genotype-specific excess sap flow within the plant to fruiting branches. Its high-throughput application has enabled large-scale quantification of stomatal sensitivity to soil drought-a long-standing aspiration in plant biology-facilitating the selection of drought-tolerant germplasm. Combining PlantRing with a soybean mutant has led to the discovery of a potential novel function of the circadian clock gene GmLNK2 in stomatal regulation. More practically, integrating PlantRing into feedback irrigation achieves simultaneous water conservation and quality improvement, signifying a paradigm shift from reliance on experience or environmental cues to plant-based feedback control. Collectively, PlantRing represents a groundbreaking tool poised to revolutionize botanical studies, agriculture, and forestry.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101322"},"PeriodicalIF":9.4,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143137/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143722016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SHATTERING ABORTION3 controls rice seed shattering by promoting abscission zone separation.","authors":"Danfeng Lv, Bingxin Dai, Yan Zhou, Yan Zhao, Jianghong Luo, Zhoulin Gu, Zhou Zhu, Yaoxin Zhang, Jiashun Miao, Rongrong Sun, Qingqing Hou, Yongchun Wang, Qi Feng, Danlin Fan, Congcong Zhou, Yiqi Lu, Qilin Tian, Yingying Yu, Zixuan Wang, Hong-Xuan Lin, Bin Han","doi":"10.1016/j.xplc.2025.101282","DOIUrl":"10.1016/j.xplc.2025.101282","url":null,"abstract":"","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101282"},"PeriodicalIF":9.4,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143131/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143411487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A molecular representation system with a common reference frame for analyzing triterpenoid structural diversity.","authors":"Nicole Babineau, Le Thanh Dien Nguyen, Davis Mathieu, Clint McCue, Nicholas Schlecht, Taylor Abrahamson, Björn Hamberger, Lucas Busta","doi":"10.1016/j.xplc.2025.101320","DOIUrl":"10.1016/j.xplc.2025.101320","url":null,"abstract":"<p><p>Researchers have uncovered hundreds of thousands of natural products, many of which contribute to medicine, materials, and agriculture. However, missing knowledge about the biosynthetic pathways of these products hinders their expanded use. Nucleotide sequencing is key to pathway elucidation efforts, and analyses of the molecular structures of natural products, although seldom discussed explicitly, also play an important role by suggesting hypothetical pathways for testing. Structural analyses are also important in drug discovery, for which many molecular representation systems-methods of representing molecular structures in a computer-friendly format-have been developed. Unfortunately, pathway elucidation investigations seldom use these representation systems. This gap likely occurs because those systems are primarily built to document molecular connectivity and topology rather than the absolute positions of bonds and atoms in a common reference frame, which would enable chemical structures to be connected with potential underlying biosynthetic steps. Here, we expand on recently developed skeleton-based molecular representation systems by implementing a common-reference-frame-oriented system. We tested this system using triterpenoid structures as a case study and explored its applications in biosynthesis and structural diversity tasks. The common-reference-frame system can identify structural regions of high or low variability on the scale of atoms and bonds and enable hierarchical clustering that is closely connected to underlying biosynthesis. Combined with information on phylogenetic distribution, the system illuminates distinct sources of structural variability, such as different enzyme families operating in the same pathway. These characteristics outline the potential of common-reference-frame molecular representation systems to support large-scale pathway elucidation efforts.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101320"},"PeriodicalIF":9.4,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143141/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143712078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular mechanisms driving the unusual pigmentation shift during eggplant fruit development.","authors":"Sayantan Panda, Louise Chappell-Maor, Luis Alejandro de Haro, Adam Jozwiak, Sachin A Gharat, Yana Kazachkova, Jianghua Cai, Andrii Vainer, Laura Toppino, Urmila Sehrawat, Guy Wizler, Margarita Pliner, Sagit Meir, Giuseppe Leonardo Rotino, Hagai Yasuor, Ilana Rogachev, Asaph Aharoni","doi":"10.1016/j.xplc.2025.101321","DOIUrl":"10.1016/j.xplc.2025.101321","url":null,"abstract":"<p><p>Fruit pigmentation is a major signal that attracts frugivores to enable seed dispersal. In most fleshy fruit, green chlorophyll typically accumulates early in development and is replaced by a range of pigments during ripening. In species such as grape and strawberry, chlorophyll is replaced by red anthocyanins produced by the flavonoid biosynthetic pathway. Eggplant (Solanum melongena) is unique, as its fruit accumulates anthocyanins beginning from fruit set, and these are later replaced by the yellow flavonoid-pathway intermediate naringenin chalcone. To decipher the genetic regulation of this extraordinary pigmentation shift, we integrated mRNA and microRNA (miRNA) profiling data obtained from developing eggplant fruit. We discovered that SQUAMOSA PROMOTER BINDING-LIKE (i.e., SPL6a, SPL10, and SPL15), MYB1, and MYB2 transcription factors (TFs) regulate anthocyanin biosynthesis in early fruit development, whereas the MYB12 TF controls later accumulation of naringenin chalcone. We further show that miRNA157 and miRNA858 negatively regulate the expression of SPLs and MYB12, respectively. Taken together, our findings suggest that opposing and complementary expression of miRNAs and TFs controls the pigmentation switch in eggplant fruit skin. Intriguingly, despite the distinctive pigmentation pattern in eggplant, fruit development in other species makes use of homologous regulatory factors to control the temporal and spatial production of different pigment classes.</p>","PeriodicalId":52373,"journal":{"name":"Plant Communications","volume":" ","pages":"101321"},"PeriodicalIF":9.4,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143153/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143722008","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}