生命科学最新文献

{"title":"Automated mass spectrometry-based profiling of multi-glycosylated glycosyl inositol phospho ceramides (GIPC) reveals specific series GIPC rearrangements during barley grain development and heat stress response","authors":"Marlene Pühringer,&nbsp;Nina Thür,&nbsp;Madeleine Schnurer,&nbsp;Leonida M. Lamp,&nbsp;Lisa Panzenboeck,&nbsp;Jürgen Hartler,&nbsp;Andrea Tanzer,&nbsp;Verena Ibl,&nbsp;Evelyn Rampler","doi":"10.1111/tpj.70279","DOIUrl":"https://doi.org/10.1111/tpj.70279","url":null,"abstract":"<p>Glycosyl inositol phospho ceramides (GIPC) are the predominant glycosphingolipids in plant membranes, essential for their membrane stability, cell signaling, stress adaptation, and pathogen resistance. However, their complex structures, characterized by a ceramide backbone and a glycan head group, have challenged comprehensive analysis using traditional methods, which often rely on separate glycan or lipid profiling. To overcome these limitations, we developed a glycosphingolipidomics assay using reversed-phase high-resolution mass spectrometry including multistage fragmentation (RP-HRMSⁿ). This method enables direct, detailed structural characterization of GIPC in plants, combining advanced chromatographic separation, multistage fragmentation, and automated annotation using decision rule-based criteria. Applied to barley grains, the assay identified 102 GIPC species, including A-, B-, C-, and D-series GIPC, previously unreported glycan branching fragments (421 and 403 <i>m/z</i>), and a huge structural variety in the ceramide moiety. Profiling at different development stages revealed dynamic GIPC regulation during grain development, with an upregulation of B- and C-series towards mature development stages. The application of heat stress induced significant remodeling of GIPC profiles, mainly through upregulation of B-series species, which emphasizes their roles in maintaining membrane stability and functionality under abiotic stress conditions. The presented glycosphingolipidomics assay enables the first automated analysis of complex GIPC through a decision rule-based identification approach. By resolving GIPC to the molecular lipid species level, the method provides novel insights into GIPC diversity, homeostasis, and their critical roles in membrane dynamics, stress adaptation, and pathogen resistance, paving the way for advanced research in plant lipidomics and stress biology.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"122 6","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70279","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144492787","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":"Bidirectional electrotropism of wheat root","authors":"Zhenhua Shi,&nbsp;Lingmin Wang,&nbsp;Yingrong Zhang,&nbsp;Zhen Yu","doi":"10.1111/tpj.70303","DOIUrl":"https://doi.org/10.1111/tpj.70303","url":null,"abstract":"<div>\u0000 \u0000 <p>The fact that all cell organisms have electron transport chains and that all cell organisms need to obtain electron donors and electron acceptors from the environment to survive inspired that all cell organisms should have innate bidirectional tropism toward both electron donors and electron acceptors. Here we confirmed this hypothesis in wheat, that is, under a certain voltage condition, the smaller the current in the culture medium, the more roots grew toward the cathode (electron donor). As the current increases, more and more roots grew toward the anode (electron acceptor). More importantly, although the root growth direction was opposite under certain voltage and current conditions, the growth rate of the plant was increased. Moreover, LC–MS/MS-based metabolomics analysis showed that metabolites involved in energy metabolism (e.g., glucose-6-phosphat, fumaric acid, and L-malic acid) and secondary metabolism (e.g., 4-methoxycinnamic acid, caffeine, and coumarin) are closely related to this behavior. The relationship between bidirectional electrotropism and energy metabolism was further confirmed by examining the gene expression level of enzymes involved in both the glycolysis pathway and tricarboxylic acid cycle, the activity of antioxidant enzymes, the level of cellular ATP, and the inhibition of malonic acid. This study is the first report of bidirectional electrotropism of living organisms, and as the behavior of bidirectional electrotropism is based on the common of all cellular organisms, the ancestral role of this behavior in the origin and evolution of life is desirable.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"122 6","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144492788","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Physical principles underpinning molecular-level protein evolution.","authors":"Jorge A Vila","doi":"10.1007/s00249-025-01776-6","DOIUrl":"https://doi.org/10.1007/s00249-025-01776-6","url":null,"abstract":"<p><p>Since protein mutations are the main driving force of evolution at a molecular level, a proper analysis of the factors controlling them-such as the proteins' robustness, the evolutionary pathways, the number of ancestors, the epistasis, the post-translational modifications, and the location and the order of mutations-will enable us to find a response to several crucial queries in evolutionary biology. Among them, we highlight the following: At the molecular level, what factors determine whether protein evolution is repeatable? Aiming at finding an answer to this and several other significant questions behind protein evolvability, we distinguish two evolutionary models in our analysis: convergent and divergent, based on whether or not a \"target sequence\" needs to be reached after n mutational steps beginning with a wild-type protein sequence (from an unknown ancestor). Preliminary results suggest-regardless of whether the evolution is convergent or divergent-a tight relationship between the thermodynamic hypothesis (or Anfinsen's dogma) and the protein evolution at the molecular level. This conjecture will allow us to uncover how fundamental physical principles guide protein evolution and to gain a deeper grasp of mutationally driven evolutionary processes and the factors that influence them. Breaking down complex evolutionary problems into manageable pieces-without compromising the vision of the problem as a whole-could lead to effective solutions to critical evolutionary biology challenges, paving the way for further progress in this field.</p>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144504421","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Inside the membrane: a closer look using elastic scattering techniques and friends.","authors":"Michael Kaltenegger, Enrico F Semeraro, Georg Pabst","doi":"10.1007/s00249-025-01761-z","DOIUrl":"https://doi.org/10.1007/s00249-025-01761-z","url":null,"abstract":"<p><p>Biological membranes are highly dynamic and adaptive interfaces that define cellular compartments, posing significant challenges for detailed characterization. Among the diverse range of experimental and computational techniques, small-angle scattering emerges as a label-free, non-invasive method capable of probing membrane structures across length scales from micrometers to subnanometers. By exploiting the complementary contrasts of X-ray and neutron scattering, combined with advanced optimization algorithms, this approach has provided unique insights into membranes with well-defined lipid and protein architectures. In this review, we highlight recent studies from the Pabst Lab, including investigations of lipid domains, asymmetric lipid membranes, and intrinsic lipid curvature. Furthermore, we explore the functional implications of these findings, such as the activity of an integral membrane enzyme and the effects of antimicrobial peptides in live cells. These examples underscore the versatility of small-angle scattering techniques in elucidating membrane functions, offering valuable perspectives for understanding cellular processes and advancing pharmaceutical applications.</p>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144493357","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Th17 cells in cancer: plasticity-driven immunopathology and therapeutic opportunity.","authors":"Henry Sutanto, Mukti Citra Ningtyas, Betty Rachma, Laras Pratiwi, Deasy Fetarayani","doi":"10.1111/imcb.70043","DOIUrl":"https://doi.org/10.1111/imcb.70043","url":null,"abstract":"<p><p>T-helper 17 (Th17) cells, a subset of CD4⁺ T cells, are key players in mucosal immunity and inflammation, distinguished by their production of IL-17 and related cytokines. In the context of cancer, Th17 cells exhibit extraordinary plasticity-adapting their phenotype and function in response to tumor microenvironmental cues. This review explores how Th17 cells mediate paradoxical roles in tumor biology, promoting either tumor progression or antitumor immunity depending on molecular context. Protumorigenic functions include fostering angiogenesis, chronic inflammation and immune evasion through IL-17-driven recruitment of neutrophils and myeloid-derived suppressor cells. Conversely, Th17 cells can transition into IFNγ-producing Th1-like cells, enhancing cytotoxic T-cell responses and tumor rejection. Key modulators of this plasticity include cytokines (IL-23, IL-12, TGF-β), hypoxia, metabolic shifts and epigenetic reprogramming. We further examine how Th17 plasticity contributes to metastasis, therapy resistance and immune modulation via interactions with tumor-associated macrophages and regulatory T cells. Finally, the review highlights emerging therapeutic strategies that target Th17 pathways through cytokine blockade, metabolic intervention, RORγ modulation and adoptive cell therapy. Understanding Th17 plasticity provides critical insights into tumor immunology and offers novel avenues for cancer immunotherapy.</p>","PeriodicalId":179,"journal":{"name":"Immunology & Cell Biology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144493279","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quadruplexes with a grain of salt: influence of cation type and concentration on DNA G4 stability.","authors":"Anne Cucchiarini, Filip Kledus, Yu Luo, Václav Brázda, Jean-Louis Mergny","doi":"10.1007/s00249-025-01772-w","DOIUrl":"https://doi.org/10.1007/s00249-025-01772-w","url":null,"abstract":"<p><p>G-quadruplexes (G4) are stabilized by intra-quartet hydrogen bonds stacking between quartets, as well as specific and non-specific ionic interactions. Cation effects on G-quadruplexes differ significantly from those on duplexes, and specific cation coordination is indeed required to stabilize G4 structures. Most studies so far involve \"standard\" concentrations of potassium or sodium cations because of their prevalence in human cells, but several other monovalent and divalent cations may promote quadruplex formation. In addition, ionic strength may be different in other organisms such as Halophiles: the intracellular cation (potassium) concentration in salt-loving organisms such as Haloferax volcanii can be extremely high. In this study, we first performed a bioinformatics analysis of G4 propensity in halophiles and analyzed the impact of altering ionic strength or ionic balance on G4 or hairpin duplex stability. We then present a detailed and quantitative assessment of salt effect on a variety of duplex and quadruplex sequences. Over a dozen different quadruplex and duplex sequences were investigated by FRET melting and UV melting experiments. In addition, changes in sodium/potassium balance possibly occurring in human cells have a modest effect on G4-duplex competition. We also confirm that lithium is rather a \"G4-indifferent\" than a G4-destabilizing cation.</p>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144482774","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RGIs-mediated root apical meristem development is essential for root hydrotropic response in Arabidopsis thaliana","authors":"Yang Ou,&nbsp;Jingxia Yuan,&nbsp;Yanqin Ma,&nbsp;Xiaopeng Li,&nbsp;Haoyong Zhang,&nbsp;Jia Li","doi":"10.1111/tpj.70273","DOIUrl":"https://doi.org/10.1111/tpj.70273","url":null,"abstract":"<div>\u0000 \u0000 <p>Hydrotropism refers to the tendency of roots which prefer to grow towards a region with more water availability. We previously detected higher responses of cytokinins on the drier sides of Arabidopsis root tips, which lead to more cell division activity there and the growth of roots towards higher water potential areas. To further verify the significance of cell division activity in controlling root hydrotropism, we analyzed the hydrotropic responses of a number of well-characterized short root mutants with reduced root apical meristem activities. The mutants used were from a RGF1-RGIs signaling pathway, including a quadruple and a quintuple mutant for the receptors of an RGF1 peptide hormone, <i>rgi1234</i> and <i>rgi12345</i>, a tyrosyl protein sulfotransferase mutant <i>tpst</i>, and a double mutant for two transcription factors, <i>plt1 plt2</i>. All these mutants showed a greatly reduced or even undetectable hydrotropic response. The expression levels of <i>TCSn::GFP</i>, a reporter system for monitoring the response of cytokinins, were drastically down-regulated in the root tips of <i>rgi1234</i>, <i>rgi12345</i>, <i>tpst</i>, and <i>plt1 plt2</i>. The introduction of <i>pRGI2::MKK4</i>^<i>DD</i>, a construct encoding a constitutively active MKK4, can significantly rescue not only the short root phenotype but also the defective responses of cytokinins and hydrotropism in <i>rgi12345</i>. Interestingly, the hydrotropic response of <i>tie1 tie2</i>, a short root double mutant with normal cell division activity in the root apical meristem but defects in the elongation region, is relatively normal. Our results substantiate the key roles of the RGF1-RGIs signaling pathway and cell division activity in determining root hydrotropism. These analyses also reveal the crosstalk between the RGF1-RGIs signaling pathway and the responses of cytokinins, which are worth being further investigated in the future.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"122 6","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144482194","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Innovative screening for mutants affected in seed oil/protein allocation identifies TRANSPARENT TESTA7 as a regulator of oil accumulation","authors":"Alain Lécureuil,&nbsp;Massimiliano Corso,&nbsp;Stéphanie Boutet,&nbsp;Sophie Le Gall,&nbsp;Regina Niñoles,&nbsp;Jose Gadea,&nbsp;Philippe Guerche,&nbsp;Sophie Jasinski","doi":"10.1111/tpj.70269","DOIUrl":"https://doi.org/10.1111/tpj.70269","url":null,"abstract":"<p>Brassicaceae species mainly accumulate oil and protein in their seeds, which are essential to human life as a source of food, but also as animal feed and resources for green chemistry. To date, Brassicaceae crops such as rapeseed have been selected mainly for their oil content. However, there is a growing interest in their seed protein content. A strong negative correlation between oil and protein content makes it difficult to increase both compounds simultaneously. In this study, an <i>Arabidopsis thaliana</i> homozygous EMS mutant library was screened for seed oil and protein content by near-infrared spectroscopy with the aim of identifying mutants with impaired oil/protein correlation. The mutant most affected in this correlation was found to be in the <i>TRANSPARENT TESTA7</i> gene, which is involved in the flavonoid biosynthetic pathway. Analysis of different mutants in the flavonoid pathway revealed that the <i>tt7</i> mutants were the only ones to show such a significant reduction in seed oil content, highlighting a phenotype never described before for the <i>tt7</i> mutants and suggesting a specific role for TT7 in the interplay between the oil and flavonoid biosynthetic pathways. Untargeted metabolomic analysis allowed the identification of metabolic features that are highly accumulated and specific to <i>tt7</i> seeds compared to the other genotypes and genetic analysis established that the accumulation of kaempferol-3-O-rhamnoside seems to be responsible for the seed oil reduction in <i>tt7</i> mutants.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"122 6","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70269","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473131","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":"NF-YCs modulate RNA polymerase II-mediated transcription to regulate FLM expression","authors":"Xiani Yao,&nbsp;Ao Chen,&nbsp;Mingyang Jian,&nbsp;Xiaoming Li,&nbsp;Xu Liu,&nbsp;Xingliang Hou,&nbsp;Chunyu Zhang,&nbsp;Kangjia Li","doi":"10.1111/tpj.70293","DOIUrl":"https://doi.org/10.1111/tpj.70293","url":null,"abstract":"<div>\u0000 \u0000 <p>The proper transition to flowering is a critical process for the success of plant reproduction and must be highly orchestrated. Nuclear Factor-Y subunit C (NF-YCs), which are closely related to histone H2A, exert diverse chromatin-mediated regulation over plant development events including flowering. However, the mechanisms by which NF-YCs regulate RNA polymerase II (Pol II) during gene transcription remain elusive. Here, we demonstrate that NF-YCs physically interact with EARLY FLOWERING 7 (ELF7), a core component of RNA Pol II-associated factor 1 complex (PAF1c), both <i>in vitro</i> and <i>in vivo</i>. We show that NF-YCs regulate flowering in an ELF7-dependent manner by repressing the expression of the floral repressor <i>FLOWERING LOCUS M</i> (<i>FLM</i>). Further analyses reveal that NF-YCs antagonize the binding of ELF7 to <i>FLM</i> chromatin, thereby suppressing ELF7-mediated RNA Pol II transcription at the <i>FLM</i> locus. Collectively, our findings uncover a novel chromatin-mediated regulatory mechanism in which NF-YCs, in association with ELF7, control the transcription of <i>FLM</i> to modulate flowering time.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"122 6","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144482191","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive analysis of imprinted genes in citrus endosperm and their contributions to seed development","authors":"Jing-Jing He,&nbsp;Gang Hu,&nbsp;Ming-Yao Shen,&nbsp;Yan-Jie Fan,&nbsp;Xiao-Shu Shi,&nbsp;Xiao-Meng Wu,&nbsp;Wen-Wu Guo,&nbsp;Qiang-Ming Xia,&nbsp;Kai-Dong Xie","doi":"10.1111/tpj.70290","DOIUrl":"https://doi.org/10.1111/tpj.70290","url":null,"abstract":"<div>\u0000 \u0000 <p>Interploidy hybridization between diploid and tetraploid has been an important approach to develop triploid hybrids in horticultural plants including citrus for seedless breeding. However, dysregulation of imprinted genes can lead to the failure of endosperm cellularization, resulting in abortion of triploid embryos before seed maturity, thereby impeding the efficiency of triploid generation. The identification of imprinted genes is essential for comprehending the impact of imprinting on endosperm cellularization and mitigating embryo abortion in interploidy hybridization. Herein, a genome-wide search for imprinted genes in citrus was performed using RNA sequencing of the endosperm collected from two pairs of reciprocal crosses and totally 296 imprinted genes were identified. Among them, the paternally imprinted genes (PEGs) showed a higher inclination toward endosperm-specific expression compared to maternally imprinted genes (MEGs), with a few demonstrating consistent imprinting across three developmental stages of endosperm and displaying homology with counterparts found in other plant species. The analysis of transposable element (TE) enrichment and DNA methylation revealed a significant enrichment of mutator TEs with higher level of DNA methylation around maternal imprinted genes, highlighting their vital role for controlling the expression of MEGs. By overexpressing the endosperm-specific expressed PEGs in <i>Arabidopsis</i>, we observed that the transgenic lines of OE-<i>CsPEG1</i> exhibited an increased frequency of seed abortion, which appeared to be correlated with delayed endosperm cellularization, resembling the observed phenotypes in 2x × 4x interploidy hybridizations. Our research provides evidence supporting the functional conservation of imprinted genes in plants, thereby identifying potential targets for genetic improvement in triploid breeding.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"122 6","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144482143","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}