生命科学最新文献

{"title":"Enhancing inositol pyrophosphate accumulation in plants alters growth, phosphate homeostasis, and insect herbivory","authors":"Caitlin Cridland,&nbsp;Ashlynn Russo,&nbsp;Branch Craige,&nbsp;Janet Donahue,&nbsp;Xuemei Missi Zhang,&nbsp;Madison Payne,&nbsp;Glenda Gillaspy,&nbsp;Catherine Freed","doi":"10.1111/tpj.70315","DOIUrl":"https://doi.org/10.1111/tpj.70315","url":null,"abstract":"<p>Phosphate (P<i>i</i>) is a critical nutrient for plants and is often a limiting factor in food production, as many agricultural soils are limited in available P<i>i</i>. Inositol pyrophosphates (PP-InsPs) are signaling molecules involved in P<i>i</i> sensing and jasmonic acid (JA)-regulated plant defense. Here, we report that overexpression of 1,3,4-trisphosphate 5/6-kinase 1 (ITPK1) and the kinase domain of the dual-domain diphosphoinositol pentakisphosphate kinase 2 (VIP2KD) in <i>Arabidopsis thaliana</i> results in unique elevations in PP-InsPs, accompanied by altered leaf growth and senescence patterns, as well as delayed time to flowering. While plants overexpressing ITPK1 and VIP2KD (ITPK1 OX and VIP2KD OX) accumulated significantly lower levels of P<i>i</i>, transcriptomic and qRT-PCR analysis revealed that these plants showed elevated expression of P<i>i</i> starvation response genes. Our transcriptomic analysis also revealed ITPK1 OX and VIP2KD OX showed a significant enrichment in differentially expressed genes relating to plant defense and hypoxia. Of the two transgenic types, VIP2KD OX had significantly higher expression of more diverse plant defense-related differentially expressed genes and showed greater resistance to <i>Trichoplusia ni</i> compared to WT and ITPK1 OX plants. ITPK1 OX, although also having elevated PP-InsPs, was fed upon by insect larvae comparably to WT plants. Taken together, our data indicate the elevation of certain PP-InsPs may be a useful strategy for developing new traits in crop plants.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70315","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144598245","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":"CsMYB219 and CsMYB196 influence epigallocatechin gallate biosynthesis in tea plant (Camellia sinensis) by regulating CsSCPL1A gene expression","authors":"Xiangxiang Huang,&nbsp;Zexin An,&nbsp;Tiyue Zhao,&nbsp;Nianci Xie,&nbsp;Juan Li,&nbsp;Mingzhi Zhu,&nbsp;Jian Zhao,&nbsp;Zhonghua Liu,&nbsp;Kunbo Wang","doi":"10.1111/tpj.70341","DOIUrl":"https://doi.org/10.1111/tpj.70341","url":null,"abstract":"<div>\u0000 \u0000 <p>Epigallocatechin gallate (EGCG) is the most abundant and biologically active catechin in tea leaves and has been widely utilized in the development of functional foods. EGCG is catalyzed by serine carboxypeptidase-like 1A (CsSCPL1A) acyltransferases in tea plants. Although <i>CsSCPL</i> family genes are regulated by several transcription factors (TFs), systematic studies on their regulation by MYB TFs are lacking. This study integrates targeted metabolomics, transcriptomics, DNA-protein, and protein–protein interaction analyses to elucidate the transcriptional regulation of EGCG biosynthesis-related genes <i>CsSCPL4</i> and <i>CsSCPL5-1</i> by R2R3-MYB TFs. CsMYB219 and CsMYB196 can specifically bind to <i>CsSCPL4</i> and <i>CsSCPL5-1</i> promoters and activate their expression. CsMYB196 also interacted with CsTT8a and CsTTG1 to activate the transcription activity of <i>CsSCPL4</i> and <i>CsSCPL5-1</i> promoters by forming a MYB/bHLH/WD40 (MBW) complex. Promoter truncation assays delineated MYB-responsive <i>cis</i>-elements in <i>CsSCPL4</i> (−613 to −1 bp with enhancers at −1967 to −1622) and <i>CsSCPL5-1</i> (−503 to −296 bp). Silencing of CsMYB219 and CsMYB196 by virus-induced gene silencing (VIGS) assay significantly reduced the expression levels of <i>CsSCPL4</i> and <i>CsSCPL5-1</i> and EGCG content in tea leaves. Transient overexpression of CsMYB219 and CsMYB196 in tea leaves upregulated <i>CsSCPL4</i> and <i>CsSCPL5-1</i> expression and elevated EGCG content. These findings enhance our understanding of the regulatory network underlying EGCG biosynthesis in tea plants and provide a solid foundation for future genetic improvement of tea plant cultivars.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144598239","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":"Continuous In-Situ Water Stable Isotopes Reveal Rapid Changes in Root Water Uptake by Fagus sylvatica During Severe Drought.","authors":"Laura Kinzinger, Simon Haberstroh, Judith Mach, Markus Weiler, Natalie Orlowski, Christiane Werner","doi":"10.1111/pce.70055","DOIUrl":"https://doi.org/10.1111/pce.70055","url":null,"abstract":"<p><p>Adaptation of root water uptake (RWU) is critical for drought resilience in temperate forest trees, yet information on water sources and uptake depths dynamics is scarce. Continuous in-situ stable isotope measurements in soil and xylem water of Fagus sylvatica during the severe drought 2022 revealed daily changes in RWU depth and water ages. Xylem water comprised mainly recent precipitation in early summer, but winter and spring precipitation contributed up to 70% during drought, with longer transit times (206 ± 60 days) compared to summer precipitation (62 ± 11 days). Concurrently, trees shifted RWU to deeper soil layers while also responding to individual precipitation events by absorbing fresh precipitation from topsoil layers within 2-4 days, demonstrating the significance of individual precipitation events for tree water dynamic. F. sylvatica used > 80% of a fresh precipitation event before drought, but < 20% during recovery, indicating potential drought legacies on precipitation use. Unravelling these rapid dynamics in RWU and water ages offers novel insights into the importance of single and seasonal precipitation events for forest water fluxes.</p>","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":" ","pages":""},"PeriodicalIF":6.0,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144599013","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":"Natural variation in the cytokinin oxidase gene ZmCKX6 influences leaf morphology and yield-related traits in maize","authors":"Houmiao Wang,&nbsp;Yuxing Yan,&nbsp;Tingting Wu,&nbsp;Yunyun Wang,&nbsp;Hui Sun,&nbsp;Wei Li,&nbsp;Tianze Zhu,&nbsp;Xiaomin Zhang,&nbsp;Xiaoyi Yang,&nbsp;Wenye Rui,&nbsp;Aiqing Yang,&nbsp;Yamin Duan,&nbsp;Chenwu Xu,&nbsp;Zefeng Yang,&nbsp;Pengcheng Li","doi":"10.1111/tpj.70332","DOIUrl":"https://doi.org/10.1111/tpj.70332","url":null,"abstract":"<div>\u0000 \u0000 <p>Leaf width (LW) is a critical determinant of maize architecture and yield. To uncover its genetic basis, we performed a genome-wide association study (GWAS) on 348 maize inbred lines and identified <i>ZmCKX6</i>, encoding cytokinin oxidase/dehydrogenase, as a key gene associated with LW. Natural variation in the <i>ZmCKX6</i> promoter significantly influenced its expression levels, leading to differences in LW across various haplotypes. Functional validation using CRISPR/Cas9 revealed that <i>ZmCKX6</i> knockout results in pleiotropic effects, including narrower leaves, reduced plant height, and decreased grain yield components. These phenotypes were accompanied by elevated levels of active cytokinins but reduced levels of auxin, gibberellins, and salicylic acid. Transcriptome analysis revealed a significant downregulation of photosynthesis-related genes, corresponding to reduced photosynthetic rates in knockout lines. Evolutionary analysis demonstrated that the allele associated with narrower leaves were preferentially selected during maize domestication and breeding. This study highlights the role of <i>ZmCKX6</i> in modulating cytokinin homeostasis and its subsequent impact on multiple agronomic traits in maize, providing insights into the complex genetic control of plant architecture and yield. The identified natural variations could be valuable for marker-assisted selection aimed at optimizing plant architecture and improving yield.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144598396","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":"Transcriptional Dynamics of Rice Under Individual, Combined, and Sequential Abiotic Stresses: Insights Across Stress Severity and Recovery in Contrasting Genotypes.","authors":"Khalid Anwar, Shivani Kansal, Rajeev Nayan Bahuguna, Saurabh Raghuvanshi, Sneh L Singla-Pareek, Rita A Sharma, Ashwani Pareek","doi":"10.1111/pce.70062","DOIUrl":"https://doi.org/10.1111/pce.70062","url":null,"abstract":"<p><p>Plants in natural environments frequently encounter multiple abiotic stresses, which may occur individually, simultaneously, or sequentially, significantly impacting crop productivity. The transcriptional response to these stresses varies across genotypes, and understanding these variations at the molecular level is critical for improving stress resilience. In a previous study, we identified two contrasting rice genotypes, Lomello (highly stress-tolerant) and C57-5043 (highly stress-sensitive), from a screen of ~400 genotypes for abiotic stress tolerance. Here, we performed time-course transcriptomic profiling to dissect the molecular basis of their differential stress responses under varying severity levels (mild, moderate, and severe) of high temperature (HT), drought (D), submergence (S), combined heat and drought stress (HTD), and post-submergence drought (PSD). Our results reveal that transcriptional responses are highly context-dependent, with distinct expression patterns emerging under individual, combined, and sequential stress conditions. Notably, while submergence induced significant transcriptomic changes within the first few days, subsequent drought exposure, particularly at higher severity levels, did not elicit a strong transcriptional response, likely due to transcriptional silencing resulting from physiological damage. Comparative analysis between genotypes showed that Lomello exhibits constitutively higher expression of genes involved in phytoalexin biosynthesis, even in the absence of stress, potentially conferring a preemptive defense advantage. Furthermore, Lomello demonstrated a robust induction of genes associated with reactive oxygen species (ROS) scavenging, abscisic acid (ABA) biosynthesis and signaling, and secondary metabolite production in response to stress, followed by a rapid reversion to near-baseline expression levels during recovery. These findings suggest that Lomello's superior stress tolerance is driven by enhanced secondary metabolite accumulation, efficient ROS detoxification, and a stronger recovery response. This study provides novel insights into genotype-specific transcriptional strategies for stress resilience, offering potential targets for breeding climate-resilient rice varieties.</p>","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":" ","pages":""},"PeriodicalIF":6.0,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144599017","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":"Efficient and versatile rapeseed transformation for new breeding technologies","authors":"Kea Ille,&nbsp;Siegbert Melzer","doi":"10.1111/tpj.70330","DOIUrl":"https://doi.org/10.1111/tpj.70330","url":null,"abstract":"<p>Many gene functions are widely studied and understood in Arabidopsis; however, the lack of efficient transformation systems often limits the application and verification of this knowledge in crop plants. <i>Brassica napus</i> L., a member of the Brassicaceae family, is usually transformed by <i>Agrobacterium</i>-mediated hypocotyl transformation, but not all growth types are equally amenable to transformation. In particular, winter rapeseed, which requires vernalization to initiate flowering, is recalcitrant to <i>in vitro</i> regeneration and transformation. The analysis of gene functions in rapeseed is further complicated by the allotetraploid nature of its genome and the genome triplication within the <i>Brassica</i> genus, which has led to the presence of a large number of gene homologs for each Arabidopsis ortholog. We have established a transformation method that facilitates the regeneration of winter rapeseed by using the <i>WUSCHEL</i> gene from <i>Beta vulgaris</i>. This allowed us to efficiently transform a winter and spring rapeseed genotype in small-scale experiments. As proof of principle, we targeted <i>BnCLV3</i> and <i>BnSPL9/15</i> with CRISPR/Cas9 and showed that entire gene families are effectively edited using this transformation protocol. This allowed us to simultaneously study many redundantly acting homologous genes in rapeseed. We observed mutant phenotypes for <i>BnCLV3</i> and <i>BnSPL9/15</i> in primary transformants, indicating that biallelic knockouts were obtained for up to eight genes. This allowed an initial phenotypic characterization to be performed already a few months after starting the experiment.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70330","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144598244","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":"Genome-Wide Identification and Characterisation of Aquaporins in the Marine Higher Plant Zostera japonica and Their Response to the Intertidal Environment.","authors":"Hongzhen Wang, Yamei Wang, Feng He, Xinqi Li, Yu Zang, Song Xue, Jiayi Xin, Xuexi Tang, Jun Chen","doi":"10.1111/pce.70056","DOIUrl":"https://doi.org/10.1111/pce.70056","url":null,"abstract":"<p><p>Zostera japonica mainly lives in the intertidal zone and is susceptible to fluctuations in abiotic stresses, making it an excellent natural model for studying plant response mechanisms in intertidal environments. Aquaporins (AQPs) play important roles in water uptake, growth and development, and stress regulation. However, studies on the functions of the AQPs of Z. japonica (ZjAQPs) in response to intertidal environments have not been reported. In this study, we identified 22 AQPs in Z. japonica. Phylogenetic analysis revealed that ZjAQPs can be divided into four subfamilies: PIP, TIP, NIP and SIP. Analysis of the cis-acting elements suggested that ZjAQPs may be responsive to stresses. The subcellular localisation of ZjAQPs in tobacco revealed that they functioned predominantly in the membrane system. Transcript expression revealed that ZjAQPs were specifically expressed in various tissues and presented complex responses to environmental variables. Furthermore, transgenic Overexpression in yeast and Arabidopsis revealed that ZjNIP2-1, ZjSIP2-3, ZjPIP1-3, and ZjTIP1-3 play pivotal roles in adaptation to drought and salinity stress. Unlike the AQP subfamily of other higher plants, NIPs and SIPs may play important roles in Z. japonica. The information provided here will help to understand the precise role of AQP in Z. japonica adaptation to intertidal environments.</p>","PeriodicalId":222,"journal":{"name":"Plant, Cell & Environment","volume":" ","pages":""},"PeriodicalIF":6.0,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144599015","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":"Overexpression of the ABA-responsive transcription factor PtrMYBH alters shoot apical meristem, xylem, root, and leaf development in Populus","authors":"Ziqi Liu,&nbsp;Xiaomeng Fan,&nbsp;Xuqing Liu,&nbsp;Zeyu Zhang,&nbsp;Xiangrong Li,&nbsp;Yingjie Yan,&nbsp;Shengcai Xiang,&nbsp;Xiaoqi Zhang,&nbsp;Tingting Lu,&nbsp;Siyu Lu,&nbsp;Dengcan Liu,&nbsp;Tian Hua,&nbsp;Mengna Zhao,&nbsp;Jun Zhang,&nbsp;Hangxiao Zhang,&nbsp;Lianfeng Gu","doi":"10.1111/tpj.70337","DOIUrl":"https://doi.org/10.1111/tpj.70337","url":null,"abstract":"<div>\u0000 \u0000 <p>Abscisic acid (ABA) mediates stress responses and growth regulation in plants, but the roles of ABA-responsive transcription factors (TFs) in <i>Populus</i> development remain poorly characterized. Here, we identified an ABA-upregulated TF and investigated its function through overexpression in transgenic poplar. The <i>PtrMYBH</i> is upregulated during ABA treatment, and its overexpression in transgenic poplar leads to leaf malformations, including reduced size and curling, with severity correlating with <i>PtrMYBH-</i>overexpression levels in three independent transgenic lines. <i>PtrMYBH</i> regulates stomatal growth and development, resulting in decreased stomatal length and aperture, along with distinct leaf structural abnormalities. Additionally, <i>PtrMYBH</i> affects root development, with overexpressing lines showing an increase in adventitious root number but shorter lengths, alongside morphological changes in the root elongation zone. Furthermore, morphological changes are observed in the shoot apical meristem (SAM) and stem-differentiating xylem (SDX) of <i>PtrMYBH-</i>overexpressing poplar. RNA-seq analyses reveal <i>PtrMYBH</i>'s influence on the expression of genes related to cellular proliferation in the SAM and developmental pathways in the SDX. Finally, in <i>PtrMYBH</i>-overexpressing lines, ABA treatment results in leaf tip damage, earlier leaf drop, and stunted growth, highlighting its critical role in the ABA response. These findings lay a foundation for further exploration of TFs like <i>PtrMYBH</i> to regulate growth in <i>Populus</i> species.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144589608","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":"SGAM1 orchestrates salt tolerance by balancing mitochondrial translation and ROS homeostasis in Arabidopsis","authors":"Jiangyan Dong,&nbsp;Zi-ang Li,&nbsp;Xiao Yan,&nbsp;Fangfang Wang,&nbsp;Huchen Zhang,&nbsp;Guanting Niu,&nbsp;Hongjuan Chen,&nbsp;Zhi Hong","doi":"10.1111/tpj.70322","DOIUrl":"https://doi.org/10.1111/tpj.70322","url":null,"abstract":"<div>\u0000 \u0000 <p>Salt stress severely hampers plant growth and crop productivity. Defects in Golgi α1,2-mannosidase I MNS1 and MNS2 proteins, essential for N-glycan maturation, lead to severe root growth inhibition and swollen tips in <i>Arabidopsis</i> under salt stress. Here, we reported <i>sgam1</i>, a suppressor of <i>mns1 mns2</i>, exhibiting threshold-dependent suppression of salt sensitivity. <i>SGAM1</i> encodes a mitochondria-localized pentatricopeptide repeat protein, and <i>sgam1</i> mutations decreased the abundance and activity of mitochondrial electron transport complex (mETC), potentially by disrupting mitoribosome assembly and protein translation. This, in turn, alleviated the mitochondrial ROS accumulation and activated the AOX-mediated alternative respiratory pathway in <i>mns1 mns2</i> under salt stress. Overexpression of <i>AOX1a</i> notably reversed the salt-sensitive root phenotype in <i>mns1 mns2</i>. Furthermore, <i>sgam1</i> also suppressed other N-glycosylation mutants, suggesting a common mechanism. Our findings highlight the cooperative importance of N-glycosylation and mitochondrial activity in maintaining ROS homeostasis during salt stress.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144589607","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":"Triple labeling of metabolites for metabolome analysis (TLEMMA): a stable isotope labeling approach for metabolite identification and network reconstruction","authors":"Yonghui Dong,&nbsp;Liron Feldberg,&nbsp;Yi Wang,&nbsp;Uwe Heinig,&nbsp;Ilana Rogachev,&nbsp;Asaph Aharoni","doi":"10.1111/tpj.70333","DOIUrl":"https://doi.org/10.1111/tpj.70333","url":null,"abstract":"<p>Metabolite identification remains a significant challenge in mass spectrometry (MS)-based metabolomics research. To address this issue, we combined a triple-labeled precursor-based isotope tracing approach (TLEMMA) with high-resolution liquid chromatography-MS for metabolite identification and metabolic network construction. As a demonstration, we fed duckweed (<i>Spirodela polyrhiza</i>) with four forms of phenylalanine (Phe) including unlabeled Phe, Phe-⁵H₂, Phe-⁸H₂, and Phe-¹³C₉¹⁵N₁. The distinctive isotopic pattern obtained from MS spectra greatly facilitated data processing, enabling comprehensive extraction of all Phe-derived metabolites. Importantly, the labeling pattern allowed efficient metabolite identification by significantly reducing the number of structural and positional isomers. Using this approach, 47 phenylalanine-derived metabolites were putatively identified. To further evaluate the efficiency of metabolite identification in relation to the number of differently labeled precursors used, we compared the number of filtered candidates based solely on the labeling patterns obtained from unlabeled, single, dual, and triple isotope-labeled precursor tracing experiments. On average, TLEMMA eliminates the number of false candidates by 99.1% compared with unlabeled samples, 95% compared with single isotope-labeled samples, and 66.7% compared with dual isotope-labeled samples. This significant reduction in the number of false positives, along with the ability to identify previously unreported metabolites, demonstrates the power of TLEMMA in advancing the field of metabolomics and metabolic network reconstruction.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70333","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144589619","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}