Metallomics最新文献

{"title":"Retraction and replacement of: Nitrogen sources enhance siderophore-mediated competition for iron between potato common scab and late blight causative agents.","authors":"","doi":"10.1093/mtomcs/mfaf037","DOIUrl":"https://doi.org/10.1093/mtomcs/mfaf037","url":null,"abstract":"","PeriodicalId":89,"journal":{"name":"Metallomics","volume":"17 11","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145511248","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The proteome-scale study of iron-binding proteins of bread wheat.","authors":"Anand Kumar Bharti, Shailender Kumar Verma","doi":"10.1093/mtomcs/mfaf036","DOIUrl":"10.1093/mtomcs/mfaf036","url":null,"abstract":"<p><p>Iron is an essential micronutrient and plays a vital role in human nutrition and plant development. In this report, we investigated iron-binding proteins (IBPs) of bread wheat at the sequence and structure levels, utilizing high-throughput systematic computational biology and bioinformatic approaches. We found that out of 133 346 wheat proteins, at least 0.97% could bind with iron ions. The analysis revealed numerous significant differences among these IBPs, which are involved in various biological functions. Most of these proteins are localized in plastids, followed by the endoplasmic reticulum, cell membrane and nucleus. But the most diverse group of IBPs are localized in the nucleus and cytoplasm region, being functionally associated with various biological processes. Out of 321 IBP unique domains, most proteins fall under GT1-Gtf-like, protein kinase domain, secretory peroxidases and CYP1. Further categorization and classification of these shortlisted IBPs revealed that most of these proteins are involved in metabolic processes, with oxidoreductase activity being the most prominent gene ontology molecular function (GO: MF), whereas biological process (GO: BP) enrichment highlighted the involvement of these IBPs in the management of reactive oxygen species. Protein interaction and identification of hub genes revealed further important IBP genes that have the potential to be used as a reference sheet for wet-lab work in the development of molecular markers for biofortification and understanding iron homeostasis in wheat.</p>","PeriodicalId":89,"journal":{"name":"Metallomics","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145399248","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Monoribbed-functionalized iron(II) clathrochelates with optically active and/or terminal biorelevant group(s): synthesis, single-crystal X-ray diffraction and quantum-chemical characterization, and their inherent versus protein-induced chirality.","authors":"Ilya P Limarev, Alexander S Belov, Alexander L Pomadchik, Yurii V Fedorov, Yan V Zubavichus, Anna V Vologzhanina, Alexander A Korlyukov, Yan Z Voloshin","doi":"10.1093/mtomcs/mfaf033","DOIUrl":"10.1093/mtomcs/mfaf033","url":null,"abstract":"<p><p>Novel monoribbed-functionalized iron(II) cage complexes with optically active and/or terminal biorelevant group(s) were designed and prepared by two-step nucleophilic substitution of their mono- and dichloroclathrochelate precursors. The single-crystal XRD structures of all of them and those of known leader iron(II)-centered cage bioeffector and of its reactive monochloroclathrochelate precursor were solved. These experimental data were used for theoretical quantum chemical calculations of electrostatic potentials for their 3D-shaped molecules. This allowed to localize the peripheral (exterior) biorelevant group(s), which are responsible for supramolecular binding of thus designed clathrochelate guests to globular proteins as the hosts. Host-guest binding in aqueous solutions between the unfolded protein macromolecules and all the aforementioned iron(II) complexes was studied by the circular dichroism method. An inherent chirality of the metalloclathrochelates with optically active ribbed substituent and a metal-centered chirality of all the prepared macrobicyclic compounds, induced by their supramolecular clathrochelate-to-protein binding, were observed.</p>","PeriodicalId":89,"journal":{"name":"Metallomics","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145172095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification and expression analysis of yellow stripe-like (YSL) genes in Nicotiana tabacum.","authors":"Haiyan Yuan, Zhijie Duan, Gang Liang","doi":"10.1093/mtomcs/mfaf035","DOIUrl":"10.1093/mtomcs/mfaf035","url":null,"abstract":"<p><p>Iron (Fe) and copper (Cu) are crucial micronutrients for plant growth and development. The yellow stripe-like (YSL) proteins play a vital role in the absorption and transport of metal chelates in plants. The YSL genes in tobacco have not been systematically identified and characterized. This study aims to explore the YSL genes in Nicotiana tabacum. A comprehensive set of 17 NtYSL genes were identified and classified into four distinct clades on the phylogenetic tree. The gene structures, characterized by the length and distribution of exons and introns, and protein motifs are relatively conserved. Genomic localization analysis revealed that the NtYSL genes are unevenly distributed across 15 chromosomes, with 11 pairs of homeologous loci identified within the genome. To investigate the functionality of these genes, we analyzed their expression levels in shoots and roots under Fe- and Cu-deficient conditions by real-time quantitative reverse transcription PCR (qRT-PCR), finding that several NtYSL genes are responsive to Cu deficiency or Fe deficiency. This study provides a systematic characterization of the NtYSL gene family in Nicotiana tabacum and offers insights into their potential roles in Fe and Cu homeostasis.</p>","PeriodicalId":89,"journal":{"name":"Metallomics","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145197375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integration of elemental imaging and spatial transcriptomic profiling for proof-of-concept metals-based pathway analysis of colon tumor microenvironment.","authors":"Aruesha Srivastava, Neha Shaik, Yunrui Lu, Matthew Chan, Alos Diallo, John Zavras, Serin Han, Tracy Punshon, Brian Jackson, Linda Vahdat, Xiaoying Liu, Vivek Mittal, Ken Lau, Jiang Gui, Louis Vaickus, Jack Hoopes, Fred Kolling, Laurent Perreard, Jonathan Marotti, Joshua Levy","doi":"10.1093/mtomcs/mfaf034","DOIUrl":"10.1093/mtomcs/mfaf034","url":null,"abstract":"<p><p>The complex interplay between metal abundance, transport mechanisms, cell distribution, and tumor progression-related biological pathways (e.g. metabolism, collagen remodeling) remains poorly understood. Traditionally, genes and metals have been studied in isolation, limiting insights into their interactions. Recent advances in spatial transcriptomics and elemental profiling now enable comprehensive exploration of tissue-wide metal-gene interactions, though integration remains challenging. In this proof-of-concept study, we investigated metal-dependent signaling within the tumor microenvironment of a unique colorectal cancer (CRC) tumor. We implemented a spatial multimodal workflow which integrated elemental imaging, gene expression, cellular composition, and histopathological features to uncover metals-related pathways through spatially resolved gene expression correlation analyses. Preliminary findings revealed significant associations, for instance: elevated iron correlated with mesenchymal phenotypes located at the tumor's proliferative front, correlating with expression of genes involved in the epithelial-to-mesenchymal transition pathways, and extracellular matrix remodeling. Preliminary observations from this single sample revealed that high copper concentrations were localized to regions of active tumor growth and were associated with increased expression of immune response genes. This proof-of-concept workflow demonstrates the feasibility of integrating elemental imaging with spatial transcriptomics to identify metals-based gene correlates. Future application of this workflow to larger patient cohorts will pave the way for expansive comparisons across the metallome and transcriptome, ultimately identifying novel targets for tumor progression biomarkers and therapeutic interventions.</p>","PeriodicalId":89,"journal":{"name":"Metallomics","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12569514/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145211086","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The interplay of iron status and manganese biomarkers in U.S. females: NHANES 2015-2018 analysis.","authors":"Yu-Sheng Lin, James L Caffrey, Babasaheb Sonawane, Miyoung Yoon, Viktor Morozov, Wen-Chao Ho","doi":"10.1093/mtomcs/mfaf032","DOIUrl":"10.1093/mtomcs/mfaf032","url":null,"abstract":"<p><p>Manganese (Mn) plays a dual role in the body, acting as an essential trace element and a potential toxicant, the effects of which depend on its levels. In addition to food, exposure can occur through polluted air and contaminated water. Animal studies suggest that increased retention and absorption of Mn might result from iron deficiency, as both share similar physicochemical properties. However, human evidence is incomplete. This study aimed to confirm and expand upon prior findings that iron status influences Mn kinetics in the U.S. female population. The analysis included 1255 non-pregnant females aged 12-49 years with valid urinary and blood Mn and iron measurements as part of the 2015-2018 National Health and Nutrition Examination Survey. Iron status was assessed with a total body iron (TBI) score calculated from measured serum ferritin and the transferrin receptor. Iron deficiency was defined as a TBI score < 0. Demographic and laboratory characteristics (e.g. age and kidney function) were recorded. Among the study participants, roughly 8.8% were found to have iron deficiency. Conversely, 16.9% of participants exhibited blood Mn levels exceeding 1.5 µg/dL, a commonly used reference. On average, blood Mn was approximately 40% higher in subjects considered iron deficient than in their counterparts after controlling for covariates such as race. Those with iron deficiency also had a lower urine-to-blood Mn ratio. The findings suggest that iron-deficient females may have greater Mn accumulation, increasing the risk of Mn toxicity. Further investigations should include male populations to complement the current findings.</p>","PeriodicalId":89,"journal":{"name":"Metallomics","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13035105/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145090836","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The interactome of the Bakers' yeast peroxiredoxin Tsa1 implicates it in redox regulation of intermediary metabolism, glycolysis, and zinc homeostasis.","authors":"Colin W MacDiarmid, Yirong Wang, Janet Taggart, Ajay Vashisht, Xin Qing, James A Wohlschlegel, David J Eide","doi":"10.1093/mtomcs/mfaf028","DOIUrl":"10.1093/mtomcs/mfaf028","url":null,"abstract":"<p><p>Zinc (Zn) is an essential nutrient supporting a range of critical processes. In the yeast Saccharomyces cerevisiae, Zn deficiency induces a transcriptional response mediated by the Zap1 activator, which controls a regulon of ∼80 genes. A subset support Zn homeostasis by promoting Zn uptake and its distribution between compartments, while the remainder mediate an 'adaptive response' to enhance fitness of Zn-deficient (ZnD) cells. The peroxiredoxin Tsa1 is a Zap1-regulated adaptive factor essential for the growth of ZnD yeast. Tsa1 can function as an antioxidant peroxidase, protein chaperone, or redox sensor: The latter activity oxidizes associated proteins via a redox relay mechanism. We previously reported that in ZnD cells, Tsa1 inhibits pyruvate kinase (Pyk1) to conserve phosphoenolpyruvate for aromatic amino acid synthesis. However, this regulation makes a relatively minor contribution to fitness in low Zn, suggesting that Tsa1 targets other pathways important to adaptation. Consistent with this model, the redox sensor function of Tsa1 was essential for growth of ZnD cells. Using a maltose binding protein-tagged version of Tsa1, we identified a redox-sensitive non-covalent interaction with Pyk1, and applied this system to identify multiple novel interacting partners. This interactome implicates Tsa1 in the regulation of critical processes including many Zn-dependent metabolic pathways. Interestingly, Zap1 is a Tsa1 target, as Tsa1 strongly promoted the oxidation of Zap1 activation domain 2 and was required for full Zap1 activity. Our findings reveal a novel posttranslational response to Zn deficiency, overlain on and interconnected with the Zap1-mediated transcriptional response.</p>","PeriodicalId":89,"journal":{"name":"Metallomics","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12368497/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144758678","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of a mechanistic connection between persulfide transfer and ATP hydrolysis in the SufBC2D scaffold of the Suf Fe-S cluster assembly pathway.","authors":"Nidhi Chhikara, Grishma Timilsina, Yu Wang, Dexter Reasons, F Wayne Outten, Patrick A Frantom","doi":"10.1093/mtomcs/mfaf029","DOIUrl":"10.1093/mtomcs/mfaf029","url":null,"abstract":"<p><p>The Suf pathway is the most common pathway for bacterial iron-sulfur cluster assembly and uses the SufBC2D complex as a scaffold for cluster formation. In most Gram-negative bacteria, the SufB subunit of SufBC2D accepts a persulfide from the transpersulfurase, SufE, for incorporation into nascent clusters. There is no reported structure for the SufBC2D-E complex and mechanistic details concerning the coordination of persulfide delivery with other SufBC2D activities are unclear. Using the Suf pathway from Escherichia coli as a model system, we report that SufE acts as a noncompetitive inhibitor of SufBC2D ATPase activity with a Ki value of 1.8 ± 0.2 µM. This value corresponds with a KD value of 1.6 ± 0.2 µM for SufE binding to the SufBC2D complex determined by fluorescence polarization. The rate of persulfide transfer from SufE to SufBC2D is impaired in the presence of ATP, suggesting that the two reactions are mutually exclusive. An AlphaFold3 model of the SufBC2D-E complex predicts electrostatic interactions between acidic residues on SufC and basic residues on the N-terminal helix of SufE. SufE variants at the K9 and R16 positions interfere with the ability of SufE to transfer persulfide to SufBC2D and to inhibit SufBC2D ATPase activity. In vivo complementation growth assays show that these SufE variants exhibit a slow-growth phenotype under iron starvation conditions, confirming the connection between SufE and SufC as important for optimal function in the Suf pathway. The mutual exclusivity of persulfide delivery from SufE and SufBC2D ATPase activity suggests an ordered mechanism for cluster assembly.</p>","PeriodicalId":89,"journal":{"name":"Metallomics","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12378399/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144758677","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The relationship between copper metabolism and p53 activity in tumors.","authors":"Wenyan Yu, Xinlin Hong, Guojuan Wang, Chen Zhong, Yuwei Yan, Qingqing Ma, Yujuan Lai, Naicheng Zhu, Xiudan Chen, Nanxin Li, Jianfeng Weng","doi":"10.1093/mtomcs/mfaf025","DOIUrl":"10.1093/mtomcs/mfaf025","url":null,"abstract":"<p><p>Cancer is an intractable global public health problem. The p53 protein encoded by the TP53 is a tumor suppressor, but it is mutated in many tumors, which promotes the initiation and progression of tumors. The mechanisms of p53 regulates tumors are focused on regulating apoptosis, cell cycle arrest, nutrient metabolism, iron metabolism, and redox levels. Copper is a necessary trace element, and abnormal copper homeostasis not only damages the organism but also affects tumor progression. It has confirmed that p53 can bind to copper, respond to copper levels, and regulate copper metabolism. Some anti-tumor mechanisms of copper-related compounds are related to p53. Herein, we focus on reviewing how to regulate copper-binding proteins by p53, as well as its involvement in copper-mediated cell death and tumor drug resistance. It summarizes the pertinent mechanisms of wild-type p53 in regulating cancers via copper metabolism, which aiming to provide new ideas for future cancer therapy.</p>","PeriodicalId":89,"journal":{"name":"Metallomics","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144657860","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Combined stress of Pb and Cd toxic effects on physiological response and potentially toxic elements accumulation characteristics in Cunninghamia lanceolata seedlings.","authors":"Chengfeng Liu, Lita Yi, Zhiwei Ge, Meihua Liu","doi":"10.1093/mtomcs/mfaf027","DOIUrl":"10.1093/mtomcs/mfaf027","url":null,"abstract":"<p><p>The extensive contamination of terrestrial ecosystems with multiple potentially toxic elements (PTEs) necessitates elucidation of plant adaptive mechanisms under combined PTEs stress. This study examines the physiological adaptations, antioxidant regulation, and PTEs allocation patterns in Cunninghamia lanceolata seedlings exposed to lead (Pb) stress (Pb4, 4.0 mg kg-1 Pb; Pb40, 40 mg kg-1 Pb), cadmium (Cd) stress (Cd2, 2 mg kg-1 Cd; Cd20, 20 mg kg-1 Cd), and combined Pb and Cd stress. Results demonstrated concentration-dependent inhibition of biomass production and chlorophyll b biosynthesis under both single and combined PTEs stress conditions. Different responses in superoxide dismutase activity were observed under combined stress compared to the controls, with lower concentration Pb stress causing notably higher enzymatic activation compared to higher concentration Pb stress. Elevated Cd concentrations resulted in significant accumulation of malondialdehyde in leaf tissues, indicating membrane damage. Lead preferentially accumulated in leaves under single Pb stress, while Cd predominantly accumulated in root systems. However, when the plants were exposed to combined Pb and Cd stress, the PTEs translocation pathways in the plants were altered, which resulted in a greater retention of Cd in the stems compared to when the plants were exposed to the single PTE stress. These findings provide insights into species-specific PTE homeostasis mechanisms under polymetallic stress, thereby providing theoretical foundations for the development of phytoremediation strategies in environments contaminated with multiple PTEs.</p>","PeriodicalId":89,"journal":{"name":"Metallomics","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144648029","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}