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Search Results (292)

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Keywords = LC-MS/MS protein identification

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14 pages, 1645 KB  
Article
Identification-Based Comparative Proteomic and Peptidomic Profiling of Vespa mandarinia and Apis mellifera Venoms Supported by De Novo Transcriptomic Annotation
by Lanfen Yang, Li Li, Jinwei Dao, Li Yang and Qi Yang
Toxins 2026, 18(8), 351; https://doi.org/10.3390/toxins18080351 - 17 Aug 2026
Viewed by 224
Abstract
Hymenopteran venoms contain diverse proteins and peptides that shape envenomation, defense, predation, and allergic responses. Honeybee venom from Apis mellifera is well characterized, while molecular resources for the Asian giant hornet Vespa mandarinia remain less curated. We compared protein- and peptide-fraction LC-MS/MS identification [...] Read more.
Hymenopteran venoms contain diverse proteins and peptides that shape envenomation, defense, predation, and allergic responses. Honeybee venom from Apis mellifera is well characterized, while molecular resources for the Asian giant hornet Vespa mandarinia remain less curated. We compared protein- and peptide-fraction LC-MS/MS identification datasets from V. mandarinia venom (VM-V) and A. mellifera venom (AM-V), supported by a de novo V. mandarinia transcriptome-derived database. Protein-level identification yielded 197 protein groups in VM-V PRO and 164 protein groups in AM-V PRO. AM-V contained well-recognized honeybee venom components, including phospholipase A2, hyaluronidase, venom acid phosphatase, venom dipeptidyl peptidase 4, melittin precursor, mast cell degranulating peptide precursor, secapin, and allergen Api m 6. VM-V PRO contained transcriptome-supported candidate venom-associated proteins, including venom dipeptidyl peptidase 4-like, hyaluronidase-like, venom allergen 5-like, serine protease-like, apolipophorin-like, and hexamerin-like entries. Peptide-fraction annotation was strongest in AM-V PEP, led by melittin precursor, whereas VM-V PEP remained largely unannotated. The study focuses on identification, annotation, and hypothesis-generating functional summaries, not replicate-level differential abundance. GO, KEGG, and STRING analyses organized functional annotation patterns and prioritized candidate protein groups. These data provide an identification-based comparative venomomics resource for VM-V and AM-V and a foundation for targeted validation of candidate V. mandarinia venom-associated components. Full article
(This article belongs to the Section Animal Venoms)
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19 pages, 4443 KB  
Article
Development and Preliminary Field Evaluation of an Indirect ELISA for Detecting Tomato Yellow Leaf Curl Virus
by Zeling Zhang, Yifan Liu, Xiangyu Zhang, Xianle Xue and Ting Xu
Viruses 2026, 18(7), 786; https://doi.org/10.3390/v18070786 - 19 Jul 2026
Viewed by 383
Abstract
Tomato yellow leaf curl virus (TYLCV) is a major threat to tomato production, creating a need for sensitive, low-cost detection methods that can be applied to early symptomatic or low-viral-load samples. Recombinant antigen configuration may influence serological assay development, although the specific contribution [...] Read more.
Tomato yellow leaf curl virus (TYLCV) is a major threat to tomato production, creating a need for sensitive, low-cost detection methods that can be applied to early symptomatic or low-viral-load samples. Recombinant antigen configuration may influence serological assay development, although the specific contribution of multiple-cloning-site (MCS)-derived intermediate sequences remains uncertain. In this study, a recombinant Trx-His-coat protein (CP) fusion antigen was produced using an MCS-free direct-fusion construct that retained the Trx-His tag while removing the MCS-derived intermediate sequence, followed by gradient refolding. No direct comparison with linker-containing, tag-cleaved, or tag-free antigen constructs was performed. The purified antigen was used to immunize rabbits and generate a high-titre polyclonal antibody (pAb). The resulting indirect enzyme-linked immunosorbent assay (ELISA) achieved a theoretical limit of detection of 1.8 ng/mL and an estimated pre-dilution equivalent the limit of detection (LOD) of 72 ng/mL after sample dilution. The assay showed favourable tolerance to crude tomato leaf matrices, with spike-recovery rates of 95.45–100.40%. In a preliminary evaluation using a balanced panel of 32 field-collected samples, ELISA absorbance correlated with droplet digital PCR quantification (R2 = 0.9819) and plant disease index values (R2 = 0.9774). Liquid chromatography–tandem mass spectrometry (LC-MS/MS) peptide mapping and AlphaFold2-based modelling were used only to provide preliminary computational context for antigen interpretation. The assay showed cross-recognition toward Tobacco curly shoot virus (TbCSV), indicating that it should not be considered strictly TYLCV species-specific. Therefore, this assay may support preliminary serological screening under the tested conditions, whereas molecular confirmation remains necessary when species-level identification is required. Full article
(This article belongs to the Section Viruses of Plants, Fungi and Protozoa)
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32 pages, 2952 KB  
Article
Fenugreek Seed Powder Attenuates Lead-Induced Hepatic Injury and Renal Dysfunction in Male Mice Co-Exposed to Escalating Lead Doses
by Muhammad Imran, Nosheen Mushtaq and Safdar Hussain
Curr. Issues Mol. Biol. 2026, 48(7), 650; https://doi.org/10.3390/cimb48070650 - 24 Jun 2026
Viewed by 300
Abstract
Lead (Pb) induces oxidative stress, inflammation, and hepatorenal injury. We evaluated whether fenugreek (Trigonella foenum-graecum) seed powder (200 mg/kg) protects against subchronic Pb-acetate exposure in male albino mice. Sixty mice were randomized to six groups (n = 10): control (G1), fenugreek-only [...] Read more.
Lead (Pb) induces oxidative stress, inflammation, and hepatorenal injury. We evaluated whether fenugreek (Trigonella foenum-graecum) seed powder (200 mg/kg) protects against subchronic Pb-acetate exposure in male albino mice. Sixty mice were randomized to six groups (n = 10): control (G1), fenugreek-only (G2), Pb 150 mg/kg (G3), and three co-exposure groups receiving fenugreek with Pb at 50, 100, and 150 mg/kg (G4–G6), gavaged daily for 8 weeks. LC–DAD–ESI–MS/MS of the seed batch tentatively identified 32 metabolites, dominated by flavonoid C-glycosides, luteolin dihydrogalloyl-glucosyl-pentosyl glucoside (15.90%), vicenin-3 (14.46%), vicenin-2 (9.66%), vicenin-1 (8.80%), kaempferol 7-O-rhamnosyl-glucoside (8.71%), with additional acylated phenolic conjugates. Pb exposure (G3) significantly reduced growth and intake, elevated serum ALT, AST, ALP, urea, and creatinine, raised blood Pb, and produced hepatic necrosis, vacuolation, and inflammation. Molecularly, Pb upregulated Nrf2, HO-1, SCD-1, TNF-α, and IL-6 and suppressed SOD-3. Fenugreek co-treatment attenuated all these changes across the three Pb doses, with greatest effect at the lowest Pb load (G4). Notably, fenugreek co-treatment reduced rather than further increased Nrf2 and HO-1 expression relative to Pb alone, a pattern most consistent with lowering the upstream oxidative stimulus rather than direct induction of these pathways. The seed’s polyphenolic profile—rich in vicenin-type C-glycosides and luteolin and kaempferol derivatives—offers a plausible chemical basis for the antioxidant, anti-inflammatory, and modest Pb-lowering effects observed; however, because whole seed powder was administered and metabolite identifications are tentative, these structure–activity relationships are presented as hypotheses for future bioactivity-guided fractionation rather than as demonstrated mechanisms. These preclinical findings support further investigation of fenugreek as a candidate dietary adjunct against environmental Pb exposure, contingent on protein-level validation, pharmacokinetic characterization, benchmarking against a standard chelator, and bioactivity-guided fractionation. Full article
(This article belongs to the Special Issue Natural Products in Biomedicine and Pharmacotherapy, 2nd Edition)
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27 pages, 18729 KB  
Article
Wolffia globosa Ethanolic Extract Protects Against Bisphenol A-Induced Osteoblast Dysfunction via Antioxidant Defense, Apoptosis Inhibition, and β-Catenin Modulation
by Benjawan Wudtiwai, Pornsiri Pitchakarn, Piya Temviriyanukul, Pattaralawan Sittiju, Woorawee Inthachat, Jirarat Karinchai, Nuttida Phunsanit, Prachya Kongtawelert and Peraphan Pothacharoen
Int. J. Mol. Sci. 2026, 27(12), 5352; https://doi.org/10.3390/ijms27125352 - 13 Jun 2026
Viewed by 637
Abstract
The prevalent endocrine disruptor bisphenol A (BPA) is associated with aging-related conditions, including metabolic disorders. It has been shown that BPA promotes bone fragility through oxidative stress-induced apoptosis and impaired osteoblast differentiation. The identification of sustainable bioactive substances that alleviate BPA-induced bone toxicity [...] Read more.
The prevalent endocrine disruptor bisphenol A (BPA) is associated with aging-related conditions, including metabolic disorders. It has been shown that BPA promotes bone fragility through oxidative stress-induced apoptosis and impaired osteoblast differentiation. The identification of sustainable bioactive substances that alleviate BPA-induced bone toxicity is thus of biomedical and environmental significance. Wolffia globosa (WG), the world’s smallest flowering aquatic plant, has recently gained attention as a high-protein, antioxidant-rich nutraceutical, yet its impact on BPA-induced osteoblast dysfunction has not been systematically investigated. This study presents a comprehensive assessment of WG ethanolic extract (WGE) in MC3T3-E1 pre-osteoblasts, incorporating thorough phytochemical characterization, acute high-dose and chronic low-dose BPA exposure models, and multi-faceted mechanistic analysis. LC-MS/MS profiling identified luteolin (116.17 ± 0.69 µg/g), rosmarinic acid (54.80 ± 2.12 µg/g), and apigenin (48.77 ± 0.61 µg/g) as the predominant bioactive compounds. WGE exhibited potent antioxidant capacity across DPPH and ABTS radical scavenging assays, complemented by high ORAC and FRAP values, reflecting broad-spectrum antioxidant mechanisms. Treatment with WGE (25 and 50 µg/mL) resulted in significant alleviation of BPA-induced cytotoxicity, decreased intracellular ROS levels, and inhibited apoptosis. WGE (12.5 µg/mL) also modulated autophagy-related markers (LC3-II, Beclin-1, and p62), suggesting potential autophagic participation, although flux verification was not conducted. Treatment with WGE (12.5 µg/mL) also restored BPA-suppressed osteogenesis under chronic exposure, as evidenced by enhanced alkaline phosphatase activity, and increased both mineralization and upregulation of osteogenic genes including runt-related transcription factor2 (Runx2), collagen type I alpha 1 (Colla1), alkaline phosphatase (ALP), and osteocalcin (OCN). These effects were accompanied by partial reactivation of Wnt/β-catenin signaling. This study is the first to demonstrate that WGE protects osteoblasts from BPA toxicity by concurrently strengthening antioxidant defenses, limiting apoptosis, modulating autophagy-related markers, and supporting β-catenin-mediated osteogenesis, highlighting WG as a promising sustainable nutraceutical candidate for the prevention of environmental toxin-related bone fragility. Full article
(This article belongs to the Special Issue Molecular Advances in Metabolic Bone Disorders)
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25 pages, 3714 KB  
Article
Decoding the Apical–Basal Surfaceome of Colon Epithelial Cells via Side-Selective Biotinylation
by Katalin Kuffa, Tamás Langó, András Czirók, Júlia Tárnoki-Zách, Szilvia Bősze, Loretta László, Virág Vas, Zoltán Szabó and Gábor E. Tusnády
Biomolecules 2026, 16(6), 865; https://doi.org/10.3390/biom16060865 - 12 Jun 2026
Viewed by 558
Abstract
Colorectal cancer (CRC) is the third most common malignancy worldwide. Detailed characterization of cell surface proteins (CSPs) is essential for the identification of prognostic biomarkers and the development of novel therapeutic strategies. Cancer progression and epithelial cell polarity influence the expression levels and [...] Read more.
Colorectal cancer (CRC) is the third most common malignancy worldwide. Detailed characterization of cell surface proteins (CSPs) is essential for the identification of prognostic biomarkers and the development of novel therapeutic strategies. Cancer progression and epithelial cell polarity influence the expression levels and subcellular localization of these proteins. However, quantitative information on the distribution of CSPs between the apical and basolateral membranes remains limited, particularly in CRC cells. Here, we developed a rapid, high-throughput method based on the enrichment of biotinylated peptides and proteins from the apical and basolateral surfaces of polarized CRC epithelial cells (HT29 and HCT116), followed by LC-MS/MS analysis. This approach enables the simultaneous identification of the side-specific distribution of ~1200 CSPs. In addition, almost 500 potential N-glycosylation sites with the canonical consensus sequence of these proteins were identified, which may serve as targets for future site-specific glycosylation analyses. To evaluate the sensitivity of the method, we altered the surface proteome by generating TKS4-knockout cells and identified several surface markers whose expression levels differed significantly from those of wild-type cells. Overall, our findings provide new insights into the role of CSPs in CRC cells and gene-edited models, particularly in the context of TKS4-dependent epithelial-to-mesenchymal transition (EMT)-like phenotypes that model cancer metastasis. Full article
(This article belongs to the Section Biomacromolecules: Proteins, Nucleic Acids and Carbohydrates)
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19 pages, 4011 KB  
Article
Identification of Novel Protein Biomarkers for Early Detection of Radon-Induced Lung Cancer: A Comparative Study in Kazakhstan
by Baglan Kazhiyakhmetova, Nursulu Altaeva, Meirat Bakhtin, Pavel Tarlykov, Yasutaka Omori, Shinji Tokonami, Chutima Kranrod, Radhia Pradana, Saowarak Musikawan, Anel Lesbek, Danara Ibrayeva, Elena Saifulina, Dana Auganova, Moldir Aumalikova, Madina Kairullova, Aigerim Shokabayeva, Dinara Bizhanova and Yerlan Kashkinbayev
Biomedicines 2026, 14(6), 1204; https://doi.org/10.3390/biomedicines14061204 - 27 May 2026
Viewed by 446
Abstract
Background: Radon exposure is the second most important risk factor for lung cancer after tobacco smoking and represents a significant but often underestimated public health problem. Due to the absence of specific clinical manifestations at early stages, the identification of molecular biomarkers reflecting [...] Read more.
Background: Radon exposure is the second most important risk factor for lung cancer after tobacco smoking and represents a significant but often underestimated public health problem. Due to the absence of specific clinical manifestations at early stages, the identification of molecular biomarkers reflecting early radon-induced carcinogenic processes is of particular importance. The aim of this study was to identify protein biomarkers associated with radon exposure in lung cancer patients residing in settlements of the Akmola and North Kazakhstan regions of Kazakhstan. Methods: Indoor radon exposure was assessed using CR-39 detectors to measure radon concentrations in residential dwellings during summer and autumn periods. The study included 57 lung cancer patients and 73 control subjects residing in areas characterized by varying levels of radon exposure. Plasma samples were collected and analyzed using liquid chromatography–tandem mass spectrometry (LC–MS/MS) to identify differentially expressed proteins associated with lung cancer and radon exposure. Statistical analyses were performed to evaluate differences between groups and associations between radon exposure and molecular biomarkers. Results: Seasonal variability in indoor radon concentrations was observed, with several settlements demonstrating levels exceeding international reference values. Proteomic analysis identified multiple proteins differentially expressed between lung cancer patients and controls, as well as between radon-exposed and non-exposed lung cancer patients. Several proteins involved in inflammation, lipid metabolism, oxidative stress, and immune regulation pathways demonstrated significant differences in expression levels, suggesting potential associations with radon-induced carcinogenic mechanisms. LC–MS/MS proteomic profiling identified multiple differentially expressed proteins associated with lung cancer and radon exposure after false discovery rate correction. Proteins involved in inflammation, oxidative stress, immune regulation, and lipid metabolism, including ORM2, AZGP1, PRDX2, IRF7, and APOC3, demonstrated significant expression differences between radon-exposed and low-exposure groups. Conclusions: The identified protein biomarkers demonstrated significant associations with both radon exposure and lung cancer status, indicating their potential relevance for early detection and risk assessment of radon-induced lung cancer. The integration of environmental exposure assessment with proteomic profiling may provide new insights into the molecular mechanisms of radon-associated carcinogenesis and support the development of preventive strategies. Full article
(This article belongs to the Section Cancer Biology and Oncology)
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18 pages, 3399 KB  
Article
The Proteomics-Based Stratification of Obese Subjects Allows for a Second Selective Level Beyond Gender Classification
by Raffaello Viganò, Jonica Campolo, Francesca Brambilla, Dario Di Silvestre, Ettore Corradi, Marina Parolini, Cinzia Dellanoce, Patrizia Tarlarini, Paolo Iadarola, Francesco Scaglione and Pierluigi Mauri
Int. J. Mol. Sci. 2026, 27(11), 4678; https://doi.org/10.3390/ijms27114678 - 22 May 2026
Viewed by 469
Abstract
Obesity is a major global health challenge characterized by chronic low-grade inflammation, oxidative stress, and an increased risk of cardiometabolic disorders. Although sex-related differences in inflammatory and redox biomarkers have been reported in obese populations, the molecular mechanisms underlying this heterogeneity remain incompletely [...] Read more.
Obesity is a major global health challenge characterized by chronic low-grade inflammation, oxidative stress, and an increased risk of cardiometabolic disorders. Although sex-related differences in inflammatory and redox biomarkers have been reported in obese populations, the molecular mechanisms underlying this heterogeneity remain incompletely understood. In this study, we applied a proteomics-based approach to investigate urinary extracellular vesicles from 45 obese individuals (BMI 30–40 kg/m2; age 50–70 years) in order to identify molecular signatures associated with metabolic dysregulation. Shotgun proteomics analysis performed by nanoLC–MS/MS enabled the identification of 3822 proteins. Hierarchical clustering of proteomic profiles revealed two distinct molecular groups, predominantly enriched in males (Group I) and females (Group II). Label-free quantitative analysis identified 466 differentially abundant proteins between the two clusters. Functional enrichment analysis highlighted pathways associated with immune response, metabolic regulation, and redox homeostasis, including glycolysis/gluconeogenesis, lysosome activity, leukocyte transendothelial migration, and glutathione, cysteine and methionine metabolism. Notably, proteins related to ferroptosis were enriched, suggesting the involvement of iron-dependent oxidative cell death mechanisms in the metabolic imbalance observed in a subset of subjects. Furthermore, the non-enzymatic glycosylation of urinary proteins was significantly higher in Group I compared with Group II (p = 0.0002), indicating increased formation of advanced glycation products in individuals with a more pronounced pro-oxidant state. Preliminary follow-up data suggested a higher incidence of pathological events, including cardiovascular complications, among individuals belonging to Group I. Overall, these findings demonstrate that urinary proteomic profiling can identify distinct molecular phenotypes among obese individuals and highlight oxidative stress, ferroptosis, and protein glycation as potential determinants of metabolic vulnerability, supporting the use of non-invasive proteomic approaches for improved risk stratification in obesity. Full article
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25 pages, 9441 KB  
Article
Quantitative Metaproteomic Characterization of Acetic Acid Bacteria Reveals Functional Dynamics During Verdejo Wine Acetification
by Cristina Campos-Vázquez, Juan C. García-García, Juan Carbonero-Pacheco, Juan J. Román-Camacho, Roger Consuegra-Rivera, Teresa García-Martínez, Isidoro García-García, Inés M. Santos-Dueñas and Juan Carlos Mauricio
Proteomes 2026, 14(2), 27; https://doi.org/10.3390/proteomes14020027 - 20 May 2026
Viewed by 2923
Abstract
Background: Acetification is a complex process driven by acetic acid bacteria (AAB), in which high ethanol and acidity levels require strong microbial metabolic adaptation. Although the microbiota involved in vinegar production has been described, the functional mechanisms that enable these bacteria to maintain [...] Read more.
Background: Acetification is a complex process driven by acetic acid bacteria (AAB), in which high ethanol and acidity levels require strong microbial metabolic adaptation. Although the microbiota involved in vinegar production has been described, the functional mechanisms that enable these bacteria to maintain metabolic activity remain poorly understood. In this study, the functional dynamics of AAB during Verdejo vinegar acetification were analyzed using a quantitative metaproteomic approach. Methods: Acetification was performed in submerged culture under semi-continuous conditions, and samples were collected at four stages of the cycle (S1–S4). Results: LC-MS/MS analysis led to the identification of 1626 proteins, of which 1409 were assigned to the Acetobacteraceae family. Komagataeibacter europaeus was the dominant species (73.7%). Hierarchical clustering revealed four protein abundance patterns, and differential analysis identified 350 proteins with increased abundance and 169 with decreased abundance, with the greatest changes observed between S1 and S4. Functional annotation and protein–protein interaction analyses indicated that the main metabolic adaptations involve pathways related to energy metabolism, amino acid biosynthesis, membrane-associated functions, cellular homeostasis, and acid stress response. Conclusions: Overall, the results show that K. europaeus concentrates most of the metabolic activity during acetification and that proteome reorganization reflects key molecular strategies for adaptation and survival under high-acidity conditions. Full article
(This article belongs to the Section Microbial Proteomics)
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20 pages, 5100 KB  
Article
Genome-Wide Identification of CYP75 Gene Family in Rhododendron simsii and Functional Analysis of Its Role in Promoting Anthocyanin Biosynthesis
by Yu-Hang Jiang, Yong-Hong Jia, Ze-Hang Wu, Gao-Yuan Hu, Bin-Ying Sun, Chen-Xin Xie, Qing-Hao Wang, Chao Yu, Hai-Chao Hu, Xiao-Hong Xie and Yue-Yan Wu
Plants 2026, 15(10), 1472; https://doi.org/10.3390/plants15101472 - 12 May 2026
Viewed by 694
Abstract
The flower color of Rhododendron is primarily determined by anthocyanin biosynthesis, with cytochrome P450 CYP75 family members, particularly flavonoid 3′,5′-hydroxylase (F3′5′H), playing a central role. However, the composition and functional characterization of CYP75 genes in Rhododendron remain insufficiently explored. This study performed genome-wide [...] Read more.
The flower color of Rhododendron is primarily determined by anthocyanin biosynthesis, with cytochrome P450 CYP75 family members, particularly flavonoid 3′,5′-hydroxylase (F3′5′H), playing a central role. However, the composition and functional characterization of CYP75 genes in Rhododendron remain insufficiently explored. This study performed genome-wide identification of the CYP75 gene family using the Rhododendron simsii reference genome and functionally characterized the corresponding F3′5′H homolog cloned from Rhododendron × hybridum petals (red cultivar and pink cultivar). Seven RsCYP75 genes were identified, categorized into two subfamilies: RsCYP75A (A1–A5) and RsCYP75B (B1–B2), with a prominent cluster on chromosome 13. All encoded proteins contained a conserved cytochrome P450 domain and typical heme-binding motifs. Among these, RhCYP75A2 showed the highest expression level in red petals at full blooming period and was designated as RhF3′5′H. RhF3′5′H encodes a basic membrane protein with the characteristic F3′5′H motif, with its transcript most abundant in flowers. Transient overexpression of RhF3′5′H in red R. × hybridum petals resulted in a 9.74-fold increase in its transcript levels and a 1.25-fold increase in anthocyanin content compared to that in the control accompanied by the up-regulation of CHS, F3H, DFR and ANS. Conversely, RhF3′5′H silencing reduced anthocyanin accumulation but increased CHS and F3H transcript levels, suggesting a compensatory transcriptional response in the upstream anthocyanin pathway. Moreover, RhF3′5′H was heterologously expressed in E. coli Rosetta as an MBP fusion protein, purified, and identified by LC-MS/MS and ELISA. The protein showed the ability to promote anthocyanin accumulation. Molecular docking analysis demonstrated that RhF3′5′H can bind to naringenin and dihydrokaempferol. These results confirm that RhF3′5′H is a functional F3′5′H-type CYP75A enzyme and a positive regulator of anthocyanin accumulation in Rhododendron petals. This work enriches the CYP75 gene catalog in Rhododendron and provides candidate genes for future studies on flower color regulation and molecular breeding. Full article
(This article belongs to the Section Plant Genetics, Genomics and Biotechnology)
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13 pages, 3706 KB  
Article
A Direct ALAD–SSUII Interaction Implies a Potential Link Between Tetrapyrrole and Terpenoid Pathways Toward Chlorophyll Biosynthesis in Plants
by Na Huang, Zihan Wang, Shuyan Song, Yufan Chen, Peiwen Nian, Fei Zhou and Shan Lu
Int. J. Mol. Sci. 2026, 27(10), 4225; https://doi.org/10.3390/ijms27104225 - 9 May 2026
Viewed by 401
Abstract
Chlorophylls are the major light-harvesting pigments in photosynthetic organisms. Their biosynthesis requires the coordinated supply of metabolic intermediates from two independent upstream branches: the methylerythritol 4-phosphate (MEP)-derived terpenoid pathway, which supplies the phytyl side chain via geranylgeranyl diphosphate (GGPP), and the tetrapyrrole biosynthesis [...] Read more.
Chlorophylls are the major light-harvesting pigments in photosynthetic organisms. Their biosynthesis requires the coordinated supply of metabolic intermediates from two independent upstream branches: the methylerythritol 4-phosphate (MEP)-derived terpenoid pathway, which supplies the phytyl side chain via geranylgeranyl diphosphate (GGPP), and the tetrapyrrole biosynthesis pathway (TBP), which provides the porphyrin ring. How flux through these two branches is coordinated remains poorly understood. In this study, we report the identification of a direct protein–protein interaction between δ-aminolevulinic acid dehydratase (ALAD), the second enzyme of the TBP, positioned immediately upstream of the first metabolic branch point, and the Type II small subunit of GGPP synthase (SSUII), a key regulator of terpenoid flux toward chlorophyll biosynthesis. ALAD was identified as a candidate SSUII-interacting protein by co-immunoprecipitation coupled with LC-MS analysis of rice leaf tissue, with a sequence coverage of 57.04%. The interactions between OsALAD1 and OsSSUII in rice, and between AtALAD1 and AtSSUII in Arabidopsis thaliana, were validated by yeast two-hybrid assay and bimolecular fluorescence complementation (BiFC) in Arabidopsis protoplasts. BiFC imaging demonstrated that the interaction is localized to the chloroplast. Sequence analysis revealed that plant ALAD proteins are highly conserved, with 92% similarity between OsALAD1 and AtALAD1, and 76.9% similarity between OsALAD1 and the green alga Chlamydomonas reinhardtii CrALAD1, indicating cross-species conservation of the ALAD–SSUII interaction. In vitro enzyme activity assays showed that AtSSUII does not directly alter AtALAD1 catalytic activity, suggesting the interaction operates through post-translational rather than direct catalytic mechanisms. Overexpression of AtALAD1 caused severe chlorosis and seedling lethality, while AtSSUII overexpression produced no distinct phenotype; neither transgene altered the transcript level of the other. Together, our results reveal a conserved cross-pathway protein–protein interaction linking the terpenoid regulatory machinery to the early TBP, suggesting a molecular possibility for the coordinated regulation of chlorophyll biosynthesis. Full article
(This article belongs to the Special Issue Chlorophylls and Carotenoids: Metabolism and Regulation in Plants)
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35 pages, 7317 KB  
Article
Mechanistic Insights into the Anti-Virulence Effects of Viroelixir, a Phenolic Blend from Green Tea and Pomegranate, on Streptococcus mutans
by Manal Dahdah, Vijaykumar D. Nimbarte, Mahmoud Rouabhia, Yasmine Ettouil, Hawraa Issa, Latifa Koussih, Mikhlid H. Almutairi and Abdelhabib Semlali
Antibiotics 2026, 15(4), 406; https://doi.org/10.3390/antibiotics15040406 - 17 Apr 2026
Cited by 3 | Viewed by 1793
Abstract
Background: Dental caries remains one of the most prevalent oral diseases worldwide, largely driven by the virulence of Streptococcus mutans. Although plant phenolics from green tea and pomegranate are known for their antimicrobial properties, their molecular mechanisms of action against key [...] Read more.
Background: Dental caries remains one of the most prevalent oral diseases worldwide, largely driven by the virulence of Streptococcus mutans. Although plant phenolics from green tea and pomegranate are known for their antimicrobial properties, their molecular mechanisms of action against key S. mutans virulence targets remain insufficiently characterized. Aim: This study investigated the antibacterial and anti-virulence properties of Viroelixir, a phenolic-rich formulation derived from green tea (Camellia sinensis) and pomegranate (Punica granatum), against S. mutans, with particular emphasis on predictive molecular docking interactions with critical virulence-associated proteins. Methods: Viroelixir phytochemical composition was characterized by LC–MS using a C18 reverse-phase column and negative electrospray ionization mode. Antibacterial activity was evaluated using growth kinetics, agar plating, and crystal violet assays. Acidogenicity, hemolytic activity, and biofilm formation were assessed using pH modulation, hemolysis assays, SEM, and biofilm biomass quantification. Virulence gene expression was analyzed by RT-qPCR. In silico molecular docking was performed to explore potential interactions between major LC–MS-supported phenolic constituents and S. mutans virulence proteins, including glucosyltransferase B (GtfB), LuxS, and SpaP. Biocompatibility was evaluated in human gingival epithelial cells. Results: The LC-MS analysis revealed a complex mixture of phenolic compounds consistent with catechins and ellagitannins. Compound identification was considered tentative and based on mass spectral range and chromatographic behavior. Viroelixir significantly inhibited S. mutans growth, acid production, hemolytic activity, and biofilm formation in a concentration-dependent manner. Key virulence genes were markedly downregulated. Docking analyses suggested stable binding of selected phenolics—particularly punicalagin, catechin, and epigallocatechin—within the active sites of GtfB, LuxS, and SpaP. Importantly, Viroelixir showed no cytotoxic effects on gingival epithelial cells. Conclusions: Viroelixir exerts potent antibacterial and anti-virulence effects against S. mutans through a multi-target mechanism combining transcriptional suppression and predictive molecular inhibition of virulence proteins, supporting its potential as a safe, natural therapeutic for caries prevention. Full article
(This article belongs to the Section Antibiofilm Strategies)
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16 pages, 1580 KB  
Article
Identification of Oral Secretion Proteins in Ostrinia furnacalis by Transcriptome and LC-MS/MS Analyses
by Xinyan Sun, Wei Hu, Dan Wang, Meichen Zhu, Cuiping Xin, Wenbo Yang, Huimin Li and Yanyong Cao
Insects 2026, 17(4), 357; https://doi.org/10.3390/insects17040357 - 24 Mar 2026
Viewed by 1150
Abstract
Oral secretions (OS) of the Asian corn borer (Ostrinia furnacalis) play pivotal roles in its interactions with host plants. To systematically characterize the composition and potential functions of OS, 245 functionally annotated proteins from O. furnacalis reared on artificial diet were [...] Read more.
Oral secretions (OS) of the Asian corn borer (Ostrinia furnacalis) play pivotal roles in its interactions with host plants. To systematically characterize the composition and potential functions of OS, 245 functionally annotated proteins from O. furnacalis reared on artificial diet were identified using an integrated approach combining transcriptomics and liquid chromatography–tandem mass spectrometry (LC-MS/MS). Bioinformatics analyses were further performed to predict 16 effector proteins. Subsequent tissue-specific expression assays were conducted to quantify the transcriptional levels of genes encoding these effector proteins in salivary glands, guts, and residual tissues. Among these genes, OfGDH2, OfPero2, OfPero3, and OfCBP were highly expressed in salivary glands, OfGDH3, OfRGD, OfEST1, OfEST2, OfMET, and Offerrin showed high expression in guts, while OfSP34 was abundantly expressed in both salivary glands and guts. This study represents the first systematic characterization of the molecular profile of O. furnacalis OS, thereby laying a solid foundation for future investigations into the molecular mechanisms underlying the host adaptation of this pest. Full article
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23 pages, 4458 KB  
Article
From Waste to Bioactive Ingredient: Integrated Extraction, Identification, and Validation of Novel Antioxidant Peptides from Xuefeng Black-Bone Chicken Bones
by Haige Yang, Fanjia Kong, Lan Mo, Yanyang Wu, Aihua Lou, Qingwu Shen, Wei Quan, Lei Zhou, Meichun Li and Yan Liu
Foods 2026, 15(5), 942; https://doi.org/10.3390/foods15050942 - 7 Mar 2026
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Abstract
The valorization of poultry bone by-products into high-value bioactive ingredients aligns with the principles of a sustainable circular bioeconomy. This study established an integrated process for the production, identification, and validation of bioactive antioxidant peptides from Xuefeng black-bone chicken bones (BCB). Alcalase was [...] Read more.
The valorization of poultry bone by-products into high-value bioactive ingredients aligns with the principles of a sustainable circular bioeconomy. This study established an integrated process for the production, identification, and validation of bioactive antioxidant peptides from Xuefeng black-bone chicken bones (BCB). Alcalase was selected as the optimal protease due to its superior performance in both the degree of hydrolysis and antioxidant activity under the optimized conditions. Using response surface methodology (RSM), the optimal hydrolysis conditions were determined as 50 °C, pH 10.18, and 4.2 h, resulting in a hydrolysate with a hydrolysis degree of 25.10% and ABTS radical scavenging activity of 84.36%. Upon ultrafiltration, the <3 kDa fraction demonstrated a significantly higher antioxidant capacity than the crude hydrolysate. Further purification through gel filtration chromatography yielded the F3 sub-fraction (predominantly <1 kDa peptides), which exhibited the most potent activity across all four antioxidant assays conducted (ABTS, DPPH, hydroxyl radical scavenging, and reducing power). A liquid chromatography–tandem mass spectrometry (LC-MS/MS) analysis of F3 led to the identification of 21 peptide sequences. An in silico screening based on bioactivity and toxicity predictions pinpointed three promising candidates: DYPF, WDY, and FGYK. These peptides were chemically synthesized and validated to possess significant in vitro radical scavenging activities against both DPPH and hydroxyl radicals. Molecular docking simulations revealed that all three peptides could spontaneously bind to the Keap1 protein with a high affinity (binding energy < −7.0 kcal/mol), primarily through hydrogen bonds and hydrophobic interactions, suggesting a possible molecular mechanism that may involve the Keap1-Nrf2-ARE antioxidant pathway. This computational insight provides a testable hypothesis for their bioactivity, the verification of which is contingent upon future studies demonstrating their cellular delivery and intracellular action. This work not only provides a sustainable strategy for BCB utilization but also identifies potent antioxidant peptides with potential applications in functional foods and nutraceuticals. Full article
(This article belongs to the Section Food Security and Sustainability)
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19 pages, 939 KB  
Review
Navigating Challenges in Mass Spectrometry Analysis of Endogenous and Synthetic Protein Modifications
by Caroline M. Hanson, Dina L. Bai and Jarrod A. Marto
Biomolecules 2026, 16(3), 367; https://doi.org/10.3390/biom16030367 - 28 Feb 2026
Cited by 1 | Viewed by 1636
Abstract
Mass spectrometry-based analysis of post-translational modifications (PTMs) is a key strategy for characterizing protein regulation and identifying disease-associated targets, with endogenous PTMs serving as biomarkers for disease diagnosis and therapeutic response. More recently, chemical proteomic strategies have adapted PTM-focused workflows to measure engagement [...] Read more.
Mass spectrometry-based analysis of post-translational modifications (PTMs) is a key strategy for characterizing protein regulation and identifying disease-associated targets, with endogenous PTMs serving as biomarkers for disease diagnosis and therapeutic response. More recently, chemical proteomic strategies have adapted PTM-focused workflows to measure engagement of covalent and photoactivatable small-molecule probes, expanding the scope of ligand discovery for these disease-associated targets. This review provides an overview of mass spectrometry-based PTM analysis workflows, including LC–MS/MS acquisition and post-acquisition data processing, with an emphasis on how modification-specific physicochemical properties influence PTM detection and identification. Common analytical challenges that limit PTM identification, including variable MS/MS fragmentation behavior and modification site localization, are discussed using modifications such as phosphorylation and photoaffinity labeling probe adducts as representative examples. Recent advances in acquisition strategies and computational tools that improve spectral quality and confidence in PTM assignment are also summarized. Additionally, approaches for the analytical validation of modification events, such as metabolic labeling strategies, are described. Together, this review outlines key considerations, capabilities, and limitations of MS-based PTM profiling and provides a framework for interpreting PTM datasets to support their effective integration into downstream biochemical and disease target validation studies. Full article
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21 pages, 2877 KB  
Article
Comprehensive Characterization of Lantana camara Essential Oil from Angola: GC-MS Profiling, Antioxidant Capacity, and Drug-likeness Prediction
by Nswadi Kinkela, Abdy Morales, Hugo A. Sánchez-Martínez, Maricselis Díaz, Nsevolo Samba, Monizi Mawunu, Juan A. Morán-Pinzón, Lúcia Silva, Jesus M. Rodilla and Estela Guerrero De León
Antioxidants 2026, 15(3), 291; https://doi.org/10.3390/antiox15030291 - 26 Feb 2026
Cited by 2 | Viewed by 1495
Abstract
Lantana camara L. (Verbenaceae) is a medicinal plant widely used in traditional medicine in Angola, especially for its anti-inflammatory effects. This study evaluated the chemical composition of L. camara essential oil from leaves (Lc-EO) collected in Uíge Province, Angola. GC–MS analysis [...] Read more.
Lantana camara L. (Verbenaceae) is a medicinal plant widely used in traditional medicine in Angola, especially for its anti-inflammatory effects. This study evaluated the chemical composition of L. camara essential oil from leaves (Lc-EO) collected in Uíge Province, Angola. GC–MS analysis enabled the identification of 96 volatile compounds, with sesquiterpenes and monoterpenes as the predominant constituents. Among them, β-caryophyllene (14.49%), sabinene (9.13%), bicyclogermacrene (8.18%), α-humulene (5.66%), nerolidol (5.29%), and 1,8-cineole (5.14%) were identified as major components. The antioxidant activity of Lc-EO was assessed using DPPH, ABTS, and superoxide anion (O2•−) assays. Lc-EO showed strong activity in the DPPH assay (IC50 = 0.72 µg/mL), moderate activity in the ABTS assay (IC50 = 87.5 µg/mL), but minimal effect on O2•− radicals (IC50 = 1491 µg/mL). It also significantly inhibited lipid peroxidation (IC50 = 236.2 µg/mL). The anti-inflammatory activity of Lc-EO was assessed through its ability to inhibit protein denaturation, exhibiting a moderate effect with 28% inhibition. In silico ADMET predictions suggested drug-like properties and low predicted systemic toxicity for major compounds. The Artemia salina lethality assay indicated moderate general toxicity (IC50 = 154.1 µg/mL), whereas the MTT viability assay revealed higher cytotoxic potency of Lc-EO (IC50 = 31.58 µg/mL), highlighting model-dependent differences in sensitivity. Overall, L. camara essential oil shows relevant bioactivity consistent with its traditional use, particularly antioxidant and anti-inflammatory effects, while its cytotoxicity highlights the need for safety evaluation. These findings indicate that the assayed oil is a promising source of bioactive compounds, but further studies are required to support its development as a safe pharmaceutical raw material. Full article
(This article belongs to the Special Issue Antioxidant Capacity of Natural Products—3rd Edition)
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