Journal of proteomics最新文献

{"title":"Assessing systemic effects of Bothrops jararaca venom in the lungs in a mouse model by label-free proteomics using DDA and DIA","authors":"Ana Luiza T. Silva ,&nbsp;Bianca C.S.C. de Barros ,&nbsp;Joanderson P.C. da Silva ,&nbsp;Isabel S. Carvalho ,&nbsp;Marcelo L. Santoro ,&nbsp;Alison F.A. Chaves ,&nbsp;Solange M.T. Serrano","doi":"10.1016/j.jprot.2025.105588","DOIUrl":"10.1016/j.jprot.2025.105588","url":null,"abstract":"<div><div>Snakebite envenomation is a critical yet underexplored public health issue, particularly in tropical and subtropical regions. <em>Bothrops jararaca</em> venom induces severe local and systemic effects, including pulmonary injury, however, the molecular mechanisms underlying lung tissue damage remain poorly understood. This study employed label- free quantitative proteomics to map protein alterations in the lung tissue in a mouse model of envenomation. Using Data-Dependent Acquisition (DDA) and Data-Independent Acquisition (DIA) approaches combined with different sample preparation methods, we provide a comprehensive proteomic profile of venom-induced pulmonary damage. Our findings reveal significant changes in proteins involved in inflammatory responses, extracellular matrix remodeling, oxidative stress, and blood coagulation. Comparative analyses highlight the superior performance of DIA over DDA, with DIA offering deeper proteome coverage, enhanced detection of low-abundance proteins, and improved resolution of venom-induced alterations. This benchmark study underscores the potential of DIA as a robust tool for elucidating complex, systemic, mammalian molecular responses to animal toxins. By bridging the gap between proteomic methodologies and pathophysiological insights, our findings contribute to a deeper understanding of viperid snake venom-induced lung injury and give insights for improved clinical management strategies.</div></div><div><h3>Significance</h3><div><em>Bothrops</em> snakebites remain a major neglected health problem, causing severe local and systemic complications. While the impact of viperid venoms on muscle and kidney tissues is well documented, the effects on the lungs — an organ critically involved in systemic envenomation outcomes — remain poorly understood. Our study provides the first comprehensive proteomic characterization of lung responses to <em>B. jararaca</em> venom in a murine model, revealing alterations in pathways related to inflammation, extracellular matrix remodeling, oxidative stress, and coagulation. These molecular insights fill an important knowledge gap by showing that proteomic disturbances occur even in the absence of overt lung pathology, highlighting the lungs as a key systemic target of envenomation. Moreover, by demonstrating that antivenom administration mitigates many of these changes, our findings underscore both the therapeutic efficacy of antivenom and the need to better understand its broader systemic footprint. This work advances both toxinology and proteomics by linking molecular-level disturbances to clinically relevant systemic outcomes.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"325 ","pages":"Article 105588"},"PeriodicalIF":2.8,"publicationDate":"2025-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145850154","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Salivary proteomics and metabolic responses to resistance training with and without blood flow restriction in young adults","authors":"Gustavo Zanete Alencar ,&nbsp;Dalton Muller Pessôa Filho ,&nbsp;Karina Oliveira Santos ,&nbsp;Anderson Geremias Macedo ,&nbsp;Henrique Basso Vitti ,&nbsp;Guilherme Neves Gasparino ,&nbsp;Larissa Tercília Grizzo Thomassian ,&nbsp;Murilo Henrique Faria ,&nbsp;Ana Carolina Magalhães","doi":"10.1016/j.jprot.2025.105587","DOIUrl":"10.1016/j.jprot.2025.105587","url":null,"abstract":"<div><div>Blood flow restriction (BFR) has been applied as alternative strategy to reproduce the effects of conventional high-load intensity training (HI) while training with low-loads (LI). Therefore, the aim of this research was to evaluate the salivary proteomic and metabolic responses to different resistance training in young adults.Ten participants were selected and underwent to training with LI (30 %1RM – one repetition maximum) plus BFR vs. HI (70 %1RM) without BFR, at 48 h-interval. Stimulated saliva was collected before and immediately after the sessions, while breath-by-breath oxygen uptake (VO₂) was measured during and after each session. Arterial blood samples for lactate concentration measurement (in EqO_2[La]) were taken at 1^st minute of resting between each exercise. For HI, there was an increase in two actin cytoplasmic isoforms and two immunoglobulin isoforms and a decrease of six hemoglobin isoforms. For LI-BFR, there was an increase in two hemoglobin isoforms, and the same immunoglobulin isoforms (<em>t</em>-test, <em>p</em> &lt; 0.05). No differences were significant between HI and LI + BRF training regarding the total energy demand (in mlO₂), absolute oxygen values (mlO₂) for oxidative response (VO_2ON), glycolytic (EqO_2[La]), and oxygen debt (VO_2OFF) (<em>p</em> &gt; 0.05). Both HI and LI + BFR protocols modulated immune system activity and exhibited divergent hemoglobin patterns.</div></div><div><h3>Significance</h3><div>The current study, which identified protein from saliva samples, a non-invasive method, and analyzed physiological markers, enabled the comparison of different resistance exercise protocols. Although no significant differences were observed in the metabolic responses to each protocol, which highlights the potential of LI + BRF to reproduce a high-intensity training stimulus, the changes in salivary protein profiles indicate specific functional adaptations that may become evident over time.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"325 ","pages":"Article 105587"},"PeriodicalIF":2.8,"publicationDate":"2025-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145843898","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MALDI Deamidation Score (MDS): A fast and flexible method for assessing deamidation in ZooMS data and its application to the Denisova Cave bone assemblage","authors":"Fei Yang ,&nbsp;Ismael Rodríguez Palomo ,&nbsp;Bharath Anila Bhuvanendran Nair ,&nbsp;Samantha Brown","doi":"10.1016/j.jprot.2025.105577","DOIUrl":"10.1016/j.jprot.2025.105577","url":null,"abstract":"&lt;div&gt;&lt;div&gt;Estimating deamidation from ZooMS spectra has frequently been achieved using the q2e method due to its high-throughput capacity and ease of use. Despite this, q2e only works with spectral data in txt format, operates slowly, and employs a genetic algorithm for fitting, which is stochastic and less interpretable. Furthermore, q2e only estimates deamidation at the peptide level and does not generate a sample-wide summary. The introduction of the Parchment Glutamine Index (PQI) presented an alternative method. Initially designed for a large ZooMS dataset of parchment, it utilises weighted least squares and a linear mixed-effects model (LME) to generate a peptide deamidation estimation and a sample level index, respectively. To address the limitations of q2e and expand the applicability of PQI to a wider range of archaeological tissues and MALDI-TOF-derived data (such as ZooMS data on bone collagen), we developed the MALDI Deamidation Score (MDS), an iteration of the PQI method optimised for handling large-scale datasets. MDS is more streamlined for analysing multi-species data with customisable peptide lists, offering dramatically reduced processing time. Using the published Denisova Cave ZooMS assemblage, we demonstrate that different peptides exhibit varying deamidation patterns over time, making the use of a single peptide to represent overall deamidation potentially biased. Such information is invaluable for investigating key questions such as protein preservation and site formation processes.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Significance&lt;/h3&gt;&lt;div&gt;We introduce the MALDI Deamidation Score (MDS), a new model that estimates deamidation at both peptide and sample levels from MALDI-derived datasets. MDS streamlines multi-species analyses with customisable peptide lists and markedly reduces processing time, enabling robust and large-scale deamidation estimation. Before MDS, deamidation in ZooMS has often been inferred from a single peptide common to Eurasian terrestrial mammals. Applied to the published Denisova Cave ZooMS assemblage, MDS reveals peptide-specific temporal deamidation patterns, showing that single-peptide proxies can be biased as peptides differ in deamidation rates and may be subject to different taphonomic processes. These results have broad relevance for studies of protein preservation and site-formation processes related to molecular taphonomy across archaeological and paleontological contexts. Looking ahead, as MDS allows a customisable peptide list, it has the potential to extend deamidation analysis of ZooMS data beyond terrestrial mammals to marine mammals and non-mammalian vertebrates (e.g., birds), and to different proteinaceous material such as keratin. It also has the potential to be compatible with different instruments used in peptide mass fingerprinting, such as MALDI-TOF, MALDI-FTICR, and TIMS-TOF. We believe that MDS will contribute greatly to our understanding of deamidation on different peptide sequences under various e","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"324 ","pages":"Article 105577"},"PeriodicalIF":2.8,"publicationDate":"2025-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145661494","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sulfur metabolism regulates endoplasmic reticulum stress survival through the interaction between cystathionine beta-synthase and Sec14 protein","authors":"Elias Nieto-Zaragoza ,&nbsp;Emilio Espinoza-Simón ,&nbsp;Damián Ramirez-Robles ,&nbsp;Emmanuel Ríos-Castro ,&nbsp;Ramiro Garza-Domínguez ,&nbsp;Francisco Torres-Quiroz","doi":"10.1016/j.jprot.2025.105573","DOIUrl":"10.1016/j.jprot.2025.105573","url":null,"abstract":"<div><div>The gasotransmitter hydrogen sulfide (H₂S) is implicated in a myriad of biological processes, including disease causing alterations. Besides acting as an antioxidant molecule, H₂S reacts with thiol groups from cysteine residues found in proteins. This post-translational modification (PTM), called S-persulfidation, plays an essential role during endoplasmic reticulum (ER) stress. Here we demonstrated that yeast cystathionine beta-synthase (Cys4), is the main responsible for ER H₂S-mediated homeostasis. We also found that during ER stress, Cys4 interacts with specific proteins that we identified with at least one cysteine residue modified by hydrogen sulfide. Finally, we focused on one interactor with reported tunicamycin sensitivity, the phospholipid transfer protein Sec14. In addition to Cys4 immunoprecipitation, we confirmed this interaction by pulling down Sec14 interactors. Deleting <em>CYS4</em> generated the accumulation of lipid droplets inside the cytosol, similar to Sec14. For the first time, we described a set of protein-protein interactions of Cys4 during ER stress with cysteines susceptible to S-persulfidation, leaving an open question about the role and regulation of the rest of the interactors.</div></div><div><h3>Significance</h3><div>In this study, we identified several interactor partners of yeast cystathionine beta synthase and analyzed cysteine residues with cysteine S-persulfidations. Although yeast have multiple H₂S producing enzymes, Cys4 seems to play a predominant role during ER stress. Temporal and spatial generation of H₂S is becoming significant in the field, and our findings contribute to that understanding. Besides, Cys4/Sec14 complex found here, seven different Cys4 complexes that may be regulated by H₂S were also reported. Because the biogenesis of this PMT is still controversial, findings like these support the hypothesis of interaction mediated biogenesis. H₂S producing enzymes specificity would help control their signaling across the cell. Finally, all Cys4 interactors with modified cysteines, including Sec14, are excellent targets to study how this PTM regulates enzyme functioning. Structural and functional assays with cysteine mutants in these proteins will shed light on new regulatory mechanisms.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"324 ","pages":"Article 105573"},"PeriodicalIF":2.8,"publicationDate":"2025-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145653287","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Opt-TMT: An optimized and scaled-down TMT labeling strategy for limited sample","authors":"Michele Martins,&nbsp;Fábio César Sousa Nogueira,&nbsp;Magno Junqueira,&nbsp;Guillaume Nugue","doi":"10.1016/j.jprot.2025.105576","DOIUrl":"10.1016/j.jprot.2025.105576","url":null,"abstract":"<div><div>Mass spectrometry-based proteomics has evolved and currently requires minimal sample quantities. However, manufacturers' isobaric labeling protocols, such as Tandem Mass Tag (TMT), are still designed for larger sample amounts, leading to significant costs and limiting research possibilities. Here, we present an optimized isobaric labeling protocol (Opt-TMT) that maintains high labeling efficiency while substantially reducing reagent consumption and sample requirements. We achieved consistent labeling efficiency even with peptide quantities as low as 6–15 μg per channel by adjusting reaction conditions, including volume reduction and increased peptide concentration. Importantly, our protocol reduces reagent costs by up to 90 % compared to the commercial protocol, while maintaining labeling efficiency above 99 %. This cost-effective approach addresses key challenges in proteomic research, especially for studies involving limited biological material or post-translational modification analyses. The Opt-TMT method provides a practical solution for researchers seeking to maximize the utility of isobaric labeling while minimizing resource expenditure, without compromising analytical quality.</div></div><div><h3>Significance</h3><div>The Opt-TMT protocol provides a major advancement for proteomics by making isobaric labeling both cost-effective and scalable to very limited sample amounts. By reducing reagent costs up to 90 % without compromising labeling efficiency (&gt;99 %), this approach enables high-quality quantitative proteomics for studies where material is scarce, such as patient-derived samples, biopsies, or post-translational modification analyses. Importantly, Opt-TMT broadens access to TMT-based workflows for laboratories with limited resources, while preserving analytical robustness. This work contributes a practical and impactful methodological improvement that directly benefits both fundamental and applied proteomics research.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"324 ","pages":"Article 105576"},"PeriodicalIF":2.8,"publicationDate":"2025-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145635030","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enhanced proteome profiling of human cerebrospinal fluid using a commercial plasma enrichment strategy","authors":"Eva Borràs ,&nbsp;Federica Anastasi ,&nbsp;Olga Pastor ,&nbsp;Marc Suárez-Calvet ,&nbsp;Eduard Sabidó","doi":"10.1016/j.jprot.2025.105575","DOIUrl":"10.1016/j.jprot.2025.105575","url":null,"abstract":"<div><div>Cerebrospinal fluid (CSF) is a valuable liquid biopsy for identifying protein biomarkers in neurological diseases, yet its proteome profiling faces challenges due to the large dynamic range of protein abundances. In this study, we assessed the effectiveness of a commercial enrichment strategy, initially developed for plasma samples, in enhancing the detection of low-abundance proteins in human CSF. We demonstrate significant improvements in protein identification and coverage depth while maintaining high reproducibility and low coefficients of variation. These findings underscore the potential of this enrichment strategy to facilitate rapid and sensitive CSF analysis, advancing biomarker discovery in neurological research.</div></div><div><h3>Significance</h3><div>This article highlights the effectiveness of a commercial plasma enrichment strategy in enhancing the detection of low-abundance proteins in human CSF. The article shows improvements in proteome coverage and it underscores the potential of this strategy to facilitate rapid and sensitive CSF analysis.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"324 ","pages":"Article 105575"},"PeriodicalIF":2.8,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145610237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Temporal proteomic profiling of mouse kidney reveals dynamic responses to Crotalus durissus terrificus envenomation","authors":"Isabela de Oliveira Cavalcante Pimentel ,&nbsp;Wellington da Silva Santos ,&nbsp;Fabio Montoni ,&nbsp;Alison Felipe Alencar Chaves ,&nbsp;Rosangela Aparecida dos Santos Eichler ,&nbsp;Ismael Feitosa Lima ,&nbsp;Talita Souza-Siqueira ,&nbsp;Milton Yutaka Nishiyama-Jr ,&nbsp;Lilian de Jesus Oliveira ,&nbsp;Emer Suavinho Ferro ,&nbsp;Leo Kei Iwai","doi":"10.1016/j.jprot.2025.105574","DOIUrl":"10.1016/j.jprot.2025.105574","url":null,"abstract":"<div><div>Snakebite envenoming by <em>Crotalus durissus terrificus</em> causes significant morbidity, particularly acute kidney injury (AKI), though its molecular mechanisms remain poorly understood. This study provides the first comprehensive temporal proteomic atlas of renal responses to <em>C. d. terrificus</em> envenomation, combining TMT-based quantitative proteomics with multivariate bioinformatics and histopathological validation in a mouse model (0.5 LD50). We identified 2567 renal proteins, with 904 significantly altered (FDR ≤ 0.05), demonstrating a proteomic crisis that peaked at 12 h (400 increased, 451 decreased) and was already evident at 6 h (15 increased, 37 decreased). Changes at 1 h and 24 h were minimal at the single-protein level. These results delineate a precise biphasic progression: from acute phase at 6 h to 12 h, characterized by oxidative stress, mitochondrial dysfunction, and loss of key tubular transport proteins dominated by maladaptive repair and fibrotic signaling. Our temporal analysis defines distinct windows for intervention: an early opportunity for antioxidant therapy to counter acute injury, followed by a critical period where anti-fibrotic strategies are required to prevent the progression to irreversible kidney damage.</div></div><div><h3>Significance</h3><div>Snakebite envenomation by <em>Crotalus durissus terrificus</em> rattlesnake venom frequently leads to acute kidney injury (AKI), yet the molecular mechanisms driving nephrotoxicity remain poorly characterized. This study provides the first comprehensive temporal proteomic atlas of renal responses to envenomation, revealing that the most robust proteomic remodeling occurs between 6 h and 12 h, with hundreds of proteins significantly altered. These changes highlight mitochondrial dysfunction, oxidative stress, and tubular injury, exemplified by decrease of CUBN and AGT, alongside shifts in cytoskeletal and ribosomal pathways. Early (1 h) and late (24 h) effects were limited at the single-protein level and are reported as exploratory trends, such as NDRG2 (hypoxia response) and ITGA3 (fibrotic signaling). Histological validation confirmed progressive tubular damage and maladaptive repair, paralleling the proteomic signatures. Together, these findings delineate a critical window of maximal molecular disruption at 12 h, providing mechanistic insights into the progression from acute injury to maladaptive remodeling. The data suggest that therapeutic strategies targeting early oxidative stress (e.g., antioxidant interventions) or late fibrotic pathways (e.g., RAS modulation) could mitigate venom-induced damage. This work bridges molecular pathophysiology with clinical outcomes, informing future translational research.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"324 ","pages":"Article 105574"},"PeriodicalIF":2.8,"publicationDate":"2025-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145634997","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lunatin-1: A peptide derived from the venom of the Hadruroides lunatus scorpion modulates signaling pathways in HL60 tumor cells to induce cytotoxic effects","authors":"Edleusa M. Lima-Batista ,&nbsp;Diana Paola Gómez-Mendoza ,&nbsp;Maurício Nogueira Moysés ,&nbsp;Kamila de Sousa Gomes ,&nbsp;Brener Cunha Carvalho ,&nbsp;Maria Elena de Lima ,&nbsp;Elaine M. Souza-Fagundes ,&nbsp;Aristóbolo Mendes da Silva ,&nbsp;Frank Kjeldsen ,&nbsp;Thiago Verano-Braga ,&nbsp;Adriano M.C. Pimenta","doi":"10.1016/j.jprot.2025.105571","DOIUrl":"10.1016/j.jprot.2025.105571","url":null,"abstract":"<div><div>Lunatin-1 is a 13-residue cytotoxic peptide derived from the venom of the scorpion <em>Hadruroides lunatus</em>. This study investigated its early effects on cellular signaling in the human promyelocytic leukemia cell line HL-60 using integrated proteomics and phosphoproteomics. Lunatin-1 regulated key mediators of apoptosis, such as caspase-2 (CASP2) and MEK1 (MAP2K1), and impacted major signaling pathways such as MAPK and PI3K/AKT. Lunatin-1 induced caspase-dependent and -independent apoptotic signaling, reduced AKT1 phosphorylation, and promoted BAX activation, consistent with mitochondrial apoptosis. These findings demonstrate that Lunatin-1 disrupts pro-survival signaling and activates multiple cell death pathways, highlighting its potential as a therapeutic candidate for hematologic malignancies.</div></div><div><h3>Significance</h3><div>This study provides a comprehensive analysis of the early molecular events triggered by Lunatin-1, a venom-derived peptide, in HL60 leukemia cells. Through integrated proteomic and phosphoproteomic approaches, we reveal that Lunatin-1 disrupts key survival pathways, notably MAPK and PI3K/AKT, and activates both caspase-dependent and -independent mechanisms of apoptosis. The peptide modulates proteins involved in DNA damage response, cell cycle regulation, and oxidative stress, offering insight into its multifaceted cytotoxic effects. These findings advance our understanding of venom-derived peptides as potential anticancer agents and underscore Lunatin-1's therapeutic promise for targeting resistant cancer cell populations.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"324 ","pages":"Article 105571"},"PeriodicalIF":2.8,"publicationDate":"2025-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145587862","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nitrate and silicate limitations induce metabolic reprogramming and lipid redistribution in Navicula incerta, enhancing biodiesel properties","authors":"José Jesús Encinas-Arzate ,&nbsp;Damaristelma De Jesús-Campos ,&nbsp;Enrique Márquez-Ríos ,&nbsp;Magdalena Hernández-Ortiz ,&nbsp;Martha Beatriz Morales-Amparano ,&nbsp;José Antonio López-Elías ,&nbsp;Wilfrido Torres-Arreola ,&nbsp;Sergio Encarnación-Guevara ,&nbsp;Juan Carlos Ramírez-Suárez ,&nbsp;María Gisela Carvallo-Ruiz ,&nbsp;Esaú Bojórquez-Velázquez ,&nbsp;José Ángel Huerta-Ocampo","doi":"10.1016/j.jprot.2025.105572","DOIUrl":"10.1016/j.jprot.2025.105572","url":null,"abstract":"<div><div>Nutrient limitations alter microalgae metabolism and fatty acid biosynthesis, modifying the lipid profile and improving the chemical properties of the resulting biodiesel. This study investigated the effects of nitrate and silicate limitations on the proteomic and lipid profiles in <em>Navicula incerta</em> and its biodiesel potential. Proteomic analysis revealed 287 differentially abundant proteins (DAPs) out of 558 identified, with silicate-limited conditions showing the highest number of DAPs (212) and nitrogen-limited conditions showing 125 DAPs (log2FC &gt; |0.57|, <em>p</em>-value &lt;0.05). These changes underpin two distinct survival strategies: nitrogen limitation forced a broad metabolic shutdown, while silicate limitation prompted a strategic reallocation of resources, maintaining core biosynthesis and enhancing internal recycling. Both stresses induced a convergent lipid remodeling characterized by decreases in saturated fatty acids and increases in monounsaturated and polyunsaturated fatty acids. This shift optimizes membrane fluidity for stress resistance and enhances key biodiesel properties, confirming the potential of <em>N. incerta</em> as a sustainable source of high-quality biodiesel. These findings highlight the diatom's metabolic flexibility in optimizing resource allocation for survival, a trait that can be harnessed to tailor lipid profiles for advanced biofuel applications. Future work should focus on the impact, efficiency, and economic feasibility of cultivating <em>N. incerta</em> under nutrient stress.</div></div><div><h3>Significance</h3><div>Understanding the relationship between nitrogen and silicate concentrations and protein accumulation is crucial for harnessing the potential of microalgae in various industries and addressing environmental challenges. The proteomic analysis and lipid profiles obtained in <em>N. incerta</em> under nitrogen and silicate limitation demonstrate remarkable metabolic flexibility in response to nutrient limitations, optimizing resource allocation to ensure survival under nutrient stress. Nitrogen limitation drives the accumulation of carbohydrates and dry biomass, along with lipid mobilization and a shift toward unsaturated fatty acids, enhancing energy efficiency and membrane functionality. Silicate limitation, while having a milder effect, prioritizes resource conservation and the redistribution of existing reserves. These adaptive responses highlight the diatom's ability to maintain critical cellular functions under adverse conditions and reveal its potential for biodiesel production.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"323 ","pages":"Article 105572"},"PeriodicalIF":2.8,"publicationDate":"2025-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145587965","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteome dynamics of chilli pepper fruits during development and ripening from two Mexican cultivars of Capsicum annuum L","authors":"David Gomez-Zepeda ,&nbsp;Felipe Cervantes-Hernández ,&nbsp;Octavio Martínez ,&nbsp;Neftalí Ochoa-Alejo ,&nbsp;José Juan Ordaz-Ortiz","doi":"10.1016/j.jprot.2025.105569","DOIUrl":"10.1016/j.jprot.2025.105569","url":null,"abstract":"<div><div>Chilli pepper (<em>Capsicum annuum</em> L., Solanaceae family), a horticultural crop native to the Americas, is esteemed for its flavour and bioactive compounds. To enhance our understanding of the molecular basis of chilli pepper fruit development and ripening, we characterised proteome dynamics from early fruit set to ripening in two Mexican cultivars. Protein profiles were analysed using label-free quantitative (LFQ) LC-MS proteomics with data-independent acquisition (DIA), resulting in the quantification of 421 proteins, predominantly involved in primary and secondary metabolism. The developmental stage was the primary factor driving proteome variation, with limited influence from cultivar differences. Clustering and relative quantification revealed intricate patterns of protein abundance across fruit maturation. Proteins associated with carotenoid and capsaicinoid biosynthesis exhibited temporal regulation consistent with their roles in determining fruit colour and pungency. This study provides insights into the molecular changes underlying chilli pepper fruit growth, development, and ripening and offers a proteomic overview for understanding some biochemical traits that define chilli pepper fruit characteristics.</div></div><div><h3>Significance</h3><div>Understanding the molecular basis of fruit growth, development, and ripening is crucial for enhancing crop quality and nutritional value. In chilli pepper, traits such as the production of valuable secondary metabolites, pigmentation, and pungency arise from finely regulated metabolic processes during fruit maturation. Here, we investigated these processes from a proteomics perspective, complemented with clustering and functional enrichment analyses. The findings reveal that developmental stage, rather than genotype, is the dominant factor shaping the fruit proteome, underscoring a conserved maturation program. Proteins involved in primary metabolism and specialised biosynthetic pathways, including those for carotenoids and capsaicinoids, show dynamic regulation consistent with their roles in fruit quality traits. These results contribute to the understanding of the molecular processes involved in fruit growth, development, and ripening and provide a proteomic framework for studying trait formation in <em>Capsicum annuum</em> and related Solanaceae crops.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"323 ","pages":"Article 105569"},"PeriodicalIF":2.8,"publicationDate":"2025-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145557108","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}