Journal of proteomics最新文献

{"title":"Proteomics analysis reveals early event molecular effectors of anti-CD19 CAR-T cell therapy in hematological cancer.","authors":"John Oluwafemi Teibo, Roberta Maraninchi Silveira, Virginia Campos Silvestrini, Izadora Archiolli, Ana PaulaMasson, Beatriz Pereira de Morais, Dayane Schmidt, Matheus Henrique Dos Santos, Germano Aguiar Ferreira, Carolina Hassibe Thomé, Dominic Helm, Raja Sekhar Nirujogi, Dairo Renato Alessi, Virginia Picanço-Castro, Lucas Eduardo Botelho de Souza, Vitor Marcel Faça","doi":"10.1016/j.jprot.2025.105507","DOIUrl":"https://doi.org/10.1016/j.jprot.2025.105507","url":null,"abstract":"<p><p>Chimeric antigen receptor T-cell (CAR-T) therapy is at the forefront of the field of cell immunotherapy. In this study, we generated an anti-CD19 CAR-Jurkat T cell line using a locally produced second-generation anti-CD19 CAR construct, which allowed us to analyse early proteomic changes that are crucial for comprehending the signalling pathways and mechanism of action of this CAR-T cell. SILAC-heavy tagged RAJI B-cells and anti-CD19 CAR-Jurkat T-cells were co-cultured for ten minutes. The proteomic profiles were acquired via DIA methodology on the Orbitrap Astral LC-MS/MS platform. The proteome was extensively covered, resulting in about 8800 protein identifications at 1 % FDR. The effector CAR-Jurkat cells showed proteomic changes involving antigen presentation by CD74. The target RAJI B-cells exhibited more significant alterations. Effector proteins, namely CD247, CD28, DAP, LCK, p38 MAPK, and CASP3, were validated, as they have critical roles in antigen presentation, T-cell activation, and apoptosis. Pharmacological inhibition of LCK using Dasatinib further suggested its pivotal role in early CAR-T signalling. This study led us to identify proteins that function as molecular effectors of anti-CD19 CAR-T cell therapy during the initial phases of CAR-T-target cell engagement, advancing our knowledge of the mechanism and signalling pathways that will support CAR-T cell development. SIGNIFICANCE: Chimeric antigen receptor T-cell (CAR-T cell) therapy is state-of-the-art in cell and immunotherapy. Determining important players in cellular communication and signalling mediated by membranes and intracellular proteins require understanding the connection between tumours and modified cells. We employed global proteomics in this study to better grasp the functional protein networks using a high-sensitivity mass spectrometric platform for protein identification and quantification. We identified proteins as molecular effectors of anti-CD19 CAR-T cell treatment during the early stages of CAR-T-target cell interaction. Our understanding of the mechanism and signalling pathways will promote the development of new CAR constructs and improve the efficacy and ability to overcome the resistance of this innovative cancer treatment strategy, which will advance the identification of adjuvant molecules for the regulation of CAR-T responses.</p>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":" ","pages":"105507"},"PeriodicalIF":2.8,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144731928","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":"Quantitative proteomic analysis of the Toxoplasma gondii cytoskeleton and bioinformatic identification of highly antigenic proteins","authors":"Karina Araujo-Ruiz ,&nbsp;Daniel Ignacio López-Flores ,&nbsp;María Karla Martínez-Muné ,&nbsp;Brenda Yomara García-Sánchez ,&nbsp;Carlos J. Ramírez-Flores ,&nbsp;Francisco Ernesto Sandoval-Rodríguez ,&nbsp;Emmanuel Ríos-Castro ,&nbsp;Mónica Edith Mondragón-Castelán ,&nbsp;Sirenia González-Pozos ,&nbsp;Ricardo Mondragón-Flores","doi":"10.1016/j.jprot.2025.105509","DOIUrl":"10.1016/j.jprot.2025.105509","url":null,"abstract":"<div><div>The <em>Toxoplasma gondii</em> cytoskeleton is a highly organized structure essential for parasite motility, replication, and host cell invasion. To identify its components, a highly enriched fraction of tachyzoite cytoskeletons was obtained and quantitatively analyzed by mass spectrometry. We identified 623 proteins classified into 18 functional groups, including 30 IMC proteins, 34 cytoskeleton proteins, and 14 uncharacterized proteins. A comprehensive bioinformatic analysis was conducted to assess protein abundance (fmol), antigenicity, accessibility, interactome, and homology, with the aim of identifying immunogenic targets. Among the top vaccine candidates were -GRA12, IMC1, ROP8, and -IMC4, with ROP8 emerging as the most promising based on epitope prediction. Data are available <em>via</em> ProteomeXchange with identifier <span><span>PXD063409</span><svg><path></path></svg></span>.</div></div><div><h3>Significance</h3><div><em>Toxoplasma gondii</em> represents one of the most virulent and successful parasites in human and veterinary pathogenesis. Since <em>T. gondii</em> is a highly dynamic parasite that depends on its cytoskeleton to invade and disseminate through tissues, knowledge of its cytoskeleton composition is essential for understanding the biological mechanisms involved in parasite-host interactions and for the design of pharmaceutical and vaccination strategies. Quantitative proteomic analysis of the <em>T. gondii</em> cytoskeleton provided new and extensive information on its composition and, through bioinformatics approaches, allowed us to suggest several candidate molecules for future immunoprotective design.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"321 ","pages":"Article 105509"},"PeriodicalIF":2.8,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144722115","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":"E cadherin appears to be an essential on/off switch for initiating bile canaliculi formation","authors":"Mireille Chevallet ,&nbsp;Thierry Rabilloud ,&nbsp;Hélène Diemer ,&nbsp;Fabrice Bertile ,&nbsp;Alexandra Fuchs ,&nbsp;Aurélien Deniaud","doi":"10.1016/j.jprot.2025.105508","DOIUrl":"10.1016/j.jprot.2025.105508","url":null,"abstract":"<div><div>The mechanisms underlying cell polarization are fundamental to biology but remain incompletely understood. This is especially true for hepatocytes, which display a particularly complex polarization that enables the formation of the bile canaliculi (BC) network crucial for liver excretory functions. To identify key proteins involved in hepatocyte polarization, BC formation, structure or function, we employed a proteomic approach comparing the human hepatocyte cell line HepG2 to its sub clone HepG2/C3A known for its markedly greater efficiency in forming mature BCs. Through this analysis, we localized LimA1 and Espin to the BC for the first time, suggesting their important role in this compartment, and confirmed the presence of NHE-RF1. Using a targeted protein repression strategy, we identified E cadherin as essential for the initiation of BC formation, unlike other adherens junction components such as N cadherin or α-catenin. Our findings demonstrate, for the first time, that in the absence of E cadherin, hepatocytes lose the capacity to form BCs.</div></div><div><h3>Significance</h3><div>This study aims to deepen our understanding of the highly specialized polarization of hepatocytes in relation to bile canaliculus formation. The major finding is the key role of E cadherin in this process, where it appears to be essential for bile canaliculus formation in both 2D and 3D culture models. Additionally, the study led to the identification of several proteins potentially localized to the bile canaliculi, whose functions remain to be elucidated.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"321 ","pages":"Article 105508"},"PeriodicalIF":2.8,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144718127","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":"Redox proteomics workflow to unveil extracellular targets of oxidation in vascular endothelial cells","authors":"Danielle Fernandes Vileigas,&nbsp;Railmara Pereira da Silva,&nbsp;Bianca Dempsey,&nbsp;Mariana Pereira Massafera,&nbsp;Mikaela Peglow Pinz,&nbsp;Flavia Carla Meotti","doi":"10.1016/j.jprot.2025.105506","DOIUrl":"10.1016/j.jprot.2025.105506","url":null,"abstract":"<div><div>Redox regulation has emerged as a key process in cellular signaling. The role of extracellular cell surface redox-sensitive proteins in redox regulation and intracellular communication has been supported by secretion of oxidoreductases that modulate thiol-disulfide switches. Despite these advances, redox-sensitive targets on the cell surface remain little explored. We established a comprehensive redox proteomic workflow using plasma membrane impermeable thiol labeling where we identified 1159 cell surface and extracellular proteins susceptible to oxidation. Treatment with diamide or urate hydroperoxide (HOOU) resulted in 377 and 12 differentially abundant redox-modulated proteins compared to control. Such proteins represent chaperones, adhesion molecules, vesicle-associated proteins, channels, receptors, cytoskeleton, and others, which may play a relevant role in several signaling pathway. Eleven oxidoreductases were redox-modulated by diamide, including members of the protein disulfide isomerase (PDI), peroxiredoxin (PRDX), and quiescin sulfhydryl oxidase (QSOX) families, with a particular focus on PDI TMX3 (TMX3), which provides the first evidence of its secretion in endothelial cells. In conclusion, our findings not only revealed potential redox-sensitive targets on the cell surface but also offer a useful tool for future investigations aiming to analyze redox regulation in the extracellular environment across diverse biological contexts.</div></div><div><h3>Significance</h3><div>Redox signaling at the cell surface is emerging as a crucial regulator of vascular function, emphasizing its role in cardiovascular disease. However, the extracellular redox proteome remains underexplored because of the complexity of the method. We developed a reproducible workflow combining differential thiol labeling and mass spectrometry to systematically map oxidized extracellular proteins in endothelial cells exposed to oxidants. Hundreds of proteins were identified as redox-sensitive targets. Key functional groups included molecular chaperones, adhesion molecules, vesicle-associated proteins, channels, receptors, and cytoskeleton. This work reveals novel insights into extracellular redox regulation, expands the repertoire of known redox-sensitive proteins, and establishes a versatile platform to investigate redox dynamics at cell surface both in vascular biology and other pathophysiological contexts.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"321 ","pages":"Article 105506"},"PeriodicalIF":2.8,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144718128","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":"Comparative proteomic analysis of subcutaneous and intraperitoneal cysts of Echinococcus multilocularis","authors":"Junmei Zhang ,&nbsp;Shanling Cao ,&nbsp;Zheng Tian ,&nbsp;Zhengzhe Zhang ,&nbsp;Yu Zhou ,&nbsp;Yixuan Wu ,&nbsp;Xuenong Luo ,&nbsp;Shuai Wang ,&nbsp;Xiaola Guo","doi":"10.1016/j.jprot.2025.105505","DOIUrl":"10.1016/j.jprot.2025.105505","url":null,"abstract":"<div><div>Alveolar echinococcosis is a zoonotic disease that poses serious threats to public health. We observed subcutaneous cysts (SCs) of <em>E. multilocularis</em> had fewer protoscoleces (PSCs) compared to intraperitoneal cysts (ICs) at 60 days post-infection. However, the mechanisms underlying the development of <em>E. multilocularis</em> cysts in different tissues remain unclear. In this study, we compared the proteomic profiles of <em>E. multilocularis</em> cysts derived from mice intraperitoneally and subcutaneously infected with PSCs at 30 days post-infection, prior to the development of mature PSCs. Proteomic analysis identified 284 differentially expressed proteins (DEPs) in SCs compared to ICs, with 147 upregulated DEPs and 137 downregulated DEPs. Enzymatic proteins involved in carbohydrate and amino acid metabolism were predominantly upregulated in SCs compared to ICs, whereas proteins associated with protein folding, sorting, a degradation were downregulated. Western blotting analysis confirmed that phosphoenolpyruvate carboxykinase (PEPCK) and fructose-bisphosphate aldolase (FBA) were upregulated, whereas transitional endoplasmic reticulum ATPase (TER ATPase) was downregulated in SCs compared to ICs. The identified DEPs may play crucial roles in shaping the unique characteristics of <em>E. multilocularis</em> cysts. This study offers valuable insights into exploring the mechanisms underlying the occurrence and development of metacestodes.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"320 ","pages":"Article 105505"},"PeriodicalIF":2.8,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144698902","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":"Palaeoproteomic characterization of archaeological dental calculus reveals precarious periodontal health in pre-Roman Italy (7th–4th century BCE)","authors":"Giulia Riccomi ,&nbsp;Lisa Rosselli ,&nbsp;Marinella Marchesi ,&nbsp;Federica Guidi ,&nbsp;Maria Taloni ,&nbsp;Giovanni Ricci ,&nbsp;Carmine Pellegrino ,&nbsp;Shevan Wilkin","doi":"10.1016/j.jprot.2025.105503","DOIUrl":"10.1016/j.jprot.2025.105503","url":null,"abstract":"<div><div>Periodontitis, a chronic inflammatory disease affecting the tooth-supporting structures, is a key indicator of oral health in palaeopathology. While poor oral hygiene, systemic diseases, and genetics are well-established contributors, the dietary impact has often been underestimated. Clinical studies, however, link diets high in fermentable carbohydrates and meat to inflammation. We investigated periodontal disease by analyzing interdental septa in 63 individuals from elite and non-elite groups in pre-Roman Italy (7th–4th centuries BCE), a period of social stratification, intensified agriculture, and increased cereal consumption. Macroscopic analysis was combined with proteomics of dental calculus from 33 individuals. Of the 1890 septa considered, 23 % displayed signs of periodontitis, with significantly higher rates in males. Prevalence increased with age in both sexes. Proteomic findings identified <em>Porphyromonas gingivalis,</em> a key periodontal pathogen, in 10 of 19 well-preserved dental calculus samples. While plaque accumulation is the main trigger for periodontitis, our findings highlight the dietary role in disease susceptibility. Carbohydrate-rich foods adhere to teeth and nourish bacteria, worsening periodontal conditions. At the same time, greater access to animal protein, particularly among emerging elites, may have contributed to inflammation. We propose that a proinflammatory diet may have been a major contributor to the proliferation of pathogenic oral microbiota.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"320 ","pages":"Article 105503"},"PeriodicalIF":2.8,"publicationDate":"2025-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144682762","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":"Corrigendum to \"Metabonomics analysis reveals the protective effect of nano‑selenium against heat stress of rainbow trout (Oncorhynchus mykiss)\" [Journal of Proteomics 259 (2022)104545/ID: JPROT-104545].","authors":"Lanlan Li, Zhe Liu, Jinqiang Quan, Junhao Lu, Guiyan Zhao, Jun Sun","doi":"10.1016/j.jprot.2025.105492","DOIUrl":"https://doi.org/10.1016/j.jprot.2025.105492","url":null,"abstract":"","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":" ","pages":"105492"},"PeriodicalIF":2.8,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144667891","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":"Unraveling the mechanism of peptidases participation in the protein digestion of the whiteleg shrimp (Litopenaeus vannamei)","authors":"Carlos Estrella-Soliz ,&nbsp;Adriana Muhlia-Almazan ,&nbsp;Esau Bojorquez-Velazquez ,&nbsp;Liliana Rojo-Arreola ,&nbsp;Humberto Gonzalez-Rios ,&nbsp;Jose A. Huerta-Ocampo","doi":"10.1016/j.jprot.2025.105504","DOIUrl":"10.1016/j.jprot.2025.105504","url":null,"abstract":"<div><div>This study aims to identify and analyze the temporal variation in the activity and relative abundance of peptidases in the midgut gland of the Pacific whiteleg shrimp, <em>Litopenaeus vannamei,</em> during digestion. The dynamic profiles of active peptidases throughout digestion were determined by zymogram profile analysis in the midgut gland of shrimp at different feeding times: preprandial, 1 h, and 3 h postprandial. Further proteomic analysis of midgut gland extracts confirmed the identity of different-class peptidases, as well as additional isoforms not previously reported, and changes in their relative abundance. Trypsins and chymotrypsins were the predominantly active peptidases throughout the digestion process. Cathepsin D was active during the preprandial time and 3 h after ingestion, whereas a metallopeptidase showed activity at preprandial time and 1 h postprandial. Additional trypsin isoforms of varying abundances were confirmed, while chymotrypsins and cathepsin L increased significantly, peaking 3 h postprandial. The results indicate significant changes in the relative abundance of new isoforms of trypsins, cathepsins, and metallopeptidases, as well as in the previously identified peptidases involved in shrimp food protein digestion over time.</div></div><div><h3>Significance</h3><div>The manuscript findings revealed the peptidases' potential participation in the digestive process of the Pacific whiteleg shrimp. The integrated results from different methods confirmed the identity and active state of some of the multiple peptidase classes in the shrimp midgut gland.</div><div>Additional trypsin, cathepsin, and metallopeptidase isoforms and their abundance changes were detected before and after ingestion. These results provide additional information about the complexity and efficiency of the protein hydrolysis mechanism of <em>L. vannamei.</em></div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"320 ","pages":"Article 105504"},"PeriodicalIF":2.8,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144675046","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":"A perspective on integrating digital pathology, proteomics, clinical data and AI analytics in cancer research","authors":"Jéssica Guedes ,&nbsp;Nicole Woldmar ,&nbsp;A. Marcell Szasz ,&nbsp;Elisabet Wieslander ,&nbsp;Krysztof Pawłowski ,&nbsp;Peter Horvatovich ,&nbsp;Johan Malm ,&nbsp;Leticia Szadai ,&nbsp;István Balázs Németh ,&nbsp;György Marko-Varga ,&nbsp;Jeovanis Gil","doi":"10.1016/j.jprot.2025.105493","DOIUrl":"10.1016/j.jprot.2025.105493","url":null,"abstract":"<div><div>Nearly 40 % of individuals will be diagnosed with cancer in their lifetime, translating to an estimated 20 million new cases annually. Despite remarkable therapeutic advances, only 15–20 % of patients achieve durable responses to immunotherapy, and the high cost of treatment (illustrated by immune checkpoint inhibitors like pembrolizumab and nivolumab, totaling roughly $191,000 per year) remains a formidable global challenge. The convergence of digital pathology, high-throughput molecular profiling, and advanced computational strategies has the potential to transform cancer research. By integrating high-resolution morphological data with proteomic, transcriptomic, and spatial molecular insights, we can elucidate the complex interplay between tumor cells and their microenvironment. In this perspective, we review how emerging techniques, from AI-driven image analysis to deep visual proteomics, can accelerate biomarker discovery, refine patient stratification, and ultimately improve clinical outcomes. We illustrate these principles with a case study in melanoma, where the integration of digital pathology and deep proteomic profiling uncovered a molecular signature predictive of recurrence in early-stage disease. As these technologies evolve, we foresee a future of precision oncology characterized by the seamless integration of morphological, clinical, and molecular data enabled by AI-driven analytics.</div></div><div><h3>Significance</h3><div>This perspective represents a pivotal step toward transforming cancer research by bridging the gap between traditional histopathological evaluation and modern molecular analytics. By integrating digital pathology with spatial proteomics and advanced AI-driven analytics, our approach provides a multidimensional view of tumor biology that captures both morphological nuances and molecular heterogeneity. This comprehensive framework not only enhances our understanding of the tumor microenvironment but also facilitates the discovery of robust biomarkers for disease recurrence and therapeutic response. Ultimately, our findings underscore the potential of precision oncology to tailor treatment strategies to individual patient profiles, thereby improving clinical outcomes and guiding the next generation of personalized cancer care.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"320 ","pages":"Article 105493"},"PeriodicalIF":2.8,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144653909","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":"Phosphoproteomics revealed salt stress tolerance mechanisms in the roots of sugar beet monomeric addition line M14","authors":"Hongli Li ,&nbsp;Zhongxu Sui ,&nbsp;Zixin Qin ,&nbsp;Sixue Chen ,&nbsp;Bing Yu ,&nbsp;Haiying Li","doi":"10.1016/j.jprot.2025.105488","DOIUrl":"10.1016/j.jprot.2025.105488","url":null,"abstract":"<div><div>Soil salinity is a major abiotic stress that limits global crop production and food security. It is necessary to explore the mechanisms of salt stress tolerance in order to cultivate high-quality salt-tolerant varieties. Sugar beet M14 line exhibits capability of salt stress tolerance. Here we conducted a phosphoproteomic study of the sugar beet M14 roots treated with 200 mM and 400 mM NaCl. Using phosphopeptide enrichment and LC-MS/MS based phosphoproteomics techniques, 1427 differential abundant phosphoproteins (DAPPs) and 983 unique phosphoproteins were identified under 200 mM NaCl. 1234 DAPPs and 769 unique phosphopeptides were identified under 400 mM NaCl. The two datasets were significantly enriched for terms associated with protein kinases and transcription factors. Meanwhile, the biological pathways enriched between 200 mM and 400 mM NaCl containing signaling pathways, metabolism and transport were prominently represented, suggesting that distinct signaling cascades may converge in key biological processes (e.g., glycolysis, transport and reactive oxygen metabolism) to mediate the salt stress response and tolerance. Furthermore, unlike the DAPPs enriched in sugar beet M14 leaves, the DAPPs enriched in roots specifically participated in the plant-pathogen interaction and prenyltransferase pathways.</div><div>Significance: Sugar beet is an important sugar-producing crop, and its roots are the primary organ usually affected by salt stress. However, the phosphoproteomics of sugar beet M14 roots under salt stress remains unclear. This study emphasizes the changes in the phosphorylation level of sugar beet M14 roots proteins under different salt concentrations. We analyzed the similarities and differences in function and participating pathways of the DAPPs and unique phosphoproteins obtained at different salt stresses. These findings not only provide important insights into the mechanisms mediated by phosphorylation modification in sugar beet M14 response to salt stress, but also will inform efforts toward improving crop yield and quality.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"320 ","pages":"Article 105488"},"PeriodicalIF":2.8,"publicationDate":"2025-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144631441","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}