ACS Publications最新文献

{"title":"Elucidating the Molecular Mechanisms of Hederagenin-Regulated Mitophagy in Cervical Cancer SiHa Cells through an Integrative Approach Combining Proteomics and Advanced Network Association Algorithm.","authors":"Hao Sun, Dan Wang, Yongquan Zheng, Yiqing Ye","doi":"10.1021/acs.jproteome.5c00022","DOIUrl":"10.1021/acs.jproteome.5c00022","url":null,"abstract":"<p><p>Hederagenin (Hed), a natural triterpenoid, exhibits antitumor potential in cervical cancer. The present study was designed to explore Hed's regulatory mechanisms on mitophagy in SiHa cervical cancer cells, employing tandem mass tag (TMT) proteomics and an advanced network association algorithm (NAA). Our findings revealed that Hed decreased SiHa cell viability, induced apoptosis, and altered mitochondrial membrane potential. Notably, Hed inhibited mitophagic flux under both normoxic and hypoxic conditions. Through TMT proteomics analysis and innovative NAA, we identified a close association between the HIF-1 signaling pathway and mitophagy. Network analysis further suggested that Hed acts on a target network centered on SRC, STAT3, AKT1, and HIF1A. Western blot analysis confirmed the expression and phosphorylation status of these targets in response to Hed. This study elucidates the molecular mechanisms underlying Hed's regulation of mitophagy in SiHa cells, offering novel insights and potential therapeutic targets for cervical cancer treatment.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"2081-2095"},"PeriodicalIF":3.8,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143707762","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":"Recent Developments in Single-Cell Metabolomics by Mass Spectrometry─A Perspective.","authors":"Boryana Petrova, Arzu Tugce Guler","doi":"10.1021/acs.jproteome.4c00646","DOIUrl":"10.1021/acs.jproteome.4c00646","url":null,"abstract":"<p><p>Recent advancements in single-cell (sc) resolution analyses, particularly in sc transcriptomics and sc proteomics, have revolutionized our ability to probe and understand cellular heterogeneity. The study of metabolism through small molecules, metabolomics, provides an additional level of information otherwise unattainable by transcriptomics or proteomics by shedding light on the metabolic pathways that translate gene expression into functional outcomes. Metabolic heterogeneity, critical in health and disease, impacts developmental outcomes, disease progression, and treatment responses. However, dedicated approaches probing the sc metabolome have not reached the maturity of other sc omics technologies. Over the past decade, innovations in sc metabolomics have addressed some of the practical limitations, including cell isolation, signal sensitivity, and throughput. To fully exploit their potential in biological research, however, remaining challenges must be thoroughly addressed. Additionally, integrating sc metabolomics with orthogonal sc techniques will be required to validate relevant results and gain systems-level understanding. This perspective offers a broad-stroke overview of recent mass spectrometry (MS)-based sc metabolomics advancements, focusing on ongoing challenges from a biologist's viewpoint, aimed at addressing pertinent and innovative biological questions. Additionally, we emphasize the use of orthogonal approaches and showcase biological systems that these sophisticated methodologies are apt to explore.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"1493-1518"},"PeriodicalIF":3.8,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142491154","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":"Microbial Butyrate Modified by Melatonin Alleviates Colon Inflammation by Inhibiting GPR109A/Caspase-1-Dependent Macrophage M1 Polarization.","authors":"Xinyu Shao, Xiuwei Mi, Xiaoyi Kuai, Diyuan Zhou, Qingliang Tai, Yang Lu, Chunli Zhou, Songbing He","doi":"10.1021/acs.jproteome.4c00915","DOIUrl":"10.1021/acs.jproteome.4c00915","url":null,"abstract":"<p><p>Recurrent ulcerative colitis (UC) seriously affects the quality of life of patients. Melatonin affects the alteration of the gut microbiota and can effectively relieve inflammation-associated diseases. In the present study, we determined that melatonin effectively alleviated intestinal inflammation and delayed weight loss in mice. Analysis of ileocecal contents in mice via 16S-rRNA and GC-MS revealed that melatonin could elevate the diversity of the gut microbiota and the abundance of short-chain fatty acids producing bacteria and promote the secretion of butyrate. Subsequently, butyrate negatively regulates the NLRP3-mediated inflammatory signaling pathway to inhibit the secretion of proinflammatory mediators such as caspase-1 and IL-1β to restrict the further development of intestinal inflammation. The NLRP3 expression increased, and the GPR109A expression was reduced significantly in the intestinal tissues of active UC patients, which was also closely related to clinical indicators CRP and ESR closely. However, disrupting the gut microbiota with broad-spectrum antibiotics (ABX) blocks melatonin's role in reducing intestinal inflammation. Collectively, we indicate that melatonin arrests UC in mice by modulating the microbiome and the NLRP3/caspase-1 inflammatory signaling pathways to skew macrophage polarization, which may have potential implications in the development of new approaches to treat acute UC.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"1871-1884"},"PeriodicalIF":3.8,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143555269","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":"Plasma IgG Glycosylation Profiling Reveals the Biological Features of Early Chronic Obstructive Pulmonary Disease.","authors":"Jinyu Zhou, Yuting Tan, Wenqian Wu, Junye Chen, Huiyuan Hu, Ziyi Yin, Siyang Liu, Chen Liu, Xiaohua Qin, Jiantao Hu, Qian Wang, Le Luo, Bin Liu, Yongqiang Wang, Peitao Zhang, Jieqiong Miao, Wei Sun, Lifeng Yang, Hongmei Zhao, Jing Wang, Lin Wang, Chen Wang","doi":"10.1021/acs.jproteome.4c00819","DOIUrl":"10.1021/acs.jproteome.4c00819","url":null,"abstract":"<p><p>Chronic inflammatory and immune dysregulation are critical drivers of the development and progression of chronic obstructive pulmonary disease (COPD). Posttranslational modifications, such as glycosylation of Immunoglobulin G (IgG), are crucial in modulating systemic inflammatory homeostasis. This study aims to profile plasma IgG glycopeptides (IgGPs) in COPD patients to uncover new insights into their pathogenesis and to identify novel biomarkers. An integrated platform that combines Fe₃O₄@PDA@DETA nanospheres enrichment with high-resolution mass spectrometry measurement was employed to analyze plasma IgG N-glycopeptides from 90 COPD patients, 45 clinically defined early COPD (CECOPD) patients, and 90 healthy individuals. To explore the underlying mechanism of COPD progression, correlations between IgG N-glycoforms and clinical parameters were assessed. Disease-specific IgGPs were identified in both the ECOPD and COPD cohorts. Notably, it was the IgG glycopattern, rather than the IgG levels themselves, that underwent changes as the disease progressed. In early COPD patients, there was a decrease in bisection, accompanied by an increase in site-specific afucosylated galactosylation and fucosylation of IgG, indicating an anti-inflammatory state. Conversely, in COPD patients, an increase in inflammation was observed, which was characterized by reduced galactosylation and sialylation. Interestingly, a subset of healthy controls displayed IgGP patterns similar to those of early COPD, possibly reflecting the impact of smoking and the associated immune responses. We finally identified 6 anti-inflammatory and 2 pro-inflammatory IgGPs as ECOPD-specific IgGP indicators. Collectively, these findings suggest that plasma IgG glycosylation holds great potential as a biomarker for early COPD diagnosis, providing valuable insights into the immune system changes during disease progression. The raw data files are publicly accessible via the ProteomeXchange Consortium with the identifier PXD056374.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"1804-1816"},"PeriodicalIF":3.8,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143555273","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":"Limelight: An Open, Web-Based Tool for Visualizing, Sharing, and Analyzing Mass Spectrometry Data from DDA Pipelines.","authors":"Michael Riffle, Alex Zelter, Daniel Jaschob, Michael R Hoopmann, Danielle A Faivre, Robert L Moritz, Trisha N Davis, Michael J MacCoss, Nina Isoherranen","doi":"10.1021/acs.jproteome.4c00968","DOIUrl":"10.1021/acs.jproteome.4c00968","url":null,"abstract":"<p><p>Liquid chromatography-tandem mass spectrometry employing data-dependent acquisition (DDA) is a mature, widely used proteomics technique routinely applied to proteome profiling, protein-protein interaction studies, biomarker discovery, and protein modification analysis. Numerous tools exist for searching DDA data and myriad file formats are output as results. While some search and post processing tools include data visualization features to aid biological interpretation, they are often limited or tied to specific software pipelines. This restricts the accessibility, sharing and interpretation of data, and hinders comparison of results between different software pipelines. We developed Limelight, an easy-to-use, open-source, freely available tool that provides data sharing, analysis and visualization and is not tied to any specific software pipeline. Limelight is a data visualization tool specifically designed to provide access to the whole \"data stack\", from raw and annotated scan data to peptide-spectrum matches, quality control, peptides, proteins, and modifications. Limelight is designed from the ground up for sharing and collaboration and to support data from any DDA workflow. We provide tools to import data from many widely used open-mass and closed-mass search software workflows. Limelight helps maximize the utility of data by providing an easy-to-use interface for finding and interpreting data, all using the native scores from respective workflows.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"1895-1906"},"PeriodicalIF":3.8,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143555354","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":"Maximizing Immunopeptidomics-Based Bacterial Epitope Discovery by Multiple Search Engines and Rescoring.","authors":"Patrick Willems, Fabien Thery, Laura Van Moortel, Margaux De Meyer, An Staes, Adillah Gul, Lyudmila Kovalchuke, Arthur Declercq, Robbe Devreese, Robbin Bouwmeester, Ralf Gabriels, Lennart Martens, Francis Impens","doi":"10.1021/acs.jproteome.4c00864","DOIUrl":"10.1021/acs.jproteome.4c00864","url":null,"abstract":"<p><p>Mass spectrometry-based discovery of bacterial immunopeptides presented by infected cells allows untargeted discovery of bacterial antigens that can serve as vaccine candidates. However, reliable identification of bacterial epitopes is challenged by their extremely low abundance. Here, we describe an optimized bioinformatic framework to enhance the confident identification of bacterial immunopeptides. Immunopeptidomics data of cell cultures infected with <i>Listeria monocytogenes</i> were searched by four different search engines, PEAKS, Comet, Sage and MSFragger, followed by data-driven rescoring with MS²Rescore. Compared with individual search engine results, this integrated workflow boosted immunopeptide identification by an average of 27% and led to the high-confidence detection of 18 additional bacterial peptides (+27%) matching 15 different <i>Listeria</i> proteins (+36%). Despite the strong agreement between the search engines, a small number of spectra (<1%) had ambiguous matches to multiple peptides and were excluded to ensure high-confidence identifications. Finally, we demonstrate our workflow with sensitive timsTOF SCP data acquisition and find that rescoring, now with inclusion of ion mobility features, identifies 76% more peptides compared to Q Exactive HF acquisition. Together, our results demonstrate how integration of multiple search engine results along with data-driven rescoring maximizes immunopeptide identification, boosting the detection of high-confidence bacterial epitopes for vaccine development.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"2141-2151"},"PeriodicalIF":3.8,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143622883","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":"3-Hydroxybutyrate Promotes Myoblast Proliferation and Differentiation through Energy Metabolism and GPR109a-Mediated Ca²⁺-NFAT Signaling Pathways.","authors":"Xu Qiu, Wenfang Wu, Shuya Zhang, Caihua Huang, Donghai Lin","doi":"10.1021/acs.jproteome.4c01150","DOIUrl":"10.1021/acs.jproteome.4c01150","url":null,"abstract":"<p><p>Skeletal muscle wasting is a critical clinical problem associated with several diseases that significantly impair patient outcomes due to the progressive loss of muscle mass and function. This study explores the potential of 3-hydroxybutyrate (3-HB) as a therapeutic agent to counteract muscle atrophy by promoting the proliferation and differentiation of C2C12 myoblasts. Using nuclear magnetic resonance (NMR)-based metabolomics analysis, we uncover the underlying mechanisms by which 3-HB exerts its effects. Our findings demonstrate that 3-HB exerts its effects through two distinct mechanisms: as a metabolic substrate and as a signaling molecule. As a metabolic substrate, 3-HB enhances myoblast energy efficiency by stimulating the expression of G protein-coupled receptor 109a (GPR109a), which subsequently upregulates the 3-HB transporters MCT1 and CD147, the utilization enzyme OXCT1, and phosphorylated AMPK, thereby increasing ATP production. As a signaling molecule, 3-HB activates GPR109a, promoting calcium influx, improving calcium homeostasis, and increasing the expression of Ca²⁺-related proteins such as CAMKK2. This signaling cascade activates calcineurin (CaN), facilitating NFAT translocation to the nucleus and gene expression that drives myoblast proliferation and differentiation. By elucidating the dual regulatory roles of 3-HB in energy metabolism and cellular signaling, this study not only advances our understanding of muscle physiology but also highlights the potential of 3-HB as a novel therapeutic approach for the prevention or treatment of skeletal muscle atrophy.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"2063-2080"},"PeriodicalIF":3.8,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143655508","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":"Redesigning CYP109E1 for Improving Catalytic Performance in 25-Hydroxyvitamin D₃ Synthesis Through Synergistic Enhancement of Electron Transfer and NADPH Regeneration.","authors":"Jiaying Ai, Ziyang Yin, Jikai Gao, Wenjing Wang, Fuping Lu, Hui-Min Qin, Shuhong Mao","doi":"10.1021/acssynbio.4c00879","DOIUrl":"https://doi.org/10.1021/acssynbio.4c00879","url":null,"abstract":"<p><p>P450 enzymes are promising biocatalysts and play an important role in the field of drug synthesis due to their high catalytic activity and stereoselectivity. CYP109E1 from <i>Bacillus megaterium</i> was used to convert VD₃ for the production of 25(OH)VD₃. However, the industrial production was still limited due to the low catalytic performance of CYP109E1. To overcome this, we constructed an engineered strain containing a modified CYP109E1 coupled with an efficient electron transfer chain and NADPH regeneration system. First, Adx_4-108T69E-Fpr was identified as the most compatible redox partner for the enzyme based on in-silico analysis. Then, targeted mutations were introduced at the substrate channel of CYP109E1, resulting in higher production efficiency. Next, the production of 25(OH)VD₃ was increased by 13.1% after introducing a double Adx_4-108T69E expression cassette. Finally, an NADPH regeneration system was introduced by overexpressing <i>zwf</i>, which increased the yield of 25(OH)VD₃ 48.7%. These results demonstrate that recombinant <i>Escherichia coli</i> BL21 (DE3) coexpressing CYP109E1_R70A-ZWF and 2Adx_4-108T69Es-Fpr is an efficient whole-cell biocatalyst for the synthesis of 25(OH)VD₃, illustrating an attractive strategy for improving the catalytic efficiency of P450 enzymes.</p>","PeriodicalId":26,"journal":{"name":"ACS Synthetic Biology","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143778574","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":"Conservation of Putative Liquid-Liquid Phase Separating Proteins in Multiple Drug-Resistant <i>Mycobacterium tuberculosis</i>: Role in Host-Pathogen Interactions?","authors":"Jasdeep Singh, Prashant Pradhan, Arti Kataria, Sanjeev Sinha, Nasreen Z Ehtesham, Peter N Monk, Seyed E Hasnain","doi":"10.1021/acsinfecdis.4c00722","DOIUrl":"https://doi.org/10.1021/acsinfecdis.4c00722","url":null,"abstract":"<p><p>We observed a high proportion of proteins in pathogenic <i>Mycobacterium</i> species that can potentially undergo liquid-liquid phase separation (LLPS) mediated biomolecular condensate formation, compared to nonpathogenic species. These proteins mainly include the PE-PPE and PE-PGRS families of proteins that have nucleic acid and protein-protein binding functions, typical of LLPS proteins. We also mapped identified LLPS proteins in <i>M. tuberculosis</i> (M.tb) drug-resistant databases PubMLST and TBProfiler, based upon the WHO 2023 catalogue of resistance-associated mutations. High sequence conservation of LLPS-associated proteins in various multiple drug-resistant M.tb isolates points to their potentially important role in virulence and host-pathogen interactions during pathogenic evolution. This analysis provides a perspective on the role of protein phase separation in the evaluation of M.tb pathogenesis and offers avenues for future research aimed at developing innovative strategies to combat M.tb infection.</p>","PeriodicalId":17,"journal":{"name":"ACS Infectious Diseases","volume":" ","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143778596","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Response of a Tethered Zn-Bis-Terpyridine Complex to an External Mechanical Force: A Computational Study of the Roles of the Tether and Solvent.","authors":"Shouryo Ghose, Anne-Sophie Duwez, Charles-André Fustin, Françoise Remacle","doi":"10.1021/acs.jpca.4c08639","DOIUrl":"https://doi.org/10.1021/acs.jpca.4c08639","url":null,"abstract":"<p><p>Polymeric materials containing weak sacrificial bonds can be designed to engineer self-healing and higher toughness, improve melt-processing, or facilitate recycling. However, they usually exhibit a lower mechanical strength and are subject to creep and fatigue. For improving their design, it is of interest to investigate their mechanical response on the molecular scale. We report on a computational study of the response to a mechanical external force of a Zinc(II) bis-methyl phenyl-terpyridine ([Zn-bis-Terpy]²⁺) complex included in a cyclic poly(ethylene glycol) (PEG) tether designed to maintain the two partners of the metal-ligand bonds in close proximity after the rupture of the complex. The mechanical response is studied as a function of the pulling distortion by using the CoGEF isometric protocol, including interactions with a polar solvent (DMSO). We show that tethering favors recombination but destabilizes the complex before bond rupture because of the interactions of the PEG units with Terpy ligands. Similar effects occur between the DMSO molecules and the complex. Our results on the molecular scale are relevant for single-molecule force spectroscopy experiments. Interactions of the complex with solvent molecules and/or with the tether lead to a dispersion of the rupture force values, which could obscure the interpretation of the results.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143778515","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}