Journal of Proteome Research最新文献_第2页

Metaproteomics as a Powerful Tool for an Extensive Characterization of Ambient Bioaerosols. 宏蛋白质组学是广泛表征环境生物气溶胶的有力工具。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-05-21 DOI: 10.1021/acs.jproteome.4c00936

Mathieu Galmiche, Lauriane Kuhn, Maurice Millet, Yannis-Nicolas François

{"title":"Metaproteomics as a Powerful Tool for an Extensive Characterization of Ambient Bioaerosols.","authors":"Mathieu Galmiche, Lauriane Kuhn, Maurice Millet, Yannis-Nicolas François","doi":"10.1021/acs.jproteome.4c00936","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00936","url":null,"abstract":"Bioaerosols are of great health and environmental concern. Current techniques for their characterization are generally designed to detect individual species or oppositely unspecific molecular tracers. Metaproteomics on the other hand features the possibility to cover a broad range of taxonomies in a single analysis. This work presents a successful application of metaproteomics to characterize the biological fraction of airborne particulate matter (PM). A bottom-up proteomic strategy was employed, including protein extraction by ultrasonication in aqueous buffer, in-solution tryptic digestion, and nanoflow liquid chromatography-high-resolution mass spectrometry analysis. Extraction parameters were optimized to enhance proteins' recovery. The method was validated on Escherichia coli extracts before its application on ambient PM10 samples collected over 12 weeks in Strasbourg, France. A total of 1,087 peptides were detected across all samples, with a weekly average of 223 ± 104 peptides corresponding to 111 ± 40 proteins. Peptides from species belonging to animals, plants, fungi, bacteria, and archaea kingdoms were inventoried. Many of them proved to be very relevant, as they were related to human allergens and pathogens, plant pathogens, or ecological indicators. In this work, the major benefits of metaproteomics, yet rather unexploited, as well as its pitfalls and challenges for a broader application in atmospheric chemistry, are discussed.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144118408","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}

引用次数: 0

Proteotranscriptomics Analysis Reveals the Key Pathways and Genes Involved in Apigenin's Anti-Liver Fibrosis Effects. 蛋白质转录组学分析揭示了芹菜素抗肝纤维化作用的关键途径和基因。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-05-21 DOI: 10.1021/acs.jproteome.5c00087

Tao Sun, Xiuzhi Zhang, Xianghua Liu, Xiaoying Li, Saifei Li, Shanfa Yu, Zhefeng Xiao, Ningning Li

{"title":"Proteotranscriptomics Analysis Reveals the Key Pathways and Genes Involved in Apigenin's Anti-Liver Fibrosis Effects.","authors":"Tao Sun, Xiuzhi Zhang, Xianghua Liu, Xiaoying Li, Saifei Li, Shanfa Yu, Zhefeng Xiao, Ningning Li","doi":"10.1021/acs.jproteome.5c00087","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00087","url":null,"abstract":"Liver fibrosis is a global health issue with limited treatments. While apigenin has demonstrated potential in alleviating liver fibrosis, its mechanisms remain unclear. This study employed an integrated proteotranscriptomic approach to elucidate the molecular mechanisms underlying apigenin's protective effects against CCl4-induced liver fibrosis. Liver tissues from mice with CCl4-induced fibrosis treated with different doses of apigenin (10, 20, and 40 mg/kg) were analyzed using transcriptomics and proteomics. Results demonstrated dose-dependent antifibrotic effects of apigenin. Notably, numerous genes and proteins were inversely regulated by CCl4 and apigenin, with generally low and variable mRNA-protein abundance correlations. We identified 82 biological processes or molecular functions that were inversely regulated by CCl4 and high-dose apigenin at both mRNA and protein levels. Among the 48 key proteins (KPs) involved, 11 and 14 KPs correlated with liver fibrosis in mouse and human data sets, respectively. Six KPs maintained consistent correlations with fibrosis severity across both species, highlighting their potential as both biomarkers for fibrosis progression and translational targets. These findings underscore apigenin's therapeutic potential and emphasize the importance of multiomics approaches in understanding complex diseases like liver fibrosis. This study also provides valuable insights for developing improved therapeutic strategies and diagnostic tools for liver fibrosis.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144118409","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}

引用次数: 0

MCQR: Enhancing the Processing and Analysis of Quantitative Proteomics Data by Incorporating Chromatography and Mass Spectrometry Information. MCQR：结合色谱和质谱信息加强定量蛋白质组学数据的处理和分析。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-05-20 DOI: 10.1021/acs.jproteome.4c01119

Thierry Balliau, Anne Frambourg, Olivier Langella, Marie-Laure Martin, Michel Zivy, Mélisande Blein-Nicolas

{"title":"MCQR: Enhancing the Processing and Analysis of Quantitative Proteomics Data by Incorporating Chromatography and Mass Spectrometry Information.","authors":"Thierry Balliau, Anne Frambourg, Olivier Langella, Marie-Laure Martin, Michel Zivy, Mélisande Blein-Nicolas","doi":"10.1021/acs.jproteome.4c01119","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c01119","url":null,"abstract":"In the field of proteomics, generating biologically relevant results from mass spectrometry (MS) signals remains a challenging task. This is partly due to the fact that the computational strategies for converting MS signals into biologically interpretable data depend heavily on the MS acquisition method. Additionally, the processing and the analysis of these data vary depending on whether the proteomic experiment was performed with or without labeling, and with or without fractionation. Several R packages have been developed for processing and analyzing MS data, but they only incorporate identification and quantification data; none of them takes into account other invaluable information collected during MS runs. To address this limitation, we introduce MCQR, an alternative R package for the in-depth exploration, processing, and analysis of quantitative proteomics data generated from either data-dependent or data-independent acquisition methods. MCQR leverages experimental retention time measurements for quality control, data filtering, and processing. Its modular architecture offers flexibility to accommodate various types of proteomics experiments, including label-free, label-based, fractionated, or those enriched for specific post-translational modifications. Its functions, designed as simple building blocks, are user-friendly, making it easy to test parameters and methods, and to construct customized analysis scenarios. These unique features position MCQR as a comprehensive toolbox, perfectly suited to the specific needs of MS-based proteomics experiments.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144109108","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}

引用次数: 0

The Proteoform Landscape of Tau from the Human Brain. 人脑中Tau蛋白的变形景观。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-05-20 DOI: 10.1021/acs.jproteome.5c00139

Tian Xu, Taojunfeng Su, Benjamin J Des Soye, Soumya Kandi, Che-Fan Huang, John T Wilkins, Rudolph J Castellani, Jared O Kafader, Steven M Patrie, Robert Vassar, Neil L Kelleher

{"title":"The Proteoform Landscape of Tau from the Human Brain.","authors":"Tian Xu, Taojunfeng Su, Benjamin J Des Soye, Soumya Kandi, Che-Fan Huang, John T Wilkins, Rudolph J Castellani, Jared O Kafader, Steven M Patrie, Robert Vassar, Neil L Kelleher","doi":"10.1021/acs.jproteome.5c00139","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00139","url":null,"abstract":"Tau is a microtubule-associated protein (MAP) and is critical for maintaining the cytoskeleton of neurons. Tau and its post-translational modifications (PTMs) have been studied for decades, yet the exact composition of intact tau and its truncation products present in the human brain has evaded study at the proteoform level. Here, we show that tau proteoform profiling and exact characterization are possible using immunoprecipitation (IP) and the new approach of individual ion mass spectrometry (I2MS). We provide a first glimpse of the tau proteoform landscape present in the CHAPS-soluble extracts from the temporal cortex of a control subject and a donor with Alzheimer's disease (AD). Profiling and identification of four isoforms (0N3R, 1N3R, 0N4R, and 1N4R), truncated products (e.g., 72-172 derived from the 0N3R/0N4R isoforms), and intact tau proteoforms harboring PTMs include phosphorylation, methylation, and acetylation. The specific tau proteoform identification typically employs proton transfer charge reduction (PTCR) and electron transfer dissociation (ETD) with spectral readout by individual ion tandem mass spectrometry (I2MS2). A precise understanding of the tau proteoform landscape over the course of neurodegeneration is critical to understand AD pathology vs related dementias. The assay approach reported here will advance AD research, gives a sense of what is technologically possible for new biomarker discovery and will assist the development of therapeutics using the most exact kind of compositional information on tau.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144109117","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}

引用次数: 0

Proteomic Profiling of Serum-Derived Extracellular Vesicles in Diffuse Idiopathic Skeletal Hyperostosis Patients. 弥漫性特发性骨质增生患者血清来源的细胞外囊泡的蛋白质组学分析。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-05-19 DOI: 10.1021/acs.jproteome.4c01015

Haicheng Zhou, Jianmin Gong, Zhentao Zhang, Bin Wang, Yong Qiu, Hongpan Xu, Xu Sun, Zhiyang Li

{"title":"Proteomic Profiling of Serum-Derived Extracellular Vesicles in Diffuse Idiopathic Skeletal Hyperostosis Patients.","authors":"Haicheng Zhou, Jianmin Gong, Zhentao Zhang, Bin Wang, Yong Qiu, Hongpan Xu, Xu Sun, Zhiyang Li","doi":"10.1021/acs.jproteome.4c01015","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c01015","url":null,"abstract":"This study focuses on the proteomic profiles of serum-derived EVs in diffuse idiopathic skeletal hyperostosis (DISH), aiming to identify the potential diagnostic biomarkers for DISH. Serum-EVs were separated using a differential centrifugation technique. Then, label-free-liquid chromatography mass spectrometry (LC-MS/MS) was utilized to identify differentially expressed proteins (DEPs) highly associated with DISH. DEPs' expression levels were tested using enzyme-linked immunosorbent assay (ELISA) and bioinformatic analyses were performed. According to ectopic ossification severity, DISH cohort was stratified into T-DISH and L-DISH subtypes. Serum-EVs' AHSG level was also compared between T-DISH and L-DISH subgroups. Additionally, the number of ossified segments of all DISH patients was assessed and its correlation with serum-EVs' AHSG was analyzed. LC-MS/MS proteomic analyses demonstrated 24 up-regulated and 6 down-regulated proteins in the DISH group. ELISA results showed that AHSG level in serum-EVs was significantly higher in the DISH group. Interestingly, serum-EVs' AHSG was found significantly higher in the L-DISH subgroup compared to the T-DISH subgroup and a strong positive correlation was demonstrated between the quantified ossified segments and serum-EVs' AHSG. Hence, serum-EVs' AHSG may be a promising biomarker for DISH and participate in the pathogenesis of heterotopic bone formation in DISH.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144092071","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}

引用次数: 0

Integrative Metabolomic and Lipidomic Signatures of SARS-CoV-2 VOCs: Correlations with Hematological and Biochemical Markers. SARS-CoV-2 VOCs的代谢组学和脂质组学综合特征：与血液学和生化标志物的相关性

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-05-19 DOI: 10.1021/acs.jproteome.4c00996

Budhadev Baral, Vaishali Saini, Siddharth Singh, Tarun Prakash Verma, Deb Kumar Rath, Jyotirmayee Bahinipati, Priyadarsini Panda, Shubhransu Patro, Namrata Misra, Manas Ranjan Behera, Kartik Muduli, Hamendra Singh Parmar, Ajay Kumar Meena, Rajesh Kumar, Sonali Agarwal, Soumya R Mohapatra, Nirmal Kumar Mohakud, Hem Chandra Jha

{"title":"Integrative Metabolomic and Lipidomic Signatures of SARS-CoV-2 VOCs: Correlations with Hematological and Biochemical Markers.","authors":"Budhadev Baral, Vaishali Saini, Siddharth Singh, Tarun Prakash Verma, Deb Kumar Rath, Jyotirmayee Bahinipati, Priyadarsini Panda, Shubhransu Patro, Namrata Misra, Manas Ranjan Behera, Kartik Muduli, Hamendra Singh Parmar, Ajay Kumar Meena, Rajesh Kumar, Sonali Agarwal, Soumya R Mohapatra, Nirmal Kumar Mohakud, Hem Chandra Jha","doi":"10.1021/acs.jproteome.4c00996","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00996","url":null,"abstract":"In the present study, we investigated biochemical, hematological, lipidomic, and metabolomic alterations associated with different SAR-CoV-2 variants of concern (VOCs), such as WT, α, β, γ, and δ, as well as their impact on COVID-19 severity. Across the first and second waves in India, a machine learning approach was used in 3134 COVID-19 patients, and nine critical biochemical and hematological parameters, namely, C-reactive protein (CRP), D-dimer, ferritin, neutrophil, WBC count, lymphocyte, urea, creatine, and lactate dehydrogenase (LDH), were identified. Furthermore, through metabolic and lipidomic profiles of lung and colon cells transfected with spike VOCs, notable dysregulation was exhibited by the delta variant correlated with characteristic pathways such as catecholamine and thyroid hormone synthesis. A corroborating meta-analysis also highlighted the involvement of urea and amino acid metabolism pathways. Overall, our study provides crucial insights into metabolic and biochemical disruptions caused by VOCs, contributing to a better understanding of COVID-19 pathogenesis and the development of targeted interventions.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144100974","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}

引用次数: 0

MultiStageSearch: An Iterative Workflow for Unbiased Taxonomic Analysis of Pathogens Using Proteogenomics. 多阶段研究：利用蛋白质基因组学对病原体进行无偏分类分析的迭代工作流程。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-05-18 DOI: 10.1021/acs.jproteome.4c00901

Julian Pipart, Tanja Holstein, Lennart Martens, Thilo Muth

{"title":"MultiStageSearch: An Iterative Workflow for Unbiased Taxonomic Analysis of Pathogens Using Proteogenomics.","authors":"Julian Pipart, Tanja Holstein, Lennart Martens, Thilo Muth","doi":"10.1021/acs.jproteome.4c00901","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00901","url":null,"abstract":"The global SARS-CoV-2 pandemic emphasized the need for accurate pathogen diagnostics. While genomics is the gold standard, integrating mass spectrometry-based proteomics offers additional benefits. However, current proteomic and genomic reference databases are often biased toward specific taxa, such as pathogenic strains or model organisms, and proteomic databases are less comprehensive. These biases and gaps can lead to inaccurate identifications. To address these issues, we introduce MultiStageSearch, a multistep database search method that combines proteome and genome databases for taxonomic analysis. Initially, a generalist proteome database is used to infer potential species. Then, MultiStageSearch generates a specialized proteogenomic database for precise identification. This database is preprocessed to filter duplicates and cluster identical open reading frames to reduce genomic database biases. The workflow operates independently of strain-level NCBI taxonomy, enabling the identification of strains not represented in existing taxonomies. We benchmarked the workflow on viral and bacterial samples, demonstrating its superior performance in strain-level taxonomic inference compared to existing methods. MultiStageSearch offers a flexible and accurate approach for pathogen research and diagnostics, overcoming incomplete search spaces and biases inherent in reference databases.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144092070","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}

引用次数: 0

Human-Derived Proteome Characterization of Tongue Coating in Colorectal Cancer. 结直肠癌患者舌苔的蛋白质组学特征。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-05-16 DOI: 10.1021/acs.jproteome.5c00120

Qubo Chen, Wanhua Li, Xiangyu Gu, Fengye Lin, Ying Chen, Hairong Su, Tao Su, Ang Li, Chuyang Wang, Xuan Zeng, Weicheng Chen, Beiping Zhang, Haiyan Zhang, Meng Gong

{"title":"Human-Derived Proteome Characterization of Tongue Coating in Colorectal Cancer.","authors":"Qubo Chen, Wanhua Li, Xiangyu Gu, Fengye Lin, Ying Chen, Hairong Su, Tao Su, Ang Li, Chuyang Wang, Xuan Zeng, Weicheng Chen, Beiping Zhang, Haiyan Zhang, Meng Gong","doi":"10.1021/acs.jproteome.5c00120","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00120","url":null,"abstract":"Most colorectal cancer (CRC) patients experience changes in tongue coating morphology, but the underlying mechanisms remain unclear. While the human-derived proteome of tongue coatings in gastric cancer and healthy individuals has been characterized, research on CRC patients remains lacking. The tongue coating collection process is painless and noninvasive, providing a more favorable examination experience. This study aims to preliminarily explore the composition and changes in the human-derived proteome of tongue coatings in CRC patients, providing insights into abnormal morphology and potential new CRC screening methods. Utilizing a \"bottom-up\" strategy and data-independent acquisition (DIA) mode, the human-derived proteome of tongue coating in healthy controls, colorectal hyperplastic polyps patients, and CRC patients was detected using the EASY-nLC 1200 chromatograph coupled with the Orbitrap Fusion Lumos Tribrid mass spectrometer. Differentially expressed proteins were validated by Western blot, and the diagnostic efficacy of tongue coating proteins compared with CRC serum markers was assessed. Our results indicate that the human tongue coating proteome undergoes significant changes in CRC, with upregulated proteins potentially involved in remodeling the tongue coating morphology. Hemopexin (HPX), fibrinogen β chain (FGB), and cystatin C (CST3) in the tongue coating are promising indicators for CRC screening.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144074893","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}

引用次数: 0

Comparative Omics Reveals Unanticipated Metabolic Rearrangements in a High-Oil Mutant of Plastid Acetyl-CoA Carboxylase. 比较组学揭示了质体乙酰辅酶a羧化酶高油突变体中意想不到的代谢重排。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-05-16 DOI: 10.1021/acs.jproteome.4c00947

Amr Kataya, Jose Roberto S Nascimento, Chunhui Xu, Matthew G Garneau, Somnath Koley, Athen Kimberlin, Thiya Mukherjee, Brian P Mooney, Dong Xu, Philip D Bates, Doug K Allen, Abraham J Koo, Jay J Thelen

{"title":"Comparative Omics Reveals Unanticipated Metabolic Rearrangements in a High-Oil Mutant of Plastid Acetyl-CoA Carboxylase.","authors":"Amr Kataya, Jose Roberto S Nascimento, Chunhui Xu, Matthew G Garneau, Somnath Koley, Athen Kimberlin, Thiya Mukherjee, Brian P Mooney, Dong Xu, Philip D Bates, Doug K Allen, Abraham J Koo, Jay J Thelen","doi":"10.1021/acs.jproteome.4c00947","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00947","url":null,"abstract":"Heteromeric acetyl-CoA carboxylase (ACCase) catalyzes the ATP-dependent carboxylation of acetyl-CoA to produce malonyl-CoA, which is the committed step for de novo fatty acid synthesis. In plants, ACCase activity is controlled at multiple levels, including negative regulation by biotin attachment domain-containing (BADC) proteins, of which the badc1/3 double mutant leads to increased seed triacylglycerol accumulation. Unexpectedly, the Arabidopsis badc1/3 mutant also accumulated more protein. The metabolic consequences from both higher oil and protein were investigated in developing badc1/3 seed using global transcriptomics, translatomics, proteomics, metabolomics, and other biomass measurements. Changes included increased storage proteins and lipid droplet-packaging proteins, increased SDP1 lipase, altered organic acid metabolism, and reduced extracellular lipid synthesis perhaps offsetting the increase in TAG. We present a model of how Arabidopsis adapted to deregulated ACCase, resulting in more oil, and altered flux through pathways that partition carbon and propose targets for future bioengineering of seed storage reserves.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144074865","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}

引用次数: 0

Comparative Proteomic Analysis Reveals Altered Ciliary Proteins in Sickle Cell Disease. 比较蛋白质组学分析揭示镰状细胞病纤毛蛋白改变

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-05-15 DOI: 10.1021/acs.jproteome.5c00168

Ashraf M Mohieldin, Madison Spencer, Carter Bernal, Wala B Fadol, Ankan Gupta, Karthikeyan Thirugnanam, Claire Delahunty, Francisco Nunez, Amy Y Pan, Amanda M Brandow, Sean P Palecek, Kevin R Rarick, Ramani Ramchandran, Rahima Zennadi, John Yates, Surya M Nauli

{"title":"Comparative Proteomic Analysis Reveals Altered Ciliary Proteins in Sickle Cell Disease.","authors":"Ashraf M Mohieldin, Madison Spencer, Carter Bernal, Wala B Fadol, Ankan Gupta, Karthikeyan Thirugnanam, Claire Delahunty, Francisco Nunez, Amy Y Pan, Amanda M Brandow, Sean P Palecek, Kevin R Rarick, Ramani Ramchandran, Rahima Zennadi, John Yates, Surya M Nauli","doi":"10.1021/acs.jproteome.5c00168","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00168","url":null,"abstract":"Sickle cell disease (SCD) is an inherited hemoglobinopathy characterized by sickle-shaped red blood cells (RBCs). Primary cilia are mechanosensory organelles and are projected in the lumen of blood vessels to detect blood flow. We previously reported that interaction between microvasculature endothelial cells and sickled RBCs resulted in altered blood flow that can elevate reactive oxygen species, leading to increased deciliation in SCD patients. However, the impact of deciliation mediated by sickled RBCs in the context of the ciliary protein profiles remains unclear. Here, we investigated cell-cilia stability under different physiological shear-stress magnitudes and examined cilia protein profiles in SCD, utilizing mouse models and human participants. Our results demonstrate that subjecting endothelial cilia to sickled RBCs at 5.0 dyn/cm2 led to significant deciliation events. The proteomic and bioinformatic analyses showed different ciliary protein profiles, distinct signaling pathways, and unique post-translational modification processes in the SCD mouse model. Consistent with the SCD mouse model results, our translational studies validated the enrichment of specific proteins, including Transferrin Receptor-1 (TfR1), Glyceraldehyde-3-Phosphate-Dehydrogenase (GAPDH), and ADP Ribosylation Factor Like GTPase-13B (ARL13B) in SCD patients. These findings underscore the clinical relevance of cilia in SCD and suggest that ciliary proteins are potential biomarkers for assessing vascular damage.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144074869","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}

引用次数: 0