Journal of proteomics最新文献

{"title":"Aberrant oxidative modifications of neutrophil myeloperoxidase in anti-neutrophil cytoplasmic antibody-associated vasculitis","authors":"Masaaki Sato ,&nbsp;Kouhei Nagai ,&nbsp;Toshiyuki Sato ,&nbsp;Ryo Yoshimoto ,&nbsp;Yuto Shibano ,&nbsp;Minori Shibahara ,&nbsp;Haruka Satokawa ,&nbsp;Masayuki Anzai ,&nbsp;Teisuke Uchida ,&nbsp;Atsuhiro Tsutiya ,&nbsp;Yukiko Takakuwa ,&nbsp;Kazuki Omoteyama ,&nbsp;Mitsumi Arito ,&nbsp;Naoya Suematsu ,&nbsp;Seido Ooka ,&nbsp;Kimito Kawahata ,&nbsp;Tomohiro Kato ,&nbsp;Manae S. Kurokawa","doi":"10.1016/j.jprot.2025.105412","DOIUrl":"10.1016/j.jprot.2025.105412","url":null,"abstract":"<div><div>Anti-neutrophil cytoplasmic antibodies directed to myeloperoxidase (MPO-ANCA) are key molecules in the pathogenesis of ANCA-associated vasculitis (AAV), however, the mechanisms of autoantibody production have not been elucidated. We hypothesized that an aberrant PTM occurs in the MPO of MPO-ANCA-positive AAV (MPO-AAV), which induces immune responses to self MPO. To test this, we purified MPO proteins from neutrophils of 8 patients with MPO-AAV and 8 healthy subjects, digested them with trypsin, and comprehensively quantified PTMs of the MPO peptides using the sequential window acquisition of all theoretical fragment ion spectra (SWATH) method of LC-MS. Among the 1034 detected MPO peptides, 38 peptides were increased in the patients with MPO-AAV relative to the healthy subjects, whereas 10 peptides were decreased in the patients (<em>p</em> &lt; 0.05). Interestingly, oxidative modifications were found in 11 of the 38 increased peptides (1.14- to 3.29-fold), but not in the decreased peptides. These included oxidation of Met577, Phe686, Met688 and Met719, dioxidation of Met409, Phe605, Trp679 and Met719, and kynurenylation of Trp255. Conversely, glycosylation was detected in 4 of the 10 decreased peptides (−1.32- to −2.32-fold), but not in the increased peptides. They were <em>O</em>-type glycans at Ser357 and Ser731, and <em>N</em>-type glycans at Asn355 and Asn729. In animal experiments, immunization of mice with in vitro oxidized or unoxidized mouse MPO (mMPO) showed that not only anti-oxidized mMPO antibodies but also anti-unoxidized mMPO antibodies were preferentially produced in the oxidized mMPO-immunized mice relative to the unoxidized mMPO-immunized mice (anti-oxidized mMPO antibodies, 6/8 vs 1/9, <em>p</em> &lt; 0.05; anti-unoxidized mMPO antibodies, 4/8 vs 0/9, <em>p</em> &lt; 0.05). Our results suggest that the increased oxidative modifications of MPO in MPO-AAV may break immune tolerance and trigger the MPO-ANCA production.</div></div><div><h3>Significance</h3><div>AAV is a systemic and refractory disease that causes life-threatening multi-organ involvement such as necrotizing glomerulonephritis and lung hemorrhage. MPO-ANCA is an autoantibody that plays a key role in the pathogenesis of AAV. Therefore, elucidation of the mechanism of MPO-ANCA production is crucial to overcoming this disease. In this study, we applied a SWATH-MS analysis to the detection of aberrant PTMs, and found increased oxidative modifications of neutrophil MPO in patients with MPO-AAV for the first time. Immunization of in vitro oxidized MPO induced autoantibodies to the intact unoxidized MPO, suggesting that the increased oxidative modifications of MPO may break the immune tolerance in MPO-AAV. This study suggests a novel trigger mechanism for MPO-ANCA production.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"315 ","pages":"Article 105412"},"PeriodicalIF":2.8,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143492518","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":"Expanded characterization and localization of male seminal fluid proteins within the female reproductive tract of the dengue vector mosquito Aedes aegypti","authors":"Sara V. Villa-Arias ,&nbsp;José Alberto Mendivil-de la Ossa ,&nbsp;Frank W. Avila ,&nbsp;Steve Dorus ,&nbsp;Catalina Alfonso-Parra","doi":"10.1016/j.jprot.2025.105410","DOIUrl":"10.1016/j.jprot.2025.105410","url":null,"abstract":"<div><div><em>Aedes aegypti</em> mosquitoes transmit numerous viruses that impact human health. Contemporary biological control programs aim to reduce <em>Aedes</em> fertility despite our limited understanding of interactions between the sexes required for reproduction. During mating, males transfer seminal fluid proteins (SFPs) to females which alter their post-mating behavior, physiology and gene regulation, but the contribution of individual SFPs to fertility remains uncharacterized. In <em>Drosophila</em>, a small subset of SFPs localize to the sperm storage organs and oviducts or enter the hemolymph which suggests their participation in specific post-mating processes. We used mass spectrometry-based proteomics in conjunction with whole animal heavy labelling to expand the characterization of the <em>Ae. aegypti</em> ejaculate and identify SFPs that leave the site of insemination and localize to other female tissues. We identified 1031 ejaculate proteins, including a suite of novel SFPs. The expanded ejaculate proteome shows low conservation amongst SFPs when compared to insect model <em>Drosophila</em>, consistent with rapid evolutionary turnover at the genetic and proteomic levels. Further, we identify 25 SFPs that localize to the spermathecae, oviducts, and/or enter the hemolymph. This study expands our knowledge of the <em>Ae. aegypti</em> seminal fluid proteome and identifies candidate SFPs that may have tissue-specific, postcopulatory roles which support fertility.</div></div><div><h3>Significance</h3><div>Male-derived seminal fluid proteins (SFPs), transferred to females along with sperm during mating, are essential for the fertility of a mating pair. SFPs in aggregate induce several physiological and behavioral changes in mated females. Studies in the insect model <em>Drosophila</em> have shown that individual SFPs often participate in specific post-mating processes. In the dengue vector mosquito <em>Aedes aegypti</em>, 177 high confidence SFPs have been identified, but the contribution of individual SFPs in female fertility has yet not been characterized. In <em>Drosophila</em>, a small subset of SFPs leave the site of insemination and localize to the oviduct and sperm storage organs of the female reproductive tract or are transported to the female hemolymph, with patterns of SFP localization suggesting participation in a specific post-mating process. We used MS/MS proteomic characterization coupled with whole animal heavy labeling to expand characterization of the <em>Ae. aegypti</em> ejaculate proteome, increasing the number of known ejaculate proteins to 1378, including identification of 40 novel SFPs. Further, we identified 25 SFPs that leave the site of insemination and localize to the oviducts and/or spermathecae or enter the hemolymph, which can now be assessed for potential tissue-specific functions in female fertility.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"315 ","pages":"Article 105410"},"PeriodicalIF":2.8,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143472520","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteomic and metabolomic analyses reveal the antibacterial mechanism of Cannabidiol against gram-positive bacteria","authors":"Huimei Zeng ,&nbsp;Xingyao Wang ,&nbsp;Jiyu Tang ,&nbsp;Peina Liu ,&nbsp;Shen Zhang ,&nbsp;Hongwei Chu ,&nbsp;Bo Chen ,&nbsp;Ming Ma","doi":"10.1016/j.jprot.2025.105411","DOIUrl":"10.1016/j.jprot.2025.105411","url":null,"abstract":"<div><div>Cannabidiol (CBD), the primary non-psychoactive cannabinoid isolated from cannabis, exhibits promising antibacterial effects. However, the antibacterial mechanism of CBD remains poorly understood. In this study, the mechanism was investigated using bacterial inhibition assays, label-free proteomics, and untargeted metabolomics, with <em>Bacillus licheniformis</em> (<em>B. licheniformis</em>), <em>Staphylococcus aureus</em> (<em>S. aureus</em>), and <em>Enterococcus faecium</em> (<em>E. faecium</em>) selected as representative Gram-positive bacteria. The results revealed that CBD caused significant damage to bacterial cell walls and membranes, leading to notable changes in proteomic and metabolic profiles. Specifically, 437, 120, and 195 proteins, as well as 52, 153, and 94 metabolites, were differentially expressed in <em>B. licheniformis</em>, <em>S. aureus</em>, and <em>E. faecium</em>, respectively. The antimicrobial mechanism of CBD shares similarities with previously known antibacterial agents, such as penicillin and cephalosporins, particularly in affecting the bacterial cell wall, but differs in its detailed mode of action. CBD disrupted the biosynthesis of primary and secondary metabolites and altered bacterial metabolism, contributing to its antibacterial activity. This study provides valuable insights into the antibacterial mechanism of CBD, supporting its potential development as an antibiotic alternative and its application in food safety.</div></div><div><h3>Significance</h3><div>It is crucial to find alternatives to antibiotics to mitigate the impact of pathogenic bacteria on food safety and reduce the use of antibiotics. CBD is the primary non-psychoactive cannabinoid derived from cannabis, and it has shown promising antibacterial effects. However, the antimicrobial mechanisms of CBD have not been well elucidated. This study provides a deep understanding of the antibacterial mechanism from the cellular to molecular level, which will contribute to the development of CBD as a novel antibacterial agent.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"315 ","pages":"Article 105411"},"PeriodicalIF":2.8,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143464022","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 proteomics and phosphoproteomics analysis reveals differential sperm motility in Mediterranean buffalo semen","authors":"Qingsong Xue ,&nbsp;Xuan Ren ,&nbsp;Tairan Xu ,&nbsp;Ting Yang ,&nbsp;Le Sun ,&nbsp;Xi Luo ,&nbsp;Shihai Huang ,&nbsp;Deshun Shi ,&nbsp;Xiangping Li","doi":"10.1016/j.jprot.2025.105401","DOIUrl":"10.1016/j.jprot.2025.105401","url":null,"abstract":"<div><div>High motility spermatozoa are good for cryopreservation and artificial insemination (AI) of mammalian semen. In this study, normal motility (NM) and low motility (LM) Mediterranean buffalo spermatozoa were compared using quantitative proteomics and phosphoproteomics techniques to screen for important proteins and phosphorylated proteins related to the motility of spermatozoa and to identify candidate protein molecular markers related to the quality of Mediterranean buffalo semen. Proteomics results identified 2550 proteins, with 119 proteins upregulated and 146 proteins downregulated in the LM spermatozoa versus the NM spermatozoa. The differentially abundant proteins were mainly involved in carbohydrate metabolism, glycolysis/gluconeogenesis, and tricarboxylic acid cycles. The phosphoproteomics analysis revealed 412 proteins, 1228 phosphorylated peptides, and 1465 phosphorylation modification sites. Compared to the NM group, 119 peptides were downregulated in the LM group, corresponding to 98 proteins, and 84 phosphorylated peptides were upregulated in the white matter, corresponding to 61 proteins. Differentially phosphorylated proteins were primarily involved in spermatogenesis, flagellate sperm motility, and glycolysis/gluconeogenesis. The combined proteomics and phosphoproteomics results identified the common proteins HMGB4, POC1B, PKM, LDHA, TBC1D21, and CBY2, whose main roles were related to spermatogenesis, sperm flagellar structure, and energy metabolism, which can be used as potential markers of Mediterranean buffalo sperm quality.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"315 ","pages":"Article 105401"},"PeriodicalIF":2.8,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143441119","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":"Higher mitochondrial protein-Succinylation detected in lung tissues of idiopathic pulmonary fibrosis patients","authors":"Yunmulan Zhao ,&nbsp;Wenyu Hou ,&nbsp;Liqing Yang ,&nbsp;Kangyin Chen ,&nbsp;Qin Lang ,&nbsp;Wei Sun ,&nbsp;Lingyun Gao","doi":"10.1016/j.jprot.2025.105400","DOIUrl":"10.1016/j.jprot.2025.105400","url":null,"abstract":"<div><div>A new pathogenic role for mitochondrial dysfunction has been associated with the development of idiopathic pulmonary fibrosis (IPF). Lysine succinylation (Ksucc) is involved in many energy metabolism pathways in mitochondria, making Ksucc highly valuable for studying IPF. We used liquid chromatography with tandem mass spectrometry (LC-MS/MS) to perform the first global profiling of Ksucc in fibrotic lung tissues from IPF patients, providing a proof of concept for the alteration of Ksucc in IPF and highlighting its potential as a therapeutic target. Selected candidate proteins were further verified by targeted proteomics using parallel reaction monitoring (PRM). In this study, we identified 1964 Ksucc sites on 628 modified proteins, with675 of these Ksucc sites on 124 modified proteins closely related to mitochondrial metabolism. 117 succinylated proteins were associated with energy metabolism in mitochondria by comparing these proteins with those previously reported in normal lung tissues. The Ksucc levels in KYAT3, HSD17B8, GRHPR, and IDH2 were different between control and IPF groups by Using PRM. This study provides insight into Ksucc profile alterations in IPF pathogenesis and Ksucc sites in proteins associated with mitochondrial energy metabolism can also serve as candidate molecules for future mechanism exploration and drug target selection in IPF.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"314 ","pages":"Article 105400"},"PeriodicalIF":2.8,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143386828","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":"TMT-label comparative proteomics reveals the vernalization mechanism in Wucai (Brassica campestris L.)","authors":"Xueqing Liu ,&nbsp;Na Liao ,&nbsp;Xiaoyan Tang ,&nbsp;Kang Wang ,&nbsp;Wenjie Wang ,&nbsp;Afrasyab Khan ,&nbsp;Chenggang Wang ,&nbsp;Lingyun Yuan ,&nbsp;Guohu Chen","doi":"10.1016/j.jprot.2025.105398","DOIUrl":"10.1016/j.jprot.2025.105398","url":null,"abstract":"<div><div>To investigate the molecular basis of vernalization in Wucai [<em>Brassica campestris</em> L. (Syn. <em>Brassica rapa</em> L.) ssp. <em>chinensis</em> var. <em>rosularis</em> Tsen], we performed differential proteomic analysis using a tandem mass tags (TMT)-based approach. Proteins from shoot apices subjected to 0, 15, and 30 days of vernalization (V0, V15, and V30) were analyzed to identify differentially abundant proteins (DAPs). A total of 8066 proteins were obtained, and 507 shared DAPs were involved in both initiation and progression of vernalization. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations revealed functional enrichment in cellular processes, metabolic pathways, and translation-related activities, including photosynthesis, glucosinolate biosynthesis, and flavonoid biosynthesis. Proteomic data showed reduced abundance of photosynthesis-related proteins and upregulation of flavonoid biosynthesis during vernalization. Transcriptional validation of 24 proteins across metabolic and regulatory pathways corroborated proteomic findings, with notable peaks in genes associated with flavonoid biosynthesis at 15 days of vernalization, such as <em>VESR1</em>,<em>CH13</em>, <em>CHS1</em>, <em>FHT</em>, and <em>FLS1</em>. The functions of these genes in vernalization will be further analyzed.</div></div><div><h3>Significance</h3><div>Wucai is prone to premature bolting and flowering under cold conditions, as vernalization plays a key role in controlling flowering time in Chinese cabbage crops. However, the proteomic basis of vernalization remains poorly understood. In this study, TMT-based proteomic analysis identified DAPs associated with vernalization. Pathway enrichment analysis highlighted key DAPs and their roles in significantly enriched pathways relevant to vernalization. Notably, genes in the flavonoid biosynthesis pathway genes, including <em>VESR1</em>, <em>CH13, CHS1</em>, <em>FHT</em>, and <em>FLS1</em>, respond to vernalization. These findings offer novel insights into the molecular mechanisms underlying flowering time regulation in Wucai.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"314 ","pages":"Article 105398"},"PeriodicalIF":2.8,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143372219","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 phosphoproteomic reveals that the induction of competence modulates protein phosphorylation in Streptococcus pneumonaie","authors":"Jean-Pierre Lavergne ,&nbsp;Adeline Page ,&nbsp;Patrice Polard ,&nbsp;Nathalie Campo ,&nbsp;Christophe Grangeasse","doi":"10.1016/j.jprot.2025.105399","DOIUrl":"10.1016/j.jprot.2025.105399","url":null,"abstract":"<div><div>Competence in the pathogenic bacterium <em>Streptococcus pneumoniae</em> (<em>S. pneumoniae</em>) is a developmental genetic program that is key for natural genetic transformation and consequently bacterial horizontal gene transfer. Phosphoproteomic studies have revealed that protein phosphorylation on serine, threonine and tyrosine residues is a widespread regulatory post-translational modification in bacteria. In this study, we performed quantitative proteomic and phosphoproteomic analyses on <em>S. pneumoniae</em> as a function of competence induction. To calculate peptide abundance ratios between non-competent and competent samples we used dimethyl-tag labeling. Titanium dioxide (TiO2) beads were used for phosphopeptide enrichment and samples were analysed by LC-MS/MS. Our proteome analysis covers approximatively 63 % of the total bacterial protein content, identifying 82 proteins with significantly different abundance ratios, including some not previously linked to competence. 248 phosphopeptides were identified including 47 having different abundance ratios. Notably, the proteins with a change in phosphorylation in competent cells are different from the proteins with a change in expression, highlighting different pathways induced by competence and regulated by phosphorylation. This is the first report that phosphorylation of some proteins is regulated during competence in <em>Streptococcus pneumoniae</em>, a key pathway for the bacteria to evade vaccines or acquire antibiotic resistance.</div></div><div><h3>Significance</h3><div><em>S. pneumoniae</em> is a prominent model for the study of competence that governs the development of natural genetic transformation. The latter largely accounts for the spread of antibiotic resistance and vaccine evasion in pneumococcal isolates. Many proteins specifically expressed during competence have been identified and extensively studied. However, the potential contribution of post-translational modifications, and notably phosphorylation, during the development of competence has never been investigated. In this study, we used a quantitative phosphoproteomic approach to determine both the protein expression and the protein phosphorylation patterns. Comparison of these patterns allows to highlight a series of proteins that are differentially phosphorylated in the two conditions. This result opens new avenues to decipher new regulatory pathways induced by competence and that are potentially key for natural genetic transformation. Interfering with theses regulatory pathways could represent a promising strategy to combat antibiotic resistance in the future.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"315 ","pages":"Article 105399"},"PeriodicalIF":2.8,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143374298","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":"P.1 and P.2 SARS-CoV-2 Brazilian variants activate the unfolded protein response with a time and pathway specificity","authors":"Vinícius de Morais Gomes ,&nbsp;Deivid Martins Santos ,&nbsp;Janaina Macedo-da-Silva ,&nbsp;Lucas C. Lazari ,&nbsp;Rafael Rahal Guaragna Machado ,&nbsp;Ancely Ferreira dos Santos ,&nbsp;Danielle Bastos Araujo ,&nbsp;João Vitor Paccini Coutinho ,&nbsp;Gabriel Santos Arini ,&nbsp;Claudia B. Angeli ,&nbsp;Edmarcia E. de Souza ,&nbsp;Rodolfo F. Marques ,&nbsp;Silvia Beatriz Boscardin ,&nbsp;Carsten Wrenger ,&nbsp;Claudio Romero Farias Marinho ,&nbsp;Danielle B.L. Oliveira ,&nbsp;Edison L. Durigon ,&nbsp;Leticia Labriola ,&nbsp;Livia Rosa-Fernandes ,&nbsp;Giuseppe Palmisano","doi":"10.1016/j.jprot.2025.105397","DOIUrl":"10.1016/j.jprot.2025.105397","url":null,"abstract":"<div><div>COVID-19 is a human respiratory syndrome caused by the infection of the SARS-CoV-2 virus that has a high rate of infection and mortality. Viruses modulate the host machinery by altering cellular mechanisms that favor their replication. One of the mechanisms that viruses exploit is the protein folding and processing of post-translational modifications that occur in the endoplasmic reticulum (ER). When ER function is impaired, there is an accumulation of misfolded proteins leading to endoplasmic reticulum stress (ER stress). To maintain homeostasis, cells trigger an adaptive signaling mechanism called the Unfolded Protein Response (UPR) which helps cells deal with stress, but under severe conditions, can activate the apoptotic cell death mechanism. This study elucidated an activation of a diversity of molecular mechanisms by Brazilian variants of SARS-CoV-2 by a time-resolved and large-scale characterization of SARS-CoV-2-infected cells proteomics and immunoblotting. Furthermore, it was shown that pharmacological UPR modulation could reduce viral release by counteracting the different viral activations of its cellular response. Analysis of human clinical specimens and disease outcomes focusing on ER stress reinforces the importance of UPR modulation as a host regulatory mechanism during viral infection and could point to novel therapeutic targets.</div></div><div><h3>Significance</h3><div>Since the emergence of SARS-CoV-2 and the consequent COVID-19 pandemic, the rapid emergence of variants of this new coronavirus has been a cause for concern since many of them have significantly higher rates of transmissibility and virulence, being called Variants of Concern (VOC). In this work, we studied the VOCs Gamma (P.1) and Zeta (P.2), also known as Brazilian variants. Constant evidence has reported that there are particularities related to each variant of SARS-CoV-2, with different rates of transmissibility, replication and modulation of host biological processes being observed, in addition to the mutations present in the variants. For this reason, this work focused on infections caused by the Brazilian variants of SARS-CoV-2 in different cell lines, in which we were able to observe that the infections caused by the variants induced endoplasmic reticulum stress in the infected cells and activated the UPR pathways, presenting specific modulations of each variant in this pathway. Furthermore, transcriptome analysis of patients revealed a correlation between ER-related genes and COVID-19 progression. Finally, we observed that the use of UPR modulators in host cells decreased viral release of all variants without affecting cell viability. The data presented in this work complement the observations of other studies that aim to understand the pathogenicity of SARS-CoV-2 VOCs and possible new therapeutic strategies, mainly targeting biological processes related to the endoplasmic reticulum.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"315 ","pages":"Article 105397"},"PeriodicalIF":2.8,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143255949","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":"Antibody-free LC-HRMS/MS method for simultaneous quantification of NGAL, CRP and SAA in serum from sepsis patients","authors":"Maxence Derbez-Morin ,&nbsp;Vincent Delatour ,&nbsp;François Fenaille ,&nbsp;Catherine Perrot ,&nbsp;Anne-Marie Dupuy ,&nbsp;Amandine Boeuf ,&nbsp;François Becher","doi":"10.1016/j.jprot.2025.105396","DOIUrl":"10.1016/j.jprot.2025.105396","url":null,"abstract":"<div><div>Liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS/MS) is a valuable alternative to ligand-binding assay, enabling specific and accurate quantification of protein biomarkers. We developed a robust antibody-free LC-HRMS/MS method for the multiplex quantification of three sepsis biomarkers in serum: NGAL, CRP and SAA. The method was thoroughly optimized from sample preparation to LC-HRMS/MS analysis, alongside the calibration. Specifically, a modified trichloroacetic acid/isopropanol protein precipitation procedure combined with an optimized Parallel Reaction Monitoring acquisition allowed the quantification of the low abundant NGAL at ng/mL levels. While reference material and reference measurement procedure were available for CRP, no such standards existed for NGAL and SAA. Well-characterized peptide calibrators traceable to the international system of units were developed for NGAL and SAA. The method demonstrated suitable trueness and precision for the quantification of NGAL, CRP, and SAA with coefficients of variation (CV%) ranging from 1.6 % to 22.4 % and bias between −12.6 % and +18.0 %. Successful application to pooled serum samples illustrated the method's effectiveness. Our results pave the way toward the development of reference systems for additional sepsis biomarkers.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"314 ","pages":"Article 105396"},"PeriodicalIF":2.8,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143123166","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":"Shotgun and targeted proteomics of Mycolicibacterium smegmatis highlight the role of arginine phosphorylation in the functional adaptation to its environment","authors":"Danyang Xu ,&nbsp;Jiahui Shi ,&nbsp;Songhao Jiang ,&nbsp;Shuhong Meng ,&nbsp;Zhiyuan Cheng ,&nbsp;Wenhui Wu ,&nbsp;Lei Chang ,&nbsp;Yuping Xie ,&nbsp;Yuan Gao ,&nbsp;Yu Xue ,&nbsp;Yao Zhang","doi":"10.1016/j.jprot.2025.105388","DOIUrl":"10.1016/j.jprot.2025.105388","url":null,"abstract":"<div><div>Although the phosphorylation of serine (S), threonine (T), and tyrosine (Y) is well-established, arginine phosphorylation (pR) has recently garnered significant attention due to its crucial role in bacteria pathogenicity and stress response. <em>Mycolicibacterium smegmatis</em>, a nonpathogenic surrogate of <em>Mycobacterium tuberculosis</em>, serves as a model for studying mycobacterial pathogenesis. A recent proteomics study identified six pR proteins in <em>M. smegmatis</em>. To gain a more comprehensive understanding, we performed pR profiling using mass spectrometry in combination with two distinct phosphopeptide enrichment strategies: titanium-immobilized metal ion affinity chromatography (Ti⁴⁺-IMAC) and Fe-NTA cartridge purification. This approach led to the identification of 1192 shared pR peptides with 1553 pR sites in <em>M. smegmatis</em> following both competitive and non-competitive scoring assessments for pR and pS/T/Y. Further stringent filtering through manual verification resulted in 58 high-confident pR sites across 57 proteins. These confirmed pR-proteins are functionally related, particularly in DNA binding and ATP binding. Alterations in the modification of three pR sites during the logarithmic and stationary phases at the phosphorylation level, but not at the total cell protein level, further suggest the role of pR in the bacterium's functional adaptation to its environment.</div></div><div><h3>Significance</h3><div>Our findings reveal that pR proteins are prevalent and play roles in DNA-binding and ATP-binding activities, providing insights into the broader biological functions of pR peptides in other genetically diverse species. The reliable identification of bacterial pR events in <em>M. smegmatis</em> not only propels the study of pR within the realm of proteomics but also paves the way for exploring its detailed function in bacteria.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"314 ","pages":"Article 105388"},"PeriodicalIF":2.8,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143066363","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}