Journal of proteomics最新文献

{"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}

{"title":"New potential susceptibility factors contributing to tomato bacterial spot disease","authors":"Lucas José de Sousa ,&nbsp;Ivonaldo Reis Santos ,&nbsp;Isabelle Souza Luz ,&nbsp;Daiane Gonzaga Ribeiro ,&nbsp;Osmundo Brilhante de Oliveira-Neto ,&nbsp;Wagner Fontes ,&nbsp;Luiz Eduardo Bassay Blum ,&nbsp;Angela Mehta","doi":"10.1016/j.jprot.2025.105387","DOIUrl":"10.1016/j.jprot.2025.105387","url":null,"abstract":"<div><div>The label-free shotgun proteomics analysis carried out in this study aimed to understand the molecular mechanisms that contribute towards tomato susceptibility to <em>Xanthomonas euvesicatoria</em> pv. <em>perforans</em> (<em>Xep</em>). To achieve this, comparative proteomics was performed on susceptible inoculated plants with the bacterium and the control group (saline solution) at 24 and 48 h after inoculation (hai). The results revealed that most of the identified proteins showed increased abundance in the infected group and were classified into different gene ontology groups. Eight of these proteins were related to susceptibility in other pathosystems, suggesting their potential involvement in the development of bacterial spot in tomato. Some of these proteins are involved in the negative regulation of salicylic acid, PR proteins and reactive oxygen species (ROS), as well as contributing to the acquisition of sugars by the pathogen. The results obtained in this study provided us with valuable information for understanding the molecular mechanisms that lead to tomato susceptibility to <em>Xep</em> and will help in developing tomato cultivars resistant to bacterial spot.</div></div><div><h3>Significance</h3><div>Our proteomic study of tomato plants during infection by <em>Xep</em> allowed for the identification of potential proteins that contribute to bacterial spot tomato disease development. These proteins can act in different ways to favor the pathogen, such as the negative modulation of phytohormones involved in plant defense, the inhibition of PR proteins and reactive oxygen species, as well as to collaborate in the acquisition of sugar for pathogen nutrition.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"314 ","pages":"Article 105387"},"PeriodicalIF":2.8,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143039406","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":"2025: A historic moment for proteomics!","authors":"Jean Armengaud","doi":"10.1016/j.jprot.2025.105385","DOIUrl":"10.1016/j.jprot.2025.105385","url":null,"abstract":"","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"313 ","pages":"Article 105385"},"PeriodicalIF":2.8,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142978902","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":"Effects of periodontal disease on the proteomic profile of the periodontal ligament","authors":"Maria Eduarda Scordamaia Lopes ,&nbsp;Camila Chierici Marcantonio ,&nbsp;Cristiane Ribeiro Salmon ,&nbsp;Luciana Souto Mofatto ,&nbsp;Francisco Humberto Nociti Junior ,&nbsp;Sigrun Eick ,&nbsp;James Deschner ,&nbsp;Joni Augusto Cirelli ,&nbsp;Andressa Vilas Boas Nogueira","doi":"10.1016/j.jprot.2025.105384","DOIUrl":"10.1016/j.jprot.2025.105384","url":null,"abstract":"<div><div>Periodontal disease affects over 1 billion people globally. This study investigated how periodontitis affects the protein profile of the periodontal ligament (PDL) in rats. Eight Holtzman rats were divided into control and experimental periodontitis groups. The PDL was isolated using laser capture microdissection and protein extracts were analyzed by mass spectrometry. Data analysis utilized specialized software, and Gene Ontology enrichment analysis identified significant protein functions. The data are available <em>via</em> ProteomeXchange with identifier <span><span>PXD055817</span><svg><path></path></svg></span>. Proteins such as SerpinB1, C5, and Lgals3 were validated through immunohistochemistry, and their gene expression was examined in an <em>in vitro</em> human PDL cell line. This study identified 1326 proteins, with 156 unique to the control group, 294 unique to the periodontitis group, and 876 common to both groups. Enrichment analysis revealed that proteins associated with the regulation of enzyme activity and RNA binding were significantly represented in the periodontitis group. There were increased levels of SerpinB1, C5, and Lgals3 in the periodontitis group based on proteomic and immunohistochemical analyses. Furthermore, these targets showed increased gene expression in stimulated human PDL cells. This study provides insights into the periodontitis-related alterations in the protein composition of the PDL and PDL cells, identifying both novel and previously known disease-associated proteins.</div></div><div><h3>Significance</h3><div>The periodontal ligament plays a crucial role in oral functions by providing structural support to the tooth. Due to the presence of undifferentiated mesenchymal cells, research into its regenerative capacity is ongoing. Pathological conditions can affect these functions and protein composition. Currently, there is a lack of comprehensive research specifically focusing on evaluating the periodontal ligament in both healthy and diseased states. This pioneering study screened for protein alterations and the mechanisms related to periodontitis. The possibility of using proteomic analysis to evaluate the protein alterations that occur in periodontitis, a disease with a high global incidence, could provide therapeutic targets and new biomarkers for future clinical studies.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"314 ","pages":"Article 105384"},"PeriodicalIF":2.8,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142971407","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":"The effect of thermal stress on the X-organ/sinus gland proteome of the estuarine blue crab Callinectes sapidus during the intermolt and premolt stages","authors":"José Thalles Lacerda ,&nbsp;Daniela Dantas David ,&nbsp;Ana Maria L. Castrucci","doi":"10.1016/j.jprot.2025.105382","DOIUrl":"10.1016/j.jprot.2025.105382","url":null,"abstract":"<div><div>Survival of brachyuran crabs is temperature-dependent and thermal stress promotes changes during molting. We aimed to decipher the impact of thermal stresses on the X-organ/sinus gland (XO/SG) complex, a temperature-sensitive neuroendocrine tissue involved in the molting regulation of <em>Callinectes sapidus</em> during the intermolt and premolt phases. We employed a proteogenomic approach using specimens subjected to control (24 °C), cold (19 °C), and heat (29 °C) temperatures. A total of 1463 protein groups with at least two unique peptides were identified and quantified. <em>C. sapidus</em> in the premolt stage exposed to the cold condition exhibited a proteome closely resembling that of the intermolt stage, as evidenced by measurements of circulating ecdysteroid levels. Compared to the intermolt at control temperature, the premolt stage exhibited increased energy metabolism, structural changes in the cuticle mediated by chitin metabolism and glycoproteins, biosynthesis of methyl farnesoate (MF), and elevated tissue levels of molt-inhibiting hormone (MIH) and crustacean hyperglycemic hormone (CHH), indicating lower secretion rates. Heat temperature (29 °C) seems to induce mitochondrial metabolism in the intermolt XO/SG, while cold temperature elicited a delayed molt cycle in the premolt phase, marked by reduced tissue levels of CHH, indicating increased secretion and Y-organ (YO) inhibition, and decreased MF production (reduced YO stimulation).</div></div><div><h3>Significance statement</h3><div>Temperature plays a pivotal role in regulating the metabolism, growth, molting, reproduction, and survival of crabs, such as the blue crab (<em>Callinectes sapidus</em>). Despite the blue crab's significance on both economic and ecological realms, there has been a notable lack of molecular information related to this species and therefore a gap in our knowledge of the blue crab's molecular makeup and genetic diversity. This research established a comprehensive proteome landscape to elucidate the molecular and functional changes in the XO/SG complex involved in the molting process of <em>C. sapidus</em>, and how thermal stresses significantly influence biotransformation processes. Utilizing a proteogenomics approach with multi-round homologous database analysis, we have generated a highly accurate protein repertoire with at least two unique peptide of XO/SG tissue proteome. This resource will be invaluable for future molecular analyses of this species. Our findings demonstrate that thermal stresses induced specific modifications in the XO/SG tissue, depending on the molt cycle phase. Temperature-mediated responses influences the biological processes, enhancing the functional morphogenesis and comprehensive metabolic adaptations on molting cycle supported by a relationship between the XO/SG tissue proteome and circulating ecdysteroid levels.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"313 ","pages":"Article 105382"},"PeriodicalIF":2.8,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142971408","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteome changes during the germination and early seedling development of carnauba palm (Copernicia prunifera) under skotomorphogenic conditions","authors":"Sheheryar Sheheryar ,&nbsp;Francisco A.S.A. Carioca ,&nbsp;Ítalo A.C. Coutinho ,&nbsp;Yara M. Silva ,&nbsp;Gilberto B. Domont ,&nbsp;Fábio C.S. Nogueira ,&nbsp;Francisco A.P. Campos","doi":"10.1016/j.jprot.2025.105386","DOIUrl":"10.1016/j.jprot.2025.105386","url":null,"abstract":"<div><div>We analyze the proteome changes during the development of the carnauba palm (<em>Copernicia prunifera</em>) seedlings under skotomorphogenic conditions, by separating the embryo into its two components: haustorium (HA) and cotyledonary petiole (CP) and established the descriptive and quantitative proteomes of these tissues across four developmental stages. 5205 proteins were identified in HA and 6028 in CP. These proteomes are rich in proteins known to maintain the skotomorphogenic state, and in a complete set of proteins involved in cellular respiration and biosynthesis of secondary metabolites. The quantitative analysis employing a label-free approach revealed that 583 proteins in HA and 383 in CP were differentially abundant, with 251 proteins shared between the datasets. The results showed that HA participates in the digestion of food reserves present in HA itself and in the endosperm, acting as a conduit of nitrogen and carbon sources for the growing embryo axis. Among the differentially abundant proteins in the CP, we identified the presence of proteins from the cellular metabolism and proteins involved in the hydrolysis of food reserves such as starch and proteins. This indicates that the CP, in addition to the endosperm and HA, serves as a source of food reserves for the embryo axis.</div></div><div><h3>Significance</h3><div>Our results also reveal the differential regulation of specific proteins involved in reactive oxygen species scavenging, cell wall remodeling, respiratory metabolism, and protein repair in seeds and seedlings of <em>C. prunifera</em>. These findings have broad implications for understanding the energy metabolism that drives the transition from seed to seedling.</div><div>For this study, we employed state-of-the-art proteomic techniques, including quantitative mass spectrometry and bioinformatic analysis, that allowed us to create a large dataset that will be a valuable resource for future research on the physiological and biochemical aspects of skotomorphogenesis, photomorphogenesis, and the transition between these states.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"313 ","pages":"Article 105386"},"PeriodicalIF":2.8,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142971131","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 combined proteomic and metabolomic analysis of the early aborted embryonic tissues with maternal COVID-19 infection","authors":"Ling Ling ,&nbsp;Guiqin Xu ,&nbsp;Miao Fang ,&nbsp;Jianquan Chen ,&nbsp;Ming Gong ,&nbsp;TianMing Wang ,&nbsp;Rong Ju ,&nbsp;Sipei Nie","doi":"10.1016/j.jprot.2025.105383","DOIUrl":"10.1016/j.jprot.2025.105383","url":null,"abstract":"<div><div>COVID-19 still spreads worldwide, and repeated infections are hard to avoid. Maternal infection during pregnancy is associated with adverse maternal and neonatal outcomes. Our study used a multi-omics profiling method to explore the proteome and metabolome alteration in early embryonic development after COVID-19 infection. A total of 30 chorionic tissues after artificial abortion (15 infection and 15 no-infection samples) were collected, and the UHPLC-MS/MS and LC-MS/MS were applied in the present study. As a result, 311 significantly differentially expressed proteins were identified. The function annotations revealed that the thermogenesis pathway is the most significantly enriched signaling pathway; PRKAG2, IGF1R, and RPS6KB2 were identified as the hub proteins. There were 359 metabolites significantly altered after infection. The functional annotations revealed that amino acid metabolism was significantly affected, especially beta-alanine metabolism, glutamate metabolism, and histidine metabolism pathways. The metabolites in ovarian steroidogenesis showed a down-regulating trend in the infection group. Finally, we combined the results of proteins and metabolomics analysis. The biosynthesis of the cofactors pathway was identified as significantly enriched in both proteomics and metabolomics datasets. Our findings provide a network of protein regulation and metabolite perturbation during early embryonic development with COVID-19 infection. Our findings can provide valuable insights for further exploration of the complex mechanism of COVID-19-associated pregnancy complications and outcomes.</div></div><div><h3>Significance</h3><div>COVID-19 has developed into the most prominent and deadliest pandemic respiratory disease in the world, and repeated infections are complicated to avoid. COVID-19 infection during pregnancy increases the risk of adverse maternal and neonatal outcomes, such as preterm birth and stillbirth. However, previous studies mainly focused on its effect on pregnant women, such as the clinical characteristics and gestation outcomes. There is no relevant report about the effects of virus infection on embryos in early pregnancy. The effects of COVID-19 infection changes of the proteins and metabolites during early embryonic development are undefined. Our findings provide an association between protein regulation, metabolite perturbation, and COVID-19 infection, which can provide valuable insights for further exploration of the complex mechanism COVID-19 COVID-19-associated pregnancy complications and adverse pregnancy outcomes.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"313 ","pages":"Article 105383"},"PeriodicalIF":2.8,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142965497","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}