Journal of proteomics最新文献

{"title":"Multi-organ proteome reveals different nursing ability between two honeybee srocks","authors":"Ronghua Wang ,&nbsp;Jianke Li ,&nbsp;Lifeng Meng","doi":"10.1016/j.jprot.2025.105417","DOIUrl":"10.1016/j.jprot.2025.105417","url":null,"abstract":"<div><div>High royal jelly production is an adaptive reproductive investment syndrome in honey bees that enhances their nursing ability to queen bee larvae. However, the biological basis of this reproduction investment at the multi-organ level remains elusive. In this study, proteome across 11 organs of two bee stocks: high royal jelly production bees (RJBs) and Italian bees (ITBs) was compared. Our analysis revealed significant differences in protein expression profiles in brain, fat body, mandibular gland, and Malpighian tubule, highlighting their crucial roles in regulating royal jelly secretion in RJBs. The increased energy turnover, protein synthesis, and lipid synthesis observed in RJBs compared to ITBs highlight their enhanced metabolic activity, which is essential for the robust secretion of royal jelly in RJBs. The elevated abundance of major royal jelly proteins (MRJPs), hexamerins, and vitellogenin suggests their critical contributions to the nutritional and material requirement necessary for royal jelly secretion. Furthermore, the high level of vitellogenin and juvenile hormone esterase may suppress juvenile hormones, which contribute to a strong royal jelly secretion and sensitivity of RJBs to larval pheromones relative to ITBs. This comprehensive dataset contributes to a better understanding of nursing behavior and reproductive investment in honey bees.</div><div>Significiance.</div><div>The royal jelly secretion syndrome is a colony level social trait dominated by the intricate interplay of multiple organs. However, previous studies have primarily focused on individual organs. In this study, the proteome of 11 organs was compared between high royal jelly production bees (RJBs) and Italian bees (ITBs) to provide knowledge on how multiple organs cooperate to boost the elevated royal jelly production by RJBs. Nutrition supply was sufficient at multiple organs of RJBs when compared to ITBs, indicating that nutrition plays an essential role in boosting energy metabolism, protein and lipid synthesis, and directly contributes to the amount of royal jelly secretion. The high level of secretion of storage proteins, such as MRJPs, hex, and vitellogenin, provides sufficient nutrition and material for royal jelly secretion. Moreover, the higher levels of vitellogenin and juvenile hormone esterase may suppress juvenile hormone synthesis, and contributing to stronger sense of RJBs to larval pheromone relative to ITBs. This suggests that nutrition can influence the hormone levels and sensory abilities of RJBs nurse bees to promote their royal jelly secretion ability. The reported data provide insights into the systematic regulation strategy of honeybee nursing behavior and reproductive investment.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"316 ","pages":"Article 105417"},"PeriodicalIF":2.8,"publicationDate":"2025-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143557274","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":"Integrative transcriptomic, proteomic, biochemical and neutralization studies on the venom of Micrurus ephippifer","authors":"Vanessa Zarzosa ,&nbsp;Edgar Neri-Castro ,&nbsp;Bruno Lomonte ,&nbsp;Julián Fernández ,&nbsp;Gibrán Rodríguez-Barrera ,&nbsp;Bruno Rodríguez-López ,&nbsp;Audrey Michelle Rodríguez-Solís ,&nbsp;Alejandro Olvera-Rodríguez ,&nbsp;Melisa Bénard-Valle ,&nbsp;Anthony Saviola ,&nbsp;Uri O. García-Vázquez ,&nbsp;Leonardo Fernández-Badillo ,&nbsp;Nallely Morales-Capellán ,&nbsp;Miguel Borja ,&nbsp;Fernando Zamudio ,&nbsp;Alejandro Alagón","doi":"10.1016/j.jprot.2025.105416","DOIUrl":"10.1016/j.jprot.2025.105416","url":null,"abstract":"<div><div>Species of the genus <em>Micrurus</em> belong to the family Elapidae and possess venoms of significant clinical importance. This study presents an analysis of the venom composition of <em>Micrurus ephippifer</em>, employing transcriptomic and proteomic methodologies. A total of 2885 venom gland transcripts were assembled, of which 42 were identified as toxins. Transcripts for three-finger toxins (3FTx) were the most abundant (80.7 %), followed by PLA₂ transcripts (16.3 %). Tryptic peptide sequences obtained through bottom-up shotgun MS/MS venom analysis were assigned to 46 distinct proteins in the SwissProt/UniProt database, of which 23 belong to the 3FTx family. Peptide spectral matching against the venom gland transcriptome database identified 24 proteins, 12 of which correspond to 3FTx, and three belong to PLA₂. Venom decomplexation by RP-HPLC followed by N-terminal amino acid sequencing of fractions allowed an estimation of the relative abundance of protein families, indicating that 3FTx comprise over 50 % of the venom. The identified toxic fractions displayed distinct lethality profiles in mice, with certain combinations exhibiting enhanced toxicity, very similar to what has been reported with Brownitoxin-I, with only the PLA₂ sequence showing similarity. Our results emphasize the importance of integrating transcriptomic and proteomic approaches to understand venom diversity and its implications for antivenom development.</div></div><div><h3>Significance</h3><div>Mexico ranks first in the Americas in snake venom diversity. Paradoxically, very little is known about the composition of coral snake venoms, and <em>Micrurus ephippifer</em> is a clear example of this gap, as nothing was known about its venom composition. This type of study provides valuable information that helps fill these knowledge gaps. This study presents the second report of coral snake venoms containing a complex of phospholipase A₂ and a three-finger toxin, offering important data that, with further research, will contribute to understanding venom evolution and evaluating the efficacy of antivenoms.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"316 ","pages":"Article 105416"},"PeriodicalIF":2.8,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143537309","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":"Proteomics and phosphoproteomics analysis of acute pancreatitis alleviated by forsythoside B","authors":"Linxiao Sun ,&nbsp;Hongmei Li ,&nbsp;Haiyan Zhang ,&nbsp;Yinchu Guo ,&nbsp;Cheng Wang ,&nbsp;Shichao Chen","doi":"10.1016/j.jprot.2025.105414","DOIUrl":"10.1016/j.jprot.2025.105414","url":null,"abstract":"&lt;div&gt;&lt;div&gt;Acute pancreatitis (AP) is a common acute abdominal condition in clinical practice, associated with high morbidity and mortality rates. Forsythia constitutes a component of traditional Chinese medicinal decoctions used for clinical AP treatment; however, the efficacy of its active monomer in treating AP has yet to be completely substantiated. Here, we engineered an AP cell and mouse model by administering a combination of caerulein and LPS. &lt;em&gt;In vitro&lt;/em&gt; experiments utilizing AR42J cells demonstrated that forsythoside B (FST·B) was the most effective monomer in mitigating cellular inflammation. Subsequently, a comprehensive evaluation of FST·B concentrations and efficacy was performed in animal models. Next Mass spectrometry analysis of pancreatic from AP mice treated with 50 mg/kg FST·B was conducted to elucidate its primary regulatory molecular signaling and key targets. FST·B effectively mitigated pathological damage in mice with acute pancreatitis, leading to a reduction in the expression of inflammatory cytokines in both pancreatic tissue and serum. Proteomics and phosphoproteomic profiles revealed that FST·B significantly enhanced the level of oxidative phosphorylation and spliceosome pathway in the AP mice. This research provides initial evidence of the regulatory molecular signals and targets of FST·B in AP, laying a potential foundation for its clinical use in treating AP.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Significance&lt;/h3&gt;&lt;div&gt;Acute pancreatitis (AP) is a common acute abdominal condition in clinical practice, associated with high morbidity and mortality rates, and the global incidence of AP has increased by approximately 25 % over the past 15 years. Despite the complexity of AP's causes and the high susceptibility of proteins to degradation during lesions, systems biology studies, such as proteomics, have been limited in investigating the molecular mechanisms involved in its pharmacological treatment. Forsythoside B, a phenylethanol glycoside isolated from the air-dried fruit of forsythia, is a traditional oriental anti-inflammatory drug commonly used in clinical practice. We demonstrated in the AP mouse model that forsythoside B can alleviate pancreatic inflammatory damage &lt;em&gt;in vivo&lt;/em&gt;. To elucidate the molecular mechanisms underlying the anti-inflammatory effect of forsythoside B, a comprehensive proteomic and phosphoproteomic analysis was conducted on AP mice models prior to and subsequent to forsythoside B intervention. Finally, 1640 significantly differentially expressed proteins, 1448 significantly differentially expressed phosphoproteins corresponding to 2496 significantly differentially expressed phosphosites were identified. Functional analysis revealed that forsythoside B significantly enhanced the level of oxidative phosphorylation in the AP mice in proteomic profiles, and the spliceosome pathway at the phosphorylation level was significantly affected by forsythoside B. This research provides initial evidence of the regul","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"315 ","pages":"Article 105414"},"PeriodicalIF":2.8,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143523797","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":"Trypanosoma cruzi cell cycle progression exhibits minimal variation in histone PTMs with unique histone H4 acetylation pattern","authors":"A.P.J. Menezes ,&nbsp;A.M. Silber ,&nbsp;M.C. Elias ,&nbsp;J.P.C. da Cunha","doi":"10.1016/j.jprot.2025.105413","DOIUrl":"10.1016/j.jprot.2025.105413","url":null,"abstract":"&lt;div&gt;&lt;div&gt;Histones are crucial proteins in eukaryotic cells that undergo extensive posttranslational modifications (PTMs) such as methylation, acetylation, and phosphorylation, which are associated to chromatin structure, gene expression, DNA damage/repair and cell cycle. In &lt;em&gt;Trypanosoma cruzi&lt;/em&gt;, the primary sequence of histones differs from that of other eukaryotes. Despite this, they display a vast range of PTMs, though their modulation throughout the cell cycle remains largely unexplored. In this study, we investigated the dynamic modulation of histone PTMs across G1/S, S, and G2/M phases of &lt;em&gt;T. cruzi&lt;/em&gt; cell cycle using hydroxyurea- synchronized parasites. We applied a workflow that included histone derivatization, trypsin digestion followed by a high-resolution mass spectrometry and data independent analysis. Quantitative analysis of 141 histone peptide isoforms revealed that there are only minor variations in histone PTM levels throughout the cell cycle. The H3K76 trimethylation remained predominant throughout all phases, with an increase in monomethylation during G2/M. Additionally, hyperacetylation of the N-terminal region of histone H4 was observed, particularly at lysine residues 2, 5, and 10, suggesting their importance in cell cycle progression. Striking, acetylation of histone H4 at K2 and K5 increases during the S-phase, mirroring the H4K5acK12ac pattern observed in mammals, which are related to histone nuclear import and chromatin deposition.&lt;/div&gt;&lt;div&gt;Overall, the results suggest that the &lt;em&gt;T. cruzi&lt;/em&gt; cell cycle maintains stable global levels of histone PTMs, relying on variations in only a few specific PTMs. Further investigations are warranted to elucidate the functional significance of these PTMs and their impact on cell cycle regulation and chromatin dynamics in &lt;em&gt;T. cruzi&lt;/em&gt;.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Significance&lt;/h3&gt;&lt;div&gt;Histone posttranslational modifications (PTMs) are key regulators of chromatin architecture and cellular processes such as gene expression and cell cycle control. In &lt;em&gt;Trypanosoma cruzi&lt;/em&gt;, the etiological agent of Chagas disease, histones have a distinct primary structure compared to other eukaryotes, yet they display a wide variety of PTMs. This study provides a comprehensive analysis of histone PTM dynamics across the G1/S, S, and G2/M phases of the &lt;em&gt;T. cruzi&lt;/em&gt; cell cycle, revealing that global histone PTM levels remain largely stable, with variations in a few specific marks. Notably, the study highlights the increased acetylation of histone H4 at lysines 2 and 5 during the S-phase, contrasting with the well-conserved acetylation at lysines 5 and 12 observed in mammals involved in nuclear import and chromatin assembly. These findings underscore the evolutionary divergence and functional specificity of histone modifications and provide a foundation for further investigations into their roles in parasite biology, with potential implications for understanding chromatin dynamics and i","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"315 ","pages":"Article 105413"},"PeriodicalIF":2.8,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143511241","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":"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}