Yunbo Kan , Shuyu Xie , Yewen Sun , Tong Ye , Yunxu Bian , Fang Guo , Mingya Zhang , Tianxian Liu , Tianqi Liu , Jing Ji , Bin Liu , Minjia Tan , Jun-Yu Xu
{"title":"Substrate and functional characterization of the lysine acetyltransferase MsKat and deacetylase MsCobB in Mycobacterium smegmatis","authors":"Yunbo Kan , Shuyu Xie , Yewen Sun , Tong Ye , Yunxu Bian , Fang Guo , Mingya Zhang , Tianxian Liu , Tianqi Liu , Jing Ji , Bin Liu , Minjia Tan , Jun-Yu Xu","doi":"10.1016/j.jprot.2024.105177","DOIUrl":"https://doi.org/10.1016/j.jprot.2024.105177","url":null,"abstract":"<div><p>Tuberculosis (TB) is a serious cause of infectious death worldwide. Recent studies have reported that about 30% of the <em>Mtb</em> proteome was modified post-translationally, indicating that their functions are essential for drug resistance, mycobacterial survival, and pathogenicity. Among them, lysine acetylation, reversibly regulated by acetyltransferase and deacetylase, has important roles involved in energy metabolism, cellular adaptation, and protein interactions. However, the substrate and biological functions of these two important regulatory enzymes remain unclear. Herein, we utilized the non-pathogenic <em>M. smegmatis</em> strain as a model and systematically investigated the dynamic proteome changes in response to the overexpressing of <em>Ms</em>Kat/<em>Ms</em>CobB in mycobacteria. A total of 4179 proteins and 1236 acetylated sites were identified in our data. Further analysis of the dynamic changes involved in proteome and acetylome showed that <em>Ms</em>Kat/<em>Ms</em>CobB played a regulatory role in various metabolic pathways and nucleic acid processes. After that, the quantitative mass spectrometric method was utilized and proved that the AMP-dependent synthetase, Citrate synthase, ATP-dependent specificity component of the Clp protease, and ATP-dependent DNA/RNA helicases were identified to be the substrates of <em>Ms</em>Kat. Overall, our study provided an important resource underlying the substrates and functions of the acetylation regulatory enzymes in mycobacteria.</p></div><div><h3>Significance</h3><p>In this study, we systematically analyzed the dynamic molecular changes in response to the <em>Ms</em>Kat/<em>Ms</em>CobB overexpression in mycobacteria at proteome and lysine acetylation level by using a TMT-based quantitative proteomic approach. Pathways related with glycolysis, degradation of branched chain amino acids, phosphotransferase system were affected after disturbance of the two regulates enzymes involved in lysine acetylation. We also proved that AMP-dependent synthetase Clp protease, ATP-dependent DNA/RNA helicases and citrate synthase was the substrate of <em>Ms</em>Kat according to our proteomic data and biological validation. Together, our study underlined the substrates and functions of the acetylation regulatory enzymes in mycobacteria.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140640776","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":"Proteomic and metabolomic insights into seed germination of Ferula assa-foetida","authors":"Ashwani Punia , Manglesh Kumari , Monika Chouhan , Vishal Saini , Robin Joshi , Ashok Kumar , Rajiv Kumar","doi":"10.1016/j.jprot.2024.105176","DOIUrl":"https://doi.org/10.1016/j.jprot.2024.105176","url":null,"abstract":"<div><p>Cold stratification is known to affect the speed of seed germination; however, its regulation at the molecular level in <em>Ferula assa-foetida</em> remains ambiguous. Here, we used cold stratification (4 °C in the dark) to induce germination in <em>F. assa-foetida</em> and adopted a proteomic and metabolomic approach to understand the molecular mechanism of germination. Compared to the control, we identified 209 non-redundant proteins and 96 metabolites in germinated <em>F. assa-foetida</em> seed. Results highlight the common and unique regulatory mechanisms like signaling cascade, reactivation of energy metabolism, activation of ROS scavenging system, DNA repair, gene expression cascade, cytoskeleton, and cell wall modulation in <em>F. assa-foetida</em> germination. A protein-protein interaction network identifies 18 hub protein species central to the interactome and could be a key player in <em>F. assa-foetida</em> germination. Further, the predominant metabolic pathways like glucosinolate biosynthesis, arginine and proline metabolism, cysteine and methionine metabolism, aminoacyl-tRNA biosynthesis, and carotenoid biosynthesis in germinating seed may indicate the regulation of carbon and nitrogen metabolism is prime essential to maintain the physiology of germinating seedlings. The findings of this study provide a better understanding of cold stratification-induced seed germination, which might be utilized for genetic modification and traditional breeding of <em>Ferula assa-foetida.</em></p></div><div><h3>Significance</h3><p>Seed germination is the fundamental checkpoint for plant growth and development, which has ecological significance. <em>Ferula assa-foetida</em> L., commonly known as “asafoetida,” is a medicinal and food crop with huge therapeutic potential. To date, our understanding of <em>F. assa-foetida</em> seed germination is rudimentary. Therefore, studying the molecular mechanism that governs dormancy decay and the onset of germination in <em>F. assa-foetida</em> is essential for understanding the basic principle of seed germination, which could offer to improve genetic modification and traditional breeding.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140551490","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}
Jeremy Altman , Shan Bai , Sharad Purohit , John White , Dennis Steed , Su Liu , Diane Hopkins , Jin-Xiong She , Ashok Sharma , Wenbo Zhi
{"title":"A candidate panel of eight urinary proteins shows potential of early diagnosis and risk assessment for diabetic kidney disease in type 1 diabetes","authors":"Jeremy Altman , Shan Bai , Sharad Purohit , John White , Dennis Steed , Su Liu , Diane Hopkins , Jin-Xiong She , Ashok Sharma , Wenbo Zhi","doi":"10.1016/j.jprot.2024.105167","DOIUrl":"https://doi.org/10.1016/j.jprot.2024.105167","url":null,"abstract":"<div><p>Diabetic kidney disease (DKD) poses a significant health challenge for individuals with diabetes. At its initial stages, DKD often presents asymptomatically, and the standard for non-invasive diagnosis, the albumin-creatinine ratio (ACR), employs discrete categorizations (normal, microalbuminuria, macroalbuminuria) with limitations in sensitivity and specificity across diverse population cohorts. Single biomarker reliance further restricts the predictive value in clinical settings. Given the escalating prevalence of diabetes, our study uses proteomic technologies to identify novel urinary proteins as supplementary DKD biomarkers. A total of 158 T1D subjects provided urine samples, with 28 (15 DKD; 13 non-DKD) used in the discovery stage and 131 (45 DKD; 40 pDKD; 46 non-DKD) used in the confirmation. We identified eight proteins (A1BG, AMBP, AZGP1, BTD, RBP4, ORM2, GM2A, and PGCP), all of which demonstrated excellent area-under-the-curve (AUC) values (0.959 to 0.995) in distinguishing DKD from non-DKD. Furthermore, this multi-marker panel successfully segregated the most ambiguous group (microalbuminuria) into three distinct clusters, with 80% of subjects aligning either as DKD or non-DKD. The remaining 20% exhibited continued uncertainty. Overall, the use of these candidate urinary proteins allowed for the better classification of DKD and offered potential for significant improvements in the early identification of DKD in T1D populations.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140539386","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":"Use of data-independent acquisition mass spectrometry to identify an objective serum indicator of the need for osteoporotic therapeutic intervention","authors":"Yusuke Nakai , Ken Kumagai , Yoko Ino , Tomoko Akiyama , Kayano Moriyama , Yuriko Takeda , Kenji Egashira , Takashi Ohira , Akihide Ryo , Tomoyuki Saito , Yutaka Inaba , Hisashi Hirano , Yayoi Kimura","doi":"10.1016/j.jprot.2024.105166","DOIUrl":"https://doi.org/10.1016/j.jprot.2024.105166","url":null,"abstract":"<div><p>Osteoporosis is characterized by weakened bone microstructure and loss of bone mass. Current diagnostic criteria for osteoporosis are based on the T-score, which is a measure of bone mineral density. However, osteoporotic fragility fractures can occur regardless of the T-score, underscoring the need for additional criteria for the early detection of patients at fracture risk. To identify indicators of reduced bone strength, we performed serum proteomic analysis using data-independent acquisition mass spectrometry with serum samples from two patient groups, one with osteoporosis but no fractures and the other with osteopenia and fragility fractures. Collective evaluation of the results identified six serum proteins that changed to a similar extent in both patient groups compared with controls. Of these, extracellular matrix protein 1 (ECM1), which contributes to bone formation, showed the most significant increase in serum levels in both patient groups. An ELISA-based assay suggested that ECM1 could serve as a serum indicator of the need for therapeutic intervention; however, further prospective studies with a larger sample size are necessary to confirm these results. The present findings may contribute to the provision of early and appropriate therapeutic strategies for patients at risk of osteoporotic fractures.</p></div><div><h3>Significance</h3><p>This study aimed to identify objective serum indicators of the need for therapeutic intervention in individuals at risk of osteoporotic fracture. Comprehensive proteome analyses of serum collected from patients with osteoporosis but no fractures, patients with osteopenia and fragility fractures, and controls were performed by data-independent acquisition mass spectrometry. Collective evaluation of the proteome analysis data and ELISA-based assays identified serum ECM1 as a potential objective marker of the risk of fragility fractures in patients with osteoporosis or osteopenia. The findings are an important step toward the development of appropriate bone health management methods to improve well-being and maintain quality of life.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1874391924000988/pdfft?md5=8d1a739e3a06e7234e652e4063c10980&pid=1-s2.0-S1874391924000988-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140539385","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}
Jorge Peinado-Izaguerri , Alexander Corbishley , Eduardo Zarzuela , Blanca Pina-Beltrán , Francesca Riva , Dorothy E.F. McKeegan , Maureen Bain , Javier Muñoz , Mangesh Bhide , Mark McLaughlin , Tom Preston
{"title":"Effect of an immune challenge and two feed supplements on broiler chicken individual breast muscle protein synthesis rate","authors":"Jorge Peinado-Izaguerri , Alexander Corbishley , Eduardo Zarzuela , Blanca Pina-Beltrán , Francesca Riva , Dorothy E.F. McKeegan , Maureen Bain , Javier Muñoz , Mangesh Bhide , Mark McLaughlin , Tom Preston","doi":"10.1016/j.jprot.2024.105158","DOIUrl":"10.1016/j.jprot.2024.105158","url":null,"abstract":"<div><p>Optimization of broiler chicken breast muscle protein accretion is key for the efficient production of poultry meat, whose demand is steadily increasing. In a context where antimicrobial growth promoters use is being restricted, it is important to find alternatives as well as to characterize the effect of immunological stress on broiler chicken's growth. Despite its importance, research on broiler chicken muscle protein dynamics has mostly been limited to the study of mixed protein turnover. The present study aims to characterize the effect of a bacterial challenge and the feed supplementation of citrus and cucumber extracts on broiler chicken individual breast muscle proteins fractional synthesis rates (FSR) using a recently developed dynamic proteomics pipeline. Twenty-one day-old broiler chickens were administered a single <sup>2</sup>H<sub>2</sub>O dose before being culled at different timepoints. A total of 60 breast muscle protein extracts from five experimental groups (Unchallenged, Challenged, Control Diet, Diet 1 and Diet 2) were analysed using a DDA proteomics approach. Proteomics data was filtered in order to reliably calculate multiple proteins FSR making use of a newly developed bioinformatics pipeline. Broiler breast muscle proteins FSR uniformly decreased following a bacterial challenge, this change was judged significant for 15 individual proteins, the two major functional clusters identified as well as for mixed breast muscle protein. Citrus or cucumber extract feed supplementation did not show any effect on the breast muscle protein FSR of immunologically challenged broilers. The present study has identified potential predictive markers of breast muscle growth and provided new information on broiler chicken breast muscle protein synthesis which could be essential for improving the efficiency of broiler chicken meat production.</p></div><div><h3>Significance</h3><p>The present study constitutes the first dynamic proteomics study conducted in a farm animal species which has characterized FSR in a large number of proteins, establishing a precedent for biomarker discovery and assessment of health and growth status. Moreover, it has been evidenced that the decrease in broiler chicken breast muscle protein following an immune challenge is a coordinated event which seems to be the main cause of the decreased growth observed in these animals.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1874391924000903/pdfft?md5=5ef346e96b45e4b245d9c470200d0242&pid=1-s2.0-S1874391924000903-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140131763","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":"Screening by Q Exactive liquid chromatography/tandem mass spectrometry identified Choline, 25-hydroxyvitamin D2, and SM(d18:0/16:1(9Z) (OH)) as biomarkers for high-grade serous ovarian cancer","authors":"Jiajia Li , Dongzhen Liu , Man Cui , Zhentong Wei","doi":"10.1016/j.jprot.2024.105154","DOIUrl":"10.1016/j.jprot.2024.105154","url":null,"abstract":"<div><p>High-grade serous ovarian cancer (HGSOC) has a high death rate and poor prognosis. The main causes of poor prognosis are asymptomatic early disease, no effective screening method at present, and advanced disease. Changes in cellular metabolism are characteristic of cancer, and plasma metabolome analysis can be used to identify biomarkers. In this study, we used Q Exactive liquid chromatography tandem mass spectrometry (LC–MS/MS, QE) to compare the differentiation between plasma samples (22 HGSOC samples and 22 normal samples). In total, we detected 124 metabolites, and an orthogonal partial least-squares-discriminant analysis (OPLS-DA) model was useful to distinguish HGSOC patients from healthy controls. Choline, 25-hydroxyvitamin D2, and sphingomyelin (d18:0/16:1(9Z) (OH))/SM(d18:0/16:1(9Z) (OH)) showed significantly differential plasma levels in HGSOC patients under the conditions of variable importance in projection (VIP) > 1, <em>p</em> < 0.05 using Student's <em>t</em><em>-</em>test, and fold change (FC) ≥ 1.5 or ≤ 0.667. Metabolic pathway analysis can provide valuable information to enhance the understanding of the underlying pathophysiology of HGSOC. In conclusion, the Q Exactive LC/MS/MS method validation-based plasma metabolomics approach may have potential as a convenient screening method for HGSOC and may be a method to monitor tumor recurrence in patients with HGSOC after surgery</p></div><div><h3>Significance</h3><p>High-grade serous ovarian cancer (HGSOC) has a high death rate and poor prognosis. The main causes of poor prognosis are asymptomatic early disease, no effective screening method at present, and advanced disease. Changes in cellular metabolism are characteristic of cancer, and plasma metabolome analysis can be used to identify biomarkers. In this study, we used Q Exactive liquid chromatography tandem mass spectrometry (LC–MS/MS, QE) to compare the differentiation between plasma samples (20 HGSOC samples and 20 normal samples). In total, we detected 124 metabolites, and an orthogonal partial least-squares-discriminant analysis (OPLS-DA) model was useful to distinguish HGSOC patients from healthy controls. Choline, 25-hydroxyvitamin D2, and sphingomyelin (d18:0/16:1(9Z) (OH))/SM(d18:0/16:1(9Z) (OH)) showed significantly differential plasma levels in HGSOC patients under the conditions of variable importance in projection (VIP) > 1, <em>p</em> < 0.05 using Student's <em>t-</em>test, and fold change (FC) ≥ 1.5 or ≤ 0.667. Metabolic pathway analysis can provide valuable information to enhance the understanding of the underlying pathophysiology of HGSOC. In conclusion, the Q Exactive LC/MS/MS method validation-based plasma metabolomics approach may have potential as a convenient screening method for HGSOC and may be a method to monitor tumor recurrence in patients with HGSOC after surgery.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1874391924000861/pdfft?md5=cb19be0c772b029c0891116a892ab81f&pid=1-s2.0-S1874391924000861-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140110494","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}
Roberta Pena da Paschoa , Vitor Batista Pinto , Jéssica Priscilla Pereira , Paulo Cezar Cavatte , Mário Luís Garbin , Tiago Godinho , Lucas Rodrigues Xavier , Tatiana Tavares Carrijo , Vanildo Silveira
{"title":"Proteomic and physiological signatures of altitude adaptation in a Myrsine coriacea population under common garden conditions","authors":"Roberta Pena da Paschoa , Vitor Batista Pinto , Jéssica Priscilla Pereira , Paulo Cezar Cavatte , Mário Luís Garbin , Tiago Godinho , Lucas Rodrigues Xavier , Tatiana Tavares Carrijo , Vanildo Silveira","doi":"10.1016/j.jprot.2024.105156","DOIUrl":"10.1016/j.jprot.2024.105156","url":null,"abstract":"<div><p>Plants exhibit phenotypic plasticity in response to environmental variations, which can lead to stable genetic and physiological adaptations if exposure to specific conditions is prolonged. <em>Myrsine coriacea</em> demonstrates this through its ability to thrive in diverse environments. The objective of the article is to investigate potential differences in protein accumulation and physiological responses of <em>M. coriacea</em> by cultivating plants from seeds collected from four populations at different altitudes in a common garden experiment. Additionally, we aim to evaluate whether these differences exhibit genetic fixation. Through integrated physiological and proteomic analyses, we identified 170 differentially accumulated proteins and observed significant physiological differences among the populations. The high-altitude population (POP1) exhibited a unique proteomic profile with significant down-regulation of proteins involved in carbon fixation and energy metabolism, suggesting a potential reduction in photosynthetic efficiency. Physiological analyses showed lower leaf nitrogen content, net CO<sub>2</sub> assimilation rate, specific leaf area, and relative growth rate in stem height for POP1, alongside higher leaf carbon isotopic composition (<em>δ13C</em>) and leaf carbon (<em>C</em>) content. These findings provide insight into the complex interplay between proteomic and physiological adaptations in <em>M. coriacea</em> and underscore the importance of local adaptations.</p></div><div><h3>Significance</h3><p>We investigate the adaptive responses of <em>M. coriacea</em>, a shrub with a broad phenotypic range, by cultivating plants from seeds collected at four different altitudes in a common garden experiment. These findings provide insight into the complex interplay between proteomic and physiological adaptations in <em>M. coriacea</em> and underscore the importance of local adaptations in the face of climate change. This study contributes to advancing our understanding of the influence of altitude-specific selection pressures on the molecular biology and physiology of plants in natural populations. Our findings provide valuable insights that enhance our ability to predict and comprehend how plants respond to climate change.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140101853","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}
Yan Gao , Juntong Li , Kaichao Hu , Shasha Wang , Songwei Yang , Qidi Ai , Jiaqing Yan
{"title":"Phosphoproteomic analysis of APP/PS1 mice of Alzheimer's disease by DIA based mass spectrometry analysis with PRM verification","authors":"Yan Gao , Juntong Li , Kaichao Hu , Shasha Wang , Songwei Yang , Qidi Ai , Jiaqing Yan","doi":"10.1016/j.jprot.2024.105157","DOIUrl":"10.1016/j.jprot.2024.105157","url":null,"abstract":"<div><p>Traditional Chinese medicine has been utilized in China for approximately thousands of years in clinical settings to prevent Alzheimer's disease (AD) and enhance memory, despite the lack of a systematic exploration of its biological underpinnings. Exciting research has corroborated the beneficial effects of tetrahydroxy stilbene glycoside (TSG), an extract derived from <em>Polygonum multiflorum</em>, in delaying learning and memory impairment in a model that mimics AD. Therefore, the primary objective of this study is to investigate the major function of TSG upon protein regulation in AD. Herein, a novel approach, encompassing data independent acquisition (DIA), DIA phosphorylated proteomics, and parallel reaction monitoring (PRM), was utilized to integrate quantitative proteomic data collected from APP/PS1 mouse model exhibiting toxic intracellular aggregation of Aβ. Initially, we deliberated upon both single and multi-dimensional data pertaining to AD model mice. Furthermore, we authenticated disparities in protein phosphorylation quantity and expression, phosphorylation function, and ultimately phosphorylation kinase analysis. In order to validate the results, we utilized PRM ion monitoring technology to identify potential protein or peptide biomarkers. In the mixed samples, targeted detection of 50 target proteins revealed that 26 to 33 target proteins were stably detected by PRM. In summary, our findings provide new candidates for AD biomarker, which have been identified and validated through protein researches conducted on mouse brains. This offers a wealth of potential resources for extensive biomarker validation in neurodegenerative diseases.</p></div><div><h3>Significance</h3><p>DIA phosphorylated proteomics technique was used to detect and analyze phosphorylated proteins in brain tissues of mice with AD. Data were analyzed by various bioinformatics tools to explore the phosphorylation events and characterize them related to TSG. The results of DIA were further verified by PRM. Besides, we mapped the major metabolite classes emerging from the analyses to key biological pathways implicated in AD to understand the potential roles of the molecules and the interactions in triggering symptom onset and progression of AD. Meanwhile, we clarified that in the context of AD onset and TSG intervention, the changes in proteins, protein phosphorylation, phosphorylation kinases, and the internal connections.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140094236","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}
Keqing Qiu , Yan Tian , Chunyan Guo , Ougen Liu , Yan Shi , Dewu Liu , Tao Luo
{"title":"Global proteomic analysis reveals lysine succinylation is involved in the pathogenesis of hypertrophic scar","authors":"Keqing Qiu , Yan Tian , Chunyan Guo , Ougen Liu , Yan Shi , Dewu Liu , Tao Luo","doi":"10.1016/j.jprot.2024.105155","DOIUrl":"10.1016/j.jprot.2024.105155","url":null,"abstract":"<div><p>Lysine succinylation (Ksucc) is a recently identified posttranslational modification that is involved in many diseases. This study examined the role of Ksucc in the pathogenesis of hypertrophic scar (HS). The presence of Ksucc in human skin was measured by immunoblotting. Ksucc occurs in many skin proteins ranging from 25 to 250 kDa, and higher levels of Ksucc are found in HS skin than in normal skin. An immunoaffinity approach coupled with LC–MS/MS was used to characterize the first succinylome of human skin, and 159 Ksucc sites in 79 proteins were identified. Among these, there were 38 increased succinylated sites in 29 proteins but no decreased succinylated sites in HS compared with normal skin. A parallel reaction monitoring assay was performed to validate the results of the succinylome and showed that the levels of Ksucc in decorin and collagens, which are involved in the pathogenesis of HS, were increased in HS than in normal skin. In addition, increasing the level of Ksucc enhanced cell proliferation and upregulated the expression of fibrosis markers (α-SMA, COL1, and COL3) in human skin fibroblasts. Our results provide global insights into the functional role of Ksucc in hypertrophic scarring.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140068461","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}
Shengqin Zang , Xiaorui Yang , Jiangfeng Ye , Xianhong Mo , Guangbin Zhou , Yi Fang
{"title":"Quantitative phosphoproteomics explain cryopreservation-induced reductions in ram sperm motility","authors":"Shengqin Zang , Xiaorui Yang , Jiangfeng Ye , Xianhong Mo , Guangbin Zhou , Yi Fang","doi":"10.1016/j.jprot.2024.105153","DOIUrl":"10.1016/j.jprot.2024.105153","url":null,"abstract":"<div><p>Sperm cryopreservation decreases motility, probably due to changes in protein phosphorylation. Our objective was to use quantitative phosphoproteomics for systematic comparative analyses of fresh versus frozen-thawed sperm to identify factors causing cryo-injury. Ejaculates were collected (artificial vagina) from six Dorper rams, pooled, extended, and frozen over liquid nitrogen. Overall, 915, 3382, and 6875 phosphorylated proteins, phosphorylated peptides, and phosphorylation sites, respectively, were identified. At least two modified sites were present in 57.94% of the 6875 phosphosites identified, of which AKAP4 protein contained up to 331 modified sites. There were 732 phosphorylated peptides significantly up-regulated and 909 significantly down-regulated in frozen-thawed versus fresh sperm. Moreover, the conserved motif [RxxS] was significantly down-regulated in frozen-thawed sperm. Phosphorylation of sperm-specific proteins, e.g., AKAP3/4, CABYR, FSIP2, GSK3A/B, GPI, and ODF1/2 make them potential biomarkers to assess the quality of frozen-thawed ram sperm. Furthermore, these differentially phosphorylated proteins and modification sites were implicated in cryopreservation-induced changes in sperm energy production, fiber sheath composition, and various biological processes. We concluded that abnormal protein phosphorylation modifications are key regulators of reduced sperm motility. These novel findings implicated specific protein phosphorylation modifications in sperm cryo-injury.</p></div><div><h3>Significance</h3><p>This study used phosphorylated TMT quantitative proteomics to explore regulation of epigenetic modifications in frozen-thawed ram sperm. This experiment demonstrated that ram sperm freezing affects phosphorylation site modifications of proteins, especially those related to functions such as sperm motility and energy production. Furthermore, it is important to link functions of phosphorylated proteins with changes in sperm quality after freezing and thawing, and to clarify intrinsic reasons for sperm quality changes, which is of great importance for elucidating mechanisms of sperm freezing damage. Based on these protein markers and combined with cryoprotectant design theory, it provides a theoretical basis and data reference to study sperm cryoprotectants.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140028276","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}