Journal of proteomics最新文献

{"title":"Lysine acetylproteome analysis reveals the lysine acetylation in developing fruit and a key acetylated protein involved in sucrose accumulation in Rosa roxburghii Tratt.","authors":"Xue Zhang ,&nbsp;Min Lu ,&nbsp;Huaming An","doi":"10.1016/j.jprot.2024.105248","DOIUrl":"10.1016/j.jprot.2024.105248","url":null,"abstract":"<div><p>Lysine acetylation is a common post-translational modification of proteins in plants. <em>Rosa roxburghii</em> Tratt. is an economically important fruit tree known for its high nutritional value. However, the characteristics of acetylome-related proteins during fruit development in this crop remain unknown. This study aimed to explore the global acetylproteome of <em>R. roxburghii</em> fruit to identify key lysine-acetylated proteins associated with its quality traits. A total of 4280 acetylated proteins were identified, among them, 981 proteins exhibited differential acetylation (DA) while 19 proteins showed increased acetylation level consistently on individual sites. Functional classification revealed that these DA proteins were primarily associated with central metabolic pathways, carbohydrate metabolism, terpenoids and polyketides metabolism, lipid metabolism, and amino acid metabolism, highlighting the importance of lysine acetylation in fruit quality formation. Notably, the most significant up-regulated acetylation occurred in sucrose synthase (SuS1), a key enzyme in sucrose biosynthesis. Enzyme assays, RNA-seq and proteome analysis indicated that SuS activity, which was independent of its transcriptome and proteome level, may be enhanced by up-acetylation, ultimately increasing sucrose accumulation. Thus, these findings offer a better understanding of the global acetylproteome of <em>R. roxburghii</em> fruit, while also uncover a novel mechanism of acetylated SuS-mediated in sucrose metabolism in plant.</p></div><div><h3>Significance</h3><p><em>Rosa roxburghii</em> Tratt. is an important horticultural crop whose commercial value is closely linked to its fruit quality. Acetylation modification is a post-translational mechanism observed in plants, which regulates the physiological functions and metabolic fluxes involved in various biological processes. The regulatory mechanism of lysine acetylation in the fruit quality formation in perennial woody plants has not been fully elucidated, while most of the research has primarily focused on annual crops. Therefore, this study, for the first time, uses Rosaceae fruits as the research material to elucidate the regulatory role of lysine-acetylated proteins in fruit development, identify key metabolic processes influencing fruit quality formation, and provide valuable insights for cultivation strategies.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"305 ","pages":"Article 105248"},"PeriodicalIF":2.8,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141534593","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":"Plasma GPI and PGD are associated with vascular normalization and may serve as novel prognostic biomarkers for lung adenocarcinoma: Multi-omics and multi-dimensional analysis","authors":"Yiran Liu ,&nbsp;Yanchi Wang ,&nbsp;Qianyao Meng ,&nbsp;Liping Mao ,&nbsp;Yang Hu ,&nbsp;Rongrong Zhao ,&nbsp;Wendi Zhang ,&nbsp;Huiwen Xu ,&nbsp;Yutong Wu ,&nbsp;Junfeng Chu ,&nbsp;Qiong Chen ,&nbsp;Xiaobo Tao ,&nbsp;Shufan Xu ,&nbsp;Lei Zhang ,&nbsp;Tian Tian ,&nbsp;Guangyu Tian ,&nbsp;Jiahua Cui ,&nbsp;Minjie Chu","doi":"10.1016/j.jprot.2024.105247","DOIUrl":"10.1016/j.jprot.2024.105247","url":null,"abstract":"<div><p>The aim of this study was to explore potential novel plasma protein biomarkers for lung adenocarcinoma (LUAD). A plasma proteomics analysis was carried out and candidate protein biomarkers were validated in 102 LUAD cases and 102 matched healthy controls. The same LUAD tumor tissues were detected to explore the correlation between the expression of candidate proteins in tissues and plasma and vascular normalization. A LUAD active metastasis mice model was constructed to explore the role of candidate proteins for lung metastasis. GPI and PGD were verified to be upregulated in plasma from LUAD patients, and the expression of GPI in tumor tissue was positively correlated with the expression of GPI in plasma and negatively correlated with the normalization of tumor blood vessels. Meanwhile, a negative correlation between the expression of GPI and PGD in plasma and tumor vascular normalization was discovered. In the LUAD active metastasis model, the lowest levels of vascular normalization and the highest expression of GPI and PGD were found in mice with lung metastases. This study found that GPI and PGD may be potential plasma biomarkers for LUAD, and monitoring those may infer the risk of metastasis and malignancy of the tumor.</p></div><div><h3>Significant</h3><p>We identified GPI and PGD as potential novel diagnostic and prognostic biomarkers for LUAD. PGD and GPI can be used as diagnostic biomarkers in combination with other available strategies to assist in the screening and diagnosis of LUAD, and as prognostic biomarkers aid in predict the risk of tumor metastasis and malignancy in patients with LUAD.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"305 ","pages":"Article 105247"},"PeriodicalIF":2.8,"publicationDate":"2024-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141476851","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":"An efficient, amine-specific iTRAQ labeling method improves the peptide and protein identification rates","authors":"Ruomeng Chang,&nbsp;Chenchen Chang,&nbsp;Yan Cai,&nbsp;Rijing Liao","doi":"10.1016/j.jprot.2024.105244","DOIUrl":"10.1016/j.jprot.2024.105244","url":null,"abstract":"<div><p>Isotope tags for relative and absolute quantification (iTRAQ) are among the most widely used proteomics quantification techniques. These tags can be rapidly coupled to the primary amines of proteins/peptides through chemical reactions under mild conditions, making this technique universally applicable to any kind of sample. However, iTRAQ reagents also partially react with the hydroxyl groups of serine, threonine and tyrosine residues, particularly when these residues coexist with a histidine residue in the same peptide. This overlabeling of peptides causes systematic biases and significantly compromises protein/peptide identification rates. In this study, we report a novel iTRAQ labeling method that overcomes the detrimental overlabeling while providing high amine labeling efficiency. The impacts of reaction temperature, reactant concentrations, reaction time, buffer compositions, and pH on iTRAQ labeling performance were investigated in-depth. In a comparison experiment between our method and the standard labeling method provided by the iTRAQ manufacturer, our method reduced the number of overlabeled peptides by 55-fold while achieving comparable amine labeling efficiency. This improvement allowed our method to eliminates the systematic bias against histidyl- and hydroxyl-containing peptides, and more importantly, enabled the identification of 23.9% more peptides and 9.8% more proteins.</p></div><div><h3>Significance</h3><p>In addition to amines, the hydroxyl groups in serine, threonine, and tyrosine residues can also partially labeled by iTRAQ reagents, which leads to systematic biases and significantly compromises the analytical sensitivity. To address this issue, we developed a novel iTRAQ labeling method that overcomes the detrimental overlabeling while providing high labeling efficiency of amines. When benchmarking our method against the standard method provided by the reagent manufacturer, our method achieved comparable labeling efficiency but reduced the overlabeled species by 55-fold. This significant improvement eliminated the systematic biases, and more importantly, enabled the identification of 23.9% more peptides and 9.8% more proteins, demonstrating its superior performance and potential to enhance proteome quantification using iTRAQ labeling.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"305 ","pages":"Article 105244"},"PeriodicalIF":2.8,"publicationDate":"2024-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141468944","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-based host-specific biomarkers for tuberculosis: The future of TB diagnosis","authors":"Divya Pandey ,&nbsp;Dipanjana Ghosh","doi":"10.1016/j.jprot.2024.105245","DOIUrl":"10.1016/j.jprot.2024.105245","url":null,"abstract":"<div><p>Tuberculosis (TB) is an infectious disease that remains one of the major global public health concerns. Early detection of Active Pulmonary TB is therefore of utmost importance for controlling lethality and disease spreading. Currently available TB diagnostics can be broadly categorized into microscopy, culture-based, and molecular approaches, all of which come with compromised sensitivity, limited efficacy, and high expenses. Hence, rapid, sensitive, and affordable diagnostic methods for TB is the current prerequisite for disease management. This review summarizes the proteomics investigations for host-specific biomarkers from serum, sputum, saliva, and urine samples of TB patients, along with patients having comorbidity. Thorough data mining from available literature led us to conclude that the host-specific proteins involved in immunity and defense, metabolic regulation, cellular adhesion, and motility, inflammatory responses, and tissue remodelling have shown significant deregulation upon <em>Mycobacterium tuberculosis</em> (<em>Mtb</em>) infection. Notably, the immunoregulatory protein orosomucoid (ORM) was up-regulated in active TB compared to non-TB individuals, as observed in multiple studies from diverse sample types. Mannose receptor C type 2 (MRC2) was identified as an upregulated, treatment response biomarker in two independent serum proteomics investigations. Thorough mechanistic investigation on these candidate proteins would be fascinating to dig into potential drug targets and customized therapeutics for TB patients, along with their diagnostic potentials.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"305 ","pages":"Article 105245"},"PeriodicalIF":2.8,"publicationDate":"2024-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141468945","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":"Candidate prognostic biomarkers and prediction models for high-grade serous ovarian cancer from urinary proteomics","authors":"Maowei Ni ,&nbsp;Danying Wan ,&nbsp;Junzhou Wu ,&nbsp;Wangang Gong ,&nbsp;Junjian Wang ,&nbsp;Zhiguo Zheng","doi":"10.1016/j.jprot.2024.105234","DOIUrl":"10.1016/j.jprot.2024.105234","url":null,"abstract":"<div><p>High-grade serous ovarian cancer (HGSOC) is one of the most common histologic types of ovarian cancer. The purpose of this study was to identify potential prognostic biomarkers in urine specimens from patients with HGSOC. First, 56 urine samples with information on relapse-free survival (RFS) months were collected and classified into good prognosis (RFS ≥ 12 months) and poor prognosis (RFS &lt; 12 months) groups. Next, data-independent acquisition (DIA)-based mass spectrometry (MS) analysis was combined with MSFragger-DIA workflow to identify potential prognostic biomarkers in a discovery set (<em>n</em> = 31). With the aid of parallel reaction monitoring (PRM) analysis, four candidate biomarkers (ANXA1, G6PI, SPB3, and SPRR3) were finally validated in both the discovery set and an independent validation set (<em>n</em> = 25). Subsequent RFS and Cox regression analyses confirmed the utility of these candidate biomarkers as independent prognostic factors affecting RFS in patients with HGSOC. Regression models were constructed to predict the 12-month RFS rate, with area under the receiver operating characteristic curve (AUC) values ranging from 0.847 to 0.905. Overall, candidate prognostic biomarkers were identified in urine specimens from patients with HGSOC and prediction models for the 12-month RFS rate constructed.</p></div><div><h3>Significance</h3><p>OC is one of the leading causes of death due to gynecological malignancies. HGSOC constitutes one of the most common histologic types of OC with aggressive characteristics, accounting for the majority of advanced cases. In cases where patients with advanced HGSOC potentially face high risk of unfavorable prognosis or disease advancement within a 12-month period, intensive medical monitoring is necessary. In the era of precision cancer medicine, accurate prediction of prognosis or 12-month RFS rate is critical for distinguishing patient groups requiring heightened surveillance. Patients could significantly benefit from timely modifications to treatment regimens based on the outcomes of clinical monitoring. Urine is an ideal resource for disease surveillance purposes due to its easy accessibility. Furthermore, molecules excreted in urine are less complex and more stable than those in other liquid samples. In the current study, we identified candidate prognostic biomarkers in urine specimens from patients with HGSOC and constructed prediction models for the 12-month RFS rate.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"304 ","pages":"Article 105234"},"PeriodicalIF":2.8,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141457634","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":"Discovery and validation of combined biomarkers for the diagnosis of esophageal intraepithelial neoplasia and esophageal squamous cell carcinoma","authors":"Ya-Qi Zheng ,&nbsp;Hai-Hua Huang ,&nbsp;Shu-Xian Chen ,&nbsp;Xiu-E Xu ,&nbsp;Zhi-Mao Li ,&nbsp;Yue-Hong Li ,&nbsp;Su-Zuan Chen ,&nbsp;Wen-Xiong Luo ,&nbsp;Yi Guo ,&nbsp;Wei Liu ,&nbsp;En-Min Li ,&nbsp;Li-Yan Xu","doi":"10.1016/j.jprot.2024.105233","DOIUrl":"10.1016/j.jprot.2024.105233","url":null,"abstract":"<div><p>Early diagnosis and intervention of esophageal squamous cell carcinoma (ESCC) can improve the prognosis. The purpose of this study was to identify biomarkers for ESCC and esophageal precancerous lesions (intraepithelial neoplasia, IEN). Based on the proteomic and genomic data of esophageal tissue including previously reported data, up-regulated proteins with copy number amplification in esophageal cancer were screened as candidate biomarkers. Five proteins, including KDM2A, RAD9A, ECT2, CYHR1 and TONSL, were confirmed by immunohistochemistry on ESCC and normal esophagus (NE). Then, we investigated the expression of 5 proteins in 236 participants (60 NEs, 93 IENs and 83 ESCCs) which were randomly divided into training set and test set. When distinguishing ESCC from NE, the area under curve (AUC) of the multiprotein model was 0.940 in the training set, while the lowest AUC of a protein was 0.735. In the test set, the results were similar. When distinguishing ESCC from IEN or distinguishing IEN from NE, the diagnostic efficiency of the multi-protein models were also improved compared with that of single protein. Our findings suggest that combined detection of KDM2A, RAD9A, ECT2, CYHR1 and TONSL can be used as potential biomarkers for the early diagnosis of ESCC and precancerous lesion development prediction.</p></div><div><h3>Significance</h3><p>Candidate biomarkers including KDM2A, RAD9A, ECT2, CYHR1 and TONSL screened by integrating genomic and proteomic data from the esophagus can be used as potential biomarkers for the early diagnosis of esophageal squamous cell carcinoma and precancerous lesion development prediction.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"304 ","pages":"Article 105233"},"PeriodicalIF":2.8,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141457635","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":"Conjugated linoleic acid (CLA) modulates bovine peripheral blood mononuclear cells (PBMC) proteome in vitro","authors":"G. Ávila ,&nbsp;F. Ceciliani ,&nbsp;D. Viala ,&nbsp;S. Dejean ,&nbsp;G. Sala ,&nbsp;C. Lecchi ,&nbsp;M. Bonnet","doi":"10.1016/j.jprot.2024.105232","DOIUrl":"10.1016/j.jprot.2024.105232","url":null,"abstract":"<div><p>Conjugated linoleic acid (CLA) is a group of natural isomers of the n-6 polyunsaturated fatty acid (PUFA) linoleic acid, exerting biological effects on cow physiology. This study assessed the impact of the mixture 50:50 (vol:vol) of CLA isomers (cis-9, trans-11 and trans-10, cis-12) on bovine peripheral blood mononuclear cells (PBMC) proteome, identifying 1608 quantifiable proteins. A supervised multivariate statistical analysis, sparse variant partial least squares – discriminant analysis (sPLS-DA) for paired data identified 407 discriminant proteins (DP), allowing the clustering between the CLA and controls. The ProteINSIDE workflow found that DP with higher abundance in the CLA group included proteins related to innate immune defenses (PLIN2, CD36, C3, C4, and AGP), with antiapoptotic (SERPINF2 and ITIH4) and antioxidant effects (HMOX1). These results demonstrated that CLA modulates the bovine PBMC proteome, supports the antiapoptotic and immunomodulatory effects observed in previous <em>in vitro</em> studies on bovine PBMC, and suggests a cytoprotective role against oxidative stress.</p></div><div><h3>Significance</h3><p>In this study, we report for the first time that the mixture 50:50 (vol:vol) of cis-9, trans-11, and trans-10, cis-12-CLA isomers modulates the bovine PBMC proteome. Our results support the immunomodulatory and antiapoptotic effects observed in bovine PBMC <em>in vitro</em>. In addition, the present study proposes a cytoprotective role of CLA mixture against oxidative stress. We suggest a molecular signature of CLA treatment based on combining a multivariate sparse discriminant analysis and a clustering method. This demonstrates the great value of sPLS-DA as an alternative option to identify discriminant proteins with relevant biological significance.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"304 ","pages":"Article 105232"},"PeriodicalIF":2.8,"publicationDate":"2024-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1874391924001647/pdfft?md5=335f7735e285899a69bbf0c6c8a9c78f&pid=1-s2.0-S1874391924001647-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141442906","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":"Shotgun proteomics of detergent-solubilized proteins from Trypanosoma evansi","authors":"Franciane Batista ,&nbsp;Renato Simões Moreira ,&nbsp;Vilmar Benetti Filho ,&nbsp;Hércules Moura ,&nbsp;Glauber Wagner ,&nbsp;Luiz Claudio Miletti","doi":"10.1016/j.jprot.2024.105231","DOIUrl":"https://doi.org/10.1016/j.jprot.2024.105231","url":null,"abstract":"<div><p><em>Trypanosoma evansi</em>, the causative agent of surra, is the most prevalent pathogenic salivarian trypanosome and affects the majority of domesticated and wild animals in endemic regions. This work aimed to analyze detergent-solubilized <em>T. evansi</em> proteins and identify potential diagnostic biomarkers for surra. Triton X-114-extracted membrane-enriched proteins (MEP) of <em>T. evansi</em> bloodstream forms were analyzed using a gel-free technique (LC-ESI-MS/MS). 247 proteins were identified following the MS analysis of three biological and technical replicates. Two of these proteins were predicted to have a GPI-anchor, 100 (40%) were predicted to have transmembrane domains, and 166 (67%) were predicted to be membrane-bound based on at least one of six features: location (WolfPSORT, DeepLoc-2.0, Protcomp-9.0), transmembrane, GPI, and gene ontology. It was predicted that 76 (30%) of proteins had membrane evidence. Typical membrane proteins for each organelle were identified, among them ISG families (64, 65, and 75 kDa), flagellar calcium-binding protein, 24 kDa calflagin, syntaxins and oligosaccharyltransferase some of which had previously been studied in other trypanosomatids<em>. T. evansi</em> lacks singletons and exclusive orthologous groups, whereas three distinct epitopes have been identified. Data are available via ProteomeXchange with identifier <span>PXD040594</span><svg><path></path></svg>.</p></div><div><h3>Significance</h3><p><em>Trypanosoma evansi</em> is a highly prevalent parasite that induces a pathological condition known as “surra” in various species of ungulates across five continents. The infection gives rise to symptoms that are not pathognomonic, thereby posing challenges in its diagnosis and leading to substantial economic losses in the livestock industry. A significant challenge arises from the absence of a diagnostic test capable of distinguishing between <em>Trypanosoma equiperdum</em> and <em>T. evansi</em>, both of which are implicated in equine diseases. Therefore, there is a pressing need to conduct research on the biochemistry of the parasite in order to identify proteins that could potentially serve as targets for differential diagnosis or therapeutic interventions.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"304 ","pages":"Article 105231"},"PeriodicalIF":2.8,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141434988","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 of sugarcane smut fungus - Sporisorium scitamineum unravels dynamic proteomic alterations during the dimorphic transition","authors":"Nalayeni Kumaravel ,&nbsp;Leonard Barnabas Ebinezer ,&nbsp;N.M.R. Ashwin ,&nbsp;Cinzia Franchin ,&nbsp;Ilaria Battisti ,&nbsp;Paolo Carletti ,&nbsp;Amalraj Ramesh Sundar ,&nbsp;Antonio Masi ,&nbsp;Palaniyandi Malathi ,&nbsp;Rasappa Viswanathan ,&nbsp;Giorgio Arrigoni","doi":"10.1016/j.jprot.2024.105230","DOIUrl":"10.1016/j.jprot.2024.105230","url":null,"abstract":"&lt;div&gt;&lt;p&gt;Life cycle of the dimorphic sugarcane smut fungi, &lt;em&gt;Sporisorium scitamineum&lt;/em&gt;, involves recognition and mating of compatible saprophytic yeast-like haploid sporidia (MAT-1 and MAT-2) that upon fusion, develop into infective dikaryotic mycelia. Although the dimorphic transition is intrinsically linked with the pathogenicity and virulence of &lt;em&gt;S. scitamineum&lt;/em&gt;, it has never been studied using a proteomic approach. In the present study, an iTRAQ-based comparative proteomic analysis of three distinct stages was carried out. The stages were: the dimorphic transition period - haploid sporidial stage (MAT-1 and MAT-2); the transition phase (24 h post co-culturing (hpc)) and the dikaryotic mycelial stage (48 hpc). Functional categorization of differentially abundant proteins showed that the most altered biological processes were energy production, primary metabolism, especially, carbohydrate, amino acid, fatty acid, followed by translation, post-translation and protein turnover. Several differentially abundant proteins (DAPs), especially in the dikaryotic mycelial stage were predicted as effectors. Taken together, key molecular mechanisms underpinning the dimorphic transition in &lt;em&gt;S. scitamineum&lt;/em&gt; at the proteome level were highlighted. The catalogue of stage-specific and dimorphic transition-associated-proteins and potential effectors identified herein represents a list of potential candidates for defective mutant screening to elucidate their functional role in the dimorphic transition and pathogenicity in &lt;em&gt;S. scitamineum&lt;/em&gt;.&lt;/p&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Biological significance&lt;/h3&gt;&lt;p&gt;Being the first comparative proteomics analysis of &lt;em&gt;S. scitamineum&lt;/em&gt;, this study comprehensively examined three pivotal life cycle stages of the pathogen: the non-pathogenic haploid phase, the transition phase, and the pathogenic dikaryotic mycelial stage. While previous studies have reported the sugarcane and &lt;em&gt;S. scitamineum&lt;/em&gt; interactions, this study endeavored to specifically identify the proteins responsible for pathogenicity. By analyzing the proteomic alterations between the haploid and dikaryotic mycelial phases, the study revealed significant changes in metabolic pathway-associated proteins linked to energy production, notably oxidative phosphorylation, and the citrate cycle. Furthermore, this study successfully identified key metabolic pathways that undergo reprogramming during the transition from the non-pathogenic to the pathogenic stage. The study also deciphered the underlying mechanisms driving the morphological and physiological alterations crucial for the &lt;em&gt;S. scitamineum&lt;/em&gt; virulence. By studying its life cycle stages, identifying the key metabolic pathways and stage-specific proteins, it provides unprecedented insights into the pathogenicity and potential avenues for intervention. As proteomics continues to advance, such studies pave the way for a deeper understanding of plant-pathogen interactions and the development of i","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"304 ","pages":"Article 105230"},"PeriodicalIF":2.8,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141432199","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":"In-gel protein digestion using acidic methanol produces a highly selective methylation of glutamic acid residues","authors":"Marta Lozano-Prieto ,&nbsp;Emilio Camafeita ,&nbsp;Inmaculada Jorge ,&nbsp;Andrea Laguillo-Gómez ,&nbsp;Rafael Barrero-Rodríguez ,&nbsp;Cristina A. Devesa ,&nbsp;Clara Pertusa ,&nbsp;Enrique Calvo ,&nbsp;Francisco Sánchez-Madrid ,&nbsp;Jesús Vázquez ,&nbsp;Noa B. Martin-Cofreces","doi":"10.1016/j.jprot.2024.105229","DOIUrl":"10.1016/j.jprot.2024.105229","url":null,"abstract":"<div><p>Mass-tolerant open search methods allow the high-throughput analysis of modified peptides by mass spectrometry. These techniques have paved the way to unbiased analysis of post-translational modifications in biological contexts, as well as of chemical modifications produced during the manipulation of protein samples. In this work, we have analyzed in-depth a wide variety of samples of different biological origin, including cells, extracellular vesicles, secretomes, centrosomes and tissue preparations, using Comet-ReCom, a recently improved version of the open search engine Comet-PTM. Our results demonstrate that glutamic acid residues undergo intensive methyl esterification when protein digestion is performed using in-gel techniques, but not using gel-free approaches. This effect was highly specific to Glu and was not found for other methylable residues such as Asp.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"304 ","pages":"Article 105229"},"PeriodicalIF":3.3,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141331226","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}