scholarly journals Tandem Mass Tag-Based Quantitative Proteomic Analysis of ISG15 Knockout PK15 Cells in Pseudorabies Virus Infection

Genes ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1557
Author(s):  
Wenfeng He ◽  
Chen Li ◽  
Liangliang Dong ◽  
Guoqing Yang ◽  
Huimin Liu
Keyword(s):  
Pseudorabies Virus ◽  
Molecular Mechanisms ◽  
Tandem Mass ◽  
Validity And Reliability ◽  
Proteomics Data ◽  
Swine Industry ◽  
Bioinformatics Analyses ◽  
Protein Targets ◽  
Tandem Mass Tag ◽  
Mass Tag

Pseudorabies virus (PRV) is recognized as one of the most important pathogens of swine and poses a serious threat to the swine industry worldwide. Available commercial vaccines fail to protect against the emergence of new PRV strains. Therefore, the new protein targets against PRV highlight the urgent need for uncovering the molecular determinants of host cellular proteins following PRV infection. Interferon-stimulated gene 15 (ISG15) demonstrates an outstanding antiviral response. However, the molecular mechanism of ISG15 that affects PRV replication is incompletely known. Here, we performed a tandem mass tag (TMT)-based approach to quantitatively identify protein expression changes in PRV-infected ISG15 knockout PK15 (ISG15−/−-PK15) cells. In total, 4958 proteins were identified by using TMT coupled with LC-MS/MS in this study. In the PRV- and mock-infected groups, 241 differentially expressed proteins (DEPs) were identified, 162 upregulated and 79 downregulated proteins at 24 h post-infection (hpi), among which AFP, Vtn, Hsp40, Herc5, and Mccc1 may play important roles in PRV propagation. To ensure the validity and reliability of the proteomics data, the randomly selected DEPs were verified by RT-qPCR and Western blot analysis, and the results were consistent with the TMT results. Bioinformatics analyses further demonstrated that the DEPs are mainly involved in various biological processes and signaling pathways, such as signal transduction, the digestive system, and the PI3K-AKT pathway. These findings may provide new insight into molecular mechanisms for PRV infection, which is helpful for identifying potential protein targets for antiviral agents.

scholarly journals Tandem Mass Tag labelling quantitative acetylome analysis of differentially modified proteins during mycoparasitism of Clonostachys chloroleuca 67–1

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Na Jiang ◽  
Binna Lv ◽  
Haixia Wu ◽  
Shidong Li ◽  
Manhong Sun
Keyword(s):  
Fungal Pathogens ◽  
Molecular Mechanisms ◽  
Tandem Mass ◽  
The Novel ◽  
Post Translational Modification ◽  
Bioinformatics Analyses ◽  
Tandem Mass Tag ◽  
Liquid Chromatography Tandem Mass ◽  
Insight Into ◽  
Mass Tag

AbstractLysine acetylation (Kac) is an important post-translational modification (PTM) of proteins in all organisms, but its functions have not been extensively explored in filamentous fungi. In this study, a Tandem Mass Tag (TMT) labelling lysine acetylome was constructed, and differentially modified Kac proteins were quantified during mycoparasitism and vegetative growth in the biocontrol fungus Clonostachys chloroleuca 67–1, using liquid chromatography-tandem mass spectrometry (LC–MS/MS). A total of 1448 Kac sites were detected on 740 Kac proteins, among which 126 sites on 103 proteins were differentially regulated. Systematic bioinformatics analyses indicate that the modified Kac proteins were from multiple subcellular localizations and involved in diverse functions including chromatin assembly, glycometabolism and redox activities. All Kac sites were characterized by 10 motifs, including the novel CxxKac motif. The results suggest that Kac proteins may have effects of broadly regulating protein interaction networks during C. chloroleuca parasitism to Sclerotinia sclerotiorum sclerotia. This is the first report of a correlation between Kac events and the biocontrol activity of C. chloroleuca. Our findings provide insight into the molecular mechanisms underlying C. chloroleuca control of plant fungal pathogens regulated by Kac proteins.

scholarly journals Oxonium Ion Guided Analysis of Quantitative Proteomics Data Reveals Site-Specific O-Glycosylation of Anterior Gradient Protein 2 (AGR2)

2021 ◽  
Vol 22 (10) ◽  
pp. 5369
Author(s):  
Martina Pirro ◽  
Yassene Mohammed ◽  
Arnoud H. de Ru ◽  
George M. C. Janssen ◽  
Rayman T. N. Tjokrodirijo ◽  
...  
Keyword(s):  
Cell Lines ◽  
Quantitative Proteomics ◽  
Glycosylation Site ◽  
Total Cell ◽  
Tandem Mass ◽  
Proteomics Data ◽  
Site Specific ◽  
Oxonium Ions ◽  
Tandem Mass Tag ◽  
Colorectal Cancer Cell Lines

Developments in mass spectrometry (MS)-based analyses of glycoproteins have been important to study changes in glycosylation related to disease. Recently, the characteristic pattern of oxonium ions in glycopeptide fragmentation spectra had been used to assign different sets of glycopeptides. In particular, this was helpful to discriminate between O-GalNAc and O-GlcNAc. Here, we thought to investigate how such information can be used to examine quantitative proteomics data. For this purpose, we used tandem mass tag (TMT)-labeled samples from total cell lysates and secreted proteins from three different colorectal cancer cell lines. Following automated glycopeptide assignment (Byonic) and evaluation of the presence and relative intensity of oxonium ions, we observed that, in particular, the ratio of the ions at m/z 144.066 and 138.055, respectively, could be used to discriminate between O-GlcNAcylated and O-GalNAcylated peptides, with concomitant relative quantification between the different cell lines. Among the O-GalNAcylated proteins, we also observed anterior gradient protein 2 (AGR2), a protein which glycosylation site and status was hitherto not well documented. Using a combination of multiple fragmentation methods, we then not only assigned the site of modification, but also showed different glycosylation between intracellular (ER-resident) and secreted AGR2. Overall, our study shows the potential of broad application of the use of the relative intensities of oxonium ions for the confident assignment of glycopeptides, even in complex proteomics datasets.

scholarly journals Quantitative Top-Down Proteomics in Complex Samples Using Protein-Level Tandem Mass Tag Labeling

2021 ◽  
Author(s):  
Dahang Yu ◽  
Zhe Wang ◽  
Kellye A. Cupp-Sutton ◽  
Yanting Guo ◽  
Qiang Kou ◽  
...  
Keyword(s):  
Protein Level ◽  
Tandem Mass ◽  
Top Down ◽  
Complex Samples ◽  
Tandem Mass Tag ◽  
Mass Tag

scholarly journals Tandem Mass Tag-Based Quantitative Proteomics and Virulence Phenotype of Hemolymph-Treated Bacillus thuringiensis kurstaki Cells Reveal New Insights on Bacterial Pathogenesis in Insects

2021 ◽  
Author(s):  
Yanyan Sun ◽  
Linlin Yang ◽  
Lianet Rodríguez-Cabrera ◽  
Yushan Ding ◽  
Chaoliang Leng ◽  
...  
Keyword(s):  
Bacillus Thuringiensis ◽  
Quantitative Proteomics ◽  
Bacterial Pathogenesis ◽  
Midgut Epithelium ◽  
Tandem Mass ◽  
Content Type ◽  
Virulence Phenotype ◽  
Bacillus Thuringiensis Kurstaki ◽  
Tandem Mass Tag ◽  
Mass Tag

After ingestion by a susceptible insect and damaging its midgut epithelium, the bacterium Bacillus thuringiensis (Bt) reaches the insect blood (hemolymph), where it propagates despite the host’s antimicrobial defenses and induces insect death by acute septicemia. Although the hemolymph stage of the Bt toxic pathway is determinant for the infested insects’ fate, the response of Bt to hemolymph and the latter’s role in bacterial pathogenesis has been poorly explored.

Tandem mass tag-based quantitative proteomics analyses reveal the response of Bacillus licheniformis to high growth temperatures

2017 ◽  
Vol 67 (7) ◽  
pp. 501-510 ◽  
Author(s):  
Zixing Dong ◽  
Zhixin Chen ◽  
Hongbin Wang ◽  
Kangming Tian ◽  
Peng Jin ◽  
...  
Keyword(s):  
Bacillus Licheniformis ◽  
Quantitative Proteomics ◽  
High Growth ◽  
Tandem Mass ◽  
Tandem Mass Tag ◽  
Mass Tag
Sign in / Sign up

Export Citation Format

Share Document