BEMAP analysis of glycosylated TW10722 YghJ
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Escherichia Coli
SUBMITTER: 
Anders Boysen
LAB HEAD: Anders Boysen
PROVIDER: PXD030322 | Pride | 2022-02-17
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| LUM2_04768.pdResult | Other | |||
| LUM2_04768.raw | Raw |
Items per page: 5 1 - 2 of 2 |
Publications
Characterization of Glycosylation-Specific Systemic and Mucosal IgA Antibody Responses to <i>Escherichia coli</i> Mucinase YghJ (SslE).
Riaz Saman S Steinsland Hans H Thorsing Mette M Andersen Ann Z AZ Boysen Anders A Hanevik Kurt K
Frontiers in immunology 20211217
Efforts to develop broadly protective vaccines against pathogenic <i>Escherichia coli</i> are ongoing. A potential antigen candidate for vaccine development is the metalloprotease YghJ, or SslE. YghJ is a conserved mucinase that is immunogenic, heavily glycosylated, and produced by most pathogenic <i>E. coli</i>. To develop efficacious YghJ-based vaccines, there is a need to investigate to what extent potentially protective antibody responses target glycosylated epitopes in YghJ and to describe ...[more]
Similar Datasets
Project description:In the present study we have further investigated the extent of YghJ glycosylation and coupled this inherent O-linked protein glycosylation to an increased antigenic potential of YghJ. We have expressed and purified glycosylated YghJ from the canonical ETEC strain H10407 and performed an in depth BEMAP analysis to identify glycosylated Ser/Thr residues
2021-08-09 | PXD025876 | Pride
Project description:The mammalian SID-1 transmembrane family member 1 (SIDT1), are multi-pass transmembrane proteins that mediate the cellular uptake and intracellular trafficking of nucleic acids, playing important roles in the immune response and tumorigenesis. We here report N-glycosylation as a key regulator of SIDT1-mediated RNA transport activities. To identify regulators whose expression was induced by N-glycan-deficient SIDT1, we further performed gene expression analysis on wild-type SIDT1 and non-N-glycosylated SIDT1overexpression HEK293F cells. Samples were subjected to RNA sequencing (RNA-seq) to reveal genes differences in SIDT1 overexpressing cells versus SIDT1N-glycan overexpressing cells. Our results indicate that the non-N-glycosylated SIDT1 is severely misfolded. These severely misfolded non-N-glycosylated SIDT1 may cause ER stress, leading to the induction of the unfolded protein response (UPR) and regulated by the ERQC system.
2023-08-09 | GSE239877 | GEO
Project description:N-linked glycosylation is a posttranslational modification affecting protein folding and protein function. The N-linked glycosylation pathway in algae is poorly characterized, and further knowledge is needed to understand the cell biology of algae and the evolution of N-linked glycosylation. This study investigated the N-linked glycosylation pathway in the open ocean diatom Thalassiosira oceanica and identified N-linked glycosylated peptides through solid-phase extraction of N-linked glycosylated peptides (SPEG). We characterized 118 N-linked glycosylated peptides from samples of cells grown in high- and low-iron conditions. The identified peptides had 81% NXT-type motifs, with X being any amino acids except proline. The presence of N-linked glycosylation sites in the iron starvation-induced protein 1a (ISIP1a) confirmed its predicted topology, contributing to the biochemical characterization of ISIP1 proteins.
2021-09-09 | PXD021782 | Pride
Project description:N-glycosylation is an important posttranslational modification in all eukaryotes, but little is known about the N-glycoproteomes in microalgal systems. Here, N-glycoproteome of the model diatom Phaeodactylum tricornutum was unveiled. Totally, 893 different N-glycosylated sites from 649 proteins were identified from P. tricornutum. The new synthesized N-glycans were principally transferred to asparagine residues within the conserved N-X-S/T (where X is a residue other than proline) sequence of nascent polypeptide chains. Functional annotation of N-glycosylated proteins showed that 70% N-glycoproteins were involved in vesicular transport and posttranslational modification, protein turnover, chaperones, indicating the N-glycosylation was important for these functions. Of the all identified N-glycoproteins 45.3% were predicted to localize on chloroplast, which implied the widespread regulatory role of N-glycosylation in chloroplast. Furthermore, the enrichment results of N-glycoproteins indicated that compared to ‘Cellular component’ and ‘Biological process’ categories proteins related with the ‘Molecular function’ category were more prone to be N-glycosylated. And it was speculated that N-glycosylation played a vital regulatory role in catalytic activity of enzymes and metabolism processes of many small molecules. 47% of all enriched proteins were related with metabolic pathways. The functional annotation and enrichment of N-glycoproteins suggested that N-glycoproteins participated in a variety of important metabolic pathways and perform different functions in P. tricornutum. 12 proteins involved in the ER quality control mechanism and ER- associated degradation pathway were identified as N-glycosylated proteins, indicating that the N-glycosylated modification was important for their functions in the protein N-glycosylation pathway. Additionally, some interacted glycoproteins were classified from this study, which provided valuable information for studying the functions of these glycoproteins. In the study, the identification of N-glycosylation on nascent proteins expands our understanding of this PTM at a proteomics scale and may facilitate the elucidation of the precise function of proteins in this model diatom.
2021-11-03 | PXD022483 | Pride
Project description:Free and glycosylated sterols play a central role in maintaining the structural integrity and proper functioning of plasma membrane, which serves as the primary sensor of cold and initiates signaling cascades to mitigate chilling-induced damage. Here we characterize the cold response of tomato (Micro-Tom) mutants with opposite glycosylated to free sterol ratio resulting from the overexpression and silencing of the sterol glycosyltransferases SlSGT2 and SlSGT1. A high ratio in the SlSGT2 overexpressing mutants increases cold tolerance, membrane stability, and oxidative stress responses, while a low ratio in the SlSGT1-silenced mutants causes the opposite phenotypes. The different cold sensitivity in these mutants is due to the altered membrane sterol profiles, rather than to a different capacity to adjust sterol levels during cold exposure. Changes in the glycosylated to free sterol ratio also trigger distinct transcriptional programs that establish a preconditioned stress-responsive state under basal conditions and a more efficient response under cold exposure in the SlSGT2 overexpressing mutants and compromise the capacity to withstand the effects of cold stress in the SlSGT1-silenced mutants. The SlSGT2 overexpressing mutants accumulate higher basal levels of jasmonates and display enhanced biosynthetic capacity under cold stress compared to SlSGT1-silenced and control plants. The elevated glycosylated to free sterol ratio in SlSGT2 overexpressing mutants facilitates JA biosynthesis and signaling, leading to the activation of cold-responsive genes, including those of the CBF–COR pathway, antioxidant defenses and polyamine biosynthesis. Our findings provide key insights into the mechanisms by which glycosylated sterols improve cold tolerance in tomato.
2025-09-30 | GSE292957 | GEO
Project description:Acquired resistance to trastuzumab, a rationally designed HER-2 targeting antibody, remains a major hurdle in management of HER-2 positive breast cancer (HER-2+ BC) patients. Potential resistance mechanisms are numerous, derived primarily from studies where HER-2 positive cell lines are chronically exposed to trastuzumab. Recent evidence suggests a role for epithelial-mesenchymal transition (EMT) in trastuzumab resistance, but a definitive link between the two has been difficult to establish because relevant model systems are lacking. When sub-populations of trastuzumab sensitive SKBR-3 cells were isolated using cloning rings, an (EMT) occurred spontaneously in several (3/8) clones. SKBR-3 EMT-clones featured increased spindle morphology, expressed N-glycosylated β1-integrin, and decreased HER-2, all characteristics shared by JIMT-1, a cell lines with intrinsic resistance to trastuzumab. SKBR-3 EMT-clones were characterized by gene expression profiling and mammosphere formation. The N-glycosylated isoform of β-itnegrin was targeted with β-integrin inhibiting antibody, AIIB2. Transcriptional profiling revealed that SKBR-3 EMT-clones underwent a shift from a luminal molecular subtype to a more aggressive mesenchymal/ basal phenotype. Isolating clones from SKBR-3 cells with enforced expression of a β-integrin isoform lacking extensive N-glycosylation failed to increase the likelihood for spontaneous EMT in SKBR-3. However, specific inhibition of the heavily N-glycosylated variant of β1-integrin expressed by SKBR-3 EMT-clones restored epithelial morphology and impaired mammosphere formation. Furthermore, when SKBR-3 EMT-clones were treated with relevant doses of trastuzumab and lapatinib, they showed “spontaneous” resistance. In this study we describe a model of spontaneous EMT following clonal selection in HER-2+ cell line, SKBR-3. Using this model we establish the first direct link between EMT and resistance to HER-2 targeted therapies. We also identify the N-glycosylated isoform of β-integrin as a potential biomarker and target in HER-2+ BC refractory to HER-2 targeted therapies.
2015-01-01 | GSE40152 | GEO
Project description:Biological functions of nuclear proteins are regulated by post-translational modifications (PTMs) that modulate gene expression and cellular physiology. However, the role of O-linked glycosylation (O-GalNAc) as a PTM of nuclear proteins in the human cell has not been previously reported. Here, we examined the initiation of O-GalNAc glycan biosynthesis, representing a novel PTM of nuclear proteins in the nucleus of human cells, with an emphasis on HeLa cells. Using affinity chromatography and MS analyses, we identified O-GalNAc glycosylated proteins in the nucleus and present solid evidence for O-GalNAc glycan synthesis in this organelle. The demonstration of O-GalNAc glycosylation of nuclear proteins in mammalian cells reported here has important implications for cell and chemical biology.
2019-04-17 | PXD013484 | Pride
Project description:Acquired resistance to trastuzumab, a rationally designed HER-2 targeting antibody, remains a major hurdle in management of HER-2 positive breast cancer (HER-2+ BC) patients. Potential resistance mechanisms are numerous, derived primarily from studies where HER-2 positive cell lines are chronically exposed to trastuzumab. Recent evidence suggests a role for epithelial-mesenchymal transition (EMT) in trastuzumab resistance, but a definitive link between the two has been difficult to establish because relevant model systems are lacking. When sub-populations of trastuzumab sensitive SKBR-3 cells were isolated using cloning rings, an (EMT) occurred spontaneously in several (3/8) clones. SKBR-3 EMT-clones featured increased spindle morphology, expressed N-glycosylated M-NM-21-integrin, and decreased HER-2, all characteristics shared by JIMT-1, a cell lines with intrinsic resistance to trastuzumab. SKBR-3 EMT-clones were characterized by gene expression profiling and mammosphere formation. The N-glycosylated isoform of M-NM-2-itnegrin was targeted with M-NM-2-integrin inhibiting antibody, AIIB2. Transcriptional profiling revealed that SKBR-3 EMT-clones underwent a shift from a luminal molecular subtype to a more aggressive mesenchymal/ basal phenotype. Isolating clones from SKBR-3 cells with enforced expression of a M-NM-2-integrin isoform lacking extensive N-glycosylation failed to increase the likelihood for spontaneous EMT in SKBR-3. However, specific inhibition of the heavily N-glycosylated variant of M-NM-21-integrin expressed by SKBR-3 EMT-clones restored epithelial morphology and impaired mammosphere formation. Furthermore, when SKBR-3 EMT-clones were treated with relevant doses of trastuzumab and lapatinib, they showed M-bM-^@M-^\spontaneousM-bM-^@M-^] resistance. In this study we describe a model of spontaneous EMT following clonal selection in HER-2+ cell line, SKBR-3. Using this model we establish the first direct link between EMT and resistance to HER-2 targeted therapies. We also identify the N-glycosylated isoform of M-NM-2-integrin as a potential biomarker and target in HER-2+ BC refractory to HER-2 targeted therapies. RNA was isolated from 10 breast cancer cell lines in triplicate. Pairwise gene expression differences were compared between each of the SKBR-3 cell lines (SKBR-3/ b1, SK-EV-C4, and SK-B1-C1). Features selected had at least a 2X difference in at least one comparison, with a one-way ANOVA corrected p-value of >0.05. In addition, expression profiles from SKBR-3/ EV and SK-B1-C1 cell were compared and a differential gene list was generated to include genes that differed by at least 1.5X, with a t-test p-value of >0.02 (unpaired, Bonferroni corrected). A total of 1940 entities met these criteria and the expression of these genes was investigated in all breast cancer cell lines.
2015-01-01 | E-GEOD-40152 | biostudies-arrayexpress
Project description:Protein glycosylation, and in particular N-linked glycans, is a hall mark of Eukaryotic cells and has been well studied in mammalian cells and parasites. However, little research has been conducted to investigate the conservation and variation of protein glycosylation pathways in other eukaryotic organisms. Euglena gracilis is an industrially important microalga, used in the production of biofuels and nutritional supplements. It is evolutionarily highly divergent from green algae and more related to Kinetoplastid pathogens. It was recently shown that E. gracilis possesses the machinery for producing a range of protein glycosylations and make simple N-glycans, but the modified proteins were not identified. This study identifies the glycosylated proteins, including transporters, extra cellular proteases and those involved in cell surface signalling. Notably, many of the most highly expressed and glycosylated proteins are not related to any known sequences and are therefore likely to be involved in important novel functions in Euglena.
2023-05-10 | PXD030579 | Pride
Project description:In this study, we identified and quantified the relative glycan distribution on UTI-Fc using nanoHILIC-MS for comprehensive mapping O-glycopeptides in UTI-Fc fusion protein. We quantified O-glycosylated peptides in the Fab domain and describe in detail for the first-time unexpected O-glycosylation at the linker and Fc region in UTI-Fc. These results highlight the improved performance of nanoHILIC-MS for characterization of biotherapeutic protein glycosylation in comparison to RP nanoLC-MS methods.
2023-03-11 | PXD033645 | Pride