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To identify the deficient enzyme(s) in the glycosylation pathway that yield incomplete maturation of (uPAR) protein

ABSTRACT: We previously demonstrated plasticity in urokinase receptor (u-PAR) display in clonal colon cancer cells (Cancer Research 66: 7957-7967 (2006)). Thus, u-PAR display oscillates 10 fold between high and low density at the cell surface. We have determined that this oscillation in u-PAR display is posttranslational in nature. Thus, while clonal cell populations with high and low u-PAR density synthesize u-PAR at the same rate, the protein is inefficiently glycosylated in cells down-shifted for u-PAR display and subsequently degraded.

ORGANISM(S): Homo sapiens

PROVIDER: GSE31929 | GEO | 2011/09/06

SECONDARY ACCESSION(S): PRJNA145035

REPOSITORIES: GEO

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To identify the deficient enzyme(s) in the glycosylation pathway that yield incomplete maturation of (uPAR) protein

Project description:We previously demonstrated plasticity in urokinase receptor (u-PAR) display in clonal colon cancer cells (Cancer Research 66: 7957-7967 (2006)). Thus, u-PAR display oscillates 10 fold between high and low density at the cell surface. We have determined that this oscillation in u-PAR display is posttranslational in nature. Thus, while clonal cell populations with high and low u-PAR density synthesize u-PAR at the same rate, the protein is inefficiently glycosylated in cells down-shifted for u-PAR display and subsequently degraded. The objective of this study is to identify the deficient enzyme(s) in the glycosylation pathway that yield incomplete maturation of the u-PAR protein and hence its premature degradation. We will compare a clonal population of the RKO colon cancer cell line (designated RKO C2) with a population derived (by FACS sorting for low u-PAR) from RKO C2 (designated RKO C2 F3).

2011-09-05 | E-GEOD-31929 | biostudies-arrayexpress

CD209L/L-SIGN N-Glycosylation and N-Glycosylation Site Occupancy

Project description:CD209L is a membrane glycoprotein with known glycan-binding properties and it also contains 2 N-glycosylation sequons at sites N92 and N361. Treatment with PNGase F in the presence of H218O, which removes N-linked glycans and isotopically labels the formerly-glycosylated site, confirmed that both unmodified and formerly-glycosylated versions of the peptide spanning the N92 N-glycosylated sequon were present. This suggests that a portion of CD209L protein is N-glycosylated at site N92. nUPLC-MS/MS analyses of CD209L digests enabled detection of a glycopeptide consistent with high-mannose type N-linked glycosylation.

2021-09-09 | PXD021309 | Pride

The role of glycans and glycosylation in cell-type specific effects on viral infectivity

2011-06-14 | GSE29924 | GEO

Cerebral organoids display dynamic clonal growth with lineage replenishment

Project description:Cerebral organoids display dynamic clonal growth with lineage replenishment

| PRJNA883958 | ENA

O-Glycosylation of Mycobacteriophage Proteins

Project description:Provided herein is the first evidence that mycobacteriophage, indeed phage of any kind, have surface proteins (capsid and/or tail tube proteins) that are O-glycosylated. The glycosyltranferases that glycosylate these proteins are encoded in the phage genomes. In addition, for the three mycobacteriophages invested in this study, the glycans appear to be attached exclusively at a C-terminal serine residue. Each phage expresses a unique and novel O-glycan. The LC-MS files deposited here are the preliminary evidence that these mycobacteriophage proteins are glycosylated. A follow-up investigation will examine the composition and structure of the O-glycans in more detail.

2024-08-10 | PXD041690 | Pride

Incomplete glycosylation during prion infection unmasks a prion protein epitope that facilitates prion detection and strain discrimination.

Project description:The causative factors underlying conformational conversion of cellular prion protein (PrPC) into its infectious counterpart (PrPSc) during prion infection remain undetermined, in part because of a lack of monoclonal antibodies (mAbs) that can distinguish these conformational isoforms. Here we show that the anti-PrP mAb PRC7 recognizes an epitope that is shielded from detection when glycans are attached to Asn-196. We observed that whereas PrPC is predisposed to full glycosylation and is therefore refractory to PRC7 detection, prion infection leads to diminished PrPSc glycosylation at Asn-196, resulting in an unshielded PRC7 epitope that is amenable to mAb recognition upon renaturation. Detection of PRC7-reactive PrPSc in experimental and natural infections with various mouse-adapted scrapie strains and with prions causing deer and elk chronic wasting disease and transmissible mink encephalopathy uncovered that incomplete PrPSc glycosylation is a consistent feature of prion pathogenesis. We also show that interrogating the conformational properties of the PRC7 epitope affords a direct means of distinguishing different prion strains. Because the specificity of our approach for prion detection and strain discrimination relies on the extent to which N-linked glycosylation shields or unshields PrP epitopes from antibody recognition, it dispenses with the requirement for additional standard manipulations to distinguish PrPSc from PrPC, including evaluation of protease resistance. Our findings not only highlight an innovative and facile strategy for prion detection and strain differentiation, but are also consistent with a mechanism of prion replication in which structural instability of incompletely glycosylated PrP contributes to the conformational conversion of PrPC to PrPSc.

| S-EPMC7383396 | biostudies-literature

Deconstruction of the GalNAc-Type O-Glycosylation Capacity of Human HEK293 Cells

Project description:Most proteins trafficking the secretory pathway of metazoan cells will acquire GalNAc-type O-glycosylation. GalNAc-type O-glycosylation is differentially regulated in cells by the expression of a repertoire of up to twenty genes encoding polypeptide GalNAc-transferase isoforms (GalNAc-Ts) that initiate O-glycosylation by catalyzing the attachment of GalNAc residues to select Ser and Thr residues. These GalNAc-Ts orchestrate the positions and patterns of O-glycans on proteins in poorly understood coordinated ways guided partly by the kinetic properties and substrate specificities of their catalytic domains and modulatory effects of their unique GalNAc-binding lectin domains. Here, we provide the hereto most comprehensive characterization of the non-redundant contributions of individual GalNAc-T isoforms to the O-glycoproteome of the human HEK293 cell line using quantitative differential O-glycoproteomics on a panel of isogenic HEK293 cell lines with knockout of GalNAc-T genes (GALNT1, T2, T3, T7, T10, or T11). We confirm that a major part of the O-glycoproteome is covered by redundancy, while distinct subsets of O-glycosites are covered by non-redundant GalNAc-T isoform-specific functions. We demonstrate that GalNAc-T7 and T10 as predicted from in vitro studies function in completion of high density O-glycosylated regions, while GalNAc-T11 selectively controls the site-specific O-glycosylation of low-density lipoprotein-related receptors in the linker regions between the ligand-binding LDLR class A repeats.

2019-06-24 | PXD009955 | Pride

The role of glycans and glycosylation in cell-type specific effects on viral infectivity

Project description:Our lab has previously used the Glyco v3 gene-chip to analyze RNA from human macrophages and T-cells, as part of a project examining the effect of cellular origin on the viral infectivity of HIV/SIV. Our experiments have led us to hypothesize that the different glycosylation pathways present in macrophages and T-cells result in the production of virions with differently glycosylated viral proteins and different glycans present on the virion surface. Furthermore, studies with glycosidases using the Glyco v3 gene-chip have indicated that these differences in the glycosylation profiles of virions derived from different cell types may influence viral infectivity. Here we used glyco v3 chips for identifying the enzymes active in the glycosylation pathways of 174xCEM and 293 cells, which are cell types commonly used in HIV and SIV research. These analyses will allow us a better understanding of the role of glycans and glycosylation in cell-type specific effects on viral infectivity because there is a much larger amount of data on virus derived from these cell types and we will be able to relate our studies more directly to previous work in our lab and other labs. RNA from 174xCEM and HEK293 cells, cell types commonly used in HIV and SIV research, was isolated and sent to Microarray Core (E). RNA was prepared in duplicate, totaling 4 samples. Samples were labeled and hybridized to the GLYCOv3 array and gene expression patterns were used to identify enzymes active in glycosylation pathways.

2011-06-14 | E-GEOD-29924 | biostudies-arrayexpress

Epigenetic age oscillates during the day

Project description:Epigenetic age oscillates during the day

| PRJNA1036603 | ENA

Exploring glycosylation of mucins with O-glycodomain reporters expressed in glycoengineered HEK293 cells

Project description:Mucins and glycoproteins with mucin-like regions contain densely O-glycosylated domains often found in tandem repeat (TR) sequences. These O-glycodomains have traditionally been difficult to characterize because of resistance to proteolytic digestion, and knowledge of positions of O-glycans is particularly limited for these regions. Mucin O-glycodomains are believed to contain important binding cues for endogenous lectin receptors and the microbiota, and it is important to develop strategies to characterize and produce these abundant molecules. Here, we took advantage of our recently developed glycoengineered cell-based platform for display and production of mucin TR reporters with custom designed O-glycosylation to characterize O-glycodomains derived from mucins and mucin-like glycoproteins. We combined intact mass and bottom-up site-specific analysis for mapping O-glycosites in MUC2, MUC20, MUC21, PSGL-1, and Syndecan-3. We found that all the potential Ser/Thr positions in these O-glycodomains were O-glycosylated when expressed in HEK293 SimpleCells (Tn-glycoform). Interestingly, while all the sites in TRs derived from secreted mucins were almost fully occupied, positions in TRs from a subset of transmembrane mucins were less efficiently processed. We further used the mucin TR reporters to characterize cleavage sites of the StcE and BT4244 glycoproteases, revealing a more restricted substrate specificities than reported. Finally, we used these for bottom-up analysis of isolated ovine submaxillary mucin (OSM) and identified the gene. The study provides insight into O-glycosylation of mucins and mucin-like domains and the strategies developed open up for wider analysis of native mucins.

2022-05-20 | PXD029885 | Pride

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