Analysis of the enzymes involved in PEN5 carbohydrate metabolism
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE29931 | GEO | 2011/06/14
SECONDARY ACCESSION(S): PRJNA140875
REPOSITORIES: GEO
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Project description:Dr. Eric Vivier's lab would like to tackle the enzymes involved in PEN5 carbohydrate metabolism. We have generated these cell lines by repeated cell sorting and cell cloning of the parental HSB-2 T cell line and the parental JY B cell line. H+ are PEN5+ HSB-2 cells, H- are PEN5- HSB-2 cells; JY+ are PEN5+ HSB-2 cells, JY- are PEN5- HSB-2 cells. We have originally described a cell surface molecule called PEN5, as a sulfated lactosamine, that is selectively expressed on a mature subset of human NK cells (Vivier, J. Exp. Med. 1993). Later, we have shown that the PEN5 carbohydrate decorates PSGL-1, confering L-selectin binding properties (André et al. PNAS, 2000). We have recently performed a Glycan Array Screening via Core H (Glycomics 917). These studies indeed reveal a very nice binding of the anti-PEN5 mAb to a subset of sulfated lactosamines. We would like to tackle the enzymes involved in PEN5 carbohydrate metabolism. We thus requesting a Gene microarray analysis performed using RNA extracted from PEN5+ and PEN5- NK cells, as well from the H+, H-, JY+ and JY- stable cell lines. We have generated these cell lines by repeated cell sorting and cell cloning of the parental HSB-2 T cell line and the parental JY B cell line. H+ are PEN5+ HSB-2 cells, H- are PEN5- HSB-2 cells; JY+ are PEN5+ HSB-2 cells, JY- are PEN5- HSB-2 cells. RNA preparations from variants of the HSB-2 (human T leukemia) and JY (human B lymphoma) cell lines, which were express or not PEN5 were sent to Microarray Core (E). These stable variants are referred to as H+ (HSB-2 cells expressing PEN5), H- (HSB-2 cells NOT expressing PEN5), JY+ (JY cells expressing PEN5), and JY- (JY cells NOT expressing PEN5). Samples were prepared at 3 different time points. The RNA was amplified, labeled, and hybridized to the GLYCOv3 microarrays. Data was sent to Dr. Eric Vivier for analysis.
2011-06-14 | E-GEOD-29931 | biostudies-arrayexpress
Project description:Aquaculture is one of the fastest growing sectors of US food production, with hybrid striped bass (HSB) considered a major species. A significant issue in HSB aquaculture stems from the large amount of variation in growth observed when growing-out these hybrids to market size adults. The goal of this study was therefore to determine if significant differences in metabolic gene expression might play a role in observed growth differences in HSB. The objective of this study was to use RNAseq on liver tissue of superior and inferior performing HSB representatives to identify global expression differences in HSB adults.
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Project description:Volvariella volvacea is one of a few commercial cultivated mushrooms mainly using straw as carbon source. In this study, the genome of V. volcacea was sequenced and assembled. A total of 286 genes encoding carbohydrate-active enzymes (CAZymes) in V. volvacea were identified and annotated. Among 15 fungi with sequenced genomes, V. volvacea ranks the seventh in the number of genes encoding CAZymes. In addition, the composition of glycoside hydrolases in V. volcacea is dramatically different from other basidiomycetes: it is particularly rich in members of the glycoside hydrolase families GH10 (hemicellulose degradation) and GH43 (hemicellulose and pectin degradation), and the lyase families PL1, PL3 and PL4 (pectin degradation) but lacks families GH5b, GH11, GH26, GH62, GH93, GH115, GH105, GH9, GH53, GH32, GH74 and CE12. Analysis of genome-wide gene expression profiles of 3 strains using 3'-tag digital gene expression (DGE) reveals that 246 CAZyme genes were expressed even in potato destrose broth medium. Our data also showed that the formation of a heterokaryon strain could dramatically increase the expression of a number of genes which were poorly expressed in its parental homokaryon strains.
2014-12-19 | GSE43019 | GEO
Project description:Volvariella volvacea is one of a few commercial cultivated mushrooms mainly using straw as carbon source. In this study, the genome of V. volcacea was sequenced and assembled. A total of 286 genes encoding carbohydrate-active enzymes (CAZymes) in V. volvacea were identified and annotated. Among 15 fungi with sequenced genomes, V. volvacea ranks the seventh in the number of genes encoding CAZymes. In addition, the composition of glycoside hydrolases in V. volcacea is dramatically different from other basidiomycetes: it is particularly rich in members of the glycoside hydrolase families GH10 (hemicellulose degradation) and GH43 (hemicellulose and pectin degradation), and the lyase families PL1, PL3 and PL4 (pectin degradation) but lacks families GH5b, GH11, GH26, GH62, GH93, GH115, GH105, GH9, GH53, GH32, GH74 and CE12. Analysis of genome-wide gene expression profiles of 3 strains using 3'-tag digital gene expression (DGE) reveals that 246 CAZyme genes were expressed even in potato destrose broth medium. Our data also showed that the formation of a heterokaryon strain could dramatically increase the expression of a number of genes which were poorly expressed in its parental homokaryon strains. Using the 3'-tag digital gene expression (DGE), we compared the gene expression profiles among 2 homokaryotic V. volvacea strains PYd15 and PYd21, and one heterokaryotic strain H1521, which is a hybrid strain of PYd15 and PYd21.
2014-12-19 | E-GEOD-43019 | biostudies-arrayexpress
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2015-12-15 | E-GEOD-75839 | biostudies-arrayexpress
Project description:Carbohydrate active enzymes often contain auxiliary binding sites located either on independent domains termed carbohydrate binding modules (CBMs) or as so-called surface binding sites (SBSs) on the catalytic module at a certain distance from the active site. The SBSs are usually critical for the activity of their cognate enzyme, though they are not readily detected in the sequence of a protein, but normally require a crystal structure of a complex for their identification. A variety of methods, including affinity electrophoresis (AE), insoluble polysaccharide pulldown (IPP) and surface plasmon resonance (SPR) have been used to study auxiliary binding sites. These techniques are complementary as AE allows monitoring of binding to soluble polysaccharides, IPP to insoluble polysaccharides and SPR to oligosaccharides. Here we show that these methods are useful not only for analyzing known binding sites, but also for identifying new ones, even without structural data available. We further verify the chosen assays discriminate between known SBS/CBM containing enzymes and negative controls. Altogether 35 enzymes are screened for the presence of SBSs or CBMs and several novel binding sites are identified, including the first SBS ever reported in a cellulase. This work demonstrates that combinations of these methods can be used as a part of routine enzyme characterization to identify new binding sites and advance the study of SBSs and CBMs, allowing them to be detected in the absence of structural data.
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Project description:In this project, we generated chronic sunitinib-treated 786-O cell, a renal cell carcinoma cell line. In order to investigate the possible effect of GPR30 agonist, G-1, on the growth-inhibtion related signaling pathways, we treated either parental both parental and chronic sunitinib-treated 786-O cells were treated either by vehicle-only (i.e. 0.1% DMSO) or 2 μM G-1 for 48 h. Therefore, there were three groups for comparison, including G-1 treatment (G-1 vs. parental), chronic sunitinib-treatment (SunR vs. parental), and G-1 treatment in SunR cells (SunR&G-1 vs. parental).
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