Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

N-Linked Glycans of Chloroviruses Sharing a Core Architecture without Precedent.

ABSTRACT: N-glycosylation is a fundamental modification of proteins and exists in the three domains of life and in some viruses, including the chloroviruses, for which a new type of core N-glycan is herein described. This N-glycan core structure, common to all chloroviruses, is a pentasaccharide with a ?-glucose linked to an asparagine residue which is not located in the typical sequon N-X-T/S. The glucose is linked to a terminal xylose unit and a hyperbranched fucose, which is in turn substituted with a terminal galactose and a second xylose residue. The third position of the fucose unit is always linked to a rhamnose, which is a semiconserved element because its absolute configuration is virus-dependent. Additional decorations occur on this core N-glycan and represent a molecular signature for each chlorovirus.

SUBMITTER: De Castro C

PROVIDER: S-EPMC4836869 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

N-Linked Glycans of Chloroviruses Sharing a Core Architecture without Precedent.

De Castro Cristina C Speciale Immacolata I Duncan Garry G Dunigan David D DD Agarkova Irina I Lanzetta Rosa R Sturiale Luisa L Palmigiano Angelo A Garozzo Domenico D Molinaro Antonio A Tonetti Michela M Van Etten James L JL

Angewandte Chemie (International ed. in English) 20151119 2

N-glycosylation is a fundamental modification of proteins and exists in the three domains of life and in some viruses, including the chloroviruses, for which a new type of core N-glycan is herein described. This N-glycan core structure, common to all chloroviruses, is a pentasaccharide with a β-glucose linked to an asparagine residue which is not located in the typical sequon N-X-T/S. The glucose is linked to a terminal xylose unit and a hyperbranched fucose, which is in turn substituted with a ...[more]

PMID: 26582281

Similar Datasets

Nucleotide composition-linked divergence of vertebrate core promoter architecture

Project description:Transcription initiation involves the recruitment of basal transcription factors to the core promoter. A variety of core promoter elements exists, however for most of these motifs the distribution across species is unknown. Here we report on the comparison of human and amphibian promoter sequences. We have used oligo-capping in combination with deep sequencing to determine transcription start sites in Xenopus tropicalis. To systematically predict regulatory elements we have developed a de novo motif finding pipeline using an ensemble of computational tools. A comprehensive comparison of human and amphibian promoter sequences revealed both similarities and differences in core promoter architecture. Some of the differences stem from a highly divergent nucleotide composition of Xenopus and human promoters. Whereas the distribution of some core promoter motifs is conserved independent of species-specific nucleotide bias, the frequency of another class of motifs correlates with the single nucleotide frequencies. This class includes the well-known TATA box and SP1 motifs, which are more abundant in Xenopus and human promoters, respectively. While these motifs are enriched above the local nucleotide background in both organisms, their frequency varies in step with this background. These differences are likely adaptive as these motifs can recruit TFIID to either CpG island or sharply initiating promoters. Our results highlight both conserved and diverged aspects of vertebrate transcription, most notably showing co-opted motif usage to recruit the transcriptional machinery to promoters with diverging nucleotide composition. This shows how sweeping changes in nucleotide composition are compatible with highly conserved mechanisms of transcription initiation. ChIP-seq profiles of TBP in Xenopus tropicalis stage 12 embryos and TSS-seq profiles of Xenopus oocytes and stage 12 embryos

2010-12-30 | E-GEOD-21482 | biostudies-arrayexpress

Manual and Automated Syntheses of the N-Linked Glycoprotein Core Glycans.

Project description:Presented herein are two complementary approaches to the synthesis of the core N-glycan pentasaccharide. The first, a traditional manual approach in solution, makes use of the H-bond-mediated aglycone delivery method for the highly diastereoselective introduction of the β-mannosidic linkage at room temperature. The synthesis of the core pentasaccharide was also accomplished using an high-performance liquid chromatography-assisted automated approach. The overall assembly was swift (8 h) and efficient (31%).

| S-EPMC8114088 | biostudies-literature

Nucleotide composition-linked divergence of vertebrate core promoter architecture.

Project description:Transcription initiation involves the recruitment of basal transcription factors to the core promoter. A variety of core promoter elements exists; however for most of these motifs, the distribution across species is unknown. Here we report on the comparison of human and amphibian promoter sequences. We have used oligo-capping in combination with deep sequencing to determine transcription start sites in Xenopus tropicalis. To systematically predict regulatory elements, we have developed a de novo motif finding pipeline using an ensemble of computational tools. A comprehensive comparison of human and amphibian promoter sequences revealed both similarities and differences in core promoter architecture. Some of the differences stem from a highly divergent nucleotide composition of Xenopus and human promoters. Whereas the distribution of some core promoter motifs is conserved independently of species-specific nucleotide bias, the frequency of another class of motifs correlates with the single nucleotide frequencies. This class includes the well-known TATA box and SP1 motifs, which are more abundant in Xenopus and human promoters, respectively. While these motifs are enriched above the local nucleotide background in both organisms, their frequency varies in step with this background. These differences are likely adaptive as these motifs can recruit TFIID to either CpG island or sharply initiating promoters. Our results highlight both the conserved and diverged aspects of vertebrate transcription, most notably showing co-opted motif usage to recruit the transcriptional machinery to promoters with diverging nucleotide composition. This shows how sweeping changes in nucleotide composition are compatible with highly conserved mechanisms of transcription initiation.

| S-EPMC3044855 | biostudies-literature

Chloroviruses.

Project description:Chloroviruses are large dsDNA, plaque-forming viruses that infect certain chlorella-like green algae; the algae are normally mutualistic endosymbionts of protists and metazoans and are often referred to as zoochlorellae. The viruses are ubiquitous in inland aqueous environments throughout the world and occasionally single types reach titers of thousands of plaque-forming units per ml of native water. The viruses are icosahedral in shape with a spike structure located at one of the vertices. They contain an internal membrane that is required for infectivity. The viral genomes are 290 to 370 kb in size, which encode up to 16 tRNAs and 330 to ~415 proteins, including many not previously seen in viruses. Examples include genes encoding DNA restriction and modification enzymes, hyaluronan and chitin biosynthetic enzymes, polyamine biosynthetic enzymes, ion channel and transport proteins, and enzymes involved in the glycan synthesis of the virus major capsid glycoproteins. The proteins encoded by many of these viruses are often the smallest or among the smallest proteins of their class. Consequently, some of the viral proteins are the subject of intensive biochemical and structural investigation.

| S-EPMC7019647 | biostudies-literature

Nucleotide composition-linked divergence of vertebrate core promoter architecture

2010-12-30 | GSE21482 | GEO

Future climate forcing potentially without precedent in the last 420 million years.

Project description:The evolution of Earth's climate on geological timescales is largely driven by variations in the magnitude of total solar irradiance (TSI) and changes in the greenhouse gas content of the atmosphere. Here we show that the slow ∼50 Wm-2 increase in TSI over the last ∼420 million years (an increase of ∼9 Wm-2 of radiative forcing) was almost completely negated by a long-term decline in atmospheric CO2. This was likely due to the silicate weathering-negative feedback and the expansion of land plants that together ensured Earth's long-term habitability. Humanity's fossil-fuel use, if unabated, risks taking us, by the middle of the twenty-first century, to values of CO2 not seen since the early Eocene (50 million years ago). If CO2 continues to rise further into the twenty-third century, then the associated large increase in radiative forcing, and how the Earth system would respond, would likely be without geological precedent in the last half a billion years.

| S-EPMC5382278 | biostudies-literature

Aberrant expression of mucin core proteins and o-linked glycans associated with progression of pancreatic cancer.

Project description:Mucin expression is a common feature of most adenocarcinomas and features prominently in current attempts to improve diagnosis and therapy for pancreatic cancer and other adenocarcinomas. We investigated the expression of a number of mucin core proteins and associated O-linked glycans expressed in pancreatic adenocarcinoma-sialyl Tn (STn), Tn, T antigen, sialyl Lewis A (CA19-9), sialyl Lewis C (SLeC), Lewis X (LeX), and sialyl LeX (SLeX)-during the progression of pancreatic cancer from early stages to metastatic disease.Immunohistochemical analyses of mucin and associated glycan expression on primary tumor and liver metastatic tumor samples were conducted with matched sets of tissues from 40 autopsy patients diagnosed with pancreatic adenocarcinoma, 14 surgically resected tissue samples, and 8 normal pancreata.There were significant changes in mucin expression patterns throughout disease progression. MUC1 and MUC4 were differentially glycosylated as the disease progressed from early pancreatic intraepithelial neoplasias to metastatic disease. De novo expression of several mucins correlated with increased metastasis indicating a potentially more invasive phenotype, and we show the expression of MUC6 in acinar cells undergoing acinar to ductal metaplasia. A "cancer field-effect" that included changes in mucin protein expression and glycosylation in the adjacent normal pancreas was also seen.There are significant alterations in mucin expression and posttranslational processing during progression of pancreatic cancer from early lesions to metastasis. The results are presented in the context of how mucins influence the biology of tumor cells and their microenvironment during progression of pancreatic cancer.

| S-EPMC3873635 | biostudies-literature

Measles virus envelope pseudotyped lentiviral vectors transduce quiescent human HSCs at an efficiency without precedent.

Project description:Hematopoietic stem cell (HSC)-based gene therapy trials are now moving toward the use of lentiviral vectors (LVs) with success. However, one challenge in the field remains: efficient transduction of HSCs without compromising their stem cell potential. Here we showed that measles virus glycoprotein-displaying LVs (hemagglutinin and fusion protein LVs [H/F-LVs]) were capable of transducing 100% of early-acting cytokine-stimulated human CD34+ (hCD34+) progenitor cells upon a single application. Strikingly, these H/F-LVs also allowed transduction of up to 70% of nonstimulated quiescent hCD34+ cells, whereas conventional vesicular stomatitis virus G (VSV-G)-LVs reached 5% at the most with H/F-LV entry occurring exclusively through the CD46 complement receptor. Importantly, reconstitution of NOD/SCIDγc-/- (NSG) mice with H/F-LV transduced prestimulated or resting hCD34+ cells confirmed these high transduction levels in all myeloid and lymphoid lineages. Remarkably, for resting CD34+ cells, secondary recipients exhibited increasing transduction levels of up to 100%, emphasizing that H/F-LVs efficiently gene-marked HSCs in the resting state. Because H/F-LVs promoted ex vivo gene modification of minimally manipulated CD34+ progenitors that maintained stemness, we assessed their applicability in Fanconi anemia, a bone marrow (BM) failure with chromosomal fragility. Notably, only H/F-LVs efficiently gene-corrected minimally stimulated hCD34+ cells in unfractionated BM from these patients. These H/F-LVs improved HSC gene delivery in the absence of cytokine stimulation while maintaining their stem cell potential. Thus, H/F-LVs will facilitate future clinical applications requiring HSC gene modification, including BM failure syndromes, for which treatment has been very challenging up to now.

| S-EPMC5728281 | biostudies-literature

A synthetic precedent for the [FeIV2(mu-O)2] diamond core proposed for methane monooxygenase intermediate Q.

Project description:Intermediate Q, the methane-oxidizing species of soluble methane monooxygenase, is proposed to have an [Fe(IV)(2)(mu-O)(2)] diamond core. In an effort to obtain a synthetic precedent for such a core, bulk electrolysis at 900 mV (versus Fc(+/0)) has been performed in MeCN at -40 degrees C on a valence-delocalized [Fe(III)Fe(IV)(mu-O)(2)(L(b))(2)](3+) complex (1b) (E(1/2) = 760 mV versus Fc(+/0)). Oxidation of 1b results in the near-quantitative formation of a deep red complex, designated 2b, that exhibits a visible spectrum with lambda(max) at 485 nm (9,800 M(-1).cm(-1)) and 875 nm (2,200 M(-1).cm(-1)). The 4.2 K Mössbauer spectrum of 2b exhibits a quadrupole doublet with delta = -0.04(1) mm.s(-1) and DeltaE(Q) = 2.09(2) mm.s(-1), parameters typical of an iron(IV) center. The Mössbauer patterns observed in strong applied fields show that 2b is an antiferromagnetically coupled diiron(IV) center. Resonance Raman studies reveal the diagnostic vibration mode of the [Fe(2)(mu-O)(2)] core at 674 cm(-1), downshifting 30 cm(-1) upon (18)O labeling. Extended x-ray absorption fine structure (EXAFS) analysis shows two O/N scatterers at 1.78 A and an Fe scatterer at 2.73 A. Based on the accumulated spectroscopic evidence, 2b thus can be formulated as [Fe(IV)(2)(mu-O)(2)(L(b))(2)](4+), the first synthetic complex with an [Fe(IV)(2)(mu-O)(2)] core. A comparison of 2b and its mononuclear analog [Fe(IV)(O)(L(b))(NCMe)](2+) (4b) reveals that 4b is 100-fold more reactive than 2b in oxidizing weak C H bonds. This surprising observation may shed further light on how intermediate Q carries out the hydroxylation of methane.

| S-EPMC2409154 | biostudies-literature

Divergent Chemoenzymatic Synthesis of Asymmetrical-Core-Fucosylated and Core-Unmodified N-Glycans.

Project description:A divergent chemoenzymaytic approach for the preparation of core-fucosylated and core-unmodified asymmetrical N-glycans from a common advances precursor is described. An undecasaccharide was synthesized by sequential chemical glycosylations of an orthogonally protected core fucosylated hexasaccharide that is common to all mammalian core fucosylated N-glycans. Antennae-selective enzymatic extension of the undecasaccharide using a panel of glycosyl transferases afforded core fucosylated asymmetrical triantennary N-glycan isomers, which are potential biomarkers for breast cancer. A unique aspect of our approach is that a fucosidase (FucA1) has been identified that selectively can cleave a core-fucoside without affecting the fucoside of a sialyl LewisX epitope to give easy access to core-unmodified compounds.

| S-EPMC5442444 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data