O-GlcNAcylation Modulates Expression and Abundance of N-Glycosylation Machinery in an Inherited Glycosylation Disorder
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PROVIDER: PRJNA1120060 | ENA |
REPOSITORIES: ENA
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Project description:Much of the N-glycosylation machinery was identified decades ago, but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process, revising the view of the relationship between different metabolic pathways. Using a multi-omic approach in a zebrafish, we discovered a mechanism where O-GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N-linked glycosylation, the nus1-encoded NgBR and Dpagt1. Here we show that phosphomannomutase (pmm2) deficiency is associated with increased levels of UDP-GlcNAc and protein O-GlcNAcylation. Biochemical studies show that O-GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O-GlcNAc levels, NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants, suggesting that O-GlcNAc mediated increases in the N-glycosylation machinery protects against more severe pathology. These findings highlight nucleotide-sugar donors as metabolic sensors that coordinate two different glycosylation pathways, demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation.
2024-12-27 | GSE269074 | GEO
Project description:O-GlcNAcylation is an essential, nutrient-sensitive post-translational modification, but its biochemical and phenotypic effects remain incompletely understood. To address this knowledge gap, we investigated the global transcriptional response to perturbations in O-GlcNAcylation. Unexpectedly, many transcriptional effects of O-GlcNAc transferase (OGT) inhibition were due to the activation of NRF2, the master regulator of redox stress tolerance. Moreover, we found that a signature of low OGT activity strongly correlates with NRF2 activation in multiple tumor expression datasets. Guided by this information, we identified KEAP1 (also known as KLHL19), the primary negative regulator of NRF2, as a direct substrate of OGT. We show that O-GlcNAcylation of KEAP1 at serine 104 is required for the efficient ubiquitination and degradation of NRF2. Interestingly, O-GlcNAc levels and NRF2 activation co-vary in response to glucose fluctuations, indicating that KEAP1 O-GlcNAcylation links nutrient sensing to downstream stress resistance. Our results reveal a novel regulatory connection between nutrient-sensitive glycosylation and NRF2 signaling, and provide a blueprint for future approaches to discover functionally important O-GlcNAcylation events on other KLHL family proteins in various experimental and disease contexts.
2017-06-26 | GSE81740 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE33049: GlcNAcylation of histone H2B facilitates its monoubiquitination [Illumina Genome Analyzer data] GSE33050: GlcNAcylation of histone H2B facilitates its monoubiquitination [Affymetrix data] Refer to individual Series
2011-10-26 | E-GEOD-33051 | biostudies-arrayexpress
Project description:We report that histone GlcNAcylation of H2B S112 is a vital histone modification which facilitates histone monoubiquitination (ub). In a genome-wide analysis, H2B S112 GlcNAcylation sites were observed widely distributed over entire chromosomes including transcribed gene loci, together with co-localization of H2B S112 GlcNAcylation and K120 ub. Examination of H2B S112 GlcNAc and H2B K120 ub in HeLa S3 cells
2011-10-27 | E-GEOD-33049 | biostudies-arrayexpress
Project description:Cellular homeostasis is ensured by myriad cellular processes that integrate environmental changes and maintain stability within the organism. Variation in nutrient availability can be reflected by the post-translational modification of many proteins by the nutrient sensor O-GlcNAcylation. Herein, we describe a molecular mechanism of transcription regulation by O-GlcNAcylation of the TATA-box binding protein (TBP). We show that O-GlcNAcylation regulates its interaction with BTAF1, hence, formation of the B-TFIID complex, and its dynamic cycling on and off of DNA. We mapped three O-GlcNAcylation sites at the N-terminus of TBP and defined T114 as a main regulator of the interaction with BTAF1. CRISPR/Cas9 editing of wild-type TBP replaced by a T114A mutant, leads to profound modification of HeLa cells’ glucose and lipid metabolism and gene expression profile. These data indicate that basal transcription machinery, via O-GlcNAcylation of TBP, can integrate nutrient availability and modulate the transcriptome, resulting in adaptation of cellular metabolism.
2020-04-14 | GSE106231 | GEO
Project description:Purpose: CREB (cAMP response element binding protein) is a transcription factor that is critical for learning and memory. The activity of CREB is mediated through its post-translational modifications (PTMs); specifically, phosphorylation at serine 133 and glycosylation at serine 40. In this study, we used RNA-Seq and weighted gene network coexpression analysis (WGCNA) to determine the CREB-mediated transcriptional programmes that are regulated by phosphorylation at serine 133 and glycosylation at serine 40 through the use of various PTM-deficient CREB mutants. Methods: The mRNA profiles of E16.5 Creb1-/- mouse cortical neurons expressing GFP, WT CREB, S40A-CREB, S133A-CREB, and S40A-S133A-CREB were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500. The sequence reads that passed quality filters were analyzed using Bowtie, aligned using TopHat, and quantified using Cufflinks in Galaxy. Results: Through differential expression analysis with glycosylation-deficient (S40A) and phosphorylation-deficient (S133A) CREB mutants, we show that CREB O-GlcNAcylation is important for neuronal activity and excitability, while phosphorylation at serine 133 regulates the expression of genes involved in neuronal differentiation. Furthermore, many of the S40A and S133A differentially-expressed genes were directly bound by (1) CREB and its co-activators, CREB-binding protein and p300, (2) activating histone modifications, (3) OGT and O-GlcNAc, and (4) Tet1, an critical regulator of neuronal activity and differentiation. Finally, we observed a positive correlation between S40A and activity- and excitotoxicity-related gene networks and a negative correlation between S133A and neuronal differentiation and amino and fatty acid metabolism-related gene networks. This study demonstrates that CREB O-GlcNAcylation at serine 40 and phosphorylation mediate mutually exclusive gene networks. Together, O-GlcNAc and phosphorylation impart a TF code, which CREB must integrate and decode to modulate neuronal activity, differentiation, and metabolism.
2020-12-17 | GSE109349 | GEO
Project description:We report that histone GlcNAcylation of H2B S112 is a vital histone modification which facilitates histone monoubiquitination (ub). In a genome-wide analysis, H2B S112 GlcNAcylation sites were observed widely distributed over entire chromosomes including transcribed gene loci, together with co-localization of H2B S112 GlcNAcylation and K120 ub.
2011-10-27 | GSE33049 | GEO
Project description:Endomembrane glycosylation and cytoplasmic O-GlcNAcylation each play essential roles in nutrient sensing, and in fact, characteristic changes in glycan patterns have been described in disease states such as diabetes and cancer. These changes in glycosylation have important functional roles and can drive disease progression. However, little is known about the molecular mechanisms underlying how these signals are integrated and transduced into biological effects. Galectins are proteins that bind glycans and are secreted by a poorly characterized non-classical secretory mechanism. Once outside the cell, galectins bind to terminal galactose residues of cell surface glycans and modulate numerous extracellular functions like clathrin independent endocytosis (CIE). Originating in the cytoplasm, galectins are predicted substrates for O-GlcNAc addition and removal; and, as we have shown, galectin 3 is a substrate for OGT. This study also shows that galectin 3 secretion is sensitive to changes in O-GlcNAc levels. We determined that there is a significant difference in O-GlcNAcylation status between cytoplasmic and secreted galectin 3. We observed dramatic alterations in galectin 3 secretion in response to nutrient conditions and these changes were dependent on dynamic O-GlcNAcylation. Importantly, we showed that these O-GlcNAc driven alterations in galectin 3 secretion drove changes in CIE. These results indicate that dynamic O-GlcNAcylation of galectin 3 plays a role in modulating its secretion and can tune its function of transducing nutrient sensing information coded in cell surface glycosylation into biological effects.
2022-04-01 | PXD028139 | Pride
Project description:Secondary metabolites play a key role in coordinating ecology and defense strategies of plants. Diversity of these metabolites arise by conjugation of core structures with diverse chemical moieties, such as sugars in glycosylation. Active pools of phytohormones, including those involved in plant stress response are also regulated by glycosylation. While, much is known about the enzymes involved in glycosylation, we know little about their regulation or coordination with other processes. We characterized the flavonoid pathway transcription factor, TRANSPARENT TESTA 8 (TT8) in Arabidopsis thaliana, using an integrative omics strategy. This approach provides a systems level understanding of the cellular machinery that is used to generate metabolite diversity by glycosylation. Metabolomics analysis of TT8 loss-of-function and inducible overexpression lines showed that TT8 coordinates glycosylation of not only flavonoids, but also nucleotides, thus, implicating TT8 in regulating pools of activated nucleotide sugars. Transcriptome and promoter network analyses revealed that TT8 regulome included sugar transporters, proteins involved in sugar binding and sequestration, and a number of carbohydrate active enzymes. Importantly, TT8 affects stress response, along with brassinosteroid and jasmonic acid biosynthesis, by directly binding to the promoters of key genes of these processes. This combined effect on metabolites glycosylation and stress hormones by TT8 inducible overexpression led to significant increase in tolerance towards multiple abiotic and biotic stresses. Conversely, loss of TT8 leads to increased sensitivity to these stresses. Thus, the transcription factor TT8 is an integrator of secondary metabolism and stress response. These findings provide novel approaches to improve broad-spectrum stress tolerance. Gene expression analysis for 6-day old Arabidopsis thaliana seedling were performed for TT8 loss-of-function line, tt8-3 (in Ws background), and its wild type background control, Ws. Two independent biological replicates for each line were hybridized onto two slides of Agilent SurePrint G2 Agilent Arabidopsis V4 (4x44K), with each slide having two technical replicates for each line. Contributors: Amit Rai, Shivshankar Umashankar, Megha, Lim Boon Kiat, Johanan Aow Shao Bing, Sanjay Swarup.
2016-07-20 | E-GEOD-59048 | biostudies-arrayexpress
Project description:Secondary metabolites play a key role in coordinating ecology and defense strategies of plants. Diversity of these metabolites arise by conjugation of core structures with diverse chemical moieties, such as sugars in glycosylation. Active pools of phytohormones, including those involved in plant stress response are also regulated by glycosylation. While, much is known about the enzymes involved in glycosylation, we know little about their regulation or coordination with other processes. We characterized the flavonoid pathway transcription factor, TRANSPARENT TESTA 8 (TT8) in Arabidopsis thaliana, using an integrative omics strategy. This approach provides a systems level understanding of the cellular machinery that is used to generate metabolite diversity by glycosylation. Metabolomics analysis of TT8 loss-of-function and inducible overexpression lines showed that TT8 coordinates glycosylation of not only flavonoids, but also nucleotides, thus, implicating TT8 in regulating pools of activated nucleotide sugars. Transcriptome and promoter network analyses revealed that TT8 regulome included sugar transporters, proteins involved in sugar binding and sequestration, and a number of carbohydrate active enzymes. Importantly, TT8 affects stress response, along with brassinosteroid and jasmonic acid biosynthesis, by directly binding to the promoters of key genes of these processes. This combined effect on metabolites glycosylation and stress hormones by TT8 inducible overexpression led to significant increase in tolerance towards multiple abiotic and biotic stresses. Conversely, loss of TT8 leads to increased sensitivity to these stresses. Thus, the transcription factor TT8 is an integrator of secondary metabolism and stress response. These findings provide novel approaches to improve broad-spectrum stress tolerance.
2016-07-20 | GSE59048 | GEO