O-GlcNAcylation Modulates Expression and Abundance of N-Glycosylation Machinery in an Inherited Glycosylation Disorder
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ABSTRACT:
PROVIDER: PRJNA1120060 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29285561_1.fastq.gz | Fastqsanger.gz | |||
| SRR29285561_2.fastq.gz | Fastqsanger.gz | |||
| SRR29285562_1.fastq.gz | Fastqsanger.gz | |||
| SRR29285562_2.fastq.gz | Fastqsanger.gz | |||
| SRR29285563_1.fastq.gz | Fastqsanger.gz |
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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:Core components of the N-glycosylation pathway are known, but the metabolic and post-translational mechanisms regulating this pathway in normal and disease states remain elusive. Using a multi-omic approach in zebrafish, we discovered a mechanism whereby O-GlcNAcylation directly impacts the expression and abundance of two rate-limiting proteins in the N-linked glycosylation pathway. We show in a model of an inherited glycosylation disorder PMM2-CDG, congenital disorders of glycosylation that phosphomannomutase deficiency is associated with increased levels of UDP-GlcNAc and protein O-GlcNAcylation. O-GlcNAc modification increases the transcript and protein abundance of both NgBR and Dpagt1 in pmm2m/m mutants. Modulating O-GlcNAc levels, NgBR abundance, or Dpagt1 activity exacerbated the cartilage phenotypes in pmm2 mutants, suggesting that O-GlcNAc-mediated increases in the N-glycosylation machinery are protective. These findings highlight nucleotide-sugar donors as metabolic sensors that regulate two spatially separated glycosylation pathways, demonstrating how their coordination is relevant to disease severity in the most common congenital disorder of glycosylation.
| S-EPMC11656453 | biostudies-literature
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:Alternative splicing (AS) is a key mechanism of gene regulation, but the full repertoire of proteins involved and the regulatory mechanisms governing this process remains poorly understood. Using TurboID-based proximity labeling coupled with mass spectrometry (PL-MS), we comprehensively mapped the Arabidopsis AS machinery, focusing on the evolutionarily conserved splicing factor ACINUS, its paralog PININ, and the stable interactor SR45. Our analysis identified a high-confidence list of 298 components, including both established and novel interactors, providing strong evidence that alternative splicing is coupled to transcription and that multiple RNA processing steps occur simultaneously in plants. Selected interactors were validated through AS readouts and phenotypic analysis. Furthermore, a systematic evaluation of O-glycosylation double mutants revealed that SECRET AGENT (O-GlcNAc transferase) and SPINDLY (O-fucose transferase) modulate AS through both ACINUS-dependent and -independent pathways.
2025-04-16 | GSE286870 | 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:Next-Generation Mapping of the ACINUS-Mediated Alternative Splicing Machinery and Its Regulation by O-glycosylation in Arabidopsis
| PRJNA1210017 | ENA