Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ubiquitin diGly site ampping on ZNFX1 autoubiquitination reactions

ABSTRACT: This experiment aimed to characterise ubiquitin chain linkage preferences generated and autoubiquitination sistes during ZNFX1 E3 reactions using diGly remnant mass spectrometry. GlyGly-modified lysine residues were identified as a qualitative proxy for ubiquitin linkage types. Spectral counts of rank-1 GlyGly-modified peptides were used to infer relative linkage abundance. Data interpretation was qualitative in nature, with no quantitative normalisation or statistical comparison applied.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Satpal Virdee

LAB HEAD: Satpal Virdee

PROVIDER: PXD073484 | Pride | 2026-05-22

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20250821_DSquair_SV_119966_03_minusRNA.raw	Raw
	20250821_DSquair_SV_119966_04_plusRNA.raw	Raw
	F300634-plusRNA.csv	Csv
	F300635-minusRNA.csv	Csv
	checksum.txt	Txt

Items per page:

1 - 5 of 5

Publications

ZNFX1 uses two-component ubiquitin circuitry to quarantine viral RNA.

Squair Daniel R DR Rivers Eilidh E Sowar Hanna H Balci Arda A Harmo Roosa R Wright David J DJ Beniwal Gaurav G Soetens Mathieu M Mathur Sunil S Tollervey Aidan A Wood Nicola T NT Pao Kuan-Chuan KC Stanton Callum C Fletcher Adam J AJ Virdee Satpal S

Molecular cell 20260301 6

The detection of viral RNA inside cells triggers a diverse range of antiviral responses, including global translation inhibition, interferon secretion, and RNA sequestration. Mutations in the gene zinc-finger NFX1-type containing 1 (ZNFX1) cause severe pediatric immunodeficiencies, including chronic viral infection and autoinflammation. Here, we show that ZNFX1 is an RNA helicase with cryptic and unusual bifurcating E3 ubiquitin ligase activity. Nucleotide-dependent RNA binding stimulates ZNFX1 ...[more]

PMID: 41861786

Similar Datasets

DiGly analysis of autoubiquitinated UBR4 (residues 4730-5183)

Project description:Human recombinant UBR4 protein, consisting of residues 4730-5183, undergoes in vitro autoubiquitination when incubated with the E2 conjugating enzyme UBE2A and the other reaction components. The autoubiquitinated protein was analysed by mass spectrometry to identify modification sites and the ubiquitin linkage types present. This was achieved by searching for diGly as a variable modification on Ser, Thr, Tyr, Cys and Lys residues. A single autoubiquitination site at K4814 was detected. However, mutation of this residue impaired autoubiquitination, indicating the presence of additional sites. The ubiquitin linkages identified were Lys33, Lys48, Lys63, Lys11 and Lys6, suggesting that UBR4 assembles these ubiquitin linkages on its substrates.

2023-11-15 | PXD046899 | Pride

Gingipain transpeptidation - Porphyromonas gingivalis Gingipains Display Transpeptidation Activity

Project description:Porphyromonas gingivalis is a keystone periodontal pathogen that has been associated with autoimmune disorders. The cell surface proteases Lys-gingipain (Kgp) and Arg-gingipains (RgpA and RgpB) are major virulence factors and their proteolytic activity is enhanced by small peptides such as glycylglycine (GlyGly). The reaction kinetics suggested that GlyGly may function as an acceptor molecule for gingipain-catalysed transpeptidation. Purified gingipains and P. gingivalis whole cells were used to digest selected substrates including human haemoglobin in the presence or absence of peptide acceptors. Mass spectrometric analysis of the substrates digested with gingipains in the presence of GlyGly showed that transpeptidation outcompeted hydrolysis while the trypsin-digested controls exhibited predominantly hydrolysis activity. The transpeptidation levels increased with increasing concentration of GlyGly. Purified gingipains and whole cells exhibited extensive transpeptidation activities on human haemoglobin. All haemoglobin cleavage sites were found to be suitable for GlyGly transpeptidation and this transpeptidation enhanced haemoglobin digestion. The transpeptidation products were often more abundant than the corresponding hydrolysis products. In the absence of GlyGly, haemoglobin peptides produced during digestion were utilised as acceptors leading to the detection of up to 116 different transpeptidation products in a single reaction. P. gingivalis cells were able to digest haemoglobin faster when acceptor peptides derived from human serum albumin were included in the reaction suggesting that gingipain-catalysed transpeptidation may be relevant for substrates encountered in vivo. The transpeptidation of host proteins in vivo may potentially lead to the breakdown of immunological tolerance culminating in autoimmune reactions.

2018-07-11 | PXD009950 | Pride

Proteome-wide identification of ISG15 sites targeted by SARS-CoV-2 PLpro

Project description:Here, we applied an ISG15-GlyGly peptidomics approach on HeLa cells producing high levels of ISGylated proteins upon stimulation with IFN-α. After obtaining cellular lysates from wild-type and Isg15-/-cells, the samples were incubated with recombinant wild-type or mutant PLpro to catalyze deISGylation of host cellular proteins. After incubation with PLpro, we continued with trypsin digestion to generate diglycine-modified peptides that were subsequently enriched by immunoprecipitation and identified and quantified by LC-MS/MS. By comparing sites across all four conditions, we uncovered 118 ISGylation sites on 95 proteins as targets of the SARS-CoV-2 protease PLpro.

2021-10-12 | PXD026748 | Pride

Glycosaminoglycan linkage region of urinary bikunin as a potentially useful biomarker for β3GalT6-deficient spondylodysplastic Ehlers-Danlos syndrome

Project description:The spondylodysplastic type of Ehlers-Danlos syndromes (spEDS) is caused by genetic defects in the B4GALT7 or B3GALT6 genes both deranging the biosynthesis of the glycosaminoglycan linkage region of chondroitin/dermatan sulfate and heparan sulfate proteoglycans. In this study we have analyzed the linkage regions of urinary chondroitin sulfate proteoglycans of three siblings, diagnosed with spEDS and carrying biallelic pathogenic variants of the B3GALT6 gene. Proteoglycans were digested with trypsin, glycopeptides enriched on anion-exchange columns, depolymerized with chondroitinase ABC and analyzed by nLC-MS/MS. In urine of the unaffected mother, the dominating glycopeptide of bikunin/protein AMBP appeared as only one dominating (99.9%) peak with the canonical tetrasaccharide linkage region modification. In contrast, the samples of the three affected siblings contained two different glycopeptide peaks, corresponding to the canonical tetrasaccharide and to the non-canonical trisaccharide linkage region modifications in individual ratios of 61/38, 73/27, 59/41.We propose that the relative distribution of glycosaminoglycan linkage regions of urinary bikunin glycopeptides may serve as a phenotypic biomarker in a diagnostic test but also as a biomarker to follow the effect of future therapies in affected individuals.

2022-06-29 | PXD033230 | Pride

Genome Wide Linkage analysis of large family with coronary artery disease

Project description:We used linkage data from CAD family to search for the responsible variant in disease. we used illumina array for linkage analysis of CAD affected family.

2014-03-28 | E-GEOD-42137 | biostudies-arrayexpress

Proteome-wide identification of ISG15 sites in HeLa cells

Project description:We employed a GlyGly-peptidomics approach to comprehensively map ISG15 modification sites in HeLa cells under three conditions: mock-transfected controls, IFN-induced cells, and cells transfected with the ISGylation machinery. Lysates from wild-type and Isg15 knockout (KO) cells were processed using S-trap, followed by trypsin digestion to generate diglycine-modified peptides. These peptides were enriched via immunoprecipitation and analyzed by LC-MS/MS for identification and quantification. Comparative analysis across conditions and genotypes revealed 671 ISG15 modification sites on 456 distinct proteins, expanding the HeLa ISGylome.

2026-03-02 | PXD065158 | Pride

Linkage Reprogramming by Tailor-made E3s Reveals Polyubiquitin Chain Requirements in DNA Damage Bypass

Project description:A polyubiquitin chain can adopt a variety of shapes, depending on how the ubiquitin monomers are joined. However, the relevance of linkage for the signaling functions of polyubiquitin chains is often poorly understood because of our inability to control or manipulate this parameter in vivo. Here we present a strategy for reprogramming polyubiquitin chain linkage by means of tailor-made, linkage- and substrate-selective ubiquitin ligases. Using the polyubiquitylation of the budding yeast replication factor PCNA in response to DNA damage as a model case, we show that altering the features of a polyubiquitin chain in vivo canchange the fate of the modified substrate. We also provide evidence for redundancy betweendistinct, but structurally similar linkages, and we demonstrate by proof-of-principle experiments that the method can be generalized to targets beyond PCNA. Our study illustrates apromising approach towards the in vivo analysis of polyubiquitin signaling.

2022-04-25 | PXD030735 | Pride

Mapping Ubiquitination Sites in Alzheimer's Disease

Project description:Alzheimer’s Disease (AD) is characterized by the deposition of protein aggregates such as neurofibrillary tangles (NFTs) and amyloid (Aβ) plaques in the brain. Post-translational modification through ubiquitylationplays critical roles in clearing misfolded protein aggregates. Investigating global ubiquitylation changes inAD brain may provide insights regarding the underlying mechanisms of proteostasis and disease pathogenesis.Here, we utilizedan immunoaffinity approach to specifically enrichubiquitinated(di-glycine) peptides frompostmortemhuman control and AD braintissues.Mass spectrometry(MS)based proteomicanalysis identified global ubiquitylation changes associated with ADand hierarchical clustering of the human brain ubiquitylome clearly classified AD cases from healthy controls based on ubiquitylation patterns. Polyubiquitin linkage analysis identified increased levels of all seven polyubiquitin linkage typesas well as total ubiquitin in the AD brain tissues.We also report novel ubiquitylation sites in the microtubulebinding repeatof Tauwith potential implicationsfor Tauaggregation. Dually modified peptides with both phosphorylation and ubiquitylationsites, many of which originated from Tauprotein are also differentially enriched in AD.Furthermore, all the KXGS motifswithin themicrotubule binding region (MTBR)of Tauprotein,which represents the core ofNFTs,are enriched among dually modified peptides. Collectively, these studieshighlight the utility of an immunoaffinity enrichment approach coupled with MSanalysis for mapping AD associated global ubiquitylome changesas well as to gain insights intounderlying proteostasis pathwaysaltered in AD brain.

2019-06-25 | PXD009199 | Pride

Hsp90 inhibition induces both protein-specific and global changes in the ubiquitinome

Project description:We used stable isotope labeling and antibody-based peptide enrichment to quantify more than 1500 protein sites modified with a Gly-Gly motif, the remnant of ubiquitination, in human T-cells treated with an Hsp90 inhibitor. We compared the data with the evolution of net protein levels in the same cells and with changes in protein decay and synthesis rates from a previous study.

2015-03-19 | PXD001549 | Pride

In colorectal metastases patients who require liver resection, does a surgeon having knowledge of liver fat measurements influence surgical planning decisions that result in improved patient outcomes.

Project description:Intervention arm – the surgeon will have knowledge of a quantitative measure of liver fat from MRI (HepaFat-Scan) Primary Outcome 1: all cause mortality as assessed by data linkage to medical records[Timepoint: within 3 months post surgery];Primary Outcome 2: postoperative complications as assessed by data linkage to medical records (e.g. ascites, urine infection, bilioma, renal failure)[Timepoint: at baseline and 6 months post surgery];Primary Outcome 3: deviations from standard surgical treatment as assessed by qualitative questionnaire designed specifically for this study[Timepoint: baseline] Study Design: Purpose: Treatment; Allocation: Randomised controlled trial; Masking: Blinded (masking used);Assignment: Parallel;Type of endpoint: Safety/efficacy

| 2462248 | ecrin-mdr-crc