Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A novel polyubiquitin chain linkage formed by viral Ubiquitin resists cleavage by deubiquitinating enzymes

ABSTRACT: The project reports the structural difference between viral Ubiquitin (vUB) and human ubiquitin, hence causing local and global destabilization in vUB. Viral Ubiquitin conjugates are degraded by proteasome machinery. The in-vitro biochemical assays suggest comparable activity of mono UB and mono-vUB against different set of E2 and E3 enzymes. The project also reports the novel isopeptide linkage in viral ubiquitin at K54 position through MS/MS, which is made by E2D2 and not by other E2s used in this study. Most importantly K54-conjugates were found to be resistant towards deubiquitinase enzymes.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Bombyx Mori (silk Moth)

SUBMITTER: Hitendra Negi

LAB HEAD: Dr. Ranabir Das

PROVIDER: PXD017215 | Pride | 2020-06-28

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

A novel polyubiquitin chain linkage formed by viral Ubiquitin is resistant to host deubiquitinating enzymes.

Negi Hitendra H Reddy Pothula Purushotham PP Vengayil Vineeth V Patole Chhaya C Laxman Sunil S Das Ranabir R

The Biochemical journal 20200601 12

The Baculoviridae family of viruses encode a viral Ubiquitin (vUb) gene. Though the vUb is homologous to the host eukaryotic Ubiquitin (Ub), its preservation in the viral genome indicates unique functions that are not compensated by the host Ub. We report the structural, biophysical, and biochemical properties of the vUb from Autographa californica multiple nucleo-polyhedrosis virus (AcMNPV). The packing of central helix α1 to the beta-sheet β1-β5 is different between vUb and Ub. Consequently, i ...[more]

PMID: 32478812

Similar Datasets

LC-MS/MS analysis of ribosome UFMylation in vitro

Project description:UFMylation, is a Ubiquitin-like modification occurring on RPL26, a ribosomal subunit, upon ribosome stalling at the ER membrane. This modification is achieved by a pool of enzymes commonly referred to as E1-activating, E2-conjugating and E3-ligase enzymes. The UFM1 E3 ligase comprises of three proteins: UFL1, UFBP1 and CDK5RAP3, referred to as UFM1 Ribosome E3 Ligase (UREL) complex. While UFL1 and UFBP1 are sufficient for E3 ligase activity in vitro, CDK5RAP3 is indispensable for ribosome UFMylation in vivo. In this work, we characterize in vitro UFMylation reaction of purified 60S ribosomes in the presence and absence of CDK5RAP3 using LC-MS/MS. Specifically, we analyse sites of UFMylation, linkage type and quantify monoUFMylation and diUFMylation on RPL26. Interestingly, we find UFMylation to occur on a specific lysine residue, K134, in the presence of UFL1/UFBP1 alone and in complex with CDK5RAP3. In addition, we also provide quantitative information on relative abundances of RPL26 mono- and di-UFMylation under these conditions.

2024-03-22 | PXD046991 | Pride

UBR7 an E3 ligase targets Sp110 via modulating IFN beta signalling in HBV-induced hepatic carcinoma

Project description:UBR7 is an E3 ubiquitin ligase. We identified that Sp110 is a novel substrate for UBR7 which promotes HBV persistence. UBR7 ubiquitinates Sp110 which leads to downregulation of type I interferon response pathway genes. Our study reports that UBR7 ubiquitinates Sp110 thereby promoting viral persistence and HBV- induced HCC.

2023-12-31 | GSE229339 | GEO

Mus musculus primary CD4+ T cell di-glycine remnant and whole cell proteomics

Project description:It is known that ubiquitination is important for T cell receptor (TCR) signaling during T cell activation but the breadth of ubiquitination events triggered during TCR signaling is not completely understood. This dataset utilizes di-glycine remnant profiling combined with mass spectrometry to identify a global landscape of ubiquitination events downstream of the TCR and to quantify changes ubiquitin abundance in response to TCR stimulation. Additionally, whole cell proteomics data were generated to measure protein abundances during TCR stimulation. Mouse primary T cells were isolated, proliferated and either remained resting or stimulated with CD3/CD28 to activate downstream signaling through the TCR and co-stimulatory pathways. Di-glycine remnant profiling and whole cell proteomics was performed on rested cells and cells that had undergone CD3/CD28 TCR stimulation for 4 hours. These data were analyzed to identify the ubiquitination events during TCR activation and to quantify the change in peptide-based ubiquitin abundance and total protein abundance over the course of the 4 hour TCR stimulation. Integration of di-glycine and whole cell proteomics was used to generate protein-specific predictions of whether ubiquitination events downstream of TCR signaling lead to a decrease in associated protein abundance. The analysis of these data suggests that T cell activation leads to an increase in ubiquitination that is not associated with proteasomal or lysosomal degradation.

2019-05-09 | PXD012831 | Pride

Proteome-wide identification of NEDD8 modification sites reveals distinct proteomes for canonical and atypical NEDDylation

Project description:The Ubiquitin-like molecule NEDD8 controls several biological processes and is a promising target for therapeutic intervention. NEDDylation occurs through specific NEDD8 enzymes (canonical) or enzymes of the Ubiquitin system (atypical). Identification of NEDD8 sites on substrates is critical for delineating the processes controlled by NEDDylation. By combining the use of the NEDD8 R74K mutant with anti-diGly antibodies we identified 1101 unique NEDDylation sites in 620 proteins. Bioinformatics analysis reveals that canonical and atypical NEDDylation have distinct proteomes; the spliceosome/mRNA surveillance/DNA replication and ribosome/proteasome respectively. The data also reveal the formation of poly-NEDD8, hybrid NEDD8-Ubiquitin and NEDD8-SUMO-2 chains as potential molecular signals. In particular, NEDD8-SUMO-2 chains are induced upon proteotoxic stress (atypical) through NEDDylation of K11 in SUMO-2 and conjugates accumulate in previously described nucleolus-related inclusions. The study uncovers a diverse proteome for NEDDylation, and is consistent with the concept of extensive cross-talk between Ubiquitin and Ubls under proteotoxic stress conditions.

2021-02-10 | PXD022812 | Pride

Bacteria conjugate ubiquitin-like proteins to interfere with phage assembly

Project description:Multiple immune pathways in humans conjugate ubiquitin-like proteins to virus and host molecules as a means of antiviral defense. Here we studied an anti-phage defense system in bacteria, comprising a ubiquitin-like protein, ubiquitin-conjugating enzymes E1 and E2, and a deubiquitinase. We show that during phage infection, this system specifically conjugates the ubiquitin-like protein to the phage central tail fiber, a protein at the tip of the tail that is essential for tail assembly as well as for recognition of the target host receptor. Following infection, cells encoding this defense system release a mixture of partially assembled, tailless phage particles, and fully assembled phages in which the central tail fiber is obstructed by the covalently attached ubiquitin-like protein. These phages exhibit severely impaired infectivity, explaining how the defense system protects the bacterial population from the spread of phage infection. Our findings demonstrate that conjugation of ubiquitin-like proteins is an antiviral strategy conserved across the tree of life.

2024-05-08 | GSE262579 | GEO

IP-MS of DCAF1/VprBP interacting proteins in mouse CD4 T cells

Project description:DCAF1, also known as VprBP (HIV-1-viral-protein-r-binding-protein), is an evolutionary conserved substrate-binding subunit of CRL4 (Cul4a-Ddb1-Roc1) ubiquitin ligase complex. It is a cellular protein targeted by HIV-1 viral protein R (Vpr). DCAF1 modulates cellular response against HIV in macrophages, controls the survival and reprogramming of oocyte, and regulates G2/M transition. DCAF1 functions through diverse mechanisms including regulating protein poly-ubiquitination, mono-ubiquitination and phosphorylation. Nonetheless, whether and how DCAF1 controls the function of primary T cell, a major cell type infected by HIV, remains unknown. We found DCAF1 is required for cell size growth and cell cycle entry from quiescence. To investigate the underlying molecular mechanisms and identify the cellular factors that associate with DCAF1 in T cells, we analyzed DCAF1-interacting proteins in T cells using VprBP immunoprecipitation and mass spectrometry.

2016-01-12 | PXD003180 | Pride

Slx5/8 alleviates replication stress by promoting mitotic progression

Project description:MCM-10 vs. wild type yeast differential analysis using label-free relative quantification and directed mass spectometry using RIPPER. Loss of Mcm10 causes replication stress. We uncovered that S. cerevisiae mcm10-1 mutants rely on the SUMO-targeted E3 ubiquitin ligase complex Slx5/8 and SUMO network for survival. How Slx5/8 suppresses replication stress has remained elusive. We developed a novel intensity-based label-free quantitative mass spectrometry approach and identified SUMO conjugates that were either enriched or depleted in mcm10-1 cells. We reasoned that sumoylated proteins that were decreased in mcm10-1 cells were potential Slx5/8 targets. Such candidates included subunits of the chromosome passenger complex (CPC), Bir1 and Sli15, which we verified to be substrates of the Slx5/8 pathway. CPC is known to positively regulate the spindle assembly checkpoint (SAC), and we show here that the ablation of CPC components and other SAC proteins supports growth of mcm10-1 cells by relieving mitotic arrest. Together, our data provide mechanistic insight into how SUMO and Slx5/8 orchestrate the replication stress response to promote cell survival.

2016-04-05 | PXD002607 | Pride

Identification of SLFN5 as an intrinsic inhibitor of viral transcription antagonized by the herpes simplex virus ubiquitin ligase ICP0

Project description:Intrinsic antiviral host factors are proteins that can confer cellular defense by limiting virus replication. Viruses hijack ubiquitin machinery to modify the cellular proteome to subvert these host defenses. The herpes simplex virus 1 (HSV-1) expresses ICP0, which functions as an E3 ubiquitin ligase required to promote infection. Cellular substrates of ICP0 have been discovered as host barriers to infection but the mechanisms for inhibition of viral gene expression are not fully understood. To identify new restriction factors antagonized by ICP0, we compared the proteomes associated with viral DNA (vDNA) during HSV-1 infection with wild-type (WT) virus and a mutant lacking functional ICP0 (ΔICP0). We identified the cellular protein Schlafen 5 (SLFN5) as a new ICP0 target that binds vDNA during HSV-1 ΔICP0 infection. We demonstrated that ICP0 mediates ubiquitination of SLFN5 which leads to its proteasomal degradation. In the absence of ICP0, we demonstrate SLFN5 binds vDNA to represses HSV-1 transcription by limiting accessibility of RNA polymerase II to viral promoters. These results identify SLFN5 as a new restriction factor that inhibits viral transcription and document the first viral countermeasure reported to overcome SLFN antiviral activity.

2020-09-14 | PXD018773 | Pride

Identification of RNF111 substrates by integrative ubiquitome and proteome analysis

Project description:In the present work, we sought to identify exhaustively the endogenous substrates ubiquitinated and degraded by the E3 ubiquitin ligase RNF111 in presence of TGF-β signaling by performing label free quantitative proteomics after enrichment of ubiquitinated proteins (ubiquitome) in parental U2OS cell line compared to U2OS CRISPR engineered clones expressing a truncated form of RNF111 devoid of C-terminal Ring domain. We compare two methods of enrichment for ubiquitinated proteins prior to mass spectrometry proteomics analysis, the diGly remnant peptide immunoprecipitation with a K-e-GG antibody and a novel approach using protein immunoprecipitation with an ubiquitin pan (Pan UB) nanobody that recognizes all ubiquitin chains and mono-ubiquitination. These ubiquitomes were compared to the corresponding proteome to identify proteins ubiquitinated and degraded by RNF111 upon TGF-β signaling pathway.

2021-11-17 | PXD025890 | Pride

SUMO-2 Orchestrates Chromatin Modifiers in Response to DNA Damage

Project description:Small Ubiquitin-like Modifiers play critical roles in the DNA Damage Response (DDR). To increase our understanding of SUMOylation in the mammalian DDR, we employed a quantitative proteomics approach to identify dynamically regulated SUMO-2 conjugates and modification sites upon treatment with the DNA damaging agent MMS. We have uncovered a dynamic set of 20 upregulated and 33 downregulated SUMO-2 conjugates, and 755 SUMO-2 sites, of which 362 were dynamic in response to MMS. In contrast to yeast, where a response is centered on homologous recombination, we identified dynamically SUMOylated interaction networks of chromatin modifiers, transcription factors, DNA repair factors and nuclear body components. SUMOylated chromatin modifiers include JARID1B/KDM5B, JARID1C/KDM5C, p300, CBP, PARP1, SetDB1 and MBD1. Whereas SUMOylated JARID1B was ubiquitylated by the SUMO-targeted ubiquitin ligase RNF4 and degraded by the proteasome in response to DNA damage, JARID1C was SUMOylated and recruited to the chromatin to demethylate histone H3K4.

2015-03-16 | PXD001810 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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