Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Pulldown of RNA binding protein using SARS CoV 2 NSP1 RNA

ABSTRACT: RNA sensing is critical for RLR activation and downstream signaling. To identify molecules that are involved in modulating viral RNA recognition, we utilized biotin-labeled 60 nt single-stranded RNA (ssRNA) from SARS-CoV-2 NSP1 coding region (NSP1 ssRNA) to pull down proteins from RAW264.7 cells. The elutes from biotin-labeled NSP1 ssRNA and control NSP1 ssRNA were subjected to coomassie blue (CBB) staining and liquid chromatography-mass spectrometry (LC-MS). CSDE1, a protein from the cold shock domain protein family, was identified as a potential NSP1 RNA interacting protein.

INSTRUMENT(S):

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Cell Culture

SUBMITTER: Yi Zheng

LAB HEAD: Yi Zheng

PROVIDER: PXD064808 | Pride | 2026-04-08

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	PE131GI.zip	Other
	PE131GI_NSP1_10.raw	Raw
	PE131GI_NSP1_20.raw	Raw
	PE131GI_NSP1_B10.raw	Raw
	PE131GI_NSP1_B20.raw	Raw

Items per page:

1 - 5 of 9

Similar Datasets

Josephin Domain Containing 2 (JOSD2) Inhibition as Pan-KRAS-Mutation-Targeting Strategy for Colorectal Cancer

Project description:KRAS is the most common mutated oncogenes in colorectal cancer (CRC), yet effective therapeutic strategies for targeting multiple KRAS-mutations remained challenging. The prolonged protein stability of KRAS mutants contribute to their robust tumor-promoting effects, but the underlying mechanism is elusive. Herein by screening deubiquitinases (DUBs) siRNA library, we identified Josephin domain containing 2 (JOSD2) functions as a potent DUB that regulates the protein stability of KRAS mutants. Mechanistically, JOSD2 directly interacted with and stabilized KRAS variants across different mutants, by reverting their proteolytic ubiquitination; while KRAS mutants reciprocally inhibited the catalytic activity of CHIP, a bona fide E3 ubiquitin ligase for JOSD2, thus forming a JOSD2/KRAS positive feedback circuit that significantly accelerated KRAS-mutant CRC growth. Inhibition of JOSD2 by RNA interference or its pharmacological inhibitor promoted the polyubiquitination and proteasomal degradation of KRAS mutants, and preferentially impeded the growth of KRAS-mutant CRC including patient-derived cells/xenografts/organoids (PDCs/PDXs/PDOs) over that harboring wild-type KRAS. Collectively, this study not only revealed the crucial roles of JOSD2/KRAS positive feedback circuit in KRAS-mutant CRC, but also provides a rationale to target JOSD2 as the promising pan-KRAS-mutation-targeting strategy for the treatment of a broad population of CRC patients with KRAS variant across different mutant types.

2025-03-01 | PXD054525 | Pride

Deubiquitinase JOSD2 promotes non-small cell lung cancer proliferation via deubiquitylation and inactivation of LKB1

Project description:Deubiquitinases (DUBs), frequently overactivated in cancers, are associated with tumorigenesis and regarded as promising therapeutic targets. However, the underlying mechanism of DUBs promoting non-small cell lung cancer (NSCLC) are poorly understood. Through a global analysis of the contribution of 97 DUBs in NSCLC survival possibilities by The Cancer Genome Atlas (TCGA) database, we found that high expression of Josephin Domain-containing protein 2 (JOSD2) predicted the poor prognosis of patients. Depletion of JOSD2 significantly impeded NSCLC growth in vivo in both cell/patient-derived xenografts. Mechanistically, JOSD2 inhibits LKB1 kinase activity by removing K6-linked polyubiquitination, which was critical for maintaining LKB1-STRAD-MO25 complex integrity. Furthermore, we identified the first small molecule inhibitor of JOSD2 and the pharmacological inhibition of JOSD2 significantly arrested NSCLC proliferation in vitro/in vivo. Notably, our findings demonstrate a crucial role of JOSD2 in hindering LKB1 activity, highlighting JOSD2 as a potential therapeutic target in NSCLC and providing its inhibitors as a promising strategy for NSCLC treatment.

2024-01-26 | PXD046139 | Pride

Cyclipostins and Cyclophostin analogs impair growth of Mycobacterium abscessus by inhibiting enzymes involved in many physiological processes

Project description:Mycobacterium abscessus is nowadays under the spotlight of the scientific community. This pathogenic mycobacteria is indeed responsible for a wide spectrum of infections involving mostly pulmonary infections in patients with cystic fibrosis. M. abscessus is intrinsically resistant to a broad range of antibiotics, including most antitubercular drugs, and is considered the most pathogenic and chemotherapy-resistant rapidly growing mycobacterium. Consequently, with very limited treatment options, the development of new therapeutic approaches to fight this pathogen are urgently needed. 38 new analogs of Cyclipostins & Cyclophostin (CyC), compounds naturally produced by Streptomyces species, have been synthesized. Their antibacterial activities against clinical isolates belonging to the M. chelonae-abscessus clade, as well as Gram-negative and Gram-positive bacteria have been evaluated by the REMA method. The intracellular activities of the CyC against intramacrophagic M. abscessus have also been investigated and compared to those of imipenem. The CyCs displayed very low toxicity towards host cells and their inhibitory activity was exclusively restricted to mycobacteria. The best candidate, CyC17, showed a high selectivity for mycobacteria with MIC values (<2 up to 40 µg/mL) comparable to those of most classical antibiotics used to treat M. abscessus infections. Of importance, several CyCs were active against extracellular M. abscessus growth (i.e., CyC17 / CyC18β / CyC25 / CyC26) or against intracellular mycobacteria inside macrophages (i.e., CyC7α,β / CyC8α,β) with MIC values similar to or better than those of standard antibiotics. Based on these results, we intended to identify the potential target enzymes of CyC17/CyC26 in M. abscessus by activity-based protein profiling (ABPP) approach coupled with mass spectrometry differential analysis.

2019-10-08 | PXD014255 | Pride

Dissecting the antibacterial activity of Oxadiazolone-core derivatives against Mycobacterium abscessus

Project description:Mycobacterium abscessus is nowadays under the spotlight of the scientific community. This pathogenic mycobacteria is indeed responsible for a wide spectrum of infections involving mostly pulmonary infections in patients with cystic fibrosis. M. abscessus is intrinsically resistant to a broad range of antibiotics, including most antitubercular drugs, and is considered the most pathogenic and chemotherapy-resistant rapidly growing mycobacterium. Consequently, with very limited treatment options, the development of new therapeutic approaches to fight this pathogen are urgently needed. In this context, 19 oxadiazolone (OX) derivatives have been investigated for their antibacterial activity against both the rough (R) and smooth (S) variants of M. abscessus. Several OXs were active against extracellular M. abscessus growth with moderated minimal inhibitory concentrations (MIC), or intracellularly by inhibiting M. abscessus growth inside infected macrophages with MIC values similar to those of imipenem. Such promising results prompted us to identify the potential target enzymes of the sole extra and intracellular inhibitor of M. abscessus growth, i.e., iBpPPOX via activity-based protein profiling combined with mass spectrometry. This approach led to the identification of 21 potential protein candidates being mostly involved in M. abscessus lipid metabolism and/or in cell wall biosynthesis.

2020-08-14 | PXD015680 | Pride

Overexpression of PBLD in HeLa cells was followed by BPIV3 infection and proteomics sequencing analysis.

Project description:In our study, we investigated the inhibitory effect of PBLD on viral replication mediated by NFKB. Through proteomics analysis, we identified the TRIM21 protein, which offered insight into the mechanism by which PBLD exerts its effects on NFKB. This discovery provided a crucial clue for directing the next steps of our research project.

2024-10-20 | PXD056953 | Pride

Identification of proteins that interact with endogenous DHX9 from HeLa cell nuclear extracts

Project description:This project aims to identify proteins that interact with DHX9.

2024-06-12 | PXD044366 | Pride

SILAC proteomics analysis to discover effect sensors of EGFR inhibition

Project description:Targeted therapies against EGFR show clinical benefit, but resistance to these agents invariably develops. Thus, there is a need for dynamic biomarkers - effect sensors - that reflect treatment with EGFR therapeutics during therapy. Making use of SILAC-labeling we aimed to discover plasma membrane proteins that become differentially expressed after treatment with EGFR inhibitor erlotinib in three erlotinib-sensitive breast cancer cell lines.

2018-10-18 | PXD005985 | Pride

The Mi-2 nucleosome remodeler and the Rpd3 histone deacetylase are involved in piRNA-guided heterochromatin formation

Project description:In eukaryotes, trimethylation of lysine 9 on histone H3 (H3K9) is associated with transcriptional silencing of transposable elements (TEs). In drosophila ovaries, this heterochromatic repressive mark is thought to be deposited by SetDB1 on TE genomic loci after the initial recognition of nascent transcripts by PIWI-interacting RNAs (piRNAs) loaded on the Piwi protein. Here, we show that the nucleosome remodeler Mi-2, in complex with its partner MEP-1, forms a subunit that is transiently associated, in a MEP-1 C-terminus-dependent manner, with known Piwi interactors, including a recently reported SUMO ligase Su(var)2-10. Together with the histone deacetylase Rpd3, this module is involved in the piRNA-dependent TE silencing, correlated with H3K9 deacetylation and trimethylation. Therefore. drosophila piRNA-mediated transcriptional silencing involves three epigenetic effectors, a remodeler, Mi-2, an eraser, Rpd3 and a writer, SetDB1, in addition to the Su(var)2-10 SUMO ligase.

2020-07-21 | PXD018749 | Pride

Truncated PARP1 promotes RNA Polymerase III during apoptosis

Project description:The N-terminal three zinc finger motifs of PARP1 are evolutionarily conserved in multicellular organism。However, during apoptosis, human PARP1 is mainly cleaved by caspase 3 at D214. As a result, the truncated PARP1 loses two N-terminal zinc finger motifs and only contains the third zinc finger motif, the BRCT domain, the WGR domain and the C-terminal catalytic domain. Interestingly, when we explored the domain architecture of PARP1 in other organisms, we found that similar to human tPARP1, PARP1 orthologs in several lower organisms do not have the N-terminal two zinc fingers or even they lack the third zinc finger motif. It indicates that even without the first two zinc finger motifs, tPARP1 may still catalyze ADP-ribosylation and play an important role in certain biological processes. To reveal the biological function of tPARP1, we performed tandem affinity purification and searched for the possible substrates.

2022-02-15 | PXD018691 | Pride

Comparing the plasma membrane proteins of Nek1+/+ and Nek1Kat2J/Kat2J MEFs

Project description:Mass spectrometry data comparing the plasma membrane proteins of Nek1-WT and Nek1-Kat2J MEFs enriched by Pierce™ Cell Surface Protein Isolation Kit.

2021-08-06 | PXD027493 | Pride