Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

JEV and ZIKV NS5 interactome

ABSTRACT: Among the flaviviral proteins, NS5 is the largest and most conserved. NS5 contains major enzymatic components of the viral replication complex. Disruption of the common key NS5-host protein-protein interactions critical for viral replication could aid in the development of broad-spectrum anti-flaviviral therapeutics. To this end, we investigated the JEV- and ZIKV-NS5 interactomes in human cells using GFP pull-downs with mass spectrometry analysis in a label-free fashion. A total of 138 cellular proteins interacting with NS5 from JEV, ZIKV, or both were identified as Protein classification analysis of identified cellular targets revealed the enrichment of RNA binding, processing and splicing including spliceosomal and spliceosome-associated proteins in both datasets. Comparison of our data with literature not only revealed several cellular NS5 interacting proteins shared among flaviviruses, but also identified proteins that have no known function in flavivirus biology such as RNA polymerase II-associated Paf1 complex, protein phosphatase 6, and s-adenosylmethionine synthetase. Our study generates the first landscape of the JEV and ZIKV NS5 interactome in human cells and identifies cellular proteins that are potentially targetable for broad-spectrum anti-flaviviral therapy.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell, Cell Culture

DISEASE(S): Disease Free

SUBMITTER: Duangnapa Kovanich

LAB HEAD: Duangnapa Kovanich

PROVIDER: PXD009523 | Pride | 2022-05-04

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	GFP1A.raw	Raw
	GFP1B.raw	Raw
	GFP2A.raw	Raw
	GFP2B.raw	Raw
	GFP3A.raw	Raw

Items per page:

1 - 5 of 20

Similar Datasets

Deep sequencing of HetR-bound DNA reveals novel HetR targets in Anabaena sp. strain PCC 7120

Project description:We employed chromatin pull-down and deep sequencing to globally identify HetR DNA targets in vivo at 6 hours after fixed-nitrogen deprivation. We identified novel DNA binding targets of tagged HetR-6xHis and defined a consensus HetR binding site from these HetR target sequences. Chromatin pull down of hetR mutant strain UHM103 carrying pAM4375, which expresses HetR-6xHis, and a wild-type control. One dataset was collected.

2013-10-31 | E-GEOD-51886 | biostudies-arrayexpress

RNAseq analyses in HEK293T-ACE2 cells infected with SARS-CoV-2 (VOC Delta, 24hours) vs untreated cells

Project description:In this study a gene expression (i.e., RNAseq) analysis was performed in HEK293T-ACE2 cellular model upon infection with viral particle belonging to VOC Delta (MOI: 0.026) for 24 hours in order to have a global picture of the transcriptome landscape in response to early phase of infection of SARS-CoV-2 ( VOC Delta infection and to evaluate the role of Ca2+ in HEK293-ACE2 cellular model and transfer to homeostasis in SARS-COV-2 patients (by Pasqualino de Antonellis1-2* and Veronica Ferrucci 1-2* (first authors) et al. and Massimo Zollo1-2# (corresponding author). Manuscript in preparation 2022 July 15th 2022. Short title "ATP2B1 (PMCA1), regulated by FOXO3, influences susceptibility to severe COVID19".

2022-12-01 | E-MTAB-11973 | biostudies-arrayexpress

PDZD8 interacts with Protrudin and Rab7 to form an ER-late endosome membrane contact site that recruits mitochondria

Project description:Endosomes regulate a plethora of cellular processes including signaling, nutrient status and organelle quality control by controlling the fate of material entering the cells. Endosomes undergo a process of maturation which specifies whether material will be shuttled back to the cell surface or degraded by the lysosome. Nevertheless, a complete inventory of factors regulating endosomal maturation is still lacking. Recently, membrane contact sites (MCSs) between the endoplasmic reticulum (ER) and endosomes have emerged as important players in endosomal sorting, dynamics and motility. Here, we identify the ER transmembrane protein PDZD8 as a new Rab7 effector that, together with the MCS component Protrudin, forms an ER-late endosome MCS. At these ER-late endosome MCSs, PDZD8 also recruits mitochondria to form a three-way contact. Our data suggest that the PDZD8/Protrudin-Rab7 MCS functions to facilitate an early stage of late endosome maturation.

2020-06-02 | PXD015523 | Pride

Detection of Dichlorvos Aducts in Hepatocyte Cell Line LC-MS/MS

Project description:Toxicity of dichlorvos (DDVP), an organophosphate (OP) pesticide, classically results from modification of the serine in the active sites of cholinesterases. However, DDVP also forms adducts on unrelated targets such as transferrin and albumin, suggesting that DDVP causes cellular perturbation by modifying non-cholinesterase targets. Here, we identify novel DDVP-modified targets in lysates of a human hepatocyte-like cell line (HepaRG) using a direct LC-MS assay of DDVP exposed lysates or using a competitive pull-down experiments with a biotin-linked organophosphorus compound (10-fluoroethoxyphosphinyl-N-biotinamidopentyldecanamide; FP-biotin), which competes with DDVP for similar binding sites. Using these strategies, we show that DDVP forms adduct to several proteins important to the cellular metabolic pathways and cellular differentiation, including glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and actin. We validated the results using purified proteins and enzymatic assays. The study not only identified novel DDVP-modified targets but also suggested that the modification directly inhibits the enzymes. The current approach provides information for future hypothesis studies to understand the underlying mechanism of toxicity of DDVP in non-neuronal tissues.

2014-07-31 | PXD001107 | Pride

Desumoylation of the RNA polymerase III lies at the core of the Sumo-Stress Response

Project description:Posttranslational modification by the small ubiquitin-like modifier Sumo regulates many cellular processes including the adaptive response to various types of stress, which has been referred to as Sumo Stress Response (SSR). However, it remains unclear whether the SSR involves a common set of core proteins regardless of the type of stress, or whether each particular type of stress induces a stress-specific SSR that targets a unique, largely non-overlapping set of Sumo substrates. In this study we used mass spectrometry to identify differentially sumoylated proteins during heat shock, hyperosmotic stress, oxidative stress, nitrogen starvation and DNA alkylation in Saccharomyces cerevisiae. Our results show that each stress triggers a specific SSR signature centered on proteins involved in transcription, translation, and chromatin regulation. Strikingly, while the various stress-specific SSRs were largely non-overlapping, all types of stresses tested here resulted in desumoylation of subunits of RNA polymerase III, which correlated with a decrease in tRNA synthesis. We conclude that desumoylation and subsequent inhibition of RNA polymerase III constitutes the core of all stress-specific SSRs.

2019-11-01 | PXD013884 | Pride

Breast cancer cell MCF7+CYP1B1-AS1 LC-MS/MS

Project description:Long non-coding Rnas (lncRNAs) can act as oncogenes or tumor suppressors to regulate cancer development. We found that CYP1B1-AS1 was down-regulated in breast cancer tissues and correlated with the prognosis of patients. Lentiviral vectors were used to overexpress CYP1B1-AS1 in MCF7 cells, and the target proteins bound to CYP1B1-AS1 were detected by pulldown assay and mass spectrometry. The function of CYP1B1-AS1 is unknown. Our study revealed the molecular mechanism of CYP1B1-AS1 inhibiting breast cancer proliferation in breast cancer, and provided a new strategy for the treatment of breast cancer targeting lncRNA.

2023-10-24 | PXD037317 | Pride

S. venezuelae HupS protein acetylated lysine mapping via bottom-up LC-MS

Project description:Nucleoid-associated proteins (NAPs) are critical during the process of chromatin compaction in Streptomyces soil bacteria. HupS is one of the two NAPs encoded in the Streptomyces genome. Its unique C-terminal domain, rich in lysine repeats (LR domain), is alike to the H2B histone found in eukaryotic cells or the HupB protein found in Mycobacterium. Project study aim was to identify post-translationally acetylated lysine residues of HupS via bottom-up LC-MS. Two approaches were uptaken. One was based on HupS enrichment from a strain expressing a recombinant HupS with a C-terminal FLAG tag (TM015) via an antiFLAG pull-down, and the other relied on a proteome-wide search of acetylated peptides in a WT strain lysate. Controls for spectral false-positives were also carried out in parallel, which were an antiFLAG pull-down with a WT strain, and a proteome-wide search of acetylated peptides in a HupS deletion mutant strain (ΔhupS) lysate. 5 lysine acetylation sites were confidently determined for the HupS protein within this study, them being Lys51, Lys85, Lys104, Lys119, and either Lys193 or Lys194.

2024-06-03 | PXD050776 | Pride

Identification of cellular protein interacting with HBV genome by protein mass spectrometry

Project description:: Hepatitis B virus (HBV) remains a major public health threat with more than 296 million people chronically infected worldwide at high risk to develop hepatocellular carcinoma. Current therapies are effective in suppressing HBV replication but rarely lead to cure. The fundamental limitation rests on the fact that current therapies do not affect the HBV covalently closed circular DNA (cccDNA), which serves as the template for viral transcription and replication and is highly stable in infected cells to ensure viral persistence. In this study, we aim to identify and elucidate the functional role of cccDNA-associated host factors using affinity purification and protein mass spectrometry in HBV-infected cells. HBV core protein (HBc) is associated with cccDNA. We used an anti-HBc antibody to pull down HBcAg-associated cccDNA complex in nuclear extract of HBV-infected HepG2-NTCP cells. By protein mass spectrometry, we identified many host proteins, including previously known proteins, that are associated with HBV cccDNA. Some of these proteins were functionally validated to play a role in HBV cccDNA activities.

2024-06-16 | PXD042733 | Pride

MS analysis of cellular targets of an engineered selective PSD-95 PDZ domain ligand

Project description:Designing highly specific modulators of protein-protein interactions (PPIs) is especially challenging in the context of multiple paralogs and conserved interaction surfaces. In this case, direct generation of selective and competitive inhibitors is hindered by high similarity within the evolutionary-related protein interfaces and PPI domains. We report here a strategy that addresses this challenge by using a semi-rational approach that separates the modulator design into two functional parts. We first achieve specificity toward a region outside of the interface by employing a selection by phage display coupled with molecular and cellular validation. Highly selective competition is then generated by appending the more degenerate interaction peptide to bind against the target interface. We have applied this approach to PSD-95, an essential multi-PDZ domain-containing synaptic scaffold protein that belongs to a larger family of paralogs. We show here that with this strategy we could specifically target a single PDZ domain within the postsynaptic protein PSD-95 over highly similar PDZ domains in PSD-93, SAP-97 and SAP-102. Our work provides the first paralog-selective and domain specific inhibitor of PSD-95, and describes a method to efficiently target other conserved PPI modules. This archive contains the comparative LC/MS/MS analysis of cellular targets of an engineered selective PSD-95 PDZ domain ligand, Xph20-ETWV, against the fusion with a naïve clone, Xph0-ETWV and a control non-binding protein (mSacrlet-i).

2019-11-12 | PXD015313 | Pride

Analysis of ZNF827 Halotag pulldown for a manuscript titled ‘ZNF827 is a single-stranded DNA binding protein that regulates the ATR-CHK1 DNA damage response pathway’

Project description:Mass spectrometry analysis of ZNF827 Halotag pulldown ZNF827 pull-downs were performed in HEK 293T cells overexpressing HaloTag ZNF827 or empty vector control using the HaloTag® Protein Pull-Down and Labelling System (Promega) according to the manufacturer’s protocol. Pull-downs were subjected mass spectrometry (MS) for purity validation.

2024-06-23 | PXD050191 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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