Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SND1 binds SARS-CoV-2 negative-sense RNA and promotes viral RNA synthesis through NSP9

ABSTRACT: Regulation of viral RNA biogenesis is fundamental to productive SARS-CoV-2 infection. To characterize host RNA-binding proteins (RBPs) involved in this process, we biochemically identified proteins bound to genomic and subgenomic SARS-CoV-2 RNAs. We find that the host protein SND1 binds the 5ʹ end of negative-sense viral RNA and is required for SARS-CoV-2 RNA synthesis. SND1-depleted cells form smaller replication organelles and display diminished virus growth kinetics. We discover that NSP9, a viral RBP and direct SND1 interaction partner, is covalently linked to the 5ʹ ends of positive and negative-sense RNAs produced during infection. These linkages occur at replication-transcription initiation sites, consistent with NSP9 priming viral RNA synthesis. Mechanistically, SND1 remodels NSP9 occupancy and alters the covalent linkage of NSP9 to initiating nucleotides in viral RNA. Our findings implicate NSP9 in the initiation of SARS-CoV-2 RNA synthesis and unravel an unsuspected role of a cellular protein in orchestrating viral RNA production.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Mathias Munschauer

LAB HEAD: Mathias Munschauer

PROVIDER: PXD037528 | Pride | 2023-10-05

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	F109225.dat	Other
	F109226.dat	Other
	F109227.dat	Other
	F109228.dat	Other
	F109230.dat	Other

Items per page:

1 - 5 of 43

Similar Datasets

The PDZ-binding motif of SARS-CoV envelope protein is a determinant of viral pathogenesis

Project description:A recombinant SARS-CoV lacking the envelope (E) protein is attenuated in vivo. Here we report that E protein PDZ-binding motif (PBM), a domain involved in protein-protein interactions, is a major virulence determinant in vivo. Elimination of SARS-CoV E protein PBM by using reverse genetics led to attenuated viruses (SARS-CoV-mutPBM) and to a reduction in the deleterious exacerbate immune response triggered during infection with the parental virus (SARS-CoV-wt). Cellular protein syntenin bound E protein PBM during SARS-CoV infection. Syntenin activates p38 MAPK leading to overexpression of inflammatory cytokines, and we have shown that active p38 MAPK was reduced in lungs of mice infected with SARS-CoVs lacking E protein PBM (SARS-CoV-mutPBM) as compared with the parental virus (SARS-CoV-wt), leading to a decreased expression of inflammatory cytokines and to viral attenuation. Therefore, E protein PBM is a virulence factor that activates pathogenic immune response most likely by using syntenin as a mediator of p38 MAPK induced inflammation. Three biological replicates were independently hybridized (one channel per slide) for each sample type (SARS-CoV-wt, SARS-CoV-mutPBM, Mock). Slides were Sure Print G3 Agilent 8x60K Mouse (G4852A-028005)

2014-10-31 | E-GEOD-52920 | biostudies-arrayexpress

Identification of protein interactors of SARS-CoV-2 NSP13 in HEK293T cells

Project description:Non-structural protein 13 (NSP13), as the helicase of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been shown to contain NTPase activity, DNA/RNA helicase activity, RNA 5′ triphosphatase activity and innate immunity antagonistic function. To study the function of SARS-CoV-2 NSP13, We detect the NSP13 interaction map in HEK293T cells by IP-MS.

2024-09-21 | PXD033076 | Pride

Capturing SARS-cov in low abundant patient samples: a comparative analysis (twist panviral NS).

Project description:In this study, we tested the efficacy of five commercial probes panels at detecting SARS-CoV-2 genome including panels from Illumina, Twist Bioscience and Arbor Bioscience. To do so, we used 19 patient nasal swab samples broken down into 5 series of 4 samples of equivalent SARS-CoV-2 viral load (cycle threshold (CT): low CT means a high viral load – CT26, CT29, CT32, CT35 and CT36+).

2022-06-01 | E-MTAB-11237 | biostudies-arrayexpress

Capturing SARS-cov in low abundant patient samples: a comparative analysis (arbo double ms) .

2022-06-01 | E-MTAB-11232 | biostudies-arrayexpress

Capturing SARS-cov in low abundant patient samples: a comparative analysis (Illumina respv NS).

2022-02-08 | E-MTAB-11233 | biostudies-arrayexpress

Capturing SARS-cov in low abundant patient samples: a comparative analysis (Twist sarscov MS).

2022-06-01 | E-MTAB-11234 | biostudies-arrayexpress

Capturing SARS-cov in low abundant patient samples: a comparative analysis (arbo single MS).

2022-06-01 | E-MTAB-11235 | biostudies-arrayexpress

Capturing SARS-cov in low abundant patient samples: a comparative analysis (metagenomics NS).

2022-06-01 | E-MTAB-11236 | biostudies-arrayexpress

Severe acute respiratory syndrome coronavirus envelope protein regulates cell stress responses and apoptosis

Project description:Severe acute respiratory syndrome virus (SARS-CoV) that lacks the envelope (E) gene (rSARS-CoV-ΔE) is attenuated in vivo [1,2]. To identify factors that contribute to rSARS-CoV-ΔE attenuation, gene expression in cells infected by SARS-CoV with or without E gene was compared. Twenty-five stress response genes were preferentially upregulated during infection in the absence of the E gene. In addition, genes involved in signal transduction, transcription, cell metabolism, immunoregulation, inflammation, apoptosis and cell cycle and differentiation were differentially regulated in cells infected with rSARS-CoV with or without the E gene. Administration of E protein in trans reduced the stress response in cells infected with rSARS-CoV-ΔE, with respiratory syncytial virus, or treated with drugs, such as tunicamycin and thapsigarcin that elicit cell stress by different mechanisms. In addition, SARS-CoV E protein down-regulated the signaling pathway inositol-requiring enzyme 1 (IRE-1) of the unfolded protein response, but not the PKR-like ER kinase (PERK) or activating transcription factor 6 (ATF-6) pathways, and reduced cell apoptosis. Overall, the activation of the IRE-1 pathway was not able to restore cell homeostasis, and apoptosis was induced probably as a meassure to protect the host by limiting virus production and dissemination. The expression of proinflammatory cytokines was reduced in rSARS-CoV-ΔE-infected cells compared to rSARS-CoV-infected cells, suggesting that the increase in stress responses and the reduction of inflammation in the absence of the E gene contributed to the attenuation of rSARS-CoV-ΔE. We used Affymetrix microarrays (Human Genome U133 plus 2.0) to compare global gene expression between SARS-CoV-infected, mock-infected and SARS-CoV-ΔE-infected cells. For ech type of sample three hybridizations were carried-out (independent biological replicates).

2012-06-20 | E-GEOD-30589 | biostudies-arrayexpress

Diagnostic Microbiology & Infectious Disease Rapid and sensitive detection of Sars-CoV-2 variants in nasopharyngeal swabs and wastewaters

Project description:The SARS-CoV-2 virus is continuously evolving, with appearance of new variants characterized by multiple genomic mutations, some of which can affect functional properties, including infectivity, interactions with host immunity, and disease severity. The rapid spread of new SARS-CoV-2 variants has highlighted the urgency to trace the virus evolution, to help limit its diffusion, and to assess effectiveness of containment strategies. We propose here a PCR-based rapid, sensitive and low-cost allelic discrimination assay panel for the identification of SARS-CoV-2 genotypes, useful for detection in different sample types, such as nasopharyngeal swabs and wastewater. The tests carried out demonstrate that this in-house assay, whose results were confirmed by SARS-CoV-2 whole-genome sequencing, can detect variations in up to 10 viral genome positions at once and is specific and highly sensitive for identification of all tested SARS-CoV-2 clades, even in the case of samples very diluted and of poor quality, particularly difficult to analyze.

2022-06-03 | E-MTAB-11261 | biostudies-arrayexpress

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