Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A viral Argonaute suppressor implements a dual program to block antiviral immunity

ABSTRACT: RAW files accompanying the PPI data in our 2018 Cell Host Microbe manuscript. AP-MS experiments exploring host interactions of the 1A viral suppressor proteins from DCV and CRPV along with mechanistically related experiments (see manuscript for details). Each file corresponds to one gel band from geLC-MS analysis of His-Flag tandem affinity purified bait proteins stably expressed in Drosophila Melanogaster S2 cell line. Each purification was run by SDS-PAGE and the entire lane was cut into 6 gel bands. 3-5 replicate purifications were performed. Five negative control purifications were performed: 2 purifications from untransfected S2 cells, and 3 purifications from tagged eGFP. The data were analyzed by looking at enrichment over the 3 control purifications with highest spectral counts for a given prey using SAINT express. A key mapping experiment to RAW file is provided as an excel file.

INSTRUMENT(S): LTQ Orbitrap Velos, Q Exactive

ORGANISM(S): Drosophila <fruit Fly, Genus> (ncbitaxon:7215) Cricket Paralysis Virus (ncbitaxon:12136) Drosophila C Virus (ncbitaxon:64279)

SUBMITTER: Raul Andino

PROVIDER: MSV000082752 | MassIVE | Mon Aug 06 16:38:00 BST 2018

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Small RNA from S2 cell infected with FHV deltaB2 particle

Project description:S2 cells were infected with FHV deltaB2 particle and the S2 cells were harvested to isolate total RNA at 96 hpi. Small RNAs were separated on a denaturing 15% polyacrylamide gel. Ligation to adapters requires 5' monophosphate and 3' OH. Note: The base quality (.qual) file corresponding to the fasta format (.fna) file linked to Sample GSM306489 is unavailable.

2008-10-16 | GSE12527 | GEO

Small RNA from S2 cell infected with FHV deltaB2 particle

2008-10-15 | E-GEOD-12527 | biostudies-arrayexpress

Small RNA loading licenses Argonaute for assembly into a transcriptional silencing complex

Project description:We analyzed the small RNAs bound to the fission yeast RITS and ARC complexes, and to Ago1 in wild-type and ARC mutant cells, to gain insight into the molecular role of ARC. We found that ARC contains longer heterochromatic siRNAs than RITS, and that ARC subunit Arb1 is required for loading small RNAs onto Ago1. Sequencing of 18-28 nt small RNAs from Tas3, Arb1 and Ago1 purifications.

2015-03-01 | E-GEOD-65223 | biostudies-arrayexpress

A Requirement for Argonaute 4 in Mammalian Antiviral Defense.

Project description:While interferon (IFN) responses are critical for mammalian antiviral defense, induction of antiviral RNA interference (RNAi) is evident. To date, individual functions of the mammalian RNAi and micro RNA (miRNA) effector proteins Argonautes 1-4 (AGO1-AGO4) during virus infection remain undetermined. AGO2 was recently implicated in mammalian antiviral defense, so we examined antiviral activity of AGO1, AGO3, or AGO4 in IFN-competent immune cells. Only AGO4-deficient cells are hyper-susceptible to virus infection. AGO4 antiviral function is both IFN dependent and IFN independent, since AGO4 promotes IFN but also maintains antiviral capacity following prevention of IFN signaling or production. We identified AGO-loaded virus-derived short interfering RNAs (vsiRNAs), a molecular marker of antiviral RNAi, in macrophages infected with influenza or influenza lacking the IFN and RNAi suppressor NS1, which are uniquely diminished without AGO4. Importantly, AGO4-deficient influenza-infected mice have significantly higher burden and viral titers in vivo. Together, our data assign an essential role for AGO4 in mammalian antiviral defense.

| S-EPMC7039342 | biostudies-literature

TF binding profiles acquired using ChEC-seq in various TF co-deletion strains

Project description:This data set contains ChEC-seq binding profiles of various TF in yeast strains deleted of other TFs. Each sample has a pair-end sequencing file and a processed file (.out) is a genomic signal track after alignment to S.cerevisiae (R64) reference genome. Mapping was done using the read end. This dataset also contains raw and processed MNase-seq data files for nucleosome occupancy. Data related to manuscript: The architecture of binding cooperativity between densely bound transcription factors.

2023-08-01 | GSE222268 | GEO

Contribution of the argonaute-1 isoforms to invertebrate antiviral defense.

Project description:Argonaute (Ago) protein, the central component of the RNA interference (RNAi) pathway, plays important roles in host innate antiviral immunity. Most organisms harbor a large number of different Ago proteins and isoforms; however, the roles of Ago isoforms in immune defense against pathogens remain unclear. In the present study, three Argonaute-1 (Ago1) isoforms, termed Ago1A, Ago1B, and Ago1C, were found in Marsupenaeus japonicus shrimp. Quantitative real-time PCR (polymerase chain reaction) revealed that isoforms Ago1A and Ago1B containing an insertion sequence in the PIWI domain, were significantly up-regulated in lymphoid organ and hemolymph, and also upon white spot syndrome virus (WSSV) challenge, indicating the involvement of Ago1A and Ago1B in antiviral immunity. The results showed that silencing of Ago1A with a sequence-specific siRNA led to a significant increase of WSSV loads. It was revealed that knockdown of Ago1B mRNA by 37-70% resulted in higher virus loads in shrimp. However, upon silencing Ago1B by more than 85%, a two-fold increase in Ago1A mRNA was observed but viral load was the same as untreated controls challenged with WSSV, suggesting that the simultaneous up-regulation of Ago1A might compensate for the loss of Ago1B. These data indicated that Ago1A played more important roles in the antiviral immune response than Ago1B. The simultaneous inhibition of Ago1A and Ago1B resulted in a greater increase in viral loads than Ago1A or Ago1B alone, indicating that Ago1A and Ago1B isoforms were involved in shrimp antiviral immunity. It was revealed that Ago1C had no effect on virus infection. Therefore, the current study presented the first report on the contribution of Ago isoforms in the invertebrate defense against virus infection.

| S-EPMC3510085 | biostudies-literature

Rapid and Easy Gel Disruption by Passing Through Pipette Tip with Centrifugation

Project description:We have developed an Easy Disruption method for Gel using pipet Tips (EDGe-Tip), in which polyacrylamide gel is passed through pipette tips by centrifugation in a few minutes to crush it into appropriately sized fragments. The size of the disrupted gel could be controlled by several parameters such as the strength of the centrifugal force and the size of the pipette tip hole. In shotgun proteomics, GeLC/MS/MS analysis combining SDS-PAGE and LC/MS/MS requires dicing and transferring gels to microtubes by hand, which are essential but annoying steps. Thus, EDGe-Tip was applied to the GeLC/MS/MS procedure instead of those steps. Peptides could be extracted more efficiently and variation in protein quantification is lower with EDGe-Tip than with manual dicing. We believe that this simple and rapid method of disrupting polyacrylamide gels can be useful for GeLC/MS/MS analysis and applied for experiments to extract biomolecules from the gels.

2024-05-31 | PXD042573 | JPOST Repository

Cricket paralysis virus antagonizes Argonaute 2 to modulate antiviral defense in Drosophila.

Project description:Insect viruses have evolved strategies to control the host RNAi antiviral defense mechanism. In nature, Drosophila melanogaster C virus (DCV) infection causes low mortality and persistent infection, whereas the closely related cricket paralysis virus (CrPV) causes a lethal infection. We show that these viruses use different strategies to modulate the host RNAi defense machinery. The DCV RNAi suppressor (DCV-1A) binds to long double-stranded RNA and prevents processing by Dicer2. In contrast, the CrPV suppressor (CrPV-1A) interacts with the endonuclease Argonaute 2 (Ago2) and inhibits its activity without affecting the microRNA (miRNA)-Ago1-mediated silencing. We examined the link between viral RNAi suppressors and the outcome of infection using recombinant Sindbis viruses encoding either CrPV-1A or DCV-1A. Flies infected with Sindbis virus expressing CrPV-1A showed a marked increase in virus production, spread and mortality. In contrast, Sindbis pathogenesis was only modestly increased by expression of DCV- 1A. We conclude that RNAi suppressors function as virulence factors in insects and can target the Drosophila RNAi pathway at different points.

| S-EPMC3815677 | biostudies-literature

Argonaute 5-mediated antiviral defense and viral counter-defense in Nicotiana benthamiana.

Project description:The argonaute (AGO) family proteins play a crucial role in preventing viral invasions through the plant antiviral RNA silencing pathway, with distinct AGO proteins recruited for specific antiviral mechanisms. Our previous study revealed that Nicotiana benthamiana AGO5 (NbAGO5) expression was significantly upregulated in response to bamboo mosaic virus (BaMV) infection. However, the roles of NbAGO5 in antiviral mechanisms remained to be explored. In this research, we examined the antiviral functions of NbAGO5 in the infections of different viruses. It was found that the accumulation of NbAGO5 was induced not only at the RNA but also at the protein level following the infections of BaMV, potato virus X (PVX), tobacco mosaic virus (TMV), and cucumber mosaic virus (CMV) in N. benthamiana. To explore the antiviral mechanism and regulatory function of NbAGO5, we generated NbAGO5 overexpression (OE-NbAGO5) and knockout (nbago5) transgenic N. benthamiana lines. Our findings reveal that NbAGO5 provides defense against BaMV, PVX, TMV, and a mutant CMV deficient in 2b gene, but not against the wild-type CMV and turnip mosaic virus (TuMV). Through affinity purification and small RNA northern blotting, we demonstrated that NbAGO5 exerts its antiviral function by binding to viral small interfering RNAs (vsiRNAs). Moreover, we observed that CMV 2b and TuMV HC-Pro interact with NbAGO5, triggering its degradation via the 26S proteasome and autophagy pathways, thereby allowing these viruses to overcome NbAGO5-mediated defense. In addition, TuMV HC-Pro provides another line of counter-defense by interfering with vsiRNA binding by NbAGO5. Our study provides further insights into the antiviral RNA interference mechanism and the complex interplay between NbAGO5 and plant viruses.

| S-EPMC10405324 | biostudies-literature

Profiling of Argonaute (AGO) 2-associated sRNAs after infection of bacterial pathogen Pseudomonas syringae

Project description:Transgenic Arabidopsis plants (AGO2::HA:AGO2) were treated with either mock (10 mM MgCl2) or Pseudomonas syringae pv. tomato (Pst) expressing avrRpt2 (R2) at a concentration of 2 x 107 cfu/ml for 14 hours. sRNAs associated with AGO1 and AGO2 were co-immunoprecipitated using antibodies against either AGO1 (AGO1-IP), or HA (hemagglutinin) (AGO2-IP). As controls, we also gel-purified the 18-28 nt fraction of the total RNAs from an AGO2 mutant (ago2-1). The co-immunoprecipitated or gel-purified RNAs were cloned and sequenced by Illumina deep sequencing.

2011-05-10 | GSE26161 | GEO

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