Browse
Submit Data
Databases
API
Help

Dataset Information

253 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

IRES-dependent ribosome repositioning directs translation of a +1 overlapping ORF that enhances viral infection

ABSTRACT: Elucidation of a novel +1 frame translational mechanism from the CrPV intergenic region IRES.

INSTRUMENT(S): 6520 Quadrupole Time-of-Flight LC/MS

ORGANISM(S): Drosophila Melanogaster (fruit Fly)

TISSUE(S): Cell Culture

SUBMITTER: Craig Kerr

LAB HEAD: Eric Jan

PROVIDER: PXD011388 | Pride | 2018-11-22

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

IRES-dependent ribosome repositioning directs translation of a +1 overlapping ORF that enhances viral infection.

Kerr Craig H CH Wang Qing S QS Moon Kyung-Mee KM Keatings Kathleen K Allan Douglas W DW Foster Leonard J LJ Jan Eric E

Nucleic acids research 20181201 22

RNA structures can interact with the ribosome to alter translational reading frame maintenance and promote recoding that result in alternative protein products. Here, we show that the internal ribosome entry site (IRES) from the dicistrovirus Cricket paralysis virus drives translation of the 0-frame viral polyprotein and an overlapping +1 open reading frame, called ORFx, via a novel mechanism whereby a subset of ribosomes recruited to the IRES bypasses 37 nucleotides downstream to resume transla ...[more]

PMID: 30418631

Similar Datasets

IRES-dependent ribosome repositioning directs translation of a +1 overlapping ORF that enhances viral infection.

Project description: Not available

| S-EPMC6294563 | biostudies-literature

Ultra-fast and controlled capturing, loading, and release of extracellular vesicles by a portable microstructured electrochemical fluidic device

Project description:In this project two sets of DIA-based proteomics studies were performed to characterize the proteome of isolated extracellular vesicles. For each set, seven biological replicates were analyzed

2023-08-07 | PXD039342 | Pride

SEC-SWATH-MS HEK293 - Complex-centric proteome profiling by SEC-SWATH-MS

Project description:Increasingly, biochemical co-fractionation-based approaches are used to study interactomes and protein complexes at high throughput. The devised methods facilitate the qualitative assignment and prediction of hundreds of putative cellular assemblies in one experiment and without dependency on genetic engineering to introduce affinity tags. The present dataset consists of a native proteome extracted by mild lysis from the HEK293 cell line and fractionated into 80 fractions along high resolution size exclusion chromatography, and each fraction analyzed via bottom-up SWATH mass spectrometry. In multi-tiered targeted analysis, from this fragment ion level chromatographic data, quantitative complex assembly information of the proteome is reconstructed in three steps, (i) peptide-centric detection of peptide analytes within each SEC fraction based on fragment ion co-elution groups; (ii) protein-centric detection of protein elution in SEC based on fragment peptide co-elution groups in SEC; (iii) complex-centric detection and quantification of protein complexes and -variants based on component subunit protein co-elution groups in SEC. The data delineate a global picture of quantitative complex formation within a human proteome, including deconvolution of novel subversions and assembly intermediates of critical cellular complexes with essential functions.

2019-01-11 | PXD007038 | Pride

Mass spectrometry-based analysis on the impact of iron status and whole blood donation on the global plasma proteome

Project description:Blood donation is generally considered to be safe, however to ensure blood donor health it is important to monitor the impact of a whole blood donation. Study design and methods Here, we used quantitative mass spectrometry to assess the global plasma proteomic impact of longitudinal whole blood donation in 5 new and 4 regular donors over a period of 180 days as well as the effect on iron status, by selecting 78 donors based on high levels of ferritin and hemoglobin. The majority of plasma proteins were stable between whole blood donors and demonstrated a low coefficient of variation, irrespective to iron status or donors status (new or regular). Longitudinal analysis showed limited differences between the plasma proteomes of regular and new upon a whole blood donation, apart from a consistent and significant short-term decrease in fibronectin. Plasma protein levels measured with MS highly correlated with blood count and lipid parameters, validating our MS-approach. Based on protein co-expression, we observed protein complexes of diverse biological processes, platelet and neutrophil signatures, complement and immune responses with a highly correlating cluster of IGHM, IGJ and CD5L. We showed higher inter- than intra-individual variation, most notably of immunoglobulins and allelic variants for alpha-1 antitrypsin. Overall, this study shows that whole blood donation has limited impact for both new and regular donors apart from short-term decreases in fibronectin and that varying iron statuses do not affect the global plasma proteome. We showed that individual specific signatures were reflected on the plasma proteome as well as detection of allelic variants

2023-02-01 | PXD035447 | Pride

Translational repression of pre-formed cytokine mRNA prevents chronic activation of memory T cells

Project description:Memory T cells are critical to protect us from recurring infections. Their instantaneous reactivity to pathogens is empowered by persistent expression of cytokine mRNA. How aberrant protein production of this pre-formed mRNA is prevented in the absence of infection, however, remains unresolved. We show that protein production in memory T cells is blocked through a 3’untranslated region (3’UTR)-mediated process, and that AU-rich elements (AREs) are key herein. Germ-line deletion of AREs leads to chronic IFN- production in bona fide memory T cells. Strikingly, the aberrant protein production does not result from increased mRNA levels and/or half-life. Rather, AREs block the recruitment of cytokine mRNA to ribosomes, a process that is mediated by the ARE-binding protein ZFP36L2. Thus, AREs are crucial elements for translational repression that allow murine and human memory T cells to contain pre-formed cytokine mRNAs, while preventing undesirable protein production in the absence of infection.

2018-05-15 | PXD008051 | Pride

Activated neutrophils exert myeloid-derived suppressor cell activity, damaging T cells beyond repair

Project description:Myeloid-derived suppressor cells (MDSCs) have the capacity to suppress T cell-mediated immune responses, and impact clinical outcome of cancer, infections and transplantation settings. Although MDSCs were initially described as bone-marrow-derived immature myeloid cells (either monocytic [m-MDSC] or granulocytic [g-MDSC]), also mature neutrophils have been shown to exert MDSC activity towards T cells, in ways that so far remained unclear. In this study, we demonstrate that human neutrophils – both from healthy donors and cancer patients – do not exert MDSC activity unless they are activated. Using neutrophils with genetically well-defined defects, we found that reactive oxygen species (ROS) and granule-derived constituents are required for MDSC activity after direct CD11b-dependent neutrophil-T cell interactions. Besides these cellular interactions, neutrophils were engaged in the uptake of pieces of T cell membrane, a process called trogocytosis. Together, these interactions led to changes in T cell morphology, mitochondrial dysfunction and ATP depletion, as indicated by electron microscopy, mass spectrometry and metabolic parameters. Our studies characterize the different steps by which activated mature neutrophils induce functional T cell non-responsiveness and irreparable cell damage.

2020-05-07 | PXD010508 | Pride

A Novel Cis-Acting RNA Structural Element Embedded in the Core Coding Region of the Hepatitis C Virus Genome Directs Internal Translation Initiation of the Overlapping Core+1 ORF.

Project description: Not available

| S-EPMC7554737 | biostudies-literature

Identification of genome wide Hoxa9 binding sites in primary murine and human AML cells

Project description:Relative overexpression of HOXA9 is a key feature of aggressive AML (acute myeloid leukemia). Here we determined genome wide binding sites of Hoxa9 in primary murine cells transformed by Hoxa9 and in a human AML cell line. In addition global H3K4 monomethylation and H3K27acetylation levels were determined in cells transformed by an inducible Hoxa9-ER construct in Hoxa9-active conditions and 72h after Hoxa9 was inactivated.

2019-04-13 | E-MTAB-7108 | biostudies-arrayexpress

A putative new SARS-CoV protein, 3c, encoded in an ORF overlapping ORF3a.

Project description: Not available

| S-EPMC7660454 | biostudies-literature

Resistance Strategies Differ Against Specialist and Generalist Cyanophages

Project description:Long-term coexistence between cyanobacteria and their lytic viruses (cyanophages) in the oceans is thought to be due to the presence of sensitive cells in which cyanophages reproduce, ultimately killing the cell, while other cyanobacteria survive due to resistance to infection. Here we investigated resistance strategies in naturally resistant cyanobacteria and compared strategies against generalist and specialist cyanophages. Resistance was extracellular in most interactions against specialist cyanophages, preventing entry into the cell. In contrast, resistance was intracellular in practically all interactions against generalist cyanophages. Intriguingly, the stage of intracellular arrest was interaction-specific, halting at various stages of the infection cycle. These findings unveil a heavy cost of promiscuous entry of generalist phages into non-host cells that is rarely paid by specialists, potential unknown mechanisms of intracellular resistance and that the range for viral-mediated horizontal gene transfer extends much beyond just hosts.

2019-08-12 | PXD013030 | 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