Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

293T cells transfected with HIV-1 proviral plasmids

ABSTRACT: The HIV-1 Gag protein orchestrates all steps of virion genesis, including RNA recruitment into virions. However, the identities of specific RNA sequences recognized by Gag in cells and virions are largely unknown. Using crosslinking-immunoprecipitation (CLIP) sequencing, we uncover dramatic changes in the RNA binding specificity of Gag during virion genesis that are induced by its membrane binding, multimerization and proteolytic maturation. Prior to assembly, and also in mature virions, the nucleocapsid domain of Gag preferentially binds to psi and Rev Response elements in the viral genome, and GU-rich mRNA sequences. However, during assembly of immature virions, this specificity changes in a manner that facilitates genome packaging, as nucleocapsid binds to many sites on the viral genome and mRNA sequences with a similar A-rich nucleotide composition. Additionally, we find that the matrix domain of Gag binds almost exclusively to specific tRNAs in the cytosol, and this association regulates Gag binding to cellular membranes.

ORGANISM(S): Homo sapiens

PROVIDER: GSE61508 | GEO | 2014/11/12

SECONDARY ACCESSION(S): PRJNA261331

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Simultaneous Membrane and RNA Binding by Tick-Borne Encephalitis Virus Capsid Protein

Project description:<p>Tick-borne encephalitis virus is an enveloped, pathogenic, RNA virus in the family Flaviviridae, genus Flavivirus. Viral particles are formed when the nucleocapsid, consisting of an RNA genome and multiple copies of the capsid protein, buds through the endoplasmic reticulum membrane and acquires the viral envelope and the associated proteins. The coordination of the nucleocapsid components to the sites of assembly and budding are poorly understood. Here, we investigate nucleocapsid assembly by characterizing the interactions of the wild-type and truncated capsid proteins with membranes by using biophysical methods and model membrane systems. We show that capsid protein initially binds membranes via electrostatic interactions with negatively-charged lipids which is followed by membrane insertion. Additionally, we show that membrane-bound capsid protein can recruit viral genomic RNA. We confirm the biological relevance of the biophysical findings by using mass spectrometry to show that purified virions contain negatively-charged lipids. Our results suggest that nucleocapsid assembly is coordinated by negatively-charged membrane patches on the endoplasmic reticulum and that the capsid protein mediates direct contacts between the nucleocapsid and the membrane.</p>

2023-01-06 | MTBLS6076 | MetaboLights

A focused deep mutational scan on the Env transmembrane and proximal cytosolic regions reveals an absence of sequence features for MA association

Project description:The HIV-1 surface glycoprotein Env binds target receptors to mediate fusion of the viral and host cell membranes during infection. Env is incorporated with very low density into virions, and in some cell types, regions within the long cytosolic C-terminal tail may mediate direct or indirect associations with Gag during virus assembly and budding. Here, the mutational landscape is determined across the transmembrane and proximal cytosolic domains of Env (001428 isolate from clade C) interacting with the MA domain of Gag at cellular membranes. No evidence is found in a derivative line of HEK293 cells for specific motifs that mediate Env/MA associations.

2019-02-07 | GSE126136 | GEO

Mass spectrometry-based characterization of the virion proteome and phosphoproteome of human cytomegalovirus

Project description:The assembly of human cytomegalovirus (HCMV) virions is an orchestrated process that requires, as an essential prerequisite, the complex crosstalk between viral structural proteins. So far, however, the mechanisms governing the successive steps in the constitution of virion protein complexes remained elusive. Protein phosphorylation is a key regulator determining the sequential changes in conformation, binding, dynamics and stability of proteins in the course of multiprotein assembly. Here, we present new results to complete knowledge on HCMV virion proteome and phosphoproteome. Thus, a novel dataset of viral and cellular proteins contained in HCMV virions has been generated, providing a basis for future analyses of individual phosphorylation steps and sites involved in the orchestrated assembly of HCMV virion-specific multiprotein complexes.

2020-06-05 | PXD012921 | Pride

Transcriptome Analysis of KSHV virions produced from BCBL1 and BAC36 in 293L cells

Project description:The objective of this study was to identify the viral transcripts packaged into the virion particles produced from BCBL1 cells as well as virions from 293L cells containing BAC36 BACs RNA from virions were extracted and analyzed by RNA sequencing

2014-10-16 | E-GEOD-62343 | biostudies-arrayexpress

The Proteome of the Infectious Bronchitis Virus Beau-R Virion

Project description:Infectious bronchitis is a highly contagious respiratory disease of poultry caused by the coronavius infectious bronchitis virus (IBV). Until recently is was thought that coronavirus virions were composed of the structural proteins nucleocapsid, envelope, spike and membrane proteins, but investigations of TGEV and SARS-CoV have shown the proteome of coronavirus virions also includes viral non-structural and group specific proteins as well as host cell proteins. To study the proteome of IBV virions, virus was grown in embryonated chicken eggs and purified by sucrose gradient ultracentrifugation. Purified virus was analysed using sensitive gel-free proteomic techniques to determine the proteome of IBV. Analysis of three preparations of purified IBV yielded a list of 39 proteins commonly associated with the IBV virion. Three of these proteins were the viral structural proteins spike, membrane and nucleocapsid, but none of the viral non-strucutral or groups specific proteins could be identified. The other 35 proteins commonly associated to the IBV virion were all found to be host cell proteins. These proteins were classified into 12 categories using pantherdb (pantherdb.org). These proteins were involved in a diverse range of functions such as cytoskeletal proteins, nucleic acid binding proteins and chaperone proteins. Some of these proteins were unique to this study, whilst others were found to be orthologous to proteins identified in the SARS-CoV protein, and indeed some were also identified in association with virions from a number of other RNA and DNA viruses.

2016-02-15 | PXD002936 | Pride

CLIP-seq analysis of NC-RNA interactions in wild-type and eccentric particles

Project description:Nucleocapsid (NC) CLIP-seq experiments were conducted on wild-type and eccentric HIV-1 virions generated in the presence of allosteric integrase inhibitor, BI-B2.

2017-06-15 | GSE100018 | GEO

An Updated overview of the Virion Proteome of Kaposi Sarcoma Associated Herpesvirus

Project description:The virion proteins of Kaposi Sarcoma Associated Herpesvirus (KSHV) were initially characterized in 2005 in two separate studies that combined detected 24 viral proteins and a few cellular components via LC-MS/MS or MALDI-TOF. Despite considerable advances in the sensitivity and specificity of mass spectrometry instrumentation in recent years, leading to significantly higher yields in detections, the KSHV virion proteome has not been revisited. In this study, we have re-examined the protein composition of purified KSHV virions via Ultra-High Resolution Qq-Time-Of-Flight mass spectrometry (UHR-QqTOF). Our results confirm the detection of all previously reported virion proteins, in addition to 17 other viral proteins, some of which have been characterized as virion-associated using other methods, and 10 novel proteins identified as virion-associated for the first time in this study. These results add KSHV ORF9, ORF23, ORF35, ORF48, ORF58, ORF72/vCyclin, K3, K9/vIRF1, K10/vIRF4, and K10.5/vIRF3 to the list of KSHV proteins that can be incorporated into virions. The addition of these proteins to the KSHV virion proteome provides novel and important insight into early events in KSHV infection mediated by virion-associated proteins.

2020-12-10 | PXD022626 | Pride

Transcriptome Analysis of KSHV virions produced from BCBL1 and BAC36 in 293L cells

2014-10-16 | GSE62343 | GEO

The host exosome biogenesis pathway is essential for human cytomegalovirus virion assembly and egress

Project description:Human Cytomegalovirus (HCMV) infects over 50% of humans, is a leading cause of congenital birth defects, and poses serious risks for immuno-compromised individuals. To expand the molecular knowledge governing virion assembly and egress, we initiated a proteomics-based investigation and identified a significant proportion of host exosome constituents in HCMV virions. Quantitative analysis of exosomes released from uninfected cells (765 proteins) revealed that over 99% of the protein cargo was subsequently integrated into virions, confirming near-complete acquisition of exosome biogenesis during infection. We confirmed VAMP3 is essential for viral trafficking and release of infectious progeny, further validating the intrinsic exploitation of the pathway by HCMV. Therefore, host exosomes serve as the molecular template for virion cargo addition, and provide an export mechanism for virion egress. Our discovery underpins future investigation of host exosome proteins as important modulators of viral maturation, and enhances the understanding of HCMV envelopment, trafficking, fusion and release.

2021-02-22 | PXD015081 | Pride

Selective packaging of cellular microRNAs into HIV-1 virions inhibits infectivity

Project description:We analyzed the incorporation of cellular microRNAs (miRNAs) into highly purified HIV-1 virions and observed that this largely, but not entirely, mirrored the level of miRNA expression in the producer CD4+ T cells. Specifically, of the 58 cellular miRNAs detected at significant levels in the producer cells, only five miRNAs were found at a 2 to 4-fold higher level in virions than predicted based on random sampling. Of note, these included two miRNAs, miR-155 and miR-92a, reported previously to at least weakly bind HIV-1 transcripts. To test whether miRNA binding induces virion incorporation, we introduced artificial miRNA target sites into the HIV-1 genome and observed a 10 to 40-fold increase in the packaging of the cognate miRNA into virions, leading to the recruitment of up to 1.6 copies into each virion. Importantly, this high level of incorporation significantly inhibited HIV-1 virion infectivity. We conclude that target sites for cellular miRNAs can inhibit RNA virus replication at two distinct steps, i.e., during infection and during viral gene expression, thus explaining why a range of different RNA viruses appear to have evolved to restrict cellular miRNA binding to their genome.

2016-12-22 | GSE89868 | GEO

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