RMCE-based insect cell platform
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB22717 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:In this work we established an analytical method of characterization for the Gag protein core and clarify the current variability of Gag stoichiometry in HIV-1 VLPs depending on the cell-based production platform, directly determining the number of Gag molecules per VLP in each case. Three Gag peptides have been validated to quantify the number of monomers using parallel reaction monitoring (PRM)
2022-12-07 | PXD021278 | Pride
Project description:The targeting of retroviral Gag polyproteins to the inner leaflet of the plasma membrane is mediated by the N-terminal matrix (MA) domain of Gag. Since retroviruses of different morphogenetic types assemble their immature particles in distinct regions of the host cell, the mechanism of plasma membrane targeting differs between distinct retroviral morphogenetic types. To address this, we have focused on possible mechanistic differences of the MA-plasma membrane targeting of the B type mouse mammary tumor virus (MMTV) and C type HIV-1, which assembles in the cytoplasm and at the plasma membrane, respectively. Molecular dynamic (MD) simulations together with surface mapping have indicated that MMTV uses, similarly to HIV-1, the myristic switch mechanism to anchor the MA to the membrane and electrostatically interacts with phosphatidylinositol 4,5-bisphosphate to stabilize MA orientation. We have observed that the affinity of the MMTV MA to the membrane is lower than the affinity of the HIV 1 MA. This might be related to their different topology and the number of basic residues in the highly basic region, which probably reflects the requirement of C-type retroviruses for tighter membrane binding, essential for the assembly, in contrast to D/B-type retroviruses, assembling in the cytoplasm. Additionally, a comparison of the membrane topology of the HIV-1 MA using the surface mapping method and MD simulations has shown that the residues located at the C-terminus of the HIV-1 MA could be responsible for the stabilization of protein-protein interactions within the HIV-1 MA lattice at the plasma membrane.
2020-05-18 | PXD018604 | Pride
Project description:Retroviruses exploit a variety of host proteins to assemble and release virions from infected cells. To date, most studies that examined possible interacting partners of retroviral Gag proteins focused on host proteins that localize primarily to the cytoplasm or plasma membrane. Given the recent findings that several full-length Gag proteins localize to the nucleus, identifying the Gag-nuclear interactome has high potential for novel findings that reveal previously unknown host processes. This dataset contains results from a mass spectrometry approach using affinity-tagged (His6) HIV-1 and RSV Gag proteins mixed with nuclear extracts, and identifies potential binding partners of HIV-1 and RSV Gag involved in several nuclear processes, including transcription, splicing, RNA modification, and chromatin structure. Although a subset of host proteins interacted with both Gag proteins, there were also unique host proteins belonging to each interactome dataset. These results provide a strong premise for future functional studies to investigate roles for these nuclear host factors that may have shared functions in the biology of both retroviruses, as well as functions specific to RSV and HIV-1, given their distinctive hosts and molecular pathology.
2024-07-03 | PXD048774 | Pride
Project description:During retroviral replication, the full-length RNA serves both as mRNA and genomic RNA (gRNA). While the simple retrovirus MLV segregates its full-length RNA into two functional populations, the HIV-1 full-length RNA was proposed to exist as a single population used indistinctly for protein synthesis or packaging. However, the mechanisms by which the HIV-1 Gag protein selects the two RNA molecules that will be packaged into nascent virions remain poorly understood. Here, we demonstrate that an epitranscriptomic switch involving the demethylation of adenosine residues present within HIV-1 5´-UTR regulates full-length RNA packaging. We further identified two conserved adenosines within the 5’-UTR that have a crucial structural and functional role and that are modulated by N6-methylation. While m6A deposition by METTL3/METTL14 onto the full-length RNA was associated with increased Gag synthesis and reduced packaging, FTO-mediated demethylation promotes the incorporation of the full-length RNA into viral particles. Interestingly, HIV-1 Gag associates with the RNA demethylase FTO in the nucleus contributing to full-length RNA demethylation. Finally, the specific inhibition of the FTO RNA demethylase activity suppressed HIV-1 full-length RNA packaging. Together, our data propose a novel epitranscriptomic mechanism allowing the selection of the full-length RNA molecules that will be used as viral genomes.
2021-01-02 | GSE130687 | GEO
Project description: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.
2014-11-12 | GSE61508 | GEO
Project description:We performed a 3' RACE of a novel HIV RNA TAR-gag in order to determine the sequence of the RNA at the 3' end. Our data had shown that TAR-gag was potentially a noncoding RNA and our hypothesis was that TAR-gag ended somewhere prior to the end of the gag region of the HIV genome. The 3' RACE experiment showed that TAR-gag actually consists of four different RNA clusters, the longest of which ends at 615 bases from the transcription start site; this is in the middle of the p17 region of the gag gene. In addition, we sequenced all host RNAs in the EVs.
2017-08-09 | GSE102364 | GEO
Project description:Transcriptional profiling to examine differences resulting from priming of virus-specific CD8 T cells in draining lymph node and in bone marrow, following intradermal injection of modified virus Ankara (MVA)-HIV gag. Transcriptional profiling of mouse pentamer H2kD-AMQMLKETI (HIV-gagP24) CD8 T cells from draining lymph nodes(LN) and bone marrow (BM ) 5 days following intradermal injection of MVA-HIV gag, and compared to naive (CD62L Hi CD44 int) CD8+ T cells from lymph node of naive mice (NTc).
2012-10-23 | GSE41736 | GEO
Project description:Progressively longer regions of the gag gene sequence in HIV-1 were codon-optimized, which introduced 11, 18 or 26 CpGs (CM22-165: codon-optimized gag from nucleotide 22 to 165, adding 11 CpGs; CM22-261: 18 CpGs; CM22-378: 26 CpGs).
2019-11-07 | GSE134159 | GEO
Project description:Successful development of HIV-vaccination strategies will also depend on the ability to use novel approaches to analyse and integrate immunogenicity data generated in vaccine trials. The ANRS VAC 18 trial evaluated the immunogenicity of HIV-LIPO-5 vaccine (5 HIV peptides coupled to a palmytoil tail) administered at W0, 4, 12 and 24 in healthy volunteers. 62-69% of vaccinees developed HIV-specific ELISpot responses by W26. Here we present extensive immunogenicity assessments in a subset of vaccinees using ELISpot, lymphoproliferation, intracellular cytokine staining (ICS), cytokine multiplex and transcriptomic analyses. Peripheral blood mononuclear cells from volunteers collected before and following vaccinations were stimulated with HIV LIPO 5 vaccine, Gag peptides contained or not in the vaccine as controls. Different time points and stimulation conditions were compared, using false discovery rate to control for test multiplicity. 74% and 30% of vaccinees had cultured ELISpot and lymphoproliferation responses at W14, respectively. Ex-vivo ICS showed mainly single IL-2 producing cells. Secretion of IFN-γ, TNF-α, IL-5, and IL-13 increased significantly in response to Gag stimulation after culture at W14 compared to W0. An induction of metallothionein genes was consistently detected after HIV-LIPO-5 stimulation at W0 and W14 related to the adjuvant effect of the lipid tail. After vaccination (W14), significant probes increased substantially (>1200 probes) including IFN-γ, CXCL9, IL2RA, TNFAIP6, CCL3L1 and IL-6 W14 (fold change > 100%). In conclusion, HIV LIPO-5 vaccination elicited memory precursor responses with a Th1 and Th2 profile. The signature profile before vaccination provides information about the adjuvant effect of the lipid tail. Consistently with cytokine responses, vaccination is associated with a modulation in gene expression. This combined approach allowed to identify new signatures of HIV vaccine response and indicates that HIV-LIPO-5 could be further developed as a prime component of heterologous prime boost strategies. PBMC mRNA of 12 healthy volunteers, stimulate in four different conditions (HIV-LIPO-5, Gag+, Gag-, NS) during 6 and 24 hours before and after vaccination (week 0 and week 14)
2013-07-30 | E-GEOD-39506 | biostudies-arrayexpress
Project description:Transcriptional profiling to examine differences resulting from priming of virus-specific CD8 T cells in draining lymph node and in bone marrow, following intradermal injection of modified virus Ankara (MVA)-HIV gag. Transcriptional profiling of mouse pentamer H2kD-AMQMLKETI (HIV-gagP24) CD8 T cells from draining lymph nodes(LN) and bone marrow (BM ) 5 days following intradermal injection of MVA-HIV gag, and compared to naive (CD62L Hi CD44 int) CD8+ T cells from lymph node of naive mice (NTc). Three-condition experiment, BM, LN and NTc. Experimental replicates: 5 BM, 5 LN, 5 NTc, RNA pooled from 3 independant experiments of 5 mice each.
2012-10-23 | E-GEOD-41736 | biostudies-arrayexpress