Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MS-based identification of proteins localized in viral factory of mimivirus

ABSTRACT: Mimivirus is a well-studied member of the family Mimiviridae which are ubiquitous in the environment. It is a fully cytoplasmic GV which is internalized into the host cell by phagocytosis. The acidic compartment of the phagosome, likely in conjugation with other unknown signals, triggers the opening of the stargate structure located at an apex of the icosahedral capsid. Once opened, the fusion of the membrane of the phagosome with the virion's internal membrane leads to the release in the cytoplasm of the core. The core contains the genome of the virus and the machinery needed to establish infection. The core consequently develops to establish a viral factory (VF), a highly dynamic and complex organelle-like structure. VF not only protects the viral DNA from cellular insults but also segregates DNA replication and transcription from translation. To identify client proteins of the viral factory, we performed co-immunoprecipitation experiments using resident protein of this strcture as baits.

INSTRUMENT(S):

ORGANISM(S): Acanthamoeba Castellanii Mimivirus Acanthamoeba Castellanii

SUBMITTER: Yohann Couté

LAB HEAD: Yohann Couté

PROVIDER: PXD054803 | Pride | 2025-08-21

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	GFP_R1.mgf	Mgf
	GFP_R1.raw	Raw
	GFP_R2.mgf	Mgf
	GFP_R2.raw	Raw
	GFP_R3.mgf	Mgf

Items per page:

1 - 5 of 43

Similar Datasets

Gene expression in mouse pre-B cells transduced with Ikaros.

Project description:Ikaros family DNA binding proteins are critical regulators of B cell development. To identify Ikaros-regulated genes in pre-B cells we performed gene expression studies at enhanced temporal resolution. We used retroviral gene transfer to express Ikaros proteins in the pre-B cell line B3. Total RNA from 2 biological replicates of B3 cells transduced with wild type Ikaros (HA-Ikaros-IRES-GFP) and DNA binding-deficient Ikaros mutant 159A (HA-159A Ikaros-IRES-GFP) was isolated 48h after infection. To increase the temporal resolution of Ikaros-regulated gene expression we transduced B3 cells with inducible Ikaros (HA-Ikaros-ERt2-IRES-GFP) and isolated total RNA from 3 biological replicates after 2 h and 6 h of exposure to 4-hydroxytamoxifen. Vector transduced B3 cells (ERt2-IRES-GFP) treated with 4-hydroxytamoxifen were used as controls.

2013-01-15 | E-GEOD-38110 | biostudies-arrayexpress

Ikaros target genes in the mouse pre-B cell line B3

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-01-15 | E-GEOD-38200 | biostudies-arrayexpress

Targeted and non-targeted proteomics to characterize the parasite proteins of Echinococcus multilocularis metacestodes

Project description:The larval stage of the cestode Echinococcus multilocularis is the causative agent of alveolar echinococcosis, a lethal disease if untreated. To date, drug treatment options are limited, non-curative and need improvement. In this project we investigated the proteomic composition of in vitro generated metacestodes that are the disease-causing stage of the parasite. We analysed the composition of the vesicle tissue (VT), the vesicle fluid (VF), as well as the changes in the surrounding culture medium (CM). Further we compared the composition of VF ex vivo material from infected mice. As antigen B (AgB) subunits were the most prominent proteins in both VFs and CM, we followed up on these specific proteins and assessed the possibility of re-uptake of AgB into the metacestode, by targeted proteomics against HA-tagged AgB.Six proteomic analyses were performed:1_ VF and VT 2_ CM (in vitro samples)3_ VF ex vivo samples from infected mice4_ HA-AgB8 calibration (in vitro samples)5_ HA-AgB8/1 uptake (in vitro samples)6_ HA-AgB8/2 uptake (in vitro samples)

2024-07-19 | PXD040274 | Pride

Gene expression in mouse primary pre-B cells transduced with Ikaros

Project description:Ikaros family DNA binding proteins are critical regulators of B cell development. To identify Ikaros-regulated genes in primary pre-B cells we performed gene expression microarrays. We used retroviral gene transfer to express Ikaros proteins. Total RNA from 3 biological replicates of primary pre-B cells transduced with wild type Ikaros (HA-Ikaros-IRES-GFP) and control vector (IRES-GFP) was isolated 48h after infection.

2013-01-15 | E-GEOD-42551 | biostudies-arrayexpress

Target RNA recognition drives PIWI* complex assembly for transposon silencing

Project description:PIWI clade Argonaute proteins and their associated piRNAs are essential guardians of genome integrity, silencing transposable elements through distinct nuclear and cytoplasmic pathways. Nuclear PIWI proteins direct heterochromatin formation to repress transposon transcription, while cytoplasmic PIWIs cleave transposon transcripts to initiate piRNA amplification. Both processes rely on target RNA recognition by PIWI–piRNA complexes, yet how this recognition leads to pathway-specific effector recruitment has remained unclear. Here, we show that target engagement triggers the formation of conserved PIWI* complexes—comprising a PIWI protein, a piRNA–target RNA duplex, a GTSF-family protein, and Maelstrom—that serve as molecular platforms to recruit downstream effectors. In Drosophila, nuclear Piwi* engages the SFiNX complex to induce transcriptional silencing, while cytoplasmic Aubergine* complexes recruit the helicase Spindle-E to promote piRNA biogenesis. Evolutionary analysis reveals that PIWI* complex formation is deeply conserved across metazoans, uncovering an ancient mechanism that couples small RNA-guided target recognition to effector function. These findings define a unifying molecular principle for piRNA-mediated silencing across cellular compartments.

2025-08-11 | PXD066474 | Pride

Genome-wide identification of Ikaros binding sites in pre-B cells

Project description:Ikaros DNA binding proteins are important regulators of haematopoiesis and genetic deletion of Ikaros results in severe developmental disturbances, including delayed thymocyte differentiation and an early and complete block in B cell development. Although Ikaros ChIP-seq data are available for mouse thymocytes and human haematopoietic progenitors, it has not been achieved in B cell progenitors. The goal of this study was to identify Ikaros binding sites in pre-B cells to define Ikaros target genes which could explain the essential role of Ikaros proteins in B cell differentiation. We carried out chromatin immunoprecipitation and high throughput sequencing (ChIP-seq) with antibodies to the C-terminus of endogenous Ikaros in B3 cells and with anti-haemagglutinin (HA) in B3 cells transduced with epitope-tagged HA-Ikaros.

2013-01-15 | E-GEOD-38169 | biostudies-arrayexpress

Transcription profiling of human melanoma-endothelial cells co-cultured vs controls to investigate cellular communication

Project description:Average life expectancy for patients with metastatic melanoma is less than 6 months, and only a handful of treatment options are available. If the disease can be stopped before it spreads to other organs, life expectancy is greatly increased. The goal of this project is to identify possible regulators of melanoma metastasis by determining genes whose expression is modulated when the cells are grown in contact with endothelial cells. Identification of genes involved in this cell-cell communication could have therapeutic implications. Experiment Overall Design: Using a lentiviral system, melanoma cell line 1205Lu was transduced with GFP, and HUVEC (human umbillical vein endothelial cells) cells at passage 2 were transduced with RFP. These labeled cells were plated at near confluency either alone (controls) or mixed at a 1:1 ratio (co-cultures) for 48 hours in endothelial growth medium (EGM-2, Cambrex). The labeled cells were then sorted by FACS and RNA was collected from all 4 cultures. There are a total of four samples: GFP-1205Lu cells grown alone, GFP-1205Lu cells separated from co-culture with RFP-HUVEC cells, RFP-HUVEC cells grown alone, and RFP-HUVEC cells separated from co-culture with GFP-1205Lu cells. The JHMI Microarray Core was responsible for sample processing and initial data processing using Affymetrix-recommended protocols (Affymetrix GeneChip Expression Analysis Technical Manual, 2004).

2008-10-18 | E-GEOD-8699 | biostudies-arrayexpress

MS-based proteomic characterization of Megavirus chilensis virions prepared from cells coinfected or not with Zamilon vitis

Project description:Nested parasitic chains are common schemes in nature, not limited to cellular organisms. Some giant viruses infecting protists are hyperparasitized by smaller viruses named virophages. Both can carry episomal plasmid-like DNA molecules known as transpovirons in their particles. They all share common transcriptional regulatory elements dictating the expression of their genes, which are transcribed within viral factories built by giant viruses in the host cytoplasm. This suggests close but as yet undetermined interactions between their respective transcriptional networks. Here, we studied the protein content of Megavirus chilensis virions produced in Acanthamoeba castellanii cells co-infected or not with the virophage Zamilon vitis.

2024-09-03 | PXD052049 | Pride

Whole genome sequencing of T-DNA reporter lines in Arabidopsis thaliana

Project description:In order to characterize precisely the T-DNA insertion(s) in three reporter lines, we performed whole genome sequencing and searched for insertion sites and T-DNA copy numbers.

2024-05-15 | E-MTAB-13442 | biostudies-arrayexpress

Interaction between GPR110 (ADGFR1) and tight junction protein occludin implicated in blood-brain barrier permeability

Project description:Identifying GPR110 interacting proteins using chemical crosslinking, affinity purification and quantitative mass spectrometry

2023-05-10 | PXD041011 | Pride