Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The Protein Composition of Human Adenovirus Replication Compartments.

ABSTRACT: Human adenoviruses are double–stranded DNA viruses that replicate in the cell nucleus and induce the formation of replication compartments (RCs) that are critical in viral replication and control of virus-host interactions. RCs are specialized virus-induced subnuclear microenvironments in which viral genome replication and expression are orchestrated, but also where host proteins known to restrict viral replication are co-opted and subverted. However, the protein composition of these RCs remains largely unexplored. In this study, we isolated adenovirus RC-enriched fractions from infected cells at different times post-infection and employed a tandem mass tag-based quantitative mass spectrometry approach to identify proteins associated with RCs. To validate the RC-protein components identified by mass spectrometry, we employed immunofluorescence and western blotting techniques. Proteins previously described to colocalize in RCs in infected cells were identified in the isolated subnuclear fractions. Moreover, we were able to validate previously unidentified RC-associated proteins, including the High Mobility Group Box 1, the SET nuclear proto-oncogene, the Structure Specific Recognition Protein 1 and the CCCTC-binding protein. These findings reveal an elaborate network of host and viral proteins potentially relevant for RC formation and function. The results also suggest potential candidate targets for therapeutic intervention and further mechanistic insights into the molecular basis of virus-host interactions

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Foreskin Fibroblast

DISEASE(S): Upper Respiratory Tract Disease

SUBMITTER: Ramón A. González

LAB HEAD: Ileana M.

PROVIDER: PXD051745 | Pride | 2024-11-20

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20180418_Exp1_Fr.msf	Msf
	20180418_Exp1_Fr1.raw	Raw
	20180418_Exp1_Fr2.raw	Raw
	20180418_Exp1_Fr3.raw	Raw
	20180418_Exp1_Fr4.raw	Raw

Items per page:

1 - 5 of 57

Similar Datasets

Genome-wide Analysis of Re-replication Reveals Inhibitory Controls that Target Multiple Stages of Replication Initiation

Project description:DNA replication must be tightly controlled during each cell cycle to prevent unscheduled replication and ensure proper genome maintenance. The currently known controls that prevent re-replication act redundantly to inhibit pre-Replicative Complex (pre-RC) assembly outside of the G1 phase of the cell cycle. We have analyzed the effects of re-replication on the S. cerevisiae genome using a combination of Comparitive Genomic Hybridization (CGH) of re-replicating strains and Genome-Wide Location Analysis of pre-RC components. These data indicate which sites in the genome assemble pre-RCs under re-replication conditions, which sites undergo re-initiation and the extent of re-replication. Keywords: comparative genomic hybridization, ChIP-chip, re-replication, DNA replication, pre-RC

2006-03-20 | GSE4487 | GEO

Gene expression profiling of liver from regulatar chow (RC) fed-mice, high fat diet (HFD)-fed mice with vehicle or nobiletin (NOB) treatment

Project description:Comparison of liver transcriptome between RC-fed mice, HFD-fed mice with vehicle or nobiletin treatment provides the possibility to identify the effects of nobiletin on gene expression altered by HFD relative to RC. We used Illumina microarrays to analyze liver transcriptome of different treatment groups following exposure to RC, HFD.Veh (denoted as the HFD group) and HFD.NOB (denoted as the NOB group). The microarray experiment was performed to investigate effects of HFD and NOB on mouse liver transcriptome. Liver tissues were collected at ZT2 and ZT14 (corresponding to 2 hours after light on and light off, respectively). The pooled RNA samples, 4 mice each group, were used for the microarray.

2016-03-03 | E-GEOD-78848 | biostudies-arrayexpress

Proteome characterization of HCMV virus microenvironment with addition of cidofovir

Project description:The control of host processes which influence cell-cell communication is central to determining the outcome of a virus infection in tissue. Despite this, it remains unclear how cells either in close or distant proximity to an infected cell differentially respond to the primary infection. Here, we established a virus infection microenvironment to resolve molecular features and functional consequences of cell spatial address within this localized niche by mass spectrometry. To rule out the possibility that neighboring cells are infected by the viral progeny from the primary infection, cidofovir is added in the system to prevent viral genome replication in order to prevent the spread of infection.

2023-05-11 | PXD040582 | Pride

Proteomic comparison of photosynthetic reaction centre-light harvesting 1 complexes in wild-type, protein-W knockout and His-tagged protein-W strains of Rhodopseudomonas palustris.

Project description:Rhodopseudomonas palustris is a species of purple phototrophic bacterium. In these species, solar energy is captured by reaction centre-light harvesting 1 (RC-LH1) complexes which reside in membranes within the cells. The RC comprises three protein subunits: H, M, L and is encircled by a ring of LH1-α and LH1-β subunit pairs. Approximately 10% of these complexes in the wild-type (WT) strain include an additional subunit called protein-W. In this project, we have determined cryo-EM structures for RC-LH1 complexes both with and without protein-W. To enable the purification of RC-LH1-W with 100% occupancy of protein-W, strain expressing a C-terminally His-tagged W was engineered. For complexes lacking W, a knockout strain was used. Proteomic analysis was employed to validate these strains and establish that the WT and W-His expressed similar levels of W relative to RC-LH1.

2021-09-09 | PXD020402 | Pride

Chromosomal Mcm2-7 distribution and the genome replication program in species from yeast to humans

Project description:The spatio-temporal program of genome replication across eukaryotes is thought to be driven both by the uneven loading of pre-replication complexes (pre-RCs) across the genome at the onset of S-phase, and by differences in the timing of activation of these complexes during S-phase. To determine the degree to which distribution of pre-RC loading alone could account for chromosomal replication patterns, we mapped the binding sites of the Mcm2-7 helicase complex (MCM) in budding yeast, fission yeast, mouse and humans. We observed identical individual MCM double-hexamer (DH) footprints across the species, but notable differences in their distribution. Nonetheless, most fluctuations in replication timing in all four organisms could be accounted for by differences in chromosomal MCM distribution. We conclude that, although certain genomic regions, most notably the inactive X-chromosome, are subject to post-licensing regulation, most differences in replication timing along the chromosome reflect uneven chromosomal distribution of stochastically firing pre-replication complexes.

2021-05-18 | GSE150800 | GEO

Genome-wide map of DNA replication origin in Schizosaccharomyces pombe

Project description:DNA replication origins, or DNA sites pre-RC is bound to, were identified by ChIP-seq of pre-RC components, Orc4 and Mcm2. DNA copy number analysis revealed that ~40% of the detected sites were efficient and early-firing origins.

2019-01-19 | GSE125335 | GEO

Protein S-Nitrosylation of host and viral proteins upon fibroblast infection with Human Cytomegalovirus

Project description:Human Cytomegalovirus (HCMV) is a ubiquitous pathogen that has co-evolved with its host and in doing so, is highly efficient in undermining antiviral responses that limit successful infections. As a result, HCMV infections are highly problematic in individuals with weakened or underdeveloped immune systems including transplant recipients and newborns. Understanding how HCMV controls the microenvironment of an infected cell so as to favor productive replication is of critical importance. To this end, we took an unbiased proteomics approach to identify the highly reversible, stress induced, post-translational modification (PTM), protein S-nitrosylation, on viral proteins to determine the biological impact on viral replication. We identified protein S-nitrosylation of 13 viral proteins during infection of highly permissive fibroblasts. One of these proteins, pp71, is critical for efficient viral replication, as it undermines host antiviral responses, including STING activation. By exploiting site-directed mutagenesis of the specific amino acids we identified in pp71 as protein S-nitrosylated, we found this pp71 PTM diminishes its ability to undermine antiviral responses induced by the STING pathway. Our results suggest a model in which protein S-nitrosylation may function as a host response to viral infection that limits viral spread.

2020-07-03 | PXD019208 | Pride

Genome-wide analysis of Dengue virus 2 infected cells

Project description:The goal of this study was to compare the transcriptional profile (RNA-seq) of Dengue virus 2 and mock infected cells at 24 and 36 hours post infection. Dengue virus NS5 protein plays multiple functions in the cytoplasm of infected cells, enabling viral RNA replication and counteracting host antiviral responses. Here, we demonstrate a novel function of NS5 in the nucleus where it interferes with cellular splicing. Using global proteomic analysis of infected cells together with functional studies, we found that NS5 binds spliceosome complexes and modulates endogenous splicing. In particular, we show that NS5 alone, or in the context of viral infection, interacts with core components of the U5 snRNP particle, CD2BP2 and DDX23, alters the inclusion/exclusion ratio of alternative splicing events, and changes mRNA isoform abundance of known antiviral factors. Interestingly, a genome wide transcriptome analysis, using recently developed bioinformatics tools, revealed an increase of intron retention upon dengue virus infection, and viral replication was improved by silencing specific U5 components. Different mechanistic studies indicate that binding of NS5 to the spliceosome reduces the efficiency of pre-mRNA processing, independently of NS5 enzymatic activities. We propose that NS5 binding to U5 snRNP proteins hijacks the splicing machinery resulting in a less restrictive environment for viral replication. A549 cells where infected with Dengue virus 2 or mock and after 24 and 36 hours post infection mRNA was purified. Then the transcriptional profile of these cells was analyzed using RNA-seq.

2016-08-09 | E-GEOD-84285 | biostudies-arrayexpress

Genome-wide localization of ORC and MCM binding sites and identification of replication origins in S. pombe

Project description:DNA replication of eukaryotic chromosomes initiates at a number of discrete loci, called replication origins. Distribution and regulation of origins are important for complete duplication of the genome. Here, we determined locations of Orc1 and Mcm6, components of pre-replicative complex (pre-RC), on whole genome of Schizosaccharomyces pombe using a high-resolution tiling array. Pre-RC sites were identified in 460 intergenic regions, where Orc1 and Mcm6 colocalized. By mapping of 5-bromo-2’-deoxyuridine (BrdU)-incorporated DNA in the presence of hydroxyurea (HU), 307 pre-RC sites were identified as early-firing origins. In contrast, 153 pre-RC sites without BrdU incorporation were considered to be late and/or inefficient origins. Early and late origins tend to distribute separately in large chromosome regions. Inactivation of replication checkpoint by deletion of Cds1 resulted in BrdU incorporation with HU specifically at the late origins. An origin-exchange experiment showed that replication timing was not intrinsic to origin but dependent on its surrounding region. Interestingly, pericentromeric heterochromatin and the silent mating type locus replicated in the presence of HU, while the inner centromere or subtelomeric heterochromatin did not. Notably, MCM did not bind to inner centromeres where ORC was located. Thus, replication is differentially regulated in chromosome domains. Keywords: ChIP-chip analysis

2007-03-05 | GSE6523 | GEO

Identifying host factors associated with DNA replicated during virus infection

Project description:Viral DNA genomes replicating in cells encounter a myriad of host factors that facilitate or hinder viral replication. Viral proteins expressed early during infection modulate host factors interacting with viral genomes, recruiting proteins to promote viral replication, and limiting access to antiviral repressors. Although some host factors manipulated by viruses have been identified, we know little about pathways exploited during infection and how these differ between viruses. To identify cellular processes manipulated during viral replication, we defined proteomes associated with viral genomes during infection with adenovirus, herpes simplex virus and vaccinia virus. We compared enrichment of host factors between virus proteomes and confirmed association with viral genomes and replication compartments. Using adenovirus as an illustrative example, we uncovered host factors deactivated by early viral proteins, and identified a subgroup of nucleolar proteins that aid virus replication. Our datasets provide valuable resources of virus-host interactions that affect proteins on viral genomes.

2017-10-04 | PXD007741 | Pride

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