Pseudomonas sp. ADP
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA296545 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:ADP array data, comprised of 2217 samples of Asian ancestry (excluding the Japanese population from ADP). Samples were genotyped on different Illumina or Affy platform.
| EGAD00010001491 | EGA
Project description:Host-pathogen conflicts are crucibles of molecular innovation. Selection for immunity to pathogens has driven the evolution of sophisticated immunity mechanisms throughout biology, including in bacteria that must evade their viral predators known as bacteriophages. Here, we characterize a toxin-antitoxin-chaperone system, CmdTAC, in Escherichia coli that provides robust defense against infection by T4 phage. During infection, newly synthesized capsid protein triggers dissociation of the chaperone CmdC from the CmdTAC complex, leading to destabilization and degradation of the antitoxin CmdA, with consequent liberation of the toxin CmdT, an ADP-ribosyltransferase. Strikingly, CmdT does not target a protein, DNA, or structured RNA, the known targets of other ADP-ribosyltransferases. Instead, CmdT modifies the N6 position of adenine in GA dinucleotides within single-stranded RNAs to robustly block mRNA translation and viral replication. Our work reveals both a new mechanism of anti-phage defense and a new class of ADP-ribosyltransferases that targets mRNA.
2024-03-09 | GSE253513 | GEO
Project description:Oxidative stress is a potent inducer of protein ADP-ribosylation. Although the proteins modified under oxidative stress have been identified, it is not clear, whether the number of modified proteins and/or the number ADP-ribosylation sites varies with stress intensity. Here, we investigated both the qualitative and quantitative changes in the HeLa cell ADP-ribosylome induced by mild (4 - 16 uM), moderate (64 - 250 uM), or severe, but non-lethal (1 mM) H2O2 concentrations using shotgun and parallel reaction monitoring mass spectrometry (PRM-MS). After moderate and severe oxidative stress, approximately 50% of proteins not ADP-ribosylated under basal conditions were induced, while ADP-ribosylation of the other 50% already ADP-ribosylated under basal conditions remained constant. In contrast, mild oxidative stress caused a reduction in detectable ADP-ribosylation of many proteins, which were induced under more severe oxidative stress. Overall, the number of ADP-ribosylation sites modified/de-modified did not change significantly under the various degrees of oxidative stress. Moreover, we applied the PRM method to study protein ADP-ribosylation in ovarian cancer cells that display different sensitivities to PARP inhibitors. These studies revealed similar ADP-ribosylation responses following H2O2 treatment, which, however, correlated in extent with ARTD1 abundance in these cells. Overall, our new MS approaches have proven to be highly useful in monitoring cellular protein ADP-ribosylation and have revealed unexpected fluctuations in proteins ADP-ribosylation depending on the degree of oxidative stress.
2016-11-13 | MSV000080334 | MassIVE
Project description:Host-pathogen conflicts are crucibles of molecular innovation. Selection for immunity to pathogens has driven the evolution of sophisticated immunity mechanisms throughout biology, including in bacteria that must evade their viral predators known as bacteriophages. Here, we characterize a toxin-antitoxin-chaperone system, CmdTAC, in Escherichia coli that provides robust defense against infection by T4 phage. During infection, newly synthesized capsid protein triggers dissociation of the chaperone CmdC from the CmdTAC complex, leading to destabilization and degradation of the antitoxin CmdA, with consequent liberation of the toxin CmdT, an ADP-ribosyltransferase. Strikingly, CmdT does not target a protein, DNA, or structured RNA, the known targets of other ADP-ribosyltransferases. Instead, CmdT modifies the N6 position of adenine in GA dinucleotides within single-stranded RNAs to robustly block mRNA translation and viral replication. Our work reveals both a new mechanism of anti-phage defense and a new class of ADP-ribosyltransferases that targets mRNA.
2024-03-09 | GSE253512 | GEO
Project description:Host-pathogen conflicts are crucibles of molecular innovation. Selection for immunity to pathogens has driven the evolution of sophisticated immunity mechanisms throughout biology, including in bacteria that must evade their viral predators known as bacteriophages. Here, we characterize a toxin-antitoxin-chaperone system, CmdTAC, in Escherichia coli that provides robust defense against infection by T4 phage. During infection, newly synthesized capsid protein triggers dissociation of the chaperone CmdC from the CmdTAC complex, leading to destabilization and degradation of the antitoxin CmdA, with consequent liberation of the toxin CmdT, an ADP-ribosyltransferase. Strikingly, CmdT does not target a protein, DNA, or structured RNA, the known targets of other ADP-ribosyltransferases. Instead, CmdT modifies the N6 position of adenine in GA dinucleotides within single-stranded RNAs to robustly block mRNA translation and viral replication. Our work reveals both a new mechanism of anti-phage defense and a new class of ADP-ribosyltransferases that targets mRNA.
2024-03-09 | GSE253511 | GEO
Project description:Based on inheritance of acquired characteristics, Lamarckian theory of evolution explains the evolution of biological systems through epigenetics. In a previous study, we have shown how microbial evolution has resulted in a persistent reduction in expression after repeatedly selecting for the lowest PGAL1-YFP-expressing cells. Applying the ATAC-seq assay on samples collected from this 28-days evolution experiment, here we show how genome-wide chromatin compaction change during evolution under selection pressure. We found that the chromatin compaction was altered not only on GAL network genes directly impacted by the selection pressure, showing an example of non-genetic memory, but also at the whole genome level. The GAL network genes experienced chromatin compaction accompanying the reduction in PGAL1-YFP reporter expression; strikingly, the fraction of global genes with differentially compacted chromatin states accounted for about a quarter of the total genome. Moreover, some of the ATAC-seq peaks followed well-defined temporal dynamics. Comparing the peak’s intensity in consecutive days, we found most of the differential compaction to occur between days 0 and 3 when the selection pressure was first applied, and between days 7 and 10 when the pressure was lifted. Among the gene sets enriched for the differential compaction events, some had increased chromatin availability once selection pressure was applied and decreased availability after the pressure was lifted (or vice versa). These results intriguingly show that, despite the lack of targeted selection, transcriptional availability of a large fraction of the genome change in a very diverse manner during evolution and these changes can occur in a relatively short number of generations.
2022-09-13 | GSE205227 | GEO
Project description:ADP-ribosylated proteins were enriched using the engineered Af1521 Macro domain (Nowak et al., https://doi.org/10.1038/s41467-020-18981-w) from transgenic A. thaliana plants expressing the Pseudomonas syringae type III effector AvrRpm1. Enriched proteins were analyzed by LC-MS/MS.
2023-09-28 | PXD045511 | Pride
Project description:ADP-ribosylated proteins were enriched using the engineered Af1521 Macro domain (Nowak et al., https://doi.org/10.1038/s41467-020-18981-w) from transgenic A. thaliana lines expressing the Pseudomonas syringae type III effector AvrRpm1. Enriched proteins were analyzed by LC-MS/MS.
2023-09-28 | PXD045638 | Pride
Project description:The gene expression analysis of bone marrow-derived macrophages (BMDM) treated with 100uM ADP was employed. Extracellular ADP is a danger signal that induces immune responses. Results provide insight into macrophage functions altered in ADP stimulation.
2020-07-07 | GSE153888 | GEO
Project description:ADP-ribosylated proteins were enriched using the engineered Af1521 Macro domain (Nowak et al., https://doi.org/10.1038/s41467-020-18981-w) from transgenic A. thaliana plants expressing the Pseudomonas syringae type III effectors AvrRpm1 or HopF2. Enriched proteins were analyzed by LC-MS/MS. Non-transgenic Col-0 plants served as control.
2023-09-28 | PXD045780 | Pride