Pseudomonas phage LUZ19 LC-MSMS
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Pseudomonas Phage Luz19
SUBMITTER: 
Pavel Roudnický
LAB HEAD: Zbynek Zdrahal
PROVIDER: PXD074244 | Pride | 2026-05-25
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| 4277_QTOF2_120IS_sample_LUZ19_GA1_01_56555.d.zip | Other | |||
| 4277_QTOF2_120IS_sample_LUZ19_GA1_01_56555.mgf | Mgf | |||
| 4277_QTOF2_120IS_sample_LUZ19_semiT.msf | Msf | |||
| checksum.txt | Txt |
Items per page: 5 1 - 4 of 4 |
Similar Datasets
Project description:There are a limited number of clinically useful serum biomarkers to predict tumour onset or treatment response in gastric cancer (GC). For this reason, we explored the serum proteome of the gp130Y757F murine model of intestinal-type gastric cancer (IGC). We identified 30 proteins with significantly elevated expression in early gp130Y757F IGC and 12 proteins that were significantly elevated in late gp130Y757F IGC compared to age and gender matched wild-type mice. Within these signatures, there was an overlap of 10 proteins commonly elevated in both early and late-stage disease. Since IGC in the gp130Y757F model can be reversed following therapeutic inhibition of Interleukin (IL)-11, we explored whether the protein signatures we identified could be used to monitor tumour regression. We compared two different therapeutic modalities and found 5 proteins to be uniquely differentially expressed between control and treated animals half-way through treatment, with 10 differentially expressed at the end of treatment. Our findings highlight the potential to identify reliable biomarkers to track IGC tumor regression in response to treatment.
2024-03-19 | PXD043224 | Pride
Project description:NF-κB has an essential role in innate immune response and inflammation and is involved in cancer development and progression. We apply the SEC-PCP-SILAC method incorporating metabolic labeling, size exclusion chromatography and protein correlation profiling to construct a complex network of interactome rearrangement in response to NF-κB modulation in breast cancer cells. Our interaction network represents a complex insight into the dynamics of MCF-7 protein interactome associated with NF-κB pathway. Our dataset could serve as a basis for future studies characterizing role of NF-κB in breast cancer cellular pathways. This PRIDE project includes results from SILAC labeled and label-free replicates from the SEC-PCP-SILAC analysis of protein complexes in MCF-7 cells with inhibited and uninhibited NF-κB pathway, results from the immunoprecipitation experiment aimed at interaction partners of NF-κB factor RELA, analysis of total proteome after NF-κB inhibition, and results from SEC fractionation of untreated and unlabeled MCF-7 cells.
2024-02-28 | PXD040125 | Pride
Project description:To identify protein composition of photosystem II (PSII) supercomplexes separated from spruce seedlings using sucrose gradient centrifugation. These supercomplexes represent mainly so called C2S2 PSII supercomplex as revealed by high-resolution cryo-EM.
2023-07-19 | PXD035272 | Pride
Project description:Bacteria shut down protein synthesis under stress, but how they resume growth remains unclear. We used an E. coli strain lacking a ribosome maturation factor RimM, which exhibits prolonged growth arrest, as a model to study bacterial recovery. Loss of this factor delays 30S ribosomal subunit assembly more than other maturation factors such as RbfA. Mass spectrometry and cryo-EM analyses revealed disrupted assembly of the 30S head domain, increased binding of initiation factors (IF1 and IF3), and recruitment of a silencing factor RsfS to the 50S subunit, collectively preventing premature 70S formation.
2026-03-04 | PXD068732 | Pride
Project description:Photosystem II (PSII) is essential for energy conversion during oxygenic photosynthesis in plants and algae. Chlorella ohadii, one of the fastest multiplying green alga, thrives under the harsh desert sun but lacks the standard PSII photoprotective mechanisms involving LhcSR/PsbS proteins or protein phosphorylation. Here, we present analysis of cryo-EM structure of the PSII supercomplex from C. ohadii at 2.9Å resolution to determine whether the exceptional resistance to desert conditions has a structural basis in PSII. The structure reveals a novel PsbO isoform and additional subunits, PsbR and PsbY, which enhance core complex stability through extensive interactions. Furthermore, the trimeric light-harvesting complexes (LHCII) are bound to the PSII core by specific light-harvesting proteins whose down-regulation in response to high light conditions implies a reduction in the number of bound LHCII trimers. These modifications play a crucial role in maintaining PSII stability and photoprotection, allowing C. ohadii to survive in extreme conditions.
2025-10-06 | PXD059509 | Pride
Project description:Hydrogen can be an important source of energy for chemolithotrophic acidophiles, especially in the deep terrestrial subsurface. Nevertheless, the current knowledge of microbial hydrogen utilization in acidic environments is minimal. A multi-omics analysis was applied on Acidithiobacillus ferrooxidans growing aerobically and anaerobically (with ferric iron) on hydrogen as an electron donor, and a respiratory model proposed from the results obtained. In this model, both [NiFe] hydrogenases, cytoplasmic uptake and membrane-bound respiratory, oxidize molecular hydrogen to two protons and two electrons. The electrons are used to reduce membrane-soluble ubiquinone to ubiquinol. Genetically associated [FeS]-binding proteins mediate electron relay from the hydrogenases to the ubiquinone pool. Under aerobic conditions, reduced ubiquinol transfers electrons to either cytochrome aa3 oxidase via cytochrome bc1 complex and cytochrome c4 or the alternate directly to cytochrome bd oxidase, resulting in proton efflux together with the reduction of molecular oxygen to water. Under anaerobic conditions, reduced ubiquinol transfers electrons to outer membrane cytochrome c (ferric iron reductase) via cytochrome bc1 complex and a cascade of electron transporters (cytochrome c4, cytochrome c552, rusticyanin, and high potential iron-sulfur protein), resulting in proton efflux together with the reduction of ferric iron to ferrous iron. The proton gradient generated by molecular hydrogen oxidation maintains the membrane potential and allows the generation of ATP via ATP synthase and NADH via NADH-ubiquinone oxidoreductase. To a lesser extent, NADH can also be generated by another bidirectional cytoplasmic hydrogenase. ATP and NADH are further utilized in the Calvin–Benson–Bassham cycle for inorganic carbon uptake and assimilation. These results further clarify the role of extremophiles in biogeochemical processes and their impact on the composition and features of the deep terrestrial subsurface from the distant past to the present.
2020-11-24 | PXD020361 | Pride
Project description:Polyglutamylation is a reversible post-translational modification initially discovered on tubulin. In eukaryotes, polyglutamylation is catalyzed by enzymes from the tubulin tyrosine ligase-like (TTLL) family, which show substrate and reaction specificities that are so far mostly explored on tubulin. By contrast, little is known on the mechanism and significance of TTLL-mediated modification of non-tubulin substrates. Here, we found that TTLL11 generates a previously unknown type of polyglutamylation by adding glutamate residues to the carboxy-terminus of a substrate protein. TTLL11 efficiently polyglutamylates the signaling protein disheveled 3 (DVL3), thereby changing the interactome of DVL3, as well as its capacity to undergo liquid-liquid phase separation (LLPS). Both carboxyterminal polyglutamylation and the resulting reduction in LLPS capacity of DVL3 were reverted by the deglutamylating enzyme CCP6, which demonstrates the causal relationship between TTLL11-mediated polyglutamylation and LLPS. We thus discovered a novel type of posttranslational modification catalyzed by a TTLL enzyme, which significantly broadens the range of proteins that can be modified by polyglutamylation, and provide first evidence that polyglutamylation can act as a regulator of protein LLPS.
2024-09-30 | PXD034237 | Pride
Project description:Signaling trough cytoplasmic or nuclear action of p53 is a major response mechanism to cellular stresses. While p53 protein levels have been shown to increase upon nutrient stresses such as starvation, the exact signaling cascade in this context remains elusive. Here, we show in a human hepatoma cell line that nutrient withdrawal leads to robust nuclear p53 stabilization and utilize various complementary omics approaches to dissect upstream and downstream networks in the response to starvation. Using the affinity purification mass spectrometry (MS) method BioID, we determine the cytoplasmic p53 interaction network within the immediate-early starvation response and show that p53 is dissociated from several metabolic enzymes and the kinase PAK2. Direct binding of p53 DNA-binding domain and N-terminal PAK2 was confirmed with nuclear magnetic resonance (NMR) interaction studies. Furthermore, rapid immunoprecipitation MS of endogenous proteins (RIME) uncovered the nuclear interactome under prolonged starvation, where we confirmed the novel p53 interactors SORBS1, involved in insulin signaling, and UGP2, a key enzyme of glycogen synthesis. Finally, transcriptomics after p53 re-expression on a CRISPR/Cas9 knock out background revealed a distinct starvation-specific transcriptome response and suggested novel nutrient-dependent p53 target genes. Together, our complementary approaches delineate several nodes of the p53 signaling cascade in response to starvation, shedding new light on the mechanisms of p53 as a nutrient stress sensor and regulator of specific transcriptional output. Given the central role of p53 in cancer biology and the beneficial effects of fasting in cancer treatment, the identified interaction partners and networks could pinpoint novel pharmacologic targets to fine-tune p53 activity.
2022-06-09 | PXD028341 | Pride
Project description:Interferon-gamma (IFNγ) is a critical cytokine required to coordinate anti-viral immunity in response to pathogens such as influenza. IFNγ signals through the JAK-STAT pathway, inducing a tyrosine-phosphorylation cascade that ensures a potent immune response. Aberrant JAK-STAT signaling can drive hyperinflammation and autoimmunity, and thus signaling is tightly and selectively regulated by the IFNγ-inducible protein, Suppressor of Cytokine Signaling 1 (SOCS1). SOCS1 inhibits signaling by directly blocking JAK kinase activity. Here we identified a SOCS1-interacting partner, ARAP2 that fine-tunes SOCS1 function. We report that tyrosine 415 in ARAP2 binds the SOCS1-Src Homology 2 (SH2) domain and limits the ability of SOCS1 to inhibit IFNγ signaling. Our findings reveal ARAP2 as a key player in influenza immunity that promotes the IFNγ response through a phosphorylation dependent interaction with the negative regulator SOCS1.
2025-10-06 | PXD060300 | Pride
Project description:Spinocerebellar ataxia type-1 is caused by an abnormally expanded polyglutamine (polyQ) tract in ataxin-1 protein. These expansions are responsible for protein misfolding and self-assembly into intranuclear inclusion bodies (IIBs) that are linked to neuronal death. Here, we describe a nuclear protein aggregation model of pathogenic human ataxin-1. Using an inducible Sleeping Beauty transposon system, we overexpressed ATXN1Q82 gene in human mesenchymal stem cells that are resistant to the early cytotoxic effects of the mutant protein. We characterized the structure and the protein composition of insoluble polyQ IIBs which gradually occupy the nuclei. In response to their formation, our transcriptome analysis reveals a cerebellum-specific perturbed protein interaction network, primarily affecting protein translation. Our study resolves the previously unknown architecture of insoluble polyQ IIBs and suggests that they affect the assembly and the function of the ribosome. Our inducible cell system faithfully models a human cerebellum at the end-stage of the disease.
2020-02-18 | PXD012709 | Pride