Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8173537_1.fastq.gz | Fastqsanger.gz | |||
| SRR8173537_2.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Mycobacterium tuberculosis can use a proteasome to degrade proteins when they are post-translationally modified with prokaryotic ubiquitin-like protein (Pup). While pupylation is reversible, mechanisms regulating depupylation have not been identified. Here, we identify a depupylation regulator, CoaX, a pseudo-pantothenate kinase. Pantothenate synthesis enzymes were more abundant in a ∆coaX mutant, including PanB, a substrate of the Pup-proteasome system. Media supplementation with pantothenate decreased PanB levels in a coaX and Pup-proteasome system-dependent manner. In vitro, CoaX accelerated depupylation of Pup~PanB, while addition of pantothenate inhibited this reaction. Collectively, we propose CoaX contributes to proteasomal degradation of PanB by modulating depupylation of Pup~PanB in response to pantothenate levels.
2024-11-01 | GSE260838 | GEO
Project description:Mycobacterium smegmatis is a soil bacterium exposed to continuously environmental changes of nitrogen availability. As member of Actinobacteria, it possesses an ubiquitin-like post-translational modification pathway called pupylation. The pathway starts when a small protein called Pup is attached to a lysine of a specific cellular target. Then the Pup-modified protein is degraded by the proteasome, as it was shown that Pup acts as degradation signal. Recent studies showed the role of pupylation in Mycobacterium smegmatis for survival under nitrogen starvation by supplying recycled amino acids. The present study is an investigation of the influence of Mycobacterium smegmatis Pup protein on the whole proteome in absence of nitrogen sources. Therefore a pup deletion mutant was generated. Applying stable isotope dimethyl labelling, low impact of the pupylation on proteome was revealed immediately after exposure to growth medium lacking nitrogen. In contrast, post 24 h of nitrogen starvation, Msm pup deletion strain showed several proteins with significant changes in abundance. Noteworthy, key proteins involved in nitrogen assimilation were significantly affected in Msm Δpup. Furthermore, we label-free quantified pupylated proteins of nitrogen starved Msm for a more extensive understanding of pupylation role in surviving and overcoming the lack of nitrogen.
2016-08-11 | PXD003229 | Pride
Project description:We introduce pupylation-based proximity labelling (PUP-IT) as a tool for protein interaction detection in plant biology. We show that PUP-IT readily confirmed and extended protein interactions for several known protein complexes, across different types of plant systems.
2025-01-10 | PXD048346 | Pride
Project description:To identify RA-regulated genes in mSSCs, we treated mSSCs with vehicle, RA and RA plus CHX. To characterize the induced spermatogenic cells by transcriptome profiling, we cultured mSSCs on pup Sertolic cells supplemented with RA. Induced differentiating spermatogonia and induced spermatocytes were collected after a 3-day- and 6-day-induction, respectively.
2016-06-16 | GSE77051 | GEO
Project description:Pupylation is a posttranslational protein modification in bacteria resembling ubiquitination in eukaryotes. The prokaryotic ubiquitin-like protein Pup is covalently attached to other proteins via an isopeptide bond between its carboxyterminal glutamate residue and a lysine residue in the target. In mycobacteria, pupylation was shown to mark proteins for unfolding by the ATPase Mpa and subsequent degradation by the proteasome. However, the occurrence of pupylation in species without a proteasome like Corynebacterium glutamicum suggests that degradation may not be the only fate of pupylated proteins. The Îpup mutant senses a stronger iron limitation than the wild type. Among the 125 genes showing at least 2-fold changes in transcript levels in the Îpup mutant (p-value ⤠0.05) were 54% of all genes known to be regulated by the master regulator of iron homeostasis DtxR (Brune et al., 2006; Wennerhold and Bott, 2006). Except for ftn, which is activated by DtxR and showed a 2-fold decreased mRNA level, the other DtxR target genes showed increased mRNA levels in the Îpup strain. These included ripA, encoding a transcriptional regulator of iron proteins, which represses a number of prominent iron-containing proteins under iron limitation, such as aconitase or succinate dehydrogenase (Wennerhold et al., 2005). 79% of the known RipA target genes showed decreased mRNA levels in the Îpup strain. DNA microarray analyses were performed to compare the mRNA levels of the C. glutamicum Îpup mutant and its parent wild type under iron-limited conditions. The two strains precultivated in CGXII medium with 4% (w/v) glucose and 1 µM FeSO4 were inoculated into fresh medium to an OD600 of 1, cultured for 2 h, and harvested on ice by centrifugation (5 min at 4,000 g and 4°C). Please note that the GPL16989 array design comprises oligos for 4 different bacterial genomes. In the GPR-files in this study, all IDs/Names (oligonucleotides) which are not from the host C. glutamicum were replaced by the text EMPTY since only C. glutamicum expression was analyzed.
2016-04-04 | E-GEOD-64866 | biostudies-arrayexpress
Project description:In a manner similar to ubiquitin, the prokaryotic ubiquitin-like protein (Pup) has been shown to target proteins for degradation via the proteasome in mycobacteria. However, not all actinobacteria possessing the Pup protein also harbor a proteasome, suggesting fates for pupylated proteins other than degradation via a proteasome or degradation at all. In the present study we set out to study pupylation in the proteasome-lacking non-pathogenic model microorganism and biotechnological workhorse Corynebacterium glutamicum. A defined pup deletion mutant of C. glutamicum ATCC 13032 grew as the control indicating that pupylation seems to be dispensable under the conditions tested. By expression of homologous Pup carrying a poly-histidine tag in C. glutamicum ATCC 13032 we purified the first pupylome of a microorganism lacking a proteasome. Multidimensional Protein Identification Technology (MudPIT) unraveled 54 proteins being pupylated in this organism. Similar to mycobacteria, the majority of pupylated proteins in C. glutamicum can be classified as enzymes of the metabolism or as involved in translation. These results help to elucidate the common target pathways of pupylation in bacteria.
2014-06-24 | GSE48038 | GEO
Project description:To identify RA-regulated genes in mSSCs, we treated mSSCs with vehicle, RA and RA plus CHX. To characterize the induced spermatogenic cells by transcriptome profiling, we cultured mSSCs on pup Sertolic cells supplemented with RA. Induced differentiating spermatogonia and induced spermatocytes were collected after a 3-day- and 6-day-induction, respectively. We carried out RNA-seq analysis of samples after different treatment and samples from different in vitro induction stages.Two biological replicates were included for each sample.
2016-06-16 | E-GEOD-77051 | biostudies-arrayexpress
Project description:Global identification of prokaryotic ubiquitin-like protein (PUP) targets from Mycobacteruim
2010-09-14 | PRD000821 | Pride
Project description:To determine if Sox9 was sufficient to drive mucous differentiation in the gastric epithelium, we bred mice carrying alleles for ROSA26rtTA.IRES.EGFP, TetO-Sox9, and Fgf20Cre.GFP. In these mice, cells expressing Cre will induce rtTA from the ROSA26rtTA.IRES.EGFP allele. To explore transcriptional changes following adult misexpression of Sox9, we isolated RNA from the corpus of Fgf20Cre.GFP/Cre.GFP; ROSA26rtTA.IRES.EGFP/rtTA.IRES.EGFP; TetO-Sox9 pup (misexpression animals) and ROSA26rtTA.IRES.EGFP/rtTA.IRES.EGFP; TetO-Sox9 pup (control) animals and performed RNA-sequencing.
2023-08-30 | GSE230101 | GEO
Project description:Nafion byproduct 2 (NBP2; CAS: 749836-20-2; Product #: 6164-3-3J; Lot: 512400; SynQuest Laboratories Alachua, FL, USA) is a polyfluoroalkyl ether sulfonic acid that was recently detected in surface water, drinking water, and human serum samples from monitoring studies in North Carolina, USA. We orally exposed pregnant Sprague-Dawley rats to NBP2 from gestation day (GD) 14–18 (0.1–30 mg/kg/d), GD17-21, and GD8 to postnatal day (PND) 2 (0.3–30 mg/kg/d) to characterize maternal, fetal, and postnatal effects. GD14-18 exposures were also conducted with perfluorooctane sulfonate (PFOS) for comparison to NBP2, as well as data previously published for hexafluoropropylene oxide-dimer acid (HFPO-DA or GenX). NBP2 produced stillbirth (30 mg/kg), reduced pup survival shortly after birth (10 mg/kg), and reduced pup body weight (10 mg/kg). Histopathological evaluation identified reduced glycogen stores in newborn pup livers and hepatocyte hypertrophy in maternal livers at ≥ 10 mg/kg. Exposure to NBP2 from GD14-18 reduced maternal serum total T3 and cholesterol concentrations (30 mg/kg). Maternal, fetal, and neonatal liver gene expression was investigated using RT-qPCR pathway arrays, while maternal and fetal livers were also analyzed using TempO-Seq transcriptomic profiling. Overall, there was limited alteration of genes in maternal or F1 livers from NBP2 exposure with significant changes mostly occurring in the top dose group (30 mg/kg) associated with lipid and carbohydrate metabolism. Metabolomic profiling indicated elevated maternal bile acids for NBP2, but not HFPO-DA or PFOS, while all three reduced 3-indolepropionic acid. Maternal and fetal serum and liver NBP2 concentrations were similar to PFOS, but ∼10–30-fold greater than HFPO-DA concentrations at a given maternal oral dose. NBP2 is a developmental toxicant in the rat, producing neonatal mortality, reduced pup body weight, reduced pup liver glycogen, reduced maternal thyroid hormones, and altered maternal and offspring lipid and carbohydrate metabolism similar to other studied PFAS, with oral toxicity for pup loss that is slightly less potent than PFOS but more potent than HFPO-DA.
2022-01-10 | GSE192589 | GEO