A synthetically methylotrophic Escherichia coli as a chassis for bioproduction
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap Fusion Lumos
ORGANISM(S): Escherichia Coli
SUBMITTER: 
Michael Reiter
LAB HEAD: Julia A. Vorholt
PROVIDER: PXD046243 | Pride | 2024-02-08
REPOSITORIES: Pride
Dataset's files
Items per page: 5 1 - 5 of 14 |
Similar Datasets
Project description:We want to quantify the proteome alteration following PROTAC mediated Glucocorticoid receptor depletion in vitro.
2023-12-11 | PXD046949 | Pride
Project description:Background. Dyslipidemia is associated with chronic kidney disease (CKD). It has been shown that inhibition of β-oxidation and lipid accumulation are common threats in the onset of kidney injury and conducive to fibrosis. We characterized the S-acylated proteome of kidneys from mice with diet-induced nephropathy, to uncover novel lipid-related biochemical changes that might contribute to the lipid-induced kidney dysfunction. Methods. We conducted total and S-acylated proteomics, and lipidomics of the renal crude membrane fractions of mice fed a high-fat diet (HFD). Then, we investigated in vitro the effect of S-acylation inhibition on megalin expression and ligand binding. Results. HFD caused albuminuria with unchanged kidney function. The dietary intervention induced a large-scale repression of protein S-acylation as well as of the most abundant ceramides and sphingomyelin species, which are highly suggestive of an overall reduction in acyl-CoA availability. S-acylation repression mostly affected proteins involved in endocytosis and intracellular transport. In particular, the kidney of the mice fed a HFD, which are characterized by albuminuria, displayed a marked decrease in the total amount and in the S-acylated form of megalin, the main tubular protein retrieval system. Further in vitro experiments indicated that S-acylation is important for total expression of megalin. Conclusions. The diet-induced derangement of fatty acids metabolism modifies the renal landscape of the S-acylated proteome during early stage of the kidney injury, which might reduce the maximal capacity of protein reabsorption by the proximal tubule.
2025-03-21 | PXD052634 | Pride
Project description:Proteomic expression analysis of Ca. Lokiarchaeum ossiferum, strain B35, grown using casein hydrolysate as the main carbon source under anaerobic conditions
2025-03-14 | PXD059733 | Pride
Project description:Abstract Background Vertebral endplate signal intensity changes visualized by magnetic resonance imaging termed Modic changes (MC) are highly prevalent in low back pain patients. Interconvertibility between the three MC subtypes (MC1, MC2, MC3) suggests different pathological stages. Histologically, granulation tissue, fibrosis, and bone marrow edema are signs of inflammation in MC1 and MC2. However, different inflammatory infiltrates and amount of fatty marrow suggest distinct inflammatory processes in MC2. Aims The aims of this study were to investigate i) the degree of bony (BEP) and cartilage endplate (CEP) degeneration in MC2, ii) to identify inflammatory MC2 pathomechanisms, and iii) to show that these marrow changes correlate with severity of endplate degeneration. Methods Pairs of axial biopsies (n=58) spanning the entire vertebral body including both CEPs were collected from human cadaveric vertebrae with MC2. From one biopsy, the bone marrow directly adjacent to the CEP was analyzed with mass spectrometry. Differentially expressed proteins (DEPs) between MC2 were identified and bioinformatic enrichment analysis was performed. The other biopsy was processed for paraffin histology and BEP/CEP degenerations were scored. Endplate scores were correlated with DEPs. Results Endplates from MC2 were significantly more degenerated. Proteomic analysis revealed an activated complement system, increased expression of extracellular matrix proteins, angiogenic, and neurogenic factors in MC2 marrow. Endplate scores correlated with upregulated complement and neurogenic proteins. Discussion The inflammatory pathomechanisms in MC2 comprises activation of the complement system. Concurrent inflammation, fibrosis, angiogenesis, and neurogenesis indicate that MC2 is a chronic inflammation. Correlation of endplate damage with complement and neurogenic proteins suggest that complement system activation and neoinnervation may be linked to endplate damage. The endplate-near marrow is the pathomechanistic site, because MC2 occur at locations with more endplate degeneration. Conclusion MC2 are fibroinflammatory changes with complement system involvement which occur adjacent to damaged endplates.
2025-03-21 | PXD038008 | Pride
Project description:Tripartite Tc toxins are virulence factors of bacterial pathogens. Although their structure and mechanism of action are well understood, it remains elusive where this large macromolecular complex is assembled and how it is released. Here we show by an integrative multiscale imaging approach that Yersinia entomophaga Tc (YenTc) toxin components are expressed only in a subpopulation of cells that are “primed” with several other potential virulence factors, including filaments of the protease M66/StcE. A phage-like lysis cassette (LC) is required for YenTc release; however, before resulting in complete cell lysis, the LC generates intermediate “ghost” cells, which may serve as assembly compartments and become densely packed with assembled YenTc holotoxins. We hypothesize that this stepwise mechanism evolved to minimize the number of cells that need to be sacrificed. The occurrence of similar lysis cassettes in diverse organisms indicates a conserved mechanism for Tc toxin release that may apply to other extracellular macromolecular machines.
2024-02-20 | PXD048008 | Pride
Project description:Staphylococcus aureus and Pseudomonas aeruginosa frequently co-occur in infections, and there is evidence that their interactions can negatively affect disease outcomes. P. aeruginosa is known to be dominant, often compromising S. aureus through the secretion of inhibitory compounds. We previously demonstrated that S. aureus can become resistant to growth-inhibitory compounds during experimental evolution. While resistance arose rapidly, the underlying mechanisms were not obvious as there were only few genetic mutations associated with resistance, while ample phenotypic changes occurred. We thus hypothesize that resistance may result from phenotypic responses in addition to genetic adaptation. Here, we tested this hypothesis using proteomics. We first focused on an evolved strain that acquired a single mutation in tcyA (encoding a transmembrane transporter unit) upon exposure to P. aeruginosa supernatant. We show that this mutation leads to a complete abolishment of transporter synthesis, which confers moderate protection against PQS and selenocystine, two toxic compounds produced by P. aeruginosa. However, this genetic effect was minor compared to the fundamental phenotypic changes observed at the proteome level when both ancestral and evolved S. aureus strains were exposed to P. aeruginosa supernatant. Major changes involved the downregulation of virulence factors, metabolic pathways and membrane transporters, and the upregulation of ROS scavengers and an efflux pump. Our results suggest that the observed multi-variate phenotypic response is a powerful adaptive strategy by itself, offering instant protection against competitors in fluctuating environments and reducing the need for hard-wired genetic adaptations.
2025-02-26 | PXD059647 | Pride
Project description:To study the role of the gap junction coupled astrocytic network, we generated inducible double knockouts to selectively delete Cx30 and Cx43 from astrocytes in adult mice. Mice carrying loxP-flanked Gjb6 (Cx30fl/fl mice) (Boulay et al., 2013) and Gja1 (Cx43fl/fl mice) (Theis et al., 2003) alleles were crossbred with mice expressing the tamoxifen-sensitive Cre-recombinase CreERT2 under the endogenous GLAST(Slc1a3)-promoter (Mori et al., 2006). Adult, 8-10 week old mice (Cx30fl/fl:Cx43fl/fl:GLASTCreERT2/+, termed cKO) and littermate control mice (Cx30fl/fl:Cx43fl/fl:GLAST+/+) were injected with tamoxifen for 5 consecutive days and hippocampi were isolated for subsequent TMT-based proteomics analysis 90 days after tamoxifen treatment, to study the consequences of astrocyte decoupling and connexin deletion.
2022-03-14 | PXD031136 | Pride
Project description:To study the role oligodendroglial Kir4.1 in regulating axonal energy metabolism, oligodendrocyte-specific Kir4.1 knockout mice and their littermate controls were used; optic nerve lysates were prepared for subsequent TMT-based proteomics.
2024-01-30 | PXD046207 | Pride
Project description:Nogo-A is a major player in neural development and regeneration, and it is the target of several clinical trials. However, its functions outside the nervous system are mostly unknown. We observed that Nogo-A is expressed in dental epithelial cells, responsible for the formation of enamel, and we showed that the deletion of Nogo-A in transgenic mouse models leads to the formation of defective enamel. We observed that Nogo-A directly interacts with molecules important for gene expression regulation, and its deletion perturbs their cellular localization. As a result, Nogo-A deletion induces overexpression of genes involved in cell differentiation and enamel production. Mechanistically, we demonstrated that intracellular Nogo-A, and not cell surface Nogo-A, is responsible for gene expression modulation. Taken together, our results indicate a new role for Nogo-A as regulator of enamel formation and suggest a new possible cell-autonomous function in regulating gene expression and cell differentiation.
2024-06-20 | PXD030386 | Pride
Project description:Hepatic fat accumulation has been widely associated with diabetes and hepatocellular carcinoma (HCC). Here, we aim to characterize the metabolic response that high fat availability elicits in livers prior to development of these diseases. We find that, after a short term on high fat diet, otherwise healthy mice show elevated hepatic glucose metabolization, activated glucose uptake, glycolysis and glucose contribution to serine as well as elevated pyruvate carboxylase activity compared to control diet mice. To understand other changes in the liver tissue after high fat diet exposure, we conducted untargeted transcriptomics and proteomics. This glucose phenotype occurred independent from transcriptional or proteomic programming, which identified increased peroxisomal and lipid metabolism pathways. Interestingly, we observe that high fat diet fed mice exhibit an increased lactate production when challenged with glucose. This trait seems to find a parallel in a human cohort, where we observe a correlation between waist circumference and lactate secretion after an oral glucose bolus across healthy individuals. In an in vitro model of hepatoma cells, we found physiologically relevant palmitate exposure stimulated production of reactive oxygen species (ROS) and glucose uptake, a similar glycolytic phenotype to the in vivo study. This effect is inhibited upon interference with peroxisomal lipid metabolism and ROS production. Furthermore, we find that with exposure to an HCC-inducing hepatic carcinogen, continuation of high fat diet enhances the formation of HCC (100% with resectable tumors) as compared to control (50% with resectable tumors) in mice. However, regardless of the dietary background, all murine tumors showed similar alterations in glucose metabolism compared to those identified in fat exposed non-transformed mouse livers. Further, the presence of tumors in high fat diet exposed mice normalized glucose tolerance. Lipidomics analysis of tumor tissue and liver tissue from high fat diet exposed mice identified tumor tissue enrichment of diacylglycerol (DG) and phosphatidylcholine (PC) species. Some of these species were also increased in high fat diet liver tissue compared to control diet liver tissue. These findings suggest that fat can induce similar metabolic changes in non-transformed liver cells than found in HCC, and that peroxisomal metabolism of lipids may be a factor in driving a glycolytic metabolism In conclusion, we show that normal, non-transformed livers respond to fat by inducing glucose metabolism.
2021-03-08 | PXD023848 | Pride