C. jejuni interaction with A. castellanii mitochondria
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Acanthamoeba Genotype T4
SUBMITTER: 
xiaoping yang
LAB HEAD: Fauzy Nasher
PROVIDER: PXD065850 | Pride | 2026-02-13
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| PR796_Fauzy_20231022.zip | Other | |||
| PR796_Fauzy_20241022_cont1.raw | Raw | |||
| PR796_Fauzy_20241028_Infected1.raw | Raw | |||
| PR796_Fauzy_20241028_Infected2.raw | Raw | |||
| PR796_Fauzy_20241028_Infected3.raw | Raw |
Items per page: 5 1 - 5 of 7 |
Similar Datasets
Project description:Cells sense and adapt to their environment. Parasitic protists for example, such as African trypanosomes, occupy distinct environments in mammalian hosts, and in insect vectors, and adapt energy metabolism and growth accordingly, but the mechanisms involved remain incompletely characterized. Here we describe environmental sensing dependent upon Trypanosoma brucei Quick IQ-motif protein 1 (QIQ1). We use a genome-scale loss-of-function genetic screen to identify knockdowns associated with gain-of-fitness, or a ‘quick’ growth phenotype, in bloodstream-form cells. The dominant hit, QIQ1 (Tb927.8.6870), encodes a flagellum-localized protein with multiple putative calmodulin-binding IQ-motifs. In a competition assay, qiq1-null cells displayed a density-dependent growth advantage, which was abrogated by calcium chelation. When cells were grown at reduced density in blood serum, with a series of supplements, only bicarbonate restored the qiq1-null competitive advantage. Proteomic analysis indicated that QIQ1 increased the expression of carnitine acetyltransferase, suggesting a role in modulating fatty acid metabolism, while expression of a flagellum-localized calmodulin was both QIQ1 and bicarbonate-dependent. We conclude that trypanosomes sense and adapt to distinct environments in a QIQ1-dependent manner. Our findings suggest that QIQ1-signaling facilitates CO2-sensing to optimize utilization of available nutrients via a pathway involving calcium, calmodulin, and carnitine.
2026-02-13 | PXD074433 | Pride
Project description:Folding of newly synthesized proteins poses challenges for a functional proteome. Dedicated protein quality control (PQC) systems promote either the folding of nascent polypeptides at ribosomes or, if this fails, ensure their degradation. While well studied for cytosolic protein biogenesis, it is not understood how these processes work for mitochondrially-encoded proteins, key subunits of the oxidative phosphorylation system (OXPHOS). Here, we identify dedicated hubs in proximity to mitoribosomal tunnel exits coordinating mitochondrial translation, protein import, assembly, and protein turnover. Conserved prohibitin/m-AAA protease supercomplexes and the availability of assembly chaperones determine the fate of newly synthesized proteins by molecular triaging. The localization of these competing activities in vicinity to the mitoribosomal tunnel exit allows for a prompt decision whether newly synthesized proteins are fed into OXPHOS assembly or degraded. This repository contains the results of the FLAG-based enrichment of the native prohibitin complex. Please note that we measured elution either with LDS sample buffer or using FLAG-peptides. In the published study, the LDS elution buffer was shown.
2023-08-14 | PXD043671 | Pride
Project description:Cellular functional pathways have evolved through selection based on fitness benefits conferred through protein intra- and inter-molecular interactions that comprise all protein conformational features and protein-protein interactions, collectively referred to as the interactome. While the interactome is regulated by proteome levels, it is also regulated independently by, post translational modification, co-factor, and ligand levels, as well as local protein environmental factors, such as osmolyte concentration, pH, ionic strength, temperature and others. In modern biomedical research, cultivatable cell lines have become an indispensable tool, with selection of optimal cell lines that exhibit specific functional profiles being critical for success in many cases. While it is clear that cell lines derived from different cell types have differential proteome levels, increased understanding of large-scale functional differences requires additional information beyond abundance level measurements, including how protein conformations and interactions are altered in certain cell types to shape functional landscapes. Here, we employed quantitative in vivo protein cross-linking coupled to mass spectrometry to probe large-scale protein conformational and interaction changes among three commonly employed human cell lines, HEK293, MCF-7, and HeLa cells. Isobaric quantitative Protein Interaction Reporter (iqPIR) technologies were used to obtain quantitative values of cross-linked peptides across three cell lines. These data illustrated highly reproducible (R2 values larger than 0.8 for all biological replicates) quantitative interactome levels across multiple biological replicates. We also measured protein abundance levels in these cells using data independent acquisition quantitative proteomics methods. Combining quantitative interactome and proteomics information allowed visualization of cell type-specific interactome changes mediated by proteome level adaptations as well as independently regulated interactome changes to gain deeper insight into possible drivers of these changes. Among the biggest detected alterations in protein interactions and conformations are changes in cytoskeletal proteins, RNA-binding proteins, chromatin remodeling complexes, mitochondrial proteins, and others. Overall, these data demonstrate the utility and reproducibility of quantitative cross-linking to study systems-level interactome variations. Moreover, these results illustrate how combined quantitative interactomics and proteomics can provide unique insight on cellular functional landscapes.
2024-09-17 | PXD055943 | Pride
Project description:Plasma proteins are considered to be the most informative source of biomarkers for disease diagnosis and monitoring. Mass spectrometry (MS)-based proteomics has been applied to discover biomarkers in plasma, but the complexity of plasma proteins and the extremely large dynamic range of protein abundances make the application of plasma proteomics in the clinic a great challenge. We have designed and synthesized zeolite-based nanoparticles for the depletion of high-abundant plasma proteins in plasma. This novel plasma proteomic assay is capable of consistently detecting around 3000 plasma proteins in a 45-minute gradient. Compared to neat and depleted plasma, the plasma proteins identified by our assay show distinct biological profile, which is validated in several public datasets. A pilot investigation of the proteomic profile of hepatocellular carcinoma (HCC) cohort identified 15 promising protein features, highlighting the diagnostic value of plasma proteome in distinguishing HCC from healthy individuals. Furthermore, this assay can be easily integrated with all current downstream protein profiling methods and potentially extended to other biofluids. In conclusion, we have established a robust and efficient plasma proteomic assay with unprecedented identification depths, paving the way for the translation of plasma proteomics into clinical applications.
2024-05-23 | PXD048186 | Pride
Project description:Effective therapies for metastatic osteosarcoma (OS) remain a major clinical unmet need. Targeting mRNA translation in metastatic OS represents an attractive option, as selective translation under stress supports the rapid synthesis of cytoprotective proteins that facilitate metastatic competence. We therefore assessed eukaryotic translation factors in OS, revealing high expression of eIF4A1 in metastatic OS. The eIF4A1 inhibitor, CR-1-31B, potently inhibited metastatic OS growth in vitro and reduced lung tumor burden in orthotopic mouse models. CR-1-31B synergized with the oxidative stress inducer, tert-butylhydroquinone (tBHQ), to enhance cell death under oxidative stress. Proteomic analysis revealed a subset of proteins that were upregulated by tBHQ alone, but inhibited by co-treatment of CR-1-31B, most notably the NRF2 antioxidant transcription factor, and NRF2 inactivation phenocopied CR-1-31B in blocking OS lung metastasis in vivo. Collectively, our data reveal that targeting eIF4A1 with CR-1-31B is highly effective in blocking OS metastasis by blunting the NRF2 antioxidant response.
2024-07-16 | PXD047420 | Pride
Project description:The mammalian oxidative phosphorylation (OXPHOS) system in the inner mitochondrial membrane comprises respiratory chain complexes I-IV (CI-CIV) and ATP synthase. Together, these protein complexes harvest metabolic energy to generate ATP, the cellular energy currency. The inner mitochondrial membrane is abundant in OXPHOS complexes and CI, CIII and CIV exhibit specific protein-protein interactions to form stable supercomplex assemblies, exemplified by the respirasome (CI-CIII2-CIV). Respirasomes are conserved in evolution, and as well documented by biochemical and structural methods. However, their physiological roles are much debated, despite a substantial literature suggesting their importance in facilitating catalysis and regulating turnover in response to metabolic demand. To investigate the in vivo role of respirasomes, we deleted a short conserved, charged loop in the UQCRC1 subunit of CIII that contacts CI. The resulting homozygous knock-in mice show profoundly decreased levels of respirasomes on blue native polyacrylamide gel electrophoresis (BN-PAGE) and complexome profiling proteomics analyses of different tissues, although the individual complexes appear unaffected. In vivo The spatial organization of respirasomes in vivo was altered in knock-in mice as shown by cross-linking experiments on intact mitochondria. Surprisingly, the mutant mice are healthy, with normal respiratory chain capacity and normal exercise tolerance. Therefore, respirasomes are dispensable for OXPHOS function in vivo.
2023-03-11 | PXD031345 | Pride
Project description:Analysis of brassinosteroid (BR) and auxin effects on gene expression in Arabidopsis roots. Our genomic results indicate that BR and auxin induce largely opposite gene expression responses in primary roots. RNA-Seq for 7-day-old Arabidopsis Col-0, dwf4, bri1-116, and bri1-116;bzr1-1D roots grown on regular medium and treated with brassinolide, auxin or mock solution for 4 hr.
2015-04-30 | E-GEOD-52966 | biostudies-arrayexpress
Project description:This study aimed to reveal the influence of co-incubation with Enterococcus faecalis, Enterococcus faecium, or Staphylococcus aureus on the proteome of C. jejuni 81–176 using data-independent-acquisition mass spectrometry (DIA-MS). We compared the proteome profiles during co-incubation with the proteome profile in response to the bile acid deoxycholate (DCA) and investigated the impact of DCA on proteomic changes during co-incubation, as C. jejuni is exposed to both factors during colonization. We identified 1,375 proteins by DIA-MS, which is notably high, approaching the theoretical maximum of 1,645 proteins. S. aureus had the highest impact on the proteome of C. jejuni with 215 up-regulated and 230 down-regulated proteins. However, these numbers are still markedly lower than the 526 up-regulated and 516 down-regulated proteins during DCA exposure.
2023-11-02 | PXD046477 | Pride
Project description:Clinical proteomics on solid tissue samples from human tumour biopsies present multiple challenges. These include limited sample availability, reducing endogenous protease activity and challenges with efficiently solubilising and digesting proteins for high throughput mass spectrometry while achieving comprehensive proteome coverage. Protocols for cancer biopsy proteomics involves three sample preparation steps: tissue washing, lysis and digestion, followed by peptide clean-up by SPE. Our team have reported improvements in all three steps that greatly reduce processing time, enabling greater automation and higher sample throughput. Our aim was to develop a universal protocol for tissue sample preparation that is quick and simple while improving protein solubilization, proteome coverage and reproducibility. Sample preparation with small (<2 mg) biopsies pose additional limitations including the risk of sample loss and introducing variability with multiple reagent additions steps. We now report a one-pot method called heat and beat (HnB). By identifying the limitations and challenges of the existing protocols, we were able to develop a new protocol with fewer steps by achieving lysis, reduction, alkylation and digestion in essentially a single step which was preceded by a 7 min sample heat treatment step. This was achieved by several changes to the existing protocol including the combined use of a beadbeater for tissue homogenisation followed by pressure cycling technology (PCT) using a Barocycler to further lyse and digest the sample. The procedure requires 38 minutes and was tested on 6 tissue types, across three tissue embedding techniques, fresh frozen, OCT embedded (FF-OCT), and FFPE. Our results show that HnB is an efficient new one-pot procedure. The protocol significantly reduced endogenous protease activity, improves peptide yield by up to 3-fold and delivers digestion efficiency of 85-90% from each sample source. We obtained an increase in the number of proteins identified of up to two-fold while reducing variability and processing time.
2025-03-26 | PXD045405 | Pride
Project description:Cells sense and adapt to their environment. Parasitic protists for example, such as African trypanosomes, occupy distinct environments in mammalian hosts, and in insect vectors, and adapt energy metabolism and growth accordingly, but the mechanisms involved remain incompletely characterized. Here we describe environmental sensing dependent upon Trypanosoma brucei Quick IQ-motif protein 1 (QIQ1). We use a genome-scale loss-of-function genetic screen to identify knockdowns associated with gain-of-fitness, or a ‘quick’ growth phenotype, in bloodstream-form cells. The dominant hit, QIQ1 (Tb927.8.6870), encodes a flagellum-localized protein with multiple putative calmodulin-binding IQ-motifs. In a competition assay, qiq1-null cells displayed a density-dependent growth advantage, which was abrogated by calcium chelation. When cells were grown at reduced density in blood serum, with a series of supplements, only bicarbonate restored the qiq1-null competitive advantage. Proteomic analysis indicated that QIQ1 increased the expression of carnitine acetyltransferase, suggesting a role in modulating fatty acid metabolism, while expression of a flagellum-localized calmodulin was both QIQ1 and bicarbonate-dependent. We conclude that trypanosomes sense and adapt to distinct environments in a QIQ1-dependent manner. Our findings suggest that QIQ1-signaling facilitates CO2-sensing to optimize utilization of available nutrients via a pathway involving calcium, calmodulin, and carnitine.
2026-02-13 | PXD074423 | Pride