Photoacclimation and functional control of stolen organelles in Mesodinium rubrum by an enslaved nucleus
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Mesodinium Rubrum
TISSUE(S): Photosynthetic Cell, Ciliated Cell
DISEASE(S): Disease Free
SUBMITTER: 
Matthew McIlvin
LAB HEAD: Mak Saito
PROVIDER: PXD035728 | Pride | 2025-01-07
REPOSITORIES: Pride
Dataset's files
Items per page: 5 1 - 5 of 100 |
Similar Datasets
Project description:Projected responses of ocean net primary productivity (NPP) to climate change are highly uncertain. The climate sensitivity of phytoplankton nutrient limitation in the low-latitude Pacific plays a crucial role, but field measurements are insufficient to provide suitable constraints. Here we quantify two decades of nutrient limitation in the Equatorial Pacific with satellite observations. Using field nutrient addition experiments, proteomics, and above-water hyperspectral radiometry, we demonstrate that physiological responses of phytoplankton to iron limitation led to ~3-fold increases in chlorophyll-normalized phytoplankton fluorescence. Extension to the >18-year satellite fluorescence record showed that Equatorial Pacific iron limitation was robust to changes in physical forcing through multiple El Niño–Southern Oscillation cycles, despite coherent fluctuations in limitation strength. In contrast, these iron limitation changes were overestimated 2-fold by a state-of-the-art climate model. Such synoptic constraints provide a powerful new approach for benchmarking the realism of model NPP projections to climate changes.
2023-06-26 | PXD030610 | Pride
Project description:Bdellovibrio bacteriovorus is a Gram-negative bacterium that is a pathogen of other Gram-negative bacteria, including many bacteria which are pathogens of humans, animals and plants. As such Bdellovibrio has potential as a biocontrol agent, or living antibiotic. B. bacteriovorus HD100 has a large genome and it is not yet known which of it encodes the molecular machinery and genetic control of predatory processes. We have tried to fill this knowledge-gap using mixtures of predator and prey mRNAs to monitor changes in Bdellovibrio gene expression at a timepoint of early-stage prey infection and prey killing in comparison to control cultures of predator and prey alone and also in comparison to Bdellovibrio growing axenically (in a prey-or host independent âHIâ manner) on artificial media containing peptone and tryptone. From this we have highlighted genes of the early predatosome with predicted roles in prey killing and digestion and have gained insights into possible regulatory mechanisms as Bdellovibrio enter and establish within the prey bdelloplast. Approximately seven percent of all Bdellovibrio genes were significantly up-regulated at 30 minutes of infection- but not in HI growth- implicating the role of these genes in prey digestion. Five percent were down-regulated significantly, implicating their role in free-swimming, attack-phase physiology. This study gives the first post- genomic insight into the predatory process and reveals some of the important genes that Bdellovibrio expresses inside the prey bacterium during the initial attack. Keywords: Transcriptional analysis 3 replicates of attack phase cells and 3 replicates of 30 minutes post-infection cells were analysed on individual arrays. Replicate 3 was normalized separately.
2010-05-18 | E-GEOD-9269 | biostudies-arrayexpress
Project description:Trichophyton rubrum, an anthropophilic and cosmopolitan fungus, is the most common agent of superficial mycoses, causing rarely deep dermatophytosis in immunocompromised hosts. In this study, an infection condition of T. rubrum was modeled by adding human skin sections into a limited medium containing glucose to monitor T. rubrum gene expression patterns using cDNA microarrays on a global level. We found that exposure to human skin resulted in up-regulation of the expression levels of T. rubrum genes related to many cellular and biological processes, including transcription and translation, metabolism and secondary transport, stress response, and signaling pathways. These results provide a reference set of T. rubrum genes whose expression patterns change upon infection and reveal previously unknown genes that probably corresponding to proteins that should be considered as virulence factor candidates and potential new drug targets for T. rubrum infections.
2011-10-02 | E-GEOD-15532 | biostudies-arrayexpress
Project description:Legumain is cysteine protease primarily localised to the endo-lysosomal system. Upregulated legumain activity is associated with inflammation, neurodegeneration, and tumorigenesis. Whilst inhibiting legumain in mouse models has demonstrated therapeutic benefit, the proteolytic mechanisms underpinning its various functions are not well known and thus, further characterisation of its physiological substrates is required. Here, we developed FAIMS-enabled N-terminomics for sensitive and streamlined identification of both protein abundance changes and N-termini in complex samples. Comparison of wildtype and legumain-deficient murine spleens identified 6,366 proteins and 2,528 N-termini, of which 235 were enriched in wildtype spleens. These included 119 with asparaginyl cleavages corresponding to 110 proteins, indicating legumain-specific activity. Surprisingly, many of these localised to the nucleus and cytoplasm, hinting at novel extra-lysosomal roles of legumain. We further confirmed the direct processing of selected substrates by legumain in vitro; together, validating FAIMS-enabled N-terminomics for protease substrate detection in an unbiased and systematic manner.
2024-07-12 | PXD043122 | Pride
Project description:Cancers harbouring loss-of-function (LOF) alterations in tumour suppressor genes lack targeted therapies, thus alternative means to characterise gene function and identify vulnerabilities in these cancer cells are required. Here, we map the in silico genetic networks of KMT2D, a frequently mutated tumour suppressor gene, to demonstrate its utility in uncovering novel functional associations and vulnerabilities in cancer cells with tumour suppressor gene LOF alterations. In silico KMT2D networks revealed associated with histone modification, DNA replication, metabolism, and immune response. We identified synthetic lethal (SL) candidates encoding exising therapeutic targets. Analysing patient data from The Cancer Genome Atlas (TCGA) and the Personalized OncoGenomics Project (NCT021556210), we showed dysregulated pathways associated with SL candidates and elevated immune checkpoint response markers in KMT2DLOF cases, bringing forth evidence supporting KMT2D as a biomarker for immune checkpoint inhibitors. Our study presents a framework for identifying targetable vulnerabilities in cancers with tumour suppressor gene alterations.
2024-10-18 | PXD048272 | Pride
Project description:Dermatophytes are highly specialized filamentous fungi which cause the majority of superficial mycoses in humans and animals. The high secreted proteolytic activity of these microorganisms during growth on proteins is assumed to be linked with their particular ability to exclusively infect keratinized host structures such as skin stratum corneum, hair and nails. Individual secreted dermatophyte proteases were recently described and linked with the in vitro digestion of keratin. However, the overall adaptation and transcriptional response of dermatophytes during protein degradation is largely unknown. To address this question, we constructed a cDNA microarray for the human pathogenic dermatophyte Trichophyton rubrum, which is based on transcripts of the fungus grown on proteins. Gene expression profiling during growth of T. rubrum on soy and keratin displayed the activation of a large set of genes encoding endo- and exoproteases. In addition, other specifically induced factors with potential implication in protein utilization were identified, including heat shock proteins, transporters, metabolic enzymes, transcription factors and hypothetical proteins with unknown function. This broad-scale transcriptional analysis of dermatophytes during growth on proteins reveals new putative pathogenicity related host adaptation mechanism of these human pathogenic fungi. Keywords: Two-condition experiment, strong proteolytic activity in the supernatant versus no proteolytic activity Three independently prepared T. rubrum replicates grown in each of the three media, Sabouraud, soy and keratin-soy medium (designated SabA/B/C, soyA/B/C and keratin-soyA/B/C) were used. Pairwise transcriptional comparisons, i.e. soy versus Sabouraud, keratin-soy versus Sabouraud and keratin-soy versus soy were done. The total number of slides in this study was 9.
2008-12-30 | E-GEOD-11711 | biostudies-arrayexpress
Project description:Legumain is cysteine protease primarily localised to the endo-lysosomal system. Upregulated legumain activity is associated with inflammation, neurodegeneration, and tumorigenesis. Whilst inhibiting legumain in mouse models has demonstrated therapeutic benefit, the proteolytic mechanisms underpinning its various functions are not well known and thus, further characterisation of its physiological substrates is required. Here, we developed FAIMS-enabled N-terminomics for sensitive and streamlined identification of both protein abundance changes and N-termini in complex samples. Comparison of wildtype and legumain-deficient murine spleens identified 6,366 proteins and 2,528 N-termini, of which 235 were enriched in wildtype spleens. These included 119 with asparaginyl cleavages corresponding to 110 proteins, indicating legumain-specific activity. Surprisingly, many of these localised to the nucleus and cytoplasm, hinting at novel extra-lysosomal roles of legumain. We further confirmed the direct processing of selected substrates by legumain in vitro; together, validating FAIMS-enabled N-terminomics for protease substrate detection in an unbiased and systematic manner.
2024-05-23 | PXD047734 | Pride
Project description:YAP and TAZ coordinate several NAD+-dependent processes like glycolysis, fatty acid oxidation and glutaminolysis in nutrient-deprivation conditions. However, correlations between NAD(H) levels and YAP/TAZ metabolic function are still poorly understood. We showed that stable silencing of YAP in the triple-negative breast cancer (TNBC) cell line MDAMB231 (MDA shYAP) rescued the toxicity of the NAD+ depletion agent FK866, both in 2D and in 3D culturing, prevented ROS accumulation and apoptosis. As MDA shYAP cells phenocopy the behavior of FK866-resistant MDAMB231 cells (RES), a comparative proteomic study between these cells lines was performed. We identified a deregulation of cell cycle in both MDA shYAP and RES, which prevents apoptosis initiation upon FK866 treatment. Moreover, we found an upregulation of mitochondrial proteins, in line with an increased mitochondrial biogenesis, function and mass, as previously observed for RES. Overall, we showed a YAP-dependent rewiring of mitochondrial metabolism and cell cycle checkpoints, which sustains the acquirement of resistance to FK866 in TNBC.
2025-02-24 | PXD046817 | Pride
Project description:INS1-EGFP-L10a stable cell lines were induced with Doxycycline (Dox) for 24 hours, then either untreated or treated for 30 minutes with 1uM Thapsigargin to induce ER stress. Total RNA was purified with Trizol, and RIP RNA samples were extracted by immunoaffinity purification using an EGFP antibody We aimed to determine which genes are enriched under ER stress at the polyribosomal level. To do this we compared expression profiles of Total RNA with and without ER stress, and Immunoaffinity purified RNA (RIP) with and without ER stress. Microarray results of INS-1 EGFP-L10a cells either untreated or treated with 1uM Thapsigargin (Tg) in triplicate. Both Total RNA and RNA isolated from ribosomal Immunoprecipitation (RIP) When unfolded proteins accumulate to irremediably high levels within the endoplasmic reticulum (ER), intracellular signaling pathways called the unfolded protein response (UPR) become hyperactivated to cause programmed cell death. We discovered that thioredoxin-interacting protein (TXNIP) is a critical node in this M-bM-^@M-^\Terminal UPRM-bM-^@M-^]. TXNIP becomes rapidly induced by hyperactivated IRE1a, an ER bifunctional kinase/endoribonuclease (RNase). IRE1a controls TXNIP mRNA stability by reducing levels of a TXNIP destabilizing micro-RNA, miR-17. In turn, elevated TXNIP protein activates the NLRP3 inflammasome, causing Caspase-1 cleavage and interleukin 1b (IL-1b) secretion. Txnip gene deletion reduces pancreatic b-cell death during ER stress, and suppresses diabetes caused by proinsulin misfolding in the Akita mouse. Finally, small molecule IRE1a RNase inhibitors suppress TXNIP production to block IL-1b secretion. In summary, the IRE1a-TXNIP pathway is used in the terminal UPR to promote sterile inflammation and programmed cell death, and may be targeted to develop new treatments for degenerative diseases driven by ER stress. There are 12 samples total all in INS-1 EGFP L10a cells- 3 untreated total RNA (reference sample), 3 treated with 1uM Tg 30 min total RNA, 3 untreated RIP RNA (reference sample), 3 treated with 1uM for 30 min RIP RNA
2012-09-01 | E-GEOD-39212 | biostudies-arrayexpress
Project description:Legumain is cysteine protease primarily localised to the endo-lysosomal system. Upregulated legumain activity is associated with inflammation, neurodegeneration, and tumorigenesis. Whilst inhibiting legumain in mouse models has demonstrated therapeutic benefit, the proteolytic mechanisms underpinning its various functions are not well known and thus, further characterisation of its physiological substrates is required. Here, we developed FAIMS-enabled N-terminomics for sensitive and streamlined identification of both protein abundance changes and N-termini in complex samples. Comparison of wildtype and legumain-deficient murine spleens identified 6,366 proteins and 2,528 N-termini, of which 235 were enriched in wildtype spleens. These included 119 with asparaginyl cleavages corresponding to 110 proteins, indicating legumain-specific activity. Surprisingly, many of these localised to the nucleus and cytoplasm, hinting at novel extra-lysosomal roles of legumain. We further confirmed the direct processing of selected substrates by legumain in vitro; together, validating FAIMS-enabled N-terminomics for protease substrate detection in an unbiased and systematic manner.
2024-05-23 | PXD047733 | Pride