Browse
Submit Data
Databases
API
Help

Dataset Information

7 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomics of intracellular freezing survival.

ABSTRACT: Panagrolaimus sp. DAW1, a nematode cultured from the Antarctic, has the extraordinary physiological ability to survive total intracellular freezing throughout all of its compartments. While a few other organisms, all nematodes, have subsequently also been found to survive freezing in this manner, P. sp. DAW1 has so far shown the highest survival rates. In addition, P. sp. DAW1 is also, depending on the rate or extent of freezing, able to undergo cryoprotective dehydration. In this study, the proteome of P. sp DAW1 is explored, highlighting a number of differentially expressed proteins and pathways that occur when the nematodes undergo intracellular freezing. Among the strongest signals after being frozen is an upregulation of proteases and the downregulation of cytoskeletal and antioxidant activity, the latter possibly accumulated before freezing much in the way the sugar trehalose has been shown to be stored during acclimation.

SUBMITTER: Thorne MAS

PROVIDER: S-EPMC7250440 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Proteomics of intracellular freezing survival.

Thorne Michael A S MAS Britovšek Nina Kočevar NK Hawkins Liam L Lilley Kathryn S KS Storey Kenneth B KB

PloS one 20200526 5

Panagrolaimus sp. DAW1, a nematode cultured from the Antarctic, has the extraordinary physiological ability to survive total intracellular freezing throughout all of its compartments. While a few other organisms, all nematodes, have subsequently also been found to survive freezing in this manner, P. sp. DAW1 has so far shown the highest survival rates. In addition, P. sp. DAW1 is also, depending on the rate or extent of freezing, able to undergo cryoprotective dehydration. In this study, the pro ...[more]

PMID: 32453791

Similar Datasets

Proteomics of Intracellular Freezing Survival

Project description:Panagrolaimus sp. DAW1, a nematode cultured from the Antarctic, has the extraordinary physiological ability to survive total intracellular freezing throughout all of its compartments. While a few other organisms, all nematodes, have subsequently also been found to survive freezing in this manner, P. sp. DAW1 has so far shown the highest survival rates. In addition, P. sp. DAW1 is also, depending on the rate or extent of freezing, able to undergo cryoprotective dehydration. In this study, the proteome of P. sp DAW1 is explored, highlighting a number of differentially expressed proteins and pathways that appear to be involved in intracellular freezing. Among the strongest signals after being frozen is an upregulation of proteases and the downregulation of cytoskeletal and antioxidant activity, the latter possibly accumulated earlier much in the way the sugar trehalose is stored during acclimation.

2020-05-01 | PXD018121 | Pride

Quantitative proteomics of intracellular Porphyromonas gingivalis.

Project description:Whole-cell quantitative proteomic analyses were conducted to investigate the change from an extracellular to intracellular lifestyle for Porphyromonas gingivalis, a Gram-negative intracellular pathogen associated with periodontal disease. Global protein abundance data for P. gingivalis strain ATCC 33277 internalized for 18 h within human gingival epithelial cells and controls exposed to gingival cell culture medium were obtained at sufficient coverage to provide strong evidence that these changes are profound. A total of 385 proteins were overexpressed in internalized P. gingivalis relative to controls; 240 proteins were shown to be underexpressed. This represented in total about 28% of the protein encoding ORFs annotated for this organism, and slightly less than half of the proteins that were observed experimentally. Production of several proteases, including the classical virulence factors RgpA, RgpB, and Kgp, was decreased. A separate validation study was carried out in which a 16-fold dilution of the P. gingivalis proteome was compared to the undiluted sample in order to assess the quantitative false negative rate (all ratios truly alternative). Truly null (no change) abundance ratios from technical replicates were used to assess the rate of quantitative false positives over the entire proteome. A global comparison between the direction of abundance change observed and previously published bioinformatic gene pair predictions for P. gingivalis will assist with future studies of P. gingivalis gene regulation and operon prediction.

| S-EPMC2660851 | biostudies-literature

Role of intracellular poroelasticity on freezing-induced deformation of cells in engineered tissues.

Project description:Freezing of biomaterials is important in a wide variety of biomedical applications, including cryopreservation and cryosurgeries. For the success of these applications to various biomaterials, biophysical mechanisms, which determine freezing-induced changes in cells and tissues, need to be well understood. Specifically, the significance of the intracellular mechanics during freezing is not well understood. Thus, we hypothesize that cells interact during freezing with the surroundings such as suspension media and the extracellular matrix (ECM) via two distinct but related mechanisms-water transport and cytoskeletal mechanics. The underlying rationale is that the cytoplasm of the cells has poroelastic nature, which can regulate both cellular water transport and cytoskeletal mechanics. A poroelasticity-based cell dehydration model is developed and confirmed to provide insight into the effects of the hydraulic conductivity and stiffness of the cytoplasm on the dehydration of cells in suspension during freezing. We further investigated the effect of the cytoskeletal structures on the cryoresponse of cells embedded in the ECM by measuring the spatio-temporal intracellular deformation with dermal equivalent as a model tissue. The freezing-induced change in cell, nucleus and cytoplasm volume was quantified, and the possible mechanism of the volumetric change was proposed. The results are discussed considering the hierarchical poroelasticity of biological tissues.

| S-EPMC5095213 | biostudies-literature

Quantitative Proteomics of Intracellular Campylobacter jejuni Reveals Metabolic Reprogramming.

Project description:Campylobacter jejuni is the major cause of bacterial food-borne illness in the USA and Europe. An important virulence attribute of this bacterial pathogen is its ability to enter and survive within host cells. Here we show through a quantitative proteomic analysis that upon entry into host cells, C. jejuni undergoes a significant metabolic downshift. Furthermore, our results indicate that intracellular C. jejuni reprograms its respiration, favoring the respiration of fumarate. These results explain the poor ability of C. jejuni obtained from infected cells to grow under standard laboratory conditions and provide the bases for the development of novel anti microbial strategies that would target relevant metabolic pathways.

| S-EPMC3297583 | biostudies-literature

Survival and recovery of Phaeocystis antarctica (Prymnesiophyceae) from prolonged darkness and freezing.

Project description:The colony-forming haptophyte Phaeocystis antarctica is an important primary producer in the Ross Sea, and must survive long periods of darkness and freezing temperature in this extreme environment. We conducted experiments on the responses of P. antarctica-dominated phytoplankton assemblages to prolonged periods of darkness and freezing. Chlorophyll and photosynthetic capacity of the alga declined nonlinearly and independently of each other in the dark, and darkness alone would potentially reduce photosynthetic capacity by only 60 per cent over 150 days (approximately the length of the Antarctic winter in the southern Ross Sea). The estimated reduction of colonial mucous carbon is higher than that of colonial cell carbon, suggesting metabolism of the colonial matrix in the dark. The alga quickly resumed growth upon return to light. Phaeocystis antarctica also survived freezing, although longer freezing durations lengthened the lag before growth resumption. Particulate dimethylsulfoniopropionate relative to chlorophyll increased upon freezing and decreased upon darkness. Taken together, the abilities of P. antarctica to survive freezing and initiate growth quickly after darkness may provide it with the capability to survive in both the ice and the water column, and help explain its repeated dominance in austral spring blooms in the Ross Sea and elsewhere in the Southern Ocean.

| S-EPMC2614241 | biostudies-literature

An Integrated Chemical Proteomics Approach for Quantitative Profiling of Intracellular ADP-Ribosylation.

Project description:ADP-ribosylation is integral to a diverse range of cellular processes such as DNA repair, chromatin regulation and RNA processing. However, proteome-wide investigation of its cellular functions has been limited due to numerous technical challenges including the complexity of the poly(ADP-ribose) (PAR) chains, low abundance of the modification and lack of sensitive enrichment methods. We herein show that an adenosine analogue with a terminal alkyne functionality at position 2 of the adenine (2-alkyne adenosine or 2YnAd) is suitable for selective enrichment, fluorescence detection and mass spectrometry proteomics analysis of the candidate ADP-ribosylome in mammalian cells. Although similar labelling profiles were observed via fluorescence imaging for 2YnAd and 6YnAd, a previously reported clickable NAD+ precursor, quantitative mass spectrometry analysis of the two probes in MDA-MB-231 breast cancer cells revealed a significant increase in protein coverage of the 2YnAd probe. To facilitate global enrichment of ADP-ribosylated proteins, we developed a dual metabolic labelling approach that involves simultaneous treatment of live cells with both 2YnAd and 6YnAd. By combining this dual metabolic labelling strategy with highly sensitive tandem mass tag (TMT) isobaric mass spectrometry and hierarchical Bayesian analysis, we have quantified the responses of thousands of endogenous proteins to clinical PARP inhibitors Olaparib and Rucaparib.

| S-EPMC6491589 | biostudies-literature

Excessive Inorganic Phosphate Burden Perturbed Intracellular Signaling: Quantitative Proteomics and Phosphoproteomics Analyses.

Project description:Inorganic phosphate (Pi) is an essential nutrient for the human body which exerts adverse health effects in excess and deficit. High Pi-mediated cytotoxicity has been shown to induce systemic organ damage, though the underlying molecular mechanisms are poorly understood. In this study, we employed proteomics and phosphoproteomics to analyze Pi-mediated changes in protein abundance and phosphorylation. Bioinformatic analyses and literature review revealed that the altered proteins and phosphorylation were enriched in signaling pathways and diverse biological processes. Western blot analysis confirms the extensive change in protein level and phosphorylation in key effectors that modulate pre-mRNA alternative splicing. Global proteome and phospho-profiling provide a bird-eye view of excessive Pi-rewired cell signaling networks, which deepens our understanding of the molecular mechanisms of phosphate toxicity.

| S-EPMC8795896 | biostudies-literature

Recovery from freezing

Project description:Screening of genes that respond to cryopreservation stress using yeast DNA microarray.: We studied the response of yeast cells after cryopreservation treatment using DNA microarray technology. Genes that contribute to "Cell rescue, defense and virulence," "energy," and "metabolism," were significantly induced. These genes were classified as encoding heat shock proteins, oxidative stress scavenger, and enzymes involved in glucose metabolism. The expression profile of mRNA after cryopreservation treatment was calculated to be closer to that following treatment with detergent or plant oils rather than by other stress factors such as heavy metals and agricultural chemicals. These results suggest that the cryopreservation treatment caused damage to the structure of the cell wall and cellular organelles. This was supported by the localization of the products of the induced genes at the cell wall and within cellular organelles. Keywords: stress response

2007-11-01 | GSE9404 | GEO

Role of catalase in Campylobacter jejuni intracellular survival.

Project description:The ability of Campylobacter jejuni to penetrate normally nonphagocytic host cells is believed to be a key virulence determinant. Recently, kinetics of C. jejuni intracellular survival have been described and indicate that the bacterium can persist and multiply within epithelial cells and macrophages in vitro. Studies conducted by Pesci et al. indicate that superoxide dismutase contributes to intraepithelial cell survival, as isogenic sod mutants are 12-fold more sensitive to intracellular killing than wild-type strains. These findings suggest that bacterial factors that combat reactive oxygen species enable the organism to persist inside host cells. Experiments were conducted to determine the contribution of catalase to C. jejuni intracellular survival. Zymographic analysis indicated that C. jejuni expresses a single catalase enzyme. The gene encoding catalase (katA) was cloned via functional complementation, and an isogenic katA mutant strain was constructed. Kinetic studies indicate that catalase provides resistance to hydrogen peroxide in vitro but does not play a role in intraepithelial cell survival. Catalase does however contribute to intramacrophage survival. Kinetic studies of C. jejuni growth in murine and porcine peritoneal macrophages demonstrated extensive killing of both wild-type and katA mutant strains shortly following internalization. Long-term cultures (72 h postinfection) of infected phagocytes permitted recovery of viable wild-type C. jejuni; in contrast, no viable katA mutant bacteria were recovered. Accordingly, inhibition of macrophage nitric oxide synthase or NADPH oxidase permitted recovery of katA mutant C. jejuni. These observations indicate that catalase is essential for C. jejuni intramacrophage persistence and growth and suggest a novel mechanism of intracellular survival.

| S-EPMC97717 | biostudies-literature

Actions of FGF2, LIF, and IGF1 on Embryo Survival and Conceptus Elongation following Slow-rate Freezing

Project description:Evaluation of FGF2, LIF, and IGF1 supplementation during embryo culture on conceptus development at day 15.

2022-11-18 | GSE215089 | GEO