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Stress responses in yeast cells

ABSTRACT: Proteomes of cytoplasmic particles from S. cerevisiae after oxidative shock (sodium azide)

INSTRUMENT(S):

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

TISSUE(S): Cell Culture

SUBMITTER: Natalia Demeshkina

LAB HEAD: Adrian R. Ferré-D'Amaré

PROVIDER: PXD053090 | Pride | 2025-08-25

REPOSITORIES: Pride

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			Action	DRS
	ySGCs_1_sd.msf	Msf
	ySGCs_1_sd.raw	Raw
	ySGCs_2_sd.msf	Msf
	ySGCs_2_sd.raw	Raw

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Publications

Large-scale purifications reveal yeast and human stress granule cores are heterogeneous particles with complex transcriptomes and proteomes.

Demeshkina Natalia A NA Ferré-D'Amaré Adrian R AR

Cell reports 20250523 6

Stress granules are a conserved response of eukaryotic cells to environmental insults. These cytoplasmic ribonucleoprotein condensates have hitherto been primarily studied by microscopy, which showed previously that they comprise dense ∼200 nm cores embedded in a diffuse shell. We have developed large-scale purifications of budding yeast and mammalian (HEK293T cell) stress granule cores that do not rely on immunoprecipitation of candidate protein constituents. These unbiased preparations reveal ...[more]

PMID: 40413746

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Stress responses in human cells

Project description:Proteomes of cytoplasmic particles from HEK293T cells after oxidative shock (sodium arsenite)

2025-08-25 | PXD053091 | Pride

Stress responses in yeast cells

Project description:Proteomes of cytoplasmic particles from S. cerevisiae after oxidative shock (sodium azide)

2025-08-25 | PXD053088 | Pride

Stress responses in yeast cells

Project description:Proteomes of cytoplasmic particles from S. cerevisiae after oxidative shock (sodium azide), strain YER165W (PABP1_GFP)

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Characterization of L1 ORF1p macromolecular complexes from Mael-/- mouse testes

Project description:piRNA-deficient Maelstrom (Mael) null mice are characterized by a strong upregulation of retrotransposon LINE-1 (L1) in meiotic spermatocytes. This defect turns out in the accumulation of L1 RNA and ORF1p in their cytoplasm and the formation of prominent ribonucleoprotein aggregates. We used 3-months-old Mael-/- male mice to characterize the protein composition of those ORF1p aggregates.

2023-05-26 | PXD039425 | Pride

Thio-triazole-biotin-labeled peptides derived from iPA probes

Project description:iPAs are minimal-tag chemical probes - propargyl analogs of putrescine (PUT), spermidine (SPD), and spermine (SPM) - that preserve charge/spacing, retain transporter compatibility, and enable high-resolution intracellular imaging following paraformaldehyde (PFA)-based crosslinking and copper-catalyzed azide-alkyne cycloaddition to a fluorescent reporter. The LC-MS/MS data submitted here support an experiment designed to assess whether intracellular iPAs undergo substantial metabolic/catabolic transformation. MCF-7 cells were treated with iPAs, lysed, and subjected to a copper-catalyzed azide-alkyne-thiol reaction in which solvent-exposed cysteines in proteins react simultaneously with alkyne-bearing probe(s) released from cells and with azide-PEG3-biotin added to the lysis buffer. Proteins were then digested with trypsin; thio-triazole-biotin-labeled peptides were enriched and analyzed by LC–MS/MS. Open-search analysis showed that the observed cysteine mass shifts predominantly correspond to incorporation of the intact, alkyne-retaining probe species. Note that this assay selectively detects alkyne-retaining species and does not quantify potential alkyne-loss products.

2025-12-16 | PXD070115 | Pride

Secretome profile of living constructs assembled from cell-to-cell crosslinking of human adipose tissue-derived mesenchymal stromal cells

Project description:We report proteomic data from living constructs assembled entirely from human cells covalently tethered via interfacial bridges with a glycosaminoglycan. Here, bioorthogonal azide groups are installed in cell surface glycoproteins via metabolic glycoengineering, allowing for catalyst-free click-chemistry coupling with a complementary hyaluronan biopolymer. This cell-to-cell tethering strategy enables the use of human cells as active crosslinkers and main building blocks of macroscale, tissue-dense living materials. In light of this, we explore the secretome profile of these constructs following a maturation period of 3 days. Bioinformatic analysis and matrisome annotation revealed the presence of a wide range of proteins related to extracellular matrix organization, assembly and remodeling, as well as proteins involved in cell signaling and migration. These findings highlight the potential of this cell-to-cell tethering strategy for creating nascent living tissue mimetics that can be explored in tissue engineering and regenerative medicine endeavors.

2024-07-25 | PXD042343 | Pride

Gene expression profile of miniature pig as animal model for toxicity evaluation by using mRNA expression profiling.

Project description:Miniature pig is a useful animal model to clarify the vital reaction and the molecular mechanisms. However, physiclogical response of pig model to sodium azide (AZIDE) stress is not reveal. To establishment of large animal model for evaluate toxic stress, whole blood of miniature pig were assessed with genomics. 7 month old clawn miniature pigs were fed AZIDE feeding. AZIDE dose of 300Âµg/kg, one hundredth of LD50 was given orally to the miniature pigs. Whole blood gene expression was measured at 0h, 6h and 24h after feeding.

2016-03-02 | E-GEOD-78769 | biostudies-arrayexpress

Proteomic Analysis of Stationary Growth Stage and Nutritional Deficiency Adaptation Reveals Brucella Abortus Virulence Mechanisms

Project description:Brucellosis, an important bacterial zoonosis caused by Brucella species, has drawn increased attention around the world. As an intracellular pathogen, the ability of Brucella to deal with stress within the host cell is closely related to its virulence. The survival pressure on Brucella within a phagosome is considered similar to that during the stationary phase. Here, label-free proteomics approach was used to study the adaptive response of Brucella abortus (B. abortus) in the stationary stage. 182 down-regulated and 140 up-regulated proteins were found in the stationary-phase B. abortus. B. abortus adapted to adverse environmental changes by regulating virulence, reproduction, transcription, translation, stress response, and energy production. In addition, both logarithmic and stationary-phase B. abortus were treated with short-term starvation. The logarithmic-phase B. abortus restricted cell reproduction and energy utilization in response to nutritional stress. Additionally, the expression levels of some virulence-related proteins were identified as being significantly regulated during the transition from logarithmic to stationary phase or under starvation treatment, such as Type IV secretion system protein (T4SS), VjbR, and integration host factor (IHF). Altogether, we outlined adaptive mechanisms that B. abortus could employ during the growth and compared the differences between logarithmic and stationary-phase B. abortus in response to starvation.

2021-09-09 | PXD020869 | Pride

renal damage in 24w2k1c v cont24w

Project description:The experiment was designed to study the effects of blood pressure on gene expressions in the kidney cortex. Non-clipped kidney cortex was harvested from eight 2k1c rats and eight sham rats after 4 and 24 weeks of clipping. The 2k1c is the experimental group which underwent a two kidney, one clip (2k1c) operation (renal artery stenosis), wheras the sham group serves as a control where no stenosis were performed.

2014-11-11 | E-MTAB-1449 | biostudies-arrayexpress

Cu-Catalyzed Azide-Alkyne-Thiol Reaction Forms Ubiquitous Background in Chemical Proteomics Studies

Project description:We report here a Cu-catalyzed azide-alkyne-thiol reaction forming thiotriazoles as the major by-product under widely used bioorthogonal protein labelling “click” conditions. The development of Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) had tremendous impact on many biological discoveries. However, the considered chemoselectivity of CuAAC is hampered by high reactivity of cysteine free thiols yielding thiotriazole protein conjugates. The reaction by-products generate false positive protein hits in “functional” proteomic studies. The reported detail investigation of conjugates between chemical probes containing terminal alkynes, azide-tags and cell lysates reveals formation of thiotriazoles, which can be readily detected by in-gel fluorescence scanning or after peptide and protein enrichment by MS-based proteomics. The produced fluorescent bands or enriched proteins may not result from the important enzymatically driven reaction and can be falsely assigned as hits. This study provides a complete list of the most common background proteins. The knowledge of this previously overlooked reactivity now leads to improved experimental design. Here, we present modified CuAAC conditions, which avoids the undesired product formation and diminishes the background.

2024-01-12 | PXD043402 | Pride

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