Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Riboproteome remodelling during quiescence exit in Saccharomyces cerevisiae

ABSTRACT: Characterization of the riboproteome composition in quiescent cells and post-translational reactivation. To characterize ribosome heterogeneity during the exit from quiescence, the protein composition of ribosomal particles from stationary phase and nutrient-stimulated cells was assessed. A label-free quantitative mass spectrometry strategy was taken to compare quiescent yeast cells with cells that had been nutrient stimulated for 30 and 60 min. To this end, crude extracts from these cells were subjected to sucrose gradient centrifugation and three fractions free (F); monosome (M=80S + 60S + 40S) and polysome (P) were analyzed by nano-HPLC-MS/MS. A total of 528 proteins were identified.

INSTRUMENT(S): Q Exactive HF

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

SUBMITTER: maria pia valacco

LAB HEAD: Paula Portela

PROVIDER: PXD047386 | Pride | 2023-12-20

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	CS16.msf	Msf
	CS16.raw	Raw
	CS17.msf	Msf
	CS17.raw	Raw
	CS18.msf	Msf

Items per page:

1 - 5 of 55

Similar Datasets

Proteome of Listeria monocytogenes FBUNT biofilm cells and response to bacteriocin AL705

Project description:L. monocytogenes FBUNT is able to form biofilm after six days at 10 ºC. Proteome under planktonic growth, lactocin AL705-treated and untreated biofilms was analyzed. Compared to planktonic cells, protein abundance shifts associated with ribosomes function and biogenesis, cell membrane functionality, carbohydrate and amino acid metabolism and transport were observed in sessile cells. When sessile cells were treated with lactocin AL705, proteins up-regulation were mostly related to carbohydrate metabolism and nutrient transport in an attempt to compensate for impaired energy generation caused by bacteriocin interacting with the cytoplasmic membrane. Notably, transport systems as β-glucosidase IIABC (lmo0027), cellobiose (lmo2763) and trehalose (lmo1255) specific PTS proteins were highly overexpressed.

2021-09-09 | PXD022168 | Pride

Translation State Array Analysis of TNF Stimulated Human Endothelial Cells

Project description:Confluent human umbilical vein endothelial cells (HUVECs) were exposed to TNF-alpha (100 units/mL) for 2 hours. Ribosomal profiling via gradient centrifugation and fractionation was used to separate monosome, or under-translated, and polysome, or actively-translated, mRNA species that were then used to probe cDNA arrays, a process known as Translation State Array Analysis (TSAA). Four samples were obtained from these experiments: control monosome, control polysome, TNF monosome and TNF polysome. using the normalized signal intensities from the GeneFilters, we calculated a translation index, or measure of movement of an mRNA molecule from the monosome to the polysome fraction upon stimulation. This calculation was made as follows: (TNF polysome/TNF monosome)/(control polysome/control monosome). Translational indices greater than 2.5 (upregulated) or lower than 0.4 (downregulated) were chosen for further study. Keywords: Translation State Array Analysis

2006-07-27 | GSE5354 | GEO

Translation State Array Analysis of Insulin Stimulated Human Endothelial Cells

Project description:Confluent human umbilical vein endothelial cells (HUVECs) were exposed to Insulin (100 micM) for 2 hours. Ribosomal profiling via gradient centrifugation and fractionation was used to separate monosome, or under-translated, and polysome, or actively-translated, mRNA species that were then used to probe cDNA arrays, a process known as Translation State Array Analysis (TSAA). Four samples were obtained from these experiments: control monosome, control polysome, Insulin monosome and Insulin polysome. using the normalized signal intensities from the GeneFilters, we calculated a translation index, or measure of movement of an mRNA molecule from the monosome to the polysome fraction upon stimulation. This calculation was made as follows: (Insulin polysome/Insulin monosome)/(control polysome/control monosome). Translational indices greater than 2.5 (upregulated) or lower than 0.4 (downregulated) were chosen for further study. Keywords: Translation State Array Analysis

2006-07-27 | GSE5353 | GEO

Translation State Array Analysis of Serum Stimulated Human Endothelial Cells

Project description:Confluent human umbilical vein endothelial cells (HUVECs) were exposed to histamine (100 mM) for 2 hours. Ribosomal profiling via gradient centrifugation and fractionation was used to separate monosome, or under-translated, and polysome, or actively translated, mRNA species that were then used to probe cDNA arrays, a process known as Translation State Array Analysis (TSAA). Four samples were obtained from these experiments, control monosome, control polysome, histamine monosome and histamine polysome. Using the normalized signal intensities from the GeneFilters, we calculated a translation index, or measure of movement of an mRNA molecule from the monosome to the polysome fraction upon stimulation. This calculation was made as follows: (histamine polysome/histamine monosome)/(control polysome/control monosome). Translational indices greater than 2.5 (upregulated) or lower than 0.4 (downregulated) were chosen for further study. Keywords: Translation State Array Analysis

2006-07-27 | GSE5386 | GEO

Translation State Array Analysis of Histamine Stimulated Human Endothelial Cells

2006-07-27 | GSE5385 | GEO

Translation State Array Analysis of LPS Stimulated Human Endothelial Cells

Project description:Confluent human umbilical vein endothelial cells (HUVECs) were exposed to LPS (1 micg/mL) for 2 hours. Ribosomal profiling via gradient centrifugation and fractionation was used to separate monosome, or under-translated, and polysome, or actively-translated, mRNA species that were then used to probe cDNA arrays, a process known as Translation State Array Analysis (TSAA). Four samples were obtained from these experiments: control monosome, control polysome, LPS monosome and LPS polysome. using the normalized signal intensities from the GeneFilters, we calculated a translation index, or measure of movement of an mRNA molecule from the monosome to the polysome fraction upon stimulation. This calculation was made as follows: (LPS polysome/LPS monosome)/(control polysome/control monosome). Translational indices greater than 2.5 (upregulated) or lower than 0.4 (downregulated) were chosen for further study. Keywords: Translation State Array Analysis

2006-07-27 | GSE5352 | GEO

Translation State Array Analysis of Thrombin Stimulated Human Endothelial Cells

Project description:Confluent human umbilical vein endothelial cells (HUVECs) were exposed to Thrombin (2 U/mL) for 2 hours. Ribosomal profiling via gradient centrifugation and fractionation was used to separate monosome, or under-translated, and polysome, or actively translated, mRNA species that were then used to probe cDNA arrays, a process known as Translation State Array Analysis (TSAA). Four samples were obtained from these experiments, Control Monosome, Control Polysome, Thrombin Monosome, and Thrombin Polysome. Using the normalized signal intensities from the GeneFilters, we calculated a translation index, or measure of movement of an mRNA molecule from the monosome to the polysome fraction upon stimulation. This calculation was made as follows: (thrombin polysome/thrombin monosome)/(control polysome/control monosome). Translational indices greater than 2.5 (upregulated) or lower than 0.4 (downregulated) were chosen for further study. TSAA data suggests that JunB is translationally regulated by thrombin stimulation. Immunocytochemistry, western blotting and RT-PCR were used to verify the results of TSAA. Keywords: Translation State Array Analysis

2006-05-31 | GSE4919 | GEO

Monosome profiling in starved HEK293 cells

Project description:Monosome profiling in starved HEK293 cells

| PRJNA533132 | ENA

Mitochondrial respiration is necessary to combat oxidative stress in quiescent cells

Project description:Mitochondrial oxidative phosphorylation (OXPHOS) makes ATP and supports biosynthesis during proliferation, but its role in non-proliferating cells, beyond ATP production, is less understood. Here we show that OXPHOS protects quiescent (but not proliferating) cells from oxidative stress. Using in vivo models of OXPHOS deficiency (whole body and endothelium-specific) we show that OXPHOS mediated resistance to ROS (i) maintains selectivity of ROS-based anticancer therapy by protecting normal tissues during treatment, and in quiescent endothelium (ii) ameliorates systemic LPS-induced inflammation and (iii) attenuates symptoms of the inflammatory bowel disease. ROS-resistance provided by OXPHOS is independent of its role in biosynthesis or NADH recycling. Instead, in quiescent cells OXPHOS constitutively generates low levels of endogenous ROS that support basal autophagic flux and protect from exogenous ROS challenge. Hence, during evolution cells acquired mitochondria to profit from oxidative metabolism, but also built in an OXPHOS-dependent mechanism to guard against the resulting oxidative stress.

2022-10-13 | PXD021376 | Pride

Quiescent vs. Activated Endothelial Cell-Derived Extracellular Vesicles

Project description:Proteomics was performed on extracellular vesicles derived from in vitro cultures of activated and quiescent human endothelial cells.

2024-01-04 | PXD038914 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data