Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic profile of yeast cells lacking the high affinity K+-transport system

ABSTRACT: Potassium is the major intracellular cation in S. cerevisiae, which can be concentrated up to 200-300 mM even from relatively low potassium (< 1 mM) environments. This is achieved by mean of a high affinity K+-transport system encoded by the genes TRK1 and TRK2. Recently, our group became interested in the effects of sudden shortage of extracellular potassium. Transcriptomic analysis indicates that lack of potassium drastically alters sulfur metabolism (mainly Met and Cys metabolism), triggers an oxidative stress response and activates the mitochondrial retrograde pathway. We also observe a dramatic halt in the expression of genes required for ribosome biogenesis and translation, as well as decrease in expression of diverse genes (cyclins, protein kinases) required for progression through the cell cycle. Only subsets of these changes were observed in a strain deleted for the TRK1 and TRK2 genes growing in the presence of sufficient potassium (50 mM). Research involving molecular genetics and metabolomic approaches aiming to clarify the primary targets for potassium requirements is currently ongoing.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE24711 | GEO | 2012/10/13

SECONDARY ACCESSION(S): PRJNA132331

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Transcriptomic changes induced in yeast cells by the lack of potassium in the medium

2012-10-13 | GSE24712 | GEO

Transcriptomic profile of yeast cells lacking the high affinity K+-transport system

Project description:Potassium is the major intracellular cation in S. cerevisiae, which can be concentrated up to 200-300 mM even from relatively low potassium (< 1 mM) environments. This is achieved by mean of a high affinity K+-transport system encoded by the genes TRK1 and TRK2. Recently, our group became interested in the effects of sudden shortage of extracellular potassium. Transcriptomic analysis indicates that lack of potassium drastically alters sulfur metabolism (mainly Met and Cys metabolism), triggers an oxidative stress response and activates the mitochondrial retrograde pathway. We also observe a dramatic halt in the expression of genes required for ribosome biogenesis and translation, as well as decrease in expression of diverse genes (cyclins, protein kinases) required for progression through the cell cycle. Only subsets of these changes were observed in a strain deleted for the TRK1 and TRK2 genes growing in the presence of sufficient potassium (50 mM). Research involving molecular genetics and metabolomic approaches aiming to clarify the primary targets for potassium requirements is currently ongoing. We compare the expression profile of two yeast strains: WT and trk1 trk2 double mutant, growing in a Translucent K-free medium containing 50 mM KCl until OD600 = 0.6. Two independent experiments were performed, and for each experiment a dye-swap was carried out. Total number of chips analyzed: 4.

2012-10-13 | E-GEOD-24711 | biostudies-arrayexpress

Transcriptomic changes induced in yeast cells by the lack of potassium in the medium

Project description:Potassium is the major intracellular cation in S. cerevisiae, which can be concentrated up to 200-300 mM even from relatively low potassium (< 1 mM) environments. This is achieved by mean of a high affinity K+-transport system encoded by the genes TRK1 and TRK2. Recently, our group became interested in the effects of sudden shortage of extracellular potassium. Transcriptomic analysis indicates that lack of potassium drastically alters sulfur metabolism (mainly Met and Cys metabolism), triggers an oxidative stress response and activates the mitochondrial retrograde pathway. We also observe a dramatic halt in the expression of genes required for ribosome biogenesis and translation, as well as decrease in expression of diverse genes (cyclins, protein kinases) required for progression through the cell cycle. Only subsets of these changes were observed in a strain deleted for the TRK1 and TRK2 genes growing in the presence of sufficient potassium (50 mM). Research involving molecular genetics and metabolomic approaches aiming to clarify the primary targets for potassium requirements is currently ongoing. The effect of a sudden shortage of extracellular potassium was studied using a wt yeast strain. Samples of cell cultures grown in either, in the presence or in the absence of potassium, were taken after 10, 20, 40, 60 and 120 min of potassium shortage. We compared the expression profile of: 1) WT w/o K vs WT w/ KCl at 10 min: 2) WT w/o K vs WT w/ KCl at 20 min. 3) WT w/o K vs WT w/ KCl at 40 min. 4) WT w/o K vs WT w/ KCl at 60 min. 5) WT w/o K vs WT w/ KCl at 120 min. Two independent experiments were performed, except for the timepoint of 10 min. For each experiment a dye-swap was carried out. Chips analyzed: 2 for 10 min 4 for 20 min 4 for 40 min 4 for 60 min 4 for 120 min Total number of chips: 18

2012-10-13 | E-GEOD-24712 | biostudies-arrayexpress

Cysteine deprivation in liver cell line

2007-12-13 | GSE9517 | GEO

Transcription profiling of human liver cell line after cysteine deprivation

Project description:First experiment: Cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM methionine + 0.1 mM cysteine (complete) or supplemented only with 0.1 mM methionine (cysteine-free). Cells were cultured in either medium for 42 h (Long + Cys; Long -Cys) or in cysteine-free medium for 36 h followed by 6 h in complete medium (Short +Cys); Second experiment: C3A/HepG2 cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM Met and 0.1 mM Cys (complete) or supplemented only with 0.1 mM Met (cysteine-devoid). Cells were cultured in complete medium for 42 h (Long +Cys) or in complete medium for 36 h followed by cysteine-devoid medium for 6 h (Short -Cys). Experiment Overall Design: First experiment: Three plates of cells were cultured under each condition. Cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM methionine + 0.1 mM cysteine (complete) or supplemented only with 0.1 mM methionine (cysteine-free). Cells were cultured in either medium for 42 h (Long + Cys; Long -Cys) or in cysteine-free medium for 36 h followed by 6 h in complete medium (Short +Cys). Experiment Overall Design: Second experiment: C3A/HepG2 cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM Met and 0.1 mM Cys (complete) or supplemented only with 0.1 mM Met (cysteine-devoid). Cells were cultured in complete medium for 42 h (Long +Cys) or in complete medium for 36 h followed by cysteine-devoid medium for 6 h (Short -Cys).

2008-06-16 | E-GEOD-9517 | biostudies-arrayexpress

Metformin preconditioning protects against myocardial stunning and preserves mitochondrial dynamics and protein translation in a mouse model of cardiac arrest

Project description:We compare microarray data from homogenized left ventricles of the heart at 24 hours after sham surgey vs 8-min potassium chloride induced sudden cardiac arrest and resuscitation

2021-08-01 | GSE176494 | GEO

WT + DOX vs tetO:HAL3 vhs3 + DOX

Project description:Maintenance of ion homeostatic mechanisms is essential for living cells, including the budding yeast S. cerevisiae. Whereas the impact of changes in phosphate metabolism on metal ion homeostasis has been recently examined, the inverse effect is still largely unexplored. We show here that depletion of potassium from the medium or alteration of diverse regulatory pathways controlling potassium uptake, such as the Trk1 potassium transporter or the Pma1 H+-ATPase, trigger a response that mimics that of phosphate (Pi) deprivation, exemplified by accumulation of the high-affinity Pi transporter Pho84. This response is mediated by and requires the integrity of the PHO signaling pathway. Removal of potassium from the medium does not alter the amount of total or free intracellular Pi, but is accompanied by decreased in the ATP and ADP levels and a rapid depletion of cellular polyphosphates. Therefore, our data do not support the notion of Pi being the major signaling molecule triggering phosphate-starvation responses. We also observe that cells with compromised potassium uptake cannot grow under limiting Pi conditions. The link between potassium and phosphate homeostasis reported here could explain the invasive phenotype, characteristic of nutrient deprivation, observed in potassium-deficient yeast cells.

2014-12-02 | GSE58985 | GEO

A global transcription study of the regulatory effects of potassium, glutamate and c-di-AMP in Bacillus subtilis

Project description:Since c-di-AMP has been implicated in the interplay of potassium and glutamate homeostasis, we analysed, using strand-specific tiling arrays (tiling step of 22 nucleotides), global gene expression in the wild type strain B. subtilis 168 at low (0.1 mM) and high (5 mM) potassium concentrations and in the presence of ammonium and glutamate as the nitrogen source as well as in the c-di-AMP free strain (∆disA, ∆cdaA, ∆cdaS) GP2222 and its isogenic suppressor mutant GP2223 that is able to grow at 5 mM potassium. In addition to strongly reduced expression of genes involved in fermentation and respiration (regulated by the NADH-responsive transcription factor Rex), genes of the SigO regulon involved in acid stress response and several competence genes was severely reduced in the mutant strain GP2222. In the wild type strain, the ktrAB and kimA genes were most strongly repressed by potassium. These genes encoding high affinity potassium uptake systems are controlled by a c-di-AMP sensitive riboswitch.Taken together, the analysis confirmed that c-di-AMP is involved in multiple cellular functions including genetic competence and revealed a particular role of genes involved in controlling NADH homeostasis.

2020-12-28 | GSE156738 | GEO

Global gene expression of Ruegeria pomeroyi DSS-3 during ammonium-limited, ribose phosphate-, methylphosphonate-, or potassium phosphate-excess growth regimes or during potassium phosphate-limited, ammonium-excess regime

Project description:We used the previously designed oligonucleotide microarrays (Bürgmann et al., 2007, Environmental Microbiology, 9: 2742-2755) to detect the mRNA transcripts of R. pomeroyi DSS-3 when the cells were cultured under steady-state conditions limited with ammonium (NH4Cl, 0.26 mM) but with an excess of D-ribose-5-phosphate (C5H9Na2O8P*2H2O, 0.5 mM), methylphosphonic acid (CH5PO3, 0.5 mM), or potassium phosphate (KH2PO4, 0.5 mM), or during ammonium excess (NH4Cl, 2.8 mM) but were limited with potassium phosphate (KH2PO4, 9.2 μM).

2014-06-02 | GSE38740 | GEO

Transcriptional response of Saccharomyces cerevisiae to potassium starvation

Project description:In this study we investigated the transcriptional response of the yeast Saccharomyces cerevisiae to potassium starvation. To this end yeast cells were grown for 60 min in media without potassium or in media with a standard potassium concnetration (50 mM KCl). Using Serial Analysis of Gene Expression (SAGE)-tag sequencing the effect of potassium starvation on the transcriptome was determined.

2014-12-11 | GSE57093 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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