The yeast osmostress response is carbon source dependent
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2500
ORGANISM(S): Saccharomyces cerevisiae
SUBMITTER: Petri-Jaan Lahtvee
PROVIDER: E-MTAB-5313 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
The yeast osmostress response is carbon source dependent.
Babazadeh Roja R Lahtvee Petri-Jaan PJ Adiels Caroline B CB Goksör Mattias M Nielsen Jens B JB Hohmann Stefan S
Scientific reports 20170420 1
Adaptation to altered osmotic conditions is a fundamental property of living cells and has been studied in detail in the yeast Saccharomyces cerevisiae. Yeast cells accumulate glycerol as compatible solute, controlled at different levels by the High Osmolarity Glycerol (HOG) response pathway. Up to now, essentially all osmostress studies in yeast have been performed with glucose as carbon and energy source, which is metabolised by glycolysis with glycerol as a by-product. Here we investigated th ...[more]
Similar Datasets
Project description:It is unclear how the amount of active nuclear MAPK over time quantitatively affects transcription. Here, we seek to address this issue by studying signal transduction and transcriptional response in a system that separates signalling from adaptation and hence signal strength from signal duration. The system is based on Saccharomyces cerevisiae osmoadaptation and allows modulation of the period of HOG-dependent responses without changing the initial stress intensity. The conditional osmotic stress system includes (i) a yeast mutant (gpd1 gpd2) unable to produce its main osmolyte glycerol, subsequently stressed with (ii) a stress inductor (polyols of different sizes) and allowed to adapt by (iii) expression of polyol flux-mediating aquaglyceroporin (rat AQP9). As there is no endogenous glycerol production, the osmoadaptation rate depends only on the size dependent equilibration rate over the plasma membrane of the polyol used as both stress inductor and compatible solute. Hence, we apply initially identical stresses but with differential durations, and determine the global transcriptional response.
2014-05-31 | GSE29716 | GEO
Project description:Talemi2016 - Yeast osmo-homoestasis
This model is described in the article:
Systems Level Analysis of
the Yeast Osmo-Stat.
Talemi SR, Tiger CF, Andersson M,
Babazadeh R, Welkenhuysen N, Klipp E, Hohmann S, Schaber J.
Sci Rep 2016; 6: 30950
Abstract:
Adaptation is an important property of living organisms
enabling them to cope with environmental stress and maintaining
homeostasis. Adaptation is mediated by signaling pathways
responding to different stimuli. Those signaling pathways might
communicate in order to orchestrate the cellular response to
multiple simultaneous stimuli, a phenomenon called crosstalk.
Here, we investigate possible mechanisms of crosstalk between
the High Osmolarity Glycerol (HOG) and the Cell Wall Integrity
(CWI) pathways in yeast, which mediate adaptation to hyper- and
hypo-osmotic challenges, respectively. We combine ensemble
modeling with experimental investigations to test in
quantitative terms different hypotheses about the crosstalk of
the HOG and the CWI pathways. Our analyses indicate that for
the conditions studied i) the CWI pathway activation employs an
adaptive mechanism with a variable volume-dependent threshold,
in contrast to the HOG pathway, whose activation relies on a
fixed volume-dependent threshold, ii) there is no or little
direct crosstalk between the HOG and CWI pathways, and iii) its
mainly the HOG alone mediating adaptation of cellular osmotic
pressure for both hyper- as well as hypo-osmotic stress. Thus,
by iteratively combining mathematical modeling with
experimentation we achieved a better understanding of
regulatory mechanisms of yeast osmo-homeostasis and formulated
new hypotheses about osmo-sensing.
This model is hosted on
BioModels Database
and identified by:
MODEL1606100000.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2017-05-18 | MODEL1606100000 | BioModels
Project description:It is unclear how the amount of active nuclear MAPK over time quantitatively affects transcription. Here, we seek to address this issue by studying signal transduction and transcriptional response in a system that separates signalling from adaptation and hence signal strength from signal duration. The system is based on Saccharomyces cerevisiae osmoadaptation and allows modulation of the period of HOG-dependent responses without changing the initial stress intensity. The conditional osmotic stress system includes (i) a yeast mutant (gpd1 gpd2) unable to produce its main osmolyte glycerol, subsequently stressed with (ii) a stress inductor (polyols of different sizes) and allowed to adapt by (iii) expression of polyol flux-mediating aquaglyceroporin (rat AQP9). As there is no endogenous glycerol production, the osmoadaptation rate depends only on the size dependent equilibration rate over the plasma membrane of the polyol used as both stress inductor and compatible solute. Hence, we apply initially identical stresses but with differential durations, and determine the global transcriptional response. Saccharomyces cerevisiae W303-1A (MATa leu2-3/112 ura3-1 trp1-1 his3-11/15 gpd1::TRP1 gpd2::URA3) osmotically stressed with 1M of glycerol, erythritol, xylitol or sorbitol. Samples are taken in triplicates (except for sorbitol 20 an 90 min and 20 min xylitol were duplicates were taken) in time course series after stress application. Total of 45 samples. RNA from from cultures of gpd1 gpd2 cells expressing rAQP9 prior to polyol exposure was used as reference RNA for all microarrays.
2014-05-31 | E-GEOD-29716 | biostudies-arrayexpress
Project description:Schaber2012 - Hog pathway in yeast
The high osmolarity glycerol (HOG) pathway in the yeast Saccharomyces cerevisiae is one of the best-studied mitogen-activated protein kinase (MAPK) pathways and serves as a prototype signalling system for eukaryotes. This pathway is necessary and sufficient to adapt to high external osmolarity. A key component of this pathway is the stress-activated protein kinase (SAPK) Hog1, which is rapidly phosphorylated by the SAPK kinase Pbs2 upon hyper-osmotic shock, and which is the terminal kinase of two parallel signalling pathways, subsequently called the Sho1 branch and the Sln1 branch, respectively. Ensemble modelling (192 models) is used to study the yeast HOG pathway, a prototype for eukaryotic mitogen-activated kinase signalling systems. The best fit model (Model Nr.22: described here) provides new insights into the function of this system, some of which are then experimentally validated.
This model is described in the article:
Modelling reveals novel roles of two parallel signalling pathways and homeostatic feedbacks in yeast.
Schaber J, Baltanas R, Bush A, Klipp E, Colman-Lerner A.
Mol Syst Biol. 2012 Nov 13;8:622.
Abstract:
The high osmolarity glycerol (HOG) pathway in yeast serves as a prototype signalling system for eukaryotes. We used an unprecedented amount of data to parameterise 192 models capturing different hypotheses about molecular mechanisms underlying osmo-adaptation and selected a best approximating model. This model implied novel mechanisms regulating osmo-adaptation in yeast. The model suggested that (i) the main mechanism for osmo-adaptation is a fast and transient non-transcriptional Hog1-mediated activation of glycerol production, (ii) the transcriptional response serves to maintain an increased steady-state glycerol production with low steady-state Hog1 activity, and (iii) fast negative feedbacks of activated Hog1 on upstream signalling branches serves to stabilise adaptation response. The best approximating model also indicated that homoeostatic adaptive systems with two parallel redundant signalling branches show a more robust and faster response than single-branch systems. We corroborated this notion to a large extent by dedicated measurements of volume recovery in single cells. Our study also demonstrates that systematically testing a model ensemble against data has the potential to achieve a better and unbiased understanding of molecular mechanisms.
This model is hosted on BioModels Database
and identified by: MODEL1209110001
.
To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
for more information.
2012-11-22 | BIOMD0000000429 | BioModels
Project description:The Saccharomyces cerevisiae SFP1 is required for proper regulation of ribosome biogenesis and cell size in response to nutrients. A mutant deleted for SFP1 shows specific traits among which a slow growth phenotype, which is particularly evident during growth on glucose. To assess the effects of nutrients on the activity of Sfp1 independent by growth rate related feedback we grew an sfp1Πmutant and its isogenic reference strain in chemostat cultures, at the same specific growth rate, under glucose/ethanol-limitation. Our data show that Sfp1 is involved in the modulation of cell size and RiBi gene expression and that these two functions are differently influenced by nutrients. The continuous cultures were then pulsed with a glucose excess generating a situation of batch growth similar to shake flask cultures. The dynamic analysis of the metabolic and transcriptional response following the glucose addition suggested that Sfp1 plays a role at the crossroads of ribosome biogenesis and central carbon metabolism regulation. Finally, we show that the down-regulation of RP genes, which was observed in an sfp1Πstrain during shake flask growth, cannot be directly ascribed to the absence of Sfp1 but is most probably a secondary effect due to the low growth potential of the mutant strain. Experiment Overall Design: After ten volume changes, few seconds after the samples for the steady state analysis were collected, the anaerobic glucose pulse experiments were started by sparging the medium reservoir and the fermenter with pure nitrogen gas (airflow of 0.5 L min-1, Hoek-Loos, Schiedam, <5 ppm O2). NorpreneTM tubing and butyl septa were used to minimize oxygen diffusion into the anaerobic culture. Two minutes after nitrogen sparging and just before the addition of glucose, the medium and the effluent pumps were switched off. At this time point (which we will refer to as time T=0) the 200 mM glucose pulse was injected aseptically through a rubber septum. Experiment Overall Design: Sampling from chemostats, total RNA extraction, probe preparation and hybridization to Affymetrix Genechip® microarrays were performed as previously described (1). Samples were collected at steady state and then at 5, 10, 30, 60 and 120 minutes after the pulse. The results relative to steady state samples were derived from three independent cultures, those relative to the time course analysis were derived from two independent cultures. Experiment Overall Design: 1) Cipollina C., van den Brink J., Daran-Lapujade P., Pronk J.T., Vai M. and de Winde J.H. (2007) Revisiting the role of yeast Sfp1 in ribosome biogenesis and cell size control: A chemostat study. Microbiology. In press.
2008-06-18 | E-GEOD-9644 | biostudies-arrayexpress
Project description:RNA-seq was performed on T. maritima wild type, three glucose evolved cultures, and three glycerol adapted cultures. Wild type and glucose evolved strains were grown on glucose minimal media and glycerol evolved cultures were grown on glycerol minimal media. All samples were harvested in exponential phase. Seven samples are included with two biological replicates for each condition.
2015-06-09 | E-GEOD-63141 | biostudies-arrayexpress
Project description:The goal of the study is to use Next generation sequencing (RNA-seq) to study the underlying regulation of glycerol metabolism in mixed culture fermentation (glucose and glycerol) of Rhodosporidium toruloides. We sequenced the RNA from 4 different samples in the mixed culture (glucose and glycerol) with 2 replicates each. Transcriptional profiles showed that glycerol might be produced intracellularly and glycerol kinase (GUT1) and glycerol 3–phosphate dehydrogenase (GUT2) enzymes were not down-regulated in the presence of glucose at the transcriptional level. It also showed that this yeast has a different regulation compared to S.cerevisiae. Certain insights into lipid biosynthesis on these mixed cultures are provided at systems level. This analysis provides interesting targets for metabolic engineering in this organism growing on glucose and glycerol.
2016-05-12 | GSE74307 | GEO
Project description:Petelenz-kurdzeil2013 - Osmo adaptation
gpd1D
This model is described in the article:
Quantitative analysis of
glycerol accumulation, glycolysis and growth under hyper
osmotic stress.
Petelenz-Kurdziel E, Kuehn C,
Nordlander B, Klein D, Hong KK, Jacobson T, Dahl P, Schaber J,
Nielsen J, Hohmann S, Klipp E.
PLoS Comput. Biol. 2013; 9(6):
e1003084
Abstract:
We provide an integrated dynamic view on a eukaryotic
osmolyte system, linking signaling with regulation of gene
expression, metabolic control and growth. Adaptation to osmotic
changes enables cells to adjust cellular activity and turgor
pressure to an altered environment. The yeast Saccharomyces
cerevisiae adapts to hyperosmotic stress by activating the HOG
signaling cascade, which controls glycerol accumulation. The
Hog1 kinase stimulates transcription of genes encoding enzymes
required for glycerol production (Gpd1, Gpp2) and glycerol
import (Stl1) and activates a regulatory enzyme in glycolysis
(Pfk26/27). In addition, glycerol outflow is prevented by
closure of the Fps1 glycerol facilitator. In order to better
understand the contributions to glycerol accumulation of these
different mechanisms and how redox and energy metabolism as
well as biomass production are maintained under such conditions
we collected an extensive dataset. Over a period of 180 min
after hyperosmotic shock we monitored in wild type and
different mutant cells the concentrations of key metabolites
and proteins relevant for osmoadaptation. The dataset was used
to parameterize an ODE model that reproduces the generated data
very well. A detailed computational analysis using
time-dependent response coefficients showed that Pfk26/27
contributes to rerouting glycolytic flux towards lower
glycolysis. The transient growth arrest following hyperosmotic
shock further adds to redirecting almost all glycolytic flux
from biomass towards glycerol production. Osmoadaptation is
robust to loss of individual adaptation pathways because of the
existence and upregulation of alternative routes of glycerol
accumulation. For instance, the Stl1 glycerol importer
contributes to glycerol accumulation in a mutant with
diminished glycerol production capacity. In addition, our
observations suggest a role for trehalose accumulation in
osmoadaptation and that Hog1 probably directly contributes to
the regulation of the Fps1 glycerol facilitator. Taken
together, we elucidated how different metabolic adaptation
mechanisms cooperate and provide hypotheses for further
experimental studies.
This model is hosted on
BioModels Database
and identified by:
BIOMD0000000610.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2016-04-20 | BIOMD0000000610 | BioModels
Project description:This approach aims at searching unidentified regulatory roles of the AreB transcription factor in the overall carbon metabolism of A. niger. A full areB gene deletion mutant was constructed and characterized in A. niger ATCC 1015. Both strains were grown on glucose or glycerol using ammonia as nitrogen source in batch cultivations and the transcriptome was analyzed using three biological replicated transcriptome experiments. Two areB gene deletion replicates, one on glucose and one on glycerol were discarded due to bad quality and therefore not included in the analysis. Samples for RNA extraction were collected and further processed for hybridization in custom designed Affymetrix microarrays containing probes for three Aspergillus species including A. niger. Triplicate batch fermentations with the two Aspergillus niger strains used, the wild type A. niger strain ATCC 1015 and the areB complete gene deletion strain were carried out and transcriptome analysis was performed. Biomass from each batch cultivation was harvested in the exponential phase of growth and further processed for RNA extraction and hybridization on Affymetrix microarrays.
2011-01-31 | E-GEOD-21015 | biostudies-arrayexpress
Project description:Expression data from batch cultivations of Aspergillus niger wild type strain ATCC 1015 and adrA, facB and creA deletion mutants constructed on ATCC 1015 background strain with glucose or glycerol as carbon sources. Genome-wide transcriptome analysis was used to identify genes either affected directly or indirectly by each transcription factor investigated during growth on a repressing or a derepressing carbon source. For this purpose, batch cultivations under well-controlled conditions were performed with Aspergillus niger wild type strain ATCC 1015 and the three deletion mutants of the corresponding transcription factors AdrA, FacB and CreA. Samples for RNA extraction were collected and further processed for hybridization in custom-designed Affymetrix microarrays containing probes for three Aspergillus species, including A. niger. Triplicate batch fermentations of each of the four Aspergillus niger strains used, the wild type A. niger strain ATCC 1015 and three gene deletion mutants, were carried out using glucose or glycerol as carbon source, and transcriptome analysis was performed. Biomass from each batch cultivation was harvested in the exponential phase of growth and further processed for RNA extraction and hybridization on Affymetrix microarrays.
2011-01-31 | E-GEOD-19952 | biostudies-arrayexpress