Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Widespread prion-based control of growth and differentiation strategies in Saccharomyces cerevisiae

ABSTRACT: Theory and experiment suggest that organisms would benefit from pre-adaptation to future stressors based on reproducible environmental fluctuations experienced by their ancestors. Yet mechanisms driving pre-adaptation remain enigmatic. We report that the [SMAUG+] prion allows yeast to anticipate nutrient repletion after periods of starvation, providing a strong selective advantage. By transforming the landscape of post-transcriptional gene expression, [SMAUG+] regulates the decision between two broad growth and survival strategies: mitotic proliferation or meiotic differentiation into a stress-resistant state. [SMAUG+] is common in laboratory yeast strains, where standard propagation practice produces regular cycles of nutrient scarcity followed by repletion. Distinct [SMAUG+] variants are also widespread in wild yeast isolates from multiple niches, establishing that prion polymorphs can be utilized in natural populations. Our data provide a striking example of how protein-based epigenetic switches, hidden in plain sight, can establish a transgenerational memory that integrates adaptive prediction into developmental decisions.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE138559 | GEO | 2020/02/05

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

A Non-Amyloid Prion Particle that Activates a Heritable Gene Expression Program.

Project description:Spatiotemporal gene regulation is often driven by RNA-binding proteins that harbor long intrinsically disordered regions in addition to folded RNA-binding domains. We report that the disordered region of the evolutionarily ancient developmental regulator Smaug drives selfassembly into gel-like condensates. These proteinaceous particles are not composed ofamyloid. Yet they are infectious, allowing them to act as a protein-based epigenetic element: a prion. In contrast to many amyloid prions, condensation of Smaug enhances its function in mRNA decay, and its self-assembly properties are conserved over large evolutionary distances. Yeast cells harboring the [SMAUG+] prion downregulate a coherent network of mRNAs and exhibit improved growth under nutrient limitation. Smaug condensates formed from purified protein can transform naïve cells to acquire the prion. Our data establish that non-amyloid selfassembly of RNA-binding proteins can drive a form of epigenetics beyond the chromosome, instilling adaptive gene expression programs that are heritable over long biological timescales.

2020-02-05 | GSE138557 | GEO

Rapid genomic response after relief from nitrogen starvation of an enological strain of Saccharomyces cerevisiae

Project description:The aim of this study was to determine how nitrogen repletion affected the genomic cell response of a Saccharomyces cerevisiae wine yeast strain, in particular within the first hour following relief from nutrient starvation. We found almost 4000 genes induced or repressed sometimes within minutes of nutrient changes. Some of the transcriptional responses to nitrogen depended on the TOR pathway which control positively ribosomal protein genes, amino acid and purine biosynthesis or amino acid permease genes and negatively stress-response genes, RTG specific TCA cycle genes and NCR sensitive genes. Some unexpected transcriptional responses concerned all the glycolytic genes, the starch and glucose metabolism and citrate cycle related genes which were down-regulated, as well as genes from the lipid metabolism.

2018-07-10 | GSE116766 | GEO

Global regulation of mRNA translation and stability in the early Drosophila embryo by the Smaug RNA-binding protein- Polysome gradient/microarray study

Project description:To gain a panoramic view of Smaug function in the early embryo we identified mRNAs that are bound to Smaug using RNA co-immunoprecipitation followed by hybridization to DNA microarrays. We also identified the mRNAs that are translationally repressed by Smaug using polysome gradients and microarrays. Comparison of the bound mRNAs to those that are translationally repressed by Smaug and those that require Smaug for their degradation suggests that a large fraction of Smaug?s target mRNAs are both translationally repressed and degraded by Smaug. Smaug directly regulates components of the TRiC/CCT chaperonin, the proteasome regulatory particle and lipid droplets as well as many metabolic enzymes, including several glycolytic enzymes.

2013-12-03 | GSE50026 | GEO

Project description:Hiding in plain sight: integrative analyses uncover a cryptic Salvia species in Europe

| PRJNA849002 | ENA

Project description:In this study we probe how prototrophic yeast from different environmental backgrounds respond to perturbing agents presented in the context of a conflicting signal, repletion of glucose after transient deprivation. To assess the contribution of genetic v

2013-03-03 | E-MTAB-1463 | biostudies-arrayexpress

Project description:Adaptation to nutrient limitation

| PRJNA388793 | ENA

Project description:Nutrient Adaptation in Pseudomonas aeruginosa

| PRJNA692838 | ENA

Regulation of the transcription factor CdnL promotes adaptation to nutrient stress in Caulobacter

Project description:In response to nutrient deprivation, bacteria activate a conserved stress response pathway called the stringent response (SR). In Caulobacter crescentus, SpoT synthesizes the secondary messengers (p)ppGpp, which affect transcriptional reprogramming by binding to RNA polymerase to downregulate anabolic gene transcription. (p)ppGpp can also impact the expression of anabolic genes by controlling the levels and activities of their transcriptional regulators. In Caulobacter, a major regulator of anabolic genes is the conserved transcription factor CdnL. If and how CdnL is controlled during the SR and why that might be functionally important is unclear. Here, we show that CdnL is regulated post-translationally in a manner dependent on SpoT and the ClpXP protease. We find that stabilization of CdnL causes misregulation of ribosomal and metabolic genes during starvation. Functionally, we demonstrate that the combined action of SR transcriptional regulators and CdnL clearance allows for rapid adaptation to nutrient repletion. We also find that cells that are unable to clear CdnL during starvation are outcompeted by wild-type cells when subjected to fluctuations in nutrients. We hypothesize that post-transcriptional clearance of CdnL during the SR, in conjunction with direct binding of (p)ppGpp and DksA to RNAP, are critical for altering the transcriptome in order to permit cell survival during nutrient stress.

2024-05-10 | GSE249185 | GEO

Transcriptomic Responses to Prion Disease in Rats

Project description:While prion infections have been extensively characterized in the laboratory mouse, little is known regarding the molecular responses to prions in other rodents. To explore these responses and make comparisons, we generated a prion disease in the laboratory rat by successive passage of mouse RML prions. Here we describe the accumulation of prions and associated pathology in the rat and describe the transcriptional impact throughout prion disease. Comparative transcriptional profiling between laboratory mice and rats suggests that similar molecular processes are unfolding in response to prion infection. At the level of individual transcripts, however, variability exists between mice and rats and many genes deregulated in mouse scrapie are not affected in rats. Notwithstanding these differences, many transcriptome responses are conserved between mice and rats infected with scrapie. Our findings highlight the usefulness of comparative approaches to understanding neurodegeneration and prion diseases in particular. We Adapted RML Mouse Scrapie into Rats and measured the resulting gene expression changes in brain as a result of disease progression. Rats were infected by intracranial inoculation with prion isolates obtained by adaptation of mouse RML scrapie prions into rats. Brain samples were collected from third and fourth passage infected rats and age-matched controls at specified timepoints and gene expression profiles obtained. For each time point, 3 diseased and control brain samples were profiled.

2015-09-01 | E-GEOD-63930 | biostudies-arrayexpress

Translational profiling of neuronal subtypes reveals early vulnerability of somatostatin-expressing neurons in pre-symptomatic fatal familial insomnia

Project description:Selective neuronal vulnerability is a common, yet poorly understood characteristic of neurodegenerative diseases and is particularly prominent in familial prion diseases, such as Creutzfeldt-Jakob disease (CJD) and fatal familial insomnia (FFI), where different mutations in the prion protein manifest as neuropathologically distinct diseases. To determine how presence of mutant prion protein influences gene expression at pre-symptomatic stages, we used RiboTag to isolate cell type-specific, translating RNA from GABAergic, glutamatergic, somatostatin- (SST) and parvalbumin-expressing neurons of 9-month-old knock-in mice of CJD and FFI.

2022-09-21 | GSE198063 | 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