Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNAseq and ribosome profiling of yeast cells grown under methionine restriction condition.

ABSTRACT: We characterize the translational and transcriptional programs induced by MetR and investigate the potential mechanisms through which methionine regulates gene expression, using the budding yeast S. cerevisiae as the model organism. Using ribosomal profiling and RNA-seq, we systematically compared the translational and transcriptional profiles of cells growing in the normal and methionine restricted media. We observed a broad spectrum of gene expression changes in response to MetR, including hundreds of genes whose transcript level and/or translational efficiency changed significantly. These genes fall into specific functional classes that are informative of the physiological state of the cell under MetR. Analysis of ribosome loading patterns of genes with increased translational efficiency suggested mechanisms both similar and different from the canonical model of translational regulation by general amino acid starvation. Analysis of the genes with decreased translational efficiency added support to the thiolation model of translational regulation by methionine. Since MetR extends the lifespan of many species, the list of genes we identified in this study can be good candidates for studying the downstream effectors of lifespan extension.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE91068 | GEO | 2017/02/24

SECONDARY ACCESSION(S): PRJNA356775

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

Transcriptomic comparison of D39 WT and SPD_0588 deletion mutant in Streptococcus pneumoniae D39 with different concentrations of methionine

Project description:metR (SPD_0588) mutant (TH9197) cannot grow in chemically defined medium (CDM) and had significant growth defect in CDM with 1 µg/ml methionine. With the increasing concentration of mehtionine, the growth of TH9197 was restored and the growth of metR mutant is as same as D39 WT (TH4306) when the concentration of methionine reaches 50 µg/ml. SPD_0588 is a putative transcriptional regulator and is homologous to MetR in Streptococcus mutans (78.9 % amino acid identity), which regulates both methionine synthesis and transport. We compared the transcriptome of WT and metR mutant in CDM with 1 µg/ml methionine by RNA-seq to see if MetR regulates the metabolism of methionine in Streptococcus pneumoniae D39. We compared the transcriptome of WT and metR mutant in CDM with 50 µg/ml methionine by RNA-seq to see if the regulation of MetR is methionine concentration-dependdent.We also want to identify the regulon of SPD_0588 in the two RNA-seq.

2021-05-18 | GSE166818 | GEO

Transcriptomic comparison of D39 WT and SPD_0588 deletion mutant in Streptococcus pneumoniae D39 with 1 µg/ml methionine

Project description:metR (SPD_0588) mutant (TH9197) cannot grow in chemically defined medium (CDM) without methionine and had significant growth defect in CDM with 1 µg/ml methionine. With the increasing concentration of mehtionine, the growth of TH9197 was restored and the growth of metR mutant is as same as D39 WT (TH4306) when the concentration of methionine reaches 50 µg/ml. SPD_0588 is a putative transcriptional regulator and is homologous to MetR in Streptococcus mutans (78.9 % amino acid identity), which regulates both methionine synthesis and transport. We compared the transcriptome of WT and metR mutant in CDM with 1 µg/ml methionine by RNA-seq to see if MetR regulates the metabolism of methionine in Streptococcus pneumoniae D39. We also want to identify the regulon of SPD_0588.

2021-06-01 | GSE142362 | GEO

ChIP-seq of Streptococcus pneumoniae D39 metR over-expression strain with 3×flag tag in CDM without methionine

Project description:In our study, we found that MetR as a transcriptional regulator may regulate the expression of genes not involved in methionine synthesis. To verify our hypothesis, we firstly construct a strain with metR over-expression in D39 and with 3×flag tag and culture this strain in chemically defined medium (CDM) without methionine. Then collect bacteria for ChIP-seq to identify the genes that can be directly transcriptionally regulated by MetR.

2021-05-18 | GSE167148 | GEO

scRNA-seq of aged Drosophila midgut under methionine restriction

Project description:Methionine restriction is known to extend lifespan in various model organisms including Drosophila melanogaster. In this analysis, we performed scRNAseq of Drosophila female midgut samples to understand the cell type specific response to methionine restriction.

2023-09-25 | GSE198149 | GEO

S-bacillithiolation of the OhrR repressor and the methionine synthase MetE protect against hypochlorite stress in Bacillus subtilis

Project description:Protein S-thiolation is a post-translational thiol-modification that controls redox-sensing transcription factors and protects active site cysteine residues against irreversible oxidation. In B. subtilis, the MarR-type repressor OhrR was shown to sense organic hydroperoxides via formation of mixed disulfides with the redox buffer bacillithiol (Cys-GlcN-Malate) termed as S-bacillithiolation. We have studied changes in the transcriptome and redox proteome caused by the strong oxidant hypochloric acid (NaOCl), the active component of house-hold bleach. The OhrR-controlled peroxiredoxin OhrA was most strongly up-regulated by NaOCl stress and conferred specific protection against NaOCl. Inactivation of the OhrR repressor was caused by S-bacillithiolation of the redox-sensing Cys15 residue in response to NaOCl. Two cobalamin-independent methionine synthases MetE and YxjG were identified as S-bacillithiolated at their essential active site cysteines resulting in hypochlorite-induced methionine limitation. In summary, our studies show that S-bacillithiolation of OhrR and the methionine synthases is the major mechanism in protection against hypochlorite stress in B. subtilis. The B. subtilis 168 wild type strain was grown in minimal medium to OD500 of 0.4 and harvested before and 10 minutes after exposure to 50 µM NaOCl. Microarray hybridizations were performed in triplicate using RNA isolated from independent cultures.

2011-07-04 | E-GEOD-27637 | biostudies-arrayexpress

The thiolation modification of tRNA is essential for plant immunity

Project description:Plants have evolved sophisticated mechanisms to regulate gene expression to activate immune responses against pathogen infections. However, how the translation system contributes to plant immunity is largely unknown. The evolutionarily conserved thiolation modification of tRNA ensures efficient decoding during translation. Here we show that tRNA thiolation is required for plant immunity in Arabidopsis. The Arabidopsis cgb mutant is hyper-susceptible to the pathogen Pseudomonas syringae. CGB encodes ROL5, a homolog of yeast NCS6 required for tRNA thiolation. ROL5 physically interacts with CTU2, a homolog of yeast NCS2. Mutations in either ROL5 or CTU2 result in loss of tRNA thiolation. Further analyses reveal that tRNA thiolation is required for both transcriptional reprogramming and translational reprogramming during immune responses. The translation efficiency of immune-related proteins reduces when tRNA thiolation is absent. Our study not only uncovers a new biological function of tRNA thiolation but also reveals a new mechanism for plant immunity.

2022-08-31 | GSE183087 | GEO

The Aspergillus nidulans metZ gene encodes a transcription factor involved in regulation of sulfur metabolism in this fungus and other Eurotiales

Project description:In Aspergillus nidulans, expression of sulfur metabolism genes is activated by the MetR transcription factor containing a basic region and leucine zipper domain (bZIP). Here we identified and characterized MetZ, a new transcriptional regulator in Aspergillus nidulans and other Eurotiales. It contains a bZIP domain similar to the corresponding region in MetR and this similarity suggests that MetZ could potentially complement the MetR deficiency. The metR and metZ genes are interrupted by unusually long introns. Transcription of metZ, unlike that of metR, is controlled by the sulfur metabolite repression system (SMR) dependent on the MetR protein. Overexpression of metZ from a MetR-independent promoter in a metR strain, activates transcription of genes encoding sulfate permease, homocysteine synthase and methionine permease, partially complementing the phenotype of the metR mutation. Thus, MetZ appears to be a second transcription factor involved in regulation of sulfur metabolism genes.

2015-03-23 | GSE62548 | GEO

Effects of 20 months Dietary Methionine Restriction on Hepatic Gene Expression in Fischer 344 Rats

Project description:Dietary methionine restriction (MR) has been shown to increase lifespan and decrease adiposity in rodents. This study was designed to examine the transcriptional effects of MR in metabolically relevant tissues. This experiment contains data from the liver. We analyzed MR-induced changes in gene expression using pooled RNA from liver of rats fed either a control purified amino acid diet (DL-methionine content of 0.86%) (CON) or a methionine-restricted diet (DL-methionine content of 0.172%)(MR). Rats were fed Purina rodent diet 5001 until 32 days of age and were then randomly assigned to be fed CON diet or MR diet for 20 months.

2012-04-07 | E-GEOD-28482 | biostudies-arrayexpress

Characterization of methionine dependence in melanoma cells [HumanMethylationEPIC]

Project description:Dietary methionine restriction is associated with a reduction in tumor growth in preclinical studies and an increase in lifespan in animal models. The mechanism by which methionine restriction inhibits tumor growth while sparing normal cells is incompletely understood, except for the observation that normal cells can utilize methionine or homocysteine interchangeably (methionine independence) while most cancer cells are strictly dependent on methionine availability. Here, we compared a typical methionine dependent and a rare methionine independent melanoma cell line. We show that replacing methionine, a methyl donor, with homocysteine generally induced hypomethylation in gene promoters. This decrease was similar in methionine dependent versus methionine independent cells. There was only a low level of pathway enrichment, suggesting that the hypomethylation is generic rather than gene specific. Whole proteome and transcriptome were also analyzed. This analysis revealed that contrarily to the effect on methylation, the replacement of methionine with homocysteine had a much greater effect on the transcriptome and proteome of methionine dependent cells than methionine independent cells. Interestingly, the methionine adenosyltransferase 2A (MAT2A), responsible for the synthesis of s-adenosylmethionine from methionine, was equally strongly upregulated in both cell lines. This suggests that the absence of methionine is equally detected but trigger different outcomesin methionine dependent versus independent cells. Our analysis reveals the importance of cell cycle control, DNA damage repair, translation, nutrient sensing, oxidative stress and tight junctions in the cellular response to methionine stress in melanoma.

2023-05-03 | GSE225944 | GEO

Effects of 20 months Dietary Methionine Restriction on Gene Expression in inguinal white adipose tissue of Fischer 344 Rats

Project description:Dietary methionine restriction (MR) has been shown to increase lifespan and decrease adiposity in rodents. This study was designed to examine the transcriptional effects of MR in metabolically relevant tissues. This experiment contains data from the inguinal white adipose tissue (IWAT). We analyzed MR-induced changes in gene expression using pooled RNA from IWAT of rats fed either a control purified amino acid diet (DL-methionine content of 0.86%) (CON) or a methionine-restricted diet (DL-methionine content of 0.172%)(MR). Rats were fed Purina rodent diet 5001 until 32 days of age and were then randomly assigned to be fed CON diet or MR diet for 20 months.

2013-07-01 | E-GEOD-28599 | biostudies-arrayexpress

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