Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Growth-phase dependent control of rRNA synthesis in Saccharomyces cerevisiae [RNA-seq]

ABSTRACT: Saccharomyces cerevisiae is one of the most well-studied model organisms used in the scientific community. Its ease of manipulation, accessible growth conditions, short life cycle, and conserved eukaryotic metabolic pathways make it a useful model organism. Consequently, yeast has been used to investigate a myriad of phenomena, from microbial to human studies. Most of the research performed using this model organism utilizes yeast cell populations when they are growing exponentially, a growth phase aptly termed exponential or log phase. However, log phase encompasses several yeast generations and ranges several hours of yeast growth, meaning that there is a potential for variability during this “homogenous” growth phase. Cells in log phase require robust ribosome biogenesis to support their rapid growth and cell division. Interestingly, during log phase, ribosomal RNA (rRNA) synthesis (which is the first and rate limiting step in ribosome biosynthesis) has been shown to decrease prior to growth rate decline in stationary phase. In this study, we utilized several genomic and biochemical methods to elucidate the relationship between subphases of log phase and rRNA synthesis. Our results indicate that as yeast cells progress through subphases of log growth both of Pol I transcription and rRNA processing are repressed. Overall, this study establishes a growth phase dependent control of rRNA synthesis that unexpectedly begins prior to the switch to stationary phase (i.e. pre-diauxic shift) as a putative mechanism of anticipating nutrient starvation.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE268168 | GEO | 2024/06/20

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Growth-phase dependent control of rRNA synthesis in Saccharomyces cerevisiae [NET-seq]

Project description:Saccharomyces cerevisiae is one of the most well-studied model organisms used in the scientific community. Its ease of manipulation, accessible growth conditions, short life cycle, and conserved eukaryotic metabolic pathways make it a useful model organism. Consequently, yeast has been used to investigate a myriad of phenomena, from microbial to human studies. Most of the research performed using this model organism utilizes yeast cell populations when they are growing exponentially, a growth phase aptly termed exponential or log phase. However, log phase encompasses several yeast generations and ranges several hours of yeast growth, meaning that there is a potential for variability during this “homogenous” growth phase. Cells in log phase require robust ribosome biogenesis to support their rapid growth and cell division. Interestingly, during log phase, ribosomal RNA (rRNA) synthesis (which is the first and rate limiting step in ribosome biosynthesis) has been shown to decrease prior to growth rate decline in stationary phase. In this study, we utilized several genomic and biochemical methods to elucidate the relationship between subphases of log phase and rRNA synthesis. Our results indicate that as yeast cells progress through subphases of log growth both of Pol I transcription and rRNA processing are repressed. Overall, this study establishes a growth phase dependent control of rRNA synthesis that unexpectedly begins prior to the switch to stationary phase (i.e. pre-diauxic shift) as a putative mechanism of anticipating nutrient starvation.

2024-06-20 | GSE268167 | GEO

Gene expression profiling of M tuberculosis BCG strain during extended stationary and resuscitation phase of growth

Project description:Objective of the study is to find out the differentially regulated genes of Mycobacterium BCG strain in extended stationary phase comparison to log phase growth and resuscitation phase. Mycobacterium BCG culture was grown in Sauton medium at 37o C without shaking. Cells at A600 0.6-0.8 were harvested as log phase culture. The cells harvested after 5 months incubation at 37oC without shaking became non culturable and were harvested as extended stationary phase cells. The extended stationary phase cells were treated with resuscitation promoting factor (Rpf) from Micrococcus luteus and harvested after 8 days. Cells of this stage were treated as resuscitation phase cells. Gene expression profiling was carried out using Agilent microarray platform. Keywords: Extended stationary phase, Log phase growth and Resuscitation phase.

2009-07-01 | GSE15642 | GEO

Mycobacterium tuberculosis H37Rv

Project description:LIX11 vs H37Rv under Log vs stationary phase growth

| PRJNA163615 | ENA

Brucella melitensis global gene expression

Project description:In this study we report that B. melitensis at the late logarithmic phase of growth are more invasive for HeLa cells than at mid logarithmic or stationary growth phases. Microarray analysis of B. melitensis gene expression identified 414 up- and 40 down-regulated genes in late-log growth phase compared to the stationary growth phase. The vast majority of the up-regulated genes in late-log cultures were those associated with DNA replication, transcription and translation, intermediate metabolism, energy production and conversion, membrane transport and cell envelope, biogenesis and outer membrane, while the down-regulated genes were distributed among several functional categories. This first Brucella global gene expression study provides novel information on growth phase-specific gene regulation important not only for understanding Brucella physiology but also the initial molecular interactions between Brucella and its host. Keywords: Comparison bacterial growth phase normalized to genomic DNA

2009-05-14 | GSE11192 | GEO

Comparison of gene expression of L. reuteri ATCC 55730 at different growth phase in LDMIII medium

Project description:Comparison of gene expression between L. reuteri ATCC 55730 in LDMIII between early log phase (T8), late log phase (T12) or early stationary phase phase (T16) or late stationary phase (T24)

2011-01-15 | GSE24570 | GEO

Comparison of gene expression of L. reuteri ATCC PTA 6475 at different growth phase in a LDMIII

Project description:Comparison of gene expression between L. reuteri ATCC PTA 6475 in LDMIII between early log phase (T8), late log phase (T12) or early stationary phase phase (T16) or late stationary phase (T24)

2011-01-15 | GSE24415 | GEO

Transcriptome analysis of E.coli MG1655 under multiple growth conditions

Project description:Investigation of comprehensive information about the expression level of RNA transcripts across the entire E.coli genome in mulitple growth conditions, including log-phase; stationary phase, heat shock and nitrogen-limiting condition.

2009-11-04 | GSE15534 | GEO

Growth phase-dependent response of Helicobacter pylori to iron starvation.

Project description:This data set was used to determine genes that are regulated by iron availability and to access the growth phase dependence on that regulation. Stationary (Stat Chelate and Stat.iron.survival)and exponential (Log Chelate and Log.iron.survival)were subjected to chelation using DPP. Growth status of the cultures was confirmed by determing the correlation coefficient of the Stat chelate T=0/control and Log Chelate T=0/control vs data generated in the TC Motility series. Arrays used for iron addback experiments are listed as FeAddBack-1-time or FeAddBack-2-time. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

2005-12-22 | GSE3888 | GEO

Human gut microbiome cultured over time responsed differently to drug stimulation

Project description:In vitro gut microbiota models are often used to study drug-microbiome interaction. Similar to culturing individual microbial strains, the biomass accumulation of in vitro gut microbiota follows a logistic growth curve. Current studies on in vitro gut microbiome responses introduce drug stimulation during different growth stages, e.g. lag phase or stationary phase. However, in vitro gut microbiota in different growth phases may respond differently to a same stimuli. Therefore, in this study, we used a 96-deep well plate-based culturing model (MiPro) to culture the human gut microbiota. Metformin, as the stimulus, was added at the lag, log and stationary phases of growth. Microbiome samples were collected at different time points for optical density and metaproteomic functional analysis. Results show that in vitro gut microbiota responded differently to metformin added during different growth phases, in terms of the growth curve, alterations of taxonomic and functional compositions. The addition of drugs at log phase leads to the greatest decline of bacterial growth. Metaproteomic analysis suggested that the strength of the metformin effect on the gut microbiome functional profile was ranked as lag phase > log phase > stationary phase. Our results showed that metformin added at lag phase resulted in a significantly reduced abundance of the Clostridiales order as well as an increased abundance of the Bacteroides genus, which was different from stimulation during the rest of the growth phase. Metformin also resulted in alterations of several pathways, including energy production and conversion, lipid transport and metabolism, translation, ribosomal structure and biogenesis. Our results indicate that the timing for drug stimulation should be considered when studying drug-microbiome interactions in vitro.

2022-03-01 | PXD017390 | Pride

Analysis of the Yarrowia lipolytica proteome reveals subtle variations in expression levels between lipogenic and non-lipogenic conditions

Project description:Y. lipolytica cells were grown in rich-medium and (nutrient limited) minimal-medium, showing accumulations of neutral lipids at 10% and 30% of dry cell weight respectively. To study the mechanisms driving this, we sampled these cultures in paired replicates during both log and stationary phases of the cell growth, and performed 1D LC-MS/MS quantitation analysis on their tryptic digests. Sample assignments were as follows: (RME1, RME2) log phase rich; (RMG3, RMG4) stationary phase rich; (RME10, RME11) log phase minimal; (RME7, RME8) stationary phase minimal. Label free quantitation yielded a log2 expression matrix of over 1800 proteins. Differential analysis showed that while the hypothesized driver of TAG storage- ATP citrate lyase- remained stable, there was up-regulation of proteins involved in the TCA cycle.

2020-10-08 | MSV000086249 | MassIVE

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