Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The cold shock response of Bacillus subtilis analyzed by RNA-sequencing: YplP regulates pyruvate transport at low temperatures

ABSTRACT: The cold shock response of B. subtilis was defined after 0.5 hr and 2 hr cold shock using RNA sequencing. We identified novel RNAs (including non-coding RNAs) that play a role during growth at low temperatures. Deletion of the cold induced protein YplP results in a cold sensitive phenotype, and a comparative RNA sequencing analysis suggests that YplP induces pftAB expression after prolonged incubation at low temperatures, thereby optimizing pyruvate transport under cold shock conditions.

ORGANISM(S): Bacillus subtilis

PROVIDER: GSE111577 | GEO | 2018/03/12

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

The cold shock response of Bacillus subtilis analyzed by RNA-sequencing: YplP regulates pyruvate transport at low temperatures

Project description:The cold shock response of Bacillus subtilis analyzed by RNA-sequencing: YplP regulates pyruvate transport at low temperatures

| PRJNA437458 | ENA

Cold acclimation

Project description:Experiment was designed to identify transcriptome changes during cold acclimation of Drosophila melanogaster male flies. Resistance to cold is often measured by recovery times from chill coma, which is induced almost immediately upon exposure to low but non-freezing temperatures (~0C), with flies becoming immobilised and losing motor activity. This paralysis is also ostensibly reversible upon return to normal temperatures, although again there can be longer term effects. Acclimation for increased cold resistance requires exposure periods ranging from hours or days to several weeks at low temperatures between 0C to 12C, and samples were taken during the cold acclimation period (1 hr, 2 hr, 3 hr, 6 hr, 12 hr, 24 hr, 36 hr and 48 hr).

2014-05-01 | E-MTAB-1607 | biostudies-arrayexpress

HSF1 mediated Gene regulation in T cells at normal (37C) and febrile (40C) temperatures

Project description:HSF1 is a major transcriptional regulator of heat shock responses. Many cells activate HSF1 in response to heat shock temperatures (>42oC) and other cellular stress causing agents. Unlike other cell types, T cells activate HSF1 in response to T cell activation or when exposed to febrile (40oC) temperatures, suggesting a role for HSF1 beyond the heat-shock response. We used microarray analysis and HSF1 knock-out mice to study the HSF1 mediated gene regulation in activated T cells under normal and fever temperatures. T cells were purifed from spleen and lymphnodes using miltenyi anti-CD3 magnetic beads and were activated for 5 hr with plate bound anti-CD3 at normal (37oC) and febrile( 40oC) temperatures in triplicate cultures. Total RNA from triplicate cultures were extracted, pooled and processed for hybridization on to whole mouse genome 430 2.0 affymetrix microarray chips.

2012-09-20 | E-GEOD-41005 | biostudies-arrayexpress

HSF1 mediated Gene regulation in T cells at normal (37C) and febrile (40C) temperatures

2012-09-20 | GSE41005 | GEO

Cold hardening gene expression

2005-12-01 | GSE2989 | GEO

Proteome cold-shock response in the extremely acidophilic archaeon, Cuniculiplasma divulgatum

Project description:The archaea Cuniculiplasma divulgatum are abundant in acidic environments with low to moderate temperatures. However, the molecular mechanisms underlying its ability to thrive at low temperatures remain unexplored. Using mass spectrometry (MS)-based proteomics, we analysed the effect of short-term (3 h) exposure to cold shock. The C. divulgatum genome encodes 2,016 protein-coding genes, from which 819 proteins were identified in the cells grown under optimal conditions. In line with the peptidolytic lifestyle of C. divulgatum, its intracellular proteome revealed the abundance of proteases, ABC transporters and cytochrome C oxidase. From 747 quantifiable polypeptides, the levels of 582 proteins showed no change after the cold shock (the core proteome), whereas 104 proteins were upregulated suggesting that they might be contributing to cold adaptation. The highest increase in protein levels was found for the metal-dependent hydrolase, FAD-dependent oxidoreductase, aspartate carbamoyltransferase regulatory chain proteins, 2-oxoacid ferredoxin oxidoreductase and ATPase-V type ATP synthase. Furthermore, the cold shock induced a substantial increase (3.5 % and 9.0 %) in the levels of two most abundant intracellular proteins, chaperonin and glutamate dehydrogenase. This study has outlined potential mechanisms of environmental fitness of Cuniculiplasma spp. allowing them to colonise and survive in acidic settings at low/ moderate temperatures.

2020-05-26 | PXD017828 | Pride

Global transcriptional response of wild type and transcription factor deletion strains of Saccharomyces cerevisiae to the environmental stress of cold shock and subsequent recovery

Project description:Previous studies on the global transcriptional response of budding yeast, Saccharomyces cerevisiae, to cold shock have revealed that the response can be divided into a set of early response genes (after 15 minutes to 2 hours of cold temperatures) and late response genes (after 12 to 60 hours of cold temperatures). The late response genes include the ESR genes induced by many environmental stresses and are regulated by the Msn2 and Msn4 transcription factors, as they are during other environmental stresses (Kandror et al. 2004 PMID:15053871; Schade et al. 2004 PMID:15483057). However, the transcription factors responsible for the induction of the early response genes, the overall regulatory mechanism governing this early response, and the transcriptional response to recovery after cold shock remain largely unknown. Thus, we measured the early transcriptional response of S. cerevisiae to cold shock and subsequent recovery using DNA microarrays. To determine which transcription factors were responsible for these changes in expression, the same cold shock and recovery microarray experiments were then performed on six strains individually deleted for the transcription factors Cin5, Gln3, Hap4, Hmo1, Swi4, and Zap1.

2018-06-22 | GSE83656 | GEO

The identification of small RNAs differentially expressed in apple buds reveals a potential role of the miR159-MYB regulatory module during dormancy

Project description:Winter dormancy is an adaptative mechanism that temperate and boreal trees have developed to protect their meristems against low temperatures. In apple trees (Malus domestica), cold temperatures induce bud dormancy at the end of summer/beginning of the fall. Apple buds stay dormant during winter until they are exposed to a period of cold, after which they can resume growth (budbreak) and initiate flowering in response to warm temperatures in spring. It is well-known that small RNAs modulate temperature responses in many plant species, but however, how small RNAs are involved in genetic networks of temperature-mediated dormancy control in fruit tree species remains unclear. Here, we have made use of a recently developed ARGONAUTE (AGO)-purification technique to isolate small RNAs from apple buds. A small RNA-seq experiment resulted in the identification of small RNAs that change their pattern of expression in apple buds during dormancy.

2021-11-30 | GSE189658 | GEO

Transcriptomic profile of pfd4 plants under low temperatures

Project description:Transcriptional profiling of two-old week pfd4/Col-0 (WT) plants in response to low temperatures

2017-12-01 | GSE90746 | GEO

Cold hardening gene expression

Project description:Cold hardening treatment, a brief exposure to low temperatures (e.g. 0°C for 2 h), can protect certain insects against subsequent exposure to temperatures sufficiently low to cause damage or lethality. Microarray analysis to examine the changes in transcript abundance associated with cold hardening has been undertaken in Drosophila melanogaster in order to gain insight into this phenomenon. Transcripts associated with 36 genes were identified, a subset of which appeared to be also differentially expressed after heat shock treatment. Quantitative RT-PCR was used to independently determine transcript abundance of a subset of these sequences. Taken together, these assays suggest that stress proteins, including Hsp23, Hsp26, Hsp83 and Frost as well as membrane-associated proteins may contribute to the cold hardening response. Co-reared flies were separated into a control group and a treatment group at random. RNA was isolated from the cold-shocked flies and the respective controls and was used for direct comparisons on cDNA microarrays. Treatments were not varied as they had been optimized in previous studies. A pilot experiment was performed using the Drosophila 7k2 array (GPL311) and subsequently three pairs of independent biological samples were evaluated with the Drosophila 12k1 array (GPL1467).

2005-11-30 | E-GEOD-2989 | biostudies-arrayexpress

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