Changes in Shewanella baltica transcriptome upon cold stress
Ontology highlight
ABSTRACT:
ORGANISM(S): Shewanella baltica
PROVIDER: GSE150927 | GEO | 2020/05/21
REPOSITORIES: GEO
Similar Datasets
Project description:Profound understanding of the mechanisms foodborne pathogenic bacteria utilize in adaptation to the environmental stress they encounter during food processing and storage is of paramount importance in design of control measures. Chill temperature is a central control measure applied in minimally processed foods; however, data on the mechanisms the foodborne pathogen Clostridium botulinum activates upon cold stress are scarce. Global gene expression analysis on the C. botulinum ATCC 3502 strain upon temperature downshift from 37 °C to 15 °C was performed to identify the cold-responsive gene set of this organism. Significant up- or down-regulation of 16 and 11 genes, respectively, was observed already 1 h after the cold shock. At 5 h after the temperature downshift, 199 and 210 genes were up- and down-regulated, respectively. Thus, the cold shock rapidly affected the expression of a gene set of a relatively small size, indicating a targeted acute response to cold shock, whereas extensive metabolic remodeling took place after prolonged exposure to cold. Induction of genes related to fatty acid biosynthesis, oxidative stress response, and iron uptake and storage was observed, in addition to mechanisms previously characterized as cold-tolerance related in bacteria. Furthermore, induction of several uncharacterized DNA-binding transcriptional regulator-encoding genes was observed, suggesting involvement of novel regulatory mechanisms in the cold shock response of C. botulinum. The role of such regulatory proteins, CBO0477 and CBO0558A, in cold tolerance of C. botulinum ATCC 3502 was demonstrated by the deteriorated growth of mutants of the respective genes at 17 °C.
2014-02-24 | GSE51465 | GEO
Project description:Profound understanding of the mechanisms foodborne pathogenic bacteria utilize in adaptation to the environmental stress they encounter during food processing and storage is of paramount importance in design of control measures. Chill temperature is a central control measure applied in minimally processed foods; however, data on the mechanisms the foodborne pathogen Clostridium botulinum activates upon cold stress are scarce. Global gene expression analysis on the C.M-BM- botulinum ATCC 3502 strain upon temperature downshift from 37 M-BM-0C to 15M-BM- M-BM-0C was performed to identify the cold-responsive gene set of this organism. Significant up- or down-regulation of 16 and 11 genes, respectively, was observed already 1 h after the cold shock. At 5 h after the temperature downshift, 199 and 210 genes were up- and down-regulated, respectively. Thus, the cold shock rapidly affected the expression of a gene set of a relatively small size, indicating a targeted acute response to cold shock, whereas extensive metabolic remodeling took place after prolonged exposure to cold. Induction of genes related to fatty acid biosynthesis, oxidative stress response, and iron uptake and storage was observed, in addition to mechanisms previously characterized as cold-tolerance related in bacteria. Furthermore, induction of several uncharacterized DNA-binding transcriptional regulator-encoding genes was observed, suggesting involvement of novel regulatory mechanisms in the cold shock response of C.M-BM- botulinum. The role of such regulatory proteins, CBO0477 and CBO0558A, in cold tolerance of C.M-BM- botulinum ATCC 3502 was demonstrated by the deteriorated growth of mutants of the respective genes at 17M-BM- M-BM-0C. C. botulinum ATCC 3502 wild type cold-shocked vs. pre-cold-shock; 3 replicates; growth at 37C in TPGY broth batch culture and subjected to cold shock to 15C; sampling at mid-log growth phase before cold shock, and 1 h and 5 h after temperature downshift to 15C (= 3 time points). Dye-swapped hybridization.
2014-02-24 | E-GEOD-51465 | biostudies-arrayexpress
Project description:Yeast magnesium starvation, 90 minutes
| PRJNA99065 | ENA
Project description:The biochemical and molecular mechanisms of insect cold acclimation prior to cold stress have been relatively well explored. The mechanisms linked to recovery and repair after cold stress received much less attention.Here we focus on recovery from cold stress in the larvae of vinegar fly (Drosophila melanogaster) that were exposed to two physiologically distinct cold stress situations; supercooling (S, survival > 90%) and freezing (F, survival < 10%), both at -5°C.The transcriptomic responses to cold stress were analyzed.
2019-01-25 | E-MTAB-7401 | biostudies-arrayexpress
Project description:Bacteria adapt to shifts from rapid to slow growth, and have developed strategies for long-term survival during prolonged starvation and stress conditions. We report the response of C. crescentus to carbon starvation, a common form of nutritional stress encountered by free-living bacteria, that induces stasis. We explored the differential gene expression changes in wild type cells and cells carrying deletions of two alternative extracytoplasmic function sigma factors, SigT and SigU. Glucose, the only carbon source in the minimal media M2G was removed from C. crescentus exponential phase cultures (wild-type (strain LS101), DSigT (strain LS3554) and DSigU (strain LS3547)). Total RNA was extracted after 15 minutes of incubation. Controls are cells that were mock washed and incubated in parallel in complete media.
2011-04-20 | E-GEOD-25998 | biostudies-arrayexpress
Project description:Cervicovaginal lavage (CVL)supernatants were heat inactivated for 30 minutes at 56°C before further processing. Total protein concentrations were determined using the Pierce Coomassie Plus (Bradford) Protein Assay (Thermo Scientific, Rockford, IL, USA). Sample protein content and volume were normalised with 25mM ammonium bicarbonate (ABC). Soluble proteins were precipitated using an equal volume of ice cold 30% (w/v) TCA in acetone and incubated at -20⁰C for 2 hours. Samples were centrifuged at 12,000g for 10 minutes (4⁰C) to pellet proteins. Pellets were washed three times with ice cold acetone and allowed to air dry. Further sample processing was performed as previously described (Armstrong et al, 2014) with minor modifications. Briefly, protein pellets were resuspended in 25 mM ABC, 0.05%(w/v) rapigest (Waters), reduced and alkylated. Digestion was performed with proteomic-grade trypsin (Sigma-Aldrich, St. Louis, MO, USA) at a protein:trypsin ratio of 50:1. Rapigest was precipitated by addition of trifluoroacetic acid to a final concentration of 0.5% (v/v). Peptide mixtures were analyzed by on-line nanoflow liquid chromatography using the nanoACQUITY-nLC system (Waters MS technologies) coupled to an LTQ-Orbitrap Velos (ThermoFisher Scientific, Bremen, Germany) mass spectrometer equipped with the manufacturer’s nanospray ion source. The gradient of the analytic column (nanoACQUITY UPLCTM BEH130 C18 15cm x 75µm, 1.7µm capillary column) consisted of 3-40% acetonitrile in 0.1% formic acid for 90 min then a ramp of 40-85% acetonitrile in 0.1% formic acid for 5min.
2016-03-15 | PXD003176 | Pride
Project description:SigE is a sigma factor found in Streptomyces species and is the key regulator of cell envelope stress response in Streptomyces coelicolor. To determine the regulon of SigE under conditions of cell envelope stress, 10 ug / ml vancomycin was used to induce cell envelope stress in the wild type and a sigE deletion strain of S. coelicolor. Samples were taken 0, 30, 60 and 90 minutes after addition of vancomycin and subjected to transcriptional profiling using Affymetrix arrays. Note – equivalent data for wild type Streptomyces coelicolor M600 is submitted as part of E-MEXP-3032. The data for both M600 (E-MEXP-3032) and J2130 (this submission) were generated at the same time employing the same protocols.
2019-04-24 | E-MTAB-7814 | biostudies-arrayexpress
Project description:This project aims to identify the proteins present in RNA granules of brown adipose tissue upon exposure to cold challenge. Wild type C57BL/6J mice were born and raised at thermoneutrality and were then subjected to cold exposure for 90 minutes. Brown adipose tissues were collected, and the protein lysates of RNA granules isolated from the brown adipose tissues were separated using SDS-PAGE gels and visualized with Coomassie stain. The protein bands were subsequently excised for downstream sample processing.
2023-11-23 | PXD044433 | Pride
Project description:Liebal2012 - B.subtilis sigB proteolysis model
An important transcription factor of B.subsilis is sigma B
. Liebal et al. (2012) have performed experiments in B.subtilis wild type and mutant straits to test and validate a mathematical model of the dynamics of sigma B
activity. The following three models were constructed and their ability to fit the experimental data were tested. 1) Transcription inhibition model (MODEL1212180000), 2) sigma B
proteolysis model (MODEL1302080000) and 3) Post-transcriptional instability model (MODEL1302080001). This model corresponds to the sigma B
proteolysis model (MODEL1302080000).
This model is described in the article:
Proteolysis of beta-galactosidase following SigmaB activation in Bacillus subtilis.
Liebal UW, Sappa PK, Millat T, Steil L, Homuth G, Völker U, Wolkenhauer O.
2012 Jun;8(6):1806-14.
Abstract:
In Bacillus subtilis the σ(B) mediated general stress response provides protection against various environmental and energy related stress conditions. To better understand the general stress response, we need to explore the mechanism by which the components interact. Here, we performed experiments in B. subtilis wild type and mutant strains to test and validate a mathematical model of the dynamics of σ(B) activity. In the mutant strain BSA115, σ(B) transcription is inducible by the addition of IPTG and negative control of σ(B) activity by the anti-sigma factor RsbW is absent. In contrast to our expectations of a continuous β-galactosidase activity from a ctc::lacZ fusion, we observed a transient activity in the mutant. To explain this experimental finding, we constructed mathematical models reflecting different hypotheses regarding the regulation of σ(B) and β-galactosidase dynamics. Only the model assuming instability of either ctc::lacZ mRNA or β-galactosidase protein is able to reproduce the experiments in silico. Subsequent Northern blot experiments revealed stable high-level ctc::lacZ mRNA concentrations after the induction of the σ(B) response. Therefore, we conclude that protein instability following σ(B) activation is the most likely explanation for the experimental observations. Our results thus support the idea that B. subtilis increases the cytoplasmic proteolytic degradation to adapt the proteome in face of environmental challenges following activation of the general stress response. The findings also have practical implications for the analysis of stress response dynamics using lacZ reporter gene fusions, a frequently used strategy for the σ(B) response.
Figure 3a of the reference article has been reproduced. beta-galactosidase (lacz in model) activity at different concentrations of IPTG (100M, 200M and 1000M) has been reproduced. SED-ML (Simulation Experiment Description Markup Language) file is available for this model (see curation tab).
This model is hosted on BioModels Database
and identified
by: MODEL1302080000
.
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.
2013-06-06 | BIOMD0000000460 | BioModels
Project description:Liebal2012 - B.subtilis transcription inhibition model
An important transcription factor of B.subsilis is sigma B
. Liebal et al. (2012) have performed experiments in B.subtilis wild type and mutant straits to test and validate a mathematical model of the dynamics of sigma B
activity. The following three models are constructed and their ability to fit the experimental data were tested. 1) Transcription inhibition model (MODEL1212180000), 2) sigma B
proteolysis model (MODEL1302080000) and 3) Post-transcriptional instability model (MODEL1302080001). This model corresponds to the Transcription inhibition model (MODEL1212180000).
This model is described in the article:
Proteolysis of beta-galactosidase following SigmaB activation in Bacillus subtilis.
Liebal UW, Sappa PK, Millat T, Steil L, Homuth G, Völker U, Wolkenhauer O.
2012 Jun;8(6):1806-14.
Abstract:
In Bacillus subtilis the σ(B) mediated general stress response provides protection against various environmental and energy related stress conditions. To better understand the general stress response, we need to explore the mechanism by which the components interact. Here, we performed experiments in B. subtilis wild type and mutant strains to test and validate a mathematical model of the dynamics of σ(B) activity. In the mutant strain BSA115, σ(B) transcription is inducible by the addition of IPTG and negative control of σ(B) activity by the anti-sigma factor RsbW is absent. In contrast to our expectations of a continuous β-galactosidase activity from a ctc::lacZ fusion, we observed a transient activity in the mutant. To explain this experimental finding, we constructed mathematical models reflecting different hypotheses regarding the regulation of σ(B) and β-galactosidase dynamics. Only the model assuming instability of either ctc::lacZ mRNA or β-galactosidase protein is able to reproduce the experiments in silico. Subsequent Northern blot experiments revealed stable high-level ctc::lacZ mRNA concentrations after the induction of the σ(B) response. Therefore, we conclude that protein instability following σ(B) activation is the most likely explanation for the experimental observations. Our results thus support the idea that B. subtilis increases the cytoplasmic proteolytic degradation to adapt the proteome in face of environmental challenges following activation of the general stress response. The findings also have practical implications for the analysis of stress response dynamics using lacZ reporter gene fusions, a frequently used strategy for the σ(B) response.
Figure 3a of the reference article has been reproduced. beta-galactosidase (lacz in model) activity at different concentrations of IPTG (100M, 200M and 1000M) has been reproduced. SED-ML (Simulation Experiment Description Markup Language) file is available for this model (see curation tab).
This model is hosted on BioModels Database
and identified
by: MODEL1212180000
.
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.
2013-06-06 | BIOMD0000000461 | BioModels