Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

9 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Prokaryotic expression profiling analysis for single or combined chaperones deletion

ABSTRACT: Chaperones have essential role in assist nascent peptides folding, prevent proteins aggregation and maintain cellular protein homeostasis. Considering spatial and temporal features of chaperones regulating in vivo, changes in single or combined chaperone-depleted E.coli strain is needed to be put into understand at transcriptional level. Here, we utilized expression microarrays to investigate global transcriptional response upon deletion of single or multiple chaperones in E. coli for understanding the transcriptional network affected by chaperones. To identify prokaryotic expression profiles in deletion of chaperones, several E.coli mutants were constructed in the following: Z116 (△tig 37℃), Z125(△dnaK37℃), Z625(△tig△dnaK 37℃ or 30℃), Z629(△tig△dnaK 30℃), NM (C-domain of tig was deleted 37℃), MC (N-domain of tig was deleted 37℃), NC (M-domain of tig was deleted 37℃). Two types of cDNA mixtures containing Cy3-labeled (or Cy5-labeled) control DNA (from BW25113) and Cy5-labeled (or Cy3-labeled) DNA targets (from mutant strain) were hybridized with E.coli microarrays in a dye-swap strategy. E.coli gene expression data of chaperone DnaK deletant compared control WT (BW25113). Please note that other mutant microarray data will be added in the future.

ORGANISM(S): Escherichia coli

SUBMITTER: Dongjie Fan

PROVIDER: E-GEOD-69912 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Prokaryotic expression profiling analysis for single or combined chaperones deletion

Project description:Chaperones have essential role in assist nascent peptides folding, prevent proteins aggregation and maintain cellular protein homeostasis. Considering spatial and temporal features of chaperones regulating in vivo, changes in single or combined chaperone-depleted E.coli strain is needed to be put into understand at transcriptional level. Here, we utilized expression microarrays to investigate global transcriptional response upon deletion of single or multiple chaperones in E. coli for understanding the transcriptional network affected by chaperones. To identify prokaryotic expression profiles in deletion of chaperones, several E.coli mutants were constructed in the following: Z116 (△tig 37℃), Z125(△dnaK37℃), Z625(△tig△dnaK 37℃ or 30℃), Z629(△tig△dnaK 30℃), NM (C-domain of tig was deleted 37℃), MC (N-domain of tig was deleted 37℃), NC (M-domain of tig was deleted 37℃). Two types of cDNA mixtures containing Cy3-labeled (or Cy5-labeled) control DNA (from BW25113) and Cy5-labeled (or Cy3-labeled) DNA targets (from mutant strain) were hybridized with E.coli microarrays in a dye-swap strategy.

2015-06-18 | GSE69912 | GEO

Expression data from an Avian pathogenic Escherichia coli strain

Project description:Avian pathogenic Escherichia coli strains frequently cause extra-intestinal infections and are responsible for significant economic losses in the poultry industry worldwide. APEC isolates are closely related to human extraintestinal pathogenic E.coli strains and may also act as pathogens for humans. In this work, three type VI secretion systems were deleted to analyze which pathogenicity characteristics would change in the mutants, compared to wild type strain (SEPT 362). Four Avian Pathogenic Escherichia coli strains (one wild type and three deleted mutants) were grown at 37°C in Dulbecco´s Modified Eagle´s Media (DMEM) media until reach O.D 600 = 0.8, for RNA extraction and hybridization on Affymatrix microarrays.

2010-09-09 | E-GEOD-21893 | biostudies-arrayexpress

Hsp70 ATP-dependent dimerization and Chaperone/Co-chaperone Interactions

Project description:Eukaryotic protein homeostasis (proteostasis) is largely dependent on the action of highly conserved Hsp70 molecular chaperones. Recent evidence indicates that apart from conserved molecular allostery, Hsp70 proteins retained and adapted throughout the evolution the ability to assemble as functionally relevant ATP-bound dimers. Here we have compared the ATP-dependent dimerization of DnaK, human stress-inducible Hsp70, Hsc70 and BiP Hsp70 proteins showing that their dimerization propensities differ with stress-inducible Hsp70 being predominantly dimeric in the presence of ATP. The structural analyses using hydrogen/deuterium exchange mass spectrometry, native electrospray ionization mass spectrometry, chemical cross-linking and small-angle X-ray scattering revealed that stress-inducible Hsp70 assembles in solution as an antiparallel dimer with the intermolecular interface closely resembling the ATP-bound dimer interfaces captured in DnaK and BiP crystal structures. ATP-dependent dimerization of stress-inducible Hsp70 is necessary for its efficient interaction with Hsp40 as shown by experiments with dimerization-deficient mutants. Moreover, dimerization of ATP-bound Hsp70 is required for its participation in high molecular weight protein complexes detected ex vivo supporting its functional role in vivo. As human cytosolic Hsp70 has the ability to interact with tetratricopeptide repeat (TPR) domain containing co-chaperones, we tested the interaction of Hsp70 ATP-dependent dimer with Chip and Tomm34 co-chaperones. While Chip associates with intact Hsp70 dimer to form a larger complex, binding of Tomm34 disrupts Hsp70 dimer and this event plays an important role in Hsp70 activity regulation. In summary, this study provides structural evidence of robust ATP-dependent antiparallel dimerization of human inducible Hsp70 protein and suggests novel role of TPR domain co-chaperones in multichaperone complexes involving Hsp70 ATP-bound dimers.

2018-12-11 | PXD010069 | Pride

Comparison of IS5 Deletion mutant to E.coli Motile and NonMotile Isolates

Project description:These series of experiments compares the expression profile of the motility variants of E.coli MG1655 ( Motile and NonMotile isolates) to an isogenic E.coli MG1655 strain in which the IS5 upstream of flhDC has been deleted. The expression profiles of genes in the E.coli MG1655 motile isolate and E.coli MG1655 Non_Motile isolate also compared. Keywords: parallel sample

2005-06-02 | GSE2694 | GEO

The Hsp70 Chaperone System Stabilizes a Thermo-sensitive Subproteome

Project description:Stress-inducible molecular chaperones have essential roles in maintaining protein homeostasis, but the extent to which they affect global proteome stability remains unclear. Here, we analyzed the effects of the DnaK (Hsp70) system on protein stability in Escherichia coli using pulse proteolysis combined with quantitative proteomics. We quantified ~1500 soluble proteins and found ~500 of them to be protease-sensitive under normal growth conditions, indicating a high prevalence of conformationally dynamic states. Acute heat stress resulted in unfolding of an additional ~200 proteins, reflected in exposure of otherwise buried hydrophobic regions. Overexpression of the DnaK chaperone system markedly stabilized most thermo-sensitive proteins, including numerous ribosomal proteins as well as large, hetero-oligomeric proteins that frequently contain the evolutionary ancient c.37 fold (P-loop nucleoside triphosphate hydrolases).

2019-06-24 | PXD012929 | Pride

Comparison of IS5 Deletion mutant to E.coli Motile and NonMotile Isolates

2010-06-09 | E-GEOD-2694 | biostudies-arrayexpress

An essential regulatory function of the DnaK chaperone dictates the decision between proliferation and maintenance in Caulobacter crescentus

Project description:Hsp70 chaperones are well known for their important functions in maintaining protein homeostasis during thermal stress conditions. In many bacteria the Hsp70 homolog DnaK is also required for growth in the absence of stress. The molecular reasons underlying Hsp70 essentiality remain in most cases unclear. Here, we demonstrate that DnaK is essential in the α-proteobacterium Caulobacter crescentus due to its regulatory function in gene expression. Using a suppressor screen we identified mutations in genes coding for different components of the transcriptional machinery as well as an ATP dependent protease that allow growth in the absence of DnaK. These mutations reduced the activity of the heat shock sigma factor σ32 by different mechanisms, suggesting that DnaK's sole essential function in the absence of stress is the inactivation of σ32. We found that σ32 inhibits growth and that its unleashed activity leads to an extensive reprogramming of global gene expression, which re-allocates cellular resources from proliferative to maintenance functions. While this re-allocation provides an advantage during heat stress, it leads to detrimental growth defects under favorable conditions. We conclude that Caulobacter has co-opted the DnaK chaperone system as an essential regulator of gene expression under conditions when its folding activity is dispensable.

2017-12-13 | GSE102372 | GEO

Tyrosine 601 of Bacillus subtilis DnaK undergoes phosphorylation and is crucial for chaperone activity and heat shock survival

Project description:In order to screen for cellular substrates of the Bacillus subtilis BY-kinase PtkA, and its cognate phosphotyrosine-protein phosphatase PtpZ, we performed a triple SILAC-based quantitative phosphoproteome analysis. Detected tyrosine phosphorylation sites for which the phosphorylation level decreased in the ΔptkA strain and increased in the ΔptpZ strain, compared to the wild type, were considered as potential substrates of PtkA/PtpZ. One of those sites was the residue tyrosine 601 of the molecular chaperone DnaK. We confirmed that DnaK is a substrate of PtkA and PtpZ by in vitro phosphorylation and dephosphorylation assays. In vitro, the non-phosphorylatable mutant DnaK Y601F exhibited impaired interaction with its co-chaperones DnaJ and GrpE, along with diminished capacity to hydrolyze ATP and assist the re-folding of denatured proteins. In vivo, loss of DnaK phosphorylation in the mutant strain dnaK Y601F, or in the strain overexpressing the phosphatase PtpZ, led to diminished survival upon heat shock, consistent with the in vitro results. The decreased survival of the mutant dnaK Y601F at an elevated temperature could be rescued by complementing with the wild type dnaK allele expressed ectopically. We concluded that the residue tyrosine 601 of DnaK can be phosphorylated and dephosphorylated by PtkA and PtpZ, respectively. Furthermore, Y601 is important for DnaK chaperone activity and heat shock survival of B. subtilis.

2016-05-09 | PXD003764 | Pride

Heat shock - kin82 mutant and wildtype

Project description:Wild type and kin82 mutant under heat shock. Cells grown at 25°C were collected by centrifugation, resuspended in an equal volume of 37°C medium, and returned to 37°C for growth. Samples were collected at 0, 5, 15, 30 and 60 minutes after transfer to 37°C. Experimental samples were used to generate Cy5-labeled cDNA probes, whereas mRNA reference pools extracted from cultures of the respective strains grown to early log phase under normal conditions, were used to generate Cy3-labeled cDNA probes. Cy5- and Cy3-labeled probes were hybridized together to microarrays printed with PCR-amplified fragments, representing 6280 of the Saccharomyces cerevisiae ORFs. Keywords: time-course

2003-04-15 | GSE406 | GEO

DnaK interaction and folding of firefly luciferase studied by hydrogen/deuterium exchange – mass spectrometry

Project description:The ATP-dependent chaperones of the Hsp70 class (DnaK in E. coli) function in protein folding in cooperation with J proteins and nucleotide exchange factors (DnaJ and GrpE in E. coli, respectively). Hsp70 prevents protein aggregation, increasing the folding yield, but whether it also enhances the rate of folding is unclear. Equilibrium hydrogen/deuterium exchange – mass spectrometry showed that DnaK stabilizes a poorly structured state of firefly luciferase (FLuc). Pulsed-label experiments, together with orthogonal analyses by spFRET, identified compact inter-domain misfolded states of FLuc that convert slowly to the native state. DnaK binding expands the misfolded region and thereby resolves the kinetically-trapped intermediates, with folding occurring upon GrpE-mediated release. By resolving misfolding and accelerating folding the Hsp70 system can maintain proteins in their native states under otherwise denaturing stress conditions.

2020-01-15 | PXD016509 | Pride

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