Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of a transcriptional factor FevR, involved in improving folding in the periplasm of Escherichia coli.

ABSTRACT: DegP (HtrA: High Temperature Requirement A) is a periplasmic protease with minor chaperone activity that plays a key role in the quality control of protein folding in the envelope of Escherichia coli. Periplasmic and outer membrane proteins that fail to fold in the periplasm can be proteolysed, while others are chaperoned to their native folded state by DegP. In a ΔdegP strain, E. coli is unable to survive the protein folding stress induced at 42º C. Utilizing this phenotype, we developed a plasmid-based selection of suppression of heat-induced lethality in a ΔdegP strain. Plasmid libraries of various prokaryotic genomes were screened for proteins that overcame heat-induced lethality. We identified FevR, a putative transcription factor from Citrobacter amalonaticus having close homologs in environmental E. coli capable of overcoming envelope stress. Through genetic characterization, FevR is shown to induce expression of a periplasmic chaperone-proline isomerase fkpA. Over-expression of FkpA alone is sufficient to suppress heat-induced lethality of a ΔdegP strain. This study demonstrates the use of genetic selections to uncover the hidden potential of E. coli to improve its protein folding capacity.

ORGANISM(S): Escherichia coli K-12

PROVIDER: GSE195509 | GEO | 2024/12/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

The role of the periplasmic chaperones SurA, Skp and DegP for fitness, outer membrane integrity, antibiotic susceptibility and virulence of Acinetobacter baumannii AB5075: same-same, but different?

Project description:The outer membrane (OM) of Gram-negative bacteria efficiently protects from harmful environmental stresses such as antibiotics, disinfectants or dryness. Main constituents of the OM are integral OM β-barrel proteins (OMPs). In Gram-negative bacteria such as Escherichia coli (Ec), Yersinia enterocolitica (Ye) and Pseudomonas aeruginosa (Pa), the insertion of OMPs depends on a sophisticated biogenesis pathway. This comprises the SecYEG translocon, which enables inner membrane (IM) passage, the chaperones SurA, Skp and DegP, which facilitate the passage of β-barrel OMPs through the periplasm, and the β-barrel assembly machinery (BAM) which facilitates insertion into the OM. In Ec, Ye and Pa the deletion of SurA is particularly detrimental and leads to a loss of OM integrity, sensitization to antibiotics, and hypovirulence. In search of targets that could be exploited to develop compounds that interfere with OM integrity in Acinetobacter baumannii (Ab), we employed the multidrug-resistant strain AB5075 to generate single gene knockout strains lacking individual periplasmic chaperones. In contrast to Ec, Ye and Pa, AB5075 tolerates the lack of SurA, Skp or DegP with only weak mutant phenotypes. While the double knockout strains surAskp and surAdegP are conditionally lethal in Ec, all double deletions were well tolerated by AB5075. Strikingly, even a triple knockout strain of AB5075, lacking surA, skp and degP, was viable. Our findings underline the extreme adaptibility of Ab and suggest the existence of mechanisms bypassing or acting redundantly to the known OMP biogenesis pathway comprising SurA, Skp and DegP.

2022-08-29 | PXD022004 | Pride

Heat and pressure resistance relates to protein folding and aggregation

Project description:The locus of heat resistance (LHR) confers extreme heat resistance in E. coli. This study explored the role of the LHR in pressure resistance of E. coli, as well as its relationship with protein folding and aggregation in vivo. The role of LHR was investigated in E. coli MG1655 expressing a ibpA-yfp fusion. The expression of proteins by the LHR was determined by mass spectrometry based proteomics; inclusion bodies of untreated and treated cells were also analysed by proteomics, and by observation with fluorescence microscope. In total, 11 proteins of LHR were expressed, including sHSP20, ClpKGI, sHSP, YdfX1 and YdfX2, HdeD, KefB, Trx, PsiE, DegP, and a hypothetical proteins. The proteomic analysis of inclusion bodies revealed a differential abundance of proteins related to oxidative stress in strains carrying the LHR. The LHR reduced the presence of inclusion bodies after heat or pressure treatment, indicating that proteins expressed by the LHR prevent or reverse protein aggregation. The phenotype of the LHR was also mediated by the expression of a fragment containing only sHSP20, ClpKGI, sHSP. The LHR and the fragment encoding only for sHSP20, ClpKGI, sHSP also enhanced pressure resistance in E. coli MG1655 but had no effect on pressure resistance of E. coli LMM1010. In conclusion, the LHR confers pressure resistance to some strains of E. coli, and reduces protein aggregation. Pressure and heat resistance, however, are also dependent on additional LHR-encoded functions.

2020-01-27 | PXD011023 | Pride

E. coli rnpb mutants: wild type proxy strain DW2/pFLP-Ec vs. DW2/pFLP-Bs strain

Project description:Transcriptional profiling of DW2 E. coli cells in exponential growth phase that have a chromosomal deletion of the rnpb gene (which encodes the catalytic subunit of Ribonuclease P). We compared the test strain DW2/pFLP-Bs that expresses Bacillus subtilis rnpb from plasmid pFLP-Bs to reference strain DW2/pFLP-Ec, which expresses E. coli rnpb from plasmid pFLP-Ec.

2013-10-25 | GSE51639 | GEO

DegP Chaperone supression of toxic inner membrane translocation intermediates

Project description:Dataset accompanying manuscript DegP Chaperone supression of toxic inner membrane translocation intermediates in PlosOne RAW files from 6 separate E coli proteomes (LC/MS/MS) analyzed by LFQ in DegP WT and null sequences with induced or uninduced pertactin expression at two separate time points after induction WT E coli Induced pertactin DegP(-) E coli uninduced pertactin DegP(-) E coli induced pertactin (eventually lethal)

2016-08-25 | MSV000080095 | MassIVE

Functional Genomic Study of Exogenous n-Butanol Stress in Escherichia coli

Project description:n-Butanol has been proposed as an alternative biofuel to ethanol, and both Escherichia coli and Saccharomyces cerevisiae have been engineered to produce it. Unfortunately, n-butanol is more toxic than ethanol to these organisms. To understand the basis for its toxicity, cell wide studies were conducted at the transcript, protein and metabolite levels to obtain a global view of the n-butanol stress response. Analysis of the data indicate that n-butanol stress has components common to other stress responses and includes perturbation in respiratory functions (nuo, cyo operons), oxidative stress (sodC, katG, yqhD), heat shock and cell envelope stress (rpoE, clpB, htpG, degP, cpxPR), metabolite transport (malE, opp operon) and biosynthesis. Inducible expression of the yqhD gene was found to improve the hostâs tolerance to exogenous n-butanol and confirms the role of this gene in coping with butanol stress. To survey for other potential candidates that may serve to improve host tolerance, mutant strains in several candidates which show changes at the transcript and protein levels were examined for sensitivity during butanol exposure. Chassis engineering based on these cues may be required in a high production titer, butanol-producing host. This comparison is between E. coli DH1 cells treated with 0.8% n-butanol and untreated cells at 0, 30, 80, and 195 minutes after addition. 3 biological replicates were grown, total RNA was extracted, labeled, and hybridized on 3 slides for each time point. http://www.microbesonline.org/cgi-bin/microarray/viewExp.cgi?expId=1266

2010-05-16 | E-GEOD-16973 | biostudies-arrayexpress

Dynamics of the Escherichia coli proteome in response to the deletion of the Tat pathway

Project description:In Escherichia coli, the Twin-arginine (Tat) secretion system is one of the main routes of the protein export to the periplasm. The Tat pathway secretes a set of proteins with important physiological functions. In our study, we investigated the influence of the deactivation of the Tat pathway on the E. coli cells. We applied a comprehensive and comparative proteomic analysis of the E. coli wild type and tat mutant. This dataset provides mass spectrometry based details on the abundances of proteins in cytoplasmic, periplasmic and membrane fractions. We observed that a tat deletion increases abundances of proteins involved in protein folding, degradation, responses to heat, oxidation, osmolarity, and cold. Moreover, the impairment of E. coli outer membrane resulted in the activation of proteins responsible for cell wall biogenesis. The tat deletion negatively affects the synthesis of iron transporters and imbalances its homeostasis in the cell.

2019-02-18 | PXD008803 | Pride

Control of gene expression by PdeL, a transcription regulator and c-di-GMP phosphodiesterase in Escherichia coli K12

Project description:PdeL is a transcription regulator and c-di-GMP specific phosphodiesterase in Escherichia coli. To address the transcription regulator function of PdeL we analyzed the transcriptomes of four E. coli K12 strains during the exponential growth phase by RNA-sequencing. These four strains included (1) wild-type E. coli K12 strain BW30270 carrying an empty vector control plasmid, (2) an isogenic pdeL deletion mutant carrying the control plasmid, as well as the pdeL mutant that was complemented with (3) a plasmid carrying pdeL under control of the IPTG-inducible tac promoter or (4) a plasmid encoding a fusion protein of the PdeL’s DNA-binding domain and the C-terminal dimerization domain of phage Lambda cI repressor (PdeL-DBD_cI-C). Expression of plasmid-encoded pdeL and pdeL-DBD_cI-C, respectively, was induced by addition of IPTG for 15 minutes prior to RNA isolation. Analyses of the RNA-seq data revealed that plasmid-provided PdeL (and PdeL-DBD_cI-C) repress transcription of class II flagellar genes and presumably regulate the transcription of additional loci, while only little differences were observed between the transcriptomes of wild-type strain BW30270 and its isogenic pdeL mutant.

2020-07-31 | GSE136273 | GEO

Global transcriptional and phenotypic analyseis of Escherichia coli O157:H7 strain Xuzhou21 and its pO157_Sal cured mutant

Project description:Escherichia coli O157:H7 is an important food-borne pathogen that can cause hemorrhagic colitis (HC) and hemolytic-uremic syndrome (HUS) in humans. pO157_Sal, a novel conjugative plasmid is present in a Chinese O157:H7 outbreak strain Xuzhou21. Here we investigated the phenotypic and transcriptional differences between the wild type strain Xuzhou21 and the pO157_Sal cured mutant strain Xuzhou21m. RNA-seq analysis found that all 52 ORFs encoded on pO157_Sal were transcribed. 168 chromosomal and pO157 genes were differentially expressed (M-bM-^IM-%2 fold difference) between Xuzhou21 and Xuzhou21m. Sixty-seven and 101 genes were up-regulated and down-regulated respectively by pO157_Sal including genes related to stress response, adaption and virulence. The plasmid-cured mutant grew slower than wild type in M9 medium under the condition of high NaCl or presence of sodium deoxycholate (NaDC), corroborating with the RNA-seq data. Seven differentially expressed genes are associated with NaDC resistance, including the adenine-specific DNA-methyltransferase gene (dam), multidrug efflux system subunit gene mdtA, hyperosmotically inducible periplasmic protein gene osmY and oxidation-reduction related genes while two differentially expressed genes (osmY and pspD) are likely to be related to resistance to osmotic pressure. A number of differentially expressed genes were virulence associated including four genes encoding T3SS effectors from the chromosome and ehxD from pO157. These findings demonstrated that the plasmid pO157_Sal affects the chromosome and pO157 genes transcription and contributes to the enhanced ability to resist stress. We conclude that pO157_Sal plays an important role in regulating global gene expression and affects virulence and adaptation of E.coli O157:H7. The total mRNA extracted from Escherichia coli O157:H7 Xuzhou21 and its plasmid cured strain Xuzhou21m were sequenced using Illumina.

2013-03-05 | E-GEOD-44846 | biostudies-arrayexpress

The FimZ regulon of E. coli in the stationary phase

Project description:To compare the transcriptional profiling of a FimZ-expressing strain or non-expressing strain in E. coli under stationary phase. For overexpression of fimZ gene was cloned into pBAD33 plasmid under control of the arabinose-inducible PBAD promoter, which was induced by addition of 0.2% arabinose. Goal was to determine the FimZ regulon in E. coli. Biological replicates: 2 replicates.

2021-08-05 | GSE181402 | GEO

Global transcriptional and phenotypic analyseis of Escherichia coli O157:H7 strain Xuzhou21 and its pO157_Sal cured mutant

Project description:Escherichia coli O157:H7 is an important food-borne pathogen that can cause hemorrhagic colitis (HC) and hemolytic-uremic syndrome (HUS) in humans. pO157_Sal, a novel conjugative plasmid is present in a Chinese O157:H7 outbreak strain Xuzhou21. Here we investigated the phenotypic and transcriptional differences between the wild type strain Xuzhou21 and the pO157_Sal cured mutant strain Xuzhou21m. RNA-seq analysis found that all 52 ORFs encoded on pO157_Sal were transcribed. 168 chromosomal and pO157 genes were differentially expressed (≥2 fold difference) between Xuzhou21 and Xuzhou21m. Sixty-seven and 101 genes were up-regulated and down-regulated respectively by pO157_Sal including genes related to stress response, adaption and virulence. The plasmid-cured mutant grew slower than wild type in M9 medium under the condition of high NaCl or presence of sodium deoxycholate (NaDC), corroborating with the RNA-seq data. Seven differentially expressed genes are associated with NaDC resistance, including the adenine-specific DNA-methyltransferase gene (dam), multidrug efflux system subunit gene mdtA, hyperosmotically inducible periplasmic protein gene osmY and oxidation-reduction related genes while two differentially expressed genes (osmY and pspD) are likely to be related to resistance to osmotic pressure. A number of differentially expressed genes were virulence associated including four genes encoding T3SS effectors from the chromosome and ehxD from pO157. These findings demonstrated that the plasmid pO157_Sal affects the chromosome and pO157 genes transcription and contributes to the enhanced ability to resist stress. We conclude that pO157_Sal plays an important role in regulating global gene expression and affects virulence and adaptation of E.coli O157:H7.

2013-03-05 | GSE44846 | GEO

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