Browse
Submit Data
Databases
API
Help

Dataset Information

42 Views

5 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 1013

Shotgun proteome analysis of Bordetella pertussis reveals a distinct influence of iron availability on the bacterial metabolism, virulence, and defense response.

ABSTRACT: Data from ProteomeXchange, PXD ID: PXD001280. File: 120313_O4_YL__Bp_Fe_1.mzml. Published as part of Proteomics. 2015 Mar 9 . From the Abstract: {{i}} One of the mechanisms involved in host immunity is the limitation of iron accessibility to pathogens, which in turn provokes the corresponding physiological adaptation of pathogens. This study reports a gel-free nanoLC-MS/MS-based comparative proteome analysis of Bordetella pertussis grown under iron-excess and iron-depleted conditions ... {{/i}}

INSTRUMENT(S): Instrument

ORGANISM(S): Bordetella_pertussis_tohama_i

DISEASE(S): Not Available

SUBMITTER: Hayes JA, et al.

PROVIDER: GPM32310018525 | GPMDB |

REPOSITORIES: GPMDB

ACCESS DATA

Json Xml

Publications

Shotgun proteome analysis of Bordetella pertussis reveals a distinct influence of iron availability on the bacterial metabolism, virulence, and defense response.

Alvarez Hayes Jimena J Lamberti Yanina Y Surmann Kristin K Schmidt Frank F Völker Uwe U Rodriguez Maria Eugenia ME

Proteomics 20150605 13

One of the mechanisms involved in host immunity is the limitation of iron accessibility to pathogens, which in turn provokes the corresponding physiological adaptation of pathogens. This study reports a gel-free nanoLC-MS/MS-based comparative proteome analysis of Bordetella pertussis grown under iron-excess and iron-depleted conditions. Out of the 926 proteins covered 98 displayed a shift in their abundance in response to low iron availability. Forty-seven of them were found to be increased in l ...[more]

PMID: 25755163

Similar Datasets

Project description:RNA-seq of CAR-Ms and Gel-CAR-Ms

| PRJNA1355556 | ENA

hymenophyllum caudiculatum , hymenophyllum dentatum proteomics

Project description:hymenophyllum caudiculatum , hymenophyllum dentatum proteomics by 2D gel ESI MS/MS

| PRJEB22971 | ENA

Shotgun sequencing data on microplankton at Mar Menor coastal lagoon (SE Spain)

Project description:Mar Menor microplankton metagenomes

| PRJEB108670 | ENA

Episomal S/MAR-based replicons do not alter expression profile of host genome

Project description:Methods: mRNA profiles of untransfected HeLa cells (wild-type; wt) were compared with mRNA profiles of HeLa cells stably maintaining an S/MAR-based episome. Results: We here report for the first time that episomally maintained S/MAR-based vectors do not alter gene expression profile of the host cell's genome. No global changes in gene expression in episome maintaining cells, compared to non-transfected cells could be observed. To identify differentially expressed genes, false discovery rate (FDR; q-value) cut off was set to 0.01. Significantly differentially expressed genes with q<0.01 and an absolute fold-change of 2 were not detected. For verification, we chose five genes with high fold-change and low q-values (q<0.05) and compared expression levels between untransfected HeLa and HeLa stably maintaining an S/MAR-based within three replicates in qPCR. Conclusions: S/MAR-based replicons used in this study do not code for viral proteins but tend to co-localise with promoter sequences and transcription start sites. Recent observations that cooperatively transcribed promoters can influence each other raise concerns that S/MAR-based replicons have the potential to alter endogenous gene expression. Therefore, we compared the transcriptome of untransfected HeLa cells with HeLa cells stably maintaining an S/MAR-based episome. Setting the FDR to <0.01, we found no significantly differentially expressed genes. This finding is of utmost importance for potential gene therapeutic application of S/MAR-based replicons.

2017-09-18 | GSE97725 | GEO

Adapted tolerance to Benzalkonium chloride in E. coli K12

Project description:Benzalkonium chloride (BC) is a commonly used disinfectant and preservative. This study describes changes in expression level on the transcriptomic and proteomic level for Escherichia coli K12 gradually adapted to a tolerance level towards BC of 7-8 times the initial MIC. Results from DNA arrays and two-dimensional (2-DE) gel electrophoresis for global gene and protein expression studies were confirmed by real time quantitative PCR. Peptide mass fingerprinting by MALDI-TOF MS was used to identify differentially expressed proteins. Changes in expression level in adapted cells were shown for porins, drug transporters, glycolytic enzymes, ribosomal subunits and several genes and proteins involved in protection against oxidative stress and antibiotics. Adapted strains showed increased tolerance to several antibiotics. In conclusion, E. coli K12 adapted to higher tolerance to BC, acquired several general resistance mechanisms including responses normally related to the multiple antibiotic resistance (Mar) regulon and protection against oxidative stress. The results revealed that BC treatment might result in superoxide stress in E. coli. Keywords: Study of resistance mechanism

2007-05-23 | GSE6712 | GEO

Host plant shift and acaricide resistance effects on gene expression in the two-spotted spider mite, T. urticae

Project description:The goal of our microarray experiments was twofold: 1) Compare the gene expression profile of acaricide resistant spider mite strains (MAR-AB and MR-VP) with that of a susceptible spider mite strain (London); 2) Study gene expression changes in spider mites from the London strain upon transfer from bean, a suitable host, to tomato, a less favorable host. These gene expression changes upon host change were measured for three timepoints (2 hour on tomato (Tomato-2h), 12 hour on tomato (Tomato-12h) and 5 generations on tomato (Tomato-5G)). 23 samples were analyzed: 6 biological replicates for MR-VP, 5 biological replicates for MAR-AB and four biological replicates each for Tomato-2h, Tomato-12h and Tomato-5G

2012-12-04 | E-GEOD-39869 | biostudies-arrayexpress

Label-free shotgun proteomics of Triton X-100 insoluble fractions of Lon and FtsH conditional mutants of Mycoplasma pneumoniae under depleting and inducing conditions

Project description:Using Mycoplasma pneumoniae as a model organism, we conditionally depleted the two essential ATP-dependent proteases (Lon and FtsH) of this bacterium, by engineering strains carrying a Lon and/or FtsH inducible expression locus. An integrative comparative study combining label-free shotgun proteomics and RNA-seq allowed us to decipher the global cellular response to Lon and FtsH depletion and to define protease substrates in this genome-reduced organism. This particular dataset corresponds to the analysis of the Triton X-100 insoluble fractions of Lon and FtsH mutants grown under inducing and depleting conditions. The dataset for the whole cell lysate is available under the identifier PXD016343.

2020-11-24 | PXD021506 | Pride

Transcriptomic analysis of A. thaliana roots in response to carbenicillin

Project description:A. thaliana plants were grown in 1/2 MS medium in the presence of carbenicillin (10 µg·mL-1) for 1 or 7 days and RNA from their roots extracted and sequenced in Illumina HiSeq 2000/5000 (2x50 bp).

2018-07-19 | GSE113243 | GEO

Comparison of viral RNA–host protein interactomes across pathogenic RNA viruses informs rapid antiviral drug discovery for SARS-CoV-2

Project description:We profiled vRNA-host protein interactomes for three RNA virus pathogens (SARS-CoV-2, Zika, and Ebola viruses) using ChIRP-MS. Comparative interactome analyses discovered both common and virus-specific host responses and vRNA-associated proteins that variously promote or restrict viral infection. In particular, SARS-CoV-2 binds and hijacks the host factor IGF2BP1 to stabilize vRNA and augment translation. Our interactome-informed drug repurposing efforts identified several FDA-approved drugs (e.g., Cepharanthine) as broad-spectrum antivirals in cells and hACE2 mice. A co-treatment comprising Cepharanthine and Trifluoperazine was highly potent against the newly emerged SARS-CoV-2 B.1.351 variant. Thus, our study illustrates the scientific and medical discovery utility of adopting a comparative vRNA-host protein interactome perspective.

2021-10-10 | GSE181866 | GEO

CSF proteome mapping: Human cerebrospinal fluid LC-MS/MS, Part 2

Project description:3 mL CSF from a pool of 21 neurologically healthy donors was separated into a bound and a depleted fraction using a MARS Hu-14 column. This experiment represents the depleted fraction. Gel separation on a gradient gel (SDS-PAGE) followed and the gel lane was cut into 46 fractions. Each fraction was in-gel trypsin digested and analyzed separately by LC-MS/MS on an Orbitrap Velos Pro mass spectrometer. Resulting data was searched using SeachGui, summarized in PeptideShaker and exported to the CSF-PR.

2014-08-04 | PXD000652 | Pride

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