Browse
Submit Data
Databases
API
Help

Dataset Information

230 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effect of nitroprusside on the proteomic expression of Desulfovibrio vulgaris Hildenborough

ABSTRACT: In this study, the effect of nitroprusside on protein expression of the model sulfate reducing bacterial isolate (Desulfovibrio vulgaris Hildenborough) was investigated. Three different experiments were done with different exposure time to nitroprusside (30 min, 1 hour, and 3 hours). In each experiment, the culture was grown in quadruplet of serum bottles containing 40 ml complex medium (Postgate medium B) under anaerobic condition at 30oC. At mid-log growth phase, each of the quadruplet culture was divided into two (20 ml each) and nitroprusside (0.25 mM) was added to one of each bottle while the other bottles were used as controls. After 30 min, 1 hour, and 3 hours of exposure to nitroprusside, the culture (1 ml) was pelleted and used for proteomic analysis.

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Desulfovibrio Vulgaris Str. Hildenborough

SUBMITTER: Maryam Ataeian

LAB HEAD: Gerrit Voordouw

PROVIDER: PXD007623 | Pride | 2018-05-17

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Synergy of Sodium Nitroprusside and Nitrate in Inhibiting the Activity of Sulfate Reducing Bacteria in Oil-Containing Bioreactors.

Fida Tekle T TT Voordouw Johanna J Ataeian Maryam M Kleiner Manuel M Okpala Gloria G Mand Jaspreet J Voordouw Gerrit G

Frontiers in microbiology 20180516

Sodium nitroprusside (SNP) disrupts microbial biofilms through the release of nitric oxide (NO). The actions of SNP on bacteria have been mostly limited to the genera Pseudomonas, Clostridium, and Bacillus. There are no reports of its biocidal action on sulfate-reducing bacteria (SRB), which couple the reduction of sulfate to sulfide with the oxidation of organic electron donors. Here, we report the inhibition and kill of SRB by low SNP concentrations [0.05 mM (15 ppm)] depe ...[more]

PMID: 29867883

Similar Datasets

Proteomes of twenty bacterial, archaeal and eukaryotic species for bench marking of Direct Protein-SIF (stable carbon isotope fingerprinting proteomics)

Project description:We developed a method that allows measuring the stable carbon isotope composition of individual species in microbial communities using metaproteomics. We call this methods “Direct Protein-SIF”. To benchmark this method, we measured twenty pure culture species using the Direct Protein-SIF method as well as Isotope Ratio Mass Spectrometry. Some of the pure cultures were measured in technical replicates to see how consistent Protein-SIF measurements are between mass spec runs. This submission thus contains 29 raw files for the pure cultures. See table in the submission for details of which species was measured for which .raw file. We also included the Direct Protein-SIF specific isotope pattern files as well as the .mzML files and PSM files required as input for the Direct Protein-SIF software. In addition to the pure culture a protein reference material (MKH files) was measured. The respective .raw files and isotopic pattern files are also included in this submission (see publication for details on how the reference material is used to calibrate the method).

2018-05-21 | PXD006762 | Pride

Labeling of Bacillus subtilis and Escherichia coli to saturation with different percentages of 13C2 labeled glucose for benchmarking of protein-based stable isotope probing proteomics (Protein-SIP)

Project description:This dataset is part of a study aimed at developing algorithms for the quantification of stable isotope content in microorganisms after labeling them with stable isotope-labeled substrates. In this dataset Escherichia coli and Bacillus subtilis cultures were labeled with different percentages of single-carbon 13C glucose (13C2). Cultures of B. subtilis and E. coli were grown in Bacillus minimal medium or M9 minimal medium (E. coli) in which a percentage of the glucose was replaced with 13C2 glucose for >10 generations to achieve close to complete labeling of cells. The following percentages of 13C2 glucose were added 0, 0.01, 0.025, 0.1, 0.25, 1, 5 and 10%. Triplicate cultures were grown for each percentage. Please note that the unlabeled glucose that was used of course had a natural content of 13C of around 1.1%, thus the 0% added label samples have an actual 13C content of 1.1% and all added label is on top of this value. We included a tab delimited table with this submission providing details on all raw files.

2022-12-30 | PXD024285 | Pride

Mixing of Escherichia coli cells labeled with 13C glucose with unlabeled E. coli cells for benchmarking of protein-based stable isotope probing proteomics (Protein-SIP)

Project description:This dataset is part of a study aimed at developing algorithms for the quantification of stable isotope content in microorganisms after labeling them with stable isotope-labeled substrates. In this dataset Escherichia coli cultures were labeled with different percentages (1% or 10%) of either single-carbon 13C glucose (13C2) or fully-labeled 13C glucose (13C1-6). Labeled cells were subsequently mixed with unlabeled E. coli cells in fixed ratios (50%, 90%, 95%, 99%). Cultures of E. coli were grown in M9 minimal medium in which a percentage of the glucose was replaced with 13C2 or 13C1-6 glucose for >10 generations to achieve close to complete labeling of cells. Triplicate cultures were grown for each percentage. Please note that the unlabeled glucose that was used of course had a natural content of 13C of around 1.1%, thus the 0% added label samples have an actual 13C content of 1.1% and all added label is on top of this value. We included a tab delimited table with this submission providing details on all raw files.

2022-12-30 | PXD024287 | Pride

Labeling of Bacillus subtilis and Escherichia coli to saturation with different percentages of fully 13C labeled glucose for benchmarking of protein-based stable isotope probing proteomics (Protein-SIP)

Project description:This dataset is part of a study aimed at developing algorithms for the quantification of stable isotope content in microorganisms after labeling them with stable isotope-labeled substrates. In this dataset Escherichia coli and Bacillus subtilis cultures were labeled with different percentages of fully labeled 13C glucose (13C6). Cultures of B. subtilis and E. coli were grown in Bacillus minimal medium or M9 minimal medium (E. coli) in which a percentage of the glucose was replaced with 13C6 glucose for >10 generations to achieve close to complete labeling of cells. The following percentages of 13C6 glucose were added 0, 0.01, 0.025, 0.1, 0.25, 1, 5 and 10%. Triplicate cultures were grown for each percentage. Please note that the unlabeled glucose that was used of course had a natural content of 13C of around 1.1%, thus the 0% added label samples have an actual 13C content of 1.1% and all added label is on top of this value. We included a tab delimited table with this submission providing details on all raw files.

2022-12-30 | PXD023693 | Pride

Mock microbial community with spike-ins of 13C-labeled Escherichia coli cells for benchmarking of protein-based stable isotope probing proteomics (Protein-SIP)

Project description:This dataset is part of a study aimed at developing algorithms for the quantification of stable isotope content in microorganisms in microbial communities after labeling them with stable isotope-labeled substrates. For this dataset Escherichia coli cultures were labeled with different percentages (1, 5 and 10%) of fully labeled 13C glucose (13C1-6) and spiked-in into a mock microbial community consisting of 32 species of bacteria, archaea, eukaryote and bacteriophages (UNEVEN Community described in Kleiner et al. 2017 Nat Communications 8(1):1558). The community also contained unlabeled E. coli cells and labeled/unlabeled E. coli cells in the spike-in sample were at a 1:1 ratio. Cultures of E. coli were grown in M9 minimal medium in which a percentage of the glucose was replaced with 13C1-6 glucose for >10 generations to achieve close to complete labeling of cells. The following percentages of 13C1-6 glucose were added 1, 5 and 10%. Triplicate cultures were grown for each percentage. Please note that the unlabeled glucose that was used of course had a natural content of 13C of around 1.1%, thus the 0% added label samples have an actual 13C content of 1.1% and all added label is on top of this value. We included a tab delimited table with this submission providing details on all raw files.

2022-12-30 | PXD024174 | Pride

Optimization of protein extraction methods for root-associated microbes in Arabidopsis

Project description:The goal of this study was to optimize protein extraction methods to study root-associated bacteria in Arabidopsis. For this we inoculated Arabidopsis seedlings grown in agar plates with a synthetic community (SynSom) composed of four different strains (Variovorax paradoxus, Arthrobacter sp, Agrobacterium sp. and Pseudomonas sp.. Twelve days after inoculation we extracted proteins from the roots using six different protein extraction methods each in triplicates. These methods were a combination of different extraction buffers (SDS or Triton-based) and mechanical disruption methods (bead-beating, N2 grinding, glass homogenizer and freeze-thaw cycles) We found that bead-beating the roots with lysing matrix E in SDT lysis buffer yielded the highest numbers of microbial protein identification and enhanced the detection of proteins derived from gram positive bacteria.

2022-09-08 | PXD026330 | Pride

Quantification of mock microbial communities with metagenomes, 16S rRNA gene amplicons and metaproteomics

Project description:In this study we developed metaproteomics based methods for quantifying taxonomic composition of microbiomes (microbial communities). We also compared metaproteomics based quantification to other quantification methods, namely metagenomics and 16S rRNA gene amplicon sequencing. The metagenomic and 16S rRNA data can be found in the European Nucleotide Archive (Study number: PRJEB19901). For the method development and comparison of the methods we analyzed three types of mock communities with all three methods. The communities contain between 28 to 32 species and strains of bacteria, archaea, eukaryotes and bacteriophage. For each community type 4 biological replicate communities were generated. All four replicates were analyzed by 16S rRNA sequencing and metaproteomics. Three replicates of each community type were analyzed with metagenomics. The "C" type communities have same cell/phage particle number for all community members (C1 to C4). The "P" type communities have the same protein content for all community members (P1 to P4). The "U" (UNEVEN) type communities cover a large range of protein amounts and cell numbers (U1 to U4). We also generated proteomic data for four pure cultures to test the specificity of the protein inference method. This data is also included in this submission.

2017-05-12 | PXD006118 | Pride

Transcription profiling of G sulfurreducens GGS nitrogen fixation

Project description:G. sulfurreducens (ATCC #51573) was obtained from the laboratory culture collection of Dr. Derek Lovley. Cells were grown under strict anaerobic conditions at 30 °C in chemostats, as previously described (for more information see Esteve-Núñez, A., M. M. Rothermich, M. Sharma, and D. R. Lovley. 2004. Growth of Geobacter sulfurreducens under nutrient-limiting conditions in continuous culture. Environ. Microbiol.:in press.), with acetate (5 mM) as the electron donor and fumarate (27.5 mM) as the electron acceptor. For growth in the absence of fixed nitrogen, the ammonium chloride (4.7 mM) was omitted from the medium and fumarate served as the electron acceptor. Therefore, cultures with ammonium chloride were limited by acetate while cultures without ammonium chloride were limited by nitrogen. Cultures were maintained at a dilution rate of 0.05 h-1 for 5 culture vessel volumes to ensure that cells were at steady-state prior to harvesting. Cells were harvested by centrifugation at 4 °C and the cell pellet was flash-frozen in liquid nitrogen and then stored at -80 °C prior to RNA extraction. Cells grown in the absence of ammonium had acetylene reduction rates of 0.012 nmol/hr compared to 0.003 nmol/hr in ammonium-grown cells, providing evidence that these cells were fixing nitrogen.. The steady-state concentration of cells in the nitrogen-fixing chemostats (0.178 mg/mL + 0.011; mean + standard deviation, n=3) was significantly lower than chemostats provided with ammonium (0.45 mg/mL + 0.007). Three cultures of acetate limited growth with fumarate as the electron acceptor and three cultures of nitrogen limited growth with fumarate as the electron acceptor were grown. Each culture vessel was harvested and extracted for total RNA separately to produce three biological replicates for this experiment.

2005-01-01 | E-TIGR-82 | biostudies-arrayexpress

Labeling Escherichia coli to saturation with 2.5 % of 15N ammonium in two conditions (aerobic and anaerobic) for benchmarking of protein-based stable isotope probing proteomics (Protein-SIP)

Project description:This dataset is part of a study aimed at developing algorithms for the quantification of stable isotope content in microorganisms after labeling them with stable isotope-labeled substrates. For this dataset Escherichia coli cultures were labeled with 2.5 % of 15N-labeled NH4Cl and grown either anaerobically or aerobically. Cultures of E. coli were grown in M9 minimal medium in which 2.5 % of the ammonium was replaced with 15N-labeled NH4Cl for >10 generations to achieve close to complete labeling of cells. Triplicate cultures were grown. Please note that the unlabeled ammonium that was used of course had a natural content of 15N of around 0.4 %, thus the 0% added label samples have an actual 15N content of 0.4 % and all added label is on top of this value. We included a tab delimited table with this submission providing details on all raw files.

2022-02-16 | PXD024288 | Pride

Proteomics of Ca. Riegeria standrea – the chemosynthetic symbionts of the marine flatworm Paracatenula from the Bay of Sant´Andrea (Elba, Italy)

Project description:Paracatenula are marine catenulid flatworms occuring in shallow water sediments. Adult Paracatenula lack a mouth and a digestive system. Instead, a trophosome containing intracellular alphaproteobacterial symbionts, namely Ca. Riegeria fill most of the worm´s body (Gruber-Vodicka et al., 2011). Paracatenula sp. ‘standrea’ that harbor Ca. Riegeria sp. 812A (standrea) were sampled in Elba, Italy in April 2016. Based on the genome of Ca. Riegeria sp. 812A (standrea) we discovered a versatile combination of storage and biosynthesis and a convergence with unrelated intracellular thiotrophic symbionts. Proteomic analyses were performed to investigate which symbiont genes related to the host nutrition were expressed.

2019-03-26 | PXD009856 | 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