Browse
Submit Data
Databases
API
Help

Dataset Information

335 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomics of Nitrospirae - Rice paddy Nitrospirae encode and express genes related to sulfate respiration: proposal of the new genus Candidatus Sulfobium

ABSTRACT: We present the draft genome of Nitrospirae bacterium Nbg-4 as a representative of this clade and couple this to in situ protein expression under sulfate-enriched and sulfate-depleted conditions in rice paddy soil. The proteins were extracted from the soil and analysed via LC-MS/MS measurements.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Bacteria

SUBMITTER: Jana Seifert

LAB HEAD: Jana Seifert

PROVIDER: PXD007817 | Pride | 2018-01-08

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Rice Paddy Nitrospirae Carry and Express Genes Related to Sulfate Respiration: Proposal of the New Genus "Candidatus Sulfobium".

Zecchin Sarah S Mueller Ralf C RC Seifert Jana J Stingl Ulrich U Anantharaman Karthik K von Bergen Martin M Cavalca Lucia L Pester Michael M

Applied and environmental microbiology 20180214 5

Nitrospirae spp. distantly related to thermophilic, sulfate-reducing Thermodesulfovibrio species are regularly observed in environmental surveys of anoxic marine and freshwater habitats. Here we present a metaproteogenomic analysis of Nitrospirae bacterium Nbg-4 as a representative of this clade. Its genome was assembled from replicated metagenomes of rice paddy soil that was used to grow rice in the presence and absence of gypsum (CaSO4·2H2O). Nbg-4 en ...[more]

PMID: 29247059

Similar Datasets

Rice Paddy Nitrospirae Carry and Express Genes Related to Sulfate Respiration: Proposal of the New Genus "Candidatus Sulfobium".

Project description: Not available

| S-EPMC5812927 | biostudies-literature

Parallel protein extraction methods increase the diversity of protein identification in Park Grass Experiment soil

Project description:We have combined a modified protein extraction method, heat/thaw/phenol/chloroform (HTPC), with the established Surfactant extraction method to identify proteins from Park Grass Experiment (PGE) soil, which has an extensively sequenced microbial database.

2022-09-20 | PXD017392 | Pride

Acid sulfate soil, Finland

Project description:Acid sulfate soil, Finland, 16S

| PRJNA433814 | ENA

Global transcriptomic profiling of Desulfovibro vulgaris Hildenborough following transitions between sulfate respiration and syntrophy

Project description:Managing tradeoffs through gene regulation is believed to be critical for the success of a generalist in a fluctuating resource environment. To investigate this hypothesis in depth, we imposed a fluctuating environment that required a representative community of the sulfate-reducing generalist Desulfovibrio vulgaris to manage tradeoffs associated with repeated ecologically-relevant shifts between retaining metabolic independence (active capacity for sulfate respiration) and becoming metabolically specialized to a mutualistic association with the hydrogen consuming Methanococcus maripaludis. Counterintuitively, the community rapidly collapsed and went extinct because extensive gene regulation during shifts drove precipitous decline in intracellular abundance of essential transcripts and proteins. We demonstrate that extensive gene regulation can be catastrophic for a generalist when resources fluctuate rapidly, and that the extinction phenomenon can be prevented by a single regulatory mutation that could then potentially serve as a stepping stone for further adaptive evolution in a variable resource environment. Two strains were profiled at early and mid-log phase of growth during Sulfate Respiration and Syntrophy, and after transition between them. 2 biological replicates, 24 samples

2015-09-17 | E-GEOD-73105 | biostudies-arrayexpress

Global transcriptomic profiling of Desulfovibro vulgaris Hildenborough following transitions between sulfate respiration and syntrophy

2015-09-17 | GSE73105 | GEO

Root transcriptome remodeling of Arabidopsis in response to high levels of magnesium sulfate

2010-09-17 | GSE20109 | GEO

Transcription profiling time series of wheat roots after re-supply of sulfate to sulfate-deficient roots in hydroponic culture

Project description:Transcriptomic study on the effects of resupply of sulfate to sulfate-deficient wheat roots grown in hydroponic culture.

2009-06-26 | E-MEXP-1694 | biostudies-arrayexpress

Thiosulfate vs Sulfate as electron acceptor in Sulfate reduction

Project description:In order to obtain a global view of energy metabolism pathways of the sulfate-reducer Desulfovibrio vulgaris Hildenborough and the proteins involved therein whole-genome microarrays were used to compare the transcriptional response of cells grown with hydrogen/sulfate, pyruvate/sulfate, lactate/thiosulfate, and pyruvate with limiting sulfate, relative to growth in standard lactate/sulfate condition. Growth with hydrogen/sulfate showed the largest number of differently expressed genes and the largest changes in expression levels. The most up-regulated energy metabolism genes were those coding for the periplasmic [NiFeSe] hydrogenase, followed by the Ech hydrogenase, and the most down-regulated were genes coding for the Coo hydrogenase. The results point to the involvement of formate cycling and the ethanol pathway during growth on hydrogen, whereas there is evidence for CO cycling during growth on lactate and pyruvate, but not on H2. Growth with thiosulfate showed the hallmarks of a reduced energy status of the cells with down regulation of the ATP synthase and the Qmo and Dsr complexes., whereas growth with pyruvate showed the smallest differences but an increased role for the Ech hydrogenase.that in this case functions in reverse from the case of growth with H2. The multiple periplasmic hydrogenases and formate dehydrogenases, do not display the same regulation pattern showing that their metabolic roles are not totally interchangeable. This result together with the observation that several genes coding for proteins that have not been biochemically characterised were considerably affected in this study, reveals a more complex energy metabolism than previously considered and provides guidance for further studies. Keywords: Growth protocol

2008-05-31 | GSE8072 | GEO

Acid Sulfate Soil, Vaasa, Finland

Project description:Acid Sulfate Soil, Vaasa, Finland Raw sequence reads

| PRJNA407753 | ENA

Root transcriptome remodeling of Arabidopsis in response to high levels of magnesium sulfate

Project description:Martian regolith (unconsolidated surface material) is a potential medium for plant growth in bioregenerative life support systems during manned missions on Mars. However, hydrated magnesium sulfate mineral levels in the regolith of Mars can reach as high as 10 wt%, and would be expected to be highly inhibitory to plant growth. A global approach was used to identify novel genes with potential to enhance tolerance to high MgSO4 stress. The early Arabidopsis root transcriptome response to elevated concentrations of magnesium sulfate was characterized in col-0, and also between col-0 and the mutant line cax1-1 – a mutant relatively tolerant of high levels of MgSO4•7H2O in soil solution. After 3 weeks of growth under hydroponic conditions, Arabidopsis thaliana col-0 roots were exposed to a basic nutrient solution (0.25 g/L MES, 1/16x MS, pH 5.7) with an additional 2.08 mM magnesium sulfate (total Ca:Mg ratio = 1:15) for 45 min., 90 min., or 180 min., while a col-0 control set was exposed to the basic nutrient solution without additional magnesium sulfate for 45 minutes. Arabidopsis thaliana cax1-1 roots were exposed to the basic nutrient solution with additional magnesium sulfate for 180 min. only. Four replicate containers were harvested for the control and each of the treatment sets, resulting in a total of 20 samples. Gene expression of the col-0 sets exposed to magnesium sulfate treatment for 45 min., 90 min., or 180 min. was compared to gene expression of the col-0 control set. Gene expression of the cax1-1 set exposed to magnesium sulfate treatment for 180 min. was compared to gene expression of the col-0 set exposed to magnesium sulfate treatment for 180 minutes.

2010-09-17 | E-GEOD-20109 | biostudies-arrayexpress

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