Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Metallosphaera cuprina cultivation on sulfur or yeast extract

ABSTRACT: By using heterotrophic proteome as reference, 169 proteins were found to change their abundance during autotrophic growth. The up-regulated proteins indicated that M. cuprina fixed CO2 through the previously identified 3-HB-CoA/4-HB-CoA cycle and obtained energy by oxidation of elemental sulfur as energy source under autotrophic growth. Enzymes/proteins involved in semi- and non-phosphorylating Entner-Doudoroff (ED) pathway were down-regulated. We also found that some transporter proteins changed their abundances, suggest that they were likely playing pivotal roles for growth under the respective conditions.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Metallosphaera

SUBMITTER: Ansgar Poetsch

LAB HEAD: Ansgar Poetsch

PROVIDER: PXD000676 | Pride | 2022-02-22

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	01_leer.RAW	Raw
	020308-01_leer.RAW	Raw
	020308-02_0240.RAW	Raw
	020308-03_5180.RAW	Raw
	020308-04_10180.RAW	Raw

Items per page:

1 - 5 of 101

Publications

Resolution of carbon metabolism and sulfur-oxidation pathways of Metallosphaera cuprina Ar-4 via comparative proteomics.

Jiang Cheng-Ying CY Liu Li-Jun LJ Guo Xu X You Xiao-Yan XY Liu Shuang-Jiang SJ Poetsch Ansgar A

Journal of proteomics 20140714

Metallosphaera cuprina is able to grow either heterotrophically on organics or autotrophically on CO2 with reduced sulfur compounds as electron donor. These traits endowed the species desirable for application in biomining. In order to obtain a global overview of physiological adaptations on the proteome level, proteomes of cytoplasmic and membrane fractions from cells grown autotrophically on CO2 plus sulfur or heterotrophically on yeast extract were compared. 169 proteins were found to change ...[more]

PMID: 25034824

Similar Datasets

M. sedula transcriptional response under "strict" carbon-limited autotrophy compared to carbon "rich" autotrophy and heterotrophy

Project description:Metallosphaera sedula is an extremely thermoacidophilic archaeon that grows heterotrophically on peptides, and chemolithoautotrophically on hydrogen, sulfur, or reduced metals as energy sources. During autotrophic growth, carbon dioxide is incorporated into cellular carbon via the 3-hydroxypropionate /4-hydroxybutyrate cycle (3HP/4HB). To date, all of the steps in the pathway have been connected to enzymes encoded in specific ORFs, except for the one responsible for ligation of coenzyme A (CoA) to 4-hydroxybutyrate (4HB). While several candidates for this step have been identified through bioinformatic analysis of the M. sedula genome, none have been shown to catalyze this biotransformation. Transcriptomic analysis of cells grown under strict H2-CO2 autotrophy was used elucidate additional candidate genes involved in carbon fixation and identify the genes which encode for 4HB-CoA synthetase. Three slide loop for Mse cells includes 3 conditions tested in duplicate (biological repeats from tandem fermentors): autotrophic carbon limited (ACL), autotrophic carbon rich (ACR), and heterotrophic (HTR). Half of an RNA sample for one condition was labeled with Cy3 while the other half was labeled with Cy5. The two differently labeled samples were run on different slides. Each probe is spotted on each slide 5 times (5 replicates; spot intensities for all replicates on slide provided in associated raw data file).

2013-03-05 | E-GEOD-39944 | biostudies-arrayexpress

Project description:Characterization of an Entner-Doudoroff pathway-activated Escherichia coli

| PRJNA818725 | ENA

Characterization of an Entner-Doudoroff pathway-activated Escherichia coli

Project description:Characterization of an Entner-Doudoroff pathway-activated Escherichia coli

| PRJNA818665 | ENA

Functional cooperation of glycine synthase-reductase pathway with Wood-Ljungdahl pathway for autotrophic growth of Clostridium drakei

Project description:The Wood-Ljungdahl pathway in acetogens converts C1 compounds, such as CO2 and CO, into acetyl-CoA. Similarly, the glycine synthase pathway assimilates C1 compounds into glycine. Partial glycine synthase genes are widely conserved in the Wood-Ljungdahl pathway gene cluster but functional relationship between the pathways in autotrophic condition remains unknown. To comprehend, we assembled Clostridium drakei genome (5.7-Mbp) with intact glycine synthase pathway and constructed a genome-scale metabolic model, iSL836, predicting increased metabolic flux rates of the Wood-Ljungdahl pathway and the glycine synthase-reductase associated reactions under autotrophic conditions. Along with the observation of significant transcriptional activation of genes in the pathways, surprisingly, 13C-labeling experiments and enzyme activity assays confirmed the strain synthesizes glycine and converts into acetyl-phosphate. This study suggests the Wood-Ljungdahl and the glycine synthase-reductase pathways convert CO2 into acetyl-CoA and acetyl-phosphate, respectively. In our knowledge, this is the first report on co-utilization of the pathways under autotrophic growth in acetogen.

2019-08-01 | GSE118519 | GEO

Project description:Microorganism of elemental sulfur autotrophic partial denitrification

| PRJNA985111 | ENA

LC-MS/MS of autotrophic culture KS, that performs nitrate reduction coupled to iron(II) oxidation (NDFO)

Project description:Nitrate-reducing iron(II)-oxidizing bacteria are widespread in the environment contribute to nitrate removal and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing iron(II)-oxidizing bacteria is rarely investigated and poorly understood. The most prominent model system for this type of studies is enrichment culture KS, which originates from a freshwater sediment in Bremen, Germany. To gain insights in the metabolism of nitrate reduction coupled to iron(II) oxidation under in the absence of organic carbon and oxygen limited conditions, we performed metagenomic, metatranscriptomic and metaproteomic analyses of culture KS. Raw sequencing data of 16S rRNA amplicon sequencing, shotgun metagenomics (short reads: Illumina; long reads: Oxford Nanopore Technologies), metagenome assembly, raw sequencing data of shotgun metatranscriptomes (2 conditions, triplicates) can be found at SRA in https://www.ncbi.nlm.nih.gov/bioproject/PRJNA682552. This dataset contains proteomics data for 2 conditions (heterotrophic and autotrophic growth conditions) in triplicates.

2021-05-17 | PXD023186 | Pride

Project description:Elemental-sulfur-based autotrophic disproportionation-denitrification (SAD2) process

| PRJNA984429 | ENA

M. sedula transcriptional response under "strict" carbon-limited autotrophy compared to carbon "rich" autotrophy and heterotrophy

2013-03-05 | GSE39944 | GEO

LC-MS/MS of autotrophic culture BP, that performs nitrate reduction coupled to iron(II) oxidation (NDFO)

Project description:Nitrate-reducing iron(II)-oxidizing (NDFO) bacteria are widespread in the environment contribute to nitrate removal and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing iron(II)-oxidizing bacteria is rarely investigated and poorly understood. The most prominent model system for this type of studies is enrichment culture KS, which originates from a freshwater sediment in Bremen, Germany. A second NDFO culture, culture BP, was obtained with a sample taken in 2015 at the same pond and cultured in a similar way. To gain insights in the metabolism of nitrate reduction coupled to iron(II) oxidation under in the absence of organic carbon and oxygen limited conditions, we performed metagenomic, metatranscriptomic and metaproteomic analyses of culture BP. Raw sequencing data of 16S rRNA amplicon sequencing (V4 region with Illumina and near full-length with PacBio), shotgun metagenomics, metagenome assembly, raw sequencing data of shotgun metatranscriptomes (2 conditions, triplicates) can be found at SRA in https://www.ncbi.nlm.nih.gov/bioproject/PRJNA693457. This dataset contains proteomics data for 2 conditions in triplicates. Samples R23, R24, and R25 are grown in autotrophic conditions, samples R26, R27, and R28 in heterotrophic conditions.

2021-05-17 | PXD023710 | Pride

Core metabolism shifts of methanol vs. methane growth in the methanotroph Methylomicrobium buryatense 5GB1

Project description:Methylomicrobium buryatense 5GB1 is an obligate methylotroph, which grows on methane or methanol with similar growth rates. Core metabolic pathways are similar on both substrates, but recent studies of methane metabolism suggest that growth on methanol might have significant differences from growth on methane. In this study, both a targeted metabolomics approach as well as a 13C tracer approach have been taken to understand core carbon metabolism in M. buryatense 5GB1 during methanol growth, to determine whether such differences occur. Targeted metabolomics analyses were performed on both methane and methanol cultures to identify metabolic nodes with altered fluxes. Several key metabolites showed significant differences in pool size. Noticeably, 2-keto-3-deoxy-6-phosphogluconate (KDPG) showed much larger pools under methanol culture, suggesting the Entner-Doudoroff (ED) pathway was more active. Intermediates in other parts of metabolism also showed differences in pool sizes under methanol growth. A systematic shift of active core metabolism is proposed to explain the changes. In order to distinguish flux partition differences at the C3-C4 node, 13C tracer analysis was also applied to methanol-grown cultures. Using the experimental results as constraints, we applied flux balance analysis to determine the metabolic flux phenotype of M. buryatense 5GB1 growing on methanol. The resulting new insights into core metabolism of this methanotroph provide an improved basis for future strain design.

2019-04-17 | GSE110541 | 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