Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Elucidating photorespiration pathways in a chemolithoautotroph

ABSTRACT: We investigate photorespiration pathways in the chemoautotroph Cupriavidus necator H16 when growing autotropically on hydrogen and carbon dioxide via the Calvin Cycle. We demonstrate an upregulation of the glycerate pathway under photorespiration (ambient carbon dioxide) conditions

ORGANISM(S): Cupriavidus necator

PROVIDER: GSE141999 | GEO | 2020/01/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Replacing the Calvin cycle with the reductive glycine pathway in Cupriavidus necator

Project description:These data belong to a metabolic engineering project that introduces the reductive glycine pathway for formate assimilation in Cupriavidus necator. As part of this project we performed short-term evolution of the bacterium Cupriavidus necator H16 to grow on glycine as sole carbon and energy source. Some mutations in a putiative glycine transporting systems facilitated growth, and we performed transcriptomics on the evolved strain growing on glycine. Analysis of these transcriptomic data lead us to the discovery of a glycine oxidase (DadA6), which we experimentally demonstrated to play a key role in the glycine assimilation pathay in C. necator.

2020-06-06 | GSE151887 | GEO

RNA-seq of C. necator H16 ΔmmsA123 ΔphaCAB cells grown with and without supplementation of aspartate

Project description:C. necator H16 can grow on aspartate as the sole carbon source. Using RNA-seq analysis here, we tried to identify genes that are overexpressed when the culture medium is supplemented with aspartate.

2022-11-21 | E-MTAB-11897 | biostudies-arrayexpress

Cupriavidus necator H16

Project description:Cupriavidus necator H16 Raw sequence reads

| PRJNA802999 | ENA

Cupriavidus necator H16

Project description:Cupriavidus necator H16 Genome sequencing and assembly

| PRJNA1086218 | ENA

Metabolite interactions in the bacterial Calvin cycle and implications for flux regulation

Project description:Metabolite-level regulation of enzyme activity is important for microbes to cope with environmental shifts. Knowledge of such regulations can also guide strain engineering to improve industrial phenotypes. Recently developed chemoproteomics workflows allow for genome-wide detection of metabolite-protein interactions that may regulate pathway activity. We applied limited proteolysis small molecule mapping (LiP-SMap) to identify and compare metabolite-protein interactions in the proteomes of two cyanobacteria and two lithoautotrophic bacteria that fix CO2 using the Calvin cycle. Clustering analysis of the hundreds of detected interactions showed that some metabolites interacted in a species-specific manner, such as interactions of glucose-6-phosphate in Cupriavidus necator and of glyoxylate in Synechocystis sp.sp PCC 6803. These are interpreted in light of the different central carbon conversion pathways present. Metabolites interacting with the Calvin cycle enzymes fructose-1,6/sedoheptulose-1,7-bisphosphatase (F/SBPase) and transketolase were tested for effects on catalytic activity in vitro. The Calvin cycle intermediate glyceraldehyde-3-phosphate activated both Synechocystis and Cupriavidus F/SBPase, which suggests a feed-forward activation of the cycle in both photoautotrophs and chemolithoautotrophs. In contrast to the stimulating effect in reduced conditions, glyceraldehyde-3-phosphate inactivated the Synechocystis F/SBPase in oxidized conditions by accelerating protein aggregation. Thus, metabolite-level regulation of the Calvin cycle is more prevalent than previously appreciated and may act in addition to redox regulation.

2023-08-23 | PXD044412 | Pride

Cupriavidus necator H16

Project description:Genome sequencing results of Cupriavidus necator H16 mutant.

| PRJNA1162438 | ENA

Comparative RNA-Seq of Cupriavidus necator H16, formerly Ralstonia eutropha H16, grown in minimal media with 3-hydroxypropionic acid (3-HP) or fructose as sole carbon source.

Project description:3-hydroxypropionic acid (3-HP) is a promising platform chemical with various industrial applications. Several metabolic routes to produce 3-HP from organic substrates such as sugars or glycerol have been implemented in yeast, enterobacterial species and other microorganisms. In this work, we investigated 3-HP metabolism of the well-studied ‘Knallgas bacterium’ Cupriavidus necator, a potential C1-chassis for the production of 3-HP and other fatty acid derivatives from CO2 and H2. When testing C. necator for its tolerance towards 3-HP, it was noted that it could utilise the compound as the sole source of carbon and energy.

2019-03-31 | E-MTAB-7701 | biostudies-arrayexpress

Transcriptomic analysis of C. jejuni grown in anaerobic jar with air mix and in Modular Atmospheric Controlled System

Project description:Transcriptomic analysis of C. jejuni HPC5 grown in anaerobic jar supplemented with air mix and in Modular Atmospheric Controlled System (MAC). C. jejuni HPC5 is a Campylobacter strain isolated from broiler chickens. Majority of the Campylobacter strains are cultured in an atmosphere containing 5-10% (v/v) oxygen or 5% hydrogen and 5-10% (v/v) carbon dioxide and the rest with nitrogen. To set up a jar (3.5L, Oxoid) to the required microaerophilic conditions, a vacuum is created to -22 psi and then air mixture of 85% v/v nitrogen, 10% v/v carbon dioxide and 5% v/v hydrogen (Air Products, Crewe, UK) is introduced into the jar. This resulted in a microaerobic atmosphere containing approximately 5.6% oxygen, 3.6% hydrogen, 7.3% carbon dioxide and 83% nitrogen. The Modular Atmospheric Controlled System (MAC; Don Whitely Scientific) is an anaerobic chamber where air mixture of 85% nitrogen, 10% carbon dioxide and 5% oxygen is used for growing Campylobacter. Differences in growth pattern were observed when Campylobacters were grown in it and transcriptomic analysis was done to prove the difference in the regulation of genes in the two conditions.

2011-04-01 | GSE17801 | GEO

Replacing the Calvin cycle with the reductive glycine pathway in Cupriavidus necator

Project description:Replacing the Calvin cycle with the reductive glycine pathway in Cupriavidus necator

| PRJNA637590 | ENA

Effect of oxygen and carbon dioxide on gene expression in Bordetella bronchiseptica strain RB50

Project description:The classical bordetellae (Bordetella pertussis, B. parapertussis, and B. bronchiseptica) are obligate aerobes that use only oxygen as their terminal electron acceptor for electron transport-coupled oxidative phosphorylation. Therefore, access to oxygen is critical for these bacteria to survive. To better understand how B. bronchiseptica changes its gene regulation when faced with different levels of oxygen, we grew liquid cultures of B. bronchiseptica RB50 in ambient air, 5% oxygen, and 2% oxygen. We also measured how the presence of 5% carbon dioxide affected gene expression in these bacteria, since they are respiratory pathogens and therefore get exposed to higher carbon dioxide levels during infection than are found in ambient air.

2024-06-07 | GSE268598 | 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