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MetabolomicsEnzyme engineering for optimizing biosynthesis of 2,4-dihydroxybutyric acid via the synthetic threose-dependent glycolaldehyde assimilation (STEGA) pathway
Ethylene glycol is a potential feedstock for next-generation biorefineries, as it can be derived from both plastic waste and carbon dioxide. The synthetic D-threose-dependent glycolaldehyde assimilation (STEGA) pathway, which is orthogonal to central metabolism of Escherichia coli, was recently cons...
2026-07-15 | MTBLS15050 | MetaboLights
ProteomicsAcetylation Coordinates the Crosstalk between Carbon Metabolism and Ammonium Assimilation
Enteric bacteria use up to 15% of their cellular energy for ammonium assimilation via glutamine synthetase (GS)/glutamate synthase (GOGAT) and glutamate dehydrogenase (GDH), in response to low or high ammonium availability. However, the sensory mechanisms for effective and appropriate coordination b...
ORGANISM(S): Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) 
2023-06-21 | PXD039658 | Pride
Ammonium assimilation Acetylation Coordination Carbon metabolism 
TranscriptomicsComparison of root transcriptomes in Arabidopsis thaliana plants supplied with different forms of inorganic nitrogen
Plants aquire nitrogen from the soil, most commonly in the form of either nitrate or ammonium. Unlike ammonium, nitrate must be reduced (with NADH and ferredoxin as electron donors) prior to assimilation. Thus, nitrate nutrition imposes a substantially greater energetic cost than ammonium nutrition....
ORGANISM(S): Arabidopsis thaliana 
2011-05-28 | E-GEOD-29589 | biostudies-arrayexpress
TranscriptomicsTranscriptome analysis of the shoots of Arabidopsis wild-type and ammonium-insensitive mutant plants grown under 10 mM ammonium as sole nitrogen source
Abundant ammonium nutrition impairs plant growth, i.e. ammonium toxicity, the primary cause of which remains to be determined. To obtain a clue about the toxic mechanism, we performed microarray experiments and compared the expression of genes responsive to toxic levels of ammonium between the wild-...
ORGANISM(S): Arabidopsis thaliana 
2021-07-24 | E-MTAB-10796 | biostudies-arrayexpress
TranscriptomicsEnhanced photorespiratory and TCA pathways by elevated CO2 to manage ammonium nutrition in tomato leaves
This work aims to study wether the increment of the atmospheric carbon dioxide (CO2) concentration, in the context of climate change, will potentially allow plants to better face ammonium nutrition. Tomato (Solanum lycopersicum L.) plants were grown for 4 week with 15 mM of nitrogen, supplied as nit...
ORGANISM(S): Solanum lycopersicum 
2024-11-29 | E-MTAB-14587 | biostudies-arrayexpress
TranscriptomicsPseudomonas pseudoalcaligenes CECT5344 response to cyanide vs. ammonium or nitrogen starvation
Transcriptional analysis of the cyanotroph Pseudomonas pseudoalcaligenes CECT5344 in response to cyanide present in wastewaters from industrial activities, such as jewelry and electroplating activities Four-conditions experiment, including three different nitrogen sources (ammonium, sodium cyanide o...
ORGANISM(S): Pseudomonas pseudoalcaligenes CECT 5344 
2016-01-27 | E-GEOD-69930 | biostudies-arrayexpress
ModelsBruggeman2005_AmmoniumAssimilation
This a model from the article: The multifarious short-term regulation of ammonium assimilation of Escherichia coli: dissection using an in silico replica. Bruggeman FJ, Boogerd FC, Westerhoff HV. FEBS J. 2005 Apr;272(8):1965-85. 15819889 ...
2024-09-02 | BIOMD0000000217 | BioModels
TranscriptomicsTranscription profiling of S. cerevisiae wild type and leu3 mutant strains in ethanol-limited and ammonium-limited conditions
Transcriptional regulation of branched-chain amino acid metabolism in Saccharomyces cerevisiae involves two key regulator proteins, Leu3p and Gcn4p. Leu3p is a pathway-specific regulator, known to regulate six genes involved in branched-chain amino acid metabolism and one gene in nitrogen assimilati...
ORGANISM(S): Saccharomyces cerevisiae 
2007-07-07 | E-GEOD-2076 | biostudies-arrayexpress
TranscriptomicsNitrobacter winogradskyi transcriptomic response to ammonia
The comparison was done in chemostats. Cultures maintained nitrite. The transcritome responses were compared at three ammonium concentrations. The comparison was done in chemostats. Single cultures maintained with 60 mM nitrite, and the ammonium supllemented as appropiate.
ORGANISM(S): Nitrobacter winogradskyi 
2015-02-20 | E-GEOD-58053 | biostudies-arrayexpress
ModelsMaeda2019_AmmoniumTransportAssimilation
The E. coli ammonium transport and assimilation network. This SBML model simulates Kim's experiment with glucose as a carbon source and external NH4+ = 4 microM for wild type (the refined active transporter model). SBML does not support some of the functions required for the complete simulations sho...
2019-04-15 | MODEL1901090001 | BioModels
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