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ProteomicsS. cerevisiae engineered chassis for dicarboxylic acid production
Chassis strain suitable for producing multiple compounds is a central concept in synthetic biology. Design of a chassis using computational, first-principle, models is particularly attractive due to the predictability and control it offers, including against phenotype reversal due to adaptive mutati...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2021-07-20 | PXD020611 | Pride
Yeast Adaptive laboratory evolution Chassis cell 
ProteomicsProteomics for Roseburia intestinalis and Parabacteroides merdae exposed to isosteviol and duloxetine.
The objective of this project was to identify changes in protein expression in R. intestinalis and P. merdae as a response to the treatment with the antidepressant duloxetine, the sweetener isosteviol and a combination of both. 18 samples before and after treatment were collected for each of the two...
ORGANISM(S): Parabacteroides merdae Roseburia intestinalis 
2026-04-30 | PXD045140 | Pride
Proteomics Antidepressant duloxetine Gut bacteria Sweetener isosteviol 
ProteomicsThermal proteome profiling in Clostridium saccharolyticum
We used thermal proteome profiling (TPP) to study the thermostability of Clostridium saccharolyticum in the presence of duloxetine.
ORGANISM(S): [Clostridium] saccharolyticum 
2021-07-01 | PXD016064 | Pride
Clostridium saccharolyticum Duloxetine Thermal proteome profiling 
ProteomicsThermal proteome profiling in Escherichia coli
We used thermal proteome profiling (TPP) to study the thermostability of Escherichia coli strains in the presence of duloxetine.
ORGANISM(S): Escherichia coli 
2021-07-01 | PXD016062 | Pride
Escherichia coli Duloxetine Thermal proteome profiling 
ProteomicsTrait tacking for predictive evolution of metabolic pheotypes
Adaptive laboratory evolution is highly effective for improving desired traits through natural selection. However, its applicability is inherently constrained to growth-correlated traits precluding traits of interest that incur a fitness cost, such as metabolite secretion. Here, we introduce the con...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2022-07-12 | PXD023171 | Pride
Ale s. cerevisiae wine aroma 
ProteomicsBenchmark dataset relating to Kamrad et al "Interspecies interactions drive bacterial proteome reorganisation and emergent metabolism"
Three co-cultures containing gram-positive and -negative species at different ratios (1:1 to 1:9) were measured in quadruplicates, as well as the same number of corresponding mono-cultures. To isolate LC-MS matrix effects in the absence of biological proteome changes, we mixed mono-culture samples i...
ORGANISM(S): Bacteroides thetaiotaomicron Agathobacter rectalis Peptoclostridium difficile (strain 630) (Clostridium difficile) 
2026-02-02 | PXD072524 | Pride
Gut bacteria Synthetic communities Microbiome 
ProteomicsKamrad et al Interspecies interactions drive proteome reorganization and emergent metabolism in gut bacteria"
Inter-species interactions shape the function and dynamics of microbial communities. Yet, the understanding of how these interactions influence the molecular physiology of interacting species remains surprisingly limited. Here, we assembled 104 synthetic pairwise co-cultures of 15 diverse gut bacter...
ORGANISM(S): Phocaeicola vulgatus Segatella copri Bacteroides uniformis Parabacteroides merdae Clostridium sporogenes Bacteroides thetaiotaomicron Bacteria Lactobacillus acidophilus [Clostridium] saccharolyticum Ruminococcus gnavus Lactobacillus gasseri Escherichia coli Collinsella aerofaciens Klebsiella aerogenes Clostridioides difficile Agathobacter rectalis 
2025-05-12 | PXD055395 | Pride
C. difficile Metaproteomics Microbiome 
ProteomicsOperation of a TCA cycle subnetwork in the mammalian nucleus
Nucleic acid and histone modifications critically depend on central metabolism for substrates and co-factors. Although a few enzymes related to the formation of these required metabolites have been reported in the nucleus, the corresponding metabolic pathways are considered to function elsewhere in ...
ORGANISM(S): Homo sapiens (Human) 
2022-10-14 | PXD032918 | Pride
Succinylation Subcellular localisation Lopit Spatial proteomics 
ProteomicsOperation of a TCA cycle subnetwork in the mammalian nucleus
Nucleic acid and histone modifications critically depend on central metabolism for substrates and co-factors. Although a few enzymes related to the formation of these metabolites have been reported in the nucleus, the corresponding metabolic pathways are considered to function elsewhere in the cell....
ORGANISM(S): Homo sapiens (Human) 
2022-10-13 | PXD022608 | Pride
Nucleus Metabolic pathways Proximity-biotinylation mass spectrometry Stable isotope metabolomics study 
ProteomicsOperation of a TCA cycle subnetwork in the mammalian nucleus_mass4tox
Nucleic acid and histone modifications critically depend on central metabolism for substrates and co-factors. Although a few enzymes related to the formation of these required metabolites have been reported in the nucleus, the corresponding metabolic pathways are considered to function elsewhere in ...
ORGANISM(S): Homo sapiens (Human) 
2022-10-14 | PXD032238 | Pride
Tricarboxylic acid (tca) cycle Nuclear proteins Non canonical metabolism compartmentalization Gene expression regulation 
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