[PDF][PDF] Multi-omics analysis of CRISPRi-knockdowns identifies mechanisms that buffer decreases of enzymes in E. coli metabolism
S Donati, M Kuntz, V Pahl, N Farke, D Beuter, T Glatter… - Cell systems, 2021 - cell.com
Enzymes maintain metabolism, and their concentration affects cellular fitness: high enzyme
levels are costly, and low enzyme levels can limit metabolic flux. Here, we used CRISPR …
levels are costly, and low enzyme levels can limit metabolic flux. Here, we used CRISPR …
[PDF][PDF] Allosteric feedback inhibition enables robust amino acid biosynthesis in E. coli by enforcing enzyme overabundance
Microbes must ensure robust amino acid metabolism in the face of external and internal
perturbations. This robustness is thought to emerge from regulatory interactions in metabolic …
perturbations. This robustness is thought to emerge from regulatory interactions in metabolic …
[HTML][HTML] Metabolome and proteome analyses reveal transcriptional misregulation in glycolysis of engineered E. coli
Synthetic metabolic pathways are a burden for engineered bacteria, but the underlying
mechanisms often remain elusive. Here we show that the misregulated activity of the transcription …
mechanisms often remain elusive. Here we show that the misregulated activity of the transcription …
[HTML][HTML] Dynamic fluctuations in a bacterial metabolic network
The operation of the central metabolism is typically assumed to be deterministic, but dynamics
and high connectivity of the metabolic network make it potentially prone to generating …
and high connectivity of the metabolic network make it potentially prone to generating …
[HTML][HTML] Systematic identification of metabolites controlling gene expression in E. coli
Metabolism controls gene expression through allosteric interactions between metabolites
and transcription factors. These interactions are usually measured with in vitro assays, but …
and transcription factors. These interactions are usually measured with in vitro assays, but …
[HTML][HTML] Systematic analysis of in-source modifications of primary metabolites during flow-injection time-of-flight mass spectrometry
N Farke, T Schramm, A Verhülsdonk, J Rapp… - Analytical …, 2023 - Elsevier
Flow-injection mass spectrometry (FI-MS) enables metabolomics studies with a very high
sample-throughput. However, FI-MS is prone to in-source modifications of analytes because …
sample-throughput. However, FI-MS is prone to in-source modifications of analytes because …
[PDF][PDF] A network approach identifies in-source modifications of primary metabolites during flow-injection mass spectrometry
N Farke, T Schramm, A Verhülsdonk… - … modelling of metabolism … - archiv.ub.uni-marburg.de
7.1 Abstract Flow-injection mass spectrometry (FI-MS) enables metabolomics studies with a
very high sample-throughput. In most FI-MS methods, samples are directly injected into the …
very high sample-throughput. In most FI-MS methods, samples are directly injected into the …
Mathematical modelling of metabolism and enzyme-level regulation to understand and infer functional regulators of metabolism
N Farke - 2022 - archiv.ub.uni-marburg.de
Der mikrobielle Stoffwechsel ist komplex und wird durch Feedback Regulation auf vielen
Ebenen reguliert. Feedback Regulation kann durch Metabolit-Protein Interaktionen ausgeführt …
Ebenen reguliert. Feedback Regulation kann durch Metabolit-Protein Interaktionen ausgeführt …
[PDF][PDF] A network approach identifies in-source modifications of primary metabolites during flow-injection mass spectrometry
T Schramm, N Farke, A Verhülsdonk… - … von Wachstum und … - archiv.ub.uni-marburg.de
Flow-injection mass spectrometry (FI-MS) enables metabolomics studies with a very high
sample-throughput. In most FI-MS methods, samples are directly injected into the electrospray …
sample-throughput. In most FI-MS methods, samples are directly injected into the electrospray …
[PDF][PDF] Acquisition of unknown MS2 fragments for low abundant and unavailable metabolites with CRISPR interference
N Farke, A Verhuelsdonk, H Link - Mathematical modelling of … - archiv.ub.uni-marburg.de
8.1 Abstract To identify metabolites, mass spectrometry-based metabolomics approaches rely
on accurate spectral databases that contain fragment signatures of all metabolites. These …
on accurate spectral databases that contain fragment signatures of all metabolites. These …