[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 …

[PDF][PDF] Allosteric feedback inhibition enables robust amino acid biosynthesis in E. coli by enforcing enzyme overabundance

T Sander, N Farke, C Diehl, M Kuntz, T Glatter, H Link - Cell systems, 2019 - cell.com
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 …

[HTML][HTML] Metabolome and proteome analyses reveal transcriptional misregulation in glycolysis of engineered E. coli

CY Wang, M Lempp, N Farke, S Donati… - Nature …, 2021 - nature.com
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 …

[HTML][HTML] Dynamic fluctuations in a bacterial metabolic network

S Bi, M Kargeti, R Colin, N Farke, H Link… - Nature …, 2023 - nature.com
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 …

[HTML][HTML] Systematic identification of metabolites controlling gene expression in E. coli

M Lempp, N Farke, M Kuntz, SA Freibert, R Lill… - Nature …, 2019 - nature.com
Metabolism controls gene expression through allosteric interactions between metabolites
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 …

[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 …

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 …

[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 …

[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 …