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Multi-omics analysis of CRISPRi-knockdowns identifies mechanisms that buffer decreases of enzymes in E. coli metabolism

MPG-Autoren
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Donati,  Stefano
Emmy Noether Research Group Dynamic Control of Metabolic Networks, Alumni, Max Planck Institute for Terrestrial Microbiology, Max Planck Society;

Kuntz,  Michelle
external;
Emmy Noether Research Group Dynamic Control of Metabolic Networks, Max Planck Institute for Terrestrial Microbiology, Max Planck Society;

Pahl,  Vanessa
external;
Emmy Noether Research Group Dynamic Control of Metabolic Networks, Max Planck Institute for Terrestrial Microbiology, Max Planck Society;

Farke,  Niklas
external;
Emmy Noether Research Group Dynamic Control of Metabolic Networks, Max Planck Institute for Terrestrial Microbiology, Max Planck Society;

/persons/resource/persons254138

Beuter,  Dominik
Emmy Noether Research Group Dynamic Control of Metabolic Networks, Max Planck Institute for Terrestrial Microbiology, Max Planck Society;

/persons/resource/persons261236

Glatter,  Timo
Core Facility Mass Spectrometry and Proteomics, Max Planck Institute for Terrestrial Microbiology, Max Planck Society;

Gomes-Filho,  Jose Vicente
external;
Max Planck Research Group Prokaryotic small RNA Biology, Alumni, Max Planck Institute for Terrestrial Microbiology, Max Planck Society;

/persons/resource/persons254626

Randau,  Lennart
Max Planck Research Group Prokaryotic small RNA Biology, Alumni, Max Planck Institute for Terrestrial Microbiology, Max Planck Society;

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Wang,  Chun-Ying
Emmy Noether Research Group Dynamic Control of Metabolic Networks, Alumni, Max Planck Institute for Terrestrial Microbiology, Max Planck Society;

/persons/resource/persons254499

Link,  Hannes
Emmy Noether Research Group Dynamic Control of Metabolic Networks, Max Planck Institute for Terrestrial Microbiology, Max Planck Society;

Externe Ressourcen

https://doi.org/10.1016/j.cels.2020.10.011
(Verlagsversion)

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Zitation

Donati, S., Kuntz, M., Pahl, V., Farke, N., Beuter, D., Glatter, T., et al. (2021). Multi-omics analysis of CRISPRi-knockdowns identifies mechanisms that buffer decreases of enzymes in E. coli metabolism. Cell Systems, 12(1), 56-67.E6. doi:10.1016/j.cels.2020.10.011.


Zitierlink: https://hdl.handle.net/21.11116/0000-0008-BE10-0
Zusammenfassung
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 interference (CRISPRi) to study the
consequences of decreasing E coli enzymes below wild-type levels. A
pooled CRISPRi screen with 7,177 strains demonstrates that metabolism
buffers fitness defects for hours after the induction of CRISPRI. We
characterized the metabolome and proteome responses in 30 CRISPRi
strains and elucidated three genespecific buffering mechanisms:
ornithine buffered the knockdown of carbamoyl phosphate synthetase
(CarAB) by increasing CarAB activity, S-adenosylmethionine buffered the
knockdown of homocysteine transmethylase (MetE) by de-repressing
expression of the methionine pathway, and 6-phosphogluconate buffered
the knockdown of 6-phosphogluconate dehydrogenase (Gnd) by activating a
bypass. In total, this work demonstrates that CRISPRi screens can reveal
global sources of metabolic robustness and identify local regulatory
mechanisms that buffer decreases of specific enzymes. A record of this
paper's transparent peer review process is included in the Supplemental
Information.