代谢组
基因敲除
代谢组学
生物
酶
CRISPR干扰
磷酸戊糖途径
生物化学
代谢途径
基因
清脆的
糖酵解
Cas9
生物信息学
作者
Stefano Donati,Michelle Kuntz,Vanessa Pahl,Niklas Farke,Dominik Beuter,Timo Glatter,José Vicente Gomes-Filho,Lennart Randau,Wang Chunying,Hannes Link
出处
期刊:Cell systems
[Elsevier]
日期:2021-01-20
卷期号:12 (1): 56-67.e6
被引量:36
标识
DOI:10.1016/j.cels.2020.10.011
摘要
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 gene-specific 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.
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