PXD022070 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | The metabolome buffers CRISPRi-knockdowns of enzymes in E. coli metabolism |
Description | Enzymes maintain metabolism and their concentration affects cellular fitness. High enzyme-levels are costly, but low enzyme-levels can limit metabolic flux. Here, we used CRISPR interference (CRISPRi) to study the consequences of decreasing metabolic enzymes in E. coli below wild-type levels. A time-resolved competition assay with a metabolism-wide CRISPRi library showed that fitness defects appeared late after induction of knockdowns. This suggested that metabolism is robust against decreases of enzymes. The metabolome and proteome of 30 CRISPRi strains revealed the mechanisms that enabled this robustness. First, substrates and allosteric effectors buffered knockdowns by increasing the activity of target-enzymes. Later, metabolite-transcription interactions compensated knockdowns by upregulating the target-pathway or bypass-pathways. For example, we found a new regulation strategy in which 6-phosphogluconate is responsible for bypassing bottlenecks in the pentose-p pathway via the Entner-Doudoroff-pathway. Thus, regulatory metabolites buffer decreases of enzyme-levels, which can occur in nature due to expression noise, mutations or environmental conditions. |
HostingRepository | PRIDE |
AnnounceDate | 2020-10-20 |
AnnouncementXML | Submission_2020-10-19_22:27:55.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Timo Glatter |
SpeciesList | scientific name: Escherichia coli; NCBI TaxID: 562; |
ModificationList | No PTMs are included in the dataset |
Instrument | Q Exactive Plus |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2020-10-19 03:54:38 | ID requested | |
⏵ 1 | 2020-10-19 22:27:55 | announced | |
2 | 2020-11-17 07:32:30 | announced | 2020-11-17: Updated project metadata. |
Publication List
Dataset with its publication pending |
Keyword List
submitter keyword: E.coli, Metabolome |
Contact List
Timo Glatter |
contact affiliation | Max Planck Institute for terrestrial Microbiology Karl von Frisch Str. 10 35043 Marburg Germany |
contact email | glatter@mpi-marburg.mpg.de |
lab head | |
Timo Glatter |
contact affiliation | MPI Marburg |
contact email | glatter@mpi-marburg.mpg.de |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD022070
- Label: PRIDE project
- Name: The metabolome buffers CRISPRi-knockdowns of enzymes in E. coli metabolism