PXD022070

PXD022070 is an original dataset announced via ProteomeXchange.

Title	Multi-omics analysis of CRISPRi-knockdowns identifies mechanisms that buffer decreases 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	2020-11-17
AnnouncementXML	Submission_2020-11-17_07:32:29.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

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.

Dataset with its publication pending

submitter keyword: E.coli, Metabolome

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

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PRIDE project URI

• PRIDE
  1. PXD022070
     1. Label: PRIDE project
     2. Name: Multi-omics analysis of CRISPRi-knockdowns identifies mechanisms that buffer decreases of enzymes in E. coli metabolism