PXD001594

PXD001594 is an original dataset announced via ProteomeXchange.

Title	Specific growth rate-dependent proteome resource allocation dynamics in Escherichia coli
Description	Cells usually respond to changing growth conditions with a change in the specific growth rate (μ) and adjustment of their proteome to adapt and maintain metabolic efficiency. Description of the principles behind proteome resource allocation is thus important for understanding metabolic regulation in responce to changing specific growth rate. We analysed the allocation dynamics of Escherichia coli proteome resources into different metabolic processes in response to changing μ. E. coli was grown on minimal and defined rich media in steady state continuous cultures at different μ and characterised by absolute quantitative LC-MS/MS based proteomics. We detected slowly growing cells investing more proteome resources in energy generation and carbohydrate transport and metabolism whereas for achieving faster growth cells needed to devote most resources to translation and processes closely related to the protein synthesis pipeline. Furthermore, down-regulation of energy generation and carbohydrate metabolism proteins with faster growth displayed very similar expression dynamics with the global transcriptional regulator CRP (cyclic AMP receptor protein), pointing to a dominant protein resource allocating role for this protein. Our data also suggest that acetate overflow may be the result of global proteome resource optimisation as cells saved proteome resources by switching from fully respiratory to respiro-fermentative growth. The presented results give a quantitative overview how E. coli adjusts its proteome to achieve faster growthin response to perturbations in μ. Quantitative understanding of proteome resource allocation could contribute to the design of more efficient cell factories through proteome optimisation towards proteins related to target molecule synthesis.
HostingRepository	PRIDE
AnnounceDate	2015-02-27
AnnouncementXML	Submission_2015-02-27_08:15:46.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Karl Peebo
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	methionine oxidation with neutral loss of 64 Da; S-carboxamidomethyl-L-cysteine; N-acetylated residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2014-12-10 02:18:42	ID requested
⏵ 1	2015-02-27 08:15:47	announced

Peebo K, Valgepea K, Maser A, Nahku R, Adamberg K, Vilu R, Proteome reallocation in Escherichia coli with increasing specific growth rate. Mol Biosyst, 11(4):1184-93(2015) [pubmed]

curator keyword: Biological

submitter keyword: E. coli label-free specific growth rate dependent data

Raivo Vilu
contact affiliation	Competence Center of Food and Fermentation Technology
contact email	raivo@tftak.eu
lab head
Karl Peebo
contact affiliation	Fermentation Department
contact email	karl@tftak.eu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD001594
     1. Label: PRIDE project
     2. Name: Specific growth rate-dependent proteome resource allocation dynamics in Escherichia coli