PXD011771-2

PXD011771 is an original dataset announced via ProteomeXchange.

Title	Laboratory evolution of Escherichia coli enables life based on fluorinated amino acids
Description	Organofluorine compounds are toxic to various living beings in different habitats. This usher the development of strategies based on the metabolic capacity of various fast-growing microbial strains to evolve an effective adaptation strategy for efficient environmental cleaning. We tackle this problem by trying to answer an essential question: can fluorinated amino acids be used as xenobiotics in general to build up biomass, or do large amounts of fluorine in the cells render them nonviable? To gain information about the effect of long-term exposure of a cellular proteome to fluorine, we constructed an experimental model based on bacterial adaptation in artificial fluorinated habitats. In particular, we propagated Escherichia coli (E. coli) in the presence of either 4- or 5-fluoroindole as essential precursors for the in situ synthesis of tryptophan (Trp) analogues. We found that full adaptation requires astonishingly few genetic mutations but is accompanied by large rearrangements in regulatory networks, membrane integrity and quality control of protein folding. These findings highlight the cellular mechanisms of the evolutionary adaption process and provide the molecular foundation for novel and innovative bioengineering of microbial strains potentially useful in bioaugmentation in fluorine-contaminated areas.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:15:30.213.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ludwig Sinn
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	5'-fluoro-L-tryptophan; 6x(13)C labeled residue; 4'-fluoro-L-tryptophan; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2018-11-21 00:15:34	ID requested
1	2020-11-23 23:08:03	announced
⏵ 2	2024-10-22 05:15:30	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

curator keyword: Biological

submitter keyword: E coli, Fluorine, SILAC, noncanonical, Evolution, Multi-Omics

Juri Rappsilber
contact affiliation	Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany. Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom.
contact email	juri.rappsilber@tu-berlin.de
lab head
Ludwig Sinn
contact affiliation	TU Berlin, Bioanalytics, J. Rappsilber PhD
contact email	l.sinn@tu-berlin.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD011771

PRIDE project URI

• PRIDE
  1. PXD011771
     1. Label: PRIDE project
     2. Name: Laboratory evolution of Escherichia coli enables life based on fluorinated amino acids