PXD050315

PXD050315 is an original dataset announced via ProteomeXchange.

Title	System-level characterization of engineered and evolved formatotrophic E. coli strains
Description	One carbon compounds like formate provide a promising and sustainable feedstock for microbial bioproduction of fuels and chemicals, as an alternative to the petro-chemical production industry. Growth of Escherichia coli on formate was recently achieved by introducing the reductive glycine pathway (rGlyP) into its genome, which is theoretically the most efficient aerobic formate assimilation pathway. While adaptive laboratory evolution was used to enhance the growth rate and biomass yield significantly, still the best performing formatotrophic E. coli strain did not approach the theoretical optimal biomass yield of the rGlyP. In this study, we investigated the metabolism of these previously engineered formatotrophic E. coli strains in order to elucidate why the biomass yield was sub-optimal and how it may be improved. Through a combination of metabolic modelling and proteomic analysis, we identified several potential metabolic bottlenecks and targets for expression tuning. This characterization study provides insights that can inform future rational engineering efforts to improve the growth of E. coli on formate.
HostingRepository	PRIDE
AnnounceDate	2025-03-10
AnnouncementXML	Submission_2025-03-10_03:07:02.795.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	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-03-04 02:24:20	ID requested
⏵ 1	2025-03-10 03:07:03	announced

Dataset with its publication pending

submitter keyword: metabolic modelling, proteomics,Escherichia coli, C1-assimilation, formate

Timo Glatter
contact affiliation	Max Planck Institute for Terrestrial Microbiology Karl-von-Frisch Str. 10 35043 Marburg Germany
contact email	timo.glatter@mpi-marburg.mpg.de
lab head
Timo Glatter
contact affiliation	Max Planck Institute for Terrestrial Microbiology Marburg
contact email	timo.glatter@mpi-marburg.mpg.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/2025/03/PXD050315

PRIDE project URI

• PRIDE
  1. PXD050315
     1. Label: PRIDE project
     2. Name: System-level characterization of engineered and evolved formatotrophic E. coli strains