PXD054993-1

PXD054993 is an original dataset announced via ProteomeXchange.

Title	Expanding the biotechnological scope of metabolic sensors through computational-aided designs
Description	Metabolic sensors are microbial strains modified such that biomass formation correlates with the availability of specific target metabolites. These sensors are essential for bioengineering (e.g. in growth-coupled selection of synthetic pathways), but their design is often time-consuming and low-throughput. In contrast, in silico analysis can accelerate their development. We present a systematic workflow for designing, implementing, and testing versatile metabolic sensors using Escherichia coli as a model. Glyoxylate, a key metabolite in synthetic CO2 fixation and carbon-conserving pathways, served as the test molecule. Through iterative screening of a compact metabolic reconstruction, we identified non-trivial growth-coupled designs that resulted in six metabolic sensors with different glyoxylate-to-biomass ratios. These metabolic sensors had a linear correlation between biomass formation and glyoxylate concentration spanning three orders of magnitude and were further adapted for glycolate sensing. We demonstrate the utility of these sensors in pathway engineering (implementing a synthetic route for one-carbon assimilation via glyoxylate) and environmental applications (quantifying glycolate produced by photosynthetic microalgae). The versatility and ease of implementation of this workflow make it suitable for designing and building multiple metabolic sensors for diverse biotechnological applications.
HostingRepository	PRIDE
AnnounceDate	2025-01-16
AnnouncementXML	Submission_2025-01-16_00:16:02.480.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	2024-08-19 05:30:47	ID requested
⏵ 1	2025-01-16 00:16:02	announced

Dataset with its publication pending

submitter keyword: shotgun proteomics,Synthetic microbiology

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/2025/01/PXD054993

PRIDE project URI

• PRIDE
  1. PXD054993
     1. Label: PRIDE project
     2. Name: Expanding the biotechnological scope of metabolic sensors through computational-aided designs