PXD047537

PXD047537 is an original dataset announced via ProteomeXchange.

Title	Synthetically primed adaptation of Pseudomonas putida to a non-native substrate D-xylose
Description	To broaden microbial cell factories´ substrate scope towards renewable substrates, rational genetic interventions are often combined with adaptive laboratory evolution (ALE). However, comprehensive studies enabling a holistic understanding of adaptation processes primed by detailed knowledge of metabolism remain scarce, especially for non-model organisms. The industrial workhorse Pseudomonas putida was engineered to utilize the non-native sugar D-xylose, but its assimilation into the bacterial biochemical network via the exogenous pathway remained unresolved. Here, we elucidated the xylose metabolism and established a foundation for further engineering followed by ALE. By de-repressing native glycolysis, we unlocked the route for xylose-derived carbon and obtained a strain with a substantially reduced lag phase on xylose. We then enhanced the pentose phosphate pathway in two lag-shortened strains and allowed ALE to fine-tune the rewired metabolism. Following the metabolism tuning, we employed multi-level analysis that provided unique insights into the parallel paths of bacterial adaptation to the non-native carbon source.
HostingRepository	PRIDE
AnnounceDate	2024-03-06
AnnouncementXML	Submission_2024-03-06_01:34:41.409.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Katerina Hanakova
SpeciesList	scientific name: Pseudomonas putida KT2440; NCBI TaxID: 160488;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-12-05 05:29:32	ID requested
⏵ 1	2024-03-06 01:34:41	announced

Dataset with its publication pending

submitter keyword: Pseudomonas putida, LC-MS/MS

Zbynek Zdrahal
contact affiliation	Proteomics Core Facility and Research Group Proteomics, CEITEC-MU, Masaryk University, Brno, Czech Republic
contact email	zdrahal@sci.muni.cz
lab head
Katerina Hanakova
contact affiliation	CEITEC MU
contact email	katerina.hanak@gmail.com
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/2024/03/PXD047537

PRIDE project URI

• PRIDE
  1. PXD047537
     1. Label: PRIDE project
     2. Name: Synthetically primed adaptation of Pseudomonas putida to a non-native substrate D-xylose