PXD054609

PXD054609 is an original dataset announced via ProteomeXchange.

Title	Adaptive lab evolution and omics characterization enable tolerance engineering of Pseudomonas putida KT2440 to produce the jet-fuel precursor isoprenol
Description	Pseudomonas putida KT2440 (KT2440) has been established as an industrially relevant chassis for the production of the jetfuel precursor isoprenol. However, this strain assimilated isoprenol as sole carbon source and also showed impaired growth at isoprenol concentrations > 2 g/L which is a significant impediment to high TRY production. In this study, we used tolerization adaptive laboratory evolution and functional genomics to demonstrate improved growth of KT2440 strains in the presence of up to 8 g/L isoprenol. DNA sequencing of the evolved strains revealed mutations – a combination of SNPs and large deletions acquired in response to both isoprenol and a trace formaldehyde impurity. Mutations associated to isoprenol tolerance in the evolved isolates were specific to SNPs in the transcriptional regulators gnuR, xxxR and xxxR and two large deletions in the regions that also encoded the multidrug efflux pump TtgABC and certain phage proteins. Proteomic analysis of selected evolved strains implied a concerted detoxification process for isoprenol and formaldehyde even in the absence of the offending trace contaminant. The evolved strains also activated different pathways to enhanced tolerance. These included either upregulation of a global stringent response regulator SpoT in one or by the action of multiple alcohol and other dehydrogenases
HostingRepository	PRIDE
AnnounceDate	2025-05-28
AnnouncementXML	Submission_2025-05-28_10:31:16.605.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christopher Petzold
SpeciesList	scientific name: Pseudomonas putida KT2440; NCBI TaxID: 160488;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-05 14:55:20	ID requested
⏵ 1	2025-05-28 10:31:17	announced

10.1016/j.ymben.2025.05.007;

Lim HG, Srinivasan A, Menchavez R, Yunus IS, Noh MH, White M, Chen Y, Gin JW, Palsson BO, Lee TS, Petzold CJ, Eng T, Mukhopadhyay A, Feist AM, Evolution-guided tolerance engineering of Pseudomonas putida KT2440 for production of the aviation fuel precursor isoprenol. Metab Eng, 91():322-335(2025) [pubmed]

submitter keyword: Pseudomonas putida, sustainable aviation fuel, isoprenol,Adaptive laboratory evolution, tolerance engineering

Christopher J.
contact affiliation	Staff Scientist Biological Systems & Engineering Division Lawrence Berkeley National Laboratory Berkeley CA 94720
contact email	cjpetzold@lbl.gov
lab head
Christopher Petzold
contact affiliation	Lawrence Berkeley National Laboratory
contact email	cjpetzold@lbl.gov
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD054609
     1. Label: PRIDE project
     2. Name: Adaptive lab evolution and omics characterization enable tolerance engineering of Pseudomonas putida KT2440 to produce the jet-fuel precursor isoprenol