PXD055215-1

PXD055215 is an original dataset announced via ProteomeXchange.

Title	Simultaneous Optimization of Multi-lignocellulosic-sugar Catabolism via Systematic Laboratory Evolution in Dynamic Conditions
Description	The development of microbial bioproduction is challenged by the complexity and variability of industrial feedstocks. This study aimed to systematically and simultaneously optimize catabolism of multiple sugars present in common renewable lignocellulose by adaptive laboratory evolution (ALE) using dynamic selection regimes. The engineered strain, JE3692, was subjected to ALE using three dynamic regimes— a high sugar mixture (HSM), low sugar mixture (LSM), and glucose-xylose-arabinose (GXA) series—and was compared with static ALE protocols using individual sugars. Physiological characterization of evolved strains revealed that the LSM strategy yielded the most significant improvements in catabolic efficiency and growth rates under industrially relevant mixed sugar conditions. Genomic analysis identified key mutations in heterologous pathways that contributed to the enhanced catabolism of xylose and arabinose, while proteomic analysis linked these mutations to changes in protein expression profiles in the LSM1 strain. The LSM1 strain demonstrated superior performance in producing the value-added product indigoidine, highlighting the potential of dynamic ALE for developing robust microbial strains for industrial bioproduction using lignocellulosic biomass
HostingRepository	PRIDE
AnnounceDate	2026-06-29
AnnouncementXML	Submission_2026-06-29_09:41:37.896.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: NEWT:160488;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-26 13:53:51	ID requested
⏵ 1	2026-06-29 09:41:38	announced

Dataset with its publication pending

submitter keyword: Pseudomonas putida,Adaptive laboratory evolution (ALE), Proteomics,lignocellulose

Christopher J. Petzold
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. PXD055215
     1. Label: PRIDE project
     2. Name: Simultaneous Optimization of Multi-lignocellulosic-sugar Catabolism via Systematic Laboratory Evolution in Dynamic Conditions