PXD050285

PXD050285 is an original dataset announced via ProteomeXchange.

Title	Multi-Functional Enzymes and Metabolic Cross-Feeding Constrain Implementation of Genome Scale Metabolic Model Based Designs
Description	Genome scale metabolic models (GSMM) are commonly used to identify gene deletion sets that result in growth coupling, pairing product formation with substrate utilization. While such approaches can improve strain performance beyond levels typically accessible using targeted strain engineering approaches, sustainable feedstocks often pose a challenge for GSMM-based methods due to incomplete underlying metabolic data. Specifically, we address a four-gene deletion design for the lignin-derived non-sugar carbon source, para-coumarate, that proved challenging to implement. We examine the performance of the fully implemented design for p-coumarate to glutamine, a useful biomanufacturing intermediate. In this study glutamine is then converted to indigoidine, an alternative sustainable pigment and a model heterologous product. Through omics, promoter-variation and growth characterization of a fully implemented gene deletion design, we provide evidence that aromatic catabolism is rate-limited by a specific fumarate hydratase isomer (PP_0897) in the citrate cycle. A metabolic cross-feeding experiment with the completed design strain reveals broader functions for this enzyme beyond its presumed annotation. Finally, a double sensitivity analysis demonstrates a strict requirement for fumarate hydratase activity in the strain where all genes in the growth coupling design have been implemented. This work highlights the challenge of precisely inactivating metabolic reactions encoded in multifunctional proteins.
HostingRepository	PRIDE
AnnounceDate	2025-03-08
AnnouncementXML	Submission_2025-03-07_19:58:56.404.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	2024-03-02 16:13:41	ID requested
⏵ 1	2025-03-07 19:58:57	announced

10.1038/s41540-024-00480-z;

Banerjee D, Menasalvas J, Chen Y, Gin JW, Baidoo EEK, Petzold CJ, Eng T, Mukhopadhyay A, Addressing genome scale design tradeoffs in Pseudomonas putida for bioconversion of an aromatic carbon source. NPJ Syst Biol Appl, 11(1):8(2025) [pubmed]

submitter keyword: Omics,GSMM, strain engineering

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. PXD050285
     1. Label: PRIDE project
     2. Name: Multi-Functional Enzymes and Metabolic Cross-Feeding Constrain Implementation of Genome Scale Metabolic Model Based Designs