PXD040697

PXD040697 is an original dataset announced via ProteomeXchange.

Title	Ensemble and iterative engineering for maximal bioconversion to the blue pigment, Indigoidine from non-canonical sustainable carbon sources.
Description	While many heterologous molecules can be produced at trace concentrations via microbial bioconversion processes, maximizing their titers, rates, and yields from lignin-derived carbon streams remains challenging. Strong growth coupling can not only increase titers and yields but also shift the production period from stationary phase to growth phase. These methods however require multi-gene edits for implementation which may be initially perceived as impractical. Here, we evaluated 4,114 potential solutions to pair growth on para-coumarate to indigoidine production and prototype two cutsets in Pseudomonas putida KT2440. The implemented design was enhanced using adaptive lab evolution and the resulting strains were characterized for emergent phenotypes. Using x-ray tomography we revealed increased cell density in this strain. Proteomics identified two upregulated peroxidases that mitigate increased reactive oxygen species formation. Nine additional stepwise modifications informed by model-guided and rational approaches realized a growth coupled strain that produced 7.3 g/L indigoidine at 77% yield in minimal salt media. These ensemble strategies provide a blueprint for producing target molecules at high product titers, rates, and yields.
HostingRepository	PRIDE
AnnounceDate	2024-02-29
AnnouncementXML	Submission_2024-02-28_16:11:06.656.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	2023-03-08 17:24:00	ID requested
⏵ 1	2024-02-28 16:11:07	announced

10.1016/J.CELREP.2023.113087;

submitter keyword: emergent cell phenotypes, lignin,Growth coupling, recombineering, proteomics analysis, ALE, bioproduction, heterologous pathway, CRISPR, indigoidine, genome scale metabolic models, strain engineering

Christopher 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. PXD040697
     1. Label: PRIDE project
     2. Name: Ensemble and iterative engineering for maximal bioconversion to the blue pigment, Indigoidine from non-canonical sustainable carbon sources.