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PXD021570 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleGenome-scale metabolic rewiring to improve titers, rates and yields of the non-native non-ribosomal peptide product indigoidine at scale
DescriptionHigh titer, rates, yields (TRY) and scalability are challenging metrics to achieve due to trade-offs between carbon use for growth and production. To achieve these metrics, we took the minimal cut set (MCS) approach that predicts metabolic reactions for elimination to couple metabolite production strongly with growth. We computed MCS solution-sets for a non-native product indigoidine, a sustainable pigment, in Pseudomonas putida KT2440, an emerging industrial microbe. From 63 computed solution-sets, our -omics guided process identified one experimentally feasible solution requiring 14 simultaneous reaction interventions. Using multiplex-CRISPRi, this is the first experimental implementation of a 14-gene MCS-based solution that shifted production from stationary to exponential phase. We achieved 25.6 g/L, 0.22 g/l/h, and ~50% maximum theoretical yield (0.33 g indigoidine/g glucose) TRY respectively. These phenotypes were maintained from batch to fed-batch mode, and across scales (100-ml shake flasks, 250-ml ambrĀ® and 2-L bioreactors).
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterChris Petzold
SpeciesList scientific name: Pseudomonas putida KT2440; NCBI TaxID: 160488;
Instrument6460 Triple Quadrupole LC/MS
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-09-18 14:57:01ID requested
12020-10-24 11:24:25announced
Publication List
Banerjee D, Eng T, Lau AK, Sasaki Y, Wang B, Chen Y, Prahl J-P, Singan VR, Herbert RA, Liu Y, Tanjore D, Petzold CJ, Keasling JD, Mukhopadhyay A. Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale. Nat Commun [Internet]. 2020;11(1):5385. Available from: https://doi.org/10.1038/s41467-020-19171-4
Keyword List
submitter keyword: Metabolic engineering, genome editing
Contact List
Chris Petzold
contact affiliationLawrence Berkeley National Laboratory
contact emailcjpetzold@lbl.gov
lab head
Chris Petzold
contact affiliationLawrence Berkeley National Laboratory
contact emailcjpetzold@lbl.gov
dataset submitter
Full Dataset Link List
Panorama Public dataset URI