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PXD011350 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleMassively parallel fitness profiling reveals multiple novel enzymes in Pseudomonas putida lysine metabolism
DescriptionThe lysine metabolism of Pseudomonas putida can produce multiple important commodity chemicals and is implicated in rhizosphere colonization. However, despite intensive study, the biochemical and genetic links between lysine metabolism and central metabolism remains unresolved in P. putida. Here, we leverage Random Barcode Transposon Sequencing (RB-TnSeq), a genome-wide assay measuring the fitness of thousands of genes in parallel, to identify multiple novel enzymes and regulators in both L- and D-lysine metabolism. We first describe three pathway enzymes that catabolize 2-aminoadipate (2AA) to 2-ketoglutarate (2KG) connecting D-lysine to the TCA cycle. One of these enzymes, PP_5260, contains a DUF1338 domain, a family without previously described biological function. We demonstrate PP_5260 converts 2-oxoadipate (2OA) to 2-hydroxyglutarate (2HG), a novel biochemical reaction. We expand on recent work showing that the glutarate hydroxylase CsiD can co-utilize 2OA and 2KG. We further show glutarate metabolism is locally regulated by two independent glutarate responsive transcription factors, and that cellular abundance of D- and L-lysine pathway proteins are highly sensitive to pathway specific substrates. This work demonstrates the utility of RB-TnSeq of discovering novel metabolic pathways in even well-studied bacterial species.
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
02018-10-12 11:46:15ID requested
12019-05-17 17:09:32announced
Publication List
Thompson MG, Blake-Hedges JM, Cruz-Morales P, Barajas JF, Curran SC, Eiben CB, Harris NC, Benites VT, Gin JW, Sharpless WA, Twigg FF, Skyrud W, Krishna RN, Pereira JH, Baidoo EEK, Petzold CJ, Adams PD, Arkin AP, Deutschbauer AM, Keasling JD, Lysine Metabolism. mBio, 10(3):(2019) [pubmed]
Keyword List
submitter keyword: targeted proteomics
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