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DataSet Summary

  • HostingRepository: PanoramaPublic
  • AnnounceDate: 2019-05-17
  • AnnouncementXML: Submission_2019-05-17_17:09:31.xml
  • DigitalObjectIdentifier:
  • ReviewLevel: Peer-reviewed dataset
  • DatasetOrigin: Original data
  • RepositorySupport: Supported dataset by repository
  • PrimarySubmitter: Chris Petzold
  • Title: Massively parallel fitness profiling reveals multiple novel enzymes in Pseudomonas putida lysine metabolism
  • Description: The 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.
  • SpeciesList: scientific name: Pseudomonas putida KT2440; NCBI TaxID: 160488;
  • ModificationList: Carbamidomethyl
  • Instrument: 6460 Triple Quadrupole LC/MS

Dataset History

VersionDatetimeStatusChangeLog Entry
02018-10-12 11:46:15ID requested
12019-05-17 17:09:32announced

Publication List

  1. 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

  1. submitter keyword: targeted proteomics

Contact List

    Chris Petzold
    • contact affiliation: Lawrence Berkeley National Laboratory
    • contact email: cjpetzold@lbl.gov
    • lab head:
    Chris Petzold
    • contact affiliation: Lawrence Berkeley National Laboratory
    • contact email: cjpetzold@lbl.gov
    • dataset submitter:

Full Dataset Link List

  1. Panorama Public dataset URI

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