Strain-specific proteogenomics accelerates the discovery of natural products via their biosynthetic pathways

Jessica C. Albright, Anthony W. Goering, James R. Doroghazi, William W. Metcalf, Neil L. Kelleher

Research output: Contribution to journalArticlepeer-review

Abstract

The use of proteomics for direct detection of expressed pathways producing natural products has yielded many new compounds, even when used in a screening mode without a bacterial genome sequence available. Here we quantify the advantages of having draft DNA-sequence available for strain-specific proteomics using the latest in ultrahigh-resolution mass spectrometry for both proteins and the small molecules they generate. Using the draft sequence of Streptomyces lilacinus NRRL B-1968, we show a >tenfold increase in the number of peptide identifications vs. using publicly available databases. Detected in this strain were six expressed gene clusters with varying homology to those known. To date, we have identified three of these clusters as encoding for the production of griseobactin (known), rakicidin D (an orphan NRPS/PKS hybrid cluster), and a putative thr and DHB-containing siderophore produced by a new non-ribosomal peptide sythetase gene cluster. The remaining three clusters show lower homology to those known, and likely encode enzymes for production of novel compounds. Using an interpreted strain-specific DNA sequence enables deep proteomics for the detection of multiple pathways and their encoded natural products in a single cultured bacterium.

Original languageEnglish (US)
Pages (from-to)451-459
Number of pages9
JournalJournal of Industrial Microbiology and Biotechnology
Volume41
Issue number2
DOIs
StatePublished - Feb 2014

Keywords

  • Genome mining
  • Mass spectrometry
  • Metabolomics
  • Natural products
  • Proteomics

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Applied Microbiology and Biotechnology

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