A proteomic survey of nonribosomal peptide and polyketide biosynthesis in actinobacteria

Yunqiu Chen, Ioanna Ntai, Kou San Ju, Michelle Unger, Leonid Zamdborg, Sarah J. Robinson, James R. Doroghazi, David P. Labeda, William W. Metcalf, Neil L. Kelleher*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

36 Scopus citations


Actinobacteria such as streptomycetes are renowned for their ability to produce bioactive natural products including nonribosomal peptides (NRPs) and polyketides (PKs). The advent of genome sequencing has revealed an even larger genetic repertoire for secondary metabolism with most of the small molecule products of these gene clusters still unknown. Here, we employed a "protein-first" method called PrISM (Proteomic Investigation of Secondary Metabolism) to screen 26 unsequenced actinomycetes using mass spectrometry-based proteomics for the targeted detection of expressed nonribosomal peptide synthetases or polyketide synthases. Improvements to the original PrISM screening approach (Nat. Biotechnol. 2009, 27, 951-956), for example, improved de novo peptide sequencing, have enabled the discovery of 10 NRPS/PKS gene clusters from 6 strains. Taking advantage of the concurrence of biosynthetic enzymes and the secondary metabolites they generate, two natural products were associated with their previously "orphan" gene clusters. This work has demonstrated the feasibility of a proteomics-based strategy for use in screening for NRP/PK production in actinomycetes (often >8 Mbp, high GC genomes) versus the bacilli (2-4 Mbp genomes) used previously.

Original languageEnglish (US)
Pages (from-to)85-94
Number of pages10
JournalJournal of Proteome Research
Issue number1
StatePublished - Jan 1 2012


  • Fourier-Transform Mass Spectrometry
  • actinobacteria
  • de novo sequencing
  • natural product biosynthesis
  • nonribosomal peptide
  • polyketide

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)


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