Fungal artificial chromosomes for mining of the fungal secondary metabolome

Jin Woo Bok, Rosa Ye, Kenneth D. Clevenger, David Mead, Megan Wagner, Amanda Krerowicz, Jessica C. Albright, Anthony Whitney Goering, Paul Martin Thomas, Neil L Kelleher*, Nancy P. Keller, Chengcang C. Wu

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

62 Scopus citations


Background: With thousands of fungal genomes being sequenced, each genome containing up to 70 secondary metabolite (SM) clusters 30-80 kb in size, breakthrough techniques are needed to characterize this SM wealth. Results: Here we describe a novel system-level methodology for unbiased cloning of intact large SM clusters from a single fungal genome for one-step transformation and expression in a model host. All 56 intact SM clusters from Aspergillus terreus were individually captured in self-replicating fungal artificial chromosomes (FACs) containing both the E. coli F replicon and an Aspergillus autonomously replicating sequence (AMA1). Candidate FACs were successfully shuttled between E. coli and the heterologous expression host A. nidulans. As proof-of-concept, an A. nidulans FAC strain was characterized in a novel liquid chromatography-high resolution mass spectrometry (LC-HRMS) and data analysis pipeline, leading to the discovery of the A. terreus astechrome biosynthetic machinery. Conclusion: The method we present can be used to capture the entire set of intact SM gene clusters and/or pathways from fungal species for heterologous expression in A. nidulans and natural product discovery.

Original languageEnglish (US)
Article number343
JournalBMC Genomics
Issue number1
StatePublished - Dec 12 2015


  • Functional genomics
  • Fungal artificial chromosome (FAC)
  • Natural product discovery
  • Secondary metabolite (SM) gene clusters

ASJC Scopus subject areas

  • Genetics
  • Biotechnology


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