Activation of cryptic biosynthetic gene clusters by fungal artificial chromosomes to produce novel secondary metabolites

Chengcang C. Wu, Andrea A. Stierle, Donald B. Stierle, Hongyu Chen, Michael Swyers, Timothy Decker, Emili Borkowski, Peter Korajczyk, Rosa Ye, Niel Mondava

Research output: Contribution to journalArticlepeer-review


In 2017, we reported the discovery of Berkeleylactone A (BPLA), a novel, potent antibiotic produced exclusively in co-culture by two extremophilic fungi, Penicillium fuscum and P. camembertii/clavigerum, which were isolated from the Berkeley Pit, an acid mine waste lake, in Butte, Montana. Neither fungus synthesized BPLA when grown in axenic culture. Recent studies suggest that secondary metabolites (SMs) are often synthesized by enzymes encoded by co-localized genes that form “biosynthetic gene clusters” (BGCs), which might remain silent (inactive) under various fermentation conditions. Fungi may also harbor cryptic BGCs that are not associated with previously characterized molecules. We turned to the tools of Fungal Artificial Chromosomes (FAC)-Next-Gen-Sequencing (NGS) to understand how co-culture activated cryptic biosynthesis of BPLA and several related berkeleylactones and to further investigate the true biosynthetic potential of these two fungi. FACNGS enables the capture of BGCs as individual FACs for heterologous expression in a modified strain of Aspergillus nidulans (heterologous host, FAC-AnHH). With this methodology, we created ten BGCFACs that yielded fourteen different SMs, including strobilurin, which was previously isolated exclusively from basidiomycetes. Eleven of these compounds were not detected in the extracts of the FAC-AnHH. Of this discrete set, only the novel compound citreohybriddional had been isolated from either Penicillium sp. before and only at very low yield. We propose that through heterologous expression, FACs activated these silent BGCs, resulting in the synthesis of new natural products (NPs) with yields as high as 50%–60% of the crude organic extracts.

Original languageEnglish
Pages (from-to)757-779
Number of pages23
JournalAIMS Microbiology
Issue number4
StatePublished - 2023


  • Fungal artificial chromosome
  • Liquid Chromatography/Mass Spectrometry (LC/MS)
  • Nuclear Magnetic Resonance (NMR)
  • cryptic biosynthesis
  • next-gen-sequencing
  • secondary metabolites


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