Yeast-based genome mining, production and mechanistic studies of the biosynthesis of fungal polyketide and peptide natural products

Abstract

In this article, we review recent successful efforts to engineer biosynthesis of several important fungal natural products through heterologous expression of relevant biosynthetic genes in Saccharomyces cerevisiae. We also describe an innovative method of rapidly cloning fungal polyketide synthase or nonribosomal peptide synthetase genes, which can be 5-20 kb or longer, from a pool of total RNA obtained from the fungus of interest using the technique we termed the "overlap extension PCR-yeast homologous recombination (ExRec)" method. The process concomitantly incorporates the cloned genes into yeast expression vectors for biosynthesis of corresponding polyketide and nonribosomal peptide compounds in our engineered S. cerevisiae strain, allowing detailed chemical characterizations to identify the activities of those previously uncharacterized biosynthetic megaenzymes. Studies reviewed here highlight yeast as a useful and versatile host not only for production of various natural products and mechanistic investigation of biosynthetic enzymes, but also for mining of uncharacterized fungal genomes for novel secondary metabolite biosynthetic pathways.

Heterologous expression of cytotoxic sesquiterpenoids from the medicinal mushroom Lignosus rhinocerotis in yeast

“…Nonetheless, sesquiterpene biosynthesis of Polyporales which consist of several medicinal mushrooms including Ganoderma lucidum [15], Antrodia cinnamomea [16], Trametes versicolor [17] and L. rhinocerotis (this study), remained largely unexplored. Given that S. cerevisiae has proven to be extremely useful for genome mining and characterisation of fungal secondary metabolite pathways [18] as well as for commercial production of terpenoids [19], we have chosen to use the yeast as an expression host for L. rhinocerotis STSs in this study. Guided by previous transcriptomic data, we cloned several sclerotium-expressed L. rhinocerotis STS genes for heterologous expression in a S. cerevisiae yeast system.…”

Genome of Diaporthe sp. provides insights into the potential inter-phylum transfer of a fungal sesquiterpenoid biosynthetic pathway

“…This can be achieved either by the native fungal producer or more commonly, in the case of low-yield or genetically intractable strains, by engineered, recombinant systems. Therefore, there is a need to identify and characterize the natural products biosynthetic enzymes and pathways for the development of such heterologous production systems, facilitating access to these chemically diverse scaffolds (Ajikumar et al, 2010; Boettger and Hertweck, 2013; Lin et al, 2013; Lin et al, 2014; Paddon et al, 2013; Spakowicz and Strobel, 2015; Tsunematsu et al, 2013; Wawrzyn et al, 2012a; Wiemann et al, 2013; Wiemann and Keller, 2014; Yaegashi et al, 2014). …”

Recent advances in genome mining of secondary metabolite biosynthetic gene clusters and the development of heterologous expression systems in Aspergillus nidulans

“…We also describe the current status of the annotation of the products of secondary metabolism genes in A. nidulans . We would also like to direct readers to the accompanying review in this issue by our collaborators Nancy Keller and Philipp Wiemann on general strategies for mining fungal natural products and to other recent reviews on this subject [10, 28, 53, 56, 61]. …”