Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

Rodrigo A Olarte,Jon Menke,Jason C Slot,Joseph W Spatafora,Alisha C Quandt,Jonathan P Badalamenti,Ying Zhang,Shawn Sullivan,Yinyin Huang,Kathryn E Bushley

doi:10.1186/s12864-018-5399-x

Abstract

BackgroundGenes involved in production of secondary metabolites (SMs) in fungi are exceptionally diverse. Even strains of the same species may exhibit differences in metabolite production, a finding that has important implications for drug discovery. Unlike in other eukaryotes, genes producing SMs are often clustered and co-expressed in fungal genomes, but the genetic mechanisms involved in the creation and maintenance of these secondary metabolite biosynthetic gene clusters (SMBGCs) remains poorly understood.ResultsIn order to address the role of genome architecture and chromosome scale structural variation in generating diversity of SMBGCs, we generated chromosome scale assemblies of six geographically diverse isolates of the insect pathogenic fungus Tolypocladium inflatum, producer of the multi-billion dollar lifesaving immunosuppressant drug cyclosporin, and utilized a Hi-C chromosome conformation capture approach to address the role of genome architecture and structural variation in generating intraspecific diversity in SMBGCs. Our results demonstrate that the exchange of DNA between heterologous chromosomes plays an important role in generating novelty in SMBGCs in fungi. In particular, we demonstrate movement of a polyketide synthase (PKS) and several adjacent genes by translocation to a new chromosome and genomic context, potentially generating a novel PKS cluster. We also provide evidence for inter-chromosomal recombination between nonribosomal peptide synthetases located within subtelomeres and uncover a polymorphic cluster present in only two strains that is closely related to the cluster responsible for biosynthesis of the mycotoxin aflatoxin (AF), a highly carcinogenic compound that is a major public health concern worldwide. In contrast, the cyclosporin cluster, located internally on chromosomes, was conserved across strains, suggesting selective maintenance of this important virulence factor for infection of insects.ConclusionsThis research places the evolution of SMBGCs within the context of whole genome evolution and suggests a role for recombination between chromosomes in generating novel SMBGCs in the medicinal fungus Tolypocladium inflatum.

Highlights

Genes involved in production of secondary metabolites (SMs) in fungi are exceptionally diverse
A previous karyotype of the NRRL8044 strain of T. inflatum suggested that T. inflatum has 6 chromosomes ranging in size from 3.8 to 6.6 Mb for a total genome size of approximately 30.45 Mb [37]
Our results demonstrate that movement of core SM genes (PKS, non-ribosomal peptide synthetases (NRPSs), Terpene synthase (TS), dimethylallyl tryptophan synthases (DMATs)) involved in production of the metabolite backbone structures may occur more frequently in fungal genomes than previously recognized and contributes substantially to the evolution of novel metabolite clusters in fungi

Summary

Introduction

Genes involved in production of secondary metabolites (SMs) in fungi are exceptionally diverse. The genes involved in production of most SMs in fungi are clustered in the genome, forming secondary metabolite biosynthetic gene clusters (SMBGCs) that are co-regulated and co-expressed [11, 12]. These SMBGCs may contain one or multiple types of “core” enzymes responsible for biosynthesis of the backbone structure of the metabolite. Multimodular NRPSs are thought to evolve through tandem duplication or deletion of these A-T-C modules [14] In addition to these core enzymes, SMBGCs harbor “modifying” enzymes, such as dehydrogenases, methyltransferases, acetyl transferases, and cytochrome P450 monooxygenases (P450s), among others, that are involved in chemical transformations of the backbone structure to produce the final metabolite. SMBGCs may contain cluster specific transcription factors that coordinately regulate expression of all genes in the cluster, as well as transporters involved in detoxification or self-protection in the producing fungus [15]

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