Recent developments of tools for genome and metabolome studies in basidiomycete fungi and their application to natural product research.

Fabrizio Alberti,Saraa Kaleem,Jack A Weaver

doi:10.1242/bio.056010

Abstract

ABSTRACTBasidiomycota are a large and diverse phylum of fungi. They can make bioactive metabolites that are used or have inspired the synthesis of antibiotics and agrochemicals. Terpenoids are the most abundant class of natural products encountered in this taxon. Other natural product classes have been described, including polyketides, peptides, and indole alkaloids. The discovery and study of natural products made by basidiomycete fungi has so far been hampered by several factors, which include their slow growth and complex genome architecture. Recent developments of tools for genome and metabolome studies are allowing researchers to more easily tackle the secondary metabolome of basidiomycete fungi. Inexpensive long-read whole-genome sequencing enables the assembly of high-quality genomes, improving the scaffold upon which natural product gene clusters can be predicted. CRISPR/Cas9-based engineering of basidiomycete fungi has been described and will have an important role in linking natural products to their genetic determinants. Platforms for the heterologous expression of basidiomycete genes and gene clusters have been developed, enabling natural product biosynthesis studies. Molecular network analyses and publicly available natural product databases facilitate data dereplication and natural product characterisation. These technological advances combined are prompting a revived interest in natural product discovery from basidiomycete fungi.This article has an associated Future Leader to Watch interview with the first author of the paper.

Highlights

Natural products (NPs) are low-molecular weight molecules that are made by living organisms and are often referred to as secondary metabolites
NPs are used by humankind for many applications, including as drugs; NPs and NP derivatives represent 25% of new anticancer and 55% of new antibacterial drugs approved by the US Food and Drug Administration (FDA) between 1981 and 2019
CRISPR/Cas9-mediated engineering of basidiomycete fungi It has long been known that genetically transforming targets is a vital tool for detailed molecular analysis, and until recently it was exceptionally difficult to do this in basidiomycete fungi

Summary

Introduction

Natural products (NPs) are low-molecular weight molecules that are made by living organisms and are often referred to as secondary metabolites. Long-read sequencing of proteins will no doubt prove invaluable to groups searching for the biosynthetic pathways responsible for producing NPs. CRISPR/Cas9-mediated engineering of basidiomycete fungi It has long been known that genetically transforming targets is a vital tool for detailed molecular analysis, and until recently it was exceptionally difficult to do this in basidiomycete fungi. In the same year CRISPR/Cas was used to form the basis of a high-throughput transformation technique, which successfully inserted luciferase and GFP into Coprinopsis cinerea to assess constitutive promoters; the authors developed an improved way of cryopreserving protoplasts (Sugano et al, 2017) Despite these successes, targeting efficiency remained low, potentially due to inefficient sgRNA and/or Cas expression (Sugano et al, 2017); the gates of CRISPR/ Cas for engineering and editing fungi of the phylum Basidiomycota were opened. The authors showed that increasing the volume of the ribonucleoprotein mix increased transformation efficiencies, and that having homology arms of over 100 bp was best practice for inducing efficient homologous recombination with this system,

Agaricus bisporus

Findings

Hygromycin B phosphotransferase gene for hygromycin B resistance