Introduction to engineering the biosynthesis of fungal natural products

Abstract

Filamentous fungi are highly diverse eukaryotes that inhabit all known ecosystems on earth. Estimates suggest that more than 2 × 10⁶ species are likely to exist, and analyses of typical fungal genomes suggest they harbour around 50 biosynthetic gene clusters on average. The biosynthetic potential of these organisms is thus vast. Fungi produce all the main classes of secondary metabolites, and numerous hybrid compounds. Many are highly useful in medicine such as the ‘classic’ special metabolites penicillins, cephalosporins, statins and mycophenolic acid, and new antimicrobial agents such as the pleuromutilins and enfumafungins that overcome specific patterns of resistance. Fungi differentiated from bacteria more than a billion years ago, so there has been plenty of time for uniquely fungal biosynthetic systems to evolve.

Russell J. Cox

Russell Cox was born in 1967 in the New Forest in the UK where he grew up. He studied chemistry at the University of Durham, and then worked with Professor David O'Hagan at the same institution for his PhD, studying the biosynthesis of fungal metabolites. Post-doctoral periods with Professor John Vederas FRS in Edmonton Alberta, and Professors David Hopwood FRS and Tom Simpson FRS at Norwich and Bristol in the UK, were followed by his appointment as a lecturer in the School of Chemistry at the University of Bristol where he rose to become a Full Professor of Organic and Biological Chemistry. He moved to become Professor of Microbiological Chemistry at the Leibniz Universität Hannover in Germany in 2013. He served as an editorial board member of Natural Product Reports until 2012, and has been past Chair of the Directing Biosynthesis series of scientific conferences. He is currently Chair of the editorial board of RSC Advances, and Head of the Institute for Organic Chemistry at the Leibniz Universität Hannover.

Tobias A. M. Gulder

Tobias Gulder holds degrees in Chemistry from the University of Würzburg (Diploma 2004, PhD 2008). After postdoctoral training at the Scripps Institution of Oceanography with Bradley Moore he started his independent work in 2010 as a Liebig and Emmy Noether Fellow at the University of Bonn. In 2014 he accepted the offer to join the Technical University of Munich as Professor of Biosystems Chemistry at the Department of Chemistry and the Center for Integrated Protein Science Munich (CIPSM). In 2019 he became Chair of Technical Biochemistry at the Technical University of Dresden. His research interests focus on the discovery and (bio-)synthesis of microbial natural products. This includes the elucidation of new biosynthetic transformations and their application to the biocatalytic synthesis of microbial products as well as the manipulation of biosynthetic pathways to generate new molecular structures.

Biosynthetic studies in fungi, built on more than a century of studies, have reached a high level of sophistication. Seminal studies focused on compound isolation and fungi are still key organisms for bioactive metabolite discovery, especially from specific ecological niches, organism families and structural groups. Later, isotopic labelling studies, in vitro enzymology supported by chemical synthesis, and study of mutant organisms, pushed the field forward. In the past two decades significant advances in genome and transcriptome sequencing, and development of new and efficient molecular tools have extended these studies to include rational mutation and knockout procedures, and work to understand fungal biosynthetic pathways through gene and pathway expression in heterologous hosts. All this is now supported by much-improved informatic tools. Fungal biosynthetic studies are now entering a new age, where the long-held goal of engineering of fungal metabolic pathways is becoming possible at last.

This themed issue of Natural Product Reports focuses on the topics and techniques that underpin current pathway engineering in filamentous fungi. These engineering efforts are being piloted at all levels. The fungal enzyme systems that build terpene, polyketide, peptide and alkaloid skeletons are understood in increasing detail, such that these synth(et)ases can now be rationally manipulated. In the case of polyketide synthases this also includes a developing understanding of how iterative systems are programmed and controlled, and how trans-acting elements have important and subtle effects. Fungal peptides, both of ribosomal and non-ribosomal origin, have distinct features that are also opening up to understanding and engineering efforts. Likewise, fungi are an important source of terpenoids and meroterpenoids where significant progress has been made, particularly via heterologous expression.

Heterologous expression is developing as the key tool for both understanding and engineering fungal biosynthetic systems. Development of new tools, and new host organisms, that allow the rapid and rational expression and manipulation of fungal biosynthetic gene clusters (BGCs) is a core technology. In many ways this technology starts to compete with traditional synthetic organic chemistry for the production of fungal metabolites. Hand-in-hand with this, the deployment of CRISPR-CAS methods speeds-up the traditionally slow fungal molecular methods, and sets the scene for new ways of recombining fungal biosynthetic genes. Fungal secondary metabolites are often highly complex, and this complexity usually arises because of the action of redox tailoring enzymes catalyzing late-stage structural modifications. Major advances in understanding the 3D structures of these tailoring enzymes also now allows engineering of individual tailoring systems, such as the non-heme iron oxygenases.

The editors hope that this special issue will both summarize recent progress, and also act as a stimulus for deepening knowledge and innovation in the area of engineering fungal specialized metabolites. Significant technological problems faced by humanity, including man-made climate change and the need to prevent carbon emissions, means that such methods that build on the inherently low-carbon processes of fungal fermentation will become of increasing importance in the future, for the provision of bioactive high value metabolites and as an alternative to often tedious total synthesis. Our growing understanding of fungal biosynthetic processes will even strongly impact the synthetic field in the future by expanding the available (bio)catalytic toolbox for complex small molecules synthesis with native and engineered fungal biosynthetic enzymes.

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