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Engineered and total biosynthesis of fungal specialized metabolites

Nature Reviews Chemistry volume 8, pages 61–78 (2024)Cite this article

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Abstract

Filamentous fungi produce a very wide range of complex and often bioactive metabolites, demonstrating their inherent ability as hosts of complex biosynthetic pathways. Recent advances in molecular sciences related to fungi have afforded the development of new tools that allow the rational total biosynthesis of highly complex specialized metabolites in a single process. Increasingly, these pathways can also be engineered to produce new metabolites. Engineering can be at the level of gene deletion, gene addition, formation of mixed pathways, engineering of scaffold synthases and engineering of tailoring enzymes. Combination of these approaches with hosts that can metabolize low-value waste streams opens the prospect of one-step syntheses from garbage.

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Fig. 1: Structures and biological activities of key fungal specialized metabolites.
Fig. 2: Overview of principles and similarity of total biosynthesis to chemical total synthesis.
Fig. 3: Specific examples of routes to engineered compounds via truncated pathways.
Fig. 4: Diversification of tropolone sesquiterpenoids.
Fig. 5: Examples of core engineering.
Fig. 6: Engineering the biosynthesis of fungal PKS–NRPS metabolites in the tenellin series.
Fig. 7: Engineering tailoring enzymes.
Fig. 8: Use of stereoselective enzymatic oxidative dearomatization for the highly efficient synthesis of fungal natural products.

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Authors and Affiliations

  1. Institute for Organic Chemistry and BMWZ, Leibniz University of Hannover, Hannover, Germany

    Russell J. Cox

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Glossary

Biosynthetic gene cluster (BGC)

A co-located group of genes that encode the biosynthesis and transport of a particular specialized metabolite.

Gene expression

The process by which a gene is transcribed into messenger RNA and translated by the ribosome into protein.

Gene knockout

The precise deletion or disruption of a gene to ensure that its encoded protein cannot be produced.

Heterologous expression

Gene expression that is performed in a non-native host organism.

Host organism

An engineered organism in which BGCs of interest are expressed. Host organisms often have properties beneficial for fermentation or genetic engineering.

Intron

A short sequence of non-coding nucleotides that must be removed (spliced) from messenger RNA to create the correct coding sequence for translation.

Mutasynthesis

A process in which a mutation (usually a gene knockout) is chemically complemented by addition of a synthetic precursor or pathway intermediate to produce a new metabolite.

Off-loading domain

Many synth(et)ases process substrates that are covalently attached via a thiolester or ester linkage. Off-loading domains hydrolyse or transesterify completed metabolites and free-up the synth(et)ase for another round of synthesis.

Precursor-directed synthesis

Addition of a chemical precursor to a fermentation so that it is incorporated into the biosynthetic pathway, usually to produce a new specialized metabolite.

Promoter sequence

A sequence of DNA upstream of biosynthetic genes that is bound by a transcription factor.

Refactoring

The process of moving genes to a heterologous host while simultaneously replacing their native promoters with new promoters with desired properties suitable for use in the heterologous host.

Synthase

A biosynthetic protein that builds the skeleton of a specialized metabolite without using adenosine triphosphate (ATP).

Synthetase

A biosynthetic protein that builds the skeleton of a specialized metabolite that requires the use of adenosine triphosphate (ATP).

Tailoring

Biosynthetic processes that occur after the action of a synth(et)ase. Tailoring often incudes redox processes, cyclization, alkylation and rearrangements.

Titre

A measure of the productivity of a fermentation usually expressed in (m)g L−1 or (m)g Kg−1 of the desired product.

Total biosynthesis

The biological equivalent of total chemical synthesis — the rational production of organic materials by the manipulation of the biosynthetic machinery.

Wild-type organism

Also referred to as the donor organism, this is the organism in which BGCs of interest are found. Wild-type or donor organisms are often unsuitable for metabolite production, scale-up or genetic engineering.

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Cox, R.J. Engineered and total biosynthesis of fungal specialized metabolites. Nat Rev Chem 8, 61–78 (2024). https://doi.org/10.1038/s41570-023-00564-0

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