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Skellam E, Rajendran S, Li L. Combinatorial biosynthesis for the engineering of novel fungal natural products. Commun Chem 2024; 7:89. [PMID: 38637654 PMCID: PMC11026467 DOI: 10.1038/s42004-024-01172-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 04/08/2024] [Indexed: 04/20/2024] Open
Abstract
Natural products are small molecules synthesized by fungi, bacteria and plants, which historically have had a profound effect on human health and quality of life. These natural products have evolved over millions of years resulting in specific biological functions that may be of interest for pharmaceutical, agricultural, or nutraceutical use. Often natural products need to be structurally modified to make them suitable for specific applications. Combinatorial biosynthesis is a method to alter the composition of enzymes needed to synthesize a specific natural product resulting in structurally diversified molecules. In this review we discuss different approaches for combinatorial biosynthesis of natural products via engineering fungal enzymes and biosynthetic pathways. We highlight the biosynthetic knowledge gained from these studies and provide examples of new-to-nature bioactive molecules, including molecules synthesized using combinations of fungal and non-fungal enzymes.
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Affiliation(s)
- Elizabeth Skellam
- Department of Chemistry, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA.
- BioDiscovery Institute, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA.
- Department of Biological Sciences, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA.
| | - Sanjeevan Rajendran
- Department of Chemistry, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA
- BioDiscovery Institute, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA
| | - Lei Li
- Department of Chemistry, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA
- BioDiscovery Institute, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA
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Effects of Disruption of Five FUM Genes on Fumonisin Biosynthesis and Pathogenicity in Fusarium proliferatum. Toxins (Basel) 2019; 11:toxins11060327. [PMID: 31181598 PMCID: PMC6628412 DOI: 10.3390/toxins11060327] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/06/2019] [Accepted: 06/06/2019] [Indexed: 02/06/2023] Open
Abstract
The mycotoxin fumonisin is known to be harmful to humans and animals, and thus it is desirable to reduce fumonisin content in crop products. We explored the functions of several genes that function in fumonisin biosynthesis (FUM1, FUM6, FUM8, FUM19, and FUM21) in Fusarium proliferatum and found that deletion of FUM1, FUM6, FUM8, or FUM21 results in a severe reduction in fumonisin biosynthesis, while loss of FUM19 does not. In addition, fumonisin-deficient strains display significantly decreased pathogenicity. Co-cultivation of the ΔFUM1, ΔFUM6, ΔFUM8, and ΔFUM19 mutants restores fumonisin synthesis. However, co-cultivation was unable to restore fumonisin synthesis in the ΔFUM21 strain. The relative expression levels of three key FUM genes (FUM1, FUM6, and FUM8) differed significantly in each mutant strain; notably, the expression levels of these three genes were significantly down-regulated in the ΔFUM21 strain. Taken together, our results demonstrate that FUM1, FUM6, FUM8, and FUM21 are essential for fumonisin synthesis, and FUM19 is non-essential. Partial mutants lost the ability to synthesize fumonisin, the co-culture of the mutants was able to restore fumonisin biosynthesis. While the pathogenicity of F. proliferatum is affected by many factors, inhibition of the synthesis of the mycotoxin fumonisin will weaken the pathogenicity of rice spikelet rot disease (RSRD).
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Mattern DJ, Valiante V, Unkles SE, Brakhage AA. Synthetic biology of fungal natural products. Front Microbiol 2015; 6:775. [PMID: 26284053 PMCID: PMC4519758 DOI: 10.3389/fmicb.2015.00775] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/14/2015] [Indexed: 01/08/2023] Open
Abstract
Synthetic biology is an ever-expanding field in science, also encompassing the research area of fungal natural product (NP) discovery and production. Until now, different aspects of synthetic biology have been covered in fungal NP studies from the manipulation of different regulatory elements and heterologous expression of biosynthetic pathways to the engineering of different multidomain biosynthetic enzymes such as polyketide synthases or non-ribosomal peptide synthetases. The following review will cover some of the exemplary studies of synthetic biology in filamentous fungi showing the capacity of these eukaryotes to be used as model organisms in the field. From the vast array of different NPs produced to the ease for genetic manipulation, filamentous fungi have proven to be an invaluable source for the further development of synthetic biology tools.
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Affiliation(s)
- Derek J Mattern
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany ; Institute for Microbiology, Friedrich Schiller University , Jena, Germany
| | - Vito Valiante
- Leibniz Junior Research Group "Biobricks of Microbial Natural Product Syntheses" , Jena, Germany
| | - Shiela E Unkles
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews , St Andrews, UK
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute , Jena, Germany ; Institute for Microbiology, Friedrich Schiller University , Jena, Germany
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Abstract
The iterative type I polyketide synthases (IPKSs) are central to the biosynthesis of an enormously diverse array of natural products in fungi. These natural products, known as polyketides, exhibit a wide range of biological activities and include clinically important drugs as well as undesirable toxins. The PKSs synthesize these structurally diverse polyketides via a series of decarboxylative condensations of malonyl-CoA extender units and β-keto modifications in a highly programmed manner. Significant progress has been made over the past few years in understanding the biosynthetic mechanism and programming of fungal PKSs. The continuously expanding fungal genome sequence data have sparked genome-directed discoveries of new fungal PKSs and associated products. The increasing number of fungal PKSs that have been linked to their products along with in-depth biochemical and structural characterizations of these large enzymes have remarkably improved our knowledge on the molecular basis for polyketide structural diversity in fungi. This Perspective highlights the recent advances and examines how the newly expanded paradigm has contributed to our ability to link fungal PKS genes to chemical structures and vice versa. The knowledge will help us navigate through the logarithmically expanding seas of genomic information for polyketide compound discovery and provided opportunities to reprogram these megasynthases to generate new chemical entities.
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Affiliation(s)
- Yit-Heng Chooi
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
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Fisch KM, Bakeer W, Yakasai AA, Song Z, Pedrick J, Wasil Z, Bailey AM, Lazarus CM, Simpson TJ, Cox RJ. Rational domain swaps decipher programming in fungal highly reducing polyketide synthases and resurrect an extinct metabolite. J Am Chem Soc 2011; 133:16635-41. [PMID: 21899331 DOI: 10.1021/ja206914q] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The mechanism of programming of iterative highly reducing polyketide synthases remains one of the key unsolved problems of secondary metabolism. We conducted rational domain swaps between the polyketide synthases encoding the biosynthesis of the closely related compounds tenellin and desmethylbassianin. Expression of the hybrid synthetases in Aspergillus oryzae led to the production of reprogrammed compounds in which the changes to the methylation pattern and chain length could be mapped to the domain swaps. These experiments reveal for the first time the origin of programming in these systems. Domain swaps combined with coexpression of two cytochrome P450 encoding genes from the tenellin biosynthetic gene cluster led to the resurrection of the extinct metabolite bassianin.
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Affiliation(s)
- Katja M Fisch
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
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Abstract
This review covers the recent literature on the release mechanisms for polyketides and nonribosomal peptides produced by microorganisms. The emphasis is on the novel enzymology and mechanistic insights revealed by the biosynthetic studies of new natural products.
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Affiliation(s)
- Liangcheng Du
- Department of Chemistry, University of Nebraska-Lincoln, NE 68588, USA.
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Gerber R, Lou L, Du L. A PLP-Dependent Polyketide Chain Releasing Mechanism in the Biosynthesis of Mycotoxin Fumonisins in Fusarium verticillioides. J Am Chem Soc 2009; 131:3148-9. [DOI: 10.1021/ja8091054] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ryan Gerber
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588
| | - Lili Lou
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588
| | - Liangcheng Du
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588
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Zhu X, Vogeler C, Du L. Functional complementation of fumonisin biosynthesis in FUM1-disrupted fusarium verticillioides by the AAL-toxin polyketide synthase gene ALT1 from Alternaria alternata f. sp. Lycopersici. JOURNAL OF NATURAL PRODUCTS 2008; 71:957-960. [PMID: 18435561 DOI: 10.1021/np8000514] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Fumonisins and AAL-toxins are mycotoxins produced by several widespread fungal pathogens of crops. The carbon backbone of the mycotoxins originates from a highly reduced, acyclic polyketide, a C18 chain for fumonisins and a C16 chain for AAL-toxins. Fungal reduced polyketides are assembled by iterative modular polyketide synthases (PKS), and their biosynthetic mechanism is not very clear. Here, we cloned the PKS gene, ALT1, from the tomato pathogen Alternaria alternata f. sp. Lycopersici and introduced it into Fusarium verticillioides 5777, which does not produce fumonisins due to a disrupted fumonisin PKS gene, FUM1. An ALT1 transformant of strain 5777 produced fumonisin B series as well as fumonisin analogues. The results provide experimental evidence for the function of ALT1, which encodes a PKS for mycotoxin biosynthesis. The results also show that the C16-synthesizing ALT1 is able to support the C18 fumonisin biosynthesis in F. verticillioides, suggesting that the final size of the fungal reduced polyketides is not determined by the PKSs alone. Unlike other PKSs, these PKSs do not have a thioesterase/cyclase domain. The release of polyketide precursors that are covalently attached to the PKSs involves a distinct mechanism, which probably determines the structure of the final products.
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Affiliation(s)
- Xiangcheng Zhu
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
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Du L, Zhu X, Gerber R, Huffman J, Lou L, Jorgenson J, Yu F, Zaleta-Rivera K, Wang Q. Biosynthesis of sphinganine-analog mycotoxins. J Ind Microbiol Biotechnol 2008; 35:455-64. [PMID: 18214562 DOI: 10.1007/s10295-008-0316-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Accepted: 01/10/2008] [Indexed: 10/22/2022]
Abstract
Sphinganine-analog mycotoxins (SAMT) are polyketide-derived natural products produced by a number of plant pathogenic fungi and are among the most economically important mycotoxins. The toxins are structurally similar to sphinganine, a key intermediate in the biosynthesis of ceramides and sphingolipids, and competitive inhibitors for ceramide synthase. The inhibition of ceramide and sphingolipid biosynthesis is associated with several fatal diseases in domestic animals and esophageal cancer and neural tube defects in humans. SAMT contains a highly reduced, acyclic polyketide carbon backbone, which is assembled by a single module polyketide synthase. The biosynthesis of SAMT involves a unique polyketide chain-releasing mechanism, in which a pyridoxal 5'-phosphate-dependent enzyme catalyzes the termination, offloading and elongation of the polyketide chain. This leads to the introduction of a new carbon-carbon bond and an amino group to the polyketide chain. The mechanism is fundamentally different from the thioesterase/cyclase-catalyzed polyketide chain releasing found in bacterial and other fungal polyketide biosynthesis. Genetic data suggest that the ketosynthase domain of the polyketide synthase and the chain-releasing enzyme are important for controlling the final product structure. In addition, several post-polyketide modifications have to take place before SAMT become mature toxins.
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Affiliation(s)
- L Du
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA.
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Cox RJ. Polyketides, proteins and genes in fungi: programmed nano-machines begin to reveal their secrets. Org Biomol Chem 2007; 5:2010-26. [PMID: 17581644 DOI: 10.1039/b704420h] [Citation(s) in RCA: 352] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fungi produce a wide variety of biologically active compounds. Among these, the polyketides form a large and structurally diverse group. These compounds are synthesised by highly programmed and very large iterative multifunctional proteins, the polyketide synthases, with nm dimensions. This review outlines the current state of knowledge regarding the links between gene sequence, protein architecture and biosynthetic programming for fungal polyketide synthases.
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Affiliation(s)
- Russell J Cox
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, UK BS8 1TS.
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Hoffmeister D, Keller NP. Natural products of filamentous fungi: enzymes, genes, and their regulation. Nat Prod Rep 2007; 24:393-416. [PMID: 17390002 DOI: 10.1039/b603084j] [Citation(s) in RCA: 378] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We review the literature on the enzymes, genes, and whole gene clusters underlying natural product biosyntheses and their regulation in filamentous fungi. We have included literature references from 1958, yet the majority of citations are between 1995 and the present. A total of 295 references are cited.
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Affiliation(s)
- Dirk Hoffmeister
- Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-University Freiburg, Stefan-Meier-Strasse 19, 79104 Freiburg, Germany.
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