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Yang H, Song C, Liu C, Wang P. Synthetic Biology Tools for Engineering Aspergillus oryzae. J Fungi (Basel) 2024; 10:34. [PMID: 38248944 PMCID: PMC10817548 DOI: 10.3390/jof10010034] [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: 10/24/2023] [Revised: 12/23/2023] [Accepted: 12/26/2023] [Indexed: 01/23/2024] Open
Abstract
For more than a thousand years, Aspergillus oryzae has been used in traditional culinary industries, including for food fermentation, brewing, and flavoring. In recent years, A. oryzae has been extensively used in deciphering the pathways of natural product synthesis and value-added compound bioproduction. Moreover, it is increasingly being used in modern biotechnology industries, such as for the production of enzymes and recombinant proteins. The investigation of A. oryzae has been significantly accelerated through the successive application of a diverse array of synthetic biology techniques and methodologies. In this review, the advancements in biological tools for the synthesis of A. oryzae, including DNA assembly technologies, gene expression regulatory elements, and genome editing systems, are discussed. Additionally, the challenges associated with the heterologous expression of A. oryzae are addressed.
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Affiliation(s)
- Hui Yang
- School of Life Science, Northeast Forestry University, Harbin 150040, China
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Chaonan Song
- School of Life Science, Northeast Forestry University, Harbin 150040, China
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Chengwei Liu
- School of Life Science, Northeast Forestry University, Harbin 150040, China
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Pengchao Wang
- School of Life Science, Northeast Forestry University, Harbin 150040, China
- Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
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2
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Cox RJ. Engineered and total biosynthesis of fungal specialized metabolites. Nat Rev Chem 2024; 8:61-78. [PMID: 38172201 DOI: 10.1038/s41570-023-00564-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2023] [Indexed: 01/05/2024]
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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Affiliation(s)
- Russell J Cox
- Institute for Organic Chemistry and BMWZ, Leibniz University of Hannover, Hannover, Germany.
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3
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Jeennor S, Anantayanon J, Panchanawaporn S, Chutrakul C, Vongsangnak W, Laoteng K. Efficient de novo production of bioactive cordycepin by Aspergillus oryzae using a food-grade expression platform. Microb Cell Fact 2023; 22:253. [PMID: 38071331 PMCID: PMC10710699 DOI: 10.1186/s12934-023-02261-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Cordycepin (3'-deoxyadenosine) is an important bioactive compound in medical and healthcare markets. The drawbacks of commercial cordycepin production using Cordyceps spp. include long cultivation periods and low cordycepin yields. To overcome these limitations and meet the increasing market demand, the efficient production of cordycepin by the GRAS-status Aspergillus oryzae strain using a synthetic biology approach was developed in this study. RESULTS An engineered strain of A. oryzae capable of cordycepin production was successfully constructed by overexpressing two metabolic genes (cns1 and cns2) involved in cordycepin biosynthesis under the control of constitutive promoters. Investigation of the flexibility of carbon utilization for cordycepin production by the engineered A. oryzae strain revealed that it was able to utilize C6-, C5-, and C12-sugars as carbon sources, with glucose being the best carbon source for cordycepin production. High cordycepin productivity (564.64 ± 9.59 mg/L/d) was acquired by optimizing the submerged fermentation conditions. CONCLUSIONS This study demonstrates a powerful production platform for bioactive cordycepin production by A. oryzae using a synthetic biology approach. An efficient and cost-effective fermentation process for cordycepin production using an engineered strain was established, offering a powerful alternative source for further upscaling.
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Affiliation(s)
- Sukanya Jeennor
- Industrial Bioprocess Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand.
| | - Jutamas Anantayanon
- Industrial Bioprocess Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Sarocha Panchanawaporn
- Industrial Bioprocess Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Chanikul Chutrakul
- Industrial Bioprocess Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok, 10900, Thailand
| | - Kobkul Laoteng
- Industrial Bioprocess Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
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4
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Sun Y, Tian D, Kuhnert E, Le Goff G, Arcile G, Ouazzani J, Cox RJ. Total biosynthesis of fungal tetraketide pyrones. Chem Commun (Camb) 2023; 59:13587-13590. [PMID: 37886844 DOI: 10.1039/d3cc04758j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Fungal tetraketide pyrones possess important and potent bioactivities, but their detailed biosynthetic pathways are unknown and synthetic routes to their production are lengthy. Here we investigated the fungal pathways to the multiforisins and compounds related to islandic acid. Heterologous expression experiments yield high titres of these compounds and pathway intermediates. The results both elucidate the pathway and offer a platform for the total biosynthesis of this class of metabolites.
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Affiliation(s)
- Yunlong Sun
- Institute for Organic Chemistry, Leibniz Universität Hannover, Hannover, Germany.
| | - Dongsong Tian
- Institute for Organic Chemistry, Leibniz Universität Hannover, Hannover, Germany.
| | - Eric Kuhnert
- Institute for Organic Chemistry, Leibniz Universität Hannover, Hannover, Germany.
| | | | | | | | - Russell J Cox
- Institute for Organic Chemistry, Leibniz Universität Hannover, Hannover, Germany.
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5
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Transcriptome-based Mining of the Constitutive Promoters for Tuning Gene Expression in Aspergillus oryzae. J Microbiol 2023; 61:199-210. [PMID: 36745334 DOI: 10.1007/s12275-023-00020-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 02/07/2023]
Abstract
Transcriptional regulation has been adopted for developing metabolic engineering tools. The regulatory promoter is a crucial genetic element for strain optimization. In this study, a gene set of Aspergillus oryzae with highly constitutive expression across different growth stages was identified through transcriptome data analysis. The candidate promoters were functionally characterized in A. oryzae by transcriptional control of β-glucuronidase (GUS) as a reporter. The results showed that the glyceraldehyde triphosphate dehydrogenase promoter (PgpdA1) of A. oryzae with a unique structure displayed the most robust strength in constitutively controlling the expression compared to the PgpdA2 and other putative promoters tested. In addition, the ubiquitin promoter (Pubi) of A. oryzae exhibited a moderate expression strength. The deletion analysis revealed that the 5' untranslated regions of gpdA1 and ubi with the length of 1028 and 811 nucleotides, counted from the putative translation start site (ATG), respectively, could efficiently drive the GUS expression. Interestingly, both promoters could function on various carbon sources for cell growth. Glucose was the best fermentable carbon source for allocating high constitutive expressions during cell growth, and the high concentrations (6-8% glucose, w/v) did not repress their functions. It was also demonstrated that the secondary metabolite gene coding for indigoidine could express under the control of PgpdA1 or Pubi promoter. These strong and moderate promoters of A. oryzae provided beneficial options in tuning the transcriptional expression for leveraging the metabolic control towards the targeted products.
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6
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Chiang YM, Lin TS, Wang CCC. Total Heterologous Biosynthesis of Fungal Natural Products in Aspergillus nidulans. JOURNAL OF NATURAL PRODUCTS 2022; 85:2484-2518. [PMID: 36173392 PMCID: PMC9621686 DOI: 10.1021/acs.jnatprod.2c00487] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Fungal natural products comprise a wide range of bioactive compounds including important drugs and agrochemicals. Intriguingly, bioinformatic analyses of fungal genomes have revealed that fungi have the potential to produce significantly more natural products than what have been discovered so far. It has thus become widely accepted that most biosynthesis pathways of fungal natural products are silent or expressed at very low levels under laboratory cultivation conditions. To tap into this vast chemical reservoir, the reconstitution of entire biosynthetic pathways in genetically tractable fungal hosts (total heterologous biosynthesis) has become increasingly employed in recent years. This review summarizes total heterologous biosynthesis of fungal natural products accomplished before 2020 using Aspergillus nidulans as heterologous hosts. We review here Aspergillus transformation, A. nidulans hosts, shuttle vectors for episomal expression, and chromosomal integration expression. These tools, collectively, not only facilitate the discovery of cryptic natural products but can also be used to generate high-yield strains with clean metabolite backgrounds. In comparison with total synthesis, total heterologous biosynthesis offers a simplified strategy to construct complex molecules and holds potential for commercial application.
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Affiliation(s)
- Yi-Ming Chiang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089, United States
- Department of Pharmacy, Chia Nan University of Pharmacy and Science, Tainan 71710, Taiwan
| | - Tzu-Shyang Lin
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089, United States
| | - Clay C C Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089, United States
- Department of Chemistry, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California 90089, United States
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7
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Mózsik L, Iacovelli R, Bovenberg RAL, Driessen AJM. Transcriptional Activation of Biosynthetic Gene Clusters in Filamentous Fungi. Front Bioeng Biotechnol 2022; 10:901037. [PMID: 35910033 PMCID: PMC9335490 DOI: 10.3389/fbioe.2022.901037] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/17/2022] [Indexed: 11/13/2022] Open
Abstract
Filamentous fungi are highly productive cell factories, many of which are industrial producers of enzymes, organic acids, and secondary metabolites. The increasing number of sequenced fungal genomes revealed a vast and unexplored biosynthetic potential in the form of transcriptionally silent secondary metabolite biosynthetic gene clusters (BGCs). Various strategies have been carried out to explore and mine this untapped source of bioactive molecules, and with the advent of synthetic biology, novel applications, and tools have been developed for filamentous fungi. Here we summarize approaches aiming for the expression of endogenous or exogenous natural product BGCs, including synthetic transcription factors, assembly of artificial transcription units, gene cluster refactoring, fungal shuttle vectors, and platform strains.
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Affiliation(s)
- László Mózsik
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Riccardo Iacovelli
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Roel A. L. Bovenberg
- DSM Biotechnology Center, Delft, Netherlands
- Department of Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Arnold J. M. Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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8
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Chutrakul C, Panchanawaporn S, Vorapreeda T, Jeennor S, Anantayanon J, Laoteng K. The Exploring Functional Role of Ammonium Transporters of Aspergillus oryzae in Nitrogen Metabolism: Challenges towards Cell Biomass Production. Int J Mol Sci 2022; 23:7567. [PMID: 35886914 PMCID: PMC9319855 DOI: 10.3390/ijms23147567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 11/30/2022] Open
Abstract
Ammonium is a source of fermentable inorganic nitrogen essential for the growth and development of filamentous fungi. It is involved in several cellular metabolic pathways underlying nitrogen transport and assimilation. Ammonium can be transferred into the cell by an ammonium transporter. This study explored the role of ammonium transporters in nitrogen metabolism and cell biomass production in Aspergillus oryzae strain BCC 7051. Specific sequences encoding ammonium transporters (Amts) in A. oryzae were identified using genomic analysis. Four of the identified ammonium transporter genes, aoamt1-aoamt4, showed similarity in deduced amino acid sequences to the proteins in the ammonium transporter/methylammonium permease (AMT/MEP) family. Transcriptional analysis showed that the expression of aoamt2 and aoamt3 was ammonium-dependent, and was highly upregulated under ammonium-limited conditions. Their functional roles are characterized by genetic perturbations. The gene disruption and overexpression of aoamt3 indicated that the protein encoded by it was a crucial ammonium transporter associated with nitrogen metabolism and was required for filamentous growth. Compared with the wild type, the aoamt3-overexpressing strain showed superior growth performance, high biomass yield, and low glucose consumption. These results shed light on further improvements in the production of potent bioproducts by A. oryzae by manipulating the ammonium uptake capacity and nitrogen metabolism.
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Affiliation(s)
- Chanikul Chutrakul
- Functional Ingredients and Food Innovation Research Group (IFIG), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (S.P.); (S.J.); (J.A.); (K.L.)
| | - Sarocha Panchanawaporn
- Functional Ingredients and Food Innovation Research Group (IFIG), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (S.P.); (S.J.); (J.A.); (K.L.)
| | - Tayvich Vorapreeda
- Biochemical Engineering and Systems Biology Research Group (IBEG), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), at King Mongkut’s University of Technology Thonburi, Bangkok 10150, Thailand;
| | - Sukanya Jeennor
- Functional Ingredients and Food Innovation Research Group (IFIG), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (S.P.); (S.J.); (J.A.); (K.L.)
| | - Jutamas Anantayanon
- Functional Ingredients and Food Innovation Research Group (IFIG), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (S.P.); (S.J.); (J.A.); (K.L.)
| | - Kobkul Laoteng
- Functional Ingredients and Food Innovation Research Group (IFIG), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (S.P.); (S.J.); (J.A.); (K.L.)
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9
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Panchanawaporn S, Chutrakul C, Jeennor S, Anantayanon J, Rattanaphan N, Laoteng K. Potential of Aspergillus oryzae as a biosynthetic platform for indigoidine, a non-ribosomal peptide pigment with antioxidant activity. PLoS One 2022; 17:e0270359. [PMID: 35737654 PMCID: PMC9223385 DOI: 10.1371/journal.pone.0270359] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 06/08/2022] [Indexed: 11/18/2022] Open
Abstract
The growing demand for natural pigments in the industrial sector is a significant driving force in the development of production processes. The production of natural blue pigments, which have wide industrial applications, using microbial systems has been gaining significant attention. In this study, we used Aspergillus oryzae as a platform cell factory to produce the blue pigment indigoidine (InK), by genetic manipulation of its non-ribosomal peptide synthetase system to overexpress the indigoidine synthetase gene (AoinK). Phenotypic analysis showed that InK production from the engineered strain was growth associated, owing to the constitutive control of gene expression. Furthermore, the initial pH, temperature, and glutamine and MgSO4 concentrations were key factors affecting InK production by the engineered strain. The pigment secretion was enhanced by addition of 1% Tween 80 solution to the culture medium. The maximum titer of total InK was 1409.22 ± 95.33 mg/L, and the maximum productivity was 265.09 ± 14.74 mg/L·d. Moreover, the recombinant InK produced by the engineered strain exhibited antioxidant activity. These results indicate that A. oryzae has the potential to be used as a fungal platform for overproduction of extracellular non-ribosomal peptide pigments.
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Affiliation(s)
- Sarocha Panchanawaporn
- Functional Ingredients and Food Innovation Research Group (IFIG), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, Thailand
| | - Chanikul Chutrakul
- Functional Ingredients and Food Innovation Research Group (IFIG), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, Thailand
- * E-mail:
| | - Sukanya Jeennor
- Functional Ingredients and Food Innovation Research Group (IFIG), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, Thailand
| | - Jutamas Anantayanon
- Functional Ingredients and Food Innovation Research Group (IFIG), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, Thailand
| | - Nakul Rattanaphan
- Functional Ingredients and Food Innovation Research Group (IFIG), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, Thailand
| | - Kobkul Laoteng
- Functional Ingredients and Food Innovation Research Group (IFIG), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, Thailand
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10
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Heterologous Expression of Secondary Metabolite Genes in Trichoderma reesei for Waste Valorization. J Fungi (Basel) 2022; 8:jof8040355. [PMID: 35448586 PMCID: PMC9032437 DOI: 10.3390/jof8040355] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 01/07/2023] Open
Abstract
Trichoderma reesei (Hypocrea jecorina) was developed as a microbial cell factory for the heterologous expression of fungal secondary metabolites. This was achieved by inactivation of sorbicillinoid biosynthesis and construction of vectors for the rapid cloning and expression of heterologous fungal biosynthetic genes. Two types of megasynth(et)ases were used to test the strain and vectors, namely a non-reducing polyketide synthase (nr-PKS, aspks1) from Acremonium strictum and a hybrid highly-reducing PKS non-ribosomal peptide synthetase (hr-PKS-NRPS, tenS + tenC) from Beauveria bassiana. The resulting engineered T. reesei strains were able to produce the expected natural products 3-methylorcinaldehyde and pretenellin A on waste materials including potato, orange, banana and kiwi peels and barley straw. Developing T. reesei as a heterologous host for secondary metabolite production represents a new method for waste valorization by the direct conversion of waste biomass into secondary metabolites.
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11
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Jeennor S, Anantayanon J, Chutrakul C, Panchanawaporn S, Laoteng K. Novel pentose-regulated promoter of Aspergillus oryzae with application in controlling heterologous gene expression. BIOTECHNOLOGY REPORTS 2022; 33:e00695. [PMID: 35004236 PMCID: PMC8718821 DOI: 10.1016/j.btre.2021.e00695] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 12/12/2021] [Accepted: 12/15/2021] [Indexed: 11/17/2022]
Abstract
A novel pentose-regulated promoter (PxyrA) identified from Aspergillus oryzae Xylose reductase promoter displayed strong regulation in gene expression of A. oryzae Inducible regulation in heterologous gene expressions in filamentous fungi Simultaneous gene expression and product optimization under PxyrA control
The potent promoter and its transcriptional control make a significant contribution to strain optimization. Using transcriptome-based approach, a novel pentose-regulated promoter of the xylose reductase gene (PxyrA) of Aspergillus oryzae was identified. The promoter analysis showed that the PxyrA was tightly regulated by pentose sugars, which xylose and xylan were favorable inducers. The PxyrA function was highly efficient as compared with the maltose-inducible promoters of A. oryzae. It also exhibited the efficient transcription induction even though certain amounts of glucose and sucrose existed in the cultures. The expression control of PxyrA was dependent on xylose consumption capacity for fungal growth. The control mode of PxyrA offers a simple operation in simultaneous gene expression and cultivation optimization in Aspergilli. This study provides a prospective development of fungal production platform using cellulosic sugars by the xylose-utilizing strains for sustainable growing in circular economy.
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12
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Investigating Fungal Biosynthetic Pathways Using Heterologous Gene Expression: Aspergillus nidulans as a Heterologous Host. Methods Mol Biol 2022; 2489:41-52. [PMID: 35524044 PMCID: PMC9873597 DOI: 10.1007/978-1-0716-2273-5_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Fungal natural products encompass an important source of pharmaceutically relevant molecules. Heterologous expression of biosynthetic pathways in chassis strains enables the discovery of new secondary metabolites and characterization of pathway enzymes. In our laboratory, biosynthetic genes in a clustered pathway have been refactored in engineered heterologous hosts such as Aspergillus nidulans. Here we describe the assembly of heterologous expression vectors, transformation into A. nidulans, and detection of new compounds in the transformant strains.
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de Mattos-Shipley KMJ, Lazarus CM, Williams K. Investigating Fungal Biosynthetic Pathways Using Heterologous Gene Expression: Aspergillus oryzae as a Heterologous Host. Methods Mol Biol 2022; 2489:23-39. [PMID: 35524043 DOI: 10.1007/978-1-0716-2273-5_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A suite of molecular techniques have been developed in recent decades, which allow gene clusters coding for the biosynthesis of fungal natural products to be investigated and characterized in great detail. Many of these involve the manipulation of the native producer, for example, to increase yields of natural products or investigate the biosynthetic pathway through gene disruptions. However, an alternative and powerful means of investigating biosynthetic pathways, which does not rely on a cooperative native host, is the refactoring and heterologous expression of pathways in a suitable host strain. This protocol aims to walk the reader through the various steps required for the heterologous expression of a fungal biosynthetic gene cluster, specifically using Aspergillus oryzae strain NSAR1 and the pTYGS series of expression vectors. Briefly, this process involves the design and construction of up to four multigene expression vectors using yeast recombination, PEG-mediation transformation of A. oryzae protoplasts, and chemical extraction of the resulting transformants to screen for the presence of metabolites.
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Affiliation(s)
| | - Colin M Lazarus
- School of Biological Sciences, University of Bristol, Bristol, UK
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14
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Feng J, Hauser M, Cox RJ, Skellam E. Engineering Aspergillus oryzae for the Heterologous Expression of a Bacterial Modular Polyketide Synthase. J Fungi (Basel) 2021; 7:1085. [PMID: 34947068 PMCID: PMC8708903 DOI: 10.3390/jof7121085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/31/2022] Open
Abstract
Microbial natural products have had phenomenal success in drug discovery and development yet form distinct classes based on the origin of their native producer. Methods that enable metabolic engineers to combine the most useful features of the different classes of natural products may lead to molecules with enhanced biological activities. In this study, we modified the metabolism of the fungus Aspergillus oryzae to enable the synthesis of triketide lactone (TKL), the product of the modular polyketide synthase DEBS1-TE engineered from bacteria. We established (2S)-methylmalonyl-CoA biosynthesis via introducing a propionyl-CoA carboxylase complex (PCC); reassembled the 11.2 kb DEBS1-TE coding region from synthetic codon-optimized gene fragments using yeast recombination; introduced bacterial phosphopantetheinyltransferase SePptII; investigated propionyl-CoA synthesis and degradation pathways; and developed improved delivery of exogenous propionate. Depending on the conditions used titers of TKL ranged from <0.01-7.4 mg/L. In conclusion, we have demonstrated that A. oryzae can be used as an alternative host for the synthesis of polyketides from bacteria, even those that require toxic or non-native substrates. Our metabolically engineered A. oryzae may offer advantages over current heterologous platforms for producing valuable and complex natural products.
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Affiliation(s)
- Jin Feng
- Institute for Organic Chemistry and Biomolekular Wirkstoff Zentrum, Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany; (J.F.); (M.H.)
| | - Maurice Hauser
- Institute for Organic Chemistry and Biomolekular Wirkstoff Zentrum, Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany; (J.F.); (M.H.)
| | - Russell J. Cox
- Institute for Organic Chemistry and Biomolekular Wirkstoff Zentrum, Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany; (J.F.); (M.H.)
| | - Elizabeth Skellam
- Institute for Organic Chemistry and Biomolekular Wirkstoff Zentrum, Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany; (J.F.); (M.H.)
- Department of Chemistry, BioDiscovery Institute, University of North Texas, 1155 Union Circle, Denton, TX 76201, USA
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15
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Shenouda ML, Ambilika M, Cox RJ. Trichoderma reesei Contains a Biosynthetic Gene Cluster That Encodes the Antifungal Agent Ilicicolin H. J Fungi (Basel) 2021; 7:1034. [PMID: 34947016 PMCID: PMC8705728 DOI: 10.3390/jof7121034] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 12/22/2022] Open
Abstract
The trili biosynthetic gene cluster (BGC) from the well-studied organism Trichoderma reesei was studied by heterologous expression in the fungal host Aspergillus oryzae. Coexpression of triliA and triliB produces two new acyl tetramic acids. Addition of the ring-expanding cytochrome P450 encoded by triliC then yields a known pyridone intermediate to ilicicolin H and a new chain-truncated shunt metabolite. Finally, addition of the intramolecular Diels-Alderase encoded by triliD affords a mixture of 8-epi ilicicolin H and ilicicolin H itself, showing that the T. reesei trili BGC encodes biosynthesis of this potent antifungal agent. Unexpected A. oryzae shunt pathways are responsible for the production of the new compounds, emphasising the role of fungal hosts in catalysing diversification reactions.
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Affiliation(s)
- Mary L. Shenouda
- Institute for Organic Chemistry and Biomolekulares Wirkstoffzentrum (BMWZ), Schneiderberg 38, 30167 Hannover, Germany; (M.L.S.); (M.A.)
- Pharmacognosy Department, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt
| | - Maria Ambilika
- Institute for Organic Chemistry and Biomolekulares Wirkstoffzentrum (BMWZ), Schneiderberg 38, 30167 Hannover, Germany; (M.L.S.); (M.A.)
| | - Russell J. Cox
- Institute for Organic Chemistry and Biomolekulares Wirkstoffzentrum (BMWZ), Schneiderberg 38, 30167 Hannover, Germany; (M.L.S.); (M.A.)
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16
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Meng X, Fang Y, Ding M, Zhang Y, Jia K, Li Z, Collemare J, Liu W. Developing fungal heterologous expression platforms to explore and improve the production of natural products from fungal biodiversity. Biotechnol Adv 2021; 54:107866. [PMID: 34780934 DOI: 10.1016/j.biotechadv.2021.107866] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/04/2021] [Accepted: 11/05/2021] [Indexed: 12/14/2022]
Abstract
Natural products from fungi represent an important source of biologically active metabolites notably for therapeutic agent development. Genome sequencing revealed that the number of biosynthetic gene clusters (BGCs) in fungi is much larger than expected. Unfortunately, most of them are silent or barely expressed under laboratory culture conditions. Moreover, many fungi in nature are uncultivable or cannot be genetically manipulated, restricting the extraction and identification of bioactive metabolites from these species. Rapid exploration of the tremendous number of cryptic fungal BGCs necessitates the development of heterologous expression platforms, which will facilitate the efficient production of natural products in fungal cell factories. Host selection, BGC assembly methods, promoters used for heterologous gene expression, metabolic engineering strategies and compartmentalization of biosynthetic pathways are key aspects for consideration to develop such a microbial platform. In the present review, we summarize current progress on the above challenges to promote research effort in the relevant fields.
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Affiliation(s)
- Xiangfeng Meng
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Yu Fang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Mingyang Ding
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Yanyu Zhang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Kaili Jia
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Zhongye Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Jérôme Collemare
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China.
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17
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Promoter exchange of the cryptic nonribosomal peptide synthetase gene for oligopeptide production in Aspergillus oryzae. J Microbiol 2021; 60:47-56. [PMID: 34751906 DOI: 10.1007/s12275-022-1442-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/07/2021] [Accepted: 10/07/2021] [Indexed: 12/12/2022]
Abstract
Oligopeptides with functional activities are of current interest in the nutraceutical and medical sectors. The development of the biosynthetic process of oligopeptides through a nonribosomal peptide synthetase (NRPS) system has become more challenging. To develop a production platform for nonribosomal peptides (NRPs), reprogramming of transcriptional regulation of the acv gene encoded ACV synthetase (ACVS) was implemented in Aspergillus oryzae using the CRISPR-Cas9 system. Awakening silent acv expression was successfully achieved by promoter substitution. Among the three exchanged promoters, AoPgpdA, AoPtef1, and PtPtoxA, the replacement of the native promoter with AoPgpdA led to the highest ACV production in A. oryzae. However, the ACV production of the AoPGpdA strain was also dependent on the medium composition, in which urea was the best nitrogen source, and a C:N ratio of 20:1 was optimal for tripeptide production. In addition to cell growth, magnesium ions are an essential element for ACV production and might participate in ACVS activity. It was also found that ACV was the growth-associated product of the engineered strain that might be a result of constitutive transcriptional control by the AoPgpdA promoter. This study offers a potential strategy for nonribosomal ACV production using the fungal system, which is applicable for redesigning bioactive oligopeptides with industrial relevance.
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18
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Abstract
The fungal kingdom has provided advances in our ability to identify biosynthetic gene clusters (BGCs) and to examine how gene composition of BGCs evolves across species and genera. However, little is known about the evolution of specific BGC regulators that mediate how BGCs produce secondary metabolites (SMs). A bioinformatics search for conservation of the Aspergillus fumigatus xanthocillin BGC revealed an evolutionary trail of xan-like BGCs across Eurotiales species. Although the critical regulatory and enzymatic genes were conserved in Penicillium expansum, overexpression (OE) of the conserved xan BGC transcription factor (TF) gene, PexanC, failed to activate the putative xan BGC transcription or xanthocillin production in P. expansum, in contrast to the role of AfXanC in A. fumigatus. Surprisingly, OE::PexanC was instead found to promote citrinin synthesis in P. expansum via trans induction of the cit pathway-specific TF, ctnA, as determined by cit BGC expression and chemical profiling of ctnA deletion and OE::PexanC single and double mutants. OE::AfxanC results in significant increases of xan gene expression and metabolite synthesis in A. fumigatus but had no effect on either xanthocillin or citrinin production in P. expansum. Bioinformatics and promoter mutation analysis led to the identification of an AfXanC binding site, 5'-AGTCAGCA-3', in promoter regions of the A. fumigatus xan BGC genes. This motif was not in the ctnA promoter, suggesting a different binding site of PeXanC. A compilation of a bioinformatics examination of XanC orthologs and the presence/absence of the 5'-AGTCAGCA-3' binding motif in xan BGCs in multiple Aspergillus and Penicillium spp. supports an evolutionary divergence of XanC regulatory targets that we speculate reflects an exaptation event in the Eurotiales. IMPORTANCE Fungal secondary metabolites (SMs) are an important source of pharmaceuticals on one hand and toxins on the other. Efforts to identify the biosynthetic gene clusters (BGCs) that synthesize SMs have yielded significant insights into how variation in the genes that compose BGCs may impact subsequent metabolite production within and between species. However, the role of regulatory genes in BGC activation is less well understood. Our finding that the bZIP transcription factor XanC, located in the xanthocillin BGC of both Aspergillus fumigatus and Penicillium expansum, has functionally diverged to regulate different BGCs in these two species emphasizes that the diversification of BGC regulatory elements may sometimes occur through exaptation, which is the co-option of a gene that evolved for one function to a novel function. Furthermore, this work suggests that the loss/gain of transcription factor binding site targets may be an important mediator in the evolution of secondary-metabolism regulatory elements.
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19
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Awakawa T, Abe I. Reconstitution of Polyketide-Derived Meroterpenoid Biosynthetic Pathway in Aspergillus oryzae. J Fungi (Basel) 2021; 7:jof7060486. [PMID: 34208768 PMCID: PMC8235479 DOI: 10.3390/jof7060486] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/12/2021] [Accepted: 06/14/2021] [Indexed: 02/03/2023] Open
Abstract
The heterologous gene expression system with Aspergillus oryzae as the host is an effective method to investigate fungal secondary metabolite biosynthetic pathways for reconstruction to produce un-natural molecules due to its high productivity and genetic tractability. In this review, we focus on biosynthetic studies of fungal polyketide-derived meroterpenoids, a group of bioactive natural products, by means of the A. oryzae heterologous expression system. The heterologous expression methods and the biosynthetic reactions are described in detail for future prospects to create un-natural molecules via biosynthetic re-design.
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Affiliation(s)
- Takayoshi Awakawa
- Laboratory of Natural Products Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
- Correspondence: (T.A.); (I.A.)
| | - Ikuro Abe
- Laboratory of Natural Products Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
- Correspondence: (T.A.); (I.A.)
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20
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Anantayanon J, Jeennor S, Panchanawaporn S, Chutrakul C, Laoteng K. Significance of two intracellular triacylglycerol lipases of Aspergillus oryzae in lipid mobilization: A perspective in industrial implication for microbial lipid production. Gene 2021; 793:145745. [PMID: 34077774 DOI: 10.1016/j.gene.2021.145745] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/05/2021] [Accepted: 05/27/2021] [Indexed: 11/24/2022]
Abstract
Microbial lipid production of oleaginous strains involves in a complex cellular metabolism controlling lipid biosynthesis, accumulation and degradation. Particular storage lipid, triacylglycerol (TAG), contributes to dynamic traits of intracellular lipids and cell growth. To explore a basis of TAG degradation in the oleaginous strain of Aspergillus oryzae, the functional role of two intracellular triacylglycerol lipases, AoTgla and AoTglb, were investigated by targeted gene disruption using CRISPR/Cas9 system. Comparative lipid profiling of different cultivation stages between the control, single and double disruptant strains (ΔAotgla, ΔAotglb and ΔAotglaΔAotglb strains) showed that the inactivation of either AoTgla or AoTglb led to the increase of total lipid contents, particularly in the TAG fraction. Moreover, the prolonged lipid-accumulating stage of all disruptant strains was obtained as indicated by a reduction in specific rate of lipid turnover, in which a holding capacity in maximal lipid and TAG levels was achieved. The involvement of AoTgls in spore production of A. oryzae was also discovered. In addition to the significance in lipid physiology of the oleaginous fungi, this study provides an impact on industrial practice by overcoming the limitation in short lipid-accumulating stage of the fungal strain, which facilitate the cell harvesting step at the maximum lipid production yield.
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Affiliation(s)
- Jutamas Anantayanon
- Industrial Bioprocess Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Sukanya Jeennor
- Industrial Bioprocess Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Sarocha Panchanawaporn
- Industrial Bioprocess Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Chanikul Chutrakul
- Industrial Bioprocess Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Kobkul Laoteng
- Industrial Bioprocess Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand.
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21
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Kahlert L, Villanueva M, Cox RJ, Skellam EJ. Biosynthesis of 6-Hydroxymellein Requires a Collaborating Polyketide Synthase-like Enzyme. Angew Chem Int Ed Engl 2021; 60:11423-11429. [PMID: 33661567 PMCID: PMC8251887 DOI: 10.1002/anie.202100969] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/22/2021] [Indexed: 12/12/2022]
Abstract
The polyketide synthase (PKS)-like protein TerB, consisting of inactive dehydratase, inactive C-methyltransferase, and functional ketoreductase domains collaborates with the iterative non reducing PKS TerA to produce 6-hydroxymellein, a key pathway intermediate during the biosynthesis of various fungal natural products. The catalytically inactive dehydratase domain of TerB appears to mediate productive interactions with TerA, demonstrating a new mode of trans-interaction between iterative PKS components.
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Affiliation(s)
- Lukas Kahlert
- Institute for Organic Chemistry and BMWZLeibniz Universität HannoverSchneiderberg 3830167HannoverGermany
| | - Miranda Villanueva
- Institute for Organic Chemistry and BMWZLeibniz Universität HannoverSchneiderberg 3830167HannoverGermany
- Current address: The Molecular Biology InstituteUCLALos AngelesCA90095-1570USA
| | - Russell J. Cox
- Institute for Organic Chemistry and BMWZLeibniz Universität HannoverSchneiderberg 3830167HannoverGermany
| | - Elizabeth J. Skellam
- Institute for Organic Chemistry and BMWZLeibniz Universität HannoverSchneiderberg 3830167HannoverGermany
- Current address: Department of Chemistry & BioDiscovery InstituteUniversity of North Texas1155 Union Circle 305220DentonTX76203USA
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22
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Kahlert L, Villanueva M, Cox RJ, Skellam EJ. Biosynthesis of 6‐Hydroxymellein Requires a Collaborating Polyketide Synthase‐like Enzyme. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Lukas Kahlert
- Institute for Organic Chemistry and BMWZ Leibniz Universität Hannover Schneiderberg 38 30167 Hannover Germany
| | - Miranda Villanueva
- Institute for Organic Chemistry and BMWZ Leibniz Universität Hannover Schneiderberg 38 30167 Hannover Germany
- Current address: The Molecular Biology Institute UCLA Los Angeles CA 90095-1570 USA
| | - Russell J. Cox
- Institute for Organic Chemistry and BMWZ Leibniz Universität Hannover Schneiderberg 38 30167 Hannover Germany
| | - Elizabeth J. Skellam
- Institute for Organic Chemistry and BMWZ Leibniz Universität Hannover Schneiderberg 38 30167 Hannover Germany
- Current address: Department of Chemistry & BioDiscovery Institute University of North Texas 1155 Union Circle 305220 Denton TX 76203 USA
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23
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Duan Y, Liu J, Du Y, Pei X, Li M. Aspergillus oryzae Biosynthetic Platform for de Novo Iridoid Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:2501-2511. [PMID: 33599481 DOI: 10.1021/acs.jafc.0c06563] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The iridoids and their derivatives monoterpene indole alkaloids (MIAs) are two broad classes of plant-derived natural products with valuable pharmaceutical properties. However, the poor source limited their application. Nepetalactol, a common iridoid scaffold of MIAs, was heterologously produced in Saccharomyces cerevisiae. Although the optimization of nepetalactol production in S. cerevisiae was achieved by metabolic engineering, the inherent metabolic constraints impose a restriction on the production. Herein, we developed a high nepetalactol-producing Aspergillus oryzae platform strain. First, the co-expression of 5 nepetalactol biosynthetic genes, in a high isopentenyl pyrophosphate (IPP)-producing strain A. oryzae AK2, succeeded in the biosynthesis of nepetalactol. Second, the improvement of the IPP supply and the suppression of the byproduct citronellol formation were simultaneously achieved. Finally, the highest titer of nepetalactol of 7.2 mg/L was obtained with the engineered strain, after the optimization of the carbon source. To the best of our knowledge, this is the highest reported titer of nepetalactol in microbial cells. The developed A. oryzae strain represents an attractive biosynthetic platform host for the de novo production of iridoids and MIAs.
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Affiliation(s)
- Yali Duan
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jiawei Liu
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yun Du
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xiaolin Pei
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, Zhejiang 310012, China
| | - Mu Li
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
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24
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Kahlert L, Schotte C, Cox RJ. Total Mycosynthesis: Rational Bioconstruction and Bioengineering of Fungal Natural Products. SYNTHESIS-STUTTGART 2021. [DOI: 10.1055/a-1401-2716] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
AbstractTotal biosynthesis in fungi is beginning to compete with traditional chemical total synthesis campaigns. Herein, the advantages, disadvantages and future opportunities are discussed within the scope of several recent examples.1 Introduction2 Synthetic Examples2.1 2-Pyridones2.2 Cytochalasans2.3 Sorbicillinoids2.4 Decalins: Solanapyrone2.5 α-Pyrone Polyenes: Citreoviridin and Aurovertin2.6 Anditomin and Related Meroterpenoids2.7 Tropolone Sesquiterpenoids3 Conclusion
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25
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Zhang H, Hantke V, Bruhnke P, Skellam EJ, Cox RJ. Chemical and Genetic Studies on the Formation of Pyrrolones During the Biosynthesis of Cytochalasans. Chemistry 2021; 27:3106-3113. [PMID: 33146923 PMCID: PMC7898483 DOI: 10.1002/chem.202004444] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Indexed: 01/17/2023]
Abstract
A key step during the biosynthesis of cytochalasans is a proposed Knoevenagel condensation to form the pyrrolone core, enabling the subsequent 4+2 cycloaddition reaction that results in the characteristic octahydroisoindolone motif of all cytochalasans. In this work, we investigate the role of the highly conserved α,β-hydrolase enzymes PyiE and ORFZ during the biosynthesis of pyrichalasin H and the ACE1 metabolite, respectively, using gene knockout and complementation techniques. Using synthetic aldehyde models we demonstrate that the Knoevenagel condensation proceeds spontaneously but results in the 1,3-dihydro-2H-pyrrol-2-one tautomer, rather than the required 1,5-dihydro-2H-pyrrol-2-one tautomer. Taken together our results suggest that the α,β-hydrolase enzymes are essential for first ring cyclisation, but the precise nature of the intermediates remains to be determined.
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Affiliation(s)
- Haili Zhang
- Institute for Organic ChemistryLeibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
- Biomolekulares Wirkstoff Zentrum (BMWZ)Leibniz Universität HannoverSchneiderberg 3830167HannoverGermany
| | - Verena Hantke
- Institute for Organic ChemistryLeibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
- Biomolekulares Wirkstoff Zentrum (BMWZ)Leibniz Universität HannoverSchneiderberg 3830167HannoverGermany
| | - Pia Bruhnke
- Institute for Organic ChemistryLeibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
- Biomolekulares Wirkstoff Zentrum (BMWZ)Leibniz Universität HannoverSchneiderberg 3830167HannoverGermany
| | - Elizabeth J. Skellam
- Institute for Organic ChemistryLeibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
- Biomolekulares Wirkstoff Zentrum (BMWZ)Leibniz Universität HannoverSchneiderberg 3830167HannoverGermany
- Current Address: Department of ChemistryUniversity of North Texas1508 W Mulberry30167DentonTexasUSA
| | - Russell J. Cox
- Institute for Organic ChemistryLeibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
- Biomolekulares Wirkstoff Zentrum (BMWZ)Leibniz Universität HannoverSchneiderberg 3830167HannoverGermany
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26
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Dao TT, de Mattos-Shipley KMJ, Prosser IM, Williams K, Zacharova MK, Lazarus CM, Willis CL, Bailey AM. Cleaning the Cellular Factory-Deletion of McrA in Aspergillus oryzae NSAR1 and the Generation of a Novel Kojic Acid Deficient Strain for Cleaner Heterologous Production of Secondary Metabolites. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:632542. [PMID: 37744117 PMCID: PMC10512265 DOI: 10.3389/ffunb.2021.632542] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/18/2021] [Indexed: 09/26/2023]
Abstract
The use of filamentous fungi as cellular factories, where natural product pathways can be refactored and expressed in a host strain, continues to aid the field of natural product discovery. Much work has been done to develop host strains which are genetically tractable, and for which there are multiple selectable markers and controllable expression systems. To fully exploit these strains, it is beneficial to understand their natural metabolic capabilities, as such knowledge can rule out host metabolites from analysis of transgenic lines and highlight any potential interplay between endogenous and exogenous pathways. Additionally, once identified, the deletion of secondary metabolite pathways from host strains can simplify the detection and purification of heterologous compounds. To this end, secondary metabolite production in Aspergillus oryzae strain NSAR1 has been investigated via the deletion of the newly discovered negative regulator of secondary metabolism, mcrA (multicluster regulator A). In all ascomycetes previously studied mcrA deletion led to an increase in secondary metabolite production. Surprisingly, the only detectable phenotypic change in NSAR1 was a doubling in the yields of kojic acid, with no novel secondary metabolites produced. This supports the previous claim that secondary metabolite production has been repressed in A. oryzae and demonstrates that such repression is not McrA-mediated. Strain NSAR1 was then modified by employing CRISPR-Cas9 technology to disrupt the production of kojic acid, generating the novel strain NSARΔK, which combines the various beneficial traits of NSAR1 with a uniquely clean secondary metabolite background.
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Affiliation(s)
- Trong T. Dao
- School of Chemistry, University of Bristol, Bristol, United Kingdom
| | | | - Ian M. Prosser
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Katherine Williams
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | | | - Colin M. Lazarus
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | | | - Andrew M. Bailey
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
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27
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Chiang YM, Lin TS, Chang SL, Ahn G, Wang CCC. An Aspergillus nidulans Platform for the Complete Cluster Refactoring and Total Biosynthesis of Fungal Natural Products. ACS Synth Biol 2021; 10:173-182. [PMID: 33375785 DOI: 10.1021/acssynbio.0c00536] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fungal natural products (NPs) comprise a vast number of bioactive molecules with diverse activities, and among them are many important drugs. However, the yields of fungal NPs from native producers are usually low, and total synthesis of structurally complex NPs is challenging. As such, downstream derivatization and optimization of lead fungal NPs can be impeded by the high cost of obtaining sufficient starting material. In recent years, reconstitution of NP biosynthetic pathways in heterologous hosts has become an attractive alternative approach to produce complex NPs. Here, we present an efficient, cloning-free strategy for the cluster refactoring and total biosynthesis of fungal NPs in Aspergillus nidulans. Our platform places our genes of interest (GOIs) under the regulation of the robust asperfuranone afo biosynthesis gene machinery, allowing for their concerted activation upon induction. We demonstrated the utility of our system by creating strains that can synthesize high-value NPs, citreoviridin (1), mutilin (2), and pleuromutilin (3), with good to high yield and purity. This platform can be used not only for producing NPs of interests (i.e., total biosynthesis) but also for elucidating cryptic biosynthesis pathways.
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Affiliation(s)
- Yi-Ming Chiang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089, United States
- Department of Pharmacy, Chia Nan University of Pharmacy and Science, Tainan 71710, Taiwan, ROC
| | - Tzu-Shyang Lin
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089, United States
| | - Shu-Lin Chang
- Department of Cosmetic Science, Chia Nan University of Pharmacy and Science, Tainan 71710, Taiwan, ROC
| | - Green Ahn
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089, United States
| | - Clay C C Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089, United States
- Department of Chemistry, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California 90089, United States
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Chutrakul C, Panchanawaporn S, Jeennor S, Anantayanon J, Vorapreeda T, Vichai V, Laoteng K. Functional Characterization of Novel U6 RNA Polymerase III Promoters: Their Implication for CRISPR-Cas9-Mediated Gene Editing in Aspergillus oryzae. Curr Microbiol 2019; 76:1443-1451. [PMID: 31541261 DOI: 10.1007/s00284-019-01770-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 09/09/2019] [Indexed: 01/04/2023]
Abstract
U6 RNA polymerase III promoter (PU6), which is a key element in controlling the generation of single-guide RNA (sgRNA) for gene editing through CRISPR-Cas9 system, was investigated in this work. Using bioinformatics approach, two novel U6 ribonucleic acid (U6 RNA) sequences of Aspergillus niger were identified, showing that they had conserved motifs similar to other U6 RNAs. The putative PU6 located at the upstream sequence of A. niger U6 RNA exhibited the consensus motif, CCAATYA, and the TATA box which shared highly conserved characteristics across Aspergilli, whereas the A- and B-boxes were found at the intragenic and downstream of the structural genes, respectively. Using Aspergillus oryzae as a workhorse system, the function of A. niger PU6s for controlling the transcripts of sgRNA was verified, in which the orotidine-5'-phosphate decarboxylase (pyrG) sequence was used as a target for gene disruption through CRISPR-Cas9 system. Quantitative reverse transcription-polymerase chain reaction (RT-qPCR) analysis of the selected pyrG auxotrophic strains showed the expression of sgRNA, indicating that the non-native promoters could efficiently drive sgRNA expression in A. oryzae. These identified promoters are useful genetic tools for precise engineering of metabolic pathways in the industrially important fungus through the empowered CRISPR-Cas9-associated gene-editing system.
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Affiliation(s)
- Chanikul Chutrakul
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathum Thani, 12120, Thailand.
| | - Sarocha Panchanawaporn
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathum Thani, 12120, Thailand
| | - Sukanya Jeennor
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathum Thani, 12120, Thailand
| | - Jutamas Anantayanon
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathum Thani, 12120, Thailand
| | - Tayvich Vorapreeda
- Biochemical Engineering and Systems Biology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC) At King Mongkut's University of Technology Thonburi, Bangkhuntien, Bangkok, 10150, Thailand
| | - Vanicha Vichai
- Biosensing and Bioprospecting Technology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathum Thani, 12120, Thailand
| | - Kobkul Laoteng
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathum Thani, 12120, Thailand
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Jeennor S, Anantayanon J, Panchanawaporn S, Chutrakul C, Laoteng K. Morphologically engineered strain of Aspergillus oryzae as a cell chassis for production development of functional lipids. Gene 2019; 718:144073. [DOI: 10.1016/j.gene.2019.144073] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/08/2019] [Accepted: 08/21/2019] [Indexed: 01/30/2023]
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Wang C, Becker K, Pfütze S, Kuhnert E, Stadler M, Cox RJ, Skellam E. Investigating the Function of Cryptic Cytochalasan Cytochrome P450 Monooxygenases Using Combinatorial Biosynthesis. Org Lett 2019; 21:8756-8760. [PMID: 31644300 DOI: 10.1021/acs.orglett.9b03372] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Tailoring enzymes in cytochalasan biosynthesis are relatively promiscuous. Exploiting this property, we deduced the function of four cryptic cytochrome P450 monooxygenases via heterologous expression of six cytochrome P450-encoding genes, originating from Hypoxylon fragiforme and Pyricularia oryzae, in pyrichalasin H ΔP450 strains. Three cryptic cytochrome P450 enzymes (HffD, HffG, and CYP1) restored pyrichalasin H production in mutant strains, while CYP3 catalyzed a site-selective epoxidation leading to the isolation of three novel cytochalasans.
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Affiliation(s)
- Chongqing Wang
- Institute for Organic Chemistry and Centre for Biomolecular Drug Research , Leibniz University Hannover , Schneiderberg 38 , Hannover 30167 , Germany
| | - Kevin Becker
- Department Microbial Drugs , Helmholtz Centre for Infection Research (HZI) , Inhoffenstraße 7 , 38124 Braunschweig , Germany
| | - Sebastian Pfütze
- Department Microbial Drugs , Helmholtz Centre for Infection Research (HZI) , Inhoffenstraße 7 , 38124 Braunschweig , Germany
| | - Eric Kuhnert
- Institute for Organic Chemistry and Centre for Biomolecular Drug Research , Leibniz University Hannover , Schneiderberg 38 , Hannover 30167 , Germany
| | - Marc Stadler
- Department Microbial Drugs , Helmholtz Centre for Infection Research (HZI) , Inhoffenstraße 7 , 38124 Braunschweig , Germany
| | - Russell J Cox
- Institute for Organic Chemistry and Centre for Biomolecular Drug Research , Leibniz University Hannover , Schneiderberg 38 , Hannover 30167 , Germany
| | - Elizabeth Skellam
- Institute for Organic Chemistry and Centre for Biomolecular Drug Research , Leibniz University Hannover , Schneiderberg 38 , Hannover 30167 , Germany
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Vassaux A, Meunier L, Vandenbol M, Baurain D, Fickers P, Jacques P, Leclère V. Nonribosomal peptides in fungal cell factories: from genome mining to optimized heterologous production. Biotechnol Adv 2019; 37:107449. [PMID: 31518630 DOI: 10.1016/j.biotechadv.2019.107449] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 12/15/2022]
Abstract
Fungi are notoriously prolific producers of secondary metabolites including nonribosomal peptides (NRPs). The structural complexity of NRPs grants them interesting activities such as antibiotic, anti-cancer, and anti-inflammatory properties. The discovery of these compounds with attractive activities can be achieved by using two approaches: either by screening samples originating from various environments for their biological activities, or by identifying the related clusters in genomic sequences thanks to bioinformatics tools. This genome mining approach has grown tremendously due to recent advances in genome sequencing, which have provided an incredible amount of genomic data from hundreds of microbial species. Regarding fungal organisms, the genomic data have revealed the presence of an unexpected number of putative NRP-related gene clusters. This highlights fungi as a goldmine for the discovery of putative novel bioactive compounds. Recent development of NRP dedicated bioinformatics tools have increased the capacity to identify these gene clusters and to deduce NRPs structures, speeding-up the screening process for novel metabolites discovery. Unfortunately, the newly identified compound is frequently not or poorly produced by native producers due to a lack of expression of the related genes cluster. A frequently employed strategy to increase production rates consists in transferring the related biosynthetic pathway in heterologous hosts. This review aims to provide a comprehensive overview about the topic of NRPs discovery, from gene cluster identification by genome mining to the heterologous production in fungal hosts. The main computational tools and methods for genome mining are herein presented with an emphasis on the particularities of the fungal systems. The different steps of the reconstitution of NRP biosynthetic pathway in heterologous fungal cell factories will be discussed, as well as the key factors to consider for maximizing productivity. Several examples will be developed to illustrate the potential of heterologous production to both discover uncharacterized novel compounds predicted in silico by genome mining, and to enhance the productivity of interesting bio-active natural products.
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Affiliation(s)
- Antoine Vassaux
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium; Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV-Institut Charles Viollette, F-59000 Lille, France
| | - Loïc Meunier
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium; InBioS-PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liege, Boulevard du Rectorat 27, B-4000 Liège, Belgium
| | - Micheline Vandenbol
- TERRA Teaching and Research Centre, Microbiologie et Génomique, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium
| | - Denis Baurain
- InBioS-PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liege, Boulevard du Rectorat 27, B-4000 Liège, Belgium
| | - Patrick Fickers
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium
| | - Philippe Jacques
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium
| | - Valérie Leclère
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV-Institut Charles Viollette, F-59000 Lille, France.
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Yang XL, Friedrich S, Yin S, Piech O, Williams K, Simpson TJ, Cox RJ. Molecular basis of methylation and chain-length programming in a fungal iterative highly reducing polyketide synthase. Chem Sci 2019; 10:8478-8489. [PMID: 31803427 PMCID: PMC6839510 DOI: 10.1039/c9sc03173a] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 07/28/2019] [Indexed: 12/28/2022] Open
Abstract
Exchange of 32 different sub-fragments of the C-methyltransferase (C-MeT), pseudo-ketoreductase (ΨKR) and ketoreductase (KR) catalytic domains of the tenellin iterative Type I polyketide synthase non ribosomal peptide synthetase (PKS-NRPS) TENS by homologous fragments from the desmethylbassianin (DMBS) and militarinone (MILS) PKS-NRPS led to the creation of chimeric synthetases in which programming fidelity was altered, resulting in the production of mixtures of products with different methylation patterns and chain lengths. Swap of KR domain subfragments with the homologous fragments from the KR of the heptaketide militarinone synthetase resulted in the synthesis of penta, hexa and heptaketides. The results of these and previous experiments are rationalised by considering the existence of competition for acyl-carrier protein (ACP) bound substrates between different catalytic domains of the PKS. In particular, competition between the C-MeT and ketoreductase domains (KR) can account for methylation programming, and competition between the KR and the off-loading NRPS accounts for chain-length selectivity.
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Affiliation(s)
- Xiao-Long Yang
- Institute for Organic Chemistry , Leibniz University of Hannover , Schneiderberg 1B , 30167 , Hannover , Germany . .,BMWZ , Leibniz University of Hannover , Schneiderberg 38 , 30167 , Hannover , Germany
| | - Steffen Friedrich
- Institute for Organic Chemistry , Leibniz University of Hannover , Schneiderberg 1B , 30167 , Hannover , Germany . .,BMWZ , Leibniz University of Hannover , Schneiderberg 38 , 30167 , Hannover , Germany
| | - Sen Yin
- Institute for Organic Chemistry , Leibniz University of Hannover , Schneiderberg 1B , 30167 , Hannover , Germany . .,BMWZ , Leibniz University of Hannover , Schneiderberg 38 , 30167 , Hannover , Germany
| | - Oliver Piech
- Institute for Organic Chemistry , Leibniz University of Hannover , Schneiderberg 1B , 30167 , Hannover , Germany . .,BMWZ , Leibniz University of Hannover , Schneiderberg 38 , 30167 , Hannover , Germany
| | - Katherine Williams
- Institute for Organic Chemistry , Leibniz University of Hannover , Schneiderberg 1B , 30167 , Hannover , Germany . .,BMWZ , Leibniz University of Hannover , Schneiderberg 38 , 30167 , Hannover , Germany.,School of Chemistry , University of Bristol , Cantock's Close , Bristol , BS8 1TS , UK
| | - Thomas J Simpson
- School of Chemistry , University of Bristol , Cantock's Close , Bristol , BS8 1TS , UK
| | - Russell J Cox
- Institute for Organic Chemistry , Leibniz University of Hannover , Schneiderberg 1B , 30167 , Hannover , Germany . .,BMWZ , Leibniz University of Hannover , Schneiderberg 38 , 30167 , Hannover , Germany
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Jeennor S, Anantayanon J, Panchanawaporn S, Khoomrung S, Chutrakul C, Laoteng K. Reengineering lipid biosynthetic pathways of Aspergillus oryzae for enhanced production of γ-linolenic acid and dihomo-γ-linolenic acid. Gene 2019; 706:106-114. [DOI: 10.1016/j.gene.2019.04.074] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/18/2019] [Accepted: 04/26/2019] [Indexed: 01/14/2023]
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Lebe KE, Cox RJ. Oxidative steps during the biosynthesis of squalestatin S1. Chem Sci 2019; 10:1227-1231. [PMID: 30774923 PMCID: PMC6349020 DOI: 10.1039/c8sc02615g] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 11/14/2018] [Indexed: 11/21/2022] Open
Abstract
The squalestatins are a class of highly complex fungal metabolites which are potent inhibitors of squalene synthase with potential use in the control of cholesterol biosynthesis. Little is known of the chemical steps involved in the construction of the 4,8-dioxa-bicyclo[3.2.1]octane core. Here, using a combination of directed gene knockout and heterologous expression experiments, we show that two putative non-heme-iron-dependent enzymes appear to catalyse a remarkable series of six consecutive oxidations which set up the bioactive core of the squalestatins. This is followed by the action of an unusual copper-dependent oxygenase which introduces a hydroxyl required for later acetylation.
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Affiliation(s)
- Karen E Lebe
- Institute for Organic Chemistry , BMWZ , Leibniz Universität Hannover , Schneiderberg 38 , 30167 Hannover , Germany .
| | - Russell J Cox
- Institute for Organic Chemistry , BMWZ , Leibniz Universität Hannover , Schneiderberg 38 , 30167 Hannover , Germany .
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35
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Bunnak W, Wonnapinij P, Sriboonlert A, Lazarus CM, Wattana-Amorn P. Heterologous biosynthesis of a fungal macrocyclic polylactone requires only two iterative polyketide synthases. Org Biomol Chem 2019; 17:374-379. [DOI: 10.1039/c8ob02773k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Formation of macrocyclic polylactone catalysed by only reducing and non-reducing polyketide synthases.
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Affiliation(s)
- Waraporn Bunnak
- Department of Chemistry
- Special Research Unit for Advanced Magnetic Resonance and Center of Excellence for Innovation in Chemistry
- Faculty of Science
- Kasetsart University
- Bangkok
| | - Passorn Wonnapinij
- Department of Genetics
- Faculty of Science
- Kasetsart University
- Bangkok
- Thailand
| | | | | | - Pakorn Wattana-Amorn
- Department of Chemistry
- Special Research Unit for Advanced Magnetic Resonance and Center of Excellence for Innovation in Chemistry
- Faculty of Science
- Kasetsart University
- Bangkok
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Griffiths SA, Cox RJ, Overdijk EJR, Mesarich CH, Saccomanno B, Lazarus CM, de Wit PJGM, Collemare J. Assignment of a dubious gene cluster to melanin biosynthesis in the tomato fungal pathogen Cladosporium fulvum. PLoS One 2018; 13:e0209600. [PMID: 30596695 PMCID: PMC6312243 DOI: 10.1371/journal.pone.0209600] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 12/07/2018] [Indexed: 12/17/2022] Open
Abstract
Pigments and phytotoxins are crucial for the survival and spread of plant pathogenic fungi. The genome of the tomato biotrophic fungal pathogen Cladosporium fulvum contains a predicted gene cluster (CfPKS1, CfPRF1, CfRDT1 and CfTSF1) that is syntenic with the characterized elsinochrome toxin gene cluster in the citrus pathogen Elsinoë fawcettii. However, a previous phylogenetic analysis suggested that CfPks1 might instead be involved in pigment production. Here, we report the characterization of the CfPKS1 gene cluster to resolve this ambiguity. Activation of the regulator CfTSF1 specifically induced the expression of CfPKS1 and CfRDT1, but not of CfPRF1. These co-regulated genes that define the CfPKS1 gene cluster are orthologous to genes involved in 1,3-dihydroxynaphthalene (DHN) melanin biosynthesis in other fungi. Heterologous expression of CfPKS1 in Aspergillus oryzae yielded 1,3,6,8-tetrahydroxynaphthalene, a typical precursor of DHN melanin. Δcfpks1 deletion mutants showed similar altered pigmentation to wild type treated with DHN melanin inhibitors. These mutants remained virulent on tomato, showing this gene cluster is not involved in pathogenicity. Altogether, our results showed that the CfPKS1 gene cluster is involved in the production of DHN melanin and suggests that elsinochrome production in E. fawcettii likely involves another gene cluster.
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Affiliation(s)
- Scott A. Griffiths
- Fungal Natural Products, Westerdijk Fungal Biodiversity Institute, CT, Utrecht, The Netherlands
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Russell J. Cox
- Institut für Organische Chemie, Leibniz Universität Hannover, Hannover
| | - Elysa J. R. Overdijk
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
- Laboratory of Cell Biology, Wageningen University, Wageningen, The Netherlands
| | - Carl H. Mesarich
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Benedetta Saccomanno
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Colin M. Lazarus
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | | | - Jérôme Collemare
- Fungal Natural Products, Westerdijk Fungal Biodiversity Institute, CT, Utrecht, The Netherlands
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
- * E-mail:
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Abstract
Strobilurins from fungi are the inspiration for the creation of the β-methoxyacrylate class of agricultural fungicides. However, molecular details of the biosynthesis of strobilurins have remained cryptic. Here we report the sequence of genomes of two fungi that produce strobilurins and show that each contains a biosynthetic gene cluster, which encodes a highly reducing polyketide synthase with very unusual C-terminal hydrolase and methyltransferase domains. Expression of stpks1 in Aspergillus oryzae leads to the production of prestrobilurin A when the fermentation is supplemented with a benzoyl coenzyme A (CoA) analogue. This enables the discovery of a previously unobserved route to benzoyl CoA. Reconstruction of the gene cluster in A. oryzae leads to the formation of prestrobilurin A, and addition of the gene str9 encoding an FAD-dependent oxygenase leads to the key oxidative rearrangement responsible for the creation of the β-methoxyacrylate toxophore. Finally, two methyltransferases are required to complete the synthesis. Strobilurins are fungal metabolites that inspired the creation of β-methoxyacrylate agricultural fungicides. Here, Nofiani et al. identify the strobilurin biosynthesis gene cluster, encoding a polyketide synthase as well as an FAD-dependent oxygenase for an oxidative rearrangement leading to β-methoxyacrylate formation.
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Facile assembly and fluorescence-based screening method for heterologous expression of biosynthetic pathways in fungi. Metab Eng 2018; 48:44-51. [PMID: 29842926 DOI: 10.1016/j.ymben.2018.05.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 05/17/2018] [Accepted: 05/25/2018] [Indexed: 11/22/2022]
Abstract
Heterologous expression of multi-gene biosynthetic pathways in eukaryotic hosts is limited by highly regulated individual monocistrons. Dissimilar to prokaryotes, each eukaryotic gene is strictly controlled by its own regulatory elements, such as promoter and terminator. Consequently, parallel transcription can occur only when a group of genes is synchronously activated. A strategy to circumvent this limitation is the concerted expression of multiple genes as a polycistron. By exploiting the "stop-carry on" mechanism of picornaviruses, we have designed a sophisticated, yet easy-to-assemble vector system to heterologously express multiple genes under the control of a single promoter. For facile selection of correctly transformed colonies by basic fluorescence microscopy, our vector includes a split gene for a fluorescent reporter protein. This method was successfully applied to produce the psychotropic mushroom alkaloid psilocybin in high yields by heterologous expression of the entire biosynthetic gene cluster in the mould Aspergillus nidulans.
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Eyles TH, Vior NM, Truman AW. Rapid and Robust Yeast-Mediated Pathway Refactoring Generates Multiple New Bottromycin-Related Metabolites. ACS Synth Biol 2018; 7:1211-1218. [PMID: 29694038 DOI: 10.1021/acssynbio.8b00038] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Heterologous expression of biosynthetic gene clusters (BGCs) represents an attractive route to the production of new natural products, but is often hampered by poor yields. It is therefore important to develop tools that enable rapid refactoring, gene insertion/deletion, and targeted mutations in BGCs. Ideally, these tools should be highly efficient, affordable, accessible, marker free, and flexible for use with a wide range of BGCs. Here, we present a one-step yeast-based method that enables efficient, cheap, and flexible modifications to BGCs. Using the BGC for the antibiotic bottromycin, we showcase multiple modifications including refactoring, gene deletions and targeted mutations. This facilitated the construction of an inducible, riboswitch-controlled pathway that achieved a 120-fold increase in pathway productivity in a heterologous streptomycete host. Additionally, an unexpected biosynthetic bottleneck resulted in the production of a suite of new bottromycin-related metabolites.
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Affiliation(s)
- Tom H. Eyles
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, U.K
| | - Natalia M. Vior
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, U.K
| | - Andrew W. Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, U.K
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Three previously unrecognised classes of biosynthetic enzymes revealed during the production of xenovulene A. Nat Commun 2018; 9:1963. [PMID: 29773797 PMCID: PMC5958101 DOI: 10.1038/s41467-018-04364-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 04/25/2018] [Indexed: 01/28/2023] Open
Abstract
Xenovulene A is a complex fungal meroterpenoid, produced by the organism hitherto known as Acremonium strictum IMI 501407, for which limited biosynthetic evidence exists. Here, we generate a draft genome and show that the producing organism is previously unknown and should be renamed as Sarocladium schorii. A biosynthetic gene cluster is discovered which bears resemblance to those involved in the biosynthesis of fungal tropolones, with additional genes of unknown function. Heterologous reconstruction of the entire pathway in Aspergillus oryzae allows the chemical steps of biosynthesis to be dissected. The pathway shows very limited similarity to the biosynthesis of other fungal meroterpenoids. The pathway features: the initial formation of tropolone intermediates; the likely involvement of a hetero Diels–Alder enzyme; a terpene cyclase with no significant sequence homology to any known terpene cyclase and two enzymes catalysing oxidative-ring contractions. Xenovulene A is a fungal compound that has the potential to be used as an antidepressant. Here, the authors unravel the pathway leading to its formation in fungi and discover a new class of enzymes, which accounts for some unusual chemistry in the synthesis of xenovulene.
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41
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He Y, Wang B, Chen W, Cox RJ, He J, Chen F. Recent advances in reconstructing microbial secondary metabolites biosynthesis in Aspergillus spp. Biotechnol Adv 2018; 36:739-783. [DOI: 10.1016/j.biotechadv.2018.02.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 01/30/2018] [Accepted: 02/01/2018] [Indexed: 11/28/2022]
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de Mattos-Shipley KMJ, Greco C, Heard DM, Hough G, Mulholland NP, Vincent JL, Micklefield J, Simpson TJ, Willis CL, Cox RJ, Bailey AM. The cycloaspeptides: uncovering a new model for methylated nonribosomal peptide biosynthesis. Chem Sci 2018; 9:4109-4117. [PMID: 29780540 PMCID: PMC5941284 DOI: 10.1039/c8sc00717a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 04/03/2018] [Indexed: 11/21/2022] Open
Abstract
The cycloaspeptide gene cluster includes a pathway-specific N-methyl transferase. Its disruption allowed incorporation of N-methylated amino acids provided in the culture medium, allowing efficient production of cycloaspeptide E and novel related products.
The cycloaspeptides are bioactive pentapeptides produced by various filamentous fungi, which have garnered interest from the agricultural industry due to the reported insecticidal activity of the minor metabolite, cycloaspeptide E. Genome sequencing, bioinformatics and heterologous expression confirmed that the cycloaspeptide gene cluster contains a minimal 5-module nonribosomal peptide synthetase (NRPS) and a new type of trans-acting N-methyltransferase (N-MeT). Deletion of the N-MeT encoding gene and subsequent feeding studies determined that two modules of the NRPS preferentially accept and incorporate N-methylated amino acids. This discovery allowed the development of a system with unprecedented control over substrate supply and thus output, both increasing yields of specific metabolites and allowing the production of novel fluorinated analogues. Furthermore, the biosynthetic pathway to ditryptophenaline, another fungal nonribosomal peptide, was shown to be similar, in that methylated phenylalanine is accepted by the ditryptophenaline NRPS. Again, this allowed the directed biosynthesis of a fluorinated analogue, through the feeding of a mutant strain. These discoveries represent a new paradigm for the production of N-methylated cyclic peptides via the selective incorporation of N-methylated free amino acids.
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Affiliation(s)
| | - Claudio Greco
- School of Chemistry , University of Bristol , Cantock's Close , Bristol , BS8 1TS , UK .
| | - David M Heard
- School of Chemistry , University of Bristol , Cantock's Close , Bristol , BS8 1TS , UK .
| | - Gemma Hough
- Syngenta Ltd. , Jealott's Hill International Research Centre Bracknell , Berkshire , RG42 6EY , UK
| | - Nicholas P Mulholland
- Syngenta Ltd. , Jealott's Hill International Research Centre Bracknell , Berkshire , RG42 6EY , UK
| | - Jason L Vincent
- Syngenta Ltd. , Jealott's Hill International Research Centre Bracknell , Berkshire , RG42 6EY , UK
| | - Jason Micklefield
- School of Chemistry , University of Manchester , Oxford Road , Manchester , M1 7DN , UK
| | - Thomas J Simpson
- School of Chemistry , University of Bristol , Cantock's Close , Bristol , BS8 1TS , UK .
| | - Christine L Willis
- School of Chemistry , University of Bristol , Cantock's Close , Bristol , BS8 1TS , UK .
| | - Russell J Cox
- Institute für Organsche Chemie , Leibniz Universität Hannover , Schneiderberg 1A , 30167 Hannover , Germany.,BMWZ , Leibniz Universität Hannover , Schneiderberg 38 , 30167 Hannover , Germany
| | - Andrew M Bailey
- School of Biological Sciences , University of Bristol , Life Sciences Building, 24 Tyndall Avenue , Bristol , BS8 1TQ , UK .
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43
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Schor R, Cox R. Classic fungal natural products in the genomic age: the molecular legacy of Harold Raistrick. Nat Prod Rep 2018. [PMID: 29537034 DOI: 10.1039/c8np00021b] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: 1893 to 2017Harold Raistrick was involved in the discovery of many of the most important classes of fungal metabolites during the 20th century. This review focusses on how these discoveries led to developments in isotopic labelling, biomimetic chemistry and the discovery, analysis and exploitation of biosynthetic gene clusters for major classes of fungal metabolites including: alternariol; geodin and metabolites of the emodin pathway; maleidrides; citrinin and the azaphilones; dehydrocurvularin; mycophenolic acid; and the tropolones. Key recent advances in the molecular understanding of these important pathways, including the discovery of biosynthetic gene clusters, the investigation of the molecular and chemical aspects of key biosynthetic steps, and the reengineering of key components of the pathways are reviewed and compared. Finally, discussion of key relationships between metabolites and pathways and the most important recent advances and opportunities for future research directions are given.
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Affiliation(s)
- Raissa Schor
- Institut für Organische Chemie, BMWZ, Leibniz Universität Hannover, Germany.
| | - Russell Cox
- Institut für Organische Chemie, BMWZ, Leibniz Universität Hannover, Germany.
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44
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Yamane M, Minami A, Liu C, Ozaki T, Takeuchi I, Tsukagoshi T, Tokiwano T, Gomi K, Oikawa H. Biosynthetic Machinery of Diterpene Pleuromutilin Isolated from Basidiomycete Fungi. Chembiochem 2017; 18:2317-2322. [PMID: 28924980 DOI: 10.1002/cbic.201700434] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Indexed: 12/11/2022]
Abstract
The diterpene pleuromutilin is a ribosome-targeting antibiotic isolated from basidiomycete fungi, such as Clitopilus pseudo-pinsitus. The functional characterization of all biosynthetic enzymes involved in pleuromutilin biosynthesis is reported and a biosynthetic pathway proposed. In vitro enzymatic reactions and mutational analysis revealed that a labdane-related diterpene synthase, Ple3, catalyzed two rounds of cyclization from geranylgeranyl diphosphate to premutilin possessing a characteristic 5-6-8-tricyclic carbon skeleton. Biotransformation experiments utilizing Aspergillus oryzae transformants possessing modification enzyme genes allowed the biosynthetic pathway from premutilin to pleuromutilin to be proposed. The present study sets the stage for the enzymatic synthesis of natural products isolated from basidiomycete fungi, which are a prolific source of structurally diverse and biologically active terpenoids.
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Affiliation(s)
- Momoka Yamane
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Atsushi Minami
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Chengwei Liu
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Taro Ozaki
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Ichiro Takeuchi
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Tae Tsukagoshi
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Tetsuo Tokiwano
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Katsuya Gomi
- Graduate School of Agricultural Science, Tohoku University, Sendai, 981-8555, Japan
| | - Hideaki Oikawa
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan
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45
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Alberti F, Khairudin K, Venegas ER, Davies JA, Hayes PM, Willis CL, Bailey AM, Foster GD. Heterologous expression reveals the biosynthesis of the antibiotic pleuromutilin and generates bioactive semi-synthetic derivatives. Nat Commun 2017; 8:1831. [PMID: 29184068 PMCID: PMC5705593 DOI: 10.1038/s41467-017-01659-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 10/06/2017] [Indexed: 11/10/2022] Open
Abstract
The rise in antibiotic resistance is a major threat for human health. Basidiomycete fungi represent an untapped source of underexploited antimicrobials, with pleuromutilin-a diterpene produced by Clitopilus passeckerianus-being the only antibiotic from these fungi leading to commercial derivatives. Here we report genetic characterisation of the steps involved in pleuromutilin biosynthesis, through rational heterologous expression in Aspergillus oryzae coupled with isolation and detailed structural elucidation of the pathway intermediates by spectroscopic methods and comparison with synthetic standards. A. oryzae was further established as a platform for bio-conversion of chemically modified analogues of pleuromutilin intermediates, and was employed to generate a semi-synthetic pleuromutilin derivative with enhanced antibiotic activity. These studies pave the way for future characterisation of biosynthetic pathways of other basidiomycete natural products in ascomycete heterologous hosts, and open up new possibilities of further chemical modification for the growing class of potent pleuromutilin antibiotics.
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Affiliation(s)
- Fabrizio Alberti
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
- School of Life Sciences and Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Khairunisa Khairudin
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | | | - Jonathan A Davies
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Patrick M Hayes
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Christine L Willis
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Andy M Bailey
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK.
| | - Gary D Foster
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK.
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46
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Chen W, Chen R, Liu Q, He Y, He K, Ding X, Kang L, Guo X, Xie N, Zhou Y, Lu Y, Cox RJ, Molnár I, Li M, Shao Y, Chen F. Orange, red, yellow: biosynthesis of azaphilone pigments in Monascus fungi. Chem Sci 2017; 8:4917-4925. [PMID: 28959415 PMCID: PMC5603960 DOI: 10.1039/c7sc00475c] [Citation(s) in RCA: 193] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/20/2017] [Indexed: 12/23/2022] Open
Abstract
Monascus azaphilone pigments (MonAzPs) are very widely used as food colorants, but their biosynthetic pathway has remained poorly characterized for more than half a century. In this study, the individual steps of MonAzPs biosynthesis in Monascus ruber M7 were elucidated by a combination of targeted gene knockouts, heterologous gene expression, and in vitro chemical and enzymatic reactions. This study describes the first rational engineering of MonAzPs biosynthesis and provides a roadmap for future pathway engineering efforts directed towards the selective production of the most valuable pigments and serves as a model for the biosynthesis of fungal azaphilones in general.
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Affiliation(s)
- Wanping Chen
- Key Laboratory of Environment Correlative Dietology , College of Food Science and Technology , Huazhong Agricultural University , Wuhan , Hubei Province 430070 , China . ; ; Tel: +86-27-87282111
| | - Runfa Chen
- Key Laboratory of Environment Correlative Dietology , College of Food Science and Technology , Huazhong Agricultural University , Wuhan , Hubei Province 430070 , China . ; ; Tel: +86-27-87282111
| | - Qingpei Liu
- Key Laboratory of Environment Correlative Dietology , College of Food Science and Technology , Huazhong Agricultural University , Wuhan , Hubei Province 430070 , China . ; ; Tel: +86-27-87282111
- Natural Products Center , The University of Arizona , 250 E. Valencia Rd. , Tucson , Arizona 85706 , USA .
| | - Yi He
- Key Laboratory of Environment Correlative Dietology , College of Food Science and Technology , Huazhong Agricultural University , Wuhan , Hubei Province 430070 , China . ; ; Tel: +86-27-87282111
| | - Kun He
- Key Laboratory of Environment Correlative Dietology , College of Food Science and Technology , Huazhong Agricultural University , Wuhan , Hubei Province 430070 , China . ; ; Tel: +86-27-87282111
| | - Xiaoli Ding
- Key Laboratory of Environment Correlative Dietology , College of Food Science and Technology , Huazhong Agricultural University , Wuhan , Hubei Province 430070 , China . ; ; Tel: +86-27-87282111
| | - Lijing Kang
- Key Laboratory of Environment Correlative Dietology , College of Food Science and Technology , Huazhong Agricultural University , Wuhan , Hubei Province 430070 , China . ; ; Tel: +86-27-87282111
| | - Xiaoxiao Guo
- Key Laboratory of Environment Correlative Dietology , College of Food Science and Technology , Huazhong Agricultural University , Wuhan , Hubei Province 430070 , China . ; ; Tel: +86-27-87282111
| | - Nana Xie
- Key Laboratory of Environment Correlative Dietology , College of Food Science and Technology , Huazhong Agricultural University , Wuhan , Hubei Province 430070 , China . ; ; Tel: +86-27-87282111
| | - Youxiang Zhou
- Institute of Quality Standard and Testing Technology for Agro-Products , Hubei Academy of Agricultural Sciences , Wuhan , Hubei Province 430064 , China .
| | - Yuanyuan Lu
- Natural Products Center , The University of Arizona , 250 E. Valencia Rd. , Tucson , Arizona 85706 , USA .
- State Key Laboratory of Natural Medicines , School of Life Science and Technology , China Pharmaceutical University , 24 Tong Jia Xiang , Nanjing 210009 , China
| | - Russell J Cox
- Institut fur Organische Chemie , BMWZ , Leibniz Universitat Hannover , Schneiderberg 1B , 30167 Hannover , Germany
| | - István Molnár
- Natural Products Center , The University of Arizona , 250 E. Valencia Rd. , Tucson , Arizona 85706 , USA .
| | - Mu Li
- Key Laboratory of Environment Correlative Dietology , College of Food Science and Technology , Huazhong Agricultural University , Wuhan , Hubei Province 430070 , China . ; ; Tel: +86-27-87282111
| | - Yanchun Shao
- Key Laboratory of Environment Correlative Dietology , College of Food Science and Technology , Huazhong Agricultural University , Wuhan , Hubei Province 430070 , China . ; ; Tel: +86-27-87282111
| | - Fusheng Chen
- Key Laboratory of Environment Correlative Dietology , College of Food Science and Technology , Huazhong Agricultural University , Wuhan , Hubei Province 430070 , China . ; ; Tel: +86-27-87282111
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47
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Alberti F, Foster GD, Bailey AM. Natural products from filamentous fungi and production by heterologous expression. Appl Microbiol Biotechnol 2017; 101:493-500. [PMID: 27966047 PMCID: PMC5219032 DOI: 10.1007/s00253-016-8034-2] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/22/2016] [Accepted: 11/25/2016] [Indexed: 01/07/2023]
Abstract
Filamentous fungi represent an incredibly rich and rather overlooked reservoir of natural products, which often show potent bioactivity and find applications in different fields. Increasing the naturally low yields of bioactive metabolites within their host producers can be problematic, and yield improvement is further hampered by such fungi often being genetic intractable or having demanding culturing conditions. Additionally, total synthesis does not always represent a cost-effective approach for producing bioactive fungal-inspired metabolites, especially when pursuing assembly of compounds with complex chemistry. This review aims at providing insights into heterologous production of secondary metabolites from filamentous fungi, which has been established as a potent system for the biosynthesis of bioactive compounds. Numerous advantages are associated with this technique, such as the availability of tools that allow enhanced production yields and directing biosynthesis towards analogues of the naturally occurring metabolite. Furthermore, a choice of hosts is available for heterologous expression, going from model unicellular organisms to well-characterised filamentous fungi, which has also been shown to allow the study of biosynthesis of complex secondary metabolites. Looking to the future, fungi are likely to continue to play a substantial role as sources of new pharmaceuticals and agrochemicals-either as producers of novel natural products or indeed as platforms to generate new compounds through synthetic biology.
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Affiliation(s)
- Fabrizio Alberti
- School of Life Sciences and Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL UK
| | - Gary D. Foster
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ UK
| | - Andy M. Bailey
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ UK
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48
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Elucidation of cladofulvin biosynthesis reveals a cytochrome P450 monooxygenase required for anthraquinone dimerization. Proc Natl Acad Sci U S A 2016; 113:6851-6. [PMID: 27274078 DOI: 10.1073/pnas.1603528113] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Anthraquinones are a large family of secondary metabolites (SMs) that are extensively studied for their diverse biological activities. These activities are determined by functional group decorations and the formation of dimers from anthraquinone monomers. Despite their numerous medicinal qualities, very few anthraquinone biosynthetic pathways have been elucidated so far, including the enzymatic dimerization steps. In this study, we report the elucidation of the biosynthesis of cladofulvin, an asymmetrical homodimer of nataloe-emodin produced by the fungus Cladosporium fulvum A gene cluster of 10 genes controls cladofulvin biosynthesis, which begins with the production of atrochrysone carboxylic acid by the polyketide synthase ClaG and the β-lactamase ClaF. This compound is decarboxylated by ClaH to yield emodin, which is then converted to chrysophanol hydroquinone by the reductase ClaC and the dehydratase ClaB. We show that the predicted cytochrome P450 ClaM catalyzes the dimerization of nataloe-emodin to cladofulvin. Remarkably, such dimerization dramatically increases nataloe-emodin cytotoxicity against mammalian cell lines. These findings shed light on the enzymatic mechanisms involved in anthraquinone dimerization. Future characterization of the ClaM enzyme should facilitate engineering the biosynthesis of novel, potent, dimeric anthraquinones and structurally related compound families.
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49
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Williams K, Szwalbe AJ, Mulholland NP, Vincent JL, Bailey AM, Willis CL, Simpson TJ, Cox RJ. Heterologous Production of Fungal Maleidrides Reveals the Cryptic Cyclization Involved in their Biosynthesis. Angew Chem Int Ed Engl 2016; 55:6784-8. [PMID: 27099957 PMCID: PMC4982102 DOI: 10.1002/anie.201511882] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/16/2015] [Indexed: 11/12/2022]
Abstract
Fungal maleidrides are an important family of bioactive secondary metabolites that consist of 7, 8, or 9-membered carbocycles with one or two fused maleic anhydride moieties. The biosynthesis of byssochlamic acid (a nonadride) and agnestadride A (a heptadride) was investigated through gene disruption and heterologous expression experiments. The results reveal that the precursors for cyclization are formed by an iterative highly reducing fungal polyketide synthase supported by a hydrolase, together with two citrate-processing enzymes. The enigmatic ring formation is catalyzed by two proteins with homology to ketosteroid isomerases, and assisted by two proteins with homology to phosphatidylethanolamine-binding proteins.
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Affiliation(s)
- Katherine Williams
- Institute for Organic Chemistry, Leibniz University of Hannover, Schneiderberg 1B, 30167, Germany.
| | - Agnieszka J Szwalbe
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | | | - Jason L Vincent
- Syngenta, Jealott's Hill, Bracknell, Berkshire, RG42 6EY, UK
| | - Andrew M Bailey
- School of Biological Sciences, Bristol Life Sciences Building, University of Bristol, 24 Tyndall Ave, Bristol, BS8 1TH, UK
| | - Christine L Willis
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Thomas J Simpson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Russell J Cox
- Institute for Organic Chemistry, Leibniz University of Hannover, Schneiderberg 1B, 30167, Germany.
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
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50
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Bailey AM, Alberti F, Kilaru S, Collins CM, de Mattos-Shipley K, Hartley AJ, Hayes P, Griffin A, Lazarus CM, Cox RJ, Willis CL, O’Dwyer K, Spence DW, Foster GD. Identification and manipulation of the pleuromutilin gene cluster from Clitopilus passeckerianus for increased rapid antibiotic production. Sci Rep 2016; 6:25202. [PMID: 27143514 PMCID: PMC4855138 DOI: 10.1038/srep25202] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/11/2016] [Indexed: 12/16/2022] Open
Abstract
Semi-synthetic derivatives of the tricyclic diterpene antibiotic pleuromutilin from the basidiomycete Clitopilus passeckerianus are important in combatting bacterial infections in human and veterinary medicine. These compounds belong to the only new class of antibiotics for human applications, with novel mode of action and lack of cross-resistance, representing a class with great potential. Basidiomycete fungi, being dikaryotic, are not generally amenable to strain improvement. We report identification of the seven-gene pleuromutilin gene cluster and verify that using various targeted approaches aimed at increasing antibiotic production in C. passeckerianus, no improvement in yield was achieved. The seven-gene pleuromutilin cluster was reconstructed within Aspergillus oryzae giving production of pleuromutilin in an ascomycete, with a significant increase (2106%) in production. This is the first gene cluster from a basidiomycete to be successfully expressed in an ascomycete, and paves the way for the exploitation of a metabolically rich but traditionally overlooked group of fungi.
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Affiliation(s)
- Andy M. Bailey
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Fabrizio Alberti
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Sreedhar Kilaru
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Catherine M. Collins
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Kate de Mattos-Shipley
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Amanda J. Hartley
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Patrick Hayes
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Alison Griffin
- GSK, Southdownview Way, Worthing, West Sussex, BN14 8QH, UK
| | - Colin M. Lazarus
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Russell J. Cox
- School of Chemistry, University of Bristol, Cantock’s Close Bristol, BS8 1TS, UK
| | - Christine L. Willis
- School of Chemistry, University of Bristol, Cantock’s Close Bristol, BS8 1TS, UK
| | - Karen O’Dwyer
- GSK, 1250 S. Collegeville Road, Collegeville, Pennsylvania, 19426-0989, United States
| | - David W. Spence
- School of Chemistry, University of Bristol, Cantock’s Close Bristol, BS8 1TS, UK
| | - Gary D. Foster
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
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