1
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Shende VV, Bauman KD, Moore BS. The shikimate pathway: gateway to metabolic diversity. Nat Prod Rep 2024; 41:604-648. [PMID: 38170905 PMCID: PMC11043010 DOI: 10.1039/d3np00037k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Covering: 1997 to 2023The shikimate pathway is the metabolic process responsible for the biosynthesis of the aromatic amino acids phenylalanine, tyrosine, and tryptophan. Seven metabolic steps convert phosphoenolpyruvate (PEP) and erythrose 4-phosphate (E4P) into shikimate and ultimately chorismate, which serves as the branch point for dedicated aromatic amino acid biosynthesis. Bacteria, fungi, algae, and plants (yet not animals) biosynthesize chorismate and exploit its intermediates in their specialized metabolism. This review highlights the metabolic diversity derived from intermediates of the shikimate pathway along the seven steps from PEP and E4P to chorismate, as well as additional sections on compounds derived from prephenate, anthranilate and the synonymous aminoshikimate pathway. We discuss the genomic basis and biochemical support leading to shikimate-derived antibiotics, lipids, pigments, cofactors, and other metabolites across the tree of life.
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Affiliation(s)
- Vikram V Shende
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Katherine D Bauman
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
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2
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Wang R, Liang JJ, Yang W, Vuong D, Kalaitzis JA, Lacey AE, Lacey E, Piggott AM, Chooi YH, Li H. Heterologous Biosynthesis of the Sterol O-Acyltransferase Inhibitor Helvamide Unveils an α-Ketoglutarate-Dependent Cross-Linking Oxygenase. Org Lett 2024; 26:1807-1812. [PMID: 38393343 DOI: 10.1021/acs.orglett.3c04310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
We have identified the biosynthetic gene cluster (hvm) for the sterol O-acyltransferase inhibitor helvamide (1) from the genome of Aspergillus rugulosus MST-FP2007. Heterologous expression of hvm in A. nidulans produced a previously unreported analog helvamide B (5). An α-ketoglutarate-dependent oxygenase Hvm1 was shown to catalyze intramolecular cyclization of 1 to yield 5. The biosynthetic branch to the related hancockiamides and helvamides was found to be controlled by the substrate selectivity of monomodular nonribosomal peptide synthetases.
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Affiliation(s)
- Rui Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Jia-Jing Liang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Wencong Yang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Daniel Vuong
- Microbial Screening Technologies Pty. Ltd., Smithfield, NSW 2164, Australia
| | - John A Kalaitzis
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Alastair E Lacey
- Microbial Screening Technologies Pty. Ltd., Smithfield, NSW 2164, Australia
| | - Ernest Lacey
- Microbial Screening Technologies Pty. Ltd., Smithfield, NSW 2164, Australia
| | - Andrew M Piggott
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Hang Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
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3
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Lacey AE, Minns SA, Chen R, Vuong D, Lacey E, Kalaitzis JA, Tan YP, Shivas RG, Butler MS, Piggott AM. Talcarpones A and B: bisnaphthazarin-derived metabolites from the Australian fungus Talaromyces johnpittii sp. nov. MST-FP2594. J Antibiot (Tokyo) 2024; 77:147-155. [PMID: 38110564 DOI: 10.1038/s41429-023-00688-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 11/02/2023] [Accepted: 11/08/2023] [Indexed: 12/20/2023]
Abstract
Talcarpones A (1) and B (2) are rare bisnaphthazarin derivatives produced by Talaromyces johnpittii (ex-type strain MST-FP2594), a newly discovered Australian fungus, which is formally described and named herein. The talcarpones were isolated along with the previously reported monomeric naphthoquinone, aureoquinone (3), suggesting a biosynthetic link between these metabolites. Talcarpone A is a lower homologue of hybocarpone (4), which was first isolated from a mycobiont of the lichen Lecanora hybocarpa. The structures of 1 and 2 were elucidated by detailed spectroscopic analysis, molecular modelling and comparison with literature data. Talcarpones 1 and 2 exhibited moderate antifungal activity (MIC 0.78-3.1 µg ml-1) and weak activity against Gram-positive bacteria (MIC 13-25 µg ml-1). The talcarpones also demonstrated noteworthy chemical reactivities, with 2 converting rapidly to 1, which in turn converted slowly to the highly coloured 3. These post-biosynthetic reactions point to a potential ecological role for the talcarpones in providing ongoing (slow-release) physicochemical protection for T. johnpittii against solar irradiation.
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Affiliation(s)
- Alastair E Lacey
- Microbial Screening Technologies, Smithfield, NSW, 2164, Australia
| | - Scott A Minns
- Microbial Screening Technologies, Smithfield, NSW, 2164, Australia
| | - Rachel Chen
- Microbial Screening Technologies, Smithfield, NSW, 2164, Australia
| | - Daniel Vuong
- Microbial Screening Technologies, Smithfield, NSW, 2164, Australia
| | - Ernest Lacey
- Microbial Screening Technologies, Smithfield, NSW, 2164, Australia
- School of Natural Sciences, Macquarie University, Macquarie Park, NSW, 2109, Australia
| | - John A Kalaitzis
- School of Natural Sciences, Macquarie University, Macquarie Park, NSW, 2109, Australia
| | - Yu Pei Tan
- Queensland Plant Pathology Herbarium, Department of Agriculture and Fisheries, Brisbane, QLD, 4102, Australia
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4350, Australia
| | - Roger G Shivas
- Queensland Plant Pathology Herbarium, Department of Agriculture and Fisheries, Brisbane, QLD, 4102, Australia
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4350, Australia
| | | | - Andrew M Piggott
- School of Natural Sciences, Macquarie University, Macquarie Park, NSW, 2109, Australia.
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4
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Janzen DJ, Zhou J, Li SM. Biosynthesis of p-Terphenyls in Aspergillus ustus Implies Enzymatic Reductive Dehydration and Spontaneous Dibenzofuran Formation. Org Lett 2023; 25:6311-6316. [PMID: 37607357 DOI: 10.1021/acs.orglett.3c02234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
p-Terphenyls contain a central benzene ring substituted with two phenyl residues at its para positions. Heterologous expression of a biosynthetic gene cluster from Aspergillus ustus led to the formation of four new p-terphenyl derivatives. Gene deletion experiments proved the formation and reductive dehydration of the terphenylquinone atromentin, followed by O-methylation and prenylation. Spontaneous dibenzofuran formation led to the final products. These results provide new insights into the biosynthesis of p-terphenyls in fungi and dibenzofuran formation in the biosynthesis of numerous natural products.
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Affiliation(s)
- Daniel J Janzen
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037 Marburg, Germany
| | - Jing Zhou
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037 Marburg, Germany
- School of Life Sciences, Hainan University, Haikou, Hainan 570228, People's Republic of China
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037 Marburg, Germany
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5
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Promsuk G, Vuttipongchaikij S, Prommarit K, Suttangkakul A, Lazarus CM, Wonnapinij P, Wattana-Amorn P. Anthranilic Acid Accumulation in Saccharomyces cerevisiae Induced by Expression of a Nonribosomal Peptide Synthetase Gene from Paecilomyces cinnamomeus BCC 9616. Chembiochem 2022; 23:e202200573. [PMID: 36250803 DOI: 10.1002/cbic.202200573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/14/2022] [Indexed: 01/25/2023]
Abstract
Heterologous expression of nrps33, a nonribosomal peptide synthetase gene, from Paecilomyces cinnamomeus BCC 9616 in Saccharomyces cerevisiae unexpectedly resulted in the accumulation of anthranilic acid, an intermediate in tryptophan biosynthesis. Based on transcriptomic and real-time quantitative polymerase chain reaction (RT-qPCR) results, expression of nrps33 affected the transcription of tryptophan biosynthesis genes especially TRP1 which is also the selectable auxotrophic marker for the expression vector used in this work. The product of nrps33 could inhibit the activity of Trp4 involved in the conversion of anthranilate to N-(5'-phosphoribosyl)anthranilate and therefore caused the accumulation of anthranilic acid. This accumulation could in turn result in down-regulation of downstream tryptophan biosynthesis genes. Anthranilic acid is typically produced by chemical synthesis and has been used as a substrate for synthesising bioactive compounds including commercial drugs; our results could provide a new biological platform for production of this compound.
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Affiliation(s)
- Gunlatida Promsuk
- Interdisciplinary Graduate Program in Bioscience Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | | | - Kamonchat Prommarit
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Anongpat Suttangkakul
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Colin M Lazarus
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Passorn Wonnapinij
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Centre for Advanced Studies in Tropical Natural Resources, Kasetsart University, Bangkok, 10900, Thailand
- Omics Centre for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok, 10900, Thailand
| | - Pakorn Wattana-Amorn
- Interdisciplinary Graduate Program in Bioscience Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Department of Chemistry Special Research Unit for Advanced Magnetic Resonance and Center of Excellence for Innovation in Chemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
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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: 10] [Impact Index Per Article: 5.0] [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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Quantitative characterization of filamentous fungal promoters on a single-cell resolution to discover cryptic natural products. SCIENCE CHINA LIFE SCIENCES 2022; 66:848-860. [PMID: 36287342 DOI: 10.1007/s11427-022-2175-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 08/15/2022] [Indexed: 11/05/2022]
Abstract
Characterization of filamentous fungal regulatory elements remains challenging because of time-consuming transformation technologies and limited quantitative methods. Here we established a method for quantitative assessment of filamentous fungal promoters based on flow cytometry detection of the superfolder green fluorescent protein at single-cell resolution. Using this quantitative method, we acquired a library of 93 native promoter elements from Aspergillus nidulans in a high-throughput format. The strengths of identified promoters covered a 37-fold range by flow cytometry. PzipA and PsltA were identified as the strongest promoters, which were 2.9- and 1.5-fold higher than that of the commonly used constitutive promoter PgpdA. Thus, we applied PzipA and PsltA to activate the silent nonribosomal peptide synthetase gene Afpes1 from Aspergillus fumigatus in its native host and the heterologous host A. nidulans. The metabolic products of Afpes1 were identified as new cyclic tetrapeptide derivatives, namely, fumiganins A and B. Our method provides an innovative strategy for natural product discovery in fungi.
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8
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LIU L, CHEN X, ZOU Y. Genome mining of fungal globin-like enzymes for catalyzing the synthesis of linear terpenes. Chin J Nat Med 2022; 20:795-800. [DOI: 10.1016/s1875-5364(22)60192-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Indexed: 11/03/2022]
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9
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Chen L, Tang JW, Liu YY, Matsuda Y. Aspcandine: A Pyrrolobenzazepine Alkaloid Synthesized by a Fungal Nonribosomal Peptide Synthetase-Polyketide Synthase Hybrid. Org Lett 2022; 24:4816-4819. [PMID: 35748771 DOI: 10.1021/acs.orglett.2c01918] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Characterization of an orphan biosynthetic gene cluster found in the fungus Aspergillus candidus CBS 102.13 resulted in the discovery of a pyrrolobenzazepine alkaloid, aspcandine (1). The unique molecular scaffold of 1 is synthesized by the nonribosomal peptide synthetase-polyketide synthase hybrid AcdB, which unusually incorporates 3-hydroxy-l-kynurenine as a building block. AcdB subsequently performs one round of chain elongation using malonyl-CoA, which is followed by the chain release to furnish the tricyclic system of 1.
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Affiliation(s)
- Lin Chen
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Jian-Wei Tang
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Yan Yee Liu
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Yudai Matsuda
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
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10
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Li H, Mirzayans PM, Butler MS, Lacey AE, Vuong D, Chen R, Kalaitzis JA, Moggach SA, Lacey E, Piggott AM, Chooi YH. Discovery of brevijanazines from Aspergillus brevijanus reveals the molecular basis for p-nitrobenzoic acid in fungi. Chem Commun (Camb) 2022; 58:6296-6299. [PMID: 35537125 DOI: 10.1039/d2cc01679f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The brevijanazines are novel p-nitrobenzoylated piperazines isolated from Aspergillus brevijanus. Their structures were elucidated by spectroscopic analysis, X-ray crystallography and total synthesis. Heterologous biosynthesis, precursor feeding and in vitro microsomal assays unveiled the biosynthetic pathway to the brevijanazines, featuring a cytochrome P450 oxygenase that converts p-aminobenzoic acid to p-nitrobenzoic acid.
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Affiliation(s)
- Hang Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China. .,School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
| | - Paul M Mirzayans
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | | | - Alastair E Lacey
- Microbial Screening Technologies Pty. Ltd., Smithfield, NSW 2164, Australia
| | - Daniel Vuong
- Microbial Screening Technologies Pty. Ltd., Smithfield, NSW 2164, Australia
| | - Rachel Chen
- Microbial Screening Technologies Pty. Ltd., Smithfield, NSW 2164, Australia
| | - John A Kalaitzis
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia. .,Microbial Screening Technologies Pty. Ltd., Smithfield, NSW 2164, Australia
| | - Stephen A Moggach
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia. .,Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, WA 6009, Australia
| | - Ernest Lacey
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia. .,Microbial Screening Technologies Pty. Ltd., Smithfield, NSW 2164, Australia
| | - Andrew M Piggott
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
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11
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Roux I, Chooi YH. Heterologous Expression of Fungal Biosynthetic Pathways in Aspergillus nidulans Using Episomal Vectors. Methods Mol Biol 2022; 2489:75-92. [PMID: 35524046 DOI: 10.1007/978-1-0716-2273-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Filamentous fungi produce a wide diversity of secondary metabolites, whose biosynthesis is encoded in biosynthetic gene clusters (BGCs). As novel BGCs are often found in fungal species that are genetically intractable or difficult to cultivate, heterologous expression is increasingly being used for compound discovery. In addition, heterologous expression is a useful strategy to elucidate the function of the genes within a BGC and shed light on their enzymatic mechanisms. Here, we describe a method for BGC elucidation using multi-marker AMA1-based pYFAC vectors for episomal expression in the fungal host Aspergillus nidulans. The pYFAC vectors have the advantage of high transformation efficiency and support high compound production. In addition, different pathway intermediates can be easily evaluated by testing different vector combinations. This protocol encompasses different AMA1-based strategies for BGC expression such as cloning of a BGC native sequence, promoter exchange or transcription factor overexpression. We also describe procedures for A. nidulans protoplasting, transformation, and small-scale culture analysis of strains containing AMA1 vectors.
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Affiliation(s)
- Indra Roux
- School of Molecular Sciences, University of Western Australia, Perth, WA, Australia
| | - Yit Heng Chooi
- School of Molecular Sciences, University of Western Australia, Perth, WA, Australia.
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12
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Xie X, Sun J. [4+3]-Cycloaddition Reaction of Sulfilimines with Cyclobutenones: Access to Benzazepinones. Org Lett 2021; 23:8921-8925. [PMID: 34723560 DOI: 10.1021/acs.orglett.1c03413] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A catalyst-free [4+3]-cycloaddition reaction of N-aryl sulfilimines with cyclobutenones is described, which provides a straightforward protocol for synthesizing 1,5-dihydro-2H-benzo[b]azepin-2-ones under mild reaction conditions. This reaction features a broad substrate scope and good functional group tolerance and does not require catalysts or additives. Moreover, using N-pyridinyl sulfilimine as the substrate, a series of pyridoazepinones have also been prepared.
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Affiliation(s)
- Xiaozhou Xie
- Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, School of Petrochemical Engineering, Changzhou University, Changzhou 213164, China
| | - Jiangtao Sun
- Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, School of Petrochemical Engineering, Changzhou University, Changzhou 213164, China
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13
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Gilchrist CLM, Chooi YH. Synthaser: a CD-Search enabled Python toolkit for analysing domain architecture of fungal secondary metabolite megasynth(et)ases. Fungal Biol Biotechnol 2021; 8:13. [PMID: 34763725 PMCID: PMC8582187 DOI: 10.1186/s40694-021-00120-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/29/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fungi are prolific producers of secondary metabolites (SMs), which are bioactive small molecules with important applications in medicine, agriculture and other industries. The backbones of a large proportion of fungal SMs are generated through the action of large, multi-domain megasynth(et)ases such as polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs). The structure of these backbones is determined by the domain architecture of the corresponding megasynth(et)ase, and thus accurate annotation and classification of these architectures is an important step in linking SMs to their biosynthetic origins in the genome. RESULTS Here we report synthaser, a Python package leveraging the NCBI's conserved domain search tool for remote prediction and classification of fungal megasynth(et)ase domain architectures. Synthaser is capable of batch sequence analysis, and produces rich textual output and interactive visualisations which allow for quick assessment of the megasynth(et)ase diversity of a fungal genome. Synthaser uses a hierarchical rule-based classification system, which can be extensively customised by the user through a web application ( http://gamcil.github.io/synthaser ). We show that synthaser provides more accurate domain architecture predictions than comparable tools which rely on curated profile hidden Markov model (pHMM)-based approaches; the utilisation of the NCBI conserved domain database also allows for significantly greater flexibility compared to pHMM approaches. In addition, we demonstrate how synthaser can be applied to large scale genome mining pipelines through the construction of an Aspergillus PKS similarity network. CONCLUSIONS Synthaser is an easy to use tool that represents a significant upgrade to previous domain architecture analysis tools. It is freely available under a MIT license from PyPI ( https://pypi.org/project/synthaser ) and GitHub ( https://github.com/gamcil/synthaser ).
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Affiliation(s)
- Cameron L M Gilchrist
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, 6009, Australia.
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, 6009, Australia.
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14
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Roux I, Bowles S, Kalaitzis JA, Vuong D, Lacey E, Chooi YH, Piggott AM. Characterisation and heterologous biosynthesis of burnettiene A, a new polyene-decalin polyketide from Aspergillus burnettii. Org Biomol Chem 2021; 19:9506-9513. [PMID: 34714309 DOI: 10.1039/d1ob01766g] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Chemical exploration of the recently described Australian fungus, Aspergillus burnettii, uncovered a new metabolite, burnettiene A. Here, we characterise the structure of burnettiene A as a polyene-decalin polyketide. Bioinformatic analysis of the genome of A. burnettii identified a putative biosynthetic gene cluster for burnettiene A (bue), consisting of eight genes and sharing similarity to the fusarielin gene cluster. Introduction of the reassembled bue gene cluster into Aspergillus nidulans for heterologous expression resulted in the production of burnettiene A under native promoters. Omission of bueE encoding a cytochrome P450 led to the production of preburnettiene A, confirming that BueE is responsible for catalysing the regiospecific multi-oxidation of terminal methyl groups to carboxylic acids. Similarly, bueF was shown to encode an ester-forming methyltransferase, with its omission resulting in the production of the tricarboxylic acid, preburnettiene B. Introduction of an additional copy of the transcription factor bueR under the regulation of the gpdA promoter significantly improved the heterologous production of the burnettienes. Burnettiene A displayed strong in vitro cytotoxicity against mouse myeloma NS-1 cells (MIC 0.8 μg mL-1).
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Affiliation(s)
- Indra Roux
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
| | - Simon Bowles
- Microbial Screening Technologies Pty. Ltd, Smithfield, NSW 2164, Australia
| | - John A Kalaitzis
- Microbial Screening Technologies Pty. Ltd, Smithfield, NSW 2164, Australia.,Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Daniel Vuong
- Microbial Screening Technologies Pty. Ltd, Smithfield, NSW 2164, Australia
| | - Ernest Lacey
- Microbial Screening Technologies Pty. Ltd, Smithfield, NSW 2164, Australia.,Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
| | - Andrew M Piggott
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
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15
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Little RF, Hertweck C. Chain release mechanisms in polyketide and non-ribosomal peptide biosynthesis. Nat Prod Rep 2021; 39:163-205. [PMID: 34622896 DOI: 10.1039/d1np00035g] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Review covering up to mid-2021The structure of polyketide and non-ribosomal peptide natural products is strongly influenced by how they are released from their biosynthetic enzymes. As such, Nature has evolved a diverse range of release mechanisms, leading to the formation of bioactive chemical scaffolds such as lactones, lactams, diketopiperazines, and tetronates. Here, we review the enzymes and mechanisms used for chain release in polyketide and non-ribosomal peptide biosynthesis, how these mechanisms affect natural product structure, and how they could be utilised to introduce structural diversity into the products of engineered biosynthetic pathways.
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Affiliation(s)
- Rory F Little
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
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16
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Gilchrist CLM, Booth TJ, van Wersch B, van Grieken L, Medema MH, Chooi YH. cblaster: a remote search tool for rapid identification and visualization of homologous gene clusters. BIOINFORMATICS ADVANCES 2021; 1:vbab016. [PMID: 36700093 PMCID: PMC9710679 DOI: 10.1093/bioadv/vbab016] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/28/2021] [Accepted: 08/03/2021] [Indexed: 01/28/2023]
Abstract
Motivation Genes involved in coordinated biological pathways, including metabolism, drug resistance and virulence, are often collocalized as gene clusters. Identifying homologous gene clusters aids in the study of their function and evolution, however, existing tools are limited to searching local sequence databases. Tools for remotely searching public databases are necessary to keep pace with the rapid growth of online genomic data. Results Here, we present cblaster, a Python-based tool to rapidly detect collocated genes in local and remote databases. cblaster is easy to use, offering both a command line and a user-friendly graphical user interface. It generates outputs that enable intuitive visualizations of large datasets and can be readily incorporated into larger bioinformatic pipelines. cblaster is a significant update to the comparative genomics toolbox. Availability and implementation cblaster source code and documentation is freely available from GitHub under the MIT license (github.com/gamcil/cblaster). Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Cameron L M Gilchrist
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia,To whom correspondence should be addressed. or or
| | - Thomas J Booth
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Bram van Wersch
- Bioinformatics Group, Wageningen University, Wageningen 6708PB, The Netherlands
| | - Liana van Grieken
- Bioinformatics Group, Wageningen University, Wageningen 6708PB, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen 6708PB, The Netherlands,To whom correspondence should be addressed. or or
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia,To whom correspondence should be addressed. or or
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17
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Hong SY, Lee DH, Lee JH, Haque MA, Cho KM. Five Surfactin Isomers Produced during Cheonggukjang Fermentation by Bacillus pumilus HY1 and Their Properties. Molecules 2021; 26:4478. [PMID: 34361631 PMCID: PMC8346962 DOI: 10.3390/molecules26154478] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 12/03/2022] Open
Abstract
The cyclic lipopeptide produced from Bacillus pumilus strain HY1 was isolated from Korean soybean sauce cheonggukjang. The chemical structures of the surfactin isomers were analyzed using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and electrospray ionization tandem mass spectrometry (ESI-MS/MS). The five potential surfactin isoforms were detected with protonated masses of m/z 994.7, 1008.7, 1022.7, 1036.7, and 1050.7 and different structures in combination with Na+, K+, and Ca2+ ions. ESI-MS/MS analysis revealed that the isolated surfactin possessed the precise amino acid sequence LLVDLL and hydroxyl fatty acids with 12 to 16 carbons. The surfactin content during cheonggukjang fermentation increased from 0.3 to 51.2 mg/kg over 60 h of fermentation. The mixture of five surfactin isoforms of cheonggukjang inhibited the growth of two cancer cell lines. The growth of both MCF-7 and Caco-2 cells was strongly inhibited with 100 μg/μL of surfactin. This study is the first-time report of five surfactin isomers of Bacillus pumilus strain HY1 during Korean soybean sauce cheonggukjang fermentation, which has cytotoxic properties.
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Affiliation(s)
- Su-Young Hong
- SBT Business Division, Food Science Research Institute, Kolmar BNH Inc., Sejong 30003, Korea;
| | - Dong-Hee Lee
- Industry Academy Cooperation Foundation, Andong National University, Andong 36729, Korea;
| | - Jin-Hwan Lee
- Department of Life Resources Industry, Dong-A University, Busan 49315, Korea;
| | - Md. Azizul Haque
- Department of Biochemistry & Molecular Biology, Hajee Mohammad Danesh Science & Technology University, Dinajpur 5200, Bangladesh;
| | - Kye-Man Cho
- Department of Food Science, Gyeongsang National University, Jinju 52725, Korea
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18
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Wu L, Qin L, Nie Y, Xu Y, Zhao YL. Computer-aided understanding and engineering of enzymatic selectivity. Biotechnol Adv 2021; 54:107793. [PMID: 34217814 DOI: 10.1016/j.biotechadv.2021.107793] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/26/2021] [Accepted: 06/28/2021] [Indexed: 12/26/2022]
Abstract
Enzymes offering chemo-, regio-, and stereoselectivity enable the asymmetric synthesis of high-value chiral molecules. Unfortunately, the drawback that naturally occurring enzymes are often inefficient or have undesired selectivity toward non-native substrates hinders the broadening of biocatalytic applications. To match the demands of specific selectivity in asymmetric synthesis, biochemists have implemented various computer-aided strategies in understanding and engineering enzymatic selectivity, diversifying the available repository of artificial enzymes. Here, given that the entire asymmetric catalytic cycle, involving precise interactions within the active pocket and substrate transport in the enzyme channel, could affect the enzymatic efficiency and selectivity, we presented a comprehensive overview of the computer-aided workflow for enzymatic selectivity. This review includes a mechanistic understanding of enzymatic selectivity based on quantum mechanical calculations, rational design of enzymatic selectivity guided by enzyme-substrate interactions, and enzymatic selectivity regulation via enzyme channel engineering. Finally, we discussed the computational paradigm for designing enzyme selectivity in silico to facilitate the advancement of asymmetric biosynthesis.
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Affiliation(s)
- Lunjie Wu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Lei Qin
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yao Nie
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Suqian Industrial Technology Research Institute of Jiangnan University, Suqian 223814, China.
| | - Yan Xu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, MOE-LSB & MOE-LSC, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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19
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Bedir E, Karakoyun Ç, Doğan G, Kuru G, Küçüksolak M, Yusufoğlu H. New Cardenolides from Biotransformation of Gitoxigenin by the Endophytic Fungus Alternaria eureka 1E1BL1: Characterization and Cytotoxic Activities. Molecules 2021; 26:molecules26103030. [PMID: 34069653 PMCID: PMC8161373 DOI: 10.3390/molecules26103030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 11/16/2022] Open
Abstract
Microbial biotransformation is an important tool in drug discovery and for metabolism studies. To expand our bioactive natural product library via modification and to identify possible mammalian metabolites, a cytotoxic cardenolide (gitoxigenin) was biotransformed using the endophytic fungus Alternaria eureka 1E1BL1. Initially, oleandrin was isolated from the dried leaves of Nerium oleander L. and subjected to an acid-catalysed hydrolysis to obtain the substrate gitoxigenin (yield; ~25%). After 21 days of incubation, five new cardenolides 1, 3, 4, 6, and 8 and three previously- identified compounds 2, 5 and 7 were isolated using chromatographic methods. Structural elucidations were accomplished through 1D/2D NMR, HR-ESI-MS and FT-IR analysis. A. eureka catalyzed oxygenation, oxidation, epimerization and dimethyl acetal formation reactions on the substrate. Cytotoxicity of the metabolites were evaluated using MTT cell viability method, whereas doxorubicin and oleandrin were used as positive controls. Biotransformation products displayed less cytotoxicity than the substrate. The new metabolite 8 exhibited the highest activity with IC50 values of 8.25, 1.95 and 3.4 µM against A549, PANC-1 and MIA PaCa-2 cells, respectively, without causing toxicity on healthy cell lines (MRC-5 and HEK-293) up to concentration of 10 µM. Our results suggest that A. eureka is an effective biocatalyst for modifying cardenolide-type secondary metabolites.
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Affiliation(s)
- Erdal Bedir
- Department of Bioengineering, Faculty of Engineering, İzmir Institute of Technology, 35430 Urla-İzmir, Turkey; (G.D.); (G.K.); (M.K.)
- Correspondence: (E.B.); (Ç.K.); Tel.: +90-232-750-7389 (E.B.); +90-232-311-2598 (Ç.K.)
| | - Çiğdem Karakoyun
- Department of Pharmacognosy, Faculty of Pharmacy, Ege University, 35100 Bornova-İzmir, Turkey
- Correspondence: (E.B.); (Ç.K.); Tel.: +90-232-750-7389 (E.B.); +90-232-311-2598 (Ç.K.)
| | - Gamze Doğan
- Department of Bioengineering, Faculty of Engineering, İzmir Institute of Technology, 35430 Urla-İzmir, Turkey; (G.D.); (G.K.); (M.K.)
| | - Gülten Kuru
- Department of Bioengineering, Faculty of Engineering, İzmir Institute of Technology, 35430 Urla-İzmir, Turkey; (G.D.); (G.K.); (M.K.)
| | - Melis Küçüksolak
- Department of Bioengineering, Faculty of Engineering, İzmir Institute of Technology, 35430 Urla-İzmir, Turkey; (G.D.); (G.K.); (M.K.)
| | - Hasan Yusufoğlu
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia;
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20
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Sbaraini N, Hu J, Roux I, Phan CS, Motta H, Rezaee H, Schrank A, Chooi YH, Staats CC. Polyketides produced by the entomopathogenic fungus Metarhizium anisopliae induce Candida albicans growth. Fungal Genet Biol 2021; 152:103568. [PMID: 33991663 DOI: 10.1016/j.fgb.2021.103568] [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: 12/20/2020] [Revised: 03/16/2021] [Accepted: 04/18/2021] [Indexed: 11/15/2022]
Abstract
Metarhizium anisopliae is an important entomopathogenic species and model for arthropod-fungus interaction studies. This fungus harbors a diverse arsenal of unexplored secondary metabolite biosynthetic gene clusters, which are suggested to perform diverse roles during host interaction and soil subsistence as a saprophytic species. Here we explored an unusual carnitine acyltransferase domain-containing highly reducing polyketide synthase found in the genome of M. anisopliae. Employing heterologous expression in Aspergillus nidulans, two new polyketides were obtained, named BAA and BAB, as well as one known polyketide [(2Z,4E,6E)-octa-2,4,6-trienedioic acid]. Intra-hemocoel injection of the most abundant compound (BAA) in the model-arthropod Galleria mellonella larvae did not induce mortality or noticeable alterations, suggesting that this compound may not harbor insecticidal activity. Also, the potential role of such molecules in polymicrobial interactions was evaluated. Determination of minimum inhibitory concentration assays using distinct fungal species revealed that BAA and BAB did not alter Cryptococcus neoformans growth, while BAA exhibited weak antifungal activity against Saccharomyces cerevisiae. Unexpectedly, these compounds increased Candida albicans growth compared to control conditions. Furthermore, BAA can mitigate the fungicidal effects of fluconazole over C. albicans. Although the exact role of these compounds on the M. anisopliae life cycle is elusive, the described results add up to the complexity of secondary metabolites produced by Metarhizium spp. Moreover, up to our knowledge, these are the first polyketides isolated from filamentous fungi that can boost the growth of another fungal species.
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Affiliation(s)
- Nicolau Sbaraini
- Centro de Biotecnologia, Programa de Pós-graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Jinyu Hu
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Indra Roux
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Chin-Soon Phan
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Heryk Motta
- Centro de Biotecnologia, Programa de Pós-graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Hamideh Rezaee
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Augusto Schrank
- Centro de Biotecnologia, Programa de Pós-graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
| | - Charley Christian Staats
- Centro de Biotecnologia, Programa de Pós-graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
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21
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Adrover-Castellano ML, Schmidt JJ, Sherman DH. Biosynthetic Cyclization Catalysts for the Assembly of Peptide and Polyketide Natural Products. ChemCatChem 2021; 13:2095-2116. [PMID: 34335987 PMCID: PMC8320681 DOI: 10.1002/cctc.202001886] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Indexed: 12/13/2022]
Abstract
Many biologically active natural products are synthesized by nonribosomal peptide synthetases (NRPSs), polyketide synthases (PKSs) and their hybrids. These megasynthetases contain modules possessing distinct catalytic domains that allow for substrate initiation, chain extension, processing and termination. At the end of a module, a terminal domain, usually a thioesterase (TE), is responsible for catalyzing the release of the NRPS or PKS as a linear or cyclized product. In this review, we address the general cyclization mechanism of the TE domain, including oligomerization and the fungal C-C bond forming Claisen-like cyclases (CLCs). Additionally, we include examples of cyclization catalysts acting within or at the end of a module. Furthermore, condensation-like (CT) domains, terminal reductase (R) domains, reductase-like domains that catalyze Dieckmann condensation (RD), thioesterase-like Dieckmann cyclases, trans-acting TEs from the penicillin binding protein (PBP) enzyme family, product template (PT) domains and others will also be reviewed. The studies summarized here highlight the remarkable diversity of NRPS and PKS cyclization catalysts for the production of biologically relevant, complex cyclic natural products and related compounds.
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Affiliation(s)
| | - Jennifer J Schmidt
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216 (USA)
| | - David H Sherman
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216 (USA)
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22
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Marshall JW, de Mattos-Shipley KMJ, Ghannam IAY, Munawar A, Killen JC, Lazarus CM, Cox RJ, Willis CL, Simpson TJ. Fusarochromene, a novel tryptophan-derived metabolite from Fusarium sacchari. Org Biomol Chem 2021; 19:182-187. [PMID: 33107888 DOI: 10.1039/d0ob02031a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fusarochromene isolated from the plant pathogenic fungus, Fusarium sacchari is closely related to a group of mycotoxins including fusarochromanone previously isolated from various Fusaria spp. Despite their assumed polyketide biogenesis, incorporation studies with 13C-labelled acetate, glycerol and tryptophans show that fusarochromene is unexpectedly derived via oxidative cleavage of the aromatic amino acid tryptophan. A putative biosynthetic gene cluster has been identified.
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Affiliation(s)
- James W Marshall
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
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23
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Li H, Lacey AE, Shu S, Kalaitzis JA, Vuong D, Crombie A, Hu J, Gilchrist CLM, Lacey E, Piggott AM, Chooi YH. Hancockiamides: phenylpropanoid piperazines from Aspergillus hancockii are biosynthesised by a versatile dual single-module NRPS pathway. Org Biomol Chem 2021; 19:587-595. [DOI: 10.1039/d0ob02243h] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The hancockiamides are an unusual new family of N-cinnamoylated piperazines from the Australian soil fungus Aspergillus hancockii, originating from mixed nonribosomal peptide and phenylpropanoid pathways.
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Affiliation(s)
- Hang Li
- School of Molecular Sciences
- The University of Western Australia
- Perth
- Australia
| | | | - Si Shu
- School of Molecular Sciences
- The University of Western Australia
- Perth
- Australia
| | | | - Daniel Vuong
- Microbial Screening Technologies Pty. Ltd
- Smithfield
- Australia
| | - Andrew Crombie
- Microbial Screening Technologies Pty. Ltd
- Smithfield
- Australia
| | - Jinyu Hu
- School of Molecular Sciences
- The University of Western Australia
- Perth
- Australia
| | | | - Ernest Lacey
- Microbial Screening Technologies Pty. Ltd
- Smithfield
- Australia
- Department of Molecular Sciences
- Macquarie University
| | | | - Yit-Heng Chooi
- School of Molecular Sciences
- The University of Western Australia
- Perth
- Australia
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24
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Dekimpe S, Masschelein J. Beyond peptide bond formation: the versatile role of condensation domains in natural product biosynthesis. Nat Prod Rep 2021; 38:1910-1937. [DOI: 10.1039/d0np00098a] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Condensation domains perform highly diverse functions during natural product biosynthesis and are capable of generating remarkable chemical diversity.
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Affiliation(s)
- Sofie Dekimpe
- Laboratory for Biomolecular Discovery & Engineering
- Department of Biology
- KU Leuven
- Leuven
- Belgium
| | - Joleen Masschelein
- Laboratory for Biomolecular Discovery & Engineering
- Department of Biology
- KU Leuven
- Leuven
- Belgium
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25
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Morshed MT, Nguyen HT, Vuong D, Crombie A, Lacey E, Ogunniyi AD, Page SW, Trott DJ, Piggott AM. Semisynthesis and biological evaluation of a focused library of unguinol derivatives as next-generation antibiotics. Org Biomol Chem 2021; 19:1022-1036. [DOI: 10.1039/d0ob02460k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Semisynthetic unguinol derivatives showed potent activity against a panel of methicillin-resistant Staphylococcus aureus strains and are promising candidates for further development.
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Affiliation(s)
| | - Hang T. Nguyen
- Australian Centre for Antimicrobial Resistance Ecology
- School of Animal and Veterinary Sciences
- The University of Adelaide
- Roseworthy
- Australia
| | - Daniel Vuong
- Microbial Screening Technologies Pty. Ltd
- Smithfield
- Australia
| | - Andrew Crombie
- Microbial Screening Technologies Pty. Ltd
- Smithfield
- Australia
| | - Ernest Lacey
- Department of Molecular Sciences
- Macquarie University
- Australia
- Microbial Screening Technologies Pty. Ltd
- Smithfield
| | - Abiodun D. Ogunniyi
- Australian Centre for Antimicrobial Resistance Ecology
- School of Animal and Veterinary Sciences
- The University of Adelaide
- Roseworthy
- Australia
| | | | - Darren J. Trott
- Australian Centre for Antimicrobial Resistance Ecology
- School of Animal and Veterinary Sciences
- The University of Adelaide
- Roseworthy
- Australia
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26
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Heterologous biosynthesis as a platform for producing new generation natural products. Curr Opin Biotechnol 2020; 66:123-130. [DOI: 10.1016/j.copbio.2020.06.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/27/2020] [Accepted: 06/30/2020] [Indexed: 12/18/2022]
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27
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Caesar LK, Kelleher NL, Keller NP. In the fungus where it happens: History and future propelling Aspergillus nidulans as the archetype of natural products research. Fungal Genet Biol 2020; 144:103477. [PMID: 33035657 DOI: 10.1016/j.fgb.2020.103477] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/21/2020] [Accepted: 09/30/2020] [Indexed: 02/08/2023]
Abstract
In 1990 the first fungal secondary metabolite biosynthetic gene was cloned in Aspergillus nidulans. Thirty years later, >30 biosynthetic gene clusters (BGCs) have been linked to specific natural products in this one fungal species. While impressive, over half of the BGCs in A. nidulans remain uncharacterized and their compounds structurally and functionally unknown. Here, we provide a comprehensive review of past advances that have enabled A. nidulans to rise to its current status as a natural product powerhouse focusing on the discovery and annotation of secondary metabolite clusters. From genome sequencing, heterologous expression, and metabolomics to CRISPR and epigenetic manipulations, we present a guided tour through the evolution of technologies developed and utilized in the last 30 years. These insights provide perspective to future efforts to fully unlock the biosynthetic potential of A. nidulans and, by extension, the potential of other filamentous fungi.
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Affiliation(s)
- Lindsay K Caesar
- Department of Chemistry, Northwestern University, Evanston, IL, United States
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, IL, United States; Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States; Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin- Madison, Madison, WI, United States; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States.
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28
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Heterologous Expression of the Unusual Terreazepine Biosynthetic Gene Cluster Reveals a Promising Approach for Identifying New Chemical Scaffolds. mBio 2020; 11:mBio.01691-20. [PMID: 32843555 PMCID: PMC7448278 DOI: 10.1128/mbio.01691-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Advances in genome sequencing have revitalized natural product discovery efforts, revealing the untapped biosynthetic potential of fungi. While the volume of genomic data continues to expand, discovery efforts are slowed due to the time-consuming nature of experiments required to characterize new molecules. To direct efforts toward uncharacterized biosynthetic gene clusters most likely to encode novel chemical scaffolds, we took advantage of comparative metabolomics and heterologous gene expression using fungal artificial chromosomes (FACs). By linking mass spectral profiles with structural clues provided by FAC-encoded gene clusters, we targeted a compound originating from an unusual gene cluster containing an indoleamine 2,3-dioxygenase (IDO). With this approach, we isolate and characterize R and S forms of the new molecule terreazepine, which contains a novel chemical scaffold resulting from cyclization of the IDO-supplied kynurenine. The discovery of terreazepine illustrates that FAC-based approaches targeting unusual biosynthetic machinery provide a promising avenue forward for targeted discovery of novel scaffolds and their biosynthetic enzymes, and it also represents another example of a biosynthetic gene cluster "repurposing" a primary metabolic enzyme to diversify its secondary metabolite arsenal.IMPORTANCE Here, we provide evidence that Aspergillus terreus encodes a biosynthetic gene cluster containing a repurposed indoleamine 2,3-dioxygenase (IDO) dedicated to secondary metabolite synthesis. The discovery of this neofunctionalized IDO not only enabled discovery of a new compound with an unusual chemical scaffold but also provided insight into the numerous strategies fungi employ for diversifying and protecting themselves against secondary metabolites. The observations in this study set the stage for further in-depth studies into the function of duplicated IDOs present in fungal biosynthetic gene clusters and presents a strategy for accessing the biosynthetic potential of gene clusters containing duplicated primary metabolic genes.
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29
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Hill RA, Sutherland A. Hot off the Press. Nat Prod Rep 2020. [DOI: 10.1039/d0np90022b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as sporormielone A from a Sporormiella species.
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