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Schmalhofer M, Vagstad AL, Zhou Q, Bode HB, Groll M. Polyketide Trimming Shapes Dihydroxynaphthalene-Melanin and Anthraquinone Pigments. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400184. [PMID: 38491909 PMCID: PMC11165489 DOI: 10.1002/advs.202400184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/28/2024] [Indexed: 03/18/2024]
Abstract
Pigments such as anthraquinones (AQs) and melanins are antioxidants, protectants, or virulence factors. AQs from the entomopathogenic bacterium Photorhabdus laumondii are produced by a modular type II polyketide synthase system. A key enzyme involved in AQ biosynthesis is PlAntI, which catalyzes the hydrolysis of the bicyclic-intermediate-loaded acyl carrier protein, polyketide trimming, and assembly of the aromatic AQ scaffold. Here, multiple crystal structures of PlAntI in various conformations and with bound substrate surrogates or inhibitors are reported. Structure-based mutagenesis and activity assays provide experimental insights into the three sequential reaction steps to yield the natural product AQ-256. For comparison, a series of ligand-complex structures of two functionally related hydrolases involved in the biosynthesis of 1,8-dihydroxynaphthalene-melanin in pathogenic fungi is determined. These data provide fundamental insights into the mechanism of polyketide trimming that shapes pigments in pro- and eukaryotes.
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Affiliation(s)
- Maximilian Schmalhofer
- TUM School of Natural SciencesDepartment of BioscienceCentre for Protein AssembliesChair of BiochemistryTechnical University of Munich85748GarchingGermany
| | - Anna L. Vagstad
- Eidgenössische Technische Hochschule (ETH) ZürichInstitute of MicrobiologyZürich8093Switzerland
| | - Qiuqin Zhou
- Department of Natural Products in Organismic InteractionsMax Planck Institute for Terrestrial Microbiology35043MarburgGermany
- Present address:
Center for Mass Spectrometry and Optical Spectroscopy (CeMOS)Mannheim University of Applied Sciences68163MannheimGermany
| | - Helge B. Bode
- Department of Natural Products in Organismic InteractionsMax Planck Institute for Terrestrial Microbiology35043MarburgGermany
- Molecular BiotechnologyDepartment of BiosciencesGoethe University Frankfurt60438FrankfurtGermany
- Department of ChemistryPhillips Universität Marburg35043MarburgGermany
- Center for Synthetic Microbiology (SYNMIKRO)Phillips Universität Marburg35043MarburgGermany
- Senckenberg Gesellschaft für Naturforschung60325FrankfurtGermany
| | - Michael Groll
- TUM School of Natural SciencesDepartment of BioscienceCentre for Protein AssembliesChair of BiochemistryTechnical University of Munich85748GarchingGermany
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2
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Zhao S, Yin R, Zhang M, Zhai Z, Shen Z, Mou Y, Xu D, Zhou L, Lai D. Efficient gene editing in the slow-growing, non-sporulating, melanized, endophytic fungus Berkleasmium sp. Dzf12 using a CRISPR/Cas9 system. World J Microbiol Biotechnol 2024; 40:176. [PMID: 38652405 DOI: 10.1007/s11274-024-03988-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/15/2024] [Indexed: 04/25/2024]
Abstract
The endophytic fungus Berkleasmium sp. Dzf12 that was isolated from Dioscorea zingiberensis, is a proficient producer of palmarumycins, which are intriguing polyketides of the spirobisnaphthalene class. These compounds displayed a wide range of bioactivities, including antibacterial, antifungal, and cytotoxic activities. However, conventional genetic manipulation of Berkleasmium sp. Dzf12 is difficult and inefficient, partially due to the slow-growing, non-sporulating, and highly pigmented behavior of this fungus. Herein, we developed a CRISPR/Cas9 system suitable for gene editing in Berkleasmium sp. Dzf12. The protoplast preparation was optimized, and the expression of Cas9 in Berkleasmium sp. Dzf12 was validated. To assess the gene disruption efficiency, a putative 1, 3, 6, 8-tetrahydroxynaphthalene synthase encoding gene, bdpks, involved in 1,8-dihydroxynaphthalene (DHN)-melanin biosynthesis, was selected as the target for gene disruption. Various endogenous sgRNA promoters were tested, and different strategies to express sgRNA were compared, resulting in the construction of an optimal system using the U6 snRNA-1 promoter as the sgRNA promoter. Successful disruption of bdpks led to a complete abolishment of the production of spirobisnaphthalenes and melanin. This work establishes a useful gene targeting disruption system for exploration of gene functions in Berkleasmium sp. Dzf12, and also provides an example for developing an efficient CRISPR/Cas9 system to the fungi that are difficult to manipulate using conventional genetic tools.
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Affiliation(s)
- Siji Zhao
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian district, Beijing, 100193, China
| | - Ruya Yin
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian district, Beijing, 100193, China
| | - Mengwei Zhang
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian district, Beijing, 100193, China
| | - Ziqi Zhai
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian district, Beijing, 100193, China
| | - Zhen Shen
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian district, Beijing, 100193, China
| | - Yan Mou
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian district, Beijing, 100193, China
| | - Dan Xu
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian district, Beijing, 100193, China
| | - Ligang Zhou
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian district, Beijing, 100193, China
| | - Daowan Lai
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian district, Beijing, 100193, China.
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Skellam E, Rajendran S, Li L. Combinatorial biosynthesis for the engineering of novel fungal natural products. Commun Chem 2024; 7:89. [PMID: 38637654 PMCID: PMC11026467 DOI: 10.1038/s42004-024-01172-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 04/08/2024] [Indexed: 04/20/2024] Open
Abstract
Natural products are small molecules synthesized by fungi, bacteria and plants, which historically have had a profound effect on human health and quality of life. These natural products have evolved over millions of years resulting in specific biological functions that may be of interest for pharmaceutical, agricultural, or nutraceutical use. Often natural products need to be structurally modified to make them suitable for specific applications. Combinatorial biosynthesis is a method to alter the composition of enzymes needed to synthesize a specific natural product resulting in structurally diversified molecules. In this review we discuss different approaches for combinatorial biosynthesis of natural products via engineering fungal enzymes and biosynthetic pathways. We highlight the biosynthetic knowledge gained from these studies and provide examples of new-to-nature bioactive molecules, including molecules synthesized using combinations of fungal and non-fungal enzymes.
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Affiliation(s)
- Elizabeth Skellam
- Department of Chemistry, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA.
- BioDiscovery Institute, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA.
- Department of Biological Sciences, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA.
| | - Sanjeevan Rajendran
- Department of Chemistry, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA
- BioDiscovery Institute, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA
| | - Lei Li
- Department of Chemistry, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA
- BioDiscovery Institute, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA
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Fang Y, Liu F, Shi Y, Yang T, Xin Y, Gu Z, Shi G, Zhang L. N-terminal lid swapping contributes to the substrate specificity and activity of thermophilic lipase TrLipE. Front Microbiol 2023; 14:1193955. [PMID: 37434709 PMCID: PMC10332459 DOI: 10.3389/fmicb.2023.1193955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 06/12/2023] [Indexed: 07/13/2023] Open
Abstract
TrLipE is a thermophilic lipase that has potential commercial applications because of its catalytic ability under extreme conditions. Consistent with most lipases, the lid of TrLipE is located over the catalytic pocket, controls the substrate channel to the active center, and regulates the substrate specificity, activity, and stability of the enzyme through conformational changes. TrLipE from Thermomicrobium roseum has potential industrial applications, which is hindered by its weak enzymatic activity. Here, 18 chimeras (TrL1-TrL18) were reconstructed by N-terminal lid swapping between TrLipE and structurally similar enzymes. The results showed that the chimeras had a similar pH range and optimum pH as wild TrLipE but a narrower temperature range of 40-80°C, and TrL17 and the other chimeras showed lower optimum temperatures of 70°C and 60°C, respectively. In addition, the half-lives of the chimeras were lower than those of TrLipE under optimum temperature conditions. Molecular dynamics simulations indicated that chimeras had high RMSD, RMSF, and B-factor values. When p-nitrophenol esters with different chains were used as substrates, compared with TrLipE, most of the chimeras had a low Km and high kcat value. The chimeras TrL2, TrL3, TrL17, and TrL18 could specifically catalyze the substrate 4-nitrophenyl benzoate, with TrL17 showing the highest kcat/Km value of 363.88 ± 15.83 L⋅min-1⋅mmol-1. Mutants were then designed by investigating the binding free energies of TrL17 and 4-nitrophenyl benzoate. The results indicated that single, double, and triple substitution variants (M89W and I206N; E33W/I206M and M89W/I206M; and M89W/I206M/L21I and M89W/I206N/L21I, respectively) presented approximately 2- to 3-fold faster catalysis of 4-nitrophenyl benzoate than the wild TrL17. Our observations will facilitate the development of the properties and industrial applications of TrLipE.
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Affiliation(s)
- Yakun Fang
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu, China
| | - Fan Liu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu, China
| | - Yi Shi
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu, China
| | - Ting Yang
- Wuxi Food Safety Inspection and Test Center, Technology Innovation Center of Special Food for State Market Regulation, Wuxi, Jiangsu, China
| | - Yu Xin
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu, China
| | - Zhenghua Gu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu, China
| | - Guiyang Shi
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu, China
| | - Liang Zhang
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu, China
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Paguirigan JAG, Kim JA, Hur JS, Kim W. Identification of a biosynthetic gene cluster for a red pigment cristazarin produced by a lichen-forming fungus Cladonia metacorallifera. PLoS One 2023; 18:e0287559. [PMID: 37352186 PMCID: PMC10289310 DOI: 10.1371/journal.pone.0287559] [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: 03/06/2023] [Accepted: 06/07/2023] [Indexed: 06/25/2023] Open
Abstract
Lichens are known to produce many novel bioactive metabolites. To date, approximately 1,000 secondary metabolites have been discovered, which are predominantly produced by the lichen mycobionts. However, despite the extensive studies on production of lichen secondary metabolites, little is known about the responsible biosynthetic gene clusters (BGCs). Here, we identified a putative BGC that is implicated in production of a red pigment, cristazarin (a naphthazarin derivative), in Cladonia metacorallifera. Previously, cristazarin was shown to be specifically induced in growth media containing fructose as a sole carbon source. Thus, we performed transcriptome analysis of C. metacorallifera growing on different carbon sources including fructose to identify the BGC for cristazarin. Among 39 polyketide synthase (PKS) genes found in the genome of C. metacorallifera, a non-reducing PKS (coined crz7) was highly expressed in growth media containing either fructose or glucose. The borders of a cristazarin gene cluster were delimited by co-expression patterns of neighboring genes of the crz7. BGCs highly conserved to the cristazarin BGC were also found in C. borealis and C. macilenta, indicating that these related species also have metabolic potentials to produce cristazarin. Phylogenetic analysis revealed that the Crz7 is sister to fungal PKSs that biosynthesize an acetylated tetrahydoxynaphthalene as a precursor of melanin pigment. Based on the phylogenetic placement of the Crz7 and putative functions of its neighboring genes, we proposed a plausible biosynthetic route for cristazarin. In this study, we identified a lichen-specific BGC that is likely involved in the biosynthesis of a naphthazarin derivative, cristazarin, and confirmed that transcriptome profiling under inducing and non-inducing conditions is an effective strategy for linking metabolites of interest to biosynthetic genes.
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Affiliation(s)
- Jaycee Augusto Gumiran Paguirigan
- Korean Lichen Research Institute, Sunchon National University, Suncheon, Korea
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines
| | - Jung A. Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon, Korea
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Sunchon National University, Suncheon, Korea
| | - Wonyong Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon, Korea
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Löhr NA, Urban MC, Eisen F, Platz L, Hüttel W, Gressler M, Müller M, Hoffmeister D. The Ketosynthase Domain Controls Chain Length in Mushroom Oligocyclic Polyketide Synthases. Chembiochem 2023; 24:e202200649. [PMID: 36507600 PMCID: PMC10108026 DOI: 10.1002/cbic.202200649] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022]
Abstract
The nonreducing iterative type I polyketide synthases (NR-PKSs) CoPKS1 and CoPKS4 of the webcap mushroom Cortinarius odorifer share 88 % identical amino acids. CoPKS1 almost exclusively produces a tricyclic octaketide product, atrochrysone carboxylic acid, whereas CoPKS4 shows simultaneous hepta- and octaketide synthase activity and also produces the bicyclic heptaketide 6-hydroxymusizin. To identify the region(s) controlling chain length, four chimeric enzyme variants were constructed and assayed for activity in Aspergillus niger as heterologous expression platform. We provide evidence that the β-ketoacyl synthase (KS) domain determines chain length in these mushroom NR-PKSs, even though their KS domains differ in only ten amino acids. A unique proline-rich linker connecting the acyl carrier protein with the thioesterase domain varies most between these two enzymes but is not involved in chain length control.
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Affiliation(s)
- Nikolai A Löhr
- Department Pharmaceutical Microbiology, Hans-Knöll-Institute, Friedrich-Schiller-Universität, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Maximilian C Urban
- Department Pharmaceutical Microbiology, Hans-Knöll-Institute, Friedrich-Schiller-Universität, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Frederic Eisen
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Lukas Platz
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Wolfgang Hüttel
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Markus Gressler
- Department Pharmaceutical Microbiology, Hans-Knöll-Institute, Friedrich-Schiller-Universität, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Dirk Hoffmeister
- Department Pharmaceutical Microbiology, Hans-Knöll-Institute, Friedrich-Schiller-Universität, Beutenbergstrasse 11a, 07745, Jena, Germany
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Gibbons JG, D’Avino P, Zhao S, Cox GW, Rinker DC, Fortwendel JR, Latge JP. Comparative Genomics Reveals a Single Nucleotide Deletion in pksP That Results in White-Spore Phenotype in Natural Variants of Aspergillus fumigatus. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:897954. [PMID: 37746219 PMCID: PMC10512363 DOI: 10.3389/ffunb.2022.897954] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/03/2022] [Indexed: 09/26/2023]
Abstract
Aspergillus fumigatus is a potentially deadly opportunistic human pathogen. A. fumigatus has evolved a variety of mechanisms to evade detection by the immune system. For example, the conidium surface is covered in a layer of 1,8-dihydroxynaphthalene (DHN) melanin which masks the antigen macrophages use for recognition. DHN melanin also protects conidia from ultraviolet radiation and gives A. fumigatus conidia their characteristic green-grayish color. Here, we conducted genomic analysis of two closely related white-spore natural variants of A. fumigatus in comparison to two closely related green-spore isolates to identify a genetic basis of the white-spore phenotype. Illumina whole-genome resequencing data of the four isolates was used to identify variants that were shared in the white-spore isolates and different from both the green-spore isolates and the Af293 reference genome (which is also a green-spore isolate). We identified 4,279 single nucleotide variants and 1,785 insertion/deletions fitting this pattern. Among these, we identified 64 variants predicted to be high impact, loss-of-function mutations. One of these variants is a single nucleotide deletion that results in a frameshift in pksP (Afu2g17600), the core biosynthetic gene in the DHN melanin encoding gene cluster. The frameshift mutation in the white-spore isolates leads to a truncated protein in which a phosphopantetheine attachment site (PP-binding domain) is interrupted and an additional PP-binding domain and a thioesterase domain are omitted. Growth rate analysis of white-spore and green-spore isolates at 37°C and 48°C revealed that white-spore isolates are thermosensitive. Growth rate of A. fumigatus Af293 and a pksP null mutant in the Af293 background suggests pksP is not directly involved in the thermosensitivity phenotype. Further, our study identified a mutation in a gene (Afu4g04740) associated with thermal sensitivity in yeasts which could also be responsible for the thermosensitivity of the white-spore mutants. Overall, we used comparative genomics to identify the mutation and protein alterations responsible for the white-spore phenotype of environmental isolates of A. fumigatus.
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Affiliation(s)
- John G. Gibbons
- Department of Food Science, University of Massachusetts, Amherst, MA, United States
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, United States
- Organismic & Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, MA, United States
| | - Paolo D’Avino
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, United States
| | - Shu Zhao
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, United States
| | - Grace W. Cox
- Department of Food Science, University of Massachusetts, Amherst, MA, United States
| | - David C. Rinker
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
| | - Jarrod R. Fortwendel
- Department of Clinical Pharmacy and Translational Science, University of Tennessee Health Science Center, Memphis, TN, United States
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Evolution-Informed Discovery of the Naphthalenone Biosynthetic Pathway in Fungi. mBio 2022; 13:e0022322. [PMID: 35616333 PMCID: PMC9239057 DOI: 10.1128/mbio.00223-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Fungi produce a wide diversity of secondary metabolites with interesting biological activities for the health, industrial, and agricultural sectors. While fungal genomes have revealed an unexpectedly high number of biosynthetic pathways that far exceeds the number of known molecules, accessing and characterizing this hidden diversity remain highly challenging. Here, we applied a combined phylogenetic dereplication and comparative genomics strategy to explore eight lichenizing fungi. The determination of the evolutionary relationships of aromatic polyketide pathways resulted in the identification of an uncharacterized biosynthetic pathway that is conserved in distant fungal lineages. The heterologous expression of the homologue from Aspergillus parvulus linked this pathway to naphthalenone compounds, which were detected in cultures when the pathway was expressed. Our unbiased and rational strategy generated evolutionary knowledge that ultimately linked biosynthetic genes to naphthalenone polyketides. Applied to many more genomes, this approach can unlock the full exploitation of the fungal kingdom for molecule discovery.
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Li F, Lin Z, Torres JP, Hill EA, Li D, Townsend CA, Schmidt EW. Sea Urchin Polyketide Synthase SpPks1 Produces the Naphthalene Precursor to Echinoderm Pigments. J Am Chem Soc 2022; 144:9363-9371. [PMID: 35588530 DOI: 10.1021/jacs.2c01416] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nearly every animal species on Earth contains a unique polyketide synthase (PKS) encoded in its genome, yet no animal-clade PKS has been biochemically characterized, and even the chemical products of these ubiquitous enzymes are known in only a few cases. The earliest animal genome-encoded PKS gene to be identified was SpPks1 from sea urchins. Previous genetic knockdown experiments implicated SpPks1 in synthesis of the sea urchin pigment echinochrome. Here, we express and purify SpPks1, performing biochemical experiments to demonstrate that the sea urchin protein is responsible for the synthesis of 2-acetyl-1,3,6,8-tetrahydroxynaphthalene (ATHN). Since ATHN is a plausible precursor of echinochromes, this result defines a biosynthetic pathway to the ubiquitous echinoderm pigments and rewrites the previous hypothesis for echinochrome biosynthesis. Truncation experiments showed that, unlike other type I iterative PKSs so far characterized, SpPks1 produces the naphthalene core using solely ketoacylsynthase (KS), acyltransferase, and acyl carrier protein domains, delineating a unique class of animal nonreducing aromatic PKSs (aPKSs). A series of amino acids in the KS domain define the family and are likely crucial in cyclization activity. Phylogenetic analyses indicate that SpPks1 and its homologs are widespread in echinoderms and their closest relatives, the acorn worms, reinforcing their fundamental importance to echinoderm biology. While the animal microbiome is known to produce aromatic polyketides, this work provides biochemical evidence that animals themselves also harbor ancient, convergent, dedicated pathways to carbocyclic aromatic polyketides. More fundamentally, biochemical analysis of SpPks1 begins to define the vast and unexplored biosynthetic space of the ubiquitous animal PKS family.
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Affiliation(s)
- Feng Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, P. R. China.,Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Joshua P Torres
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Eric A Hill
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Dehai Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, P. R. China
| | - Craig A Townsend
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Eric W Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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10
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Zhang X, Liu XX, Xing YN, Zhang M, Zhao Y, Wei YY, Zhang B, Jiao RH. Alternatones A and B, two polyketides possessing novel skeletons from entophyte Alternaria alternate L-10. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2022; 24:353-360. [PMID: 34142621 DOI: 10.1080/10286020.2021.1935893] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 05/24/2021] [Indexed: 06/12/2023]
Abstract
On our ongoing searching for bioactive natural products derived from entophytes, two polyketides possessing novel skeletons, alternatones A-B (1-2), were identified from the culture of Alternaria alternate L-10. Their structures were established by a combination of spectroscopic and single-crystal X-ray diffraction with Cu Ka radiation. Alternatone A (1) exhibited cytotoxic activity against human hepatoma carcinoma HepG-2 cell line. The putative biosynthetic pathways for compounds 1-2 were also proposed.
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Affiliation(s)
- Xuan Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Nanjing University, Nanjing 210023, China
| | - Xian-Xian Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Nanjing University, Nanjing 210023, China
| | - Yin-Nan Xing
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Nanjing University, Nanjing 210023, China
| | - Mei Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Nanjing University, Nanjing 210023, China
| | - Yang Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Nanjing University, Nanjing 210023, China
| | - Yuan-Yuan Wei
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Nanjing University, Nanjing 210023, China
| | - Bo Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Nanjing University, Nanjing 210023, China
| | - Rui-Hua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Nanjing University, Nanjing 210023, China
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Motoyama T, Kondoh Y, Shimizu T, Hayashi T, Honda K, Uchida M, Osada H. Identification of Scytalone Dehydratase Inhibitors Effective against Melanin Biosynthesis Dehydratase Inhibitor-Resistant Pyricularia oryzae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:3109-3116. [PMID: 35234040 DOI: 10.1021/acs.jafc.1c04984] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Melanin is a secondary metabolite required for the infection of the rice blast fungus Pyricularia oryzae. Melanin biosynthesis enzymes are targets for controlling rice blast disease, and three types of commercial melanin biosynthesis inhibitors (MBIs) including MBI-R, MBI-D, and MBI-P have been developed. However, the occurrence of MBI-D-resistant strains containing scytalone dehydratase (SDH1/RSY1) with V75M mutations has been recently reported. In this study, we aimed to identify inhibitors of SDH1-V75M. We screened the RIKEN Natural Products Depository chemical library using chemical array technology and evaluated the inhibition of SDH1-V75M by candidate compounds. NPD13731 strongly inhibited the activity of wild-type and mutant SDH1. The structure-activity relationship data were used to create a more potent inhibitor 16, which controlled rice blast disease in rice plants infected with MBI-D-resistant P. oryzae. Compound 16, which we named melabiostin, may be used to develop fungicides for controlling rice blast infections.
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Affiliation(s)
- Takayuki Motoyama
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yasumitsu Kondoh
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Takeshi Shimizu
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Teruo Hayashi
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kaori Honda
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Motoko Uchida
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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12
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Tang S, Men P, Zhang W, Li H, Li Z, Huang X, Lu X. Identification of a polyketide biosynthesis gene cluster by transcriptional regulator activation in Aspergillus terreus. Fungal Genet Biol 2022; 160:103690. [DOI: 10.1016/j.fgb.2022.103690] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/10/2022] [Accepted: 03/23/2022] [Indexed: 11/27/2022]
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13
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Motoyama T, Yun CS, Osada H. Biosynthesis and biological function of secondary metabolites of the rice blast fungus Pyricularia oryzae. J Ind Microbiol Biotechnol 2021; 48:kuab058. [PMID: 34379774 PMCID: PMC8788799 DOI: 10.1093/jimb/kuab058] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/05/2021] [Indexed: 11/18/2022]
Abstract
Filamentous fungi have many secondary metabolism genes and produce a wide variety of secondary metabolites with complex and unique structures. However, the role of most secondary metabolites remains unclear. Moreover, most fungal secondary metabolism genes are silent or poorly expressed under laboratory conditions and are difficult to utilize. Pyricularia oryzae, the causal pathogen of rice blast disease, is a well-characterized plant pathogenic fungus. P. oryzae also has a large number of secondary metabolism genes and appears to be a suitable organism for analyzing secondary metabolites. However, in case of this fungus, biosynthetic genes for only four groups of secondary metabolites have been well characterized. Among two of the four groups of secondary metabolites, biosynthetic genes were identified by activating secondary metabolism. These secondary metabolites include melanin, a polyketide compound required for rice infection; tenuazonic acid, a well-known mycotoxin produced by various plant pathogenic fungi and biosynthesized by a unique nonribosomal peptide synthetase-polyketide synthase hybrid enzyme; nectriapyrones, antibacterial polyketide compounds produced mainly by symbiotic fungi, including plant pathogens and endophytes, and pyriculols, phytotoxic polyketide compounds. This review mainly focuses on the biosynthesis and biological functions of the four groups of P. oryzae secondary metabolites.
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Affiliation(s)
- Takayuki Motoyama
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Choong-Soo Yun
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
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14
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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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15
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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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16
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Piras M, Patruno I, Nikolakopoulou C, Willment JA, Sloan NL, Zanato C, Brown GD, Zanda M. Synthesis of the Fungal Metabolite YWA1 and Related Constructs as Tools to Study MelLec-Mediated Immune Response to Aspergillus Infections†. J Org Chem 2021; 86:6044-6055. [PMID: 33884881 DOI: 10.1021/acs.joc.0c02324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe the chemical synthesis of the fungal naphthopyrones YWA1 and fonsecin B, as well as their functionalization with an amine-spacer arm and the conjugation of the resulting molecules to three different functional tags (i.e., biotin, Oregon green, 1-[3-(succinimidyloxycarbonyl)benzyl]-4-[5-(4-methoxyphenyl)-2-oxazolyl]pyridinium bromide (PyMPO)). The naphthopyrone-biotin and -PyMPO constructs maintained the ability to bind the C-type lectin receptor MelLec, whose interaction with immunologically active fungal metabolites (i.e., 1,8-dihydroxynaphthalene-(DHN)-melanin and YWA1) is a key step in host recognition and induction of protective immune responses against Aspergillus fumigatus. The fluorescent Fonsecin B-PyMPO construct 21 was used to selectively visualize MelLec-expressing cells, thus validating the potential of this strategy for studying the role and functions of MelLec in immunity.
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Affiliation(s)
- Monica Piras
- Kosterlitz Centre for Therapeutics, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, U.K
| | - Ilaria Patruno
- Kosterlitz Centre for Therapeutics, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, U.K
| | - Christina Nikolakopoulou
- Aberdeen Fungal Group, MRC Centre for Medical Mycology, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, U.K.,Medical Research Council Centre for Medical Mycology at the University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, U.K
| | - Janet A Willment
- Aberdeen Fungal Group, MRC Centre for Medical Mycology, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, U.K.,Medical Research Council Centre for Medical Mycology at the University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, U.K
| | - Nikki L Sloan
- Chemistry Department, Loughborough University, Loughborough LE113TU, U.K
| | - Chiara Zanato
- CY Cergy Paris Université, CNRS, BioCIS, 95000 Cergy Pontoise, France
| | - Gordon D Brown
- Aberdeen Fungal Group, MRC Centre for Medical Mycology, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, U.K.,Medical Research Council Centre for Medical Mycology at the University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, U.K
| | - Matteo Zanda
- Kosterlitz Centre for Therapeutics, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, U.K.,Chemistry Department, Loughborough University, Loughborough LE113TU, U.K.,C.N.R.-SCITEC, via Mancinelli 7, 20131 Milan, Italy
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17
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Labib MM, Amin MK, Alzohairy AM, Elashtokhy MMA, Samir O, Hassanein SE. Inhibition analysis of aflatoxin by in silico targeting the thioesterase domain of polyketide synthase enzyme in Aspergillus ssp. J Biomol Struct Dyn 2020; 40:4328-4340. [PMID: 33308034 DOI: 10.1080/07391102.2020.1856186] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The spread of fungal growth causes enormous economic, agricultural, and health problems for humans, such as Aspergillus sp., which produce aflatoxins. Thus, the inhibition of aflatoxin production became a precious target. In this research, the thioesterase (TE) domain from Polyketide synthase enzyme was selected to employ the in silico docking, using AutoDock Vina, against 623 natural compounds from the South African natural compound database (SANCDB), to identify potential inhibitors that can selectively inhibit thioesterase domain. The top ten inhibitors components were pinocembrin, typhaphthalide, p-coumaroylputrescine, dilemmaone A, 9-angelylplatynecine, 2,4,6-octatrienal, 4,8-dichloro-3,7-dimethyl-, (2e,4z,6e)-, lilacinobiose, 1,3,7-octatriene, 5,6-dichloro-2-(dichloromethyl)-6-methyl-, [r*,s*-(e)]-(-)- (9ci), lilacinobiose, 1,3,7-octatriene, 5,6-dichloro-2-(dichloromethyl)-6-methyl-, [r*,s*-(e)]-(-)- (9ci), 1,3,7-octatriene, 1,5,6-trichloro-2-(dichloromethyl)-6-methyl-, [r*,s*-(z,e)] and 9-angelylhastanecine and that depending on the lowest binding energy, the best chemical interactions and the best drug-likeness. The results of those components gave successful inhibition with the thioesterase domain. So, they can be used for inhibition and controlling aflatoxin contamination of agriculture crop yields, specially, pinocembrin which gave promising results.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mai M Labib
- Agriculture Genetic Engineering Research Institute (AGERI), Cairo, Egypt
| | - M K Amin
- Faculty of Agriculture Department of Genetics, Zagazig University, Zagazig, Egypt
| | - A M Alzohairy
- Faculty of Agriculture Department of Genetics, Zagazig University, Zagazig, Egypt
| | - M M A Elashtokhy
- Faculty of Agriculture Department of Genetics, Zagazig University, Zagazig, Egypt
| | - O Samir
- Children's Cancer Hospital Foundation, Cairo, Egypt
| | - S E Hassanein
- Agriculture Genetic Engineering Research Institute (AGERI), Cairo, Egypt.,Misr University for Science and Technology (MUST), Al Jizah, Egypt
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18
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Secondary Metabolites of the Rice Blast Fungus Pyricularia oryzae: Biosynthesis and Biological Function. Int J Mol Sci 2020; 21:ijms21228698. [PMID: 33218033 PMCID: PMC7698770 DOI: 10.3390/ijms21228698] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/10/2020] [Accepted: 11/17/2020] [Indexed: 02/07/2023] Open
Abstract
Plant pathogenic fungi produce a wide variety of secondary metabolites with unique and complex structures. However, most fungal secondary metabolism genes are poorly expressed under laboratory conditions. Moreover, the relationship between pathogenicity and secondary metabolites remains unclear. To activate silent gene clusters in fungi, successful approaches such as epigenetic control, promoter exchange, and heterologous expression have been reported. Pyricularia oryzae, a well-characterized plant pathogenic fungus, is the causal pathogen of rice blast disease. P. oryzae is also rich in secondary metabolism genes. However, biosynthetic genes for only four groups of secondary metabolites have been well characterized in this fungus. Biosynthetic genes for two of the four groups of secondary metabolites have been identified by activating secondary metabolism. This review focuses on the biosynthesis and roles of the four groups of secondary metabolites produced by P. oryzae. These secondary metabolites include melanin, a polyketide compound required for rice infection; pyriculols, phytotoxic polyketide compounds; nectriapyrones, antibacterial polyketide compounds produced mainly by symbiotic fungi including endophytes and plant pathogens; and tenuazonic acid, a well-known mycotoxin produced by various plant pathogenic fungi and biosynthesized by a unique NRPS-PKS enzyme.
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19
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Cogan DP, Ly J, Nair SK. Structural Basis for Enzymatic Off-Loading of Hybrid Polyketides by Dieckmann Condensation. ACS Chem Biol 2020; 15:2783-2791. [PMID: 33017142 DOI: 10.1021/acschembio.0c00579] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
While several bioactive natural products that contain tetramate or pyridone heterocycles have been described, information on the enzymology underpinning these functionalities has been limited. Here we biochemically characterize an off-loading Dieckmann cyclase, NcmC, that installs the tetramate headgroup in nocamycin, a hybrid polyketide/nonribosomal peptide natural product. Crystal structures of the enzyme (1.6 Å) and its covalent complex with the epoxide cerulenin (1.6 Å) guide additional structure-based mutagenesis and product-profile analyses. Our results offer mechanistic insights into how the conserved thioesterase-like scaffold has been adapted to perform a new chemical reaction, namely, heterocyclization. Additional bioinformatics combined with docking and modeling identifies likely candidates for heterocycle formation in underexplored gene clusters and uncovers a modular basis of substrate recognition by the two subdomains of these Dieckmann cyclases.
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20
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Hantke V, Wang C, Skellam EJ, Cox RJ. Function of pathway specific regulators in the ACE1 and pyrichalasin H biosynthetic gene clusters. RSC Adv 2019; 9:35797-35802. [PMID: 35528102 PMCID: PMC9074748 DOI: 10.1039/c9ra07028a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 10/28/2019] [Indexed: 11/21/2022] Open
Abstract
Ectopic expression of BC1 which encodes a putative pathway specific transcription factor from the ACE1 biosynthetic gene cluster of the rice pathogen Pyricularia oryzae Guy11 did not lead to the production of ACE1-related compounds. However the known compound hinnulin A was formed. A putative partial gene cluster potentially involved in the biosynthesis of hinnulin A and DHN melanin was validated by RT-PCR and a possible biosynthetic pathway is proposed. Ectopic expression of pyiR which encodes a pathway specific transcription factor from the pyrichalasin H biosynthetic gene cluster in Magnaporthe grisea NI980 led to the apparent up-regulation of the pyi cluster and a 3-fold increase in pyrichalasin production under standard fermentation conditions, but did not lead to the formation of new compounds.
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Affiliation(s)
- Verena Hantke
- Institute for Organic Chemistry and BMWZ, Leibniz Universität Hannover Schneiderberg 38 30167 Hannover Germany
| | - Chongqing Wang
- 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
| | - Russell J Cox
- Institute for Organic Chemistry and BMWZ, Leibniz Universität Hannover Schneiderberg 38 30167 Hannover Germany
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21
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Yi X, Zhao Q, Tian Z, Jia X, Cao W, Liu W, He Q. Insights into the Functionalization of the Methylsalicyclic Moiety during the Biosynthesis of Chlorothricin by Comparative Kinetic Assays of the Activities of Two KAS III‐like Acyltransferases. CHINESE J CHEM 2019. [DOI: 10.1002/cjoc.201900134] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xuan Yi
- Department of Chemistry, Innovative Drug Research CenterShanghai University 99 Shangda Road, Shanghai 200444 China
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence on Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences 345 Lingling Road, Shanghai 200032 China
| | - Qunfei Zhao
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence on Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences 345 Lingling Road, Shanghai 200032 China
| | - Zhenhua Tian
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence on Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences 345 Lingling Road, Shanghai 200032 China
| | - Xinying Jia
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence on Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences 345 Lingling Road, Shanghai 200032 China
| | - Weiguo Cao
- Department of Chemistry, Innovative Drug Research CenterShanghai University 99 Shangda Road, Shanghai 200444 China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence on Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences 345 Lingling Road, Shanghai 200032 China
- Huzhou Center of Bio‐Synthetic Innovation 1366 Hongfeng Road, Huzhou, Zhejiang 313000 China
| | - Qing‐Li He
- Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine 1200 Cai Lun Road, Shanghai 201203 China
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22
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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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23
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Mafezoli J, Xu YM, Hilário F, Freidhof B, Espinosa-Artiles P, dos Santos LC, de Oliveira MCF, Gunatilaka AAL. Modulation of polyketide biosynthetic pathway of the endophytic fungus, Anteaglonium sp. FL0768, by copper (II) and anacardic acid. PHYTOCHEMISTRY LETTERS 2018; 28:157-163. [PMID: 31354886 PMCID: PMC6660184 DOI: 10.1016/j.phytol.2018.10.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In an attempt to explore the biosynthetic potential of endosymbiotic fungi, the secondary metabolite profiles of the endophytic fungus, Anteaglonium sp. FL0768, cultured under a variety of conditions were investigated. In potato dextrose broth (PDB) medium, Anteaglonium sp. FL0768 produced the heptaketides, herbaridine A (1), herbarin (2), 1-hydroxydehydroherbarin (3), scorpinone (4), and the methylated hexaketide 9S,11R-(+)-ascosalitoxin (5). Incorporation of commonly used epigenetic modifiers, 5-azacytidine and suberoylanilide hydroxamic acid, into the PDB culture medium of this fungus had no effect on its secondary metabolite profile. However, the histone acetyl transferase inhibitor, anacardic acid, slightly affected the metabolite profile affording scorpinone (4) as the major metabolite together with 1-hydroxydehydroherbarin (3) and a different methylated hexaketide, ascochitine (6). Intriguingly, incorporaion of Cu2+ into the PDB medium enhanced production of metabolites and drastically affected the biosynthetic pathway resulting in the production of pentaketide dimers, palmarumycin CE4 (7), palmarumycin CP4 (8), and palmarumycin CP1 (9), in addition to ascochitine (6). The structure of the new metabolite 7 was established with the help of spectroscopic data and by MnO2 oxidation to the known pentaketide dimer, palmarumycin CP3 (10). Biosynthetic pathways to some metabolites in Anteaglonium sp. FL0768 are presented and possible effects of AA and Cu2+ on these pathways are discussed.
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Affiliation(s)
- Jair Mafezoli
- Southwest Center for Natural Products Research, School of Natural Resources and the Environment, College of Agriculture and Life Sciences, The University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, USA
- Departamento de Química Orgânica e Inorgânica, Universidade Federal do Ceará, Campus do Pici, Caixa Postal 6044, Fortaleza-CE, 60455-970, Brazil
| | - Ya-ming Xu
- Southwest Center for Natural Products Research, School of Natural Resources and the Environment, College of Agriculture and Life Sciences, The University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, USA
| | - Felipe Hilário
- Southwest Center for Natural Products Research, School of Natural Resources and the Environment, College of Agriculture and Life Sciences, The University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, USA
- Departamento de Química Orgânica, Instituto de Química, UNESP, Universidade Estadual Paulista, Araraquara, Sao Paulo, 14800-900, Brazil
| | - Brandon Freidhof
- Southwest Center for Natural Products Research, School of Natural Resources and the Environment, College of Agriculture and Life Sciences, The University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, USA
| | - Patricia Espinosa-Artiles
- Southwest Center for Natural Products Research, School of Natural Resources and the Environment, College of Agriculture and Life Sciences, The University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, USA
| | - Lourdes C. dos Santos
- Departamento de Química Orgânica, Instituto de Química, UNESP, Universidade Estadual Paulista, Araraquara, Sao Paulo, 14800-900, Brazil
| | - Maria C. F. de Oliveira
- Southwest Center for Natural Products Research, School of Natural Resources and the Environment, College of Agriculture and Life Sciences, The University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, USA
- Departamento de Química Orgânica e Inorgânica, Universidade Federal do Ceará, Campus do Pici, Caixa Postal 6044, Fortaleza-CE, 60455-970, Brazil
| | - A. A. Leslie Gunatilaka
- Southwest Center for Natural Products Research, School of Natural Resources and the Environment, College of Agriculture and Life Sciences, The University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, USA
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24
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Zhou ZZ, Zhu HJ, Lin LP, Zhang X, Ge HM, Jiao RH, Tan RX. Dalmanol biosyntheses require coupling of two separate polyketide gene clusters. Chem Sci 2018; 10:73-82. [PMID: 30746075 PMCID: PMC6335865 DOI: 10.1039/c8sc03697g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Accepted: 11/21/2018] [Indexed: 11/29/2022] Open
Abstract
Polyketide–polyketide hybrids are unique natural products with promising bioactivity, but the hybridization processes remain poorly understood.
Polyketide–polyketide hybrids are unique natural products with promising bioactivity, but the hybridization processes remain poorly understood. Herein, we present that the biosynthetic pathways of two immunosuppressants, dalmanol A and acetodalmanol A, result from an unspecific monooxygenase triggered hybridization of two distinct polyketide (naphthalene and chromane) biosynthetic gene clusters. The orchestration of the functional dimorphism of the polyketide synthase (ChrA) ketoreductase (KR) domain (shortened as ChrA KR) with that of the KR partner (ChrB) in the bioassembly line increases the polyketide diversity and allows the fungal generation of plant chromanes (e.g., noreugenin) and phloroglucinols (e.g., 2,4,6-trihydroxyacetophenone). The simultaneous fungal biosynthesis of 1,3,6,8- and 2-acetyl-1,3,6,8-tetrahydroxynaphthalenes was addressed as well. Collectively, the work may symbolize a movement in understanding the multiple-gene-cluster involved natural product biosynthesis, and highlights the possible fungal generations of some chromane- and phloroglucinol-based phytochemicals.
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Affiliation(s)
- Zhen Zhen Zhou
- State Key Laboratory of Pharmaceutical Biotechnology , Institute of Functional Biomolecules , Nanjing University , Nanjing 210023 , China .
| | - Hong Jie Zhu
- State Key Laboratory of Pharmaceutical Biotechnology , Institute of Functional Biomolecules , Nanjing University , Nanjing 210023 , China .
| | - Li Ping Lin
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy , Nanjing University of Chinese Medicine , Nanjing 210023 , China.,State Key Laboratory Elemento-Organic Chemistry , Nankai University , Tianjin 300071 , China
| | - Xuan Zhang
- State Key Laboratory of Pharmaceutical Biotechnology , Institute of Functional Biomolecules , Nanjing University , Nanjing 210023 , China .
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology , Institute of Functional Biomolecules , Nanjing University , Nanjing 210023 , China .
| | - Rui Hua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology , Institute of Functional Biomolecules , Nanjing University , Nanjing 210023 , China .
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology , Institute of Functional Biomolecules , Nanjing University , Nanjing 210023 , China . .,State Key Laboratory Cultivation Base for TCM Quality and Efficacy , Nanjing University of Chinese Medicine , Nanjing 210023 , China
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25
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Zhang X, Wang TT, Xu QL, Xiong Y, Zhang L, Han H, Xu K, Guo WJ, Xu Q, Tan RX, Ge HM. Genome Mining and Comparative Biosynthesis of Meroterpenoids from Two Phylogenetically Distinct Fungi. Angew Chem Int Ed Engl 2018; 57:8184-8188. [DOI: 10.1002/anie.201804317] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/20/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Xuan Zhang
- State Key Laboratory of Pharmaceutical BiotechnologyInstitute of Functional BiomoleculesSchool of Life SciencesNanjing University Nanjing 210023 China
| | - Ting Ting Wang
- State Key Laboratory of Pharmaceutical BiotechnologyInstitute of Functional BiomoleculesSchool of Life SciencesNanjing University Nanjing 210023 China
| | - Qin Lan Xu
- State Key Laboratory of Pharmaceutical BiotechnologyInstitute of Functional BiomoleculesSchool of Life SciencesNanjing University Nanjing 210023 China
| | - Ying Xiong
- State Key Laboratory of Pharmaceutical BiotechnologyInstitute of Functional BiomoleculesSchool of Life SciencesNanjing University Nanjing 210023 China
| | - Li Zhang
- State Key Laboratory of Pharmaceutical BiotechnologyInstitute of Functional BiomoleculesSchool of Life SciencesNanjing University Nanjing 210023 China
| | - Hao Han
- State Key Laboratory of Pharmaceutical BiotechnologyInstitute of Functional BiomoleculesSchool of Life SciencesNanjing University Nanjing 210023 China
| | - Kuang Xu
- State Key Laboratory of Pharmaceutical BiotechnologyInstitute of Functional BiomoleculesSchool of Life SciencesNanjing University Nanjing 210023 China
| | - Wen Jie Guo
- State Key Laboratory of Pharmaceutical BiotechnologyInstitute of Functional BiomoleculesSchool of Life SciencesNanjing University Nanjing 210023 China
| | - Qiang Xu
- State Key Laboratory of Pharmaceutical BiotechnologyInstitute of Functional BiomoleculesSchool of Life SciencesNanjing University Nanjing 210023 China
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical BiotechnologyInstitute of Functional BiomoleculesSchool of Life SciencesNanjing University Nanjing 210023 China
- State Key Laboratory Cultivation Base for TCM Quality and EfficacyNanjing University of Chinese Medicine Nanjing 210023 China
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical BiotechnologyInstitute of Functional BiomoleculesSchool of Life SciencesNanjing University Nanjing 210023 China
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26
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Zhang X, Wang TT, Xu QL, Xiong Y, Zhang L, Han H, Xu K, Guo WJ, Xu Q, Tan RX, Ge HM. Genome Mining and Comparative Biosynthesis of Meroterpenoids from Two Phylogenetically Distinct Fungi. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804317] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Xuan Zhang
- State Key Laboratory of Pharmaceutical BiotechnologyInstitute of Functional BiomoleculesSchool of Life SciencesNanjing University Nanjing 210023 China
| | - Ting Ting Wang
- State Key Laboratory of Pharmaceutical BiotechnologyInstitute of Functional BiomoleculesSchool of Life SciencesNanjing University Nanjing 210023 China
| | - Qin Lan Xu
- State Key Laboratory of Pharmaceutical BiotechnologyInstitute of Functional BiomoleculesSchool of Life SciencesNanjing University Nanjing 210023 China
| | - Ying Xiong
- State Key Laboratory of Pharmaceutical BiotechnologyInstitute of Functional BiomoleculesSchool of Life SciencesNanjing University Nanjing 210023 China
| | - Li Zhang
- State Key Laboratory of Pharmaceutical BiotechnologyInstitute of Functional BiomoleculesSchool of Life SciencesNanjing University Nanjing 210023 China
| | - Hao Han
- State Key Laboratory of Pharmaceutical BiotechnologyInstitute of Functional BiomoleculesSchool of Life SciencesNanjing University Nanjing 210023 China
| | - Kuang Xu
- State Key Laboratory of Pharmaceutical BiotechnologyInstitute of Functional BiomoleculesSchool of Life SciencesNanjing University Nanjing 210023 China
| | - Wen Jie Guo
- State Key Laboratory of Pharmaceutical BiotechnologyInstitute of Functional BiomoleculesSchool of Life SciencesNanjing University Nanjing 210023 China
| | - Qiang Xu
- State Key Laboratory of Pharmaceutical BiotechnologyInstitute of Functional BiomoleculesSchool of Life SciencesNanjing University Nanjing 210023 China
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical BiotechnologyInstitute of Functional BiomoleculesSchool of Life SciencesNanjing University Nanjing 210023 China
- State Key Laboratory Cultivation Base for TCM Quality and EfficacyNanjing University of Chinese Medicine Nanjing 210023 China
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical BiotechnologyInstitute of Functional BiomoleculesSchool of Life SciencesNanjing University Nanjing 210023 China
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27
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Diversity and evolution of polyketide biosynthesis gene clusters in the Ceratocystidaceae. Fungal Biol 2018; 122:856-866. [PMID: 30115319 DOI: 10.1016/j.funbio.2018.04.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 03/30/2018] [Accepted: 04/25/2018] [Indexed: 01/26/2023]
Abstract
Polyketides are secondary metabolites with diverse biological activities. Polyketide synthases (PKS) are often encoded from genes clustered in the same genomic region. Functional analyses and genomic studies show that most fungi are capable of producing a repertoire of polyketides. We considered the potential of Ceratocystidaceae for producing polyketides using a comparative genomics approach. Our aims were to identify the putative polyketide biosynthesis gene clusters, to characterize them and predict the types of polyketide compounds they might produce. We used sequences from nineteen species in the genera, Ceratocystis, Endoconidiophora, Davidsoniella, Huntiella, Thielaviopsis and Bretziella, to identify and characterize PKS gene clusters, by employing a range of bioinformatics and phylogenetic tools. We showed that the genomes contained putative clusters containing a non-reducing type I PKS and a type III PKS. Phylogenetic analyses suggested that these genes were already present in the ancestor of the Ceratocystidaceae. By contrast, the various reducing type I PKS-containing clusters identified in these genomes appeared to have distinct evolutionary origins. Although one of the identified clusters potentially allows for the production of melanin, their functional characterization will undoubtedly reveal many novel and important compounds implicated in the biology of the Ceratocystidaceae.
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28
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Liu L, Zhang Z, Shao CL, Wang CY. Analysis of the Sequences, Structures, and Functions of Product-Releasing Enzyme Domains in Fungal Polyketide Synthases. Front Microbiol 2017; 8:1685. [PMID: 28928723 PMCID: PMC5591372 DOI: 10.3389/fmicb.2017.01685] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 08/21/2017] [Indexed: 11/14/2022] Open
Abstract
Product-releasing enzyme (PRE) domains in fungal non-reducing polyketide synthases (NR-PKSs) play a crucial role in catalysis and editing during polyketide biosynthesis, especially accelerating final biosynthetic reactions accompanied with product offloading. However, up to date, the systematic knowledge about PRE domains is deficient. In the present study, the relationships between sequences, structures, and functions of PRE domains were analyzed with 574 NR-PKSs of eight groups (I–VIII). It was found that the PRE domains in NR-PKSs could be mainly classified into three types, thioesterase (TE), reductase (R), and metallo-β-lactamase-type TE (MβL-TE). The widely distributed TE or TE-like domains were involved in NR-PKSs of groups I–IV, VI, and VIII. The R domains appeared in NR-PKSs of groups IV and VII, while the physically discrete MβL-TE domains were employed by most NR-PKSs of group V. The changes of catalytic sites and structural characteristics resulted in PRE functional differentiations. The phylogeny revealed that the evolution of TE domains was accompanied by complex functional divergence. The diverse sequence lengths of TE lid-loops affected substrate specificity with different chain lengths. The volume diversification of TE catalytic pockets contributed to catalytic mechanisms with functional differentiations. The above findings may help to understand the crucial catalysis of fungal aromatic polyketide biosyntheses and govern recombination of NR-PKSs to obtain unnatural target products.
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Affiliation(s)
- Lu Liu
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of ChinaQingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China
| | - Zheng Zhang
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong UniversityJinan, China
| | - Chang-Lun Shao
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of ChinaQingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China
| | - Chang-Yun Wang
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of ChinaQingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China.,Institute of Evolution and Marine Biodiversity, Ocean University of ChinaQingdao, China
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29
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Chisuga T, Miyanaga A, Kudo F, Eguchi T. Structural analysis of the dual-function thioesterase SAV606 unravels the mechanism of Michael addition of glycine to an α,β-unsaturated thioester. J Biol Chem 2017; 292:10926-10937. [PMID: 28522606 PMCID: PMC5491777 DOI: 10.1074/jbc.m117.792549] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 05/11/2017] [Indexed: 01/14/2023] Open
Abstract
Thioesterases catalyze hydrolysis of acyl thioesters to release carboxylic acid or macrocyclization to produce the corresponding macrocycle in the biosynthesis of fatty acids, polyketides, or nonribosomal peptides. Recently, we reported that the thioesterase CmiS1 from Streptomyces sp. MJ635-86F5 catalyzes the Michael addition of glycine to an α,β-unsaturated fatty acyl thioester followed by thioester hydrolysis in the biosynthesis of the macrolactam antibiotic cremimycin. However, the molecular mechanisms of CmiS1-catalyzed reactions are unclear. Here, we report on the functional and structural characterization of the CmiS1 homolog SAV606 from Streptomyces avermitilis MA-4680. In vitro analysis indicated that SAV606 catalyzes the Michael addition of glycine to crotonic acid thioester and subsequent hydrolysis yielding (R)-N-carboxymethyl-3-aminobutyric acid. We also determined the crystal structures of SAV606 both in ligand-free form at 2.4 Å resolution and in complex with (R)-N-carboxymethyl-3-aminobutyric acid at 2.0 Å resolution. We found that SAV606 adopts an α/β hotdog fold and has an active site at the dimeric interface. Examining the complexed structure, we noted that the substrate-binding loop comprising Tyr-53-Asn-61 recognizes the glycine moiety of (R)-N-carboxymethyl-3-aminobutyric acid. Moreover, we found that SAV606 does not contain an acidic residue at the active site, which is distinct from canonical hotdog thioesterases. Site-directed mutagenesis experiments revealed that His-59 plays a crucial role in both the Michael addition and hydrolysis via a water molecule. These results allow us to propose the reaction mechanism of the SAV606-catalyzed Michael addition and thioester hydrolysis and provide new insight into the multiple functions of a thioesterase family enzyme.
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Affiliation(s)
- Taichi Chisuga
- From the Department of Chemistry and Materials Science and
| | - Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Tadashi Eguchi
- From the Department of Chemistry and Materials Science and
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
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30
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Zhang P, Wang X, Fan A, Zheng Y, Liu X, Wang S, Zou H, Oakley BR, Keller NP, Yin WB. A cryptic pigment biosynthetic pathway uncovered by heterologous expression is essential for conidial development inPestalotiopsis fici. Mol Microbiol 2017; 105:469-483. [DOI: 10.1111/mmi.13711] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2017] [Indexed: 01/15/2023]
Affiliation(s)
- Peng Zhang
- State Key Laboratory of Mycology; Institute of Microbiology, Chinese Academy of Sciences; Beijing People's Republic of China
- College of Life Science, University of Chinese Academy of Sciences; Beijing People's Republic of China
| | - Xiuna Wang
- State Key Laboratory of Mycology; Institute of Microbiology, Chinese Academy of Sciences; Beijing People's Republic of China
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences; Fujian Agriculture and Forestry University; Fuzhou People's Republic of China
| | - Aili Fan
- State Key Laboratory of Mycology; Institute of Microbiology, Chinese Academy of Sciences; Beijing People's Republic of China
| | - Yanjing Zheng
- Zhejiang Provincial (Wenzhou) Key Lab for Water Environment and Marine Biological Resources Protection, College of Life and Environmental Science; Wenzhou University; Wenzhou People's Republic of China
| | - Xingzhong Liu
- State Key Laboratory of Mycology; Institute of Microbiology, Chinese Academy of Sciences; Beijing People's Republic of China
| | - Shihua Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences; Fujian Agriculture and Forestry University; Fuzhou People's Republic of China
| | - Huixi Zou
- Zhejiang Provincial (Wenzhou) Key Lab for Water Environment and Marine Biological Resources Protection, College of Life and Environmental Science; Wenzhou University; Wenzhou People's Republic of China
| | - Berl R. Oakley
- Department of Molecular Biosciences; University of Kansas; Lawrence KS USA
| | - Nancy P. Keller
- Department of Medical Microbiology and Immunology; University of Wisconsin-Madison; Madison Wisconsin, WI USA
| | - Wen-Bing Yin
- State Key Laboratory of Mycology; Institute of Microbiology, Chinese Academy of Sciences; Beijing People's Republic of China
- College of Life Science, University of Chinese Academy of Sciences; Beijing People's Republic of China
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31
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Chen XP, Shi T, Wang XL, Wang J, Chen Q, Bai L, Zhao YL. Theoretical Studies on the Mechanism of Thioesterase-Catalyzed Macrocyclization in Erythromycin Biosynthesis. ACS Catal 2016. [DOI: 10.1021/acscatal.6b01154] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Xiong-Ping Chen
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic and Developmental Sciences, MOE-LSC, School
of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Ting Shi
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic and Developmental Sciences, MOE-LSC, School
of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xiao-Lei Wang
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic and Developmental Sciences, MOE-LSC, School
of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jitao Wang
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic and Developmental Sciences, MOE-LSC, School
of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Qihua Chen
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic and Developmental Sciences, MOE-LSC, School
of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Linquan Bai
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic and Developmental Sciences, MOE-LSC, School
of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yi-Lei Zhao
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic and Developmental Sciences, MOE-LSC, School
of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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32
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Horsman ME, Hari TPA, Boddy CN. Polyketide synthase and non-ribosomal peptide synthetase thioesterase selectivity: logic gate or a victim of fate? Nat Prod Rep 2016; 33:183-202. [DOI: 10.1039/c4np00148f] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thioesterases (TEs) are product offloading enzymes from FAS, PKS, and NRPS complexes. We review the diversity, structure, and mechanism of PKS and NRPS TEs and analyze TE loading and release steps as possible logic gates with a view to predicting TE function in new pathways.
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Affiliation(s)
- Mark E. Horsman
- Department of chemistry
- Centre for Catalysis Research and Innovation
- University of Ottawa
- Canada
| | - Taylor P. A. Hari
- Department of chemistry
- Centre for Catalysis Research and Innovation
- University of Ottawa
- Canada
| | - Christopher N. Boddy
- Department of chemistry
- Centre for Catalysis Research and Innovation
- University of Ottawa
- Canada
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33
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Schumacher J. DHN melanin biosynthesis in the plant pathogenic fungusBotrytis cinereais based on two developmentally regulated key enzyme (PKS)-encoding genes. Mol Microbiol 2015; 99:729-48. [DOI: 10.1111/mmi.13262] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2015] [Indexed: 12/28/2022]
Affiliation(s)
- Julia Schumacher
- Institut für Biologie und Biotechnologie der Pflanzen (IBBP); Westfälische Wilhelms-Universität (WWU) Münster; Schlossplatz 8 48143 Münster Germany
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34
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Bioinformatical analysis of the sequences, structures and functions of fungal polyketide synthase product template domains. Sci Rep 2015; 5:10463. [PMID: 25995122 PMCID: PMC5386248 DOI: 10.1038/srep10463] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 04/15/2015] [Indexed: 11/08/2022] Open
Abstract
The product template (PT) domains, specifically in fungal non-reducing polyketide synthases (NR-PKSs), mediate the regioselective cyclization of polyketides dominating the final structures. However, up to date, the systematic knowledge about PT domains has been insufficient. In present study, the relationships between sequences, structures and functions of the PT domains were analyzed with 661 NR-PKS sequences. Based on the phylogenetic analysis, the PT domains were classified into prominent eight groups (I–VIII) corresponding with the representative compounds and cyclization regioselectivity (C2-C7, C4-C9, and C6-C11). Most of the cavity lining residue (CLR) sites in all groups were common, while the regional CLR site mutations resulted in the appearance of finger-like regions with different orientation. The cavity volumes and shapes, even the catalytic dyad positions of PT domains in different groups were corresponding with characteristic cyclization regioselectivity and compound sizes. The conservative residues in PT sequences were responsible for the cyclization functions and the evolution of the key residues resulted in the differentiations of cyclization functions. The above findings may help to better understand the cyclization mechanisms of PT domains and even predict the structural types of the aromatic polyketide products.
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35
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Chen X, Ji R, Jiang X, Yang R, Liu F, Xin Y. Iterative type I polyketide synthases involved in enediyne natural product biosynthesis. IUBMB Life 2014; 66:587-95. [PMID: 25278375 DOI: 10.1002/iub.1316] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 09/14/2014] [Indexed: 12/12/2022]
Abstract
Enediyne natural products are potent antibiotics structurally characterized by an enediyne core containing two acetylenic groups conjugated to a double bond in a 9- or 10-membered carbocycle. The biosynthetic gene clusters for enediynes encode a novel iterative type I polyketide synthase (PKSE), which is generally believed to initiate the biosynthetic process of enediyne cores. This review article will cover research efforts made since its discovery to elucidate the role of the PKSE in enediyne core biosynthesis. Topics covered include the unique domain architecture, identification, and characterization of turnover products, and interaction with partner thioesterase protein.
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Affiliation(s)
- Xiaolei Chen
- Department of Chemistry, Dartmouth College, Hanover, NH, USA
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36
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Diversity-oriented combinatorial biosynthesis of benzenediol lactone scaffolds by subunit shuffling of fungal polyketide synthases. Proc Natl Acad Sci U S A 2014; 111:12354-9. [PMID: 25049383 DOI: 10.1073/pnas.1406999111] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Combinatorial biosynthesis aspires to exploit the promiscuity of microbial anabolic pathways to engineer the synthesis of new chemical entities. Fungal benzenediol lactone (BDL) polyketides are important pharmacophores with wide-ranging bioactivities, including heat shock response and immune system modulatory effects. Their biosynthesis on a pair of sequentially acting iterative polyketide synthases (iPKSs) offers a test case for the modularization of secondary metabolic pathways into "build-couple-pair" combinatorial synthetic schemes. Expression of random pairs of iPKS subunits from four BDL model systems in a yeast heterologous host created a diverse library of BDL congeners, including a polyketide with an unnatural skeleton and heat shock response-inducing activity. Pairwise heterocombinations of the iPKS subunits also helped to illuminate the innate, idiosyncratic programming of these enzymes. Even in combinatorial contexts, these biosynthetic programs remained largely unchanged, so that the iPKSs built their cognate biosynthons, coupled these building blocks into chimeric polyketide intermediates, and catalyzed intramolecular pairing to release macrocycles or α-pyrones. However, some heterocombinations also provoked stuttering, i.e., the relaxation of iPKSs chain length control to assemble larger homologous products. The success of such a plug and play approach to biosynthesize novel chemical diversity bodes well for bioprospecting unnatural polyketides for drug discovery.
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37
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Chooi YH, Muria-Gonzalez MJ, Solomon PS. A genome-wide survey of the secondary metabolite biosynthesis genes in the wheat pathogen Parastagonospora nodorum.. Mycology 2014; 5:192-206. [PMID: 25379341 PMCID: PMC4205913 DOI: 10.1080/21501203.2014.928386] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 05/22/2014] [Indexed: 12/02/2022] Open
Abstract
The model pathogen Parastagonospora nodorum is a necrotroph and the causal agent of the wheat disease Septoria nodorum blotch (SNB). The sequenced P. nodorum genome has revealed that the fungus harbours a large number of secondary metabolite genes. Secondary metabolites are known to play important roles in the virulence of plant pathogens, but limited knowledge is available about the SM repertoire of this wheat pathogen. Here, we review the secondary metabolites that have been isolated from P. nodorum and related species of the same genus and provide an in-depth genome-wide overview of the secondary metabolite gene clusters encoded in the P. nodorum genome. The secondary metabolite gene survey reveals that P. nodorum is capable of producing a diverse range of small molecules and exciting prospects exist for discovery of novel virulence factors and bioactive molecules.
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Affiliation(s)
- Yit-Heng Chooi
- Plant Sciences Division, Research School of Biology, The Australian National University , Canberra , 0200 , Australia
| | - Mariano Jordi Muria-Gonzalez
- Plant Sciences Division, Research School of Biology, The Australian National University , Canberra , 0200 , Australia
| | - Peter S Solomon
- Plant Sciences Division, Research School of Biology, The Australian National University , Canberra , 0200 , Australia
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38
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Newman AG, Vagstad AL, Storm P, Townsend CA. Systematic domain swaps of iterative, nonreducing polyketide synthases provide a mechanistic understanding and rationale for catalytic reprogramming. J Am Chem Soc 2014; 136:7348-62. [PMID: 24815013 PMCID: PMC4046768 DOI: 10.1021/ja5007299] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Indexed: 11/29/2022]
Abstract
Iterative, nonreducing polyketide synthases (NR-PKSs) are multidomain enzymes responsible for the construction of the core architecture of aromatic polyketide natural products in fungi. Engineering these enzymes for the production of non-native metabolites has been a long-standing goal. We conducted a systematic survey of in vitro "domain swapped" NR-PKSs using an enzyme deconstruction approach. The NR-PKSs were dissected into mono- to multidomain fragments and recombined as noncognate pairs in vitro, reconstituting enzymatic activity. The enzymes used in this study produce aromatic polyketides that are representative of the four main chemical features set by the individual NR-PKS: starter unit selection, chain-length control, cyclization register control, and product release mechanism. We found that boundary conditions limit successful chemistry, which are dependent on a set of underlying enzymatic mechanisms. Crucial for successful redirection of catalysis, the rate of productive chemistry must outpace the rate of spontaneous derailment and thioesterase-mediated editing. Additionally, all of the domains in a noncognate system must interact efficiently if chemical redirection is to proceed. These observations refine and further substantiate current understanding of the mechanisms governing NR-PKS catalysis.
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Affiliation(s)
- Adam G. Newman
- Department of Chemistry, The Johns Hopkins
University, 3400 N. Charles
Street, Baltimore, Maryland 21218, United States
| | | | - Philip
A. Storm
- Department of Chemistry, The Johns Hopkins
University, 3400 N. Charles
Street, Baltimore, Maryland 21218, United States
| | - Craig A. Townsend
- Department of Chemistry, The Johns Hopkins
University, 3400 N. Charles
Street, Baltimore, Maryland 21218, United States
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Xu Y, Zhou T, Espinosa-Artiles P, Tang Y, Zhan J, Molnár I. Insights into the biosynthesis of 12-membered resorcylic acid lactones from heterologous production in Saccharomyces cerevisiae. ACS Chem Biol 2014; 9:1119-27. [PMID: 24597618 PMCID: PMC4033647 DOI: 10.1021/cb500043g] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
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The phytotoxic fungal polyketides
lasiodiplodin and resorcylide
inhibit human blood coagulation factor XIIIa, mineralocorticoid receptors,
and prostaglandin biosynthesis. These secondary metabolites belong
to the 12-membered resorcylic acid lactone (RAL12) subclass
of the benzenediol lactone (BDL) family. Identification of genomic
loci for the biosynthesis of lasiodiplodin from Lasiodiplodia
theobromae and resorcylide from Acremonium zeae revealed collaborating iterative polyketide synthase (iPKS) pairs
whose efficient heterologous expression in Saccharomyces cerevisiae provided a convenient access to the RAL12 scaffolds desmethyl-lasiodiplodin
and trans-resorcylide, respectively. Lasiodiplodin
production was reconstituted in the heterologous host by co-expressing
an O-methyltransferase also encoded in the lasiodiplodin
cluster, while a glutathione-S-transferase was found
not to be necessary for heterologous production. Clarification of
the biogenesis of known resorcylide congeners in the heterologous
host helped to disentangle the roles that biosynthetic irregularities
and chemical interconversions play in generating chemical diversity.
Observation of 14-membered RAL homologues during in vivo heterologous biosynthesis of RAL12 metabolites revealed
“stuttering” by fungal iPKSs. The close global and domain-level
sequence similarities of the orthologous BDL synthases across different
structural subclasses implicate repeated horizontal gene transfers
and/or cluster losses in different fungal lineages. The absence of
straightforward correlations between enzyme sequences and product
structural features (the size of the macrocycle, the conformation
of the exocyclic methyl group, or the extent of reduction by the hrPKS)
suggest that BDL structural variety is the result of a select few
mutations in key active site cavity positions.
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Affiliation(s)
- Yuquan Xu
- Biotechnology
Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun
South St., Beijing 100081, People’s Republic of China
- Natural
Products Center, School of Natural Resources and the Environment,
College of Agriculture and Life Sciences, The University of Arizona, 250 E. Valencia Rd., Tucson, Arizona 85706, United States
| | - Tong Zhou
- Department
of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, Utah 84322, United States
| | - Patricia Espinosa-Artiles
- Natural
Products Center, School of Natural Resources and the Environment,
College of Agriculture and Life Sciences, The University of Arizona, 250 E. Valencia Rd., Tucson, Arizona 85706, United States
| | - Ying Tang
- Natural
Products Center, School of Natural Resources and the Environment,
College of Agriculture and Life Sciences, The University of Arizona, 250 E. Valencia Rd., Tucson, Arizona 85706, United States
- College
of Sciences, Sichuan University, Chengdu, Sichuan 610064, People’s Republic of China
| | - Jixun Zhan
- Department
of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, Utah 84322, United States
| | - István Molnár
- Natural
Products Center, School of Natural Resources and the Environment,
College of Agriculture and Life Sciences, The University of Arizona, 250 E. Valencia Rd., Tucson, Arizona 85706, United States
- Bio5
Institute, The University of Arizona, 1657 E. Helen St., Tucson, Arizona 85721, United States
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He HY, Tang MC, Zhang F, Tang GL. Cis-Double Bond Formation by Thioesterase and Transfer by Ketosynthase in FR901464 Biosynthesis. J Am Chem Soc 2014; 136:4488-91. [DOI: 10.1021/ja500942y] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hai-Yan He
- State
Key Laboratory of Bio-organic
and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Man-Cheng Tang
- State
Key Laboratory of Bio-organic
and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Feng Zhang
- State
Key Laboratory of Bio-organic
and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Gong-Li Tang
- State
Key Laboratory of Bio-organic
and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
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41
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Gaudelli NM, Townsend CA. Epimerization and substrate gating by a TE domain in β-lactam antibiotic biosynthesis. Nat Chem Biol 2014; 10:251-8. [PMID: 24531841 PMCID: PMC3961552 DOI: 10.1038/nchembio.1456] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 12/30/2013] [Indexed: 12/01/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) are versatile engines of bioactive natural product biosynthesis that function according to the multiple carrier thiotemplate mechanism. C-terminal thioesterase (TE) domains of these giant modular proteins typically catalyze product release by hydrolysis or macrocylization. We now report an unprecedented, dual-function TE involved in nocardicin A biosynthesis, the paradigm monocyclic β-lactam antibiotic. Contrary to expectation, a stereodefined series of potential peptide substrates for the nocardicin TE domain failed to undergo hydrolysis. The stringent discrimination against peptide intermediates was dramatically overcome by prior monocyclic β-lactam formation at an L-seryl site. Kinetic data are interpreted such that the TE domain acts as a gatekeeper to hold the assembling peptide on an upstream domain until β-lactam formation takes place and then rapidly catalyzes epimerization, not previously observed as a TE catalytic function, and thioesterase cleavage to discharge a fully fledged pentapeptide β-lactam harboring nocardicin G, the universal precursor of the nocardicins.
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Affiliation(s)
- Nicole M Gaudelli
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland, USA
| | - Craig A Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland, USA
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Assembly of Melleolide Antibiotics Involves a Polyketide Synthase with Cross-Coupling Activity. ACTA ACUST UNITED AC 2013; 20:1101-6. [DOI: 10.1016/j.chembiol.2013.07.009] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 07/15/2013] [Accepted: 07/16/2013] [Indexed: 01/28/2023]
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43
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Xu Y, Zhou T, Zhang S, Xuan LJ, Zhan J, Molnár I. Thioesterase domains of fungal nonreducing polyketide synthases act as decision gates during combinatorial biosynthesis. J Am Chem Soc 2013; 135:10783-91. [PMID: 23822773 PMCID: PMC3780601 DOI: 10.1021/ja4041362] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A crucial step during the programmed biosynthesis of fungal polyketide natural products is the release of the final polyketide intermediate from the iterative polyketide synthases (iPKSs), most frequently by a thioesterase (TE) domain. Realization of combinatorial biosynthesis with iPKSs requires TE domains that can accept altered polyketide intermediates generated by hybrid synthase enzymes and successfully release "unnatural products" with the desired structure. Achieving precise control over product release is of paramount importance with O-C bond-forming TE domains capable of macrocyclization, hydrolysis, transesterification, and pyrone formation that channel reactive, pluripotent polyketide intermediates to defined structural classes of bioactive secondary metabolites. By exploiting chimeric iPKS enzymes to offer substrates with controlled structural variety to two orthologous O-C bond-forming TE domains in situ, we show that these enzymes act as nonequivalent decision gates, determining context-dependent release mechanisms and overall product flux. Inappropriate choice of a TE could eradicate product formation in an otherwise highly productive chassis. Conversely, a judicious choice of a TE may allow the production of a desired hybrid metabolite. Finally, a serendipitous choice of a TE may reveal the unexpected productivity of some chassis. The ultimate decision gating role of TE domains influences the observable outcome of combinatorial domain swaps, emphasizing that the deduced programming rules are context dependent. These factors may complicate engineering the biosynthesis of a desired "unnatural product" but may also open additional avenues to create biosynthetic novelty based on fungal nonreduced polyketides.
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Affiliation(s)
- Yuquan Xu
- Natural Products Center, School of Natural Resources and the Environment, The University of Arizona, 250 E. Valencia Rd., Tucson, AZ 85706, USA
| | - Tong Zhou
- Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT 84322, USA
| | - Shuwei Zhang
- Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT 84322, USA
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, 501 Haike Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
| | - Li-Jiang Xuan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, 501 Haike Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
| | - Jixun Zhan
- Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT 84322, USA
| | - István Molnár
- Natural Products Center, School of Natural Resources and the Environment, The University of Arizona, 250 E. Valencia Rd., Tucson, AZ 85706, USA
- Bio5 Institute, The University of Arizona, 1657 E. Helen St., Tucson, AZ 85721, USA
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44
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Vagstad AL, Newman AG, Storm PA, Belecki K, Crawford JM, Townsend CA. Combinatorial Domain Swaps Provide Insights into the Rules of Fungal Polyketide Synthase Programming and the Rational Synthesis of Non-Native Aromatic Products. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208550] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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45
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Vagstad AL, Newman AG, Storm PA, Belecki K, Crawford JM, Townsend CA. Combinatorial domain swaps provide insights into the rules of fungal polyketide synthase programming and the rational synthesis of non-native aromatic products. Angew Chem Int Ed Engl 2013; 52:1718-21. [PMID: 23283670 DOI: 10.1002/anie.201208550] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Indexed: 11/11/2022]
Affiliation(s)
- Anna L Vagstad
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles St, Baltimore, MD 21218, USA
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46
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Newman AG, Vagstad AL, Belecki K, Scheerer JR, Townsend CA. Analysis of the cercosporin polyketide synthase CTB1 reveals a new fungal thioesterase function. Chem Commun (Camb) 2012; 48:11772-4. [PMID: 23108075 DOI: 10.1039/c2cc36010a] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The polyketide synthase CTB1 is demonstrated to catalyze pyrone formation thereby expanding the known biosynthetic repertoire of thioesterase domains in iterative, non-reducing polyketide synthases.
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Affiliation(s)
- Adam G Newman
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
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