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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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2
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Ahmad N, Ritz M, Calchera A, Otte J, Schmitt I, Brueck T, Mehlmer N. Biosynthetic gene cluster synteny: Orthologous polyketide synthases in Hypogymnia physodes, Hypogymnia tubulosa, and Parmelia sulcata. Microbiologyopen 2023; 12:e1386. [PMID: 37877655 PMCID: PMC10582450 DOI: 10.1002/mbo3.1386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/15/2023] [Accepted: 09/26/2023] [Indexed: 10/26/2023] Open
Abstract
Lichens are symbiotic associations consisting of a photobiont (algae or cyanobacteria) and a mycobiont (fungus), which together generate a variety of unique secondary metabolites. To access this biosynthetic potential for biotechnological applications, deeper insights into the biosynthetic pathways and corresponding gene clusters are necessary. Here, we provide a comparative view of the biosynthetic gene clusters of three lichen mycobionts derived from Hypogymnia physodes, Hypogymnia tubulosa, and Parmelia sulcata. In addition, we present a high-quality PacBio metagenome of Parmelia sulcata, from which we extracted the mycobiont bin containing 214 biosynthetic gene clusters. Most biosynthetic gene clusters in these genomes were associated with T1PKSs, followed by NRPSs and terpenes. This study focused on biosynthetic gene clusters related to polyketide synthesis. Based on ketosynthase homology, we identified nine highly syntenic clusters present in all three species. Among the four clusters belonging to nonreducing PKSs, two are putatively linked to lichen substances derived from orsellinic acid (orcinol depsides and depsidones, e.g., lecanoric acid, physodic acid, lobaric acid), one to compounds derived from methylated forms of orsellinic acid (beta orcinol depsides, e.g., atranorin), and one to melanins. Five clusters with orthologs in all three species are linked to reducing PKSs. Our study contributes to sorting and dereplicating the vast PKS diversity found in lichenized fungi. High-quality sequences of biosynthetic gene clusters of these three common species provide a foundation for further exploration into biotechnological applications and the molecular evolution of lichen substances.
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Affiliation(s)
- Nadim Ahmad
- Department of Chemistry, Werner Siemens Chair of Synthetic Biotechnology, TUM School of Natural SciencesTechnical University of Munich (TUM)GarchingGermany
| | - Manfred Ritz
- Department of Chemistry, Werner Siemens Chair of Synthetic Biotechnology, TUM School of Natural SciencesTechnical University of Munich (TUM)GarchingGermany
| | - Anjuli Calchera
- Senckenberg Biodiversity and Climate Research Centre (SBiK‐F)Frankfurt am MainGermany
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (SBiK‐F)Frankfurt am MainGermany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (SBiK‐F)Frankfurt am MainGermany
- Institute of Ecology, Evolution and DiversityGoethe University FrankfurtFrankfurt am MainGermany
| | - Thomas Brueck
- Department of Chemistry, Werner Siemens Chair of Synthetic Biotechnology, TUM School of Natural SciencesTechnical University of Munich (TUM)GarchingGermany
| | - Norbert Mehlmer
- Department of Chemistry, Werner Siemens Chair of Synthetic Biotechnology, TUM School of Natural SciencesTechnical University of Munich (TUM)GarchingGermany
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3
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Wang J, Deng Z, Liang J, Wang Z. Structural enzymology of iterative type I polyketide synthases: various routes to catalytic programming. Nat Prod Rep 2023; 40:1498-1520. [PMID: 37581222 DOI: 10.1039/d3np00015j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
Time span of literature covered: up to mid-2023Iterative type I polyketide synthases (iPKSs) are outstanding natural chemists: megaenzymes that repeatedly utilize their catalytic domains to synthesize complex natural products with diverse bioactivities. Perhaps the most fascinating but least understood question about type I iPKSs is how they perform the iterative yet programmed reactions in which the usage of domain combinations varies during the synthetic cycle. The programmed patterns are fulfilled by multiple factors, and strongly influence the complexity of the resulting natural products. This article reviews selected reports on the structural enzymology of iPKSs, focusing on the individual domain structures followed by highlighting the representative programming activities that each domain may contribute.
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Affiliation(s)
- Jialiang Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Jingdan Liang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Zhijun Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
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Yan F, Fang J, Ding W, Tang X, Chen X, Ma Z, Wang J. Structurally Diverse Metabolites from the Marine-Derived Streptomyces sp. DS-27 Based on Two Different Culture Conditions. Chem Biodivers 2023; 20:e202301017. [PMID: 37603393 DOI: 10.1002/cbdv.202301017] [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: 07/13/2023] [Accepted: 08/03/2023] [Indexed: 08/22/2023]
Abstract
Nine new compounds, including streptothiomycin A-E (1-5), two cyclopentenones (6, 7), one α-pyrone (8), wailupemycin Q (20), along with sixteen known compounds were identified from a rhizosphere strain Streptomyces sp. DS-27 derived from the marine cordgrass Spartina alterniflora under two different culture conditions. All of the structures were elucidated by extensive analysis of 1D/2D NMR and HR-ESI-MS data. The absolute configurations were determined by NOESY analysis, ECD, specific rotation and GIAO NMR calculations, and DP4+ probability analysis. Bioactivity investigation showed that compounds 5 and 7 exhibited significant inhibitory effects on LPS-induced NO production in a dose-dependent manner, which indicates their anti-inflammatory potential.
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Affiliation(s)
- Feihang Yan
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, China
| | - Jiebin Fang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, China
| | - Wanjing Ding
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, China
- Hainan Institute of Zhejiang University, Sanya, 572025, China
| | - Xinyi Tang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, China
| | - Xiaoming Chen
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, China
| | - Zhongjun Ma
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, China
- Hainan Institute of Zhejiang University, Sanya, 572025, China
| | - Jinhui Wang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, China
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5
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Ahmad N, Ritz M, Calchera A, Otte J, Schmitt I, Brueck T, Mehlmer N. Biosynthetic Potential of Hypogymnia Holobionts: Insights into Secondary Metabolite Pathways. J Fungi (Basel) 2023; 9:jof9050546. [PMID: 37233257 DOI: 10.3390/jof9050546] [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: 04/07/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023] Open
Abstract
Lichens are symbiotic associations consisting of a photobiont (algae or cyanobacteria) and a mycobiont (fungus). They are known to produce a variety of unique secondary metabolites. To access this biosynthetic potential for biotechnological applications, deeper insights into the biosynthetic pathways and corresponding gene clusters are necessary. Here we provide a comprehensive view of the biosynthetic gene clusters of all organisms comprising a lichen thallus: fungi, green algae, and bacteria. We present two high-quality PacBio metagenomes, in which we identified a total of 460 biosynthetic gene clusters. Lichen mycobionts yielded 73-114 clusters, other lichen associated ascomycetes 8-40, green algae of the genus Trebouxia 14-19, and lichen-associated bacteria 101-105 clusters. The mycobionts contained mainly T1PKSs, followed by NRPSs, and terpenes; Trebouxia reads harbored mainly clusters linked to terpenes, followed by NRPSs and T3PKSs. Other lichen-associated ascomycetes and bacteria contained a mix of diverse biosynthetic gene clusters. In this study, we identified for the first time the biosynthetic gene clusters of entire lichen holobionts. The yet untapped biosynthetic potential of two species of the genus Hypogymnia is made accessible for further research.
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Affiliation(s)
- Nadim Ahmad
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Manfred Ritz
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Anjuli Calchera
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue-Straße 13, 60438 Frankfurt am Main, Germany
| | - Thomas Brueck
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Norbert Mehlmer
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
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6
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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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7
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Chen L, Wei X, Matsuda Y. Depside Bond Formation by the Starter-Unit Acyltransferase Domain of a Fungal Polyketide Synthase. J Am Chem Soc 2022; 144:19225-19230. [PMID: 36223511 DOI: 10.1021/jacs.2c08585] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Depsides are polyphenolic molecules comprising two or more phenolic acid derivatives linked by an ester bond, which is called a depside bond in these molecules. Despite more than a century of intensive research on depsides, the biosynthetic mechanism of depside bond formation remains unclear. In this study, we discovered a polyketide synthase, DrcA, from the fungus Aspergillus duricaulis CBS 481.65 and found that DrcA synthesizes CJ-20,557 (1), a heterodimeric depside composed of 3-methylorsellinic acid and 3,5-dimethylorsellinic acid. Moreover, we determined that depside bond formation is catalyzed by the starter-unit acyltransferase (SAT) domain of DrcA. Remarkably, this is a previously undescribed form of SAT domain chemistry. Further investigation revealed that 1 is transformed into duricamidepside (2), a depside-amino acid conjugate, by the single-module nonribosomal peptide synthetase DrcB.
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Affiliation(s)
- Lin Chen
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Xingxing Wei
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Yudai Matsuda
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China.,City University of Hong Kong Shenzhen Research Institute, Shenzhen, Guangdong 518057, China
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8
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Woydziak ZR, Yucel AJ, Chamberlin AR. Tautomycetin Synthetic Analogues: Selective Inhibitors of Protein Phosphatase I. ChemMedChem 2021; 16:839-850. [PMID: 33301228 PMCID: PMC8582298 DOI: 10.1002/cmdc.202000801] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Indexed: 01/21/2023]
Abstract
Ser/Thr protein phosphatases (PPs) regulate a substantial range of cellular processes with protein phosphatases 1 (PP1) and 2 A (PP2A) accounting for over 90 % of the activity within cells. Nevertheless, tools to study PPs are limited as PPs inhibitors, particularly those selective for PP1 inhibition, are relatively scarce. Two examples of PP1-selective inhibitors, which share structural similarities, are tautomycin (TTM) and tautomycetin (TTN). This work describes the development of PP1/PP2A inhibitors that incorporate key structural features of TTM and TTN and are designed to conserve regions known to bind the active site of PP1/PP2A but vary regions that differentially contact the hydrophobic groove of PP1/PP2A. In all 28 TTN analogues were synthetically generated that inhibit PP1/PP2A activity at <250 mM; seven possessed inhibition activity at 100 nM. The IC50 values were determined for the seven most active analogues, which ranged from 34 to 1500 nM (PP1) and 70 to 6800 nM (PP2A). Four of the seven analogues possessed PP1 selectivity, and one demonstrated eightfold selectivity in the nanomolar range (PP1 IC50 =34 nM, PP2A IC50 =270 nM). A rationale is given for the observed differences in selectivity.
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Affiliation(s)
- Zachary R Woydziak
- Department of Physical and Life Sciences, Nevada State College, 1300, Nevada State Dr., Henderson, NV 89002, USA
| | - A John Yucel
- Department of Pharmaceutical Sciences, University of California, Irvine, 147 Biol. Sci. Admin., Irvine, CA 92697, USA
| | - A Richard Chamberlin
- Department of Pharmaceutical Sciences, University of California, Irvine, 147 Biol. Sci. Admin., Irvine, CA 92697, USA
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Zhu M, Wang L, He J. Repurposing the 3‐Isocyanobutanoic Acid Adenylation Enzyme SfaB for Versatile Amidation and Thioesterification. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202010042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Mengyi Zhu
- State Key Laboratory of Agricultural Microbiology College of Life Science and Technology Huazhong Agricultural University No. 1 Shizishan Street Wuhan 430070 P. R. China
| | - Lijuan Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology RNAM Center for Marine Microbiology South China Sea Institute of Oceanology Chinese Academy of Sciences 164 West Xingang Road Guangzhou 510301 P. R. China
| | - Jing He
- State Key Laboratory of Agricultural Microbiology College of Life Science and Technology Huazhong Agricultural University No. 1 Shizishan Street Wuhan 430070 P. R. China
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10
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Zhu M, Wang L, He J. Repurposing the 3-Isocyanobutanoic Acid Adenylation Enzyme SfaB for Versatile Amidation and Thioesterification. Angew Chem Int Ed Engl 2020; 60:2030-2035. [PMID: 33026145 DOI: 10.1002/anie.202010042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/15/2020] [Indexed: 11/09/2022]
Abstract
Genome mining of microbial natural products enables chemists not only to discover the bioactive molecules with novel skeletons, but also to identify the enzymes that catalyze diverse chemical reactions. Exploring the substrate promiscuity and catalytic mechanism of those biosynthetic enzymes facilitates the development of potential biocatalysts. SfaB is an acyl adenylate-forming enzyme that adenylates a unique building block, 3-isocyanobutanoic acid, in the biosynthetic pathway of the diisonitrile natural product SF2768 produced by Streptomyces thioluteus, and this AMP-ligase was demonstrated to accept a broad range of short-chain fatty acids (SCFAs). Herein, we repurpose SfaB to catalyze amidation or thioesterification between those SCFAs and various amine or thiol nucleophiles, thereby providing an alternative enzymatic approach to prepare the corresponding amides and thioesters in vitro.
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Affiliation(s)
- Mengyi Zhu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Street, Wuhan, 430070, P. R. China
| | - Lijuan Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, P. R. China
| | - Jing He
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Street, Wuhan, 430070, P. R. China
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Wang C, Wang X, Zhang L, Yue Q, Liu Q, Xu YM, Gunatilaka AAL, Wei X, Xu Y, Molnár I. Intrinsic and Extrinsic Programming of Product Chain Length and Release Mode in Fungal Collaborating Iterative Polyketide Synthases. J Am Chem Soc 2020; 142:17093-17104. [PMID: 32833442 DOI: 10.1021/jacs.0c07050] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Combinatorial biosynthesis with fungal polyketide synthases (PKSs) promises to produce unprecedented bioactive "unnatural" natural products (uNPs) for drug discovery. Genome mining of the dothideomycete Rhytidhysteron rufulum uncovered a collaborating highly reducing PKS (hrPKS)-nonreducing PKS (nrPKS) pair. These enzymes produce trace amounts of rare S-type benzenediol macrolactone congeners with a phenylacetate core in a heterologous host. However, subunit shuffling and domain swaps with voucher enzymes demonstrated that all PKS domains are highly productive. This contradiction led us to reveal novel programming layers exerted by the starter unit acyltransferase (SAT) and the thioesterase (TE) domains on the PKS system. First, macrocyclic vs linear product formation is dictated by the intrinsic biosynthetic program of the TE domain. Next, the chain length of the hrPKS product is strongly influenced in trans by the off-loading preferences of the nrPKS SAT domain. Last, TE domains are size-selective filters that facilitate or obstruct product formation from certain priming units. Thus, the intrinsic programs of the SAT and TE domains are both part of the extrinsic program of the hrPKS subunit and modulate the observable metaprogram of the whole PKS system. Reconstruction of SAT and TE phylogenies suggests that these domains travel different evolutionary trajectories, with the resulting divergence creating potential conflicts in the PKS metaprogram. Such conflicts often emerge in chimeric PKSs created by combinatorial biosynthesis, reducing biosynthetic efficiency or even incapacitating the system. Understanding the points of failure for such engineered biocatalysts is pivotal to advance the biosynthetic production of uNPs.
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Affiliation(s)
- Chen Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.,Southwest Center for Natural Products Research, University of Arizona, 250 East Valencia Road, Tucson, Arizona 85706, United States
| | - Xiaojing Wang
- Microbial Pharmacology Laboratory, Shanghai University of Medicine and Health Sciences, 279 Zhouzhu Highway, Pudong New Area, Shanghai 201318, P. R. China
| | - Liwen Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Qun Yue
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Qingpei Liu
- Southwest Center for Natural Products Research, University of Arizona, 250 East Valencia Road, Tucson, Arizona 85706, United States.,School of Pharmaceutical Sciences, South-Central University for Nationalities, 182 Minyuan Road, Hongshan District, Wuhan 430074, P. R. China
| | - Ya-Ming Xu
- Southwest Center for Natural Products Research, University of Arizona, 250 East Valencia Road, Tucson, Arizona 85706, United States
| | - A A Leslie Gunatilaka
- Southwest Center for Natural Products Research, University of Arizona, 250 East Valencia Road, Tucson, Arizona 85706, United States
| | - Xiaoyi Wei
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, P. R. China
| | - Yuquan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - István Molnár
- Southwest Center for Natural Products Research, University of Arizona, 250 East Valencia Road, Tucson, Arizona 85706, United States
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12
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Diversity and antimicrobial activity of culturable fungi associated with sea anemone Anthopleura xanthogrammica. ELECTRON J BIOTECHN 2020. [DOI: 10.1016/j.ejbt.2020.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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13
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Storm PA, Pal P, Huitt-Roehl CR, Townsend CA. Exploring Fungal Polyketide C-Methylation through Combinatorial Domain Swaps. ACS Chem Biol 2018; 13:3043-3048. [PMID: 30350943 DOI: 10.1021/acschembio.8b00429] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Polyketide C-methylation occurs during a programmed sequence of dozens of reactions carried out by multidomain polyketide synthases (PKSs). Fungal PKSs perform these reactions iteratively, where a domain may be exposed to and act upon multiple enzyme-tethered intermediates during biosynthesis. We surveyed a collection of C-methyltransferase (CMeT) domains from nonreducing fungal PKSs to gain insight into how different methylation patterns are installed. Our in vitro results show that control of methylation resides primarily with the CMeT, and CMeTs can intercept and methylate intermediates from noncognate nonreducing PKS domains. Furthermore, the methylation pattern is likely imposed by a competition between methylation or ketosynthase-catalyzed extension for each intermediate. Understanding site-specific polyketide C-methylation may facilitate targeted C-C bond formation in engineered biosynthetic pathways.
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Affiliation(s)
- Philip A. Storm
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Paramita Pal
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Callie R. Huitt-Roehl
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Craig A. Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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14
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Abstract
Covering: up to mid of 2018 Type I fatty acid synthases (FASs) are giant multienzymes catalyzing all steps of the biosynthesis of fatty acids from acetyl- and malonyl-CoA by iterative precursor extension. Two strikingly different architectures of FAS evolved in yeast (as well as in other fungi and some bacteria) and metazoans. Yeast-type FAS (yFAS) assembles into a barrel-shaped structure of more than 2 MDa molecular weight. Catalytic domains of yFAS are embedded in an extensive scaffolding matrix and arranged around two enclosed reaction chambers. Metazoan FAS (mFAS) is a 540 kDa X-shaped dimer, with lateral reaction clefts, minimal scaffolding and pronounced conformational variability. All naturally occurring yFAS are strictly specialized for the production of saturated fatty acids. The yFAS architecture is not used for the biosynthesis of any other secondary metabolite. On the contrary, mFAS is related at the domain organization level to major classes of polyketide synthases (PKSs). PKSs produce a variety of complex and potent secondary metabolites; they either act iteratively (iPKS), or are linked via directed substrate transfer into modular assembly lines (modPKSs). Here, we review the architectures of yFAS, mFAS, and iPKSs. We rationalize the evolution of the yFAS assembly, and provide examples for re-engineering of yFAS. Recent studies have provided novel insights into the organization of iPKS. A hybrid crystallographic model of a mycocerosic acid synthase-like Pks5 yielded a comprehensive visualization of the organization and dynamics of fully-reducing iPKS. Deconstruction experiments, structural and functional studies of specialized enzymatic domains, such as the product template (PT) and the starter-unit acyltransferase (SAT) domain have revealed functional principles of non-reducing iterative PKS (NR-PKSs). Most recently, a six-domain loading region of an NR-PKS has been visualized at high-resolution together with cryo-EM studies of a trapped loading intermediate. Altogether, these data reveal the related, yet divergent architectures of mFAS, iPKS and also modPKSs. The new insights highlight extensive dynamics, and conformational coupling as key features of mFAS and iPKS and are an important step towards collection of a comprehensive series of snapshots of PKS action.
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Affiliation(s)
- Dominik A Herbst
- Department Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland.
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15
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Strategies for Engineering Natural Product Biosynthesis in Fungi. Trends Biotechnol 2018; 37:416-427. [PMID: 30316556 DOI: 10.1016/j.tibtech.2018.09.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 09/02/2018] [Accepted: 09/12/2018] [Indexed: 01/22/2023]
Abstract
Fungi are a prolific source of bioactive compounds, some of which have been developed as essential medicines and life-enhancing drugs. Genome sequencing has revealed that fungi have the potential to produce considerably more natural products (NPs) than are typically observed in the laboratory. Recently, there have been significant advances in the identification, understanding, and engineering of fungal biosynthetic gene clusters (BGCs). This review briefly describes examples of the engineering of fungal NP biosynthesis at the global, pathway, and enzyme level using in vivo and in vitro approaches and refers to the range and scale of heterologous expression systems available, developments in combinatorial biosynthesis, progress in understanding how fungal BGCs are regulated, and the applications of these novel biosynthetic enzymes as biocatalysts.
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16
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Curran SC, Hagen A, Poust S, Chan LJG, Garabedian BM, de Rond T, Baluyot MJ, Vu JT, Lau AK, Yuzawa S, Petzold CJ, Katz L, Keasling JD. Probing the Flexibility of an Iterative Modular Polyketide Synthase with Non-Native Substrates in Vitro. ACS Chem Biol 2018; 13:2261-2268. [PMID: 29912551 DOI: 10.1021/acschembio.8b00422] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the search for molecular machinery for custom biosynthesis of valuable compounds, the modular type I polyketide synthases (PKSs) offer great potential. In this study, we investigate the flexibility of BorM5, the iterative fifth module of the borrelidin synthase, with a panel of non-native priming substrates in vitro. BorM5 differentially extends various aliphatic and substituted substrates. Depending on substrate size and substitution BorM5 can exceed the three iterations it natively performs. To probe the effect of methyl branching on chain length regulation, we engineered a BorM5 variant capable of incorporating methylmalonyl- and malonyl-CoA into its intermediates. Intermediate methylation did not affect overall chain length, indicating that the enzyme does not to count methyl branches to specify the number of iterations. In addition to providing regulatory insight about BorM5, we produced dozens of novel methylated intermediates that might be used for production of various hydrocarbons or pharmaceuticals. These findings enable rational engineering and recombination of BorM5 and inform the study of other iterative modules.
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Affiliation(s)
- Samuel C. Curran
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Andrew Hagen
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
| | - Sean Poust
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
| | - Leanne Jade G. Chan
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Brett M. Garabedian
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Tristan de Rond
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Marian-Joy Baluyot
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jonathan T. Vu
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Andrew K. Lau
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
| | - Satoshi Yuzawa
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Christopher J. Petzold
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Leonard Katz
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jay D. Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
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17
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Tsai SC(S. The Structural Enzymology of Iterative Aromatic Polyketide Synthases: A Critical Comparison with Fatty Acid Synthases. Annu Rev Biochem 2018; 87:503-531. [DOI: 10.1146/annurev-biochem-063011-164509] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Polyketides are a large family of structurally complex natural products including compounds with important bioactivities. Polyketides are biosynthesized by polyketide synthases (PKSs), multienzyme complexes derived evolutionarily from fatty acid synthases (FASs). The focus of this review is to critically compare the properties of FASs with iterative aromatic PKSs, including type II PKSs and fungal type I nonreducing PKSs whose chemical logic is distinct from that of modular PKSs. This review focuses on structural and enzymological studies that reveal both similarities and striking differences between FASs and aromatic PKSs. The potential application of FAS and aromatic PKS structures for bioengineering future drugs and biofuels is highlighted.
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Affiliation(s)
- Shiou-Chuan (Sheryl) Tsai
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, California 92697, USA
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18
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Saccharomonopyrones A-C, New α-Pyrones from a Marine Sediment-Derived Bacterium Saccharomonospora sp. CNQ-490. Mar Drugs 2017; 15:md15080239. [PMID: 28771166 PMCID: PMC5577594 DOI: 10.3390/md15080239] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 07/13/2017] [Accepted: 07/25/2017] [Indexed: 12/16/2022] Open
Abstract
Intensive study of the organic extract of the marine-derived bacterium Saccharomonospora sp. CNQ-490 has yielded three new α-pyrones, saccharomonopyrones A-C (1-3). The chemical structures of these compounds were assigned from the interpretation of 1D, 2D NMR and mass spectrometry data. Saccharomonopyrone A (1) is the first α-pyrone microbial natural product bearing the ethyl-butyl ether chain in the molecule, while saccharomonopyrones B and C possess unusual 3-methyl and a 6-alkyl side-chain within a 3,4,5,6-tetrasubstituted α-pyrone moiety. Saccharomonopyrone A exhibited weak antioxidant activity using a cation radical scavenging activity assay with an IC50 value of 140 μM.
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19
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Storm PA, Herbst DA, Maier T, Townsend CA. Functional and Structural Analysis of Programmed C-Methylation in the Biosynthesis of the Fungal Polyketide Citrinin. Cell Chem Biol 2017; 24:316-325. [PMID: 28238725 DOI: 10.1016/j.chembiol.2017.01.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 11/30/2016] [Accepted: 01/30/2017] [Indexed: 01/09/2023]
Abstract
Fungal polyketide synthases (PKSs) are large, multidomain enzymes that biosynthesize a wide range of natural products. A hallmark of these megasynthases is the iterative use of catalytic domains to extend and modify a series of enzyme-bound intermediates. A subset of these iterative PKSs (iPKSs) contains a C-methyltransferase (CMeT) domain that adds one or more S-adenosylmethionine (SAM)-derived methyl groups to the carbon framework. Neither the basis by which only specific positions on the growing intermediate are methylated ("programming") nor the mechanism of methylation are well understood. Domain dissection and reconstitution of PksCT, the fungal non-reducing PKS (NR-PKS) responsible for the first isolable intermediate in citrinin biosynthesis, demonstrates the role of CMeT-catalyzed methylation in precursor elongation and pentaketide formation. The crystal structure of the S-adenosyl-homocysteine (SAH) coproduct-bound PksCT CMeT domain reveals a two-subdomain organization with a novel N-terminal subdomain characteristic of PKS CMeT domains and provides insights into co-factor and ligand recognition.
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Affiliation(s)
- Philip A Storm
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Dominik A Herbst
- Department Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Timm Maier
- Department Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Craig A Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA.
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20
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Zhang X, Li S. Expansion of chemical space for natural products by uncommon P450 reactions. Nat Prod Rep 2017; 34:1061-1089. [DOI: 10.1039/c7np00028f] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This review focuses on unusual P450 reactions related to new chemistry, skeleton construction, structure re-shaping, and protein–protein interactions in natural product biosynthesis, which play significant roles in chemical space expansion for natural products.
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Affiliation(s)
- Xingwang Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology
- CAS Key Laboratory of Biofuels at Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao
- China
| | - Shengying Li
- Shandong Provincial Key Laboratory of Synthetic Biology
- CAS Key Laboratory of Biofuels at Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao
- China
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21
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Franke J, Hertweck C. Biomimetic Thioesters as Probes for Enzymatic Assembly Lines: Synthesis, Applications, and Challenges. Cell Chem Biol 2016; 23:1179-1192. [PMID: 27693058 DOI: 10.1016/j.chembiol.2016.08.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/09/2016] [Accepted: 08/31/2016] [Indexed: 10/20/2022]
Abstract
Thioesters play essential roles in many biosynthetic pathways to fatty acids, esters, polyketides, and non-ribosomal peptides. Coenzyme A (CoA) and related phosphopantetheine thioesters are typically employed as activated acyl units for diverse C-C, C-O, and C-N coupling reactions. To study and control these enzymatic assembly lines in vitro and in vivo structurally simplified analogs such as N-acetylcysteamine (NAC) thioesters have been developed. This review gives an overview on experimental strategies enabled by synthetic NAC thioesters, such as the elucidation of complex biosynthetic pathways and enzyme mechanisms as well as precursor-directed biosynthesis and mutasynthesis. The review also summarizes synthetic protocols and protection group strategies to access these versatile synthetic tools, which are reactive and often unstable compounds. In addition, alternative phosphopantetheine thioester mimics are presented that can be used as protein tags or suicide inhibitors for protein crosslinking and off-loading probes to elucidate polyketide intermediates.
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Affiliation(s)
- Jakob Franke
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745 Jena, Germany; Friedrich Schiller University, 07743 Jena, Germany.
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22
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Hii KS, Lim PT, Kon NF, Takata Y, Usup G, Leaw CP. Physiological and transcriptional responses to inorganic nutrition in a tropical Pacific strain of Alexandrium minutum: Implications for the saxitoxin genes and toxin production. HARMFUL ALGAE 2016; 56:9-21. [PMID: 28073499 DOI: 10.1016/j.hal.2016.04.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/12/2016] [Accepted: 04/12/2016] [Indexed: 06/06/2023]
Abstract
Saxitoxins (STXs) constitute a family of potent sodium channel blocking toxins, causative agents of paralytic shellfish poisoning (PSP), and are produced by several species of marine dinoflagellates and cyanobacteria. Two STX-core genes, sxtA and sxtG, have been well elucidated in Alexandrium but the expression of these genes under various nutritional modes in tropical species remains unclear. This study investigates the physiological responses of a tropical Pacific strain of Alexandrium minutum growing with nitrate or ammonium, and with various nitrogen to phosphorus (N:P) supply ratios. The transcriptional responses of the sxt genes were observed. Likewise, a putative sxtI encoding O-carbamoyltransferase (herein designated as AmsxtI) was recovered from the transcriptomic data, and its expression was investigated. The results revealed that the cellular toxin quota (Qt) was higher in P-depleted, nitrate-grown cultures. With cultures at similar N:P (<16), cells grown with excess ammonium showed a higher Qt than those grown with nitrate. sxtA1 was not expressed under any culture conditions, suggesting that this gene might not be involved in STX biosynthesis by this strain. Conversely, sxtA4 and sxtG showed positive correlations with Qt, and were up-regulated in P-depleted, nitrate-grown cultures and with excess ambient ammonium. On the other hand, AmsxtI was expressed only when induced by P-depletion, suggesting that this gene may play an important role in P-recycling metabolism, while simultaneously enhancing toxin production.
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Affiliation(s)
- Kieng Soon Hii
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, Kota Samarahan 94300, Sarawak, Malaysia
| | - Po Teen Lim
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, Bachok 16310, Kelantan, Malaysia.
| | - Nyuk Fong Kon
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, Kota Samarahan 94300, Sarawak, Malaysia
| | - Yoshinobu Takata
- The University of Tokyo, Yayoi 1-1-1, Bunkyo-Ku, Tokyo 113-8657, Japan
| | - Gires Usup
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Chui Pin Leaw
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, Bachok 16310, Kelantan, Malaysia.
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23
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Insight into different environmental niches adaptation and allergenicity from the Cladosporium sphaerospermum genome, a common human allergy-eliciting Dothideomycetes. Sci Rep 2016; 6:27008. [PMID: 27243961 PMCID: PMC4886633 DOI: 10.1038/srep27008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/10/2016] [Indexed: 11/09/2022] Open
Abstract
Cladosporium sphaerospermum, a dematiaceous saprophytic fungus commonly found in diverse environments, has been reported to cause allergy and other occasional diseases in humans. However, its basic biology and genetic information are largely unexplored. A clinical isolate C. sphaerospermum genome, UM 843, was re-sequenced and combined with previously generated sequences to form a model 26.89 Mb genome containing 9,652 predicted genes. Functional annotation on predicted genes suggests the ability of this fungus to degrade carbohydrate and protein complexes. Several putative peptidases responsible for lung tissue hydrolysis were identified. These genes shared high similarity with the Aspergillus peptidases. The UM 843 genome encodes a wide array of proteins involved in the biosynthesis of melanin, siderophores, cladosins and survival in high salinity environment. In addition, a total of 28 genes were predicted to be associated with allergy. Orthologous gene analysis together with 22 other Dothideomycetes showed genes uniquely present in UM 843 that encode four class 1 hydrophobins which may be allergens specific to Cladosporium. The mRNA of these hydrophobins were detected by RT-PCR. The genomic analysis of UM 843 contributes to the understanding of the biology and allergenicity of this widely-prevalent species.
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24
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Bai J, Lu Y, Xu YM, Zhang W, Chen M, Lin M, Gunatilaka AAL, Xu Y, Molnár I. Diversity-Oriented Combinatorial Biosynthesis of Hybrid Polyketide Scaffolds from Azaphilone and Benzenediol Lactone Biosynthons. Org Lett 2016; 18:1262-5. [PMID: 26934205 DOI: 10.1021/acs.orglett.6b00110] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two disparate polyketide families, the benzenediol lactones and the azaphilones, are produced by fungi using iterative polyketide synthase (iPKS) enzymes consisting of collaborating partner subunits. Exploitation of this common biosynthetic logic using iPKS subunit shuffling allowed the diversity-oriented combinatorial biosynthesis of unprecedented polyketide scaffolds new to nature, bearing structural motifs from both of these orthogonal natural product families. Starter unit acyltransferase domain replacements proved necessary but not sufficient to guarantee communication between iPKS subunits.
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Affiliation(s)
- Jing Bai
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences , 12 Zhongguancun South Street, Beijing 100081, P. R. China.,Natural Products Center, School of Natural Resources and the Environment, The University of Arizona , 250 East Valencia Road, Tucson, Arizona 85706, United States
| | - Yuanyuan Lu
- Natural Products Center, School of Natural Resources and the Environment, The University of Arizona , 250 East Valencia Road, Tucson, Arizona 85706, United States.,State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University , 24 Tong Jia Xiang, Nanjing 210009, P. R. China
| | - Ya-ming Xu
- Natural Products Center, School of Natural Resources and the Environment, The University of Arizona , 250 East Valencia Road, Tucson, Arizona 85706, United States
| | - Wei Zhang
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences , 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Ming Chen
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences , 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Min Lin
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences , 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - A A Leslie Gunatilaka
- Natural Products Center, School of Natural Resources and the Environment, The University of Arizona , 250 East Valencia Road, Tucson, Arizona 85706, United States
| | - Yuquan Xu
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences , 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - István Molnár
- Natural Products Center, School of Natural Resources and the Environment, The University of Arizona , 250 East Valencia Road, Tucson, Arizona 85706, United States
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25
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Parascandolo JS, Havemann J, Potter HK, Huang F, Riva E, Connolly J, Wilkening I, Song L, Leadlay PF, Tosin M. Insights into 6-Methylsalicylic Acid Bio-assembly by Using Chemical Probes. Angew Chem Int Ed Engl 2016; 55:3463-7. [PMID: 26833898 PMCID: PMC4797705 DOI: 10.1002/anie.201509038] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 11/19/2015] [Indexed: 01/21/2023]
Abstract
Chemical probes capable of reacting with KS (ketosynthase)-bound biosynthetic intermediates were utilized for the investigation of the model type I iterative polyketide synthase 6-methylsalicylic acid synthase (6-MSAS) in vivo and in vitro. From the fermentation of fungal and bacterial 6-MSAS hosts in the presence of chain termination probes, a full range of biosynthetic intermediates was isolated and characterized for the first time. Meanwhile, in vitro studies of recombinant 6-MSA synthases with both nonhydrolyzable and hydrolyzable substrate mimics have provided additional insights into substrate recognition, providing the basis for further exploration of the enzyme catalytic activities.
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Affiliation(s)
- James S Parascandolo
- Department of Chemistry, University of Warwick, Library Road, Coventry, CV4 7AL, UK
| | - Judith Havemann
- Department of Chemistry, University of Warwick, Library Road, Coventry, CV4 7AL, UK
| | - Helen K Potter
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Fanglu Huang
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Elena Riva
- Department of Chemistry, University of Warwick, Library Road, Coventry, CV4 7AL, UK
| | - Jack Connolly
- Department of Chemistry, University of Warwick, Library Road, Coventry, CV4 7AL, UK
- School of Biosciences, The University of Birmingham, Birmingham, B15 2TT, UK
| | - Ina Wilkening
- Department of Chemistry, University of Warwick, Library Road, Coventry, CV4 7AL, UK
| | - Lijiang Song
- Department of Chemistry, University of Warwick, Library Road, Coventry, CV4 7AL, UK
| | - Peter F Leadlay
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Manuela Tosin
- Department of Chemistry, University of Warwick, Library Road, Coventry, CV4 7AL, UK.
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26
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Parascandolo JS, Havemann J, Potter HK, Huang F, Riva E, Connolly J, Wilkening I, Song L, Leadlay PF, Tosin M. Insights into 6-Methylsalicylic Acid Bio-assembly by Using Chemical Probes. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 128:3524-3528. [PMID: 27478274 PMCID: PMC4950124 DOI: 10.1002/ange.201509038] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 11/19/2015] [Indexed: 01/19/2023]
Abstract
Chemical probes capable of reacting with KS (ketosynthase)-bound biosynthetic intermediates were utilized for the investigation of the model type I iterative polyketide synthase 6-methylsalicylic acid synthase (6-MSAS) in vivo and in vitro. From the fermentation of fungal and bacterial 6-MSAS hosts in the presence of chain termination probes, a full range of biosynthetic intermediates was isolated and characterized for the first time. Meanwhile, in vitro studies of recombinant 6-MSA synthases with both nonhydrolyzable and hydrolyzable substrate mimics have provided additional insights into substrate recognition, providing the basis for further exploration of the enzyme catalytic activities.
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Affiliation(s)
| | - Judith Havemann
- Department of ChemistryUniversity of WarwickLibrary RoadCoventryCV4 7ALUK
| | - Helen K. Potter
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Fanglu Huang
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- Department of BiochemistryUniversity of Cambridge80 Tennis Court RoadCambridgeCB2 1GAUK
| | - Elena Riva
- Department of ChemistryUniversity of WarwickLibrary RoadCoventryCV4 7ALUK
| | - Jack Connolly
- Department of ChemistryUniversity of WarwickLibrary RoadCoventryCV4 7ALUK
- School of BiosciencesThe University of BirminghamBirminghamB15 2TTUK
| | - Ina Wilkening
- Department of ChemistryUniversity of WarwickLibrary RoadCoventryCV4 7ALUK
| | - Lijiang Song
- Department of ChemistryUniversity of WarwickLibrary RoadCoventryCV4 7ALUK
| | - Peter F. Leadlay
- Department of BiochemistryUniversity of Cambridge80 Tennis Court RoadCambridgeCB2 1GAUK
| | - Manuela Tosin
- Department of ChemistryUniversity of WarwickLibrary RoadCoventryCV4 7ALUK
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27
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Abstract
Polyketides are a diverse group of natural products that form the basis of many important drugs. The engineering of the polyketide synthase (PKS) enzymes responsible for the formation of these compounds has long been considered to have great potential for producing new bioactive molecules. Recent advances in this field have contributed to the understanding of this powerful and complex enzymatic machinery, particularly with regard to domain activity and engineering, unique building block formation and incorporation, and programming rules and limitations. New developments in tools for
in vitro biochemical analysis, full-length megasynthase structural studies, and
in vivo heterologous expression will continue to improve our fundamental understanding of polyketide synthesis as well as our ability to engineer the production of polyketides.
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Affiliation(s)
- Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
| | - Joyce Liu
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
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28
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Harnessing natural product assembly lines: structure, promiscuity, and engineering. J Ind Microbiol Biotechnol 2015; 43:371-87. [PMID: 26527577 DOI: 10.1007/s10295-015-1704-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/18/2015] [Indexed: 10/22/2022]
Abstract
Many therapeutically relevant natural products are biosynthesized by the action of giant mega-enzyme assembly lines. By leveraging the specificity, promiscuity, and modularity of assembly lines, a variety of strategies has been developed that enables the biosynthesis of modified natural products. This review briefly summarizes recent structural advances related to natural product assembly lines, discusses chemical approaches to probing assembly line structures in the absence of traditional biophysical data, and surveys efforts that harness the inherent or engineered promiscuity of assembly lines for the synthesis of non-natural polyketides and non-ribosomal peptide analogues.
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Winter JM, Cascio D, Dietrich D, Sato M, Watanabe K, Sawaya MR, Vederas JC, Tang Y. Biochemical and Structural Basis for Controlling Chemical Modularity in Fungal Polyketide Biosynthesis. J Am Chem Soc 2015; 137:9885-93. [PMID: 26172141 DOI: 10.1021/jacs.5b04520] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Modular collaboration between iterative fungal polyketide synthases (IPKSs) is an important mechanism for generating structural diversity of polyketide natural products. Inter-PKS communication and substrate channeling are controlled in large by the starter unit acyl carrier protein transacylase (SAT) domain found in the accepting IPKS module. Here, we reconstituted the modular biosynthesis of the benzaldehyde core of the chaetoviridin and chaetomugilin azaphilone natural products using the IPKSs CazF and CazM. Our studies revealed a critical role of CazM's SAT domain in selectively transferring a highly reduced triketide product from CazF. In contrast, a more oxidized triketide that is also produced by CazF and required in later stages of biosynthesis of the final product is not recognized by the SAT domain. The structural basis for the acyl unit selectivity was uncovered by the first X-ray structure of a fungal SAT domain, highlighted by a covalent hexanoyl thioester intermediate in the SAT active site. The crystal structure of SAT domain will enable protein engineering efforts aimed at mixing and matching different IPKS modules for the biosynthesis of new compounds.
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Affiliation(s)
- Jaclyn M Winter
- †Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, United States
| | - Duilio Cascio
- §Department of Energy (DOE) Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, United States
| | - David Dietrich
- ∥Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Michio Sato
- ⊥Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Kenji Watanabe
- ⊥Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Michael R Sawaya
- §Department of Energy (DOE) Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, United States
| | - John C Vederas
- ∥Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Yi Tang
- †Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, United States.,‡Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
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