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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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Nickles GR, Oestereicher B, Keller NP, Drott M. Mining for a new class of fungal natural products: the evolution, diversity, and distribution of isocyanide synthase biosynthetic gene clusters. Nucleic Acids Res 2023; 51:7220-7235. [PMID: 37427794 PMCID: PMC10415135 DOI: 10.1093/nar/gkad573] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/16/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023] Open
Abstract
The products of non-canonical isocyanide synthase (ICS) biosynthetic gene clusters (BGCs) mediate pathogenesis, microbial competition, and metal-homeostasis through metal-associated chemistry. We sought to enable research into this class of compounds by characterizing the biosynthetic potential and evolutionary history of these BGCs across the Fungal Kingdom. We amalgamated a pipeline of tools to predict BGCs based on shared promoter motifs and located 3800 ICS BGCs in 3300 genomes, making ICS BGCs the fifth largest class of specialized metabolites compared to canonical classes found by antiSMASH. ICS BGCs are not evenly distributed across fungi, with evidence of gene-family expansions in several Ascomycete families. We show that the ICS dit1/2 gene cluster family (GCF), which was prior only studied in yeast, is present in ∼30% of all Ascomycetes. The dit variety ICS exhibits greater similarity to bacterial ICS than other fungal ICS, suggesting a potential convergence of the ICS backbone domain. The evolutionary origins of the dit GCF in Ascomycota are ancient and these genes are diversifying in some lineages. Our results create a roadmap for future research into ICS BGCs. We developed a website (https://isocyanides.fungi.wisc.edu/) that facilitates the exploration and downloading of all identified fungal ICS BGCs and GCFs.
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Affiliation(s)
- Grant R Nickles
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, WI 53706, USA
| | | | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, WI 53706, USA
- Department of Plant Pathology, University of Wisconsin—Madison, Madison, WI 53706, USA
| | - Milton T Drott
- USDA-ARS Cereal Disease Lab (CDL), St. Paul, MN 55108, USA
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3
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Nickles GR, Oestereicher B, Keller NP, Drott MT. Mining for a New Class of Fungal Natural Products: The Evolution, Diversity, and Distribution of Isocyanide Synthase Biosynthetic Gene Clusters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.17.537281. [PMID: 37131656 PMCID: PMC10153163 DOI: 10.1101/2023.04.17.537281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The products of non-canonical isocyanide synthase (ICS) biosynthetic gene clusters (BGCs) have notable bioactivities that mediate pathogenesis, microbial competition, and metal-homeostasis through metal-associated chemistry. We sought to enable research into this class of compounds by characterizing the biosynthetic potential and evolutionary history of these BGCs across the Fungal Kingdom. We developed the first genome-mining pipeline to identify ICS BGCs, locating 3,800 ICS BGCs in 3,300 genomes. Genes in these clusters share promoter motifs and are maintained in contiguous groupings by natural selection. ICS BGCs are not evenly distributed across fungi, with evidence of gene-family expansions in several Ascomycete families. We show that the ICS dit1 / 2 gene cluster family (GCF), which was thought to only exist in yeast, is present in ∼30% of all Ascomycetes, including many filamentous fungi. The evolutionary history of the dit GCF is marked by deep divergences and phylogenetic incompatibilities that raise questions about convergent evolution and suggest selection or horizontal gene transfers have shaped the evolution of this cluster in some yeast and dimorphic fungi. Our results create a roadmap for future research into ICS BGCs. We developed a website ( www.isocyanides.fungi.wisc.edu ) that facilitates the exploration, filtering, and downloading of all identified fungal ICS BGCs and GCFs.
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Affiliation(s)
- Grant R. Nickles
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, WI 53706, USA
| | | | - Nancy P. Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, WI 53706, USA
- Department of Plant Pathology, University of Wisconsin—Madison, Madison, WI 53706, USA
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4
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Zhang L, Wang C, Chen K, Zhong W, Xu Y, Molnár I. Engineering the biosynthesis of fungal nonribosomal peptides. Nat Prod Rep 2023; 40:62-88. [PMID: 35796260 DOI: 10.1039/d2np00036a] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Covering: 2011 up to the end of 2021.Fungal nonribosomal peptides (NRPs) and the related polyketide-nonribosomal peptide hybrid products (PK-NRPs) are a prolific source of bioactive compounds, some of which have been developed into essential drugs. The synthesis of these complex natural products (NPs) utilizes nonribosomal peptide synthetases (NRPSs), multidomain megaenzymes that assemble specific peptide products by sequential condensation of amino acids and amino acid-like substances, independent of the ribosome. NRPSs, collaborating polyketide synthase modules, and their associated tailoring enzymes involved in product maturation represent promising targets for NP structure diversification and the generation of small molecule unnatural products (uNPs) with improved or novel bioactivities. Indeed, reprogramming of NRPSs and recruiting of novel tailoring enzymes is the strategy by which nature evolves NRP products. The recent years have witnessed a rapid development in the discovery and identification of novel NRPs and PK-NRPs, and significant advances have also been made towards the engineering of fungal NRP assembly lines to generate uNP peptides. However, the intrinsic complexities of fungal NRP and PK-NRP biosynthesis, and the large size of the NRPSs still present formidable conceptual and technical challenges for the rational and efficient reprogramming of these pathways. This review examines key examples for the successful (and for some less-successful) re-engineering of fungal NRPS assembly lines to inform future efforts towards generating novel, biologically active peptides and PK-NRPs.
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Affiliation(s)
- Liwen Zhang
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - Chen Wang
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - Kang Chen
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - Weimao Zhong
- Southwest Center for Natural Products Research, University of Arizona, 250 E. Valencia Rd., Tucson, AZ 85706, USA
| | - Yuquan Xu
- Biotechnology Research Institute, The 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 E. Valencia Rd., Tucson, AZ 85706, USA.,VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Espoo, Finland.
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5
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Wang C, Xiao D, Dun B, Yin M, Tsega AS, Xie L, Li W, Yue Q, Wang S, Gao H, Lin M, Zhang L, Molnár I, Xu Y. Chemometrics and genome mining reveal an unprecedented family of sugar acid-containing fungal nonribosomal cyclodepsipeptides. Proc Natl Acad Sci U S A 2022; 119:e2123379119. [PMID: 35914151 PMCID: PMC9371744 DOI: 10.1073/pnas.2123379119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 06/23/2022] [Indexed: 02/03/2023] Open
Abstract
Xylomyrocins, a unique group of nonribosomal peptide secondary metabolites, were discovered in Paramyrothecium and Colletotrichum spp. fungi by employing a combination of high-resolution tandem mass spectrometry (HRMS/MS)-based chemometrics, comparative genome mining, gene disruption, stable isotope feeding, and chemical complementation techniques. These polyol cyclodepsipeptides all feature an unprecedented d-xylonic acid moiety as part of their macrocyclic scaffold. This biosynthon is derived from d-xylose supplied by xylooligosaccharide catabolic enzymes encoded in the xylomyrocin biosynthetic gene cluster, revealing a novel link between carbohydrate catabolism and nonribosomal peptide biosynthesis. Xylomyrocins from different fungal isolates differ in the number and nature of their amino acid building blocks that are nevertheless incorporated by orthologous nonribosomal peptide synthetase (NRPS) enzymes. Another source of structural diversity is the variable choice of the nucleophile for intramolecular macrocyclic ester formation during xylomyrocin chain termination. This nucleophile is selected from the multiple available alcohol functionalities of the polyol moiety, revealing a surprising polyspecificity for the NRPS terminal condensation domain. Some xylomyrocin congeners also feature N-methylated amino acid residues in positions where the corresponding NRPS modules lack N-methyltransferase (M) domains, providing a rare example of promiscuous methylation in the context of an NRPS with an otherwise canonical, collinear biosynthetic program.
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Affiliation(s)
- Chen Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| | - Dongliang Xiao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| | - Baoqing Dun
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| | - Miaomiao Yin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| | - Adigo Setargie Tsega
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| | - Linan Xie
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| | - Wenhua Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| | - Qun Yue
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| | - Sibao Wang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, P.R. China
| | - Han Gao
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, P.R. China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| | - Liwen Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| | - István Molnár
- Southwest Center for Natural Products Research, University of Arizona, Tucson, AZ 85706
- VTT Technical Research Centre of Finland, FI-02044 VTT, Espoo, Finland
| | - Yuquan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
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Xu G, Yang S. Diverse evolutionary origins of microbial [4 + 2]-cyclases in natural product biosynthesis. Int J Biol Macromol 2021; 182:154-161. [PMID: 33836196 DOI: 10.1016/j.ijbiomac.2021.04.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 10/21/2022]
Abstract
Natural [4 + 2]-cyclases catalyze concerted cycloaddition during biosynthesis of over 400 natural products reported. Microbial [4 + 2]-cyclases are structurally diverse with a broad range of substrates. Thus far, about 52 putative microbial [4 + 2]-cyclases of 13 different types have been characterized, with over 20 crystal structures. However, how these cyclases have evolved during natural product biosynthesis remains elusive. Structural and phylogenetic analyses suggest that these different types of [4 + 2]-cyclases might have diverse evolutionary origins, such as reductases, dehydratases, methyltransferases, oxidases, etc. Divergent evolution of enzyme function might have occurred in these different families. Understanding the independent evolutionary history of these cyclases would provide new insights into their catalysis mechanisms and the biocatalyst design.
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Affiliation(s)
- Gangming Xu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
| | - Suiqun Yang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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Dekimpe S, Masschelein J. Beyond peptide bond formation: the versatile role of condensation domains in natural product biosynthesis. Nat Prod Rep 2021; 38:1910-1937. [DOI: 10.1039/d0np00098a] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Condensation domains perform highly diverse functions during natural product biosynthesis and are capable of generating remarkable chemical diversity.
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Affiliation(s)
- Sofie Dekimpe
- Laboratory for Biomolecular Discovery & Engineering
- Department of Biology
- KU Leuven
- Leuven
- Belgium
| | - Joleen Masschelein
- Laboratory for Biomolecular Discovery & Engineering
- Department of Biology
- KU Leuven
- Leuven
- Belgium
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8
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Zhang L, Fasoyin OE, Molnár I, Xu Y. Secondary metabolites from hypocrealean entomopathogenic fungi: novel bioactive compounds. Nat Prod Rep 2020; 37:1181-1206. [PMID: 32211639 PMCID: PMC7529686 DOI: 10.1039/c9np00065h] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: 2014 up to the third quarter of 2019 Entomopathogens constitute a unique, specialized trophic subgroup of fungi, most of whose members belong to the order Hypocreales (class Sordariomycetes, phylum Ascomycota). These Hypocrealean Entomopathogenic Fungi (HEF) produce a large variety of secondary metabolites (SMs) and their genomes rank highly for the number of predicted, unique SM biosynthetic gene clusters. SMs from HEF have diverse roles in insect pathogenicity as virulence factors by modulating various interactions between the producer fungus and its insect host. In addition, these SMs also defend the carcass of the prey against opportunistic microbial invaders, mediate intra- and interspecies communication, and mitigate abiotic and biotic stresses. Thus, these SMs contribute to the role of HEF as commercial biopesticides in the context of integrated pest management systems, and provide lead compounds for the development of chemical pesticides for crop protection. These bioactive SMs also underpin the widespread use of certain HEF as nutraceuticals and traditional remedies, and allowed the modern pharmaceutical industry to repurpose some of these molecules as life-saving human medications. Herein, we survey the structures and biological activities of SMs described from HEF, and summarize new information on the roles of these metabolites in fungal virulence.
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Affiliation(s)
- Liwen Zhang
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P.R. China.
| | - Opemipo Esther Fasoyin
- Biotechnology Research Institute, The 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 E. Valencia Rd., Tucson, AZ 85706, USA.
| | - Yuquan Xu
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P.R. China.
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9
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Li H, Wei H, Hu J, Lacey E, Sobolev AN, Stubbs KA, Solomon PS, Chooi YH. Genomics-Driven Discovery of Phytotoxic Cytochalasans Involved in the Virulence of the Wheat Pathogen Parastagonospora nodorum. ACS Chem Biol 2020; 15:226-233. [PMID: 31815421 DOI: 10.1021/acschembio.9b00791] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The etiology of fungal pathogenesis of grains is critical to global food security. The large number of orphan biosynthetic gene clusters uncovered in fungal plant pathogen genome sequencing projects suggests that we have a significant knowledge gap about the secondary metabolite repertoires of these pathogens and their roles in plant pathogenesis. Cytochalasans are a family of natural products of significant interest due to their ability to bind to actin and interfere with cellular processes that involved actin polymerization; however, our understanding of their biosynthesis and biological roles remains incomplete. Here, we identified a putative polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS) gene cluster (phm) that was upregulated in the pathogen Parastagonospora nodorum during its infection on wheat. Overexpression of the transcription factor gene phmR encoded in the phm gene cluster resulted in the production of two leucine-derived cytochalasans, phomacins D and E (1 and 2, respectively), and an acetonyl adduct phomacin F. Heterologous expression of the PKS-NRPS gene phmA and the trans-enoyl reductase (ER) gene phmE in Aspergillus nidulans resulted in the production of a novel 2-pyrrolidone precursor prephomacin. Reverse genetics and wheat seedling infection assays showed that ΔphmA mutants exhibited significantly reduced virulence compared to the wild type. We further demonstrated that both 1 and 2 showed potent actin polymerization-inhibitory activities and exhibited potentially monocot-specific antigerminative activities. The findings from this study have advanced our knowledge based on the biosynthesis and biological roles of cytochalasans, the latter of which could have significant implications for our understanding of the molecular mechanisms of fungus-plant interactions.
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Affiliation(s)
| | - Haochen Wei
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | | | - Ernest Lacey
- Microbial Screening Technologies Pty. Ltd., Smithfield, New South Wales 2164, Australia
| | | | | | - Peter S. Solomon
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
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10
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Theobald S, Vesth TC, Andersen MR. Genus level analysis of PKS-NRPS and NRPS-PKS hybrids reveals their origin in Aspergilli. BMC Genomics 2019; 20:847. [PMID: 31722662 PMCID: PMC6854747 DOI: 10.1186/s12864-019-6114-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 09/20/2019] [Indexed: 11/10/2022] Open
Abstract
Background Filamentous fungi produce a vast amount of bioactive secondary metabolites (SMs) synthesized by e.g. hybrid polyketide synthase-nonribosomal peptide synthetase enzymes (PKS-NRPS; NRPS-PKS). While their domain structure suggests a common ancestor with other SM proteins, their evolutionary origin and dynamics in fungi are still unclear. Recent rational engineering approaches highlighted the possibility to reassemble hybrids into chimeras — suggesting molecular recombination as diversifying mechanism. Results Phylogenetic analysis of hybrids in 37 species – spanning 9 sections of Aspergillus and Penicillium chrysogenum – let us describe their dynamics throughout the genus Aspergillus. The tree topology indicates that three groups of PKS-NRPS as well as one group of NRPS-PKS hybrids developed independently from each other. Comparison to other SM genes lead to the conclusion that hybrids in Aspergilli have several PKS ancestors; in contrast, hybrids are monophyletic when compared to available NRPS genes — with the exception of a small group of NRPSs. Our analysis also revealed that certain NRPS-likes are derived from NRPSs, suggesting that the NRPS/NRPS-like relationship is dynamic and proteins can diverge from one function to another. An extended phylogenetic analysis including bacterial and fungal taxa revealed multiple ancestors of hybrids. Homologous hybrids are present in all sections which suggests frequent horizontal gene transfer between genera and a finite number of hybrids in fungi. Conclusion Phylogenetic distances between hybrids provide us with evidence for their evolution: Large inter-group distances indicate multiple independent events leading to the generation of hybrids, while short intra-group distances of hybrids from different taxonomic sections indicate frequent horizontal gene transfer. Our results are further supported by adding bacterial and fungal genera. Presence of related hybrid genes in all Ascomycetes suggests a frequent horizontal gene transfer between genera and a finite diversity of hybrids — also explaining their scarcity. The provided insights into relations of hybrids and other SM genes will serve in rational design of new hybrid enzymes.
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Affiliation(s)
- Sebastian Theobald
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, Kgs. Lyngby, Denmark.,Current address: Novozymes A/S, Krogshøjvej 36, Bagsværd, Denmark
| | - Tammi C Vesth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, Kgs. Lyngby, Denmark.,Current address: Chr. Hansen, Bøge Alle, Hørsholm, Denmark
| | - Mikael R Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, Kgs. Lyngby, Denmark. .,Current address: Novozymes A/S, Krogshøjvej 36, Bagsværd, Denmark.
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11
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Li H, Gilchrist CLM, Lacey HJ, Crombie A, Vuong D, Pitt JI, Lacey E, Chooi YH, Piggott AM. Discovery and Heterologous Biosynthesis of the Burnettramic Acids: Rare PKS-NRPS-Derived Bolaamphiphilic Pyrrolizidinediones from an Australian Fungus, Aspergillus burnettii. Org Lett 2019; 21:1287-1291. [DOI: 10.1021/acs.orglett.8b04042] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hang Li
- School of Molecular Sciences, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - Cameron L. M. Gilchrist
- School of Molecular Sciences, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - Heather J. Lacey
- Microbial Screening Technologies Pty. Ltd., Smithfield, New South Wales 2164, Australia
| | - Andrew Crombie
- Microbial Screening Technologies Pty. Ltd., Smithfield, New South Wales 2164, Australia
| | - Daniel Vuong
- Microbial Screening Technologies Pty. Ltd., Smithfield, New South Wales 2164, Australia
| | - John I. Pitt
- Commonwealth Scientific and Industrial Research Organisation, North Ryde, New South Wales 2113, Australia
| | - Ernest Lacey
- Microbial Screening Technologies Pty. Ltd., Smithfield, New South Wales 2164, Australia
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - Andrew M. Piggott
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
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12
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Wang L, Yuan M, Zheng J. Crystal structure of the condensation domain from lovastatin polyketide synthase. Synth Syst Biotechnol 2018; 4:10-15. [PMID: 30533541 PMCID: PMC6260248 DOI: 10.1016/j.synbio.2018.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/01/2018] [Accepted: 11/15/2018] [Indexed: 12/03/2022] Open
Abstract
The highly reducing iterative polyketide synthases responsible for lovastatin biosynthesis contains a section homologous to condensation (CON) domain observed in nonribosomal peptide synthetases (NRPSs). In the present study, we expressed the isolated lovastatin CON domain and solved the crystal structure to 1.79 Å resolution. The overall structure shows similarity to canonical condensation domains of NRPSs, containing the N-terminal and C-terminal subdomains that resemble enzymes of chloramphenicol acetyltransferase family, whereas distinct structural features are observed at the active site. The acceptor entry of the substrate channel is blocked by a flexible loop, thereby preventing the loading of substrate for a new round of chain elongation. The mutation of conserved catalytic motif located at the midpoint of substrate channel agrees with the incapability of CON to catalyzed amide-bond formation. The structure helps to understand the function of CON in lovastatin biosynthesis.
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13
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Hai Y, Tang Y. Biosynthesis of Long-Chain N-Acyl Amide by a Truncated Polyketide Synthase-Nonribosomal Peptide Synthetase Hybrid Megasynthase in Fungi. J Am Chem Soc 2018; 140:1271-1274. [PMID: 29343058 DOI: 10.1021/jacs.7b13350] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Truncated iterative polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS) megasynthases in which only the C domain is present are widespread in fungi, yet nearly all members have unknown functions. Bioinformatics analysis showed that the C domains of such PKS-C enzymes are noncanonical due to substitution at the second histidine in the active site HHxxxDG motif. Here, we used genome mining strategy to characterize a cryptic PKS-C hybrid from Talaromyces wortmanii and discovered the products are reduced long-chain polyketides amidated with a specific ω-amino acid 5-aminopentanoic acid (5PA). The wortmanamides resemble long-chain N-acyl-amide signaling lipids that target diverse receptors including GPCRs. The noncanonical C domain of this PKS-C hybrid was also demonstrated to be a bona fide condensation domain that specifically selects 5PA and catalyzes amidation to release polyketide chain.
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Affiliation(s)
- Yang Hai
- Department of Chemical and Biomolecular Engineering, ‡Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, ‡Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States
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14
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Miyanaga A, Kudo F, Eguchi T. Protein–protein interactions in polyketide synthase–nonribosomal peptide synthetase hybrid assembly lines. Nat Prod Rep 2018; 35:1185-1209. [DOI: 10.1039/c8np00022k] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The protein–protein interactions in polyketide synthase–nonribosomal peptide synthetase hybrids are summarized and discussed.
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Affiliation(s)
- Akimasa Miyanaga
- Department of Chemistry
- Tokyo Institute of Technology
- Tokyo 152-8551
- Japan
| | - Fumitaka Kudo
- Department of Chemistry
- Tokyo Institute of Technology
- Tokyo 152-8551
- Japan
| | - Tadashi Eguchi
- Department of Chemistry
- Tokyo Institute of Technology
- Tokyo 152-8551
- Japan
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Zhao Y, Ding J, Yuan W, Huang J, Huang W, Wang Y, Zheng W. Production of a fungal furocoumarin by a polyketide synthase gene cluster confers the chemo-resistance of Neurospora crassa to the predation by fungivorous arthropods. Environ Microbiol 2017; 19:3920-3929. [PMID: 28485098 DOI: 10.1111/1462-2920.13791] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 04/28/2017] [Accepted: 04/28/2017] [Indexed: 12/25/2022]
Abstract
The formation of sexual fruiting bodies and production of polyketides are believed to be the most important strategies for fungal survival in environmental insults. In Neurospora crassa, the backbone gene of polyketide synthase gene cluster 6 (pks-6), which is expressed at lower level under vegetative growth, is highly expressed during perithecia development. Intriguingly, deletion of pks-6 does not affect perithecia maturation. How the expression of pks-6 correlates with fungal sexual development remains to be established. Here, we showed that overexpression of pks-6 results in an enhanced production of an insecticidal furocoumarin (neurosporin A). Deletion of pks-6, however, abolished neurosporin A biosynthesis. Moreover, the content of neurosporin A negatively associates with the food preference of fungivores, where the pks-6 knockout strain is more prone to be grazed by collembolans Sinella curviseta. Additionally, during vegetative growth, confrontation with Drosophila melanogaster also results in an enhanced expression of pks-6 and production of neurosporin A. Thus, high expression of pks-6 positively interrelates with the chemo-resistance of N. crassa to arthropod predation. Our findings suggest that pks-6 confers the production of insecticidal neurosporin A counteracting the feeding attack by arthropods during sexual development of N. crassa.
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Affiliation(s)
- Yanxia Zhao
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Jianing Ding
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Weihua Yuan
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Jinjin Huang
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Wenxiu Huang
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Yan Wang
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Weifa Zheng
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
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Linker Flexibility Facilitates Module Exchange in Fungal Hybrid PKS-NRPS Engineering. PLoS One 2016; 11:e0161199. [PMID: 27551732 PMCID: PMC4994942 DOI: 10.1371/journal.pone.0161199] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 08/01/2016] [Indexed: 11/19/2022] Open
Abstract
Polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) each give rise to a vast array of complex bioactive molecules with further complexity added by the existence of natural PKS-NRPS fusions. Rational genetic engineering for the production of natural product derivatives is desirable for the purpose of incorporating new functionalities into pre-existing molecules, or for optimization of known bioactivities. We sought to expand the range of natural product diversity by combining modules of PKS-NRPS hybrids from different hosts, hereby producing novel synthetic natural products. We succeeded in the construction of a functional cross-species chimeric PKS-NRPS expressed in Aspergillus nidulans. Module swapping of the two PKS-NRPS natural hybrids CcsA from Aspergillus clavatus involved in the biosynthesis of cytochalasin E and related Syn2 from rice plant pathogen Magnaporthe oryzae lead to production of novel hybrid products, demonstrating that the rational re-design of these fungal natural product enzymes is feasible. We also report the structure of four novel pseudo pre-cytochalasin intermediates, niduclavin and niduporthin along with the chimeric compounds niduchimaeralin A and B, all indicating that PKS-NRPS activity alone is insufficient for proper assembly of the cytochalasin core structure. Future success in the field of biocombinatorial synthesis of hybrid polyketide-nonribosomal peptides relies on the understanding of the fundamental mechanisms of inter-modular polyketide chain transfer. Therefore, we expressed several PKS-NRPS linker-modified variants. Intriguingly, the linker anatomy is less complex than expected, as these variants displayed great tolerance with regards to content and length, showing a hitherto unreported flexibility in PKS-NRPS hybrids, with great potential for synthetic biology-driven biocombinatorial chemistry.
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Wolf T, Shelest V, Nath N, Shelest E. CASSIS and SMIPS: promoter-based prediction of secondary metabolite gene clusters in eukaryotic genomes. Bioinformatics 2016; 32:1138-43. [PMID: 26656005 PMCID: PMC4824125 DOI: 10.1093/bioinformatics/btv713] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 11/28/2015] [Indexed: 01/07/2023] Open
Abstract
MOTIVATION Secondary metabolites (SM) are structurally diverse natural products of high pharmaceutical importance. Genes involved in their biosynthesis are often organized in clusters, i.e., are co-localized and co-expressed. In silico cluster prediction in eukaryotic genomes remains problematic mainly due to the high variability of the clusters' content and lack of other distinguishing sequence features. RESULTS We present Cluster Assignment by Islands of Sites (CASSIS), a method for SM cluster prediction in eukaryotic genomes, and Secondary Metabolites by InterProScan (SMIPS), a tool for genome-wide detection of SM key enzymes ('anchor' genes): polyketide synthases, non-ribosomal peptide synthetases and dimethylallyl tryptophan synthases. Unlike other tools based on protein similarity, CASSIS exploits the idea of co-regulation of the cluster genes, which assumes the existence of common regulatory patterns in the cluster promoters. The method searches for 'islands' of enriched cluster-specific motifs in the vicinity of anchor genes. It was validated in a series of cross-validation experiments and showed high sensitivity and specificity. AVAILABILITY AND IMPLEMENTATION CASSIS and SMIPS are freely available at https://sbi.hki-jena.de/cassis CONTACT thomas.wolf@leibniz-hki.de or ekaterina.shelest@leibniz-hki.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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18
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Donzelli B, Krasnoff S. Molecular Genetics of Secondary Chemistry in Metarhizium Fungi. GENETICS AND MOLECULAR BIOLOGY OF ENTOMOPATHOGENIC FUNGI 2016; 94:365-436. [DOI: 10.1016/bs.adgen.2016.01.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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19
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Abstract
Filamentous fungi are historically known as rich sources for production of biologically active natural products, so-called secondary metabolites. One particularly pharmaceutically relevant chemical group of secondary metabolites is the nonribosomal peptides synthesized by nonribosomal peptide synthetases (NRPSs). As most of the fungal NRPS gene clusters leading to production of the desired molecules are not expressed under laboratory conditions, efforts to overcome this impediment are crucial to unlock the full chemical potential of each fungal species. One way to activate these silent clusters is by overexpressing and deleting global regulators of secondary metabolism. The conserved fungal-specific regulator of secondary metabolism, LaeA, was shown to be a valuable target for sleuthing of novel gene clusters and metabolites. Additionally, modulation of chromatin structures by either chemical or genetic manipulation has been shown to activate cryptic metabolites. Furthermore, NRPS-derived molecules seem to be affected by cross talk between the specific gene clusters and some of these metabolites have a tissue- or developmental-specific regulation. This chapter summarizes how this knowledge of different tiers of regulation can be combined to increase production of NRPS-derived metabolites in fungal species.
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Affiliation(s)
- Alexandra A Soukup
- Department of Genetics, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI, 53706, USA
| | - Nancy P Keller
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI, 53706, USA.
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, 3455 Microbial Sciences, 1550 Linden Drive, Madison, WI, 53706, USA.
| | - Philipp Wiemann
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, 3455 Microbial Sciences, 1550 Linden Drive, Madison, WI, 53706, USA
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20
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Liu L, Zhang J, Chen C, Teng J, Wang C, Luo D. Structure and biosynthesis of fumosorinone, a new protein tyrosine phosphatase 1B inhibitor firstly isolated from the entomogenous fungus Isaria fumosorosea. Fungal Genet Biol 2015; 81:191-200. [DOI: 10.1016/j.fgb.2015.03.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 03/26/2015] [Accepted: 03/30/2015] [Indexed: 11/24/2022]
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21
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Franke J, Ishida K, Hertweck C. Plasticity of the Malleobactin Pathway and Its Impact on Siderophore Action in Human Pathogenic Bacteria. Chemistry 2015; 21:8010-4. [DOI: 10.1002/chem.201500757] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Indexed: 12/23/2022]
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22
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Zou Y, Xu W, Tsunematsu Y, Tang M, Watanabe K, Tang Y. Methylation-dependent acyl transfer between polyketide synthase and nonribosomal peptide synthetase modules in fungal natural product biosynthesis. Org Lett 2014; 16:6390-3. [PMID: 25494235 PMCID: PMC4275151 DOI: 10.1021/ol503179v] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Biochemical studies of purified and dissected fungal polyketide synthase and nonribosomal peptide synthetase (PKS-NRPS) hybrid enzymes involved in biosynthesis of pseurotin and aspyridone indicate that one α-methylation step during polyketide synthesis is a prerequisite and a key checkpoint for chain transfer between PKS and NRPS modules. In the absence of the resulting γ-methyl feature, the completed polyketide intermediate is offloaded as an α-pyrone instead of being aminoacylated by the NRPS domain. These examples illustrate that precisely timed tailoring domain activities play critical roles in the overall programming of the iterative PKS (and NRPS) functions.
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Affiliation(s)
- Yi Zou
- Department of Chemical and Biomolecular Engineering and ‡Department of Chemistry and Biochemistry, University of California , Los Angeles, California 90095, United States
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23
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Kakule TB, Lin Z, Schmidt EW. Combinatorialization of Fungal Polyketide Synthase–Peptide Synthetase Hybrid Proteins. J Am Chem Soc 2014; 136:17882-90. [DOI: 10.1021/ja511087p] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Thomas B. Kakule
- 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
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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Hiratsuka T, Suzuki H, Kariya R, Seo T, Minami A, Oikawa H. Biosynthesis of the Structurally Unique Polycyclopropanated Polyketide-Nucleoside Hybrid Jawsamycin (FR-900848). Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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25
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Hiratsuka T, Suzuki H, Kariya R, Seo T, Minami A, Oikawa H. Biosynthesis of the Structurally Unique Polycyclopropanated Polyketide-Nucleoside Hybrid Jawsamycin (FR-900848). Angew Chem Int Ed Engl 2014; 53:5423-6. [DOI: 10.1002/anie.201402623] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Indexed: 02/06/2023]
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26
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Leitão AL, Enguita FJ. Fungal extrolites as a new source for therapeutic compounds and as building blocks for applications in synthetic biology. Microbiol Res 2014; 169:652-65. [PMID: 24636745 DOI: 10.1016/j.micres.2014.02.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 02/15/2014] [Accepted: 02/16/2014] [Indexed: 01/07/2023]
Abstract
Secondary metabolic pathways of fungal origin provide an almost unlimited resource of new compounds for medical applications, which can fulfill some of the, currently unmet, needs for therapeutic alternatives for the treatment of a number of diseases. Secondary metabolites secreted to the extracellular medium (extrolites) belong to diverse chemical and structural families, but the majority of them are synthesized by the condensation of a limited number of precursor building blocks including amino acids, sugars, lipids and low molecular weight compounds also employed in anabolic processes. In fungi, genes related to secondary metabolic pathways are frequently clustered together and show a modular organization within fungal genomes. The majority of fungal gene clusters responsible for the biosynthesis of secondary metabolites contain genes encoding a high molecular weight condensing enzyme which is responsible for the assembly of the precursor units of the metabolite. They also contain other auxiliary genes which encode enzymes involved in subsequent chemical modification of the metabolite core. Synthetic biology is a branch of molecular biology whose main objective is the manipulation of cellular components and processes in order to perform logically connected metabolic functions. In synthetic biology applications, biosynthetic modules from secondary metabolic processes can be rationally engineered and combined to produce either new compounds, or to improve the activities and/or the bioavailability of the already known ones. Recently, advanced genome editing techniques based on guided DNA endonucleases have shown potential for the manipulation of eukaryotic and bacterial genomes. This review discusses the potential application of genetic engineering and genome editing tools in the rational design of fungal secondary metabolite pathways by taking advantage of the increasing availability of genomic and biochemical data.
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Affiliation(s)
- Ana Lúcia Leitão
- Departamento de Ciências e Tecnologia da Biomassa, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, Caparica 2829-516, Portugal.
| | - Francisco J Enguita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisboa 1649-028, Portugal.
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27
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Kakule TB, Sardar D, Lin Z, Schmidt EW. Two related pyrrolidinedione synthetase loci in Fusarium heterosporum ATCC 74349 produce divergent metabolites. ACS Chem Biol 2013; 8:1549-57. [PMID: 23614392 DOI: 10.1021/cb400159f] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Equisetin synthetase (EqiS), from the filamentous fungus Fusarium heterosporum ATCC 74349, was initially assigned on the basis of genetic knockout and expression analysis. Increasing inconsistencies in experimental results led us to question this assignment. Here, we sequenced the F. heterosporum genome, revealing two hybrid polyketide-peptide proteins that were candidates for the equisetin synthetase. The surrounding genes in both clusters had the needed auxiliary genes that might be responsible for producing equisetin. Genetic mutation, biochemical analysis, and recombinant expression in the fungus enabled us to show that the initially assigned EqiS does not produce equisetin but instead produces a related 2,4-pyrrolidinedione, fusaridione A, that was previously unknown. Fusaridione A is methylated in the 3-position of the pyrrolidinedione, which has not otherwise been found in natural products, leading to spontaneous reverse-Dieckmann reactions. A newly described gene cluster, eqx, is responsible for producing equisetin.
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Affiliation(s)
- Thomas B. Kakule
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Debosmita Sardar
- 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
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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28
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Chen L, Yue Q, Zhang X, Xiang M, Wang C, Li S, Che Y, Ortiz-López FJ, Bills GF, Liu X, An Z. Genomics-driven discovery of the pneumocandin biosynthetic gene cluster in the fungus Glarea lozoyensis. BMC Genomics 2013; 14:339. [PMID: 23688303 PMCID: PMC3672099 DOI: 10.1186/1471-2164-14-339] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 05/09/2013] [Indexed: 11/15/2022] Open
Abstract
Background The antifungal therapy caspofungin is a semi-synthetic derivative of pneumocandin B0, a lipohexapeptide produced by the fungus Glarea lozoyensis, and was the first member of the echinocandin class approved for human therapy. The nonribosomal peptide synthetase (NRPS)-polyketide synthases (PKS) gene cluster responsible for pneumocandin biosynthesis from G. lozoyensis has not been elucidated to date. In this study, we report the elucidation of the pneumocandin biosynthetic gene cluster by whole genome sequencing of the G. lozoyensis wild-type strain ATCC 20868. Results The pneumocandin biosynthetic gene cluster contains a NRPS (GLNRPS4) and a PKS (GLPKS4) arranged in tandem, two cytochrome P450 monooxygenases, seven other modifying enzymes, and genes for L-homotyrosine biosynthesis, a component of the peptide core. Thus, the pneumocandin biosynthetic gene cluster is significantly more autonomous and organized than that of the recently characterized echinocandin B gene cluster. Disruption mutants of GLNRPS4 and GLPKS4 no longer produced the pneumocandins (A0 and B0), and the Δglnrps4 and Δglpks4 mutants lost antifungal activity against the human pathogenic fungus Candida albicans. In addition to pneumocandins, the G. lozoyensis genome encodes a rich repertoire of natural product-encoding genes including 24 PKSs, six NRPSs, five PKS-NRPS hybrids, two dimethylallyl tryptophan synthases, and 14 terpene synthases. Conclusions Characterization of the gene cluster provides a blueprint for engineering new pneumocandin derivatives with improved pharmacological properties. Whole genome estimation of the secondary metabolite-encoding genes from G. lozoyensis provides yet another example of the huge potential for drug discovery from natural products from the fungal kingdom.
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Affiliation(s)
- Li Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
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29
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Xu W, Chooi YH, Choi JW, Li S, Vederas JC, Da Silva NA, Tang Y. LovG: the thioesterase required for dihydromonacolin L release and lovastatin nonaketide synthase turnover in lovastatin biosynthesis. Angew Chem Int Ed Engl 2013; 52:6472-5. [PMID: 23653178 DOI: 10.1002/anie.201302406] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Wei Xu
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
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30
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Xu W, Chooi YH, Choi JW, Li S, Vederas JC, Da Silva NA, Tang Y. LovG: The Thioesterase Required for Dihydromonacolin L Release and Lovastatin Nonaketide Synthase Turnover in Lovastatin Biosynthesis. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302406] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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32
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Boettger D, Hertweck C. Molecular Diversity Sculpted by Fungal PKS-NRPS Hybrids. Chembiochem 2012; 14:28-42. [DOI: 10.1002/cbic.201200624] [Citation(s) in RCA: 155] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Indexed: 12/22/2022]
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