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Hu Y, Zhao X, Song Y, Jiang J, Long T, Cong M, Miao Y, Liu Y, Yang Z, Zhu Y, Wang J. Anti-inflammatory and Neuroprotective α-Pyrones from a Marine-Derived Strain of the Fungus Arthrinium arundinis and Their Heterologous Expression. JOURNAL OF NATURAL PRODUCTS 2024; 87:1975-1982. [PMID: 38687877 DOI: 10.1021/acs.jnatprod.4c00393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Fungal linear polyketides, such as α-pyrones with a 6-alkenyl chain, have been a rich source of biologically active compounds. Two new (1 and 2) and four known (3-6) 6-alkenylpyrone polyketides were isolated from a marine-derived strain of the fungus Arthrinium arundinis. Their structures were determined based on extensive spectroscopic analysis. The biosynthetic gene cluster (alt) for alternapyrones was identified from A. arundinis ZSDS-F3 and validated by heterologous expression in Aspergillus nidulans A1145 ΔSTΔEM, which revealed that the cytochrome P450 monooxygenase Alt2' could convert the methyl group 26-CH3 to a carboxyl group to produce 4 from 3. Another cytochrome P450 monooxygenase, Alt3', catalyzed successive hydroxylation, epoxidation, and oxidation steps to produce 1, 2, 5, and 6 from 4. Alternapyrone G (1) not only suppressed M1 polarization in lipopolysaccharide (LPS)-stimulated BV2 microglia but also stimulated dendrite regeneration and neuronal survival after Aβ treatment, suggesting alternapyrone G may be utilized as a privileged scaffold for Alzheimer's disease drug discovery.
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Affiliation(s)
- Yiwei Hu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Xiaoyang Zhao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Yue Song
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Jiahui Jiang
- College of Food Science and Technology, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Ocean University, Zhanjiang 524088, China
| | - Ting Long
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Mengjing Cong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Yuhua Miao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Yonghong Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
- Sanya Institute of Marine Ecology and Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Zhiyou Yang
- College of Food Science and Technology, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yiguang Zhu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
- Sanya Institute of Marine Ecology and Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Junfeng Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
- Sanya Institute of Marine Ecology and Engineering, Yazhou Scientific Bay, Sanya 572000, China
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Khodadadi F, Luciano-Rosario D, Gottschalk C, Jurick WM, Aćimović SG. Unveiling the Arsenal of Apple Bitter Rot Fungi: Comparative Genomics Identifies Candidate Effectors, CAZymes, and Biosynthetic Gene Clusters in Colletotrichum Species. J Fungi (Basel) 2024; 10:493. [PMID: 39057378 PMCID: PMC11278308 DOI: 10.3390/jof10070493] [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: 05/29/2024] [Revised: 07/05/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
The bitter rot of apple is caused by Colletotrichum spp. and is a serious pre-harvest disease that can manifest in postharvest losses on harvested fruit. In this study, we obtained genome sequences from four different species, C. chrysophilum, C. noveboracense, C. nupharicola, and C. fioriniae, that infect apple and cause diseases on other fruits, vegetables, and flowers. Our genomic data were obtained from isolates/species that have not yet been sequenced and represent geographic-specific regions. Genome sequencing allowed for the construction of phylogenetic trees, which corroborated the overall concordance observed in prior MLST studies. Bioinformatic pipelines were used to discover CAZyme, effector, and secondary metabolic (SM) gene clusters in all nine Colletotrichum isolates. We found redundancy and a high level of similarity across species regarding CAZyme classes and predicted cytoplastic and apoplastic effectors. SM gene clusters displayed the most diversity in type and the most common cluster was one that encodes genes involved in the production of alternapyrone. Our study provides a solid platform to identify targets for functional studies that underpin pathogenicity, virulence, and/or quiescence that can be targeted for the development of new control strategies. With these new genomics resources, exploration via omics-based technologies using these isolates will help ascertain the biological underpinnings of their widespread success and observed geographic dominance in specific areas throughout the country.
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Affiliation(s)
- Fatemeh Khodadadi
- Department of Plant Pathology and Microbiology, University of California, Riverside, Riverside, CA 92521, USA;
| | - Dianiris Luciano-Rosario
- Food Quality Laboratory, U.S. Department of Agriculture, Agriculture Research Service, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA; (D.L.-R.)
| | - Christopher Gottschalk
- Appalachian Fruit Research Station, U.S. Department of Agriculture, Agriculture Research Service, Kearneysville, WV 25430, USA;
| | - Wayne M. Jurick
- Food Quality Laboratory, U.S. Department of Agriculture, Agriculture Research Service, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA; (D.L.-R.)
| | - Srđan G. Aćimović
- Alson H. Smith Jr. Agricultural Research and Extension Center, School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Winchester, VA 22602, USA
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Chen D, Song Z, Han J, Liu J, Liu H, Dai J. Targeted Discovery of Glycosylated Natural Products by Tailoring Enzyme-Guided Genome Mining and MS-Based Metabolome Analysis. J Am Chem Soc 2024; 146:9614-9622. [PMID: 38545685 DOI: 10.1021/jacs.3c12895] [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: 04/11/2024]
Abstract
Glycosides make up a biomedically important class of secondary metabolites. Most naturally occurring glycosides were isolated from plants and bacteria; however, the chemical diversity of glycosylated natural products in fungi remains largely unexplored. Herein, we present a paradigm to specifically discover diverse and bioactive glycosylated natural products from fungi by combining tailoring enzyme-guided genome mining with mass spectrometry (MS)-based metabolome analysis. Through in vivo genes deletion and heterologous expression, the first fungal C-glycosyltransferase AuCGT involved in the biosynthesis of stromemycin was identified from Aspergillus ustus. Subsequent homology-based genome mining for fungal glycosyltransferases by using AuCGT as a probe revealed a variety of biosynthetic gene clusters (BGCs) containing its homologues in diverse fungi, of which the glycoside-producing capability was corroborated by high-performance liquid chromatography-mass spectrometry (HPLC-MS) analysis. Consequently, 28 fungal aromatic polyketide C/O-glycosides, including 20 new compounds, were efficiently discovered and isolated from the three selected fungi. Moreover, several novel fungal C/O-glycosyltransferases, especially three novel α-pyrone C-glycosyltransferases, were functionally characterized and verified in the biosynthesis of these glycosides. In addition, a proof of principle for combinatorial biosynthesis was applied to design the production of unnatural glycosides in Aspergillus nidulans. Notably, the newly discovered glycosides exhibited significant antiviral, antibacterial, and antidiabetic activities. Our work demonstrates the promise of tailoring enzyme-guided genome-mining approach for the targeted discovery of fungal glycosides and promotes the exploration of a broader chemical space for natural products with a target structural motif in microbial genomes.
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Affiliation(s)
- Dawei Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs and NHC Key Laboratory of Biosynthesis of Natural Products, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Zhijun Song
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs and NHC Key Laboratory of Biosynthesis of Natural Products, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Junjie Han
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jimei Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs and NHC Key Laboratory of Biosynthesis of Natural Products, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Hongwei Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jungui Dai
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs and NHC Key Laboratory of Biosynthesis of Natural Products, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
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Liang X, Yu W, Meng Y, Shang S, Tian H, Zhang Z, Rollins JA, Zhang R, Sun G. Genome comparisons reveal accessory genes crucial for the evolution of apple Glomerella leaf spot pathogenicity in Colletotrichum fungi. MOLECULAR PLANT PATHOLOGY 2024; 25:e13454. [PMID: 38619507 PMCID: PMC11018114 DOI: 10.1111/mpp.13454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/16/2024]
Abstract
Apple Glomerella leaf spot (GLS) is an emerging fungal disease caused by Colletotrichum fructicola and other Colletotrichum species. These species are polyphyletic and it is currently unknown how these pathogens convergently evolved to infect apple. We generated chromosome-level genome assemblies of a GLS-adapted isolate and a non-adapted isolate in C. fructicola using long-read sequencing. Additionally, we resequenced 17 C. fructicola and C. aenigma isolates varying in GLS pathogenicity using short-read sequencing. Genome comparisons revealed a conserved bipartite genome architecture involving minichromosomes (accessory chromosomes) shared by C. fructicola and other closely related species within the C. gloeosporioides species complex. Moreover, two repeat-rich genomic regions (1.61 Mb in total) were specifically conserved among GLS-pathogenic isolates in C. fructicola and C. aenigma. Single-gene deletion of 10 accessory genes within the GLS-specific regions of C. fructicola identified three that were essential for GLS pathogenicity. These genes encoded a putative non-ribosomal peptide synthetase, a flavin-binding monooxygenase and a small protein with unknown function. These results highlight the crucial role accessory genes play in the evolution of Colletotrichum pathogenicity and imply the significance of an unidentified secondary metabolite in GLS pathogenesis.
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Affiliation(s)
- Xiaofei Liang
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Plant Protection, Northwest A&F UniversityYanglingChina
| | - Wei Yu
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Plant Protection, Northwest A&F UniversityYanglingChina
| | - Yanan Meng
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Plant Protection, Northwest A&F UniversityYanglingChina
| | - Shengping Shang
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Plant Protection, Northwest A&F UniversityYanglingChina
| | - Huanhuan Tian
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Plant Protection, Northwest A&F UniversityYanglingChina
| | - Zhaohui Zhang
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Plant Protection, Northwest A&F UniversityYanglingChina
| | | | - Rong Zhang
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Plant Protection, Northwest A&F UniversityYanglingChina
| | - Guangyu Sun
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Plant Protection, Northwest A&F UniversityYanglingChina
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Lin C, Feng XL, Liu Y, Li ZC, Li XZ, Qi J. Bioinformatic Analysis of Secondary Metabolite Biosynthetic Potential in Pathogenic Fusarium. J Fungi (Basel) 2023; 9:850. [PMID: 37623621 PMCID: PMC10455296 DOI: 10.3390/jof9080850] [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: 07/13/2023] [Revised: 08/11/2023] [Accepted: 08/13/2023] [Indexed: 08/26/2023] Open
Abstract
Fusarium species are among the filamentous fungi with the most pronounced impact on agricultural production and human health. The mycotoxins produced by pathogenic Fusarium not only attack various plants including crops, causing various plant diseases that lead to reduced yields and even death, but also penetrate into the food chain of humans and animals to cause food poisoning and consequent health hazards. Although sporadic studies have revealed some of the biosynthetic pathways of Fusarium toxins, they are insufficient to satisfy the need for a comprehensive understanding of Fusarium toxin production. In this study, we focused on 35 serious pathogenic Fusarium species with available genomes and systematically analyzed the ubiquity of the distribution of identified Fusarium- and non-Fusarium-derived fungal toxin biosynthesis gene clusters (BGCs) in these species through the mining of core genes and the comparative analysis of corresponding BGCs. Additionally, novel sesterterpene synthases and PKS_NRPS clusters were discovered and analyzed. This work is the first to systematically analyze the distribution of related mycotoxin biosynthesis in pathogenic Fusarium species. These findings enhance the knowledge of mycotoxin production and provide a theoretical grounding for the prevention of fungal toxin production using biotechnological approaches.
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Affiliation(s)
- Chao Lin
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Xi-long Feng
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yu Liu
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Zhao-chen Li
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Xiu-Zhang Li
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal and Veterinary Sciences, Qinghai University, Xining 810016, China
| | - Jianzhao Qi
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
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Yang R, Feng J, Xiang H, Cheng B, Shao LD, Li YP, Wang H, Hu QF, Xiao WL, Matsuda Y, Wang WG. Ketoreductase Domain-Catalyzed Polyketide Chain Release in Fungal Alkyl Salicylaldehyde Biosynthesis. J Am Chem Soc 2023; 145:11293-11300. [PMID: 37172192 DOI: 10.1021/jacs.3c02011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Alkyl salicylaldehyde derivatives are polyketide natural products, which are widely distributed in fungi and exhibit great structural diversity. Their biosynthetic mechanisms have recently been intensively studied; however, how the polyketide synthases (PKSs) involved in the fungal alkyl salicylaldehyde biosyntheses release their products remained elusive. In this study, we discovered an orphan biosynthetic gene cluster of salicylaldehyde derivatives in the fungus Stachybotrys sp. g12. Intriguingly, the highly reducing PKS StrA, encoded by the gene cluster, performs a reductive polyketide chain release, although it lacks a C-terminal reductase domain, which is typically required for such a reductive release. Our study revealed that the chain release is achieved by the ketoreductase (KR) domain of StrA, which also conducts cannonical β-keto reductions during polyketide chain elongation. Furthermore, we found that the cupin domain-containing protein StrC plays a critical role in the aromatization reaction. Collectively, we have provided an unprecedented example of a KR domain-catalyzed polyketide chain release and a clearer image of how the salicylaldehyde scaffold is generated in fungi.
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Affiliation(s)
- Run Yang
- Key Laboratory of Natural Products Synthetic Biology of Ethnic Medicinal Endophytes, State Ethnic Affairs Commission, Key Laboratory of Chemistry in Ethnic Medicinal Resources, Ministry of Education, Yunnan Minzu University, Kunming 650031, Yunnan, China
| | - Jian Feng
- Key Laboratory of Natural Products Synthetic Biology of Ethnic Medicinal Endophytes, State Ethnic Affairs Commission, Key Laboratory of Chemistry in Ethnic Medicinal Resources, Ministry of Education, Yunnan Minzu University, Kunming 650031, Yunnan, China
| | - Hao Xiang
- Key Laboratory of Natural Products Synthetic Biology of Ethnic Medicinal Endophytes, State Ethnic Affairs Commission, Key Laboratory of Chemistry in Ethnic Medicinal Resources, Ministry of Education, Yunnan Minzu University, Kunming 650031, Yunnan, China
| | - Bin Cheng
- Key Laboratory of Medicinal Chemistry for Natural Resource of Ministry of Education, Yunnan Characteristic Plant Extraction Laboratory and Yunnan Provincial Center of Natural Products, School of Pharmacy, Yunnan University, Kunming 650091, Yunnan, China
| | - Li-Dong Shao
- Yunnan Key Laboratory of Southern Medicinal Utilization, School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming 650500 Yunnan, China
| | - Yan-Ping Li
- Yunnan Key Laboratory of Southern Medicinal Utilization, School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming 650500 Yunnan, China
| | - Hang Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Qiu-Fen Hu
- Key Laboratory of Natural Products Synthetic Biology of Ethnic Medicinal Endophytes, State Ethnic Affairs Commission, Key Laboratory of Chemistry in Ethnic Medicinal Resources, Ministry of Education, Yunnan Minzu University, Kunming 650031, Yunnan, China
| | - Wei-Lie Xiao
- Key Laboratory of Medicinal Chemistry for Natural Resource of Ministry of Education, Yunnan Characteristic Plant Extraction Laboratory and Yunnan Provincial Center of Natural Products, School of Pharmacy, Yunnan University, Kunming 650091, Yunnan, 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
| | - Wei-Guang Wang
- Key Laboratory of Natural Products Synthetic Biology of Ethnic Medicinal Endophytes, State Ethnic Affairs Commission, Key Laboratory of Chemistry in Ethnic Medicinal Resources, Ministry of Education, Yunnan Minzu University, Kunming 650031, Yunnan, China
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Sayari M, Dolatabadian A, El-Shetehy M, Rehal PK, Daayf F. Genome-Based Analysis of Verticillium Polyketide Synthase Gene Clusters. BIOLOGY 2022; 11:biology11091252. [PMID: 36138731 PMCID: PMC9495618 DOI: 10.3390/biology11091252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Fungi can produce many types of secondary metabolites, including mycotoxins. Poisonous mushrooms and mycotoxins that cause food spoilage have been known for a very long time. For example, Aspergillus flavus, which can grow on grains and nuts, produces highly toxic substances called Aflatoxins. Despite their menace to other living organisms, mycotoxins can be used for medicinal purposes, i.e., as antibiotics, growth-promoting compounds, and other kinds of drugs. These and other secondary metabolites produced by plant-pathogenic fungi may cause host plants to display disease symptoms and may play a substantial role in disease progression. Therefore, the identification and characterization of the genes involved in their biosynthesis are essential for understanding the molecular mechanism involved in their biosynthetic pathways and further promoting sustainable knowledge-based crop production. Abstract Polyketides are structurally diverse and physiologically active secondary metabolites produced by many organisms, including fungi. The biosynthesis of polyketides from acyl-CoA thioesters is catalyzed by polyketide synthases, PKSs. Polyketides play roles including in cell protection against oxidative stress, non-constitutive (toxic) roles in cell membranes, and promoting the survival of the host organisms. The genus Verticillium comprises many species that affect a wide range of organisms including plants, insects, and other fungi. Many are known as causal agents of Verticillium wilt diseases in plants. In this study, a comparative genomics approach involving several Verticillium species led us to evaluate the potential of Verticillium species for producing polyketides and to identify putative polyketide biosynthesis gene clusters. The next step was to characterize them and predict the types of polyketide compounds they might produce. We used publicly available sequences from ten species of Verticillium including V. dahliae, V. longisporum, V. nonalfalfae, V. alfalfae, V. nubilum, V. zaregamsianum, V. klebahnii, V. tricorpus, V. isaacii, and V. albo-atrum to identify and characterize PKS gene clusters by utilizing a range of bioinformatic and phylogenetic approaches. We found 32 putative PKS genes and possible clusters in the genomes of Verticillium species. All the clusters appear to be complete and functional. In addition, at least five clusters including putative DHN-melanin-, cytochalasin-, fusarielien-, fujikurin-, and lijiquinone-like compounds may belong to the active PKS repertoire of Verticillium. These results will pave the way for further functional studies to understand the role of these clusters.
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Affiliation(s)
- Mohammad Sayari
- Department of Plant Science, Faculty of Agricultural and Food Sciences, University of Manitoba, 222 Agriculture Building, Winnipeg, MB R3T 2N2, Canada
| | - Aria Dolatabadian
- Department of Plant Science, Faculty of Agricultural and Food Sciences, University of Manitoba, 222 Agriculture Building, Winnipeg, MB R3T 2N2, Canada
| | - Mohamed El-Shetehy
- Department of Plant Science, Faculty of Agricultural and Food Sciences, University of Manitoba, 222 Agriculture Building, Winnipeg, MB R3T 2N2, Canada
- Department of Botany, Faculty of Science, Tanta University, Tanta 31527, Egypt
| | - Pawanpuneet Kaur Rehal
- Department of Plant Science, Faculty of Agricultural and Food Sciences, University of Manitoba, 222 Agriculture Building, Winnipeg, MB R3T 2N2, Canada
| | - Fouad Daayf
- Department of Plant Science, Faculty of Agricultural and Food Sciences, University of Manitoba, 222 Agriculture Building, Winnipeg, MB R3T 2N2, Canada
- Correspondence:
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Phakeovilay J, Imaram W, Vuttipongchaikij S, Bunnak W, Lazarus CM, Wattana-Amorn P. C-Methylation controls the biosynthetic programming of alternapyrone. Org Biomol Chem 2022; 20:5050-5054. [PMID: 35695066 DOI: 10.1039/d2ob00947a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Alternapyrone is a highly methylated polyene α-pyrone biosynthesised by a highly reducing polyketide synthase. Mutations of the catalytic dyad residues, H1578A/Q and E1604A, of the C-methyltransferase domain resulted in either significantly reduced or no production of alternapyrone, indicating the importance of C-methylation for alternapyrone biosynthesis.
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Affiliation(s)
- Jaiyfungkhong Phakeovilay
- Interdisciplinary Program in Genetic Engineering and Bioinformatics, Graduate School, Kasetsart University, Bangkok, 10900, Thailand.
| | - Witcha Imaram
- Department of Chemistry, Special Research Unit for Advanced Magnetic Resonance and Center of Excellence for Innovation in Chemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | | | - Waraporn Bunnak
- Department of Chemistry, Special Research Unit for Advanced Magnetic Resonance and Center of Excellence for Innovation in Chemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Colin M Lazarus
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Pakorn Wattana-Amorn
- Interdisciplinary Program in Genetic Engineering and Bioinformatics, Graduate School, Kasetsart University, Bangkok, 10900, Thailand. .,Department of Chemistry, Special Research Unit for Advanced Magnetic Resonance and Center of Excellence for Innovation in Chemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
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Williams K, de Mattos-Shipley KMJ, Willis CL, Bailey AM. In silico analyses of maleidride biosynthetic gene clusters. Fungal Biol Biotechnol 2022; 9:2. [PMID: 35177129 PMCID: PMC8851701 DOI: 10.1186/s40694-022-00132-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/23/2022] [Indexed: 01/09/2023] Open
Abstract
Maleidrides are a family of structurally related fungal natural products, many of which possess diverse, potent bioactivities. Previous identification of several maleidride biosynthetic gene clusters, and subsequent experimental work, has determined the 'core' set of genes required to construct the characteristic medium-sized alicyclic ring with maleic anhydride moieties. Through genome mining, this work has used these core genes to discover ten entirely novel putative maleidride biosynthetic gene clusters, amongst both publicly available genomes, and encoded within the genome of the previously un-sequenced epiheveadride producer Wicklowia aquatica CBS 125634. We have undertaken phylogenetic analyses and comparative bioinformatics on all known and putative maleidride biosynthetic gene clusters to gain further insights regarding these unique biosynthetic pathways.
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Affiliation(s)
- Katherine Williams
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Ave, Bristol, BS8 1TQ, UK.
| | - Kate M J de Mattos-Shipley
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Ave, Bristol, BS8 1TQ, UK
| | - Christine L Willis
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Andrew M Bailey
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Ave, Bristol, BS8 1TQ, UK
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10
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Biosynthetic potential of the endophytic fungus Helotiales sp. BL73 revealed via compound identification and genome mining. Appl Environ Microbiol 2022; 88:e0251021. [PMID: 35108081 DOI: 10.1128/aem.02510-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Endophytic fungi have been recognized as prolific producers of chemically diverse secondary metabolites. In this work, we describe a new representative of the order Helotiales isolated from the medicinal plant Bergenia pacumbis. Several bioactive secondary metabolites were produced by this Helotiales sp. BL 73 isolate grown on rice medium, including cochlioquinones and isofusidienols. Sequencing and analysis of the approx. 59 Mb genome revealed at least 77 secondary metabolite biosynthesis gene clusters, several of which could be associated with detected compounds or linked to previously reported molecules. Four terpene synthase genes identified in the BL73 genome were codon-optimized and expressed, together with farnesyl-, geranyl- and geranylgeranyl-pyrophosphate synthases, in Streptomyces spp. Analysis of recombinant strains revealed production of linalool and its oxidized form, terpenoids typically associated with plants, as well as a yet unidentified terpenoid. This study demonstrates the importance of a complex approach to the investigation of the biosynthetic potential of endophytic fungi using both conventional methods and genome mining. Importance Endophytic fungi represent as yet underexplored source of secondary metabolites, some of which may have industrial and medical applications. We isolated a slow-growing fungus belonging to the order Helotiales from the traditional medicinal plant Bergenia pacumbis and characterized its potential to biosynthesize secondary metabolites. We used both cultivation of the isolate with subsequent analysis of compounds produced, bioinformatics-based mining of the genome, and heterologous expression of several terpene synthase genes. Our study revealed enormous potential of this Helotiales isolate to produce structurally diverse natural products, including polyketides, non-ribosomally synthesized peptides, terpenoids and RiPPs. Identification of meroterpenoids and xanthones, along with establishing a link between these molecules and their putative biosynthetic genes sets a stage for investigation of the respective biosynthetic pathways. Heterologous production of terpenoids suggests that this approach can be used for the discovery of new compounds belonging to this chemical class using Streptomyces bacteria as hosts.
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11
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Gao YL, Yu C, Li L. Heterologous expression of a natural product biosynthetic gene cluster from Cordyceps militaris. J Antibiot (Tokyo) 2021; 75:16-20. [PMID: 34548637 DOI: 10.1038/s41429-021-00478-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 07/20/2021] [Accepted: 08/24/2021] [Indexed: 12/22/2022]
Abstract
Cordyceps is a genus of ascomycete fungi widely used in old Chinese medicine, and many investigations have focus on uncovering their biological activities. Until now, only a few compounds have been identified from Cordyceps, mainly due to their poor yield. So as to make full use of Cordyceps, we used the strategy of genome mining and heterologous expression to discover natural products (NPs) from Cordyceps militaris. Analysis of the genome sequence of Cordyceps militaris CM01 showed the presence of a cryptic gene cluster encoding a highly-reducing polyketide synthetase (HR-PKS), enoyl-reductase (ER) and cytochrome P450. Heterologous expression in Aspergillus nidulans enabled the identification of two new polyketides, cordypyrone A and B. Their structures were determined by 1D and 2D NMR techniques. They showed only modest activities against pathogenic bacteria including methicillin-resistant Staphylococcus aureus (MRSA), Mycobacteria tuberculosis and Bacillus cereus.
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Affiliation(s)
- Yang-Le Gao
- Engineering Research Center of Industrial Microbiology, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Cui Yu
- Engineering Research Center of Industrial Microbiology, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Li Li
- Engineering Research Center of Industrial Microbiology, College of Life Sciences, Fujian Normal University, Fuzhou, China.
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12
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Genetic Relationships in the Toxin-Producing Fungal Endophyte, Alternaria oxytropis Using Polyketide Synthase and Non-Ribosomal Peptide Synthase Genes. J Fungi (Basel) 2021; 7:jof7070538. [PMID: 34356917 PMCID: PMC8306250 DOI: 10.3390/jof7070538] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 01/16/2023] Open
Abstract
The legume Oxytropis sericea hosts a fungal endophyte, Alternaria oxytropis, which produces secondary metabolites (SM), including the toxin swainsonine. Polyketide synthase (PKS) and non-ribosomal peptide synthase (NRPS) enzymes are associated with biosynthesis of fungal SM. To better understand the origins of the SM, an unannotated genome of A. oxytropis was assessed for protein sequences similar to known PKS and NRPS enzymes of fungi. Contigs exhibiting identity with known genes were analyzed at nucleotide and protein levels using available databases. Software were used to identify PKS and NRPS domains and predict identity and function. Confirmation of sequence for selected gene sequences was accomplished using PCR. Thirteen PKS, 5 NRPS, and 4 PKS-NRPS hybrids were identified and characterized with functions including swainsonine and melanin biosynthesis. Phylogenetic relationships among closest amino acid matches with Alternaria spp. were identified for seven highly conserved PKS and NRPS, including melanin synthesis. Three PKS and NRPS were most closely related to other fungi within the Pleosporaceae family, while five PKS and PKS-NRPS were closely related to fungi in the Pleosporales order. However, seven PKS and PKS-NRPS showed no identity with fungi in the Pleosporales or the class Dothideomycetes, suggesting a different evolutionary origin for those genes.
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13
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Gluck-Thaler E, Haridas S, Binder M, Grigoriev IV, Crous PW, Spatafora JW, Bushley K, Slot JC. The Architecture of Metabolism Maximizes Biosynthetic Diversity in the Largest Class of Fungi. Mol Biol Evol 2021; 37:2838-2856. [PMID: 32421770 PMCID: PMC7530617 DOI: 10.1093/molbev/msaa122] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Ecological diversity in fungi is largely defined by metabolic traits, including the ability to produce secondary or “specialized” metabolites (SMs) that mediate interactions with other organisms. Fungal SM pathways are frequently encoded in biosynthetic gene clusters (BGCs), which facilitate the identification and characterization of metabolic pathways. Variation in BGC composition reflects the diversity of their SM products. Recent studies have documented surprising diversity of BGC repertoires among isolates of the same fungal species, yet little is known about how this population-level variation is inherited across macroevolutionary timescales. Here, we applied a novel linkage-based algorithm to reveal previously unexplored dimensions of diversity in BGC composition, distribution, and repertoire across 101 species of Dothideomycetes, which are considered the most phylogenetically diverse class of fungi and known to produce many SMs. We predicted both complementary and overlapping sets of clustered genes compared with existing methods and identified novel gene pairs that associate with known secondary metabolite genes. We found that variation among sets of BGCs in individual genomes is due to nonoverlapping BGC combinations and that several BGCs have biased ecological distributions, consistent with niche-specific selection. We observed that total BGC diversity scales linearly with increasing repertoire size, suggesting that secondary metabolites have little structural redundancy in individual fungi. We project that there is substantial unsampled BGC diversity across specific families of Dothideomycetes, which will provide a roadmap for future sampling efforts. Our approach and findings lend new insight into how BGC diversity is generated and maintained across an entire fungal taxonomic class.
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Affiliation(s)
- Emile Gluck-Thaler
- Department of Plant Pathology, The Ohio State University, Columbus, OH.,Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA
| | - Sajeet Haridas
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA
| | | | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA
| | - Pedro W Crous
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR
| | - Kathryn Bushley
- Department of Plant and Microbial Biology, University of Minnesota, Minneapolis, MN
| | - Jason C Slot
- Department of Plant Pathology, The Ohio State University, Columbus, OH
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14
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Seibold PS, Lenz C, Gressler M, Hoffmeister D. The Laetiporus polyketide synthase LpaA produces a series of antifungal polyenes. J Antibiot (Tokyo) 2020; 73:711-720. [PMID: 32820242 PMCID: PMC7473843 DOI: 10.1038/s41429-020-00362-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/19/2020] [Accepted: 07/21/2020] [Indexed: 01/20/2023]
Abstract
The conspicuous bright golden to orange-reddish coloration of species of the basidiomycete genus Laetiporus is a hallmark feature of their fruiting bodies, known among mushroom hunters as the "chicken of the woods". This report describes the identification of an eight-domain mono-modular highly reducing polyketide synthase as sole enzyme necessary for laetiporic acid biosynthesis. Heterologous pathway reconstitution in both Aspergillus nidulans and Aspergillus niger verified that LpaA functions as a multi-chain length polyene synthase, which produces a cocktail of laetiporic acids with a methyl-branched C26-C32 main chain. Laetiporic acids show a marked antifungal activity on Aspergillus protoplasts. Given the multiple products of a single biosynthesis enzyme, our work underscores the diversity-oriented character of basidiomycete natural product biosynthesis.
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Affiliation(s)
| | - Claudius Lenz
- Pharmaceutical Microbiology, Friedrich Schiller University, Jena, Germany
| | - Markus Gressler
- Pharmaceutical Microbiology, Friedrich Schiller University, Jena, Germany
| | - Dirk Hoffmeister
- Pharmaceutical Microbiology, Friedrich Schiller University, Jena, Germany.
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15
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Genetic localization of the orevactaene/epipyrone biosynthetic gene cluster in Epicoccum nigrum. Bioorg Med Chem Lett 2020; 30:127242. [DOI: 10.1016/j.bmcl.2020.127242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/01/2020] [Accepted: 05/01/2020] [Indexed: 10/24/2022]
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16
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Moolhuijzen PM, Muria-Gonzalez MJ, Syme R, Rawlinson C, See PT, Moffat CS, Ellwood SR. Expansion and Conservation of Biosynthetic Gene Clusters in Pathogenic Pyrenophora spp. Toxins (Basel) 2020; 12:toxins12040242. [PMID: 32283749 PMCID: PMC7232245 DOI: 10.3390/toxins12040242] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/02/2020] [Accepted: 04/04/2020] [Indexed: 12/28/2022] Open
Abstract
Pyrenophora is a fungal genus responsible for a number of major cereal diseases. Although fungi produce many specialised or secondary metabolites for defence and interacting with the surrounding environment, the repertoire of specialised metabolites (SM) within Pyrenophora pathogenic species remains mostly uncharted. In this study, an in-depth comparative analysis of the P. teres f. teres, P teres f. maculata and P. tritici-repentis potential to produce SMs, based on in silico predicted biosynthetic gene clusters (BGCs), was conducted using genome assemblies from PacBio DNA reads. Conservation of BGCs between the Pyrenophora species included type I polyketide synthases, terpene synthases and the first reporting of a type III polyketide synthase in P teres f. maculata. P. teres isolates exhibited substantial expansion of non-ribosomal peptide synthases relative to P. tritici-repentis, hallmarked by the presence of tailoring cis-acting nitrogen methyltransferase domains. P. teres isolates also possessed unique non-ribosomal peptide synthase (NRPS)-indole and indole BGCs, while a P. tritici-repentis phytotoxin BGC for triticone production was absent in P. teres. These differences highlight diversification between the pathogens that reflects their different evolutionary histories, host adaption and lifestyles.
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Affiliation(s)
- Paula M. Moolhuijzen
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, WA 6102, Australia
- Correspondence:
| | - Mariano Jordi Muria-Gonzalez
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, WA 6102, Australia
| | - Robert Syme
- Canadian Centre for Computational Genomics, McGill University and Genome Quebec Innovation Center, Montréal, QC H3A 0G1, Canada
| | - Catherine Rawlinson
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, WA 6102, Australia
| | - Pao Theen See
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, WA 6102, Australia
| | - Caroline S. Moffat
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, WA 6102, Australia
| | - Simon R. Ellwood
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, WA 6102, Australia
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17
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Fujii I, Hashimoto M, Konishi K, Unezawa A, Sakuraba H, Suzuki K, Tsushima H, Iwasaki M, Yoshida S, Kudo A, Fujita R, Hichiwa A, Saito K, Asano T, Ishikawa J, Wakana D, Goda Y, Watanabe A, Watanabe M, Masumoto Y, Kanazawa J, Sato H, Uchiyama M. Shimalactone Biosynthesis Involves Spontaneous Double Bicyclo-Ring Formation with 8π-6π Electrocyclization. Angew Chem Int Ed Engl 2020; 59:8464-8470. [PMID: 32129542 DOI: 10.1002/anie.202001024] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/25/2020] [Indexed: 11/08/2022]
Abstract
Shimalactones A and B are neuritogenic polyketides possessing characteristic oxabicyclo[2.2.1]heptane and bicyclo[4.2.0]octadiene ring systems that are produced by the marine fungus Emericella variecolor GF10. We identified a candidate biosynthetic gene cluster and conducted heterologous expression analysis. Expression of ShmA polyketide synthase in Aspergillus oryzae resulted in the production of preshimalactone. Aspergillus oryzae and Saccharomyces cerevisiae transformants expressing ShmA and ShmB produced shimalactones A and B, thus suggesting that the double bicyclo-ring formation reactions proceed non-enzymatically from preshimalactone epoxide. DFT calculations strongly support the idea that oxabicyclo-ring formation and 8π-6π electrocyclization proceed spontaneously after opening of the preshimalactone epoxide ring through protonation. We confirmed the formation of preshimalactone epoxide in vitro, followed by its non-enzymatic conversion to shimalactones in the dark.
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Affiliation(s)
- Isao Fujii
- Division of Natural Product Sciences, School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Makoto Hashimoto
- Division of Natural Product Sciences, School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate, 028-3694, Japan.,Current address: Research Institute of Pharmaceutical Sciences, Musashino University, 1-1-20 Shinmachi, Nishitokyo-shi, Tokyo, 202-8585, Japan
| | - Kaori Konishi
- Division of Natural Product Sciences, School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Akiko Unezawa
- Division of Natural Product Sciences, School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Haruka Sakuraba
- Division of Natural Product Sciences, School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Kenta Suzuki
- Division of Natural Product Sciences, School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Harue Tsushima
- Division of Natural Product Sciences, School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Miho Iwasaki
- Division of Natural Product Sciences, School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Satsuki Yoshida
- Division of Natural Product Sciences, School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Akane Kudo
- Division of Natural Product Sciences, School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Rina Fujita
- Division of Natural Product Sciences, School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Aika Hichiwa
- Division of Natural Product Sciences, School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Koharu Saito
- Division of Natural Product Sciences, School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Takashi Asano
- Division of Natural Product Sciences, School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Jun Ishikawa
- Department of Bioactive Molecules, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Daigo Wakana
- National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kanagawa, 210-9501, Japan.,Current address: Department of Organic Chemistry, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan
| | - Yukihiro Goda
- National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kanagawa, 210-9501, Japan
| | - Ayumi Watanabe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Mamoru Watanabe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yui Masumoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Junichiro Kanazawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hajime Sato
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Cluster for Pioneering Research (CPR), Advanced Elements Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
| | - Masanobu Uchiyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Cluster for Pioneering Research (CPR), Advanced Elements Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
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18
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Fujii I, Hashimoto M, Konishi K, Unezawa A, Sakuraba H, Suzuki K, Tsushima H, Iwasaki M, Yoshida S, Kudo A, Fujita R, Hichiwa A, Saito K, Asano T, Ishikawa J, Wakana D, Goda Y, Watanabe A, Watanabe M, Masumoto Y, Kanazawa J, Sato H, Uchiyama M. Shimalactone Biosynthesis Involves Spontaneous Double Bicyclo‐Ring Formation with 8π‐6π Electrocyclization. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Isao Fujii
- Division of Natural Product Sciences School of Pharmacy Iwate Medical University 1-1-1 Idaidori Yahaba Iwate 028-3694 Japan
| | - Makoto Hashimoto
- Division of Natural Product Sciences School of Pharmacy Iwate Medical University 1-1-1 Idaidori Yahaba Iwate 028-3694 Japan
- Current address: Research Institute of Pharmaceutical Sciences Musashino University 1-1-20 Shinmachi, Nishitokyo-shi Tokyo 202-8585 Japan
| | - Kaori Konishi
- Division of Natural Product Sciences School of Pharmacy Iwate Medical University 1-1-1 Idaidori Yahaba Iwate 028-3694 Japan
| | - Akiko Unezawa
- Division of Natural Product Sciences School of Pharmacy Iwate Medical University 1-1-1 Idaidori Yahaba Iwate 028-3694 Japan
| | - Haruka Sakuraba
- Division of Natural Product Sciences School of Pharmacy Iwate Medical University 1-1-1 Idaidori Yahaba Iwate 028-3694 Japan
| | - Kenta Suzuki
- Division of Natural Product Sciences School of Pharmacy Iwate Medical University 1-1-1 Idaidori Yahaba Iwate 028-3694 Japan
| | - Harue Tsushima
- Division of Natural Product Sciences School of Pharmacy Iwate Medical University 1-1-1 Idaidori Yahaba Iwate 028-3694 Japan
| | - Miho Iwasaki
- Division of Natural Product Sciences School of Pharmacy Iwate Medical University 1-1-1 Idaidori Yahaba Iwate 028-3694 Japan
| | - Satsuki Yoshida
- Division of Natural Product Sciences School of Pharmacy Iwate Medical University 1-1-1 Idaidori Yahaba Iwate 028-3694 Japan
| | - Akane Kudo
- Division of Natural Product Sciences School of Pharmacy Iwate Medical University 1-1-1 Idaidori Yahaba Iwate 028-3694 Japan
| | - Rina Fujita
- Division of Natural Product Sciences School of Pharmacy Iwate Medical University 1-1-1 Idaidori Yahaba Iwate 028-3694 Japan
| | - Aika Hichiwa
- Division of Natural Product Sciences School of Pharmacy Iwate Medical University 1-1-1 Idaidori Yahaba Iwate 028-3694 Japan
| | - Koharu Saito
- Division of Natural Product Sciences School of Pharmacy Iwate Medical University 1-1-1 Idaidori Yahaba Iwate 028-3694 Japan
| | - Takashi Asano
- Division of Natural Product Sciences School of Pharmacy Iwate Medical University 1-1-1 Idaidori Yahaba Iwate 028-3694 Japan
| | - Jun Ishikawa
- Department of Bioactive Molecules National Institute of Infectious Diseases 1-23-1 Toyama, Shinjuku-ku Tokyo 162-8640 Japan
| | - Daigo Wakana
- National Institute of Health Sciences 3-25-26 Tonomachi, Kawasaki-ku Kanagawa 210-9501 Japan
- Current address: Department of Organic Chemistry Hoshi University 2-4-41 Ebara, Shinagawa-ku Tokyo 142-8501 Japan
| | - Yukihiro Goda
- National Institute of Health Sciences 3-25-26 Tonomachi, Kawasaki-ku Kanagawa 210-9501 Japan
| | - Ayumi Watanabe
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Mamoru Watanabe
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Yui Masumoto
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Junichiro Kanazawa
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Hajime Sato
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
- Cluster for Pioneering Research (CPR) Advanced Elements Chemistry Laboratory RIKEN 2-1 Hirosawa Wako-shi Saitama 351-0198 Japan
| | - Masanobu Uchiyama
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
- Cluster for Pioneering Research (CPR) Advanced Elements Chemistry Laboratory RIKEN 2-1 Hirosawa Wako-shi Saitama 351-0198 Japan
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19
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Oikawa H. Reconstitution of biosynthetic machinery of fungal natural products in heterologous hosts. Biosci Biotechnol Biochem 2020; 84:433-444. [DOI: 10.1080/09168451.2019.1690976] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
ABSTRACT
Ascomycota and basidiomycota fungi are prolific sources of biologically active natural products. Recent genomic data and bioinformatic analysis indicate that fungi possess a large number of biosynthetic gene clusters for bioactive natural products but more than 90% are silent. Heterologous expression in the filamentous fungi as hosts is one of the powerful tools to expression of the silent gene clusters. This review introduces recent studies on the total biosynthesis of representative family members via common platform intermediates, genome mining of novel di- and sesterterpenoids including detailed cyclization pathway, and development of expression host for basidiomycota genes with efficient genome editing method. In addition, this review will discuss the several strategies, for the generation of structural diversity, which are found through these studies.
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Affiliation(s)
- Hideaki Oikawa
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
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20
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Wang M, Liu B, Ruan R, Zeng Y, Luo J, Li H. Genomic Sequencing of Phyllosticta citriasiana Provides Insight Into Its Conservation and Diversification With Two Closely Related Phyllosticta Species Associated With Citrus. Front Microbiol 2020; 10:2979. [PMID: 31998266 PMCID: PMC6965161 DOI: 10.3389/fmicb.2019.02979] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 12/10/2019] [Indexed: 11/25/2022] Open
Abstract
Phyllosticta capitalensis, Phyllosticta citricarpa, and Phyllosticta citriasiana are three very important Phyllosticta species associated with citrus. P. capitalensis is an endophyte fungus of citrus while P. citricarpa can cause black spot of citrus (e.g., oranges and mandarins). P. citriasiana was identified recently which is the causal agent of the pomelo tan spot. Here, we present the ∼34 Mb genome of P. citriasiana. The genome is organized in 92 contigs, encompassing 9202 predicted genes. Comparative genomic analyses with two other Phyllosticta species (P. citricarpa and P. capitalensis) associated with citrus was conducted to understand their evolutionary conservation and diversification. Pair-wise genome alignments revealed that these species are highly syntenic. All species encode similar numbers of CAZymes and secreted proteins. However, the molecular functions of the secretome showed that each species contains some enzymes with distinct activities. The three Phyllosticta species investigated shared a core set of 7261 protein families. P. capitalensis had the largest set of orphan genes (1991), in complete contrast to that of P. citriasiana (364) and P. citricarpa (262). Most of the orphan genes are functionally unknown, but they contain a certain number of species-specific secreted proteins. A total of 23 secondary metabolites biosynthesis clusters were identified in the three Phyllosticta species, 21 of them being highly conserved among these species while the remaining two showed whole cluster gain and loss polymorphisms or gene content polymorphisms. Taken together, our study reveals insights into the genetic mechanisms of host adaptation of three species of Phyllosticta associated with citrus and paves the way to identify effectors that function in infection of citrus plants.
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Affiliation(s)
- Mingshuang Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Bei Liu
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Ruoxin Ruan
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Yibing Zeng
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Jinshui Luo
- Fujian Institute of Tropical Crops, Zhangzhou, China
| | - Hongye Li
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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OIKAWA H. Heterologous production of fungal natural products: Reconstitution of biosynthetic gene clusters in model host Aspergillus oryzae. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2020; 96:420-430. [PMID: 33177296 PMCID: PMC7725655 DOI: 10.2183/pjab.96.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
While exploring phytotoxic metabolites from phytopathogenic fungi in the 1970s, we became interested in biosynthetic enzymes that catalyze Diels-Alder reactions involving biosynthesis of several phytotoxins that we isolated. Target enzymes were successfully characterized, and this triggered the identification of various Diels-Alderases in a recent decade. Through our Diels-Alderase project in 1990s, we recognized a highly efficient expression system of various biosynthetic genes with Aspergillus oryzae as a host. With the development of tools such as genomic data and bioinformatics analysis to identify biosynthetic gene clusters for natural products, we developed a highly reliable methodology such as hot spot knock-in to elucidate the biosynthetic pathways of representative fungal metabolites including phytotoxic substances. This methodology allows total biosynthesis of natural products and genome mining using silent biosynthetic gene clusters to obtain novel bioactive metabolites. Further applications of this technology are discussed.
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Affiliation(s)
- Hideaki OIKAWA
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Hokkaido, Japan
- Correspondence should be addressed: H. Oikawa, Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10 Jo Nishi 8-Chome, Kita-ku, Sapporo 060-0810, Japan (e-mail: )
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Phytotoxic Metabolites Produced by Legume-Associated Ascochyta and Its Related Genera in the Dothideomycetes. Toxins (Basel) 2019; 11:toxins11110627. [PMID: 31671808 PMCID: PMC6891577 DOI: 10.3390/toxins11110627] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/27/2019] [Accepted: 10/28/2019] [Indexed: 12/20/2022] Open
Abstract
Phytotoxins, secondary metabolites toxic to plants and produced by fungi, are believed to play an important role in disease development by targeting host cellular machineries and/or interfering with host immune responses. The Ascochyta blight diseases on different legume plants are caused by Ascochyta and related taxa, such as Phoma. The causal agents of the Ascochyta blight are often associated with specific legume plants, showing a relatively narrow host range. The legume-associated Ascochyta and Phoma are known to produce a diverse array of polyketide-derived secondary metabolites, many of which exhibited significant phytotoxicity and have been claimed as virulence or pathogenicity factors. In this article, we reviewed the current state of knowledge on the diversity and biological activities of the phytotoxic compounds produced by Ascochyta and Phoma species. Also, we touched on the secondary metabolite biosynthesis gene clusters identified thus far and discussed the role of metabolites in the fungal biology.
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Hashimoto M, Ichijo H, Fujiwara K, Sugasawa H, Abo S, Matsudo K, Uchiyama N, Goda Y, Fujii I. Functional expression of a highly-reducing polyketide synthase of Emericella variecolor IFM42010, an asteltoxin-producing strain, resulted in production of two polyenoic β-ketolactones with opposite stereochemistry. Bioorg Med Chem Lett 2019; 29:126686. [PMID: 31678008 DOI: 10.1016/j.bmcl.2019.126686] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/05/2019] [Accepted: 09/13/2019] [Indexed: 02/06/2023]
Abstract
The asteltoxin-producing fungus Emericella variecolor IFM42010 possesses 22 highly-reducing polyketide synthase (HR-PKS) genes. Of these, an HR-PKS with a methyltransferase domain but lacking an enoylreductase domain could be involved in the biosynthesis of asteltoxin and related compounds. From six such candidate HR-PKS genes, Ev460pks was analyzed by gene disruption in E. variecolor and heterologous expression in Aspergillus oryzae. The Ev460pks-disrupted strain retained asteltoxin production ability, indicating that Ev460pks is not involved in asteltoxin biosynthesis. The A. oryzae transformant harboring the Ev460pks gene produced compounds 1 and 2, along with several unidentified products possibly decomposed from 2. Spectroscopic analyses revealed that 1 was a 4-methyl-β-ketolactone with a methylheptatriene side-chain at the C-5 position, and 2 was also a 4-methyl-β-ketolactone, bearing a dimethyltetradecahexaene side-chain at the same position. The relative configuration at C-4 in compounds 1 and 2 was opposite.
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Affiliation(s)
- Makoto Hashimoto
- School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate 028-3694, Japan; Research Institute of Pharmaceutical Sciences, Musashino University, 1-1-20, Shinmachi, Nishitokyo, Tokyo 202-8585, Japan.
| | - Hitomi Ichijo
- School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate 028-3694, Japan
| | - Kotaro Fujiwara
- School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate 028-3694, Japan
| | - Hitoshi Sugasawa
- School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate 028-3694, Japan
| | - Seika Abo
- School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate 028-3694, Japan
| | - Kimihito Matsudo
- School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate 028-3694, Japan
| | - Nahoko Uchiyama
- National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, Kanagawa 210-9501, Japan
| | - Yukihiro Goda
- National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, Kanagawa 210-9501, Japan
| | - Isao Fujii
- School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate 028-3694, Japan.
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Kishimoto S, Tsunematsu Y, Matsushita T, Hara K, Hashimoto H, Tang Y, Watanabe K. Functional and Structural Analyses of trans C-Methyltransferase in Fungal Polyketide Biosynthesis. Biochemistry 2019; 58:3933-3937. [DOI: 10.1021/acs.biochem.9b00702] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Shinji Kishimoto
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Yuta Tsunematsu
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Takuma Matsushita
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Kodai Hara
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Hiroshi Hashimoto
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - 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
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
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Noar RD, Thomas E, Xie DY, Carter ME, Ma D, Daub ME. A polyketide synthase gene cluster associated with the sexual reproductive cycle of the banana pathogen, Pseudocercospora fijiensis. PLoS One 2019; 14:e0220319. [PMID: 31344104 PMCID: PMC6657885 DOI: 10.1371/journal.pone.0220319] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 07/12/2019] [Indexed: 11/19/2022] Open
Abstract
Disease spread of Pseudocercospora fijiensis, causal agent of the black Sigatoka disease of banana, depends on ascospores produced through the sexual reproductive cycle. We used phylogenetic analysis to identify P. fijiensis homologs (PKS8-4 and Hybrid8-3) to the PKS4 polyketide synthases (PKS) from Neurospora crassa and Sordaria macrospora involved in sexual reproduction. These sequences also formed a clade with lovastatin, compactin, and betaenone-producing PKS sequences. Transcriptome analysis showed that both the P. fijiensis Hybrid8-3 and PKS8-4 genes have higher expression in infected leaf tissue compared to in culture. Domain analysis showed that PKS8-4 is more similar than Hybrid8-3 to PKS4. pPKS8-4:GFP transcriptional fusion transformants showed expression of GFP in flask-shaped structures in mycelial cultures as well as in crosses between compatible and incompatible mating types. Confocal microscopy confirmed expression in spermagonia in leaf substomatal cavities, consistent with a role in sexual reproduction. A disruption mutant of pks8-4 retained normal pathogenicity on banana, and no differences were observed in growth, conidial production, and spermagonia production. GC-MS profiling of the mutant and wild type did not identify differences in polyketide metabolites, but did identify changes in saturated fatty acid methyl esters and alkene and alkane derivatives. To our knowledge, this is the first report of a polyketide synthase pathway associated with spermagonia.
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Affiliation(s)
- Roslyn D. Noar
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, United States of America
| | - Elizabeth Thomas
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States of America
| | - De-Yu Xie
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States of America
| | - Morgan E. Carter
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States of America
| | - Dongming Ma
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States of America
| | - Margaret E. Daub
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States of America
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Li H, Hu J, Wei H, Solomon PS, Vuong D, Lacey E, Stubbs KA, Piggott AM, Chooi YH. Chemical Ecogenomics-Guided Discovery of Phytotoxic α-Pyrones from the Fungal Wheat Pathogen Parastagonospora nodorum. Org Lett 2018; 20:6148-6152. [DOI: 10.1021/acs.orglett.8b02617] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Hang Li
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Jinyu Hu
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Haochen Wei
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Peter S. Solomon
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Daniel Vuong
- Microbial Screening Technologies Pty Ltd, Smithfield, NSW 2164, Australia
| | - Ernest Lacey
- Microbial Screening Technologies Pty Ltd, Smithfield, NSW 2164, Australia
| | - Keith A. Stubbs
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Andrew M. Piggott
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
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He Y, Wang B, Chen W, Cox RJ, He J, Chen F. Recent advances in reconstructing microbial secondary metabolites biosynthesis in Aspergillus spp. Biotechnol Adv 2018; 36:739-783. [DOI: 10.1016/j.biotechadv.2018.02.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 01/30/2018] [Accepted: 02/01/2018] [Indexed: 11/28/2022]
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Medina FE, Neves RPP, Ramos MJ, Fernandes PA. A QM/MM study of the reaction mechanism of human β-ketoacyl reductase. Phys Chem Chem Phys 2018; 19:347-355. [PMID: 27905606 DOI: 10.1039/c6cp07014k] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Human fatty acid synthase (hFAS) is a multifunctional enzyme involved in a wide diversity of biological functions. For instance, it is a precursor of phospholipids and other complex processes such as the de novo synthesis of long chain fatty acid. Human FAS is also a component of biological membranes and it is implicated in the overexpression of several types of cancers. In this work, we describe the catalytic mechanism of β-ketoreductase (KR), which is a catalytic domain of the hFAS enzyme that catalyzes the reduction of β-ketoacyl to β-hydroxyacyl with the concomitant oxidation of the NADPH cofactor. The catalysis by KR is an intermediate step in the cycle of reactions that elongate the substrate's carbon chain until the final product is obtained. We study and propose the catalytic mechanism of the KR domain determined using the hybrid QM/MM methodology, at the ONIOM(B3LYP/6-311+G(2d,2p):AMBER) level of theory. The results indicate that the reaction mechanism occurs in two stages: (i) nucleophilic attack by a NADPH hydride to the β-carbon of the substrate, together with an asynchronous deprotonation of the Tyr2034 by the oxygen of the β-alkoxide to hold the final alcohol product; and (ii) an asynchronous deprotonation of the hydroxyl in the NADP+'s ribose by Tyr2034, and of the Lys1995 by the resulting alkoxide in the former ribose to restore the protonation state of Tyr2034. The reduction step occurs with a Gibbs energy barrier of 11.7 kcal mol-1 and a Gibbs reaction energy of -10.6 kcal mol-1. These results have provided an understanding of the catalytic mechanism of the KR hFAS domain, a piece of the heavy hFAS biosynthetic machinery.
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Affiliation(s)
- Fabiola E Medina
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.
| | - Rui P P Neves
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.
| | - Maria J Ramos
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.
| | - Pedro A Fernandes
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.
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29
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Zaccaron AZ, Bluhm BH. The genome sequence of Bipolaris cookei reveals mechanisms of pathogenesis underlying target leaf spot of sorghum. Sci Rep 2017; 7:17217. [PMID: 29222463 PMCID: PMC5722872 DOI: 10.1038/s41598-017-17476-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 11/24/2017] [Indexed: 11/23/2022] Open
Abstract
Bipolaris cookei (=Bipolaris sorghicola) causes target leaf spot, one of the most prevalent foliar diseases of sorghum. Little is known about the molecular basis of pathogenesis in B. cookei, in large part due to a paucity of resources for molecular genetics, such as a reference genome. Here, a draft genome sequence of B. cookei was obtained and analyzed. A hybrid assembly strategy utilizing Illumina and Pacific Biosciences sequencing technologies produced a draft nuclear genome of 36.1 Mb, organized into 321 scaffolds with L50 of 31 and N50 of 378 kb, from which 11,189 genes were predicted. Additionally, a finished mitochondrial genome sequence of 135,790 bp was obtained, which contained 75 predicted genes. Comparative genomics revealed that B. cookei possessed substantially fewer carbohydrate-active enzymes and secreted proteins than closely related Bipolaris species. Novel genes involved in secondary metabolism, including genes implicated in ophiobolin biosynthesis, were identified. Among 37 B. cookei genes induced during sorghum infection, one encodes a putative effector with a limited taxonomic distribution among plant pathogenic fungi. The draft genome sequence of B. cookei provided novel insights into target leaf spot of sorghum and is an important resource for future investigation.
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Affiliation(s)
- Alex Z Zaccaron
- Department of Plant Pathology, University of Arkansas, Division of Agriculture, Fayetteville, AR, 72701, USA
| | - Burton H Bluhm
- Department of Plant Pathology, University of Arkansas, Division of Agriculture, Fayetteville, AR, 72701, USA.
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30
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Zaccaron AZ, Woloshuk CP, Bluhm BH. Comparative genomics of maize ear rot pathogens reveals expansion of carbohydrate-active enzymes and secondary metabolism backbone genes in Stenocarpella maydis. Fungal Biol 2017; 121:966-983. [PMID: 29029703 DOI: 10.1016/j.funbio.2017.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 08/15/2017] [Accepted: 08/18/2017] [Indexed: 12/11/2022]
Abstract
Stenocarpella maydis is a plant pathogenic fungus that causes Diplodia ear rot, one of the most destructive diseases of maize. To date, little information is available regarding the molecular basis of pathogenesis in this organism, in part due to limited genomic resources. In this study, a 54.8 Mb draft genome assembly of S. maydis was obtained with Illumina and PacBio sequencing technologies, and analyzed. Comparative genomic analyses with the predominant maize ear rot pathogens Aspergillus flavus, Fusarium verticillioides, and Fusarium graminearum revealed an expanded set of carbohydrate-active enzymes for cellulose and hemicellulose degradation in S. maydis. Analyses of predicted genes involved in starch degradation revealed six putative α-amylases, four extracellular and two intracellular, and two putative γ-amylases, one of which appears to have been acquired from bacteria via horizontal transfer. Additionally, 87 backbone genes involved in secondary metabolism were identified, which represents one of the largest known assemblages among Pezizomycotina species. Numerous secondary metabolite gene clusters were identified, including two clusters likely involved in the biosynthesis of diplodiatoxin and chaetoglobosins. The draft genome of S. maydis presented here will serve as a useful resource for molecular genetics, functional genomics, and analyses of population diversity in this organism.
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Affiliation(s)
- Alex Z Zaccaron
- Department of Plant Pathology, University of Arkansas, Division of Agriculture, Fayetteville, AR 72701, USA
| | - Charles P Woloshuk
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, USA
| | - Burton H Bluhm
- Department of Plant Pathology, University of Arkansas, Division of Agriculture, Fayetteville, AR 72701, USA.
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Dallery JF, Lapalu N, Zampounis A, Pigné S, Luyten I, Amselem J, Wittenberg AHJ, Zhou S, de Queiroz MV, Robin GP, Auger A, Hainaut M, Henrissat B, Kim KT, Lee YH, Lespinet O, Schwartz DC, Thon MR, O’Connell RJ. Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters. BMC Genomics 2017; 18:667. [PMID: 28851275 PMCID: PMC5576322 DOI: 10.1186/s12864-017-4083-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 08/21/2017] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND The ascomycete fungus Colletotrichum higginsianum causes anthracnose disease of brassica crops and the model plant Arabidopsis thaliana. Previous versions of the genome sequence were highly fragmented, causing errors in the prediction of protein-coding genes and preventing the analysis of repetitive sequences and genome architecture. RESULTS Here, we re-sequenced the genome using single-molecule real-time (SMRT) sequencing technology and, in combination with optical map data, this provided a gapless assembly of all twelve chromosomes except for the ribosomal DNA repeat cluster on chromosome 7. The more accurate gene annotation made possible by this new assembly revealed a large repertoire of secondary metabolism (SM) key genes (89) and putative biosynthetic pathways (77 SM gene clusters). The two mini-chromosomes differed from the ten core chromosomes in being repeat- and AT-rich and gene-poor but were significantly enriched with genes encoding putative secreted effector proteins. Transposable elements (TEs) were found to occupy 7% of the genome by length. Certain TE families showed a statistically significant association with effector genes and SM cluster genes and were transcriptionally active at particular stages of fungal development. All 24 subtelomeres were found to contain one of three highly-conserved repeat elements which, by providing sites for homologous recombination, were probably instrumental in four segmental duplications. CONCLUSION The gapless genome of C. higginsianum provides access to repeat-rich regions that were previously poorly assembled, notably the mini-chromosomes and subtelomeres, and allowed prediction of the complete SM gene repertoire. It also provides insights into the potential role of TEs in gene and genome evolution and host adaptation in this asexual pathogen.
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Affiliation(s)
- Jean-Félix Dallery
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Nicolas Lapalu
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Antonios Zampounis
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
- Present Address: Department of Deciduous Fruit Trees, Institute of Plant Breeding and Plant Genetic Resources, Hellenic Agricultural Organization ‘Demeter’, Naoussa, Greece
| | - Sandrine Pigné
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | | | | | | | - Shiguo Zhou
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin USA
| | - Marisa V. de Queiroz
- Laboratório de Genética Molecular de Fungos, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Guillaume P. Robin
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Annie Auger
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Matthieu Hainaut
- CNRS UMR 7257, Aix-Marseille University, Marseille, France
- INRA, USC 1408 AFMB, Marseille, France
| | - Bernard Henrissat
- CNRS UMR 7257, Aix-Marseille University, Marseille, France
- INRA, USC 1408 AFMB, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ki-Tae Kim
- Department of Agricultural Biotechnology, Center for Fungal Genetic Resources, Seoul National University, Seoul, Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Center for Fungal Genetic Resources, Seoul National University, Seoul, Korea
| | - Olivier Lespinet
- Laboratoire de Recherche en Informatique, CNRS, Université Paris-Sud, Orsay, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Orsay, France
| | - David C. Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin USA
| | - Michael R. Thon
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Richard J. O’Connell
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
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Brandt P, García-Altares M, Nett M, Hertweck C, Hoffmeister D. Induced Chemical Defense of a Mushroom by a Double-Bond-Shifting Polyene Synthase. Angew Chem Int Ed Engl 2017; 56:5937-5941. [DOI: 10.1002/anie.201700767] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Philip Brandt
- Department Pharmaceutical Microbiology at the Hans Knöll Institute; Friedrich-Schiller-Universität; Winzerlaer Strasse 2 07745 Jena Germany
| | - María García-Altares
- Department Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology; Beutenbergstrasse 11a 07745 Jena Germany
| | - Markus Nett
- Department of Biochemical and Chemical Engineering; Technical University Dortmund; Emil-Figge-Strasse 66 44227 Dortmund Germany
| | - Christian Hertweck
- Department Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology; Beutenbergstrasse 11a 07745 Jena Germany
| | - Dirk Hoffmeister
- Department Pharmaceutical Microbiology at the Hans Knöll Institute; Friedrich-Schiller-Universität; Winzerlaer Strasse 2 07745 Jena Germany
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Brandt P, García-Altares M, Nett M, Hertweck C, Hoffmeister D. Induzierte chemische Verteidigung eines Ständerpilzes durch eine doppelbindungsverschiebende Polyensynthase. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700767] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Philip Brandt
- Department Pharmazeutische Mikrobiologie am Hans-Knöll-Institut; Friedrich-Schiller-Universität; Winzerlaer Str. 2 07745 Jena Deutschland
| | - María García-Altares
- Department Biomolekulare Chemie; Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie; Beutenbergstr. 11a 07745 Jena Deutschland
| | - Markus Nett
- Fakultät Bio- und Chemieingenieurwesen; Technische Universität Dortmund; Emil-Figge-Straße 66 44227 Dortmund Deutschland
| | - Christian Hertweck
- Department Biomolekulare Chemie; Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie; Beutenbergstr. 11a 07745 Jena Deutschland
| | - Dirk Hoffmeister
- Department Pharmazeutische Mikrobiologie am Hans-Knöll-Institut; Friedrich-Schiller-Universität; Winzerlaer Str. 2 07745 Jena Deutschland
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Paulus C, Rebets Y, Tokovenko B, Nadmid S, Terekhova LP, Myronovskyi M, Zotchev SB, Rückert C, Braig S, Zahler S, Kalinowski J, Luzhetskyy A. New natural products identified by combined genomics-metabolomics profiling of marine Streptomyces sp. MP131-18. Sci Rep 2017; 7:42382. [PMID: 28186197 PMCID: PMC5301196 DOI: 10.1038/srep42382] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 01/10/2017] [Indexed: 01/13/2023] Open
Abstract
Marine actinobacteria are drawing more and more attention as a promising source of new natural products. Here we report isolation, genome sequencing and metabolic profiling of new strain Streptomyces sp. MP131-18 isolated from marine sediment sample collected in the Trondheim Fjord, Norway. The 16S rRNA and multilocus phylogenetic analysis showed that MP131-18 belongs to the genus Streptomyces. The genome of MP131-18 isolate was sequenced, and 36 gene clusters involved in the biosynthesis of 18 different types of secondary metabolites were predicted using antiSMASH analysis. The combined genomics-metabolics profiling of the strain led to the identification of several new biologically active compounds. As a result, the family of bisindole pyrroles spiroindimicins was extended with two new members, spiroindimicins E and F. Furthermore, prediction of the biosynthetic pathway for unusual α-pyrone lagunapyrone isolated from MP131-18 resulted in foresight and identification of two new compounds of this family – lagunapyrones D and E. The diversity of identified and predicted compounds from Streptomyces sp. MP131-18 demonstrates that marine-derived actinomycetes are not only a promising source of new natural products, but also represent a valuable pool of genes for combinatorial biosynthesis of secondary metabolites.
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Affiliation(s)
- Constanze Paulus
- Helmholtz-Institute for Pharmaceutical Research Saarland, Actinobacteria Metabolic Engineering Group, Saarbrücken, Germany
| | - Yuriy Rebets
- Helmholtz-Institute for Pharmaceutical Research Saarland, Actinobacteria Metabolic Engineering Group, Saarbrücken, Germany
| | - Bogdan Tokovenko
- Helmholtz-Institute for Pharmaceutical Research Saarland, Actinobacteria Metabolic Engineering Group, Saarbrücken, Germany
| | - Suvd Nadmid
- Helmholtz-Institute for Pharmaceutical Research Saarland, Actinobacteria Metabolic Engineering Group, Saarbrücken, Germany
| | - Larisa P Terekhova
- Gause Institute of New Antibiotics, Russian Academy of Medical Sciences, Moscow, Russia
| | - Maksym Myronovskyi
- Helmholtz-Institute for Pharmaceutical Research Saarland, Actinobacteria Metabolic Engineering Group, Saarbrücken, Germany
| | - Sergey B Zotchev
- Department of Biotechnology, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Pharmacognosy, University of Vienna, Vienna, Austria
| | | | - Simone Braig
- Department of Pharmacy - Center for Drug Research, University of Munich, Munich, Germany
| | - Stefan Zahler
- Department of Pharmacy - Center for Drug Research, University of Munich, Munich, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Andriy Luzhetskyy
- Helmholtz-Institute for Pharmaceutical Research Saarland, Actinobacteria Metabolic Engineering Group, Saarbrücken, Germany.,Universität des Saarlandes, Pharmaceutical Biotechnology, Saarbrücken, Germany
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Genomic and transcriptomic analyses of the tangerine pathotype of Alternaria alternata in response to oxidative stress. Sci Rep 2016; 6:32437. [PMID: 27582273 PMCID: PMC5007530 DOI: 10.1038/srep32437] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 08/09/2016] [Indexed: 12/19/2022] Open
Abstract
The tangerine pathotype of Alternaria alternata produces the A. citri toxin (ACT) and is the causal agent of citrus brown spot that results in significant yield losses worldwide. Both the production of ACT and the ability to detoxify reactive oxygen species (ROS) are required for A. alternata pathogenicity in citrus. In this study, we report the 34.41 Mb genome sequence of strain Z7 of the tangerine pathotype of A. alternata. The host selective ACT gene cluster in strain Z7 was identified, which included 25 genes with 19 of them not reported previously. Of these, 10 genes were present only in the tangerine pathotype, representing the most likely candidate genes for this pathotype specialization. A transcriptome analysis of the global effects of H2O2 on gene expression revealed 1108 up-regulated and 498 down-regulated genes. Expressions of those genes encoding catalase, peroxiredoxin, thioredoxin and glutathione were highly induced. Genes encoding several protein families including kinases, transcription factors, transporters, cytochrome P450, ubiquitin and heat shock proteins were found associated with adaptation to oxidative stress. Our data not only revealed the molecular basis of ACT biosynthesis but also provided new insights into the potential pathways that the phytopathogen A. alternata copes with oxidative stress.
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Noar RD, Daub ME. Bioinformatics Prediction of Polyketide Synthase Gene Clusters from Mycosphaerella fijiensis. PLoS One 2016; 11:e0158471. [PMID: 27388157 PMCID: PMC4936691 DOI: 10.1371/journal.pone.0158471] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/16/2016] [Indexed: 01/07/2023] Open
Abstract
Mycosphaerella fijiensis, causal agent of black Sigatoka disease of banana, is a Dothideomycete fungus closely related to fungi that produce polyketides important for plant pathogenicity. We utilized the M. fijiensis genome sequence to predict PKS genes and their gene clusters and make bioinformatics predictions about the types of compounds produced by these clusters. Eight PKS gene clusters were identified in the M. fijiensis genome, placing M. fijiensis into the 23rd percentile for the number of PKS genes compared to other Dothideomycetes. Analysis of the PKS domains identified three of the PKS enzymes as non-reducing and two as highly reducing. Gene clusters contained types of genes frequently found in PKS clusters including genes encoding transporters, oxidoreductases, methyltransferases, and non-ribosomal peptide synthases. Phylogenetic analysis identified a putative PKS cluster encoding melanin biosynthesis. None of the other clusters were closely aligned with genes encoding known polyketides, however three of the PKS genes fell into clades with clusters encoding alternapyrone, fumonisin, and solanapyrone produced by Alternaria and Fusarium species. A search for homologs among available genomic sequences from 103 Dothideomycetes identified close homologs (>80% similarity) for six of the PKS sequences. One of the PKS sequences was not similar (< 60% similarity) to sequences in any of the 103 genomes, suggesting that it encodes a unique compound. Comparison of the M. fijiensis PKS sequences with those of two other banana pathogens, M. musicola and M. eumusae, showed that these two species have close homologs to five of the M. fijiensis PKS sequences, but three others were not found in either species. RT-PCR and RNA-Seq analysis showed that the melanin PKS cluster was down-regulated in infected banana as compared to growth in culture. Three other clusters, however were strongly upregulated during disease development in banana, suggesting that they may encode polyketides important in pathogenicity.
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Affiliation(s)
- Roslyn D. Noar
- Department of Plant Pathology, North Carolina State University, Raleigh, North Carolina, 27695-7616, United States of America
| | - Margaret E. Daub
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, 27695-7612, United States of America
- * E-mail:
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Ugai T, Minami A, Gomi K, Oikawa H. Genome mining approach for harnessing the cryptic gene cluster in Alternaria solani: production of PKS–NRPS hybrid metabolite, didymellamide B. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.05.043] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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38
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Lin TS, Chiang YM, Wang CCC. Biosynthetic Pathway of the Reduced Polyketide Product Citreoviridin in Aspergillus terreus var. aureus Revealed by Heterologous Expression in Aspergillus nidulans. Org Lett 2016; 18:1366-9. [DOI: 10.1021/acs.orglett.6b00299] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tzu-Shyang Lin
- Department
of Pharmacology and Pharmaceutical Sciences, University of Southern California, School of Pharmacy, 1985 Zonal Avenue, Los Angeles, California 90089, United States
| | - Yi-Ming Chiang
- Department
of Pharmacology and Pharmaceutical Sciences, University of Southern California, School of Pharmacy, 1985 Zonal Avenue, Los Angeles, California 90089, United States
- Department
of Pharmacy, Chia Nan University of Pharmacy and Science, Tainan 71710, Taiwan
| | - Clay C. C. Wang
- Department
of Pharmacology and Pharmaceutical Sciences, University of Southern California, School of Pharmacy, 1985 Zonal Avenue, Los Angeles, California 90089, United States
- Department
of Chemistry, University of Southern California, College of Letters, Arts, and Sciences, Los Angeles, California 90089, United States
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Insights into natural products biosynthesis from analysis of 490 polyketide synthases from Fusarium. Fungal Genet Biol 2016; 89:37-51. [PMID: 26826610 DOI: 10.1016/j.fgb.2016.01.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 01/14/2016] [Accepted: 01/16/2016] [Indexed: 01/02/2023]
Abstract
Species of the fungus Fusarium collectively cause disease on almost all crop plants and produce numerous natural products (NPs), including some of the mycotoxins of greatest concern to agriculture. Many Fusarium NPs are derived from polyketide synthases (PKSs), large multi-domain enzymes that catalyze sequential condensation of simple carboxylic acids to form polyketides. To gain insight into the biosynthesis of polyketide-derived NPs in Fusarium, we retrieved 488 PKS gene sequences from genome sequences of 31 species of the fungus. In addition to these apparently functional PKS genes, the genomes collectively included 81 pseudogenized PKS genes. Phylogenetic analysis resolved the PKS genes into 67 clades, and based on multiple lines of evidence, we propose that homologs in each clade are responsible for synthesis of a polyketide that is distinct from those synthesized by PKSs in other clades. The presence and absence of PKS genes among the species examined indicated marked differences in distribution of PKS homologs. Comparisons of Fusarium PKS genes and genes flanking them to those from other Ascomycetes provided evidence that Fusarium has the genetic potential to synthesize multiple NPs that are the same or similar to those reported in other fungi, but that have not yet been reported in Fusarium. The results also highlight ways in which such analyses can help guide identification of novel Fusarium NPs and differences in NP biosynthetic capabilities that exist among fungi.
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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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Fujii R, Matsu Y, Minami A, Nagamine S, Takeuchi I, Gomi K, Oikawa H. Biosynthetic Study on Antihypercholesterolemic Agent Phomoidride: General Biogenesis of Fungal Dimeric Anhydrides. Org Lett 2015; 17:5658-61. [DOI: 10.1021/acs.orglett.5b02934] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ryuya Fujii
- Division
of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Yusuke Matsu
- Division
of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Atsushi Minami
- Division
of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Shota Nagamine
- Division
of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Ichiro Takeuchi
- Division
of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Katsuya Gomi
- Graduate
School of Agricultural Science, Tohoku University, Sendai 981-8555, Japan
| | - Hideaki Oikawa
- Division
of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
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42
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Hashimoto M, Wakana D, Ueda M, Kobayashi D, Goda Y, Fujii I. Product identification of non-reducing polyketide synthases with C-terminus methyltransferase domain from Talaromyces stipitatus using Aspergillus oryzae heterologous expression. Bioorg Med Chem Lett 2015; 25:1381-4. [PMID: 25770780 DOI: 10.1016/j.bmcl.2015.02.057] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 02/20/2015] [Accepted: 02/23/2015] [Indexed: 01/26/2023]
Abstract
Talaromyces stipitatus ATCC 10500 possesses 17 non-reducing polyketide synthase (NR-PKS) genes. During the course of our functional analysis of PKS genes with a C-terminus methyltransferase domain from T. stipitatus, we expressed tspks2, tspks3 and tspks4 genes in the heterologous host Aspergillus oryzae, respectively. Although the tspks4 transformant gave no apparent product in HPLC analysis, a novel azaphilone pentaketide (3) was identified along with two known related products from the tspks2 transformant. Of four hexaketide products from the tspks3 transformant, two new compounds were identified to be 2-acetyl-7-methyl-3,6,8-trihydroxynaphthalene (4) and its derivative fused with α-methyl-α,β-unsaturated γ-lactone (7).
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Affiliation(s)
- Makoto Hashimoto
- School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Iwate 028-3694, Japan
| | - Daigo Wakana
- National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Miki Ueda
- School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Iwate 028-3694, Japan
| | - Daisuke Kobayashi
- School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Iwate 028-3694, Japan
| | - Yukihiro Goda
- National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Isao Fujii
- School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Iwate 028-3694, Japan.
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43
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Anyaogu DC, Mortensen UH. Heterologous production of fungal secondary metabolites in Aspergilli. Front Microbiol 2015; 6:77. [PMID: 25713568 PMCID: PMC4322707 DOI: 10.3389/fmicb.2015.00077] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 01/21/2015] [Indexed: 12/24/2022] Open
Abstract
Fungal natural products comprise a wide range of compounds. Some are medically attractive as drugs and drug leads, some are used as food additives, while others are harmful mycotoxins. In recent years the genome sequence of several fungi has become available providing genetic information of a large number of putative biosynthetic pathways. However, compound discovery is difficult as the genes required for the production of the compounds often are silent or barely expressed under laboratory conditions. Furthermore, the lack of available tools for genetic manipulation of most fungal species hinders pathway discovery. Heterologous expression of the biosynthetic pathway in model systems or cell factories facilitates product discovery, elucidation, and production. This review summarizes the recent strategies for heterologous expression of fungal biosynthetic pathways in Aspergilli.
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Affiliation(s)
- Diana Chinyere Anyaogu
- Section for Eukaryotic Biotechnology, Department of Systems Biology, Technical University of Denmark Kongens Lyngby, Denmark
| | - Uffe Hasbro Mortensen
- Section for Eukaryotic Biotechnology, Department of Systems Biology, Technical University of Denmark Kongens Lyngby, Denmark
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44
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Ugai T, Minami A, Fujii R, Tanaka M, Oguri H, Gomi K, Oikawa H. Heterologous expression of highly reducing polyketide synthase involved in betaenone biosynthesis. Chem Commun (Camb) 2015; 51:1878-81. [DOI: 10.1039/c4cc09512j] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Heterologous expression of highly reducing polyketide synthase and trans-acting enoyl reductase provides insights into the skeletal construction of betaenones.
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Affiliation(s)
- Takahiro Ugai
- Division of Chemistry
- Graduate School of Science
- Hokkaido University
- Japan
| | - Atsushi Minami
- Division of Chemistry
- Graduate School of Science
- Hokkaido University
- Japan
| | - Ryuya Fujii
- Division of Chemistry
- Graduate School of Science
- Hokkaido University
- Japan
| | - Mizuki Tanaka
- Graduate School of Agricultural Science
- Tohoku University
- Japan
| | - Hiroki Oguri
- Division of Chemistry
- Graduate School of Science
- Hokkaido University
- Japan
| | - Katsuya Gomi
- Graduate School of Agricultural Science
- Tohoku University
- Japan
| | - Hideaki Oikawa
- Division of Chemistry
- Graduate School of Science
- Hokkaido University
- Japan
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45
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Chooi YH, Solomon PS. A chemical ecogenomics approach to understand the roles of secondary metabolites in fungal cereal pathogens. Front Microbiol 2014; 5:640. [PMID: 25477876 PMCID: PMC4237128 DOI: 10.3389/fmicb.2014.00640] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 11/06/2014] [Indexed: 11/19/2022] Open
Abstract
Secondary metabolites (SMs) are known to play important roles in the virulence and lifestyle of fungal plant pathogens. The increasing availability of fungal pathogen genome sequences and next-generation genomic tools have allowed us to survey the SM gene cluster inventory in individual fungi. Thus, there is immense opportunity for SM discovery in these plant pathogens. Comparative genomics and transcriptomics have been employed to obtain insights on the genetic features that enable fungal pathogens to adapt in individual ecological niches and to adopt the different pathogenic lifestyles. Here, we will discuss how we can use these tools to search for ecologically important SM gene clusters in fungi, using cereal pathogens as models. This ecological genomics approach, combined with genome mining and chemical ecology tools, is likely to advance our understanding of the natural functions of SMs and accelerate bioactive molecule discovery.
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Affiliation(s)
- Yit-Heng Chooi
- Plant Sciences Division, Research School of Biology, The Australian National University Canberra, ACT, Australia
| | - Peter S Solomon
- Plant Sciences Division, Research School of Biology, The Australian National University Canberra, ACT, Australia
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Chooi YH, Muria-Gonzalez MJ, Solomon PS. A genome-wide survey of the secondary metabolite biosynthesis genes in the wheat pathogen Parastagonospora nodorum.. Mycology 2014; 5:192-206. [PMID: 25379341 PMCID: PMC4205913 DOI: 10.1080/21501203.2014.928386] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 05/22/2014] [Indexed: 12/02/2022] Open
Abstract
The model pathogen Parastagonospora nodorum is a necrotroph and the causal agent of the wheat disease Septoria nodorum blotch (SNB). The sequenced P. nodorum genome has revealed that the fungus harbours a large number of secondary metabolite genes. Secondary metabolites are known to play important roles in the virulence of plant pathogens, but limited knowledge is available about the SM repertoire of this wheat pathogen. Here, we review the secondary metabolites that have been isolated from P. nodorum and related species of the same genus and provide an in-depth genome-wide overview of the secondary metabolite gene clusters encoded in the P. nodorum genome. The secondary metabolite gene survey reveals that P. nodorum is capable of producing a diverse range of small molecules and exciting prospects exist for discovery of novel virulence factors and bioactive molecules.
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Affiliation(s)
- Yit-Heng Chooi
- Plant Sciences Division, Research School of Biology, The Australian National University , Canberra , 0200 , Australia
| | - Mariano Jordi Muria-Gonzalez
- Plant Sciences Division, Research School of Biology, The Australian National University , Canberra , 0200 , Australia
| | - Peter S Solomon
- Plant Sciences Division, Research School of Biology, The Australian National University , Canberra , 0200 , Australia
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47
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Total Biosynthesis of Diterpene Aphidicolin, a Specific Inhibitor of DNA Polymerase α: Heterologous Expression of Four Biosynthetic Genes inAspergillus oryzae. Biosci Biotechnol Biochem 2014; 75:1813-7. [DOI: 10.1271/bbb.110366] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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48
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Collemare J, Griffiths S, Iida Y, Karimi Jashni M, Battaglia E, Cox RJ, de Wit PJGM. Secondary metabolism and biotrophic lifestyle in the tomato pathogen Cladosporium fulvum. PLoS One 2014; 9:e85877. [PMID: 24465762 PMCID: PMC3895014 DOI: 10.1371/journal.pone.0085877] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 12/03/2013] [Indexed: 01/07/2023] Open
Abstract
Cladosporium fulvum is a biotrophic fungal pathogen that causes leaf mould of tomato. Analysis of its genome suggested a high potential for production of secondary metabolites (SM), which might be harmful to plants and animals. Here, we have analysed in detail the predicted SM gene clusters of C. fulvum employing phylogenetic and comparative genomic approaches. Expression of the SM core genes was measured by RT-qrtPCR and produced SMs were determined by LC-MS and NMR analyses. The genome of C. fulvum contains six gene clusters that are conserved in other fungal species, which have undergone rearrangements and gene losses associated with the presence of transposable elements. Although being a biotroph, C. fulvum has the potential to produce elsinochrome and cercosporin toxins. However, the corresponding core genes are not expressed during infection of tomato. Only two core genes, PKS6 and NPS9, show high expression in planta, but both are significantly down regulated during colonization of the mesophyll tissue. In vitro SM profiling detected only one major compound that was identified as cladofulvin. PKS6 is likely involved in the production of this pigment because it is the only core gene significantly expressed under these conditions. Cladofulvin does not cause necrosis on Solanaceae plants and does not show any antimicrobial activity. In contrast to other biotrophic fungi that have a reduced SM production capacity, our studies on C. fulvum suggest that down-regulation of SM biosynthetic pathways might represent another mechanism associated with a biotrophic lifestyle.
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Affiliation(s)
- Jérôme Collemare
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
- Centre for Biosystems Genomics, Wageningen, The Netherlands
- * E-mail:
| | - Scott Griffiths
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Yuichiro Iida
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
- National Institute of Vegetable and Tea Science, Tsu, Japan
| | - Mansoor Karimi Jashni
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
- Department of Plant Pathology, Tarbiat Modares University, Tehran, Iran
| | - Evy Battaglia
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Russell J. Cox
- School of Chemistry, University of Bristol, Bristol, United Kingdom
| | - Pierre J. G. M. de Wit
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
- Centre for Biosystems Genomics, Wageningen, The Netherlands
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49
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Recent advances in genome mining of secondary metabolite biosynthetic gene clusters and the development of heterologous expression systems in Aspergillus nidulans. J Ind Microbiol Biotechnol 2013; 41:433-42. [PMID: 24342965 DOI: 10.1007/s10295-013-1386-z] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 11/20/2013] [Indexed: 12/31/2022]
Abstract
Fungi are prolific producers of secondary metabolites (SMs) that show a variety of biological activities. Recent advances in genome sequencing have shown that fungal genomes harbor far more SM gene clusters than are expressed under conventional laboratory conditions. Activation of these "silent" gene clusters is a major challenge, and many approaches have been taken to attempt to activate them and, thus, unlock the vast treasure chest of fungal SMs. This review will cover recent advances in genome mining of SMs in Aspergillus nidulans. We will also discuss current updates in gene annotation of A. nidulans and recent developments in A. nidulans as a molecular genetic system, both of which are essential for rapid and efficient experimental verification of SM gene clusters on a genome-wide scale. Finally, we will describe advances in the use of A. nidulans as a heterologous expression system to aid in the analysis of SM gene clusters from other fungal species that do not have an established molecular genetic system.
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50
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Manning VA, Pandelova I, Dhillon B, Wilhelm LJ, Goodwin SB, Berlin AM, Figueroa M, Freitag M, Hane JK, Henrissat B, Holman WH, Kodira CD, Martin J, Oliver RP, Robbertse B, Schackwitz W, Schwartz DC, Spatafora JW, Turgeon BG, Yandava C, Young S, Zhou S, Zeng Q, Grigoriev IV, Ma LJ, Ciuffetti LM. Comparative genomics of a plant-pathogenic fungus, Pyrenophora tritici-repentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence. G3 (BETHESDA, MD.) 2013; 3:41-63. [PMID: 23316438 PMCID: PMC3538342 DOI: 10.1534/g3.112.004044] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 11/02/2012] [Indexed: 12/31/2022]
Abstract
Pyrenophora tritici-repentis is a necrotrophic fungus causal to the disease tan spot of wheat, whose contribution to crop loss has increased significantly during the last few decades. Pathogenicity by this fungus is attributed to the production of host-selective toxins (HST), which are recognized by their host in a genotype-specific manner. To better understand the mechanisms that have led to the increase in disease incidence related to this pathogen, we sequenced the genomes of three P. tritici-repentis isolates. A pathogenic isolate that produces two known HSTs was used to assemble a reference nuclear genome of approximately 40 Mb composed of 11 chromosomes that encode 12,141 predicted genes. Comparison of the reference genome with those of a pathogenic isolate that produces a third HST, and a nonpathogenic isolate, showed the nonpathogen genome to be more diverged than those of the two pathogens. Examination of gene-coding regions has provided candidate pathogen-specific proteins and revealed gene families that may play a role in a necrotrophic lifestyle. Analysis of transposable elements suggests that their presence in the genome of pathogenic isolates contributes to the creation of novel genes, effector diversification, possible horizontal gene transfer events, identified copy number variation, and the first example of transduplication by DNA transposable elements in fungi. Overall, comparative analysis of these genomes provides evidence that pathogenicity in this species arose through an influx of transposable elements, which created a genetically flexible landscape that can easily respond to environmental changes.
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Affiliation(s)
- Viola A. Manning
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
| | - Iovanna Pandelova
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
| | - Braham Dhillon
- Department of Forest Sciences, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z4
| | - Larry J. Wilhelm
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
- Carbone/Ferguson Laboratories, Division of Neuroscience, Oregon National Primate Research Center (ONPRC), Beaverton, Oregon 97006
| | - Stephen B. Goodwin
- USDA–Agricultural Research Service, Purdue University, West Lafayette, Indiana 47907
| | | | - Melania Figueroa
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
- USDA-Agricultural Research Service, Forage Seed and Cereal Research Unit, Oregon State University, Corvallis, Oregon 97331
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
| | - James K. Hane
- Commonwealth Scientific and Industrial Research Organization−Plant Industry, Centre for Environment and Life Sciences, Floreat, Western Australia 6014, Australia
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Centre National de la Recherche Scientifique, 13288 Marseille cedex 9, France
| | - Wade H. Holman
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
| | - Chinnappa D. Kodira
- The Broad Institute, Cambridge, Massachusetts 02142
- Roche 454, Branford, Connecticut 06405
| | - Joel Martin
- US DOE Joint Genome Institute, Walnut Creek, California 94598
| | - Richard P. Oliver
- Australian Centre for Necrotrophic Fungal Pathogens, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia 6845, Australia
| | - Barbara Robbertse
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Centre National de la Recherche Scientifique, 13288 Marseille cedex 9, France
| | | | - David C. Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin 53706
| | - Joseph W. Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
| | - B. Gillian Turgeon
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14850
| | | | - Sarah Young
- The Broad Institute, Cambridge, Massachusetts 02142
| | - Shiguo Zhou
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin 53706
| | | | | | - Li-Jun Ma
- The Broad Institute, Cambridge, Massachusetts 02142
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003
| | - Lynda M. Ciuffetti
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
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