1
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Zhou J, Chen X, Li SM. Construction of an expression platform for fungal secondary metabolite biosynthesis in Penicillium crustosum. Appl Microbiol Biotechnol 2024; 108:427. [PMID: 39046587 PMCID: PMC11269504 DOI: 10.1007/s00253-024-13259-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/08/2024] [Accepted: 07/16/2024] [Indexed: 07/25/2024]
Abstract
Filamentous fungi are prolific producers of bioactive natural products and play a vital role in drug discovery. Yet, their potential cannot be fully exploited since many biosynthetic genes are silent or cryptic under laboratory culture conditions. Several strategies have been applied to activate these genes, with heterologous expression as one of the most promising approaches. However, successful expression and identification of new products are often hindered by host-dependent factors, such as low gene targeting efficiencies, a high metabolite background, or a lack of selection markers. To overcome these challenges, we have constructed a Penicillium crustosum expression host in a pyrG deficient strain by combining the split-marker strategy and CRISPR-Cas9 technology. Deletion of ligD and pcribo improved gene targeting efficiencies and enabled the use of an additional selection marker in P. crustosum. Furthermore, we reduced the secondary metabolite background by inactivation of two highly expressed gene clusters and abolished the formation of the reactive ortho-quinone methide. Finally, we replaced the P. crustosum pigment gene pcr4401 with the commonly used Aspergillus nidulans wA expression site for convenient use of constructs originally designed for A. nidulans in our P. crustosum host strain. As proof of concept, we successfully expressed a single polyketide synthase gene and an entire gene cluster at the P. crustosum wA locus. Resulting transformants were easily detected by their albino phenotype. With this study, we provide a highly efficient platform for heterologous expression of fungal genes. KEY POINTS: Construction of a highly efficient Penicillium crustosum heterologous expression host Reduction of secondary metabolite background by genetic dereplication strategy Integration of wA site to provide an alternative host besides Aspergillus nidulans.
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Affiliation(s)
- Jenny Zhou
- Institut Für Pharmazeutische Biologie Und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037, Marburg, Germany
| | - Xiaoling Chen
- Institut Für Pharmazeutische Biologie Und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037, Marburg, Germany
| | - Shu-Ming Li
- Institut Für Pharmazeutische Biologie Und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037, Marburg, Germany.
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2
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Gene complementation strategies for filamentous fungi biotechnology. Process Biochem 2023. [DOI: 10.1016/j.procbio.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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3
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Woodcraft C, Chooi YH, Roux I. The expanding CRISPR toolbox for natural product discovery and engineering in filamentous fungi. Nat Prod Rep 2023; 40:158-173. [PMID: 36205232 DOI: 10.1039/d2np00055e] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Covering: up to May 2022Fungal genetics has transformed natural product research by enabling the elucidation of cryptic metabolites and biosynthetic steps. The enhanced capability to add, subtract, modulate, and rewrite genes via CRISPR/Cas technologies has opened up avenues for the manipulation of biosynthetic gene clusters across diverse filamentous fungi. This review discusses the innovative and diverse strategies for fungal natural product discovery and engineering made possible by CRISPR/Cas-based tools. We also provide a guide into multiple angles of CRISPR/Cas experiment design, and discuss current gaps in genetic tool development for filamentous fungi and the promising opportunities for natural product research.
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Affiliation(s)
- Clara Woodcraft
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
| | - Indra Roux
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
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4
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Liu YN, Wu FY, Tian RY, Shi YX, Xu ZQ, Liu JY, Huang J, Xue FF, Liu BY, Liu GQ. The bHLH-zip transcription factor SREBP regulates triterpenoid and lipid metabolisms in the medicinal fungus Ganoderma lingzhi. Commun Biol 2023; 6:1. [PMID: 36596887 PMCID: PMC9810662 DOI: 10.1038/s42003-022-04154-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 10/21/2022] [Indexed: 01/04/2023] Open
Abstract
Ganoderic acids (GAs) are well recognized as important pharmacological components of the medicinal species belonging to the basidiomycete genus Ganoderma. However, transcription factors directly regulating the expression of GA biosynthesis genes remain poorly understood. Here, the genome of Ganoderma lingzhi is de novo sequenced. Using DNA affinity purification sequencing, we identify putative targets of the transcription factor sterol regulatory element-binding protein (SREBP), including the genes of triterpenoid synthesis and lipid metabolism. Interactions between SREBP and the targets are verified by electrophoretic mobility gel shift assay. RNA-seq shows that SREBP targets, mevalonate kinase and 3-hydroxy-3-methylglutaryl coenzyme A synthetase in mevalonate pathway, sterol isomerase and lanosterol 14-demethylase in ergosterol biosynthesis, are significantly upregulated in the SREBP overexpression (OE::SREBP) strain. In addition, 3 targets involved in glycerophospholipid/glycerolipid metabolism are upregulated. Then, the contents of mevalonic acid, lanosterol, ergosterol and 13 different GAs as well as a variety of lipids are significantly increased in this strain. Furthermore, the effects of SREBP overexpression on triterpenoid and lipid metabolisms are recovered when OE::SREBP strain are treated with exogenous fatostatin, a specific inhibitor of SREBP. Taken together, our genome-wide study clarify the role of SREBP in triterpenoid and lipid metabolisms of G. lingzhi.
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Affiliation(s)
- Yong-Nan Liu
- grid.440660.00000 0004 1761 0083Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry & Technology, Changsha, Hunan 410004 China ,grid.440660.00000 0004 1761 0083International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry & Technology, Changsha, Hunan 410004 China ,Microbial Variety Creation Center, Yuelushan Laboratory of Seed Industry, Changsha, 410004 China
| | - Feng-Yuan Wu
- grid.440660.00000 0004 1761 0083Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry & Technology, Changsha, Hunan 410004 China ,grid.440660.00000 0004 1761 0083International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry & Technology, Changsha, Hunan 410004 China ,Microbial Variety Creation Center, Yuelushan Laboratory of Seed Industry, Changsha, 410004 China
| | - Ren-Yuan Tian
- grid.440660.00000 0004 1761 0083Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry & Technology, Changsha, Hunan 410004 China ,grid.440660.00000 0004 1761 0083International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry & Technology, Changsha, Hunan 410004 China ,Microbial Variety Creation Center, Yuelushan Laboratory of Seed Industry, Changsha, 410004 China
| | - Yi-Xin Shi
- grid.440660.00000 0004 1761 0083Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry & Technology, Changsha, Hunan 410004 China ,grid.440660.00000 0004 1761 0083International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry & Technology, Changsha, Hunan 410004 China ,Microbial Variety Creation Center, Yuelushan Laboratory of Seed Industry, Changsha, 410004 China
| | - Zi-Qi Xu
- grid.440660.00000 0004 1761 0083Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry & Technology, Changsha, Hunan 410004 China ,grid.440660.00000 0004 1761 0083International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry & Technology, Changsha, Hunan 410004 China ,Microbial Variety Creation Center, Yuelushan Laboratory of Seed Industry, Changsha, 410004 China
| | - Ji-Ye Liu
- grid.440660.00000 0004 1761 0083Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry & Technology, Changsha, Hunan 410004 China ,grid.440660.00000 0004 1761 0083International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry & Technology, Changsha, Hunan 410004 China ,Microbial Variety Creation Center, Yuelushan Laboratory of Seed Industry, Changsha, 410004 China
| | - Jia Huang
- grid.440660.00000 0004 1761 0083Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry & Technology, Changsha, Hunan 410004 China ,grid.440660.00000 0004 1761 0083International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry & Technology, Changsha, Hunan 410004 China ,Microbial Variety Creation Center, Yuelushan Laboratory of Seed Industry, Changsha, 410004 China
| | - Fei-Fei Xue
- grid.440660.00000 0004 1761 0083Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry & Technology, Changsha, Hunan 410004 China ,grid.440660.00000 0004 1761 0083International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry & Technology, Changsha, Hunan 410004 China ,Microbial Variety Creation Center, Yuelushan Laboratory of Seed Industry, Changsha, 410004 China
| | - Bi-Yang Liu
- grid.440660.00000 0004 1761 0083Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry & Technology, Changsha, Hunan 410004 China ,grid.440660.00000 0004 1761 0083International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry & Technology, Changsha, Hunan 410004 China ,Microbial Variety Creation Center, Yuelushan Laboratory of Seed Industry, Changsha, 410004 China
| | - Gao-Qiang Liu
- grid.440660.00000 0004 1761 0083Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry & Technology, Changsha, Hunan 410004 China ,grid.440660.00000 0004 1761 0083International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry & Technology, Changsha, Hunan 410004 China ,Microbial Variety Creation Center, Yuelushan Laboratory of Seed Industry, Changsha, 410004 China
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5
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Shinkado S, Saito H, Yamazaki M, Kotera S, Arazoe T, Arie T, Kamakura T. Genome editing using a versatile vector-based CRISPR/Cas9 system in Fusarium species. Sci Rep 2022; 12:16243. [PMID: 36171473 PMCID: PMC9519947 DOI: 10.1038/s41598-022-20697-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/16/2022] [Indexed: 11/30/2022] Open
Abstract
Fusarium species include important filamentous fungal pathogens that can infect plants, animals, and humans. Meanwhile, some nonpathogenic Fusarium species are promising biocontrol agents against plant pathogens. Here, we developed a genome editing technology using a vector-based CRISPR/Cas9 system for Fusarium oxysporum f. sp. lycopersici (Fol). This optimized CRISPR/Cas9 system, harboring an endogenous U6 small nuclear RNA promoter for the expression of single-guide RNA and an endogenous H2B nuclear localization signal for the localization of Cas9, enabled efficient targeted gene knock-out, including in the accessory chromosomal regions in Fol. We further demonstrated single crossover-mediated targeted base editing and endogenous gene tagging. This system was also applicable for genome editing in F. oxysporum f. sp. spinaciae and F. commune without any modifications, suggesting that this CRISPR/Cas9 vector has a potential application for a broad range of researches on other Fusarium species.
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Affiliation(s)
- Sota Shinkado
- Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Hiroki Saito
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology (TUAT), 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-0054, Japan
- Graduate School of Biological Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara, 630-0192, Japan
| | - Masaya Yamazaki
- Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Shunsuke Kotera
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology (TUAT), 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-0054, Japan
| | - Takayuki Arazoe
- Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan.
| | - Tsutomu Arie
- Faculty of Agriculture, Institute of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-0054, Japan.
| | - Takashi Kamakura
- Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan.
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6
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Zhang C, Chen M, Yang L, Cheng Y, Qin Y, Zang Y, Wang B, Sun B, Wang C. Effects of mokF gene deletion and overexpression on the Monacolin K metabolism yields of Monascus purpureus. Appl Microbiol Biotechnol 2022; 106:3069-3080. [PMID: 35435455 DOI: 10.1007/s00253-022-11913-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/30/2022] [Accepted: 04/02/2022] [Indexed: 12/27/2022]
Abstract
Monascus purpureus is a fungus known for producing various physiologically active secondary metabolites. Of these, Monacolin K, a compound with hypocholesterolemic effects, is controlled by the biosynthetic gene mokF. Here, mokF deletion and overexpression strains (F2 and C3, respectively) were constructed using genetic engineering and compared with the M. purpureus wild strain (M1). The results showed that Monacolin K production was reduced by 50.86% in F2 and increased by 74.19% in C3. Of the three strains, C3 showed the highest production of Monacolin K and the most abnormal morphology. In addition, mokF influenced the expression level of mokA-mokI and might play an important role in regulating the biosynthesis of secondary metabolites in M. purpureus. Overall, our study verified the function of mokF in M. purpureus using gene deletion and overexpression technology. KEY POINTS: • The deletion and overexpression strains of mokF gene were successfully constructed. • The deletion or overexpression of mokF gene directly affected Monacolin K production. •The mokF gene had little effect on Monascus pigments and cell biomass.
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Affiliation(s)
- Chan Zhang
- Beijing Technology & Business University (BTBU), Beijing, 100048, China. .,Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology & Business University (BTBU), Beijing, 100048, China. .,Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing, 100048, China. .,Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University, No. 11 Fucheng Road, Haidian District, Beijing, 100048, China.
| | - Mengxue Chen
- Beijing Technology & Business University (BTBU), Beijing, 100048, China
| | - Le Yang
- Beijing Technology & Business University (BTBU), Beijing, 100048, China
| | - Ying Cheng
- Beijing Technology & Business University (BTBU), Beijing, 100048, China
| | - Yuhui Qin
- Beijing Technology & Business University (BTBU), Beijing, 100048, China
| | - Yueming Zang
- Beijing Technology & Business University (BTBU), Beijing, 100048, China
| | - Bei Wang
- Beijing Technology & Business University (BTBU), Beijing, 100048, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology & Business University (BTBU), Beijing, 100048, China.,Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing, 100048, China
| | - Baoguo Sun
- Beijing Technology & Business University (BTBU), Beijing, 100048, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology & Business University (BTBU), Beijing, 100048, China.,Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing, 100048, China
| | - Chengtao Wang
- Beijing Technology & Business University (BTBU), Beijing, 100048, China. .,Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology & Business University (BTBU), Beijing, 100048, China. .,Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing, 100048, China. .,Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University, No. 11 Fucheng Road, Haidian District, Beijing, 100048, China.
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7
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Meng X, Fang Y, Ding M, Zhang Y, Jia K, Li Z, Collemare J, Liu W. Developing fungal heterologous expression platforms to explore and improve the production of natural products from fungal biodiversity. Biotechnol Adv 2021; 54:107866. [PMID: 34780934 DOI: 10.1016/j.biotechadv.2021.107866] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/04/2021] [Accepted: 11/05/2021] [Indexed: 12/14/2022]
Abstract
Natural products from fungi represent an important source of biologically active metabolites notably for therapeutic agent development. Genome sequencing revealed that the number of biosynthetic gene clusters (BGCs) in fungi is much larger than expected. Unfortunately, most of them are silent or barely expressed under laboratory culture conditions. Moreover, many fungi in nature are uncultivable or cannot be genetically manipulated, restricting the extraction and identification of bioactive metabolites from these species. Rapid exploration of the tremendous number of cryptic fungal BGCs necessitates the development of heterologous expression platforms, which will facilitate the efficient production of natural products in fungal cell factories. Host selection, BGC assembly methods, promoters used for heterologous gene expression, metabolic engineering strategies and compartmentalization of biosynthetic pathways are key aspects for consideration to develop such a microbial platform. In the present review, we summarize current progress on the above challenges to promote research effort in the relevant fields.
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Affiliation(s)
- Xiangfeng Meng
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Yu Fang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Mingyang Ding
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Yanyu Zhang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Kaili Jia
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Zhongye Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Jérôme Collemare
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China.
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8
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Zhang Y, Chen Z, Wen Q, Xiong Z, Cao X, Zheng Z, Zhang Y, Huang Z. An overview on the biosynthesis and metabolic regulation of monacolin K/lovastatin. Food Funct 2021; 11:5738-5748. [PMID: 32555902 DOI: 10.1039/d0fo00691b] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lovastatin/monacolin K (MK) is used as a lipid lowering drug, due to its effective hypercholesterolemic properties, comparable to synthetic statins. Lovastatin's biosynthetic pathway and gene cluster composition have been studied in depth in Aspergillus terreus. Evidence shows that the MK biosynthetic pathway and gene cluster in Monascus sp. are similar to those of lovastatin in A. terreus. Currently, research efforts have been focusing on the metabolic regulation of MK/lovastatin synthesis, and the evidence shows that a combination of extracellular and intracellular factors is essential for proper MK/lovastatin metabolism. Here, we comprehensively review the research progress on MK/lovastatin biosynthetic pathways, its synthetic precursors and inducing substances and metabolic regulation, with a view to providing reference for future research on fungal metabolism regulation and metabolic engineering for MK/lovastatin production.
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Affiliation(s)
- Yaru Zhang
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China. and Fujian Provincial Key Laboratory of Quality Science and Processing Technology in Special Starch, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhiting Chen
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China. and Fujian Provincial Key Laboratory of Quality Science and Processing Technology in Special Starch, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qinyou Wen
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China. and Fujian Provincial Key Laboratory of Quality Science and Processing Technology in Special Starch, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zixiao Xiong
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China. and Fujian Provincial Key Laboratory of Quality Science and Processing Technology in Special Starch, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaohua Cao
- Key Laboratory of Crop Biotechnology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou 350002, China
| | - Zhenghuai Zheng
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yangxin Zhang
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Zhiwei Huang
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China. and Fujian Provincial Key Laboratory of Quality Science and Processing Technology in Special Starch, Fujian Agriculture and Forestry University, Fuzhou 350002, China and China-Ireland International Cooperation Centre for Food Material Science and Structure Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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9
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Barrios-González J, Pérez-Sánchez A, Bibián ME. New knowledge about the biosynthesis of lovastatin and its production by fermentation of Aspergillus terreus. Appl Microbiol Biotechnol 2020; 104:8979-8998. [PMID: 32930839 DOI: 10.1007/s00253-020-10871-x] [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: 03/05/2020] [Revised: 08/10/2020] [Accepted: 08/31/2020] [Indexed: 12/21/2022]
Abstract
Lovastatin, and its semisynthetic derivative simvastatine, has great medical and economic importance, besides great potential for other uses. In the last years, a deeper and more complex view of secondary metabolism regulation has emerged, with the incorporation of cluster-specific and global transcription factors, and their relation to signaling cascades, as well as the new level of epigenetic regulation. Recently, a new mechanism, which regulates lovastatin biosynthesis, at transcriptional level, has been discovered: reactive oxygen species (ROS) regulation; also new unexpected environmental stimuli have been identified, which induce the synthesis of lovastatin, like quorum sensing-type molecules and support stimuli. The present review describes this new panorama and uses this information, together with the knowledge on lovastatin biosynthesis and genomics, as the foundation to analyze literature on optimization of fermentation parameters and medium composition, and also to fully understand new strategies for strain genetic improvement. This new knowledge has been applied to the development of more effective culture media, with the addition of molecules like butyrolactone I, oxylipins, and spermidine, or with addition of ROS-generating molecules to increase internal ROS levels in the cell. It has also been applied to the development of new strategies to generate overproducing strains of Aspergillus terreus, including engineering of the cluster-specific transcription factor (lovE), global transcription factors like the ones implicated in ROS regulation (or even mitochondrial alternative respiration aox gen), or the global regulator LaeA. Moreover, there is potential to apply some of these findings to the development of novel unconventional production systems. KEY POINTS: • New findings in regulation of lovastatin biosynthesis, like ROS regulation. • Induction by unexpected stimuli: autoinducer molecules and support stimuli. • Recent reports on culture medium and process optimization from this stand point. • Applications to molecular genetic strain improvement methods and production systems.
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Affiliation(s)
- Javier Barrios-González
- Departamento de Biotecnología, Universidad Autónoma Metropolitana -Iztapalapa, Av. San Rafael Atlixco 186, Col. Vicentina, 09340, Iztapalapa, Ciudad de México, Mexico.
| | - Ailed Pérez-Sánchez
- Departamento de Biotecnología, Universidad Autónoma Metropolitana -Iztapalapa, Av. San Rafael Atlixco 186, Col. Vicentina, 09340, Iztapalapa, Ciudad de México, Mexico
| | - María Esmeralda Bibián
- Departamento de Biotecnología, Universidad Autónoma Metropolitana -Iztapalapa, Av. San Rafael Atlixco 186, Col. Vicentina, 09340, Iztapalapa, Ciudad de México, Mexico
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10
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Yamato T, Handa A, Arazoe T, Kuroki M, Nozaka A, Kamakura T, Ohsato S, Arie T, Kuwata S. Single crossover-mediated targeted nucleotide substitution and knock-in strategies with CRISPR/Cas9 system in the rice blast fungus. Sci Rep 2019; 9:7427. [PMID: 31092866 PMCID: PMC6520371 DOI: 10.1038/s41598-019-43913-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/01/2019] [Indexed: 01/10/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated genome editing has become a promising approach for efficient and versatile genetic engineering in various organisms; however, simple and precise nucleotide modification methods in filamentous fungi have been restricted to double crossover type homologous recombination (HR). In this study, we developed a novel genome editing strategy via single crossover-mediated HR in the model filamentous fungus Pyricularia (Magnaporthe) oryzae. This method includes the CRISPR/Cas9 system and a donor vector harboring a single homology arm with point mutations at the CRISPR/Cas9 cleavage site. Using this strategy, we demonstrated highly efficient and freely programmable base substitutions within the desired genomic locus, and target gene disrupted mutants were also obtained via a shortened (100-1000 bp) single homology arm. We further demonstrated that this method allowed a one-step GFP gene knock-in at the C-terminus of the targeted gene. Since the genomic recombination does not require an intact protospacer-adjacent motif within the donor construct and any additional modifications of host components, this method can be used in various filamentous fungi for CRISPR/Cas9-based basic and applied biological analyses.
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Affiliation(s)
- Tohru Yamato
- Graduate School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Ai Handa
- Graduate School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Takayuki Arazoe
- Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan.
| | - Misa Kuroki
- Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Akihito Nozaka
- Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Takashi Kamakura
- Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Shuichi Ohsato
- Graduate School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Tsutomu Arie
- Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-0509, Japan
| | - Shigeru Kuwata
- Graduate School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan.
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11
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Kan E, Katsuyama Y, Maruyama JI, Tamano K, Koyama Y, Ohnishi Y. Production of the plant polyketide curcumin in Aspergillus oryzae: strengthening malonyl-CoA supply for yield improvement. Biosci Biotechnol Biochem 2019; 83:1372-1381. [PMID: 31023165 DOI: 10.1080/09168451.2019.1606699] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The filamentous fungus Aspergillus oryzae was recently used as a heterologous host for fungal secondary metabolite production. Here, we aimed to produce the plant polyketide curcumin in A. oryzae. Curcumin is synthesized from feruloyl-coenzyme A (CoA) and malonyl-CoA by curcuminoid synthase (CUS). A. oryzae expressing CUS produced curcumin (64 μg/plate) on an agar medium containing feruloyl-N-acetylcysteamine (a feruloyl-CoA analog). To increase curcumin yield, we attempted to strengthen the supply of malonyl-CoA using two approaches: enhancement of the reaction catalyzed by acetyl-CoA carboxylase (ACC), which produces malonyl-CoA from acetyl-CoA, and inactivation of the acetyl-CoA-consuming sterol biosynthesis pathway. Finally, we succeeded in increasing curcumin yield sixfold by the double disruption of snfA and SCAP; SnfA is a homolog of SNF1, which inhibits ACC activity by phosphorylation in Saccharomyces cerevisiae and SCAP is positively related to sterol biosynthesis in Aspergillus terreus. This study provided useful information for heterologous polyketide production in A. oryzae.
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Affiliation(s)
- Eiichiro Kan
- a Department of Biotechnology, Graduate School of Agriculture and Life Sciences , The University of Tokyo , Bunkyo-ku , Japan.,b Noda Institute for Scientific Research , Noda City , Japan
| | - Yohei Katsuyama
- a Department of Biotechnology, Graduate School of Agriculture and Life Sciences , The University of Tokyo , Bunkyo-ku , Japan.,c Collaborative Research Institute for Innovative Microbiology , The University of Tokyo , Bunkyo-ku , Japan
| | - Jun-Ichi Maruyama
- a Department of Biotechnology, Graduate School of Agriculture and Life Sciences , The University of Tokyo , Bunkyo-ku , Japan.,c Collaborative Research Institute for Innovative Microbiology , The University of Tokyo , Bunkyo-ku , Japan
| | - Koichi Tamano
- d Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) , Toyohira-ku, Sapporo , Japan
| | - Yasuji Koyama
- b Noda Institute for Scientific Research , Noda City , Japan
| | - Yasuo Ohnishi
- a Department of Biotechnology, Graduate School of Agriculture and Life Sciences , The University of Tokyo , Bunkyo-ku , Japan.,c Collaborative Research Institute for Innovative Microbiology , The University of Tokyo , Bunkyo-ku , Japan
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12
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Itoh H, Miura A, Takeda I, Matsui M, Tamano K, Machida M, Shibata T. Search for transcription factors affecting productivity of the polyketide FR901512 in filamentous fungal sp. No. 14919 and identification of Drf1, a novel negative regulator of the biosynthetic gene cluster. Biosci Biotechnol Biochem 2019; 83:1163-1170. [PMID: 30821612 DOI: 10.1080/09168451.2019.1584519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In order to increase secondary metabolite production in filamentous fungi, a transcription factor gene in the biosynthetic gene cluster and global regulator genes such as laeA are considered plausible as targets for overexpression by genetic modification. In this study, we examined these overexpression effect in fungal sp. No. 14919 that produces FR901512, an HMG-CoA reductase inhibitor. Resultantly, the productivity was improved at 1.7-1.8 fold by overexpressing frlE, a transcription factor gene in the biosynthetic gene cluster, whereas productivity did not change by overexpression of laeA and veA. Furthermore, we searched for extra transcription factors affecting the productivity by transcriptome analysis between wild-type strain and highly productive UV mutants. After verifying productivity decrease by overexpression, Drf1, a novel transcription factor encoded by drf1 was identified as the negative regulator. Because each frlE product (FrlE) and Drf1 worked on the same cluster in positive and negative regulatory manners, their network was analyzed.
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Affiliation(s)
- Hiroya Itoh
- a Biotechnology Labs., Astellas Pharma Inc ., Tsukuba , Japan.,b Technology Research Association of Highly Efficient Gene Design (TRAHED) , Tokyo , Japan
| | - Ai Miura
- c Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) , Sapporo , Japan
| | - Itaru Takeda
- c Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) , Sapporo , Japan
| | - Makoto Matsui
- b Technology Research Association of Highly Efficient Gene Design (TRAHED) , Tokyo , Japan.,d Pharmaceutical Science & Technology Labs ., Astellas Pharma Inc ., Tsukuba , Japan
| | - Koichi Tamano
- c Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) , Sapporo , Japan
| | - Masayuki Machida
- b Technology Research Association of Highly Efficient Gene Design (TRAHED) , Tokyo , Japan.,c Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) , Sapporo , Japan
| | - Takashi Shibata
- b Technology Research Association of Highly Efficient Gene Design (TRAHED) , Tokyo , Japan.,d Pharmaceutical Science & Technology Labs ., Astellas Pharma Inc ., Tsukuba , Japan
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13
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Parvez A, Giri S, Bisht R, Saxena P. New Insights on Cyclization Specificity of Fungal Type III Polyketide Synthase, PKSIII Nc in Neurospora crassa. Indian J Microbiol 2018; 58:268-277. [PMID: 30013270 PMCID: PMC6023819 DOI: 10.1007/s12088-018-0738-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 05/03/2018] [Indexed: 12/13/2022] Open
Abstract
Type III polyketide synthases (PKSs) biosynthesize varied classes of metabolites with diverse bio-functionalities. Inherent promiscuous substrate specificity, multiple elongations of reaction intermediates and several modes of ring-closure, confer the proteins with the ability to generate unique scaffolds from limited substrate pools. Structural studies have identified crucial amino acid residues that dictate type III PKS functioning, though cyclization specific residues need further investigation. PKSIIINc, a functionally and structurally characterized type III PKS from the fungus, Neurospora crassa, is known to biosynthesize alkyl-resorcinol, alkyl-triketide- and alkyl-tetraketide-α-pyrone products. In this study, we attempted to identify residue positions governing cyclization specificity in PKSIIINc through comparative structural analysis. Structural comparisons with other type III PKSs revealed a motif with conserved hydroxyl/thiol groups that could dictate PKSIIINc catalysis. Site-directed mutagenesis of Cys120 and Ser186 to Ser and Cys, respectively, altered product profiles of mutant proteins. While both C120S and S186C proteins retained wild-type PKSIIINc product activity, S186C favoured lactonization and yielded higher amounts of the α-pyrone products. Notably, C120S gained new cyclization capability and biosynthesized acyl-phloroglucinol in addition to wild-type PKSIIINc products. Generation of alkyl-resorcinol and acyl-phloroglucinol by a single protein is a unique observation in fungal type III PKS family. Mutation of Cys120 to bulky Phe side-chain abrogated formation of tetraketide products and adversely affected overall protein stability as revealed by molecular dynamics simulation studies. Our investigations identify residue positions governing cyclization programming in PKSIIINc protein and provide insights on how subtle variations in protein cores dictate product profiles in type III PKS family.
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Affiliation(s)
- Amreesh Parvez
- Chemical Biology Group, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021 India
| | - Samir Giri
- Chemical Biology Group, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021 India
- Present Address: Department of Ecology, School of Biology, University of Osnabrück, Osnabrück, 49076 Germany
| | - Renu Bisht
- Chemical Biology Group, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021 India
| | - Priti Saxena
- Chemical Biology Group, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021 India
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14
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Hasan H, Abd Rahim MH, Campbell L, Carter D, Abbas A, Montoya A. Overexpression of acetyl-CoA carboxylase in Aspergillus terreus to increase lovastatin production. N Biotechnol 2018; 44:64-71. [PMID: 29727712 DOI: 10.1016/j.nbt.2018.04.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 04/30/2018] [Accepted: 04/30/2018] [Indexed: 02/08/2023]
Abstract
The present work describes the application of homologous recombination techniques in a wild-type Aspergillus terreus (ATCC 20542) strain to increase the flow of precursors towards the lovastatin biosynthesis pathway. A new strain was generated to overexpress acetyl-CoA carboxylase (ACCase) by replacing the native ACCase promoter with a strong constitutive PadhA promoter from Aspergillus nidulans. Glycerol and a mixture of lactose and glycerol were used independently as the carbon feedstock to determine the degree of response by the A. terreus strains towards the production of acetyl-CoA, and malonyl-CoA. The new strain increased the levels of malonyl-CoA and acetyl-CoA by 240% and 14%, respectively, compared to the wild-type strain. As a result, lovastatin production was increased by 40% and (+)-geodin was decreased by 31% using the new strain. This study shows for the first time that the metabolism of Aspergillus terreus can be manipulated to attain higher levels of precursors and valuable secondary metabolites.
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Affiliation(s)
- Hanan Hasan
- University of Sydney, School of Chemical and Biomolecular Engineering, Australia; Universiti Putra Malaysia, Faculty of Food Science and Technology, Malaysia
| | - Muhammad Hafiz Abd Rahim
- University of Sydney, School of Chemical and Biomolecular Engineering, Australia; Universiti Putra Malaysia, Faculty of Food Science and Technology, Malaysia
| | - Leona Campbell
- University of Sydney, School of Life and Environmental Sciences, Australia
| | - Dee Carter
- University of Sydney, School of Life and Environmental Sciences, Australia
| | - Ali Abbas
- University of Sydney, School of Chemical and Biomolecular Engineering, Australia
| | - Alejandro Montoya
- University of Sydney, School of Chemical and Biomolecular Engineering, Australia.
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