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Long H, Zhou J, Ren Y, Lu J, Wang N, Liu H, Zhou X, Cai M. Comparative omics directed gene discovery and rewiring for normal temperature-adaptive red pigment synthesis by polar psychrotrophic fungus Geomyces sp. WNF-15A. Synth Syst Biotechnol 2024; 9:842-852. [PMID: 39149535 PMCID: PMC11326490 DOI: 10.1016/j.synbio.2024.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 08/17/2024] Open
Abstract
The Antarctic fungus Geomyces sp. WNF-15A can produce high-quality red pigments (AGRP) with good prospects for the use in food and cosmetic area. However, efficient AGRP synthesis relies on low-temperature and thus limits its industrial development. Here genome sequencing and comparative analysis were performed on the wild-type versus to four mutants derived from natural mutagenesis and transposon insertion mutation. Eleven mutated genes were identified from 2309 SNPs and 256 Indels. A CRISPR-Cas9 gene-editing system was established for functional analysis of these genes. Deficiency of scaffold1.t692 and scaffold2.t704 with unknown functions highly improved AGRP synthesis at all tested temperatures. Of note, the two mutants produced comparable levels of AGRP at 20 °C to the wild-type at 14 °C. They also broke the normal-temperature limitation and effectively synthesized AGRP at 25 °C. Comparative metabolomic analysis revealed that deficiency of scaffold1.t692 improved AGRP synthesis by regulation of global metabolic pathways especially downregulation of the competitive pathways. Knockout of key genes responsible for the differential metabolites confirmed the metabolomic results. This study shows new clues for cold-adaptive regulatory mechanism of polar fungi. It also provides references for exploitation and utilization of psychrotrophic fungal resources.
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Affiliation(s)
- Haoyu Long
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Jiawei Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Yanna Ren
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Jian Lu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Nengfei Wang
- School of Chemistry & Chemical Engineering, Linyi University, Linyi, 276005, China
| | - Haifeng Liu
- China Resources Angde Biotech Pharma Co., Ltd., 78 E-jiao Street, Liaocheng, China
| | - Xiangshan Zhou
- China Resources Biopharmaceutical Co., Ltd., 1301-84 Sightseeing Road, Shenzhen, China
| | - Menghao Cai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
- Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai, 200237, China
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2
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Lu C, Huang Y, Cui J, Wu J, Jiang C, Gu X, Cao Y, Yin S. Toward Practical Applications of Engineered Living Materials with Advanced Fabrication Techniques. ACS Synth Biol 2024; 13:2295-2312. [PMID: 39002162 DOI: 10.1021/acssynbio.4c00259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2024]
Abstract
Engineered Living Materials (ELMs) are materials composed of or incorporating living cells as essential functional units. These materials can be created using bottom-up approaches, where engineered cells spontaneously form well-defined aggregates. Alternatively, top-down methods employ advanced materials science techniques to integrate cells with various kinds of materials, creating hybrids where cells and materials are intricately combined. ELMs blend synthetic biology with materials science, allowing for dynamic responses to environmental stimuli such as stress, pH, humidity, temperature, and light. These materials exhibit unique "living" properties, including self-healing, self-replication, and environmental adaptability, making them highly suitable for a wide range of applications in medicine, environmental conservation, and manufacturing. Their inherent biocompatibility and ability to undergo genetic modifications allow for customized functionalities and prolonged sustainability. This review highlights the transformative impact of ELMs over recent decades, particularly in healthcare and environmental protection. We discuss current preparation methods, including the use of endogenous and exogenous scaffolds, living assembly, 3D bioprinting, and electrospinning. Emphasis is placed on ongoing research and technological advancements necessary to enhance the safety, functionality, and practical applicability of ELMs in real-world contexts.
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Affiliation(s)
- Chenjing Lu
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Yaying Huang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Jian Cui
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Junhua Wu
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250021, China
- Medical School, Nanjing University, Nanjing 210093, China
| | - Chunping Jiang
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250021, China
- Medical School, Nanjing University, Nanjing 210093, China
| | - Xiaosong Gu
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250021, China
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250021, China
- Institute for Brain Sciences, Nanjing University, Nanjing 210093, China
- Chemistry and Biomedicine innovation center, Nanjing University, Nanjing 210093, China
- Chemistry and Biomedicine innovation center, MOE Key Laboratory of High Performance Polymer Materials and Technology, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Sheng Yin
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250021, China
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3
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Hu Z, Liu Q, Ouyang B, Wang G, Wei C, Zhao X. Recent advances in genetic engineering to enhance plant-polysaccharide-degrading enzyme expression in Penicillium oxalicum: A brief review. Int J Biol Macromol 2024; 278:134775. [PMID: 39153674 DOI: 10.1016/j.ijbiomac.2024.134775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 08/13/2024] [Accepted: 08/13/2024] [Indexed: 08/19/2024]
Abstract
With the depletion of non-renewable fossil fuels, there has been an increasing emphasis on renewable biomass. Penicillium oxalicum is notable for its exceptional capacity to secrete a diverse array of enzymes that degrade plant polysaccharides into monosaccharides. These valuable monosaccharides can be harnessed in the production of bioethanol and other sustainable forms of energy. By enhancing the production of plant-polysaccharide-degrading enzymes (PPDEs) in P. oxalicum, we can optimize the utilization of plant biomass. This paper presents recent advances in augmenting PPDE expression in P. oxalicum through genetic engineering strategies involving protoplast preparation, transformation, and factors influencing PPDE gene expression.
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Affiliation(s)
- Ziyan Hu
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Qiling Liu
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Bei Ouyang
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Guoping Wang
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Chenyang Wei
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Xihua Zhao
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China.
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4
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Erdmann EA, Brandhorst AKM, Gorbushina AA, Schumacher J. The Tet-on system for controllable gene expression in the rock-inhabiting black fungus Knufia petricola. Extremophiles 2024; 28:38. [PMID: 39105933 PMCID: PMC11303440 DOI: 10.1007/s00792-024-01354-2] [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: 03/05/2024] [Accepted: 07/22/2024] [Indexed: 08/07/2024]
Abstract
Knufia petricola is a black fungus that colonizes sun-exposed surfaces as extreme and oligotrophic environments. As ecologically important heterotrophs and biofilm-formers on human-made surfaces, black fungi form one of the most resistant groups of biodeteriorating organisms. Due to its moderate growth rate in axenic culture and available protocols for its transformation and CRISPR/Cas9-mediated genome editing, K. petricola is used for studying the morpho-physiological adaptations shared by extremophilic and extremotolerant black fungi. In this study, the bacteria-derived tetracycline (TET)-dependent promoter (Tet-on) system was implemented to enable controllable gene expression in K. petricola. The functionality i.e., the dose-dependent inducibility of TET-regulated constructs was investigated by using GFP fluorescence, pigment synthesis (melanin and carotenoids) and restored uracil prototrophy as reporters. The newly generated cloning vectors containing the Tet-on construct, and the validated sites in the K. petricola genome for color-selectable or neutral insertion of expression constructs complete the reverse genetics toolbox. One or multiple genes can be expressed on demand from different genomic loci or from a single construct by using 2A self-cleaving peptides, e.g., for localizing proteins and protein complexes in the K. petricola cell or for using K. petricola as host for the expression of heterologous genes.
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Affiliation(s)
- Eileen A Erdmann
- Bundesanstalt für Materialforschung und -prüfung (BAM), Berlin, Germany
- Freie Universität Berlin, Berlin, Germany
| | - Antonia K M Brandhorst
- Bundesanstalt für Materialforschung und -prüfung (BAM), Berlin, Germany
- Freie Universität Berlin, Berlin, Germany
| | - Anna A Gorbushina
- Bundesanstalt für Materialforschung und -prüfung (BAM), Berlin, Germany
- Freie Universität Berlin, Berlin, Germany
| | - Julia Schumacher
- Bundesanstalt für Materialforschung und -prüfung (BAM), Berlin, Germany.
- Freie Universität Berlin, Berlin, Germany.
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Fritsche S, Reinfurt A, Fronek F, Steiger MG. NHEJ and HDR can occur simultaneously during gene integration into the genome of Aspergillus niger. Fungal Biol Biotechnol 2024; 11:10. [PMID: 39103967 DOI: 10.1186/s40694-024-00180-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 07/07/2024] [Indexed: 08/07/2024] Open
Abstract
Non-homologous end joining (NHEJ) and homology-directed repair (HDR) are two mechanisms in filamentous fungi to repair DNA damages. NHEJ is the dominant response pathway to rapidly join DNA double-strand breaks, but often leads to insertions or deletions. On the other hand, HDR is more precise and utilizes a homologous DNA template to restore the damaged sequence. Both types are exploited in genetic engineering approaches ranging from knock-out mutations to precise sequence modifications.In this study, we evaluated the efficiency of an HDR based gene integration system designed for the pyrG locus of Aspergillus niger. While gene integration was achieved at a rate of 91.4%, we also discovered a mixed-type repair (MTR) mechanism with simultaneous repair of a Cas9-mediated double-strand break by both NHEJ and HDR. In 20.3% of the analyzed transformants the donor DNA was integrated by NHEJ at the 3' end and by HDR at the 5' end of the double-strand break. Furthermore, sequencing of the locus revealed different DNA repair mechanisms at the site of the NHEJ event.Together, the results support the applicability of the genome integration system and a novel DNA repair type with implication on the diversity of genetic modifications in filamentous fungi.
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Affiliation(s)
- Susanne Fritsche
- Austrian Centre of Industrial Biotechnology, Muthgasse 18, Vienna, Austria
- Institute of Chemical, Environmental and Bioscience Engineering, Research Group Biochemistry, Technische Universität Wien, Gumpendorferstrasse 1A, Vienna, 1060, Austria
| | - Aline Reinfurt
- Austrian Centre of Industrial Biotechnology, Muthgasse 18, Vienna, Austria
- Institute of Chemical, Environmental and Bioscience Engineering, Research Group Biochemistry, Technische Universität Wien, Gumpendorferstrasse 1A, Vienna, 1060, Austria
| | - Felix Fronek
- Austrian Centre of Industrial Biotechnology, Muthgasse 18, Vienna, Austria
- Institute of Chemical, Environmental and Bioscience Engineering, Research Group Biochemistry, Technische Universität Wien, Gumpendorferstrasse 1A, Vienna, 1060, Austria
| | - Matthias G Steiger
- Austrian Centre of Industrial Biotechnology, Muthgasse 18, Vienna, Austria.
- Institute of Chemical, Environmental and Bioscience Engineering, Research Group Biochemistry, Technische Universität Wien, Gumpendorferstrasse 1A, Vienna, 1060, Austria.
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6
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Thomsen PT, Nielsen SR, Borodina I. Recent advances in engineering microorganisms for the production of natural food colorants. Curr Opin Chem Biol 2024; 81:102477. [PMID: 38878611 DOI: 10.1016/j.cbpa.2024.102477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/11/2024] [Accepted: 05/23/2024] [Indexed: 08/13/2024]
Abstract
Food colorants are frequently added to processed foods since color is an important tool in the marketing of food products, influencing consumer perceptions, preferences, and purchasing behavior. While synthetic dyes currently dominate the food colorant market, consumer concern regarding their safety and sustainability is driving a demand for their replacement with naturally derived alternatives. However, natural colorants are costly compared to their synthetic counterparts as the pigment content in the native sources is usually very low and extraction can be challenging. Recent advances in the engineering of microbial metabolism have sparked interest in the development of cell factories capable of producing natural colorants from renewable resources. This review summarizes major developments within metabolic engineering for the production of nature-identical food colorants by fermentation. Additionally, it highlights common applications, formulations, and physicochemical characteristics of prevalent pigment classes. Lastly, it outlines a workflow for accelerating the optimization of cell factories for the production or derivatization of nature-identical food colorants.
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Affiliation(s)
- Philip Tinggaard Thomsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark
| | - Susanne Roenfeldt Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark.
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7
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Chen X, Moran Torres JP, Tedjai SVK, Lugones LG, Wösten HAB. Functional analysis of FlbA-regulated transcription factor genes in Aspergillus niger using a multiplexed CRISPRoff system. Int J Biol Macromol 2024; 277:134326. [PMID: 39089555 DOI: 10.1016/j.ijbiomac.2024.134326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/31/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024]
Abstract
FlbA of Aspergillus niger (indirectly) regulates 36 transcription factor (TF) genes. As a result, it promotes sporulation and represses vegetative growth, protein secretion and lysis. In this study, the functions of part of the FlbA-regulated TF genes were studied by using CRISPRoff. This system was recently introduced as an epigenetic tool for modulating gene expression in A. niger. A plasmid encompassing an optimized CRISPRoff system as well as a library of sgRNA genes that target the promoters of the 36 FlbA-regulated TF genes was introduced in A. niger. Out of 24 transformants that exhibited a sporulation phenotype, 12 and 18 strains also showed a biomass and secretion phenotype, respectively. The transforming sgRNAs, and thus the genes responsible for the phenotypes, were identified from five of the transformants. The results show that the genes dofA, dofB, dofC, dofD, and socA are involved in sporulation and extracellular enzyme activity, while dofA and socA also play roles in biomass formation. Overall, this study shows that the multiplexed CRISPRoff system can be effectively used for functional analysis of genes in a fungus.
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Affiliation(s)
- Xiaoyi Chen
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, the Netherlands.
| | - Juan P Moran Torres
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, the Netherlands.
| | - S Vyanjan K Tedjai
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, the Netherlands.
| | - Luis G Lugones
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, the Netherlands.
| | - Han A B Wösten
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, the Netherlands.
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Tarafder E, Nizamani MM, Karunarathna SC, Das D, Zeng X, Rind RA, Wang Y, Tian F. Advancements in genetic studies of mushrooms: a comprehensive review. World J Microbiol Biotechnol 2024; 40:275. [PMID: 39034336 DOI: 10.1007/s11274-024-04079-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 07/10/2024] [Indexed: 07/23/2024]
Abstract
Genetic studies in mushrooms, driven by innovations such as CRISPR-Cas9 genome editing and RNA interference, transform our understanding of these enigmatic fungi and their multifaceted roles in agriculture, medicine, and conservation. This comprehensive review explores the rationale and significance of genetic research in mushrooms, delving into the ethical, regulatory, and ecological dimensions of this field. CRISPR-Cas9 emerges as a game-changing technology, enabling precise genome editing, targeted gene knockouts, and pathway manipulation. RNA interference complements these efforts by downregulating genes for improved crop yield and enhanced pest and disease resistance. Genetic studies also contribute to the conservation of rare species and developing more robust mushroom strains, fostering sustainable cultivation practices. Moreover, they unlock the potential for discovering novel medicinal compounds, offering new horizons in pharmaceuticals and nutraceuticals. As emerging technologies and ethical considerations shape the future of mushroom research, these studies promise to revolutionize our relationship with these fungi, paving the way for a more sustainable and innovative world.
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Affiliation(s)
- Entaj Tarafder
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, Guizhou, 550025, People's Republic of China
| | - Mir Muhammad Nizamani
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, Guizhou, 550025, People's Republic of China
| | - Samantha C Karunarathna
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan, 655011, People's Republic of China
- National Institute of Fundamental Studies, Kandy, Sri Lanka
| | - Diptosh Das
- Molecular and Applied Mycology and Plant Pathology Laboratory, Centre of Advanced Study, Department of Botany, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, West Bengal, 700019, India
| | - Xiangyu Zeng
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, Guizhou, 550025, People's Republic of China
| | - Raza Ali Rind
- Department of Plant Breeding and Genetics, Sindh Agriculture University Tandojam, Hyderabad, Pakistan
| | - Yong Wang
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, Guizhou, 550025, People's Republic of China.
| | - Fenghua Tian
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, Guizhou, 550025, People's Republic of China.
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Catanzaro I, Gerrits R, Feldmann I, Gorbushina AA, Onofri S, Schumacher J. Deletion of the polyketide synthase-encoding gene pks1 prevents melanization in the extremophilic fungus Cryomyces antarcticus. IUBMB Life 2024. [PMID: 39011777 DOI: 10.1002/iub.2895] [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: 02/05/2024] [Accepted: 05/15/2024] [Indexed: 07/17/2024]
Abstract
Cryomyces antarcticus, a melanized cryptoendolithic fungus endemic to Antarctica, can tolerate environmental conditions as severe as those in space. Particularly, its ability to withstand ionizing radiation has been attributed to the presence of thick and highly melanized cell walls, which-according to a previous investigation-may contain both 1,8-dihydroxynaphthalene (DHN) and L-3,4 dihydroxyphenylalanine (L-DOPA) melanin. The genes putatively involved in the synthesis of DHN melanin were identified in the genome of C. antarcticus. Most important is capks1 encoding a non-reducing polyketide synthase (PKS) and being the ortholog of the functionally characterized kppks1 from the rock-inhabiting fungus Knufia petricola. The co-expression of CaPKS1 or KpPKS1 with a 4'-phosphopantetheinyl transferase in Saccharomyces cerevisiae resulted in the formation of a yellowish pigment, suggesting that CaPKS1 is the enzyme providing the precursor for DHN melanin. To dissect the composition and function of the melanin layer in the outer cell wall of C. antarcticus, non-melanized mutants were generated by CRISPR/Cas9-mediated genome editing. Notwithstanding its slow growth (up to months), three independent non-melanized Δcapks1 mutants were obtained. The mutants exhibited growth similar to the wild type and a light pinkish pigmentation, which is presumably due to carotenoids. Interestingly, visible light had an adverse effect on growth of both melanized wild-type and non-melanized Δcapks1 strains. Further evidence that light can pass the melanized cell walls derives from a mutant expressing a H2B-GFP fusion protein, which can be detected by fluorescence microscopy. In conclusion, the study reports on the first genetic manipulation of C. antarcticus, resulting in non-melanized mutants and demonstrating that the melanin is rather of the DHN type. These mutants will allow to elucidate the relevance of melanization for surviving extreme conditions found in the natural habitat as well as in space.
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Affiliation(s)
- Ilaria Catanzaro
- Department Materials and the Environment, Bundesanstalt für Materialforschung und -prüfung (BAM), Berlin, Germany
- Department of Ecological and Biological Sciences (DEB), Università degli Studi della Tuscia, Viterbo, Italy
| | - Ruben Gerrits
- Department Materials and the Environment, Bundesanstalt für Materialforschung und -prüfung (BAM), Berlin, Germany
| | - Ines Feldmann
- Department Materials and the Environment, Bundesanstalt für Materialforschung und -prüfung (BAM), Berlin, Germany
| | - Anna A Gorbushina
- Department Materials and the Environment, Bundesanstalt für Materialforschung und -prüfung (BAM), Berlin, Germany
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Silvano Onofri
- Department of Ecological and Biological Sciences (DEB), Università degli Studi della Tuscia, Viterbo, Italy
| | - Julia Schumacher
- Department Materials and the Environment, Bundesanstalt für Materialforschung und -prüfung (BAM), Berlin, Germany
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany
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10
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Ropero-Pérez C, Marcos JF, Manzanares P, Garrigues S. Increasing the efficiency of CRISPR/Cas9-mediated genome editing in the citrus postharvest pathogen Penicillium digitatum. Fungal Biol Biotechnol 2024; 11:8. [PMID: 39003486 PMCID: PMC11245846 DOI: 10.1186/s40694-024-00179-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 07/07/2024] [Indexed: 07/15/2024] Open
Abstract
BACKGROUND Penicillium digitatum is a fungal plant pathogen that causes the green mold disease in harvested citrus fruits. Due to its economical relevance, many efforts have focused on the development of genetic engineering tools for this fungus. Adaptation of the CRISPR/Cas9 technology was previously accomplished with self-replicative AMA1-based plasmids for marker-free gene editing, but the resulting efficiency (10%) limited its practical implementation. In this study, we aimed to enhance the efficiency of the CRISPR/Cas9-mediated gene editing in P. digitatum to facilitate its practical use. RESULTS Increasing the culture time by performing additional culture streaks under selection conditions in a medium that promotes slower growth rates significantly improved the gene editing efficiency in P. digitatum up to 54-83%. To prove this, we disrupted five candidate genes that were chosen based on our previous high-throughput gene expression studies aimed at elucidating the transcriptomic response of P. digitatum to the antifungal protein PdAfpB. Two of these genes lead to visual phenotypic changes (PDIG_53730/pksP, and PDIG_54100/arp2) and allowed to start the protocol optimization. The other three candidates (PDIG_56860, PDIG_33760/rodA and PDIG_68680/dfg5) had no visually associated phenotype and were targeted to confirm the high efficiency of the protocol. CONCLUSION Genome editing efficiency of P. digitatum was significantly increased from 10% to up to 83% through the modification of the selection methodology, which demonstrates the feasibility of the CRISPR/Cas9 system for gene disruption in this phytopathogenic fungus. Moreover, the approach described in this study might help increase CRISPR/Cas9 gene editing efficiencies in other economically relevant fungal species for which editing efficiency via CRISPR/Cas9 is still low.
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Affiliation(s)
- Carolina Ropero-Pérez
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Catedrático Agustín Escardino Benlloch 7, Paterna, Valencia, 46980, Spain
| | - Jose F Marcos
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Catedrático Agustín Escardino Benlloch 7, Paterna, Valencia, 46980, Spain
| | - Paloma Manzanares
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Catedrático Agustín Escardino Benlloch 7, Paterna, Valencia, 46980, Spain
| | - Sandra Garrigues
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Catedrático Agustín Escardino Benlloch 7, Paterna, Valencia, 46980, Spain.
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11
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Zhou J, Pan Q, Xue Y, Dong Y, Chen Y, Huang L, Zhang B, Liu ZQ, Zheng Y. Synthetic biology for Monascus: From strain breeding to industrial production. Biotechnol J 2024; 19:e2400180. [PMID: 39014924 DOI: 10.1002/biot.202400180] [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: 03/19/2024] [Revised: 06/25/2024] [Accepted: 06/29/2024] [Indexed: 07/18/2024]
Abstract
Traditional Chinese food therapies often motivate the development of modern medicines, and learning from them will bring bright prospects. Monascus, a conventional Chinese fungus with centuries of use in the food industry, produces various metabolites, including natural pigments, lipid-lowering substances, and other bioactive ingredients. Recent Monascus studies focused on the metabolite biosynthesis mechanisms, strain modifications, and fermentation process optimizations, significantly advancing Monascus development on a lab scale. However, the advanced manufacture for Monascus is lacking, restricting its scale production. Here, the synthetic biology techniques and their challenges for engineering filamentous fungi were summarized, especially for Monascus. With further in-depth discussions of automatic solid-state fermentation manufacturing and prospects for combining synthetic biology and process intensification, the industrial scale production of Monascus will succeed with the help of Monascus improvement and intelligent fermentation control, promoting Monascus applications in food, cosmetic, agriculture, medicine, and environmental protection industries.
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Affiliation(s)
- Junping Zhou
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Qilu Pan
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Yinan Xue
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Yaping Dong
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Yihong Chen
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Lianggang Huang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Bo Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Zhi-Qiang Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Yuguo Zheng
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
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12
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Huang L, Li N, Song Y, Gao J, Nian L, Zhou J, Zhang B, Liu Z, Zheng Y. Development of a marker recyclable CRISPR/Cas9 system for scarless and multigene editing in Fusarium fujikuroi. Biotechnol J 2024; 19:e2400164. [PMID: 39014928 DOI: 10.1002/biot.202400164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 06/28/2024] [Accepted: 07/02/2024] [Indexed: 07/18/2024]
Abstract
Iterative metabolic engineering of Fusarium fujikuroi has traditionally been hampered by its low homologous recombination efficiency and scarcity of genetic markers. Thus, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas9) system has emerged as a promising tool for precise genome editing in this organism. Some integrated CRISPR/Cas9 strategies have been used to engineer F. fujikuroi to improve GA3 production capabilities, but low editing efficiency and possible genomic instability became the major obstacle. Herein, we developed a marker recyclable CRISPR/Cas9 system for scarless and multigene editing in F. fujikuroi. This system, based on an autonomously replicating sequence, demonstrated the capability of a single plasmid harboring all editing components to achieve 100%, 75%, and 37.5% editing efficiency for single, double, and triple gene targets, respectively. Remarkably, even with a reduction in homologous arms to 50 bp, we achieved a 12.5% gene editing efficiency. By employing this system, we successfully achieved multicopy integration of the truncated 3-hydroxy-3-methyl glutaryl coenzyme A reductase gene (tHMGR), leading to enhanced GA3 production. A key advantage of our plasmid-based gene editing approach was the ability to recycle selective markers through a simplified protoplast preparation and recovery process, which eliminated the need for additional genetic markers. These findings demonstrated that the single-plasmid CRISPR/Cas9 system enables rapid and precise multiple gene deletions/integrations, laying a solid foundation for future metabolic engineering efforts aimed at industrial GA3 production.
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Affiliation(s)
- Lianggang Huang
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Ningning Li
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Yixin Song
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Jie Gao
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Lu Nian
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Junping Zhou
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Bo Zhang
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Zhiqiang Liu
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Yuguo Zheng
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
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13
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Tang T, Ding Y, Guo W. Development of an Efficient CRISPR/Cas9 System in Fusarium verticillioides and Its Application in Reducing Mycotoxin Contamination. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:14229-14240. [PMID: 38797952 DOI: 10.1021/acs.jafc.4c01914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Fusarium verticillioides (F. verticillioides) is a globally recognized and highly impactful fungal pathogen of maize, causing yield losses and producing harmful mycotoxins that pose a threat to human and animal health. However, the genetic tools available for studying this crucial fungus are currently limited in comparison to other important fungal pathogens. To address this, an efficient CRISPR/Cas9 genome editing system based on an autonomously replicating plasmid with an AMA1 sequence was established in this study. First, gene disruption of pyrG and pyrE via nonhomologous end-joining (NHEJ) pathway was successfully achieved, with efficiency ranging from 66 to 100%. Second, precise gene deletions were achieved with remarkable efficiency using a dual sgRNA expression strategy. Third, the developed genome editing system can be applied to generate designer chromosomes in F. verticillioides, as evidenced by the deletion of a crucial 38 kb fragment required for fumonisin biosynthesis. Fourth, the pyrG recycling system has been established and successfully applied in F. verticillioides. Lastly, the developed ΔFUM1 and ΔFUM mutants can serve as biocontrol agents to reduce the fumonisin B1 (FB1) contamination produced by the toxigenic strain. Taken together, these significant advancements in genetic manipulation and biocontrol strategies provide valuable tools for studying and mitigating the impact of F. verticillioides on maize crops.
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Affiliation(s)
- Tingting Tang
- Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Institute of Food Science and Technology, Beijing 100193, P. R. China
| | - Yi Ding
- Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Institute of Food Science and Technology, Beijing 100193, P. R. China
| | - Wei Guo
- Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Institute of Food Science and Technology, Beijing 100193, P. R. China
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14
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Coca-Ruiz V, Cabrera-Gómez N, Collado IG, Aleu J. Improved Protoplast Production Protocol for Fungal Transformations Mediated by CRISPR/Cas9 in Botrytis cinerea Non-Sporulating Isolates. PLANTS (BASEL, SWITZERLAND) 2024; 13:1754. [PMID: 38999594 PMCID: PMC11244380 DOI: 10.3390/plants13131754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/18/2024] [Accepted: 06/21/2024] [Indexed: 07/14/2024]
Abstract
Botrytis cinerea is a necrotrophic fungus that causes considerable economic losses in commercial crops. Fungi of the genus Botrytis exhibit great morphological and genetic variability, ranging from non-sporogenic and non-infective isolates to highly virulent sporogenic ones. There is growing interest in the different isolates in terms of their methodological applications aimed at gaining a deeper understanding of the biology of these fungal species for more efficient control of the infections they cause. This article describes an improvement in the protoplast production protocol from non-sporogenic isolates, resulting in viable protoplasts with regenerating capacity. The method improvements consist of a two-day incubation period with mycelium plugs and orbital shaking. Special mention is made of our preference for the VinoTaste Pro enzyme in the KC buffer as a replacement for Glucanex, as it enhances the efficacy of protoplast isolation in B459 and B371 isolates. The methodology described here has proven to be very useful for biotechnological applications such as genetic transformations mediated by the CRISPR/Cas9 tool.
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Affiliation(s)
- Víctor Coca-Ruiz
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
- Instituto de Investigación en Biomoléculas (INBIO), Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
| | - Nuria Cabrera-Gómez
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
- Instituto de Investigación en Biomoléculas (INBIO), Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
| | - Isidro G Collado
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
- Instituto de Investigación en Biomoléculas (INBIO), Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
| | - Josefina Aleu
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
- Instituto de Investigación en Biomoléculas (INBIO), Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
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15
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Wassano NS, da Silva GB, Reis AH, A Gerhardt J, Antoniel EP, Akiyama D, Rezende CP, Neves LX, Vasconcelos EJR, de Figueiredo FL, Almeida F, de Castro PA, Pinzan CF, Goldman GH, Paes Leme AF, Fill TP, Moretti NS, Damasio A. Sirtuin E deacetylase is required for full virulence of Aspergillus fumigatus. Commun Biol 2024; 7:704. [PMID: 38851817 PMCID: PMC11162503 DOI: 10.1038/s42003-024-06383-3] [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: 10/03/2023] [Accepted: 05/24/2024] [Indexed: 06/10/2024] Open
Abstract
Aspergillus fumigatus represents a public health problem due to the high mortality rate in immunosuppressed patients and the emergence of antifungal-resistant isolates. Protein acetylation is a crucial post-translational modification that controls gene expression and biological processes. The strategic manipulation of enzymes involved in protein acetylation has emerged as a promising therapeutic approach for addressing fungal infections. Sirtuins, NAD+-dependent lysine deacetylases, regulate protein acetylation and gene expression in eukaryotes. However, their role in the human pathogenic fungus A. fumigatus remains unclear. This study constructs six single knockout strains of A. fumigatus and a strain lacking all predicted sirtuins (SIRTKO). The mutant strains are viable under laboratory conditions, indicating that sirtuins are not essential genes. Phenotypic assays suggest sirtuins' involvement in cell wall integrity, secondary metabolite production, thermotolerance, and virulence. Deletion of sirE attenuates virulence in murine and Galleria mellonella infection models. The absence of SirE alters the acetylation status of proteins, including histones and non-histones, and triggers significant changes in the expression of genes associated with secondary metabolism, cell wall biosynthesis, and virulence factors. These findings encourage testing sirtuin inhibitors as potential therapeutic strategies to combat A. fumigatus infections or in combination therapy with available antifungals.
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Affiliation(s)
- Natália S Wassano
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- National Institute of Science and Technology in Human Pathogenic Fungi, Ribeirão Preto, Brazil
| | - Gabriela B da Silva
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- National Institute of Science and Technology in Human Pathogenic Fungi, Ribeirão Preto, Brazil
- Department of Microbiology, Immunology and Parasitology, Paulist School of Medicine, Federal University of São Paulo, São Paulo, Brazil
| | - Artur H Reis
- Department of Microbiology, Immunology and Parasitology, Paulist School of Medicine, Federal University of São Paulo, São Paulo, Brazil
| | - Jaqueline A Gerhardt
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Everton P Antoniel
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Daniel Akiyama
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, Brazil
| | - Caroline P Rezende
- Department of Biochemistry and Immunology, Faculty of Medicine from Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Leandro X Neves
- Brazilian Bioscience National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | | | - Fernanda L de Figueiredo
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Fausto Almeida
- Department of Biochemistry and Immunology, Faculty of Medicine from Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Patrícia A de Castro
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Camila F Pinzan
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Gustavo H Goldman
- National Institute of Science and Technology in Human Pathogenic Fungi, Ribeirão Preto, Brazil
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Adriana F Paes Leme
- Brazilian Bioscience National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Taicia P Fill
- National Institute of Science and Technology in Human Pathogenic Fungi, Ribeirão Preto, Brazil
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, Brazil
| | - Nilmar S Moretti
- Department of Microbiology, Immunology and Parasitology, Paulist School of Medicine, Federal University of São Paulo, São Paulo, Brazil.
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, Canada.
- The Research Group on Infectious Diseases in Production Animals (GREMIP), Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, Canada.
| | - André Damasio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil.
- National Institute of Science and Technology in Human Pathogenic Fungi, Ribeirão Preto, Brazil.
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16
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Peng T, Guo J, Tong X. Advances in biosynthesis and metabolic engineering strategies of cordycepin. Front Microbiol 2024; 15:1386855. [PMID: 38903790 PMCID: PMC11188397 DOI: 10.3389/fmicb.2024.1386855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 04/26/2024] [Indexed: 06/22/2024] Open
Abstract
Cordyceps militaris, also called as bei-chong-cao, is an insect-pathogenic fungus from the Ascomycota phylum and the Clavicipitaceae family. It is a valuable filamentous fungus with medicinal and edible properties that has been utilized in traditional Chinese medicine (TCM) and as a nutritious food. Cordycepin is the bioactive compound firstly isolated from C. militaris and has a variety of nutraceutical and health-promoting properties, making it widely employed in nutraceutical and pharmaceutical fields. Due to the low composition and paucity of wild resources, its availability from natural sources is limited. With the elucidation of the cordycepin biosynthetic pathway and the advent of synthetic biology, a green cordycepin biosynthesis in Saccharomyces cerevisiae and Metarhizium robertsii has been developed, indicating a potential sustainable production method of cordycepin. Given that, this review primarily focused on the metabolic engineering and heterologous biosynthesis strategies of cordycepin.
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Affiliation(s)
| | - Jinlin Guo
- The Ministry of Education Key Laboratory of Standardization of Chinese Medicine, Key Laboratory of Systematic Research of Distinctive Chinese Medicine Resources in Southwest China, Resources Breeding Base of Co-Founded, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Xinxin Tong
- The Ministry of Education Key Laboratory of Standardization of Chinese Medicine, Key Laboratory of Systematic Research of Distinctive Chinese Medicine Resources in Southwest China, Resources Breeding Base of Co-Founded, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
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17
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Chen X, Moran Torres JP, Jan Vonk P, Damen JMA, Reiding KR, Dijksterhuis J, Lugones LG, Wösten HAB. The pleiotropic phenotype of FlbA of Aspergillus niger is explained in part by the activity of seven of its downstream-regulated transcription factors. Fungal Genet Biol 2024; 172:103894. [PMID: 38657897 DOI: 10.1016/j.fgb.2024.103894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 04/03/2024] [Accepted: 04/22/2024] [Indexed: 04/26/2024]
Abstract
Inactivation of flbA in Aspergillus niger results in thinner cell walls, increased cell lysis, abolished sporulation, and an increased secretome complexity. A total of 36 transcription factor (TF) genes are differentially expressed in ΔflbA. Here, seven of these genes (abaA, aslA, aslB, azf1, htfA, nosA, and srbA) were inactivated. Inactivation of each of these genes affected sporulation and, with the exception of abaA, cell wall integrity and protein secretion. The impact on secretion was strongest in the case of ΔaslA and ΔaslB that showed increased pepsin, cellulase, and amylase activity. Biomass was reduced of agar cultures of ΔabaA, ΔaslA, ΔnosA, and ΔsrbA, while biomass was higher in liquid shaken cultures of ΔaslA and ΔaslB. The ΔaslA and ΔhtfA strains showed increased resistance to H2O2, while ΔaslB was more sensitive to this reactive oxygen species. Together, inactivation of the seven TF genes impacted biomass formation, sporulation, protein secretion, and stress resistance, and thereby these genes explain at least part of the pleiotropic phenotype of ΔflbA of A. niger.
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Affiliation(s)
- Xiaoyi Chen
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Juan P Moran Torres
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Peter Jan Vonk
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - J Mirjam A Damen
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Karli R Reiding
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Jan Dijksterhuis
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
| | - Luis G Lugones
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Han A B Wösten
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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18
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Steinert K, Atanasoff-Kardjalieff AK, Messner E, Gorfer M, Niehaus EM, Humpf HU, Studt-Reinhold L, Kalinina SA. Tools to make Stachybotrys chartarum genetically amendable: Key to unlocking cryptic biosynthetic gene clusters. Fungal Genet Biol 2024; 172:103892. [PMID: 38636782 DOI: 10.1016/j.fgb.2024.103892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 04/12/2024] [Accepted: 04/13/2024] [Indexed: 04/20/2024]
Abstract
The soil and indoor fungus Stachybotrys chartarum can induce respiratory disorders, collectively referred to as stachybotryotoxicosis, owing to its prolific production of diverse bioactive secondary metabolites (SMs) or mycotoxins. Although many of these toxins responsible for the harmful effects on animals and humans have been identified in the genus Stachybotrys, however a number of SMs remain elusive. Through in silico analyses, we have identified 37 polyketide synthase (PKS) genes, highlighting that the chemical profile potential of Stachybotrys is far from being fully explored. Additionally, by leveraging phylogenetic analysis of known SMs produced by non-reducing polyketide synthases (NR-PKS) in other filamentous fungi, we showed that Stachybotrys possesses a rich reservoir of untapped SMs. To unravel natural product biosynthesis in S. chartarum, genetic engineering methods are crucial. For this purpose, we have developed a reliable protocol for the genetic transformation of S. chartarum and applied it to the ScPKS14 biosynthetic gene cluster. This cluster is homologous to the already known Claviceps purpurea CpPKS8 BGC, responsible for the production of ergochromes. While no novel SMs were detected, we successfully applied genetic tools, such as the generation of deletionand overexpression strains of single cluster genes. This toolbox can now be readily employed to unravel not only this particular BGC but also other candidate BGCs present in S. chartarum, making this fungus accessible for genetic engineering.
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Affiliation(s)
| | - Anna K Atanasoff-Kardjalieff
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln an der Donau, Austria
| | - Elias Messner
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln an der Donau, Austria
| | - Markus Gorfer
- Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Eva-Maria Niehaus
- Institute of Food Chemistry, University of Münster, Münster, Germany
| | - Hans-Ulrich Humpf
- Institute of Food Chemistry, University of Münster, Münster, Germany
| | - Lena Studt-Reinhold
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln an der Donau, Austria.
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19
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Guo Y, Liu JZ, Limwachiranon J, Xu F, Han Y, Xu L, Xiong Z, Zhang N, Ding G, Scharf DH. Reconstitution of the Early Stage of Chetomin Biosynthesis in Aspergillus fumigatus Leads to the Production of Epipolythiodioxopiperazines. Org Lett 2024; 26:4469-4474. [PMID: 38767929 DOI: 10.1021/acs.orglett.4c01274] [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: 05/22/2024]
Abstract
Using CRISPR-Cas9 technology and a microhomology-mediated end-joining repair system, we substituted genes of the gliotoxin pathway in Aspergillus fumigatus with genes responsible for chetomin biosynthesis from Chaetomium cochliodes, leading to the production of three new epipolythiodioxopiperazines (ETPs). This work represents the first successful endeavor to produce ETPs in a non-native host. Additionally, the simultaneous disruption of five genes in a single transformation marks the most extensive gene knockout event in filamentous fungi to date.
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Affiliation(s)
- Yaojie Guo
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, People's Republic of China
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310052, People's Republic of China
| | - Jian-Zi Liu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, People's Republic of China
| | - Jarukitt Limwachiranon
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Fan Xu
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Yi Han
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Liru Xu
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Zhenzhen Xiong
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Nan Zhang
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Gang Ding
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, People's Republic of China
| | - Daniel H Scharf
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, People's Republic of China
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang 322000, People's Republic of China
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20
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Wasim M, Ghaffar U, Javed MR, Nawaz H, Majeed MI, Ijaz A, Ishtiaq S, Rehman N, Razaq R, Younas S, Bano A, Kanwal N, Imran M. Surface-Enhanced Raman Spectroscopy for Monitoring the Biochemical Changes Due to DNA Mutations Induced by CRISPR-Cas9 Genome Editing in the Aspergillus niger Fungus. ACS OMEGA 2024; 9:15202-15209. [PMID: 38585125 PMCID: PMC10993282 DOI: 10.1021/acsomega.3c09563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/22/2024] [Accepted: 03/04/2024] [Indexed: 04/09/2024]
Abstract
In this study, surface-enhanced Raman spectroscopy (SERS) technique, along with principal component analysis (PCA) and partial least-squares discriminant analysis (PLS-DA), is used as a simple, quick, and cost-effective analysis method for identifying biochemical changes occurring due to induced mutations in the Aspergillus niger fungus strain. The goal of this study is to identify the biochemical changes in the mutated fungal cells (cell mass) as compared to the control/nonmutated cells. Furthermore, multivariate data analysis tools, including PCA and PLS-DA, are used to further confirm the differentiating SERS spectral features among fungal samples. The mutations are caused in A. niger by the clustered regularly interspaced palindromic repeat CRISPR-Cas9 genomic editing method to improve their biotechnological potential for the production of cellulase enzyme. SERS was employed to detect the changes in the cells of mutated A. niger fungal strains, including one mutant producing low levels of an enzyme and another mutant producing high levels of the enzyme as a result of mutation as compared with an unmutated fungal strain as a control sample. The distinctive features of SERS corresponding to nucleic acids and proteins appear at 546, 622, 655, 738, 802, 835, 959, 1025, 1157, 1245, 1331, 1398, and 1469 cm-1. Furthermore, PLS-DA is used to confirm the 89% accuracy, 87.7% precision, 87% sensitivity, and 88.9% specificity of this method, and the value of the area under the curve (AUROC) is 0.67. It has been shown that surface-enhanced Raman spectroscopy is an effective method for identifying and differentiating biochemical changes in genome-modified fungal samples.
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Affiliation(s)
- Muhammad Wasim
- Department
of Chemistry, University of Agriculture
Faisalabad, Faisalabad 38000, Pakistan
| | - Usman Ghaffar
- Department
of Chemistry, University of Agriculture
Faisalabad, Faisalabad 38000, Pakistan
| | - Muhammad Rizwan Javed
- Biocatalysis
and Protein Engineering Research Group (BPERG), Department of Bioinformatics
and Biotechnology, Government College University
Faisalabad (GCUF), Allama
Iqbal Road, Faisalabad 38000, Pakistan
| | - Haq Nawaz
- Department
of Chemistry, University of Agriculture
Faisalabad, Faisalabad 38000, Pakistan
| | - Muhammad Irfan Majeed
- Department
of Chemistry, University of Agriculture
Faisalabad, Faisalabad 38000, Pakistan
| | - Anam Ijaz
- Biocatalysis
and Protein Engineering Research Group (BPERG), Department of Bioinformatics
and Biotechnology, Government College University
Faisalabad (GCUF), Allama
Iqbal Road, Faisalabad 38000, Pakistan
| | - Shazra Ishtiaq
- Department
of Chemistry, University of Agriculture
Faisalabad, Faisalabad 38000, Pakistan
| | - Nimra Rehman
- Department
of Chemistry, University of Agriculture
Faisalabad, Faisalabad 38000, Pakistan
| | - Rabeea Razaq
- Department
of Chemistry, University of Agriculture
Faisalabad, Faisalabad 38000, Pakistan
| | - Sobia Younas
- Department
of Chemistry, University of Agriculture
Faisalabad, Faisalabad 38000, Pakistan
| | - Aqsa Bano
- Department
of Chemistry, University of Agriculture
Faisalabad, Faisalabad 38000, Pakistan
| | - Naeema Kanwal
- Department
of Chemistry, University of Agriculture
Faisalabad, Faisalabad 38000, Pakistan
| | - Muhammad Imran
- Department
of Chemistry, Faculty of Science, King Khalid
University, P.O. Box 9004, Abha 61413, Saudi Arabia
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Shen Q, Ruan H, Zhang H, Wu T, Zhu K, Han W, Dong R, Ming T, Qi H, Zhang Y. Utilization of CRISPR-Cas genome editing technology in filamentous fungi: function and advancement potentiality. Front Microbiol 2024; 15:1375120. [PMID: 38605715 PMCID: PMC11007153 DOI: 10.3389/fmicb.2024.1375120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/04/2024] [Indexed: 04/13/2024] Open
Abstract
Filamentous fungi play a crucial role in environmental pollution control, protein secretion, and the production of active secondary metabolites. The evolution of gene editing technology has significantly improved the study of filamentous fungi, which in the past was laborious and time-consuming. But recently, CRISPR-Cas systems, which utilize small guide RNA (sgRNA) to mediate clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas), have demonstrated considerable promise in research and application for filamentous fungi. The principle, function, and classification of CRISPR-Cas, along with its application strategies and research progress in filamentous fungi, will all be covered in the review. Additionally, we will go over general matters to take into account when editing a genome with the CRISPR-Cas system, including the creation of vectors, different transformation methodologies, multiple editing approaches, CRISPR-mediated transcriptional activation (CRISPRa) or interference (CRISPRi), base editors (BEs), and Prime editors (PEs).
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Affiliation(s)
| | - Haihua Ruan
- Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
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Sun Z, Wu Y, Long S, Feng S, Jia X, Hu Y, Ma M, Liu J, Zeng B. Aspergillus oryzae as a Cell Factory: Research and Applications in Industrial Production. J Fungi (Basel) 2024; 10:248. [PMID: 38667919 PMCID: PMC11051239 DOI: 10.3390/jof10040248] [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: 02/08/2024] [Revised: 03/15/2024] [Accepted: 03/15/2024] [Indexed: 04/28/2024] Open
Abstract
Aspergillus oryzae, a biosafe strain widely utilized in bioproduction and fermentation technology, exhibits a robust hydrolytic enzyme secretion system. Therefore, it is frequently employed as a cell factory for industrial enzyme production. Moreover, A. oryzae has the ability to synthesize various secondary metabolites, such as kojic acid and L-malic acid. Nevertheless, the complex secretion system and protein expression regulation mechanism of A. oryzae pose challenges for expressing numerous heterologous products. By leveraging synthetic biology and novel genetic engineering techniques, A. oryzae has emerged as an ideal candidate for constructing cell factories. In this review, we provide an overview of the latest advancements in the application of A. oryzae-based cell factories in industrial production. These studies suggest that metabolic engineering and optimization of protein expression regulation are key elements in realizing the widespread industrial application of A. oryzae cell factories. It is anticipated that this review will pave the way for more effective approaches and research avenues in the future implementation of A. oryzae cell factories in industrial production.
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Affiliation(s)
- Zeao Sun
- College of Chemistry and Chemical Engineering, Jiangxi Science and Technology Normal University, Nanchang 330013, China; (Z.S.); (S.F.)
- College of Pharmacy, Shenzhen Technology University, Shenzhen 518118, China; (Y.W.); (S.L.); (X.J.); (Y.H.); (M.M.)
| | - Yijian Wu
- College of Pharmacy, Shenzhen Technology University, Shenzhen 518118, China; (Y.W.); (S.L.); (X.J.); (Y.H.); (M.M.)
| | - Shihua Long
- College of Pharmacy, Shenzhen Technology University, Shenzhen 518118, China; (Y.W.); (S.L.); (X.J.); (Y.H.); (M.M.)
| | - Sai Feng
- College of Chemistry and Chemical Engineering, Jiangxi Science and Technology Normal University, Nanchang 330013, China; (Z.S.); (S.F.)
- College of Pharmacy, Shenzhen Technology University, Shenzhen 518118, China; (Y.W.); (S.L.); (X.J.); (Y.H.); (M.M.)
| | - Xiao Jia
- College of Pharmacy, Shenzhen Technology University, Shenzhen 518118, China; (Y.W.); (S.L.); (X.J.); (Y.H.); (M.M.)
| | - Yan Hu
- College of Pharmacy, Shenzhen Technology University, Shenzhen 518118, China; (Y.W.); (S.L.); (X.J.); (Y.H.); (M.M.)
| | - Maomao Ma
- College of Pharmacy, Shenzhen Technology University, Shenzhen 518118, China; (Y.W.); (S.L.); (X.J.); (Y.H.); (M.M.)
| | - Jingxin Liu
- College of Pharmacy, Shenzhen Technology University, Shenzhen 518118, China; (Y.W.); (S.L.); (X.J.); (Y.H.); (M.M.)
| | - Bin Zeng
- College of Pharmacy, Shenzhen Technology University, Shenzhen 518118, China; (Y.W.); (S.L.); (X.J.); (Y.H.); (M.M.)
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Chen X, Moran Torres JP, Wösten HAB. The role of the Flb protein family in the life cycle of Aspergillus niger. Antonie Van Leeuwenhoek 2024; 117:58. [PMID: 38502333 PMCID: PMC10950988 DOI: 10.1007/s10482-024-01957-x] [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: 01/16/2024] [Accepted: 03/04/2024] [Indexed: 03/21/2024]
Abstract
Genes flbA-E are involved in sporulation and vegetative growth in Aspergillus nidulans. Inactivation of either of these genes results in a fluffy phenotype with delayed or even abolished sporulation. Previously, a non-sporulating phenotype was obtained by inactivating flbA in Aspergillus niger, which was accompanied by lysis, thinner cell walls, and an increased secretome complexity. Here, we further studied the role of the flb genes of A. niger. Strains ΔflbA, ΔflbB and ΔflbE showed increased biomass formation, while inactivation of flbA-D reduced, or even abolished, formation of conidia. Strain ΔflbA was more sensitive to H2O2, DTT, and the cell wall integrity stress compounds SDS and Congo Red (CR). Also, ΔflbC was more sensitive to SDS, while ΔflbB, ΔflbD, and ΔflbE were more sensitive to CR. On the other hand, inactivation of flbE increased resistance to H2O2. Enzyme secretion was impacted when the Δflb strains were grown on xylose. Strain ΔflbE showed reduced xylanase, cellulase and amylase secretion. On the other hand, amylase secretion at the periphery of the ΔflbA colony was reduced but not in its center, while secretion of this enzyme was increased in the center of the ΔflbB colony but not at its periphery. Inactivation of flbC and flbD also impacted zonal cellulase and amylase activity. Together, the Flb protein family of A. niger function in biomass formation, sporulation, stress response, and protein secretion.
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Affiliation(s)
- Xiaoyi Chen
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Juan P Moran Torres
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Han A B Wösten
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
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Palma D, Oliva V, Montanares M, Gil-Durán C, Travisany D, Chávez R, Vaca I. Expanding the Toolbox for Genetic Manipulation in Pseudogymnoascus: RNAi-Mediated Silencing and CRISPR/Cas9-Mediated Disruption of a Polyketide Synthase Gene Involved in Red Pigment Production in P. verrucosus. J Fungi (Basel) 2024; 10:157. [PMID: 38392828 PMCID: PMC10889956 DOI: 10.3390/jof10020157] [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: 11/03/2023] [Revised: 01/25/2024] [Accepted: 02/13/2024] [Indexed: 02/24/2024] Open
Abstract
Fungi belonging to the genus Pseudogymnoascus have garnered increasing attention in recent years. One of the members of the genus, P. destructans, has been identified as the causal agent of a severe bat disease. Simultaneously, the knowledge of Pseudogymnoascus species has expanded, in parallel with the increased availability of genome sequences. Moreover, Pseudogymnoascus exhibits great potential as a producer of specialized metabolites, displaying a diverse array of biological activities. Despite these significant advancements, the genetic landscape of Pseudogymnoascus remains largely unexplored due to the scarcity of suitable molecular tools for genetic manipulation. In this study, we successfully implemented RNAi-mediated gene silencing and CRISPR/Cas9-mediated disruption in Pseudogymnoascus, using an Antarctic strain of Pseudogymnoascus verrucosus as a model. Both methods were applied to target azpA, a gene involved in red pigment biosynthesis. Silencing of the azpA gene to levels of 90% or higher eliminated red pigment production, resulting in transformants exhibiting a white phenotype. On the other hand, the CRISPR/Cas9 system led to a high percentage (73%) of transformants with a one-nucleotide insertion, thereby inactivating azpA and abolishing red pigment production, resulting in a white phenotype. The successful application of RNAi-mediated gene silencing and CRISPR/Cas9-mediated disruption represents a significant advancement in Pseudogymnoascus research, opening avenues for comprehensive functional genetic investigations within this underexplored fungal genus.
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Affiliation(s)
- Diego Palma
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Vicente Oliva
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Mariana Montanares
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Carlos Gil-Durán
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, USACH, Santiago 9170022, Chile
| | - Dante Travisany
- Núcleo de Investigación en Data Science, Facultad de Ingeniería y Negocios, Universidad de Las Américas, Santiago 7500975, Chile
| | - Renato Chávez
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, USACH, Santiago 9170022, Chile
| | - Inmaculada Vaca
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
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Zhang J, Li K, Sun Y, Yao C, Liu W, Liu H, Zhong Y. An efficient CRISPR/Cas9 genome editing system based on a multiple sgRNA processing platform in Trichoderma reesei for strain improvement and enzyme production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:22. [PMID: 38342915 DOI: 10.1186/s13068-024-02468-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 01/29/2024] [Indexed: 02/13/2024]
Abstract
BACKGROUND The CRISPR/Cas9 technology is being employed as a convenient tool for genetic engineering of the industrially important filamentous fungus Trichoderma reesei. However, multiplex gene editing is still constrained by the sgRNA processing capability, hindering strain improvement of T. reesei for the production of lignocellulose-degrading enzymes and recombinant proteins. RESULTS Here, a CRISPR/Cas9 system based on a multiple sgRNA processing platform was established for genome editing in T. reesei. The platform contains the arrayed tRNA-sgRNA architecture directed by a 5S rRNA promoter to generate multiple sgRNAs from a single transcript by the endogenous tRNA processing system. With this system, two sgRNAs targeting cre1 (encoding the carbon catabolite repressor 1) were designed and the precise deletion of cre1 was obtained, demonstrating the efficiency of sgRNAs processing in the tRNA-sgRNA architecture. Moreover, overexpression of xyr1-A824V (encoding a key activator for cellulase/xylanase expression) at the ace1 (encoding a repressor for cellulase/xylanase expression) locus was achieved by designing two sgRNAs targeting ace1 in the system, resulting in the significantly enhanced production of cellulase (up to 1- and 18-fold on the Avicel and glucose, respectively) and xylanase (up to 11- and 41-fold on the Avicel and glucose, respectively). Furthermore, heterologous expression of the glucose oxidase gene from Aspergillus niger ATCC 9029 at the cbh1 locus with the simultaneous deletion of cbh1 and cbh2 (two cellobiohydrolase coding genes) by designing four sgRNAs targeting cbh1 and cbh2 in the system was acquired, and the glucose oxidase produced by T. reesei reached 43.77 U/mL. Besides, it was found the ER-associated protein degradation (ERAD) level was decreased in the glucose oxidase-producing strain, which was likely due to the reduction of secretion pressure by deletion of the major endogenous cellulase-encoding genes. CONCLUSIONS The tRNA-gRNA array-based CRISPR-Cas9 editing system was successfully developed in T. reesei. This system would accelerate engineering of T. reesei for high-level production of enzymes including lignocellulose-degrading enzymes and other recombinant enzymes. Furthermore, it would expand the CRISPR toolbox for fungal genome editing and synthetic biology.
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Affiliation(s)
- Jiaxin Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Kehang Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Yu Sun
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Cheng Yao
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Hong Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China.
| | - Yaohua Zhong
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China.
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Liu XL, Xie J, Xie ZN, Zhong C, Liu H, Zhang SH, Jin J. Identification of squalene epoxidase in triterpenes biosynthesis in Poria cocos by molecular docking and CRISPR-Cas9 gene editing. Microb Cell Fact 2024; 23:34. [PMID: 38273342 PMCID: PMC10809676 DOI: 10.1186/s12934-024-02306-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/14/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Squalene epoxidase is one of the rate-limiting enzymes in the biosynthetic pathway of membrane sterols and triterpenoids. The enzyme catalyzes the formation of oxidized squalene, which is a common precursor of sterols and triterpenoids. RESULT In this study, the squalene epoxidase gene (PcSE) was evaluated in Poria cocos. Molecular docking between PcSE and squalene was performed and the active amino acids were identified. The sgRNA were designed based on the active site residues. The effect on triterpene synthesis in P. cocos was consistent with the results from ultra-high-performance liquid chromatography-quadruplex time-of-flight-double mass spectrometry (UHPLC-QTOF-MS/MS) analysis. The results showed that deletion of PcSE inhibited triterpene synthesis. In vivo verification of PcSE function was performed using a PEG-mediated protoplast transformation approach. CONCLUSION The findings from this study provide a foundation for further studies on heterologous biosynthesis of P. cocos secondary metabolites.
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Affiliation(s)
- Xiao-Liu Liu
- Institute of Chinese Medicine Resources, Hunan Academy of Chinese Medicine, Changsha, 410013, China
- Hunan Academy of Chinese Medicine, Hunan University of Traditional Chinese Medicine, Changsha, 410208, China
| | - Jing Xie
- Institute of Chinese Medicine Resources, Hunan Academy of Chinese Medicine, Changsha, 410013, China
- Hunan Academy of Chinese Medicine, Hunan University of Traditional Chinese Medicine, Changsha, 410208, China
| | - Zhen-Ni Xie
- Institute of Chinese Medicine Resources, Hunan Academy of Chinese Medicine, Changsha, 410013, China
- Hunan Academy of Chinese Medicine, Hunan University of Traditional Chinese Medicine, Changsha, 410208, China
| | - Can Zhong
- Institute of Chinese Medicine Resources, Hunan Academy of Chinese Medicine, Changsha, 410013, China
| | - Hao Liu
- Institute of Chinese Medicine Resources, Hunan Academy of Chinese Medicine, Changsha, 410013, China.
| | - Shui-Han Zhang
- Institute of Chinese Medicine Resources, Hunan Academy of Chinese Medicine, Changsha, 410013, China
- Hunan Academy of Chinese Medicine, Hunan University of Traditional Chinese Medicine, Changsha, 410208, China
| | - Jian Jin
- Institute of Chinese Medicine Resources, Hunan Academy of Chinese Medicine, Changsha, 410013, China.
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Gong Y, Li S, Liu Q, Chen F, Shao Y. CRISPR/Cas9 system is a suitable gene targeting editing tool to filamentous fungus Monascus pilosus. Appl Microbiol Biotechnol 2024; 108:154. [PMID: 38240803 PMCID: PMC10799099 DOI: 10.1007/s00253-023-12865-x] [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: 06/04/2023] [Revised: 10/08/2023] [Accepted: 10/18/2023] [Indexed: 01/22/2024]
Abstract
Monascus pilosus has been used to produce lipid-lowering drugs rich in monacolin K (MK) for a long period. Genome mining reveals there are still many potential genes worth to be explored in this fungus. Thereby, efficient genetic manipulation tools will greatly accelerate this progress. In this study, we firstly developed the protocol to prepare protoplasts for recipient of CRISPR/Cas9 system. Subsequently, the vector and donor DNA were co-transformed into recipients (106 protoplasts/mL) to produce 60-80 transformants for one test. Three genes (mpclr4, mpdot1, and mplig4) related to DNA damage response (DDR) were selected to compare the gene replacement frequencies (GRFs) of Agrobacterium tumefaciens-mediated transformation (ATMT) and CRISPR/Cas9 gene editing system (CGES) in M. pilosus MS-1. The results revealed that GRF of CGES was approximately five times greater than that of ATMT, suggesting that CGES was superior to ATMT as a targeting gene editing tool in M. pilosus MS-1. The inactivation of mpclr4 promoted DDR via the non-homologous end-joining (NHEJ) and increased the tolerances to DNA damaging agents. The inactivation of mpdot1 blocked DDR and led to the reduced tolerances to DNA damaging agents. The inactivation of mplig4 mainly blocked the NHEJ pathway and led to obviously reduced tolerances to DNA damaging agents. The submerged fermentation showed that the ability to produce MK in strain Δmpclr4 was improved by 52.6% compared to the wild type. This study provides an idea for more effective exploration of gene functions in Monascus strains. KEY POINTS: • A protocol of high-quality protoplasts for CGES has been developed in M. pilosus. • The GRF of CGES was about five times that of ATMT in M. pilosus. • The yield of MK for Δmpclr4 was enhanced by 52.6% compared with the wild type.
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Affiliation(s)
- Yunxia Gong
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shengfa Li
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qianrui Liu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fusheng Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yanchun Shao
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, 430070, China.
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28
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Joehnk B, Ali N, Voorhies M, Walcott K, Sil A. Recyclable CRISPR/Cas9-mediated gene disruption and deletions in Histoplasma. mSphere 2023; 8:e0037023. [PMID: 37819140 PMCID: PMC10732100 DOI: 10.1128/msphere.00370-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 07/17/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE Histoplasma is a primary fungal pathogen with the ability to infect otherwise healthy mammalian hosts, causing systemic and sometimes life-threatening disease. Thus far, molecular genetic manipulation of this organism has utilized RNA interference, random insertional mutagenesis, and a homologous recombination protocol that is highly variable and often inefficient. Targeted gene manipulations have been challenging due to poor rates of homologous recombination events in Histoplasma. Interrogation of the virulence strategies of this organism would be highly accelerated by a means of efficiently generating targeted mutations. We have developed a recyclable CRISPR/Cas9 system that can be used to introduce gene disruptions in Histoplasma with high efficiency, thereby allowing disruption of multiple genes.
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Affiliation(s)
- Bastian Joehnk
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Nebat Ali
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Mark Voorhies
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Keith Walcott
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Anita Sil
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, USA
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29
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Pepe M, Hesami M, de la Cerda KA, Perreault ML, Hsiang T, Jones AMP. A journey with psychedelic mushrooms: From historical relevance to biology, cultivation, medicinal uses, biotechnology, and beyond. Biotechnol Adv 2023; 69:108247. [PMID: 37659744 DOI: 10.1016/j.biotechadv.2023.108247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/04/2023]
Abstract
Psychedelic mushrooms containing psilocybin and related tryptamines have long been used for ethnomycological purposes, but emerging evidence points to the potential therapeutic value of these mushrooms to address modern neurological, psychiatric health, and related disorders. As a result, psilocybin containing mushrooms represent a re-emerging frontier for mycological, biochemical, neuroscience, and pharmacology research. This work presents crucial information related to traditional use of psychedelic mushrooms, as well as research trends and knowledge gaps related to their diversity and distribution, technologies for quantification of tryptamines and other tryptophan-derived metabolites, as well as biosynthetic mechanisms for their production within mushrooms. In addition, we explore the current state of knowledge for how psilocybin and related tryptamines are metabolized in humans and their pharmacological effects, including beneficial and hazardous human health implications. Finally, we describe opportunities and challenges for investigating the production of psychedelic mushrooms and metabolic engineering approaches to alter secondary metabolite profiles using biotechnology integrated with machine learning. Ultimately, this critical review of all aspects related to psychedelic mushrooms represents a roadmap for future research efforts that will pave the way to new applications and refined protocols.
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Affiliation(s)
- Marco Pepe
- Department of Plant Agriculture, University of Guelph, Ontario N1G 2W1, Guelph, Canada
| | - Mohsen Hesami
- Department of Plant Agriculture, University of Guelph, Ontario N1G 2W1, Guelph, Canada
| | - Karla A de la Cerda
- School of Environmental Sciences, University of Guelph, Ontario N1G 2W1, Guelph, Canada
| | - Melissa L Perreault
- Departments of Biomedical Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Ontario N1G 2W1, Guelph, Canada
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Seekles SJ, van den Brule T, Punt M, Dijksterhuis J, Arentshorst M, Ijadpanahsaravi M, Roseboom W, Meuken G, Ongenae V, Zwerus J, Ohm RA, Kramer G, Wösten HAB, de Winde JH, Ram AFJ. Compatible solutes determine the heat resistance of conidia. Fungal Biol Biotechnol 2023; 10:21. [PMID: 37957766 PMCID: PMC10644514 DOI: 10.1186/s40694-023-00168-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Asexually developed fungal spores (conidia) are key for the massive proliferation and dispersal of filamentous fungi. Germination of conidia and subsequent formation of a mycelium network give rise to many societal problems related to human and animal fungal diseases, post-harvest food spoilage, loss of harvest caused by plant-pathogenic fungi and moulding of buildings. Conidia are highly stress resistant compared to the vegetative mycelium and therefore even more difficult to tackle. RESULTS In this study, complementary approaches are used to show that accumulation of mannitol and trehalose as the main compatible solutes during spore maturation is a key factor for heat resistance of conidia. Compatible solute concentrations increase during conidia maturation, correlating with increased heat resistance of mature conidia. This maturation only occurs when conidia are attached to the conidiophore. Moreover, conidia of a mutant Aspergillus niger strain, constructed by deleting genes involved in mannitol and trehalose synthesis and consequently containing low concentrations of these compatible solutes, exhibit a sixteen orders of magnitude more sensitive heat shock phenotype compared to wild-type conidia. Cultivation at elevated temperature results in adaptation of conidia with increased heat resistance. Transcriptomic and proteomic analyses revealed two putative heat shock proteins to be upregulated under these conditions. However, conidia of knock-out strains lacking these putative heat shock proteins did not show a reduced heat resistance. CONCLUSIONS Heat stress resistance of fungal conidia is mainly determined by the compatible solute composition established during conidia maturation. To prevent heat resistant fungal spore contaminants, food processing protocols should consider environmental conditions stimulating compatible solute accumulation and potentially use compatible solute biosynthesis as a novel food preservation target.
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Affiliation(s)
- Sjoerd J Seekles
- TiFN, P.O. Box 557, 6700 AN, Wageningen, the Netherlands
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Sylviusweg 72, 2333 BE, Leiden, the Netherlands
| | - Tom van den Brule
- TiFN, P.O. Box 557, 6700 AN, Wageningen, the Netherlands
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands
| | - Maarten Punt
- TiFN, P.O. Box 557, 6700 AN, Wageningen, the Netherlands
- Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Jan Dijksterhuis
- TiFN, P.O. Box 557, 6700 AN, Wageningen, the Netherlands
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands
| | - Mark Arentshorst
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Sylviusweg 72, 2333 BE, Leiden, the Netherlands
| | - Maryam Ijadpanahsaravi
- Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Winfried Roseboom
- Mass Spectrometry of Biomolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1090 GE, Amsterdam, the Netherlands
| | - Gwendolin Meuken
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Sylviusweg 72, 2333 BE, Leiden, the Netherlands
| | - Véronique Ongenae
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Sylviusweg 72, 2333 BE, Leiden, the Netherlands
| | - Jordy Zwerus
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Sylviusweg 72, 2333 BE, Leiden, the Netherlands
| | - Robin A Ohm
- TiFN, P.O. Box 557, 6700 AN, Wageningen, the Netherlands
- Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Gertjan Kramer
- Mass Spectrometry of Biomolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1090 GE, Amsterdam, the Netherlands
| | - Han A B Wösten
- TiFN, P.O. Box 557, 6700 AN, Wageningen, the Netherlands
- Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Johannes H de Winde
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Sylviusweg 72, 2333 BE, Leiden, the Netherlands
| | - Arthur F J Ram
- TiFN, P.O. Box 557, 6700 AN, Wageningen, the Netherlands.
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Sylviusweg 72, 2333 BE, Leiden, the Netherlands.
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Cosseboom SD, Agarwal C, Hu M. CRISPR-enabled investigation of fitness costs associated with the E198A mutation in β-tubulin of Colletotrichum siamense. FRONTIERS IN PLANT SCIENCE 2023; 14:1278133. [PMID: 38023927 PMCID: PMC10654983 DOI: 10.3389/fpls.2023.1278133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023]
Abstract
Introduction Understanding fitness costs associated with fungicide resistance is critical to improve resistance management strategies. E198A in b-tubulin confers resistance to the fungicide thiophanate-methyl and has been widely reported in several plant pathogens including Colletotrichum siamense. Method To better understand potential fitness costs associated with the resistance, a ribonucleoprotein (RNP) complex mediated CRISPR/Cas9 system was used to create a point mutation (E198A) through homology directed repair (HDR) in each of the sensitive (E198) C. siamense isolates collected from strawberries, raspberries, and peaches. The RNP complex was delivered into fungal protoplasts using polyethylene glycol-mediated (PEG) transfection. Results The transformation efficiency, the proportion of transformants of sensitive parental isolates containing the E198A mutation, averaged 72%. No off-target mutations were observed when sequences similar to the b-tubulin target region with a maximum of four mismatch sites were analyzed, suggesting that the CRISPR/Cas9 system used in this study was highly specific for genome editing in C. siamense. Of the 41 comparisons of fitness between mutant and wild type isolates through in vitro and detached fruit assays, mutant isolates appeared to be as fit (24 of 41 comparisons), if not more fit than wild-type isolates (10 of 41 comparisons). Discussion The use of CRISPR/Cas9 to evaluate fitness costs associated with point mutations in this study represents a novel and useful method, since wild-type and mutant isolates were genetically identical except for the target mutation.
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Affiliation(s)
| | | | - Mengjun Hu
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, United States
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Yonehara K, Kumakura N, Motoyama T, Ishihama N, Dallery J, O'Connell R, Shirasu K. Efficient multiple gene knockout in Colletotrichum higginsianum via CRISPR/Cas9 ribonucleoprotein and URA3-based marker recycling. MOLECULAR PLANT PATHOLOGY 2023; 24:1451-1464. [PMID: 37522511 PMCID: PMC10576178 DOI: 10.1111/mpp.13378] [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: 04/14/2023] [Revised: 05/21/2023] [Accepted: 06/26/2023] [Indexed: 08/01/2023]
Abstract
Colletotrichum higginsianum is a hemibiotrophic pathogen that causes anthracnose disease on crucifer hosts, including Arabidopsis thaliana. Despite the availability of genomic and transcriptomic information and the ability to transform both organisms, identifying C. higginsianum genes involved in virulence has been challenging due to recalcitrance to gene targeting and redundancy of virulence factors. To overcome these obstacles, we developed an efficient method for multiple gene disruption in C. higginsianum by combining CRISPR/Cas9 and a URA3-based marker recycling system. Our method significantly increased the efficiency of gene knockout via homologous recombination by introducing genomic DNA double-strand breaks. We demonstrated the applicability of the URA3-based marker recycling system for multiple gene targeting in the same strain. Using our technology, we successfully targeted two melanin biosynthesis genes, SCD1 and PKS1, which resulted in deficiency in melanization and loss of pathogenicity in the mutants. Our findings demonstrate the effectiveness of our methods in analysing virulence factors in C. higginsianum, thus accelerating research on plant-fungus interactions.
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Affiliation(s)
- Katsuma Yonehara
- RIKEN Center for Sustainable Resource ScienceYokohamaJapan
- Department of Biological Science, Graduate School of ScienceThe University of TokyoTokyoJapan
| | | | | | | | | | | | - Ken Shirasu
- RIKEN Center for Sustainable Resource ScienceYokohamaJapan
- Department of Biological Science, Graduate School of ScienceThe University of TokyoTokyoJapan
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Arentshorst M, Kooloth Valappil P, Mózsik L, Regensburg-Tuïnk TJG, Seekles SJ, Tjallinks G, Fraaije MW, Visser J, Ram AFJ. A CRISPR/Cas9-based multicopy integration system for protein production in Aspergillus niger. FEBS J 2023; 290:5127-5140. [PMID: 37335926 DOI: 10.1111/febs.16891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/25/2023] [Accepted: 06/16/2023] [Indexed: 06/21/2023]
Abstract
The filamentous fungus Aspergillus niger is well known for its high protein secretion capacity and a preferred host for homologous and heterologous protein production. To improve the protein production capacity of A. niger even further, a set of dedicated protein production strains was made containing up to 10 glucoamylase landing sites (GLSs) at predetermined sites in the genome. These GLSs replace genes encoding enzymes abundantly present or encoding unwanted functions. Each GLS contains the promotor and terminator region of the glucoamylase gene (glaA), one of the highest expressed genes in A. niger. Integrating multiple gene copies, often realized by random integration, is known to boost protein production yields. In our approach the GLSs allow for rapid targeted gene replacement using CRISPR/Cas9-mediated genome editing. By introducing the same or different unique DNA sequences (dubbed KORE sequences) in each GLS and designing Cas9-compatible single guide RNAs, one is able to select at which GLS integration of a target gene occurs. In this way a set of identical strains with different copy numbers of the gene of interest can be easily and rapidly made to compare protein production levels. As an illustration of its potential, we successfully used the expression platform to generate multicopy A. niger strains producing the Penicillium expansum PatE::6xHis protein catalysing the final step in patulin biosynthesis. The A. niger strain expressing 10 copies of the patE::6xHis expression cassette produced about 70 μg·mL-1 PatE protein in the culture medium with a purity just under 90%.
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Affiliation(s)
- Mark Arentshorst
- Microbial Sciences, Fungal Genetics and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
| | - Prajeesh Kooloth Valappil
- Microbial Sciences, Fungal Genetics and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
| | - László Mózsik
- Microbial Sciences, Fungal Genetics and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
| | - Tonny J G Regensburg-Tuïnk
- Microbial Sciences, Fungal Genetics and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
| | - Sjoerd J Seekles
- Microbial Sciences, Fungal Genetics and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
| | - Gwen Tjallinks
- Molecular Enzymology, University of Groningen, The Netherlands
| | - Marco W Fraaije
- Molecular Enzymology, University of Groningen, The Netherlands
| | - Jaap Visser
- Microbial Sciences, Fungal Genetics and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
| | - Arthur F J Ram
- Microbial Sciences, Fungal Genetics and Biotechnology, Institute of Biology Leiden, Leiden University, The Netherlands
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Dai Z. Novel genetic tools improve Penicillium expansum patulin synthase production in Aspergillus niger. FEBS J 2023; 290:5094-5097. [PMID: 37794568 DOI: 10.1111/febs.16956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 09/11/2023] [Indexed: 10/06/2023]
Abstract
Since the first CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) system was developed for creating double-stranded DNA breaks, it has been adapted and improved for different biotechnological applications. In this issue of The FEBS Journal, Arentshorst et al. developed a novel approach to enhance transgene expression of a specific protein, patulin synthase (PatE) from Penicillium expansum, in the important industrial filamentous fungus Aspergillus niger. Their technique involved the disruption of selected genes with counter-effects on targeted protein production and simultaneous integration of glucoamylase landing sites into the disrupted gene locus such as protease regulator (prtT) in an ATP-dependent DNA helicase II subunit 1 (kusA or ku70)-deletion strain. Multiple copies of the PatE transgene expression cassette were introduced by CRISPR-Cas9-mediated insertion. The purified PatE was further used for structural and functional studies, and the technique laid the foundation for elevating the overall production of various proteins or chemicals in those industrially important fungi.
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Affiliation(s)
- Ziyu Dai
- Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, WA, Richland, USA
- Joint Bioenergy Institute, Emeryville, CA, United States
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Liu H, Lin J, Phan QT, Gravelat FN, Sheppard DC, Filler SG. Use of a human small airway epithelial cell line to study the interactions of Aspergillus fumigatus with pulmonary epithelial cells. mSphere 2023; 8:e0031423. [PMID: 37578262 PMCID: PMC10597448 DOI: 10.1128/msphere.00314-23] [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: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 08/15/2023] Open
Abstract
During the initiation of invasive aspergillosis, inhaled Aspergillus fumigatus conidia are deposited on the epithelial cells lining the bronchi, terminal bronchioles, and alveoli. While the interactions of A. fumigatus with bronchial and type II alveolar cell lines have been investigated in vitro, little is known about the interactions of this fungus with terminal bronchiolar epithelial cells. Using the HSAEC1-KT human small airway epithelial (HSAE) cell line, we developed an in vitro model to study the interaction of two strains of A. fumigatus with these cells. We then compared the interactions of A. fumigatus with the A549 type II alveolar epithelial cell line and the HSAE cell line. We found that A. fumigatus conidia were poorly endocytosed by A549 cells, but avidly endocytosed by HSAE cells. A. fumigatus germlings invaded both cell types by induced endocytosis, but not by active penetration. A549 cell endocytosis of A. fumigatus was independent of fungal viability, more dependent on host microfilaments than microtubules, and induced by A. fumigatus CalA interacting with host cell integrin α5β1. By contrast, HSAE cell endocytosis required fungal viability, was more dependent on microtubules than microfilaments, and did not require CalA or integrin α5β1. HSAE cells were more susceptible than A549 cells to damage caused by direct contact with killed A. fumigatus germlings and by secreted fungal products. In response to A. fumigatus infection, A549 cells secreted a broader profile of cytokines and chemokines than HSAE cells. Taken together, these results demonstrate that studies of HSAE cells provide complementary data to A549 cells and thus represent a useful model for probing the interactions of A. fumigatus with bronchiolar epithelial cells in vitro. Importance During the initiation of invasive aspergillosis, Aspergillus fumigatus interacts with the epithelial cells that line the airways and alveoli. Previous studies of A. fumigatus-epithelial cell interactions in vitro used either large airway epithelial cell lines or the A549 type II alveolar epithelial cell line; the interactions of fungi with terminal bronchiolar epithelial cells were not investigated. Using the TERT-immortalized human small airway epithelial HSAEC1-KT (HSAE) cell line, we developed an in vitro model of the interactions of A. fumigatus with bronchiolar epithelial cells. We discovered that A. fumigatus invades and damages A549 and HSAE cell lines by distinct mechanisms. Also, the proinflammatory responses of the cell lines to A. fumigatus are different. These results provide insight into how A. fumigatus interacts with different types of epithelial cells during invasive aspergillosis and demonstrate that HSAE cells are useful in vitro model for investigating the interactions of this fungus with bronchiolar epithelial cells.
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Affiliation(s)
- Hong Liu
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Jianfeng Lin
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Quynh T. Phan
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Fabrice N. Gravelat
- Department of Medicine, Infectious Diseases, and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Donald C. Sheppard
- Department of Medicine, Infectious Diseases, and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Scott G. Filler
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
- David Geffen School of Medicine at UCLA, Los Angeles, California, USA
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Wang S, Xue Y, Zhang P, Yan Q, Li Y, Jiang Z. CRISPR/Cas9 System-Mediated Multi-copy Expression of an Alkaline Serine Protease in Aspergillus niger for the Production of XOD-Inhibitory Peptides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:15194-15203. [PMID: 37807677 DOI: 10.1021/acs.jafc.3c04138] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
CRISPR/Cas9 system-mediated multi-copy expression of an alkaline serine protease (AoproS8) from Aspergillus oryzae was successfully built in Aspergillus niger. Furthermore, AoproS8 was continuously knocked in the glaA, amyA, and aamy gene loci in A. niger to construct multi-copy expression strains. The yield of the AoproS8 3.0 strain was 2.1 times higher than that of the AoproS8 1.0 strain. Then, a high protease activity of 11,023.2 U/mL with a protein concentration of 10.8 mg/mL was obtained through fed-batch fermentation in a 5 L fermenter. This is the first report on the high-level expression of alkaline serine proteases in A. niger. AoproS8 showed optimal activity at pH 9.0 and 40 °C. It was used for the production of xanthine oxidase (XOD)-inhibitory peptides from eight food processing protein by-products. Among them, the duck hemoglobin hydrolysates showed the highest XOD-inhibitory activity with an IC50 value of 2.39 mg/mL. Thus, our work provides a useful way for efficient expression of proteases in A. niger and high-value utilization of protein by-products.
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Affiliation(s)
- Shounan Wang
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yibin Xue
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Peng Zhang
- College of Engineering, China Agricultural University, Beijing 100083, China
| | - Qiaojuan Yan
- College of Engineering, China Agricultural University, Beijing 100083, China
| | - Yanxiao Li
- College of Engineering, China Agricultural University, Beijing 100083, China
| | - Zhengqiang Jiang
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Food Laboratory of Zhongyuan, Luohe City 462000, Henan Province, China
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Gil-Durán C, Palma D, Marcano Y, Palacios JL, Martínez C, Rojas-Aedo JF, Levicán G, Vaca I, Chávez R. CRISPR/Cas9-Mediated Disruption of the pcz1 Gene and Its Impact on Growth, Development, and Penicillin Production in Penicillium rubens. J Fungi (Basel) 2023; 9:1010. [PMID: 37888266 PMCID: PMC10607824 DOI: 10.3390/jof9101010] [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: 08/04/2023] [Revised: 10/02/2023] [Accepted: 10/11/2023] [Indexed: 10/28/2023] Open
Abstract
Penicillium rubens is a filamentous fungus of great biotechnological importance due to its role as an industrial producer of the antibiotic penicillin. However, despite its significance, our understanding of the regulatory mechanisms governing biological processes in this fungus is still limited. In fungi, zinc finger proteins containing a Zn(II)2Cys6 domain are particularly interesting regulators. Although the P. rubens genome harbors many genes encoding proteins with this domain, only two of them have been investigated thus far. In this study, we employed CRISPR-Cas9 technology to disrupt the pcz1 gene, which encodes a Zn(II)2Cys6 protein in P. rubens. The disruption of pcz1 resulted in a decrease in the production of penicillin in P. rubens. This decrease in penicillin production was accompanied by the downregulation of the expression of pcbAB, pcbC and penDE genes, which form the biosynthetic gene cluster responsible for penicillin production. Moreover, the disruption of pcz1 also impacts on asexual development, leading to decreased growth and conidiation, as well as enhanced conidial germination. Collectively, our results indicate that pcz1 acts as a positive regulator of penicillin production, growth, and conidiation, while functioning as a negative regulator of conidial germination in P. rubens. To the best of our knowledge, this is the first report involving a gene encoding a Zn(II)2Cys6 protein in the regulation of penicillin biosynthesis in P. rubens.
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Affiliation(s)
- Carlos Gil-Durán
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile; (C.G.-D.); (Y.M.); (J.F.R.-A.); (G.L.)
| | - Diego Palma
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile;
| | - Yudethzi Marcano
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile; (C.G.-D.); (Y.M.); (J.F.R.-A.); (G.L.)
| | - José-Luis Palacios
- Centro de Estudios en Ciencia y Tecnología de los Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile; (J.-L.P.); (C.M.)
| | - Claudio Martínez
- Centro de Estudios en Ciencia y Tecnología de los Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile; (J.-L.P.); (C.M.)
- Departamento de Ciencia y Tecnología de los Alimentos, Facultad Tecnológica, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile
| | - Juan F. Rojas-Aedo
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile; (C.G.-D.); (Y.M.); (J.F.R.-A.); (G.L.)
| | - Gloria Levicán
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile; (C.G.-D.); (Y.M.); (J.F.R.-A.); (G.L.)
| | - Inmaculada Vaca
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile;
| | - Renato Chávez
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile; (C.G.-D.); (Y.M.); (J.F.R.-A.); (G.L.)
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Wassano NS, da Silva GB, Reis AH, Gerhardt JA, Antoniel EP, Akiyama D, Rezende CP, Neves LX, Vasconcelos E, Figueiredo FL, Almeida F, de Castro PA, Pinzan CF, Goldman GH, Leme AFP, Fill TP, Moretti NS, Damasio A. Deacetylation by sirtuins is important for Aspergillus fumigatus pathogenesis and virulence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.558961. [PMID: 37808717 PMCID: PMC10557594 DOI: 10.1101/2023.09.25.558961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Protein acetylation is a crucial post-translational modification that controls gene expression and a variety of biological processes. Sirtuins, a prominent class of NAD + -dependent lysine deacetylases, serve as key regulators of protein acetylation and gene expression in eukaryotes. In this study, six single knockout strains of fungal pathogen Aspergillus fumigatus were constructed, in addition to a strain lacking all predicted sirtuins (SIRTKO). Phenotypic assays suggest that sirtuins are involved in cell wall integrity, secondary metabolite production, thermotolerance, and virulence. AfsirE deletion resulted in attenuation of virulence, as demonstrated in murine and Galleria infection models. The absence of AfSirE leads to altered acetylation status of proteins, including histones and non-histones, resulting in significant changes in the expression of genes associated with secondary metabolism, cell wall biosynthesis, and virulence factors. These findings encourage testing sirtuin inhibitors as potential therapeutic strategies to combat A. fumigatus infections or in combination therapy with available antifungals.
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Marcano Y, Montanares M, Gil-Durán C, González K, Levicán G, Vaca I, Chávez R. Pr laeA Affects the Production of Roquefortine C, Mycophenolic Acid, and Andrastin A in Penicillium roqueforti, but It Has Little Impact on Asexual Development. J Fungi (Basel) 2023; 9:954. [PMID: 37888210 PMCID: PMC10607316 DOI: 10.3390/jof9100954] [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: 07/28/2023] [Revised: 09/14/2023] [Accepted: 09/20/2023] [Indexed: 10/28/2023] Open
Abstract
The regulation of fungal specialized metabolism is a complex process involving various regulators. Among these regulators, LaeA, a methyltransferase protein originally discovered in Aspergillus spp., plays a crucial role. Although the role of LaeA in specialized metabolism has been studied in different fungi, its function in Penicillium roqueforti remains unknown. In this study, we employed CRISPR-Cas9 technology to disrupt the laeA gene in P. roqueforti (PrlaeA) aiming to investigate its impact on the production of the specialized metabolites roquefortine C, mycophenolic acid, and andrastin A, as well as on asexual development, because they are processes that occur in the same temporal stages within the physiology of the fungus. Our results demonstrate a substantial reduction in the production of the three metabolites upon disruption of PrlaeA, suggesting a positive regulatory role of LaeA in their biosynthesis. These findings were further supported by qRT-PCR analysis, which revealed significant downregulation in the expression of genes associated with the biosynthetic gene clusters (BGCs) responsible for producing roquefortine C, mycophenolic acid, and andrastin A in the ΔPrlaeA strains compared with the wild-type P. roqueforti. Regarding asexual development, the disruption of PrlaeA led to a slight decrease in colony growth rate, while conidiation and conidial germination remained unaffected. Taken together, our results suggest that LaeA positively regulates the expression of the analyzed BGCs and the production of their corresponding metabolites in P. roqueforti, but it has little impact on asexual development.
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Affiliation(s)
- Yudethzi Marcano
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile; (Y.M.); (C.G.-D.); (K.G.); (G.L.)
| | - Mariana Montanares
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile;
| | - Carlos Gil-Durán
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile; (Y.M.); (C.G.-D.); (K.G.); (G.L.)
| | - Kathia González
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile; (Y.M.); (C.G.-D.); (K.G.); (G.L.)
| | - Gloria Levicán
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile; (Y.M.); (C.G.-D.); (K.G.); (G.L.)
| | - Inmaculada Vaca
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile;
| | - Renato Chávez
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile; (Y.M.); (C.G.-D.); (K.G.); (G.L.)
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40
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Igarashi T, Katayama T, Maruyama JI. CRISPR/Cas9 genome editing for comparative genetic analysis related to soy sauce brewing in Aspergillus sojae industrial strains. Biosci Biotechnol Biochem 2023; 87:1236-1248. [PMID: 37500264 DOI: 10.1093/bbb/zbad101] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/11/2023] [Indexed: 07/29/2023]
Abstract
Aspergillus sojae has traditionally been used in soy sauce brewing. Genetic modification techniques have been established in A. sojae, but it is difficult to apply them to various industrial strains. Although we have previously developed a CRISPR/Cpf1 system for genetic modification of A. sojae, another genome editing system was required for versatile modification. In addition, repetitive genetic modification using the CRISPR system has not been established in A. sojae. In this study, we demonstrated mutagenesis, gene deletion/integration, and large deletion of a chromosomal region in A. sojae using the CRISPR/Cas9 system. We also successfully performed repetitive genetic modification using a method that involved forced recycling of genome-editing plasmids. Moreover, we demonstrated that the effects of genetic modification related to soy sauce brewing differed among A. sojae industrial strains. These results showed that our technique of using the CRISPR/Cas9 system is a powerful tool for genetic modification in A. sojae.
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Affiliation(s)
- Takayuki Igarashi
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Takuya Katayama
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Jun-Ichi Maruyama
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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41
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Bauer I, Sarikaya Bayram Ö, Bayram Ö. The use of immunoaffinity purification approaches coupled with LC-MS/MS offers a powerful strategy to identify protein complexes in filamentous fungi. Essays Biochem 2023; 67:877-892. [PMID: 37681641 DOI: 10.1042/ebc20220253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023]
Abstract
Fungi are a diverse group of organisms that can be both beneficial and harmful to mankind. They have advantages such as producing food processing enzymes and antibiotics, but they can also be pathogens and produce mycotoxins that contaminate food. Over the past two decades, there have been significant advancements in methods for studying fungal molecular biology. These advancements have led to important discoveries in fungal development, physiology, pathogenicity, biotechnology, and natural product research. Protein complexes and protein-protein interactions (PPIs) play crucial roles in fungal biology. Various methods, including yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC), are used to investigate PPIs. However, affinity-based PPI methods like co-immunoprecipitation (Co-IP) are highly preferred because they represent the natural conditions of PPIs. In recent years, the integration of liquid chromatography coupled with mass spectrometry (LC-MS/MS) has been used to analyse Co-IPs, leading to the discovery of important protein complexes in filamentous fungi. In this review, we discuss the tandem affinity purification (TAP) method and single affinity purification methods such as GFP, HA, FLAG, and MYC tag purifications. These techniques are used to identify PPIs and protein complexes in filamentous fungi. Additionally, we compare the efficiency, time requirements, and material usage of Sepharose™ and magnetic-based purification systems. Overall, the advancements in fungal molecular biology techniques have provided valuable insights into the complex interactions and functions of proteins in fungi. The methods discussed in this review offer powerful tools for studying fungal biology and will contribute to further discoveries in this field.
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Affiliation(s)
- Ingo Bauer
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Özgür Bayram
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
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42
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Yang J, Zhou Z, Chen Y, Song Y, Ju J. Characterization of the depsidone gene cluster reveals etherification, decarboxylation and multiple halogenations as tailoring steps in depsidone assembly. Acta Pharm Sin B 2023; 13:3919-3929. [PMID: 37719379 PMCID: PMC10501868 DOI: 10.1016/j.apsb.2023.05.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/17/2023] [Accepted: 05/12/2023] [Indexed: 09/19/2023] Open
Abstract
Depsides and depsidones have attracted attention for biosynthetic studies due to their broad biological activities and structural diversity. Previous structure‒activity relationships indicated that triple halogenated depsidones display the best anti-pathogenic activity. However, the gene cluster and the tailoring steps responsible for halogenated depsidone nornidulin (3) remain enigmatic. In this study, we disclosed the complete biosynthetic pathway of the halogenated depsidone through in vivo gene disruption, heterologous expression and in vitro biochemical experiments. We demonstrated an unusual depside skeleton biosynthesis process mediated by both highly-reducing polyketide synthase and non-reducing polyketide synthase, which is distinct from the common depside skeleton biosynthesis. This skeleton was subsequently modified by two in-cluster enzymes DepG and DepF for the ether bond formation and decarboxylation, respectively. In addition, the decarboxylase DepF exhibited substrate promiscuity for different scaffold substrates. Finally, and interestingly, we discovered a halogenase encoded remotely from the biosynthetic gene cluster, which catalyzes triple-halogenation to produce the active end product nornidulin (3). These discoveries provide new insights for further understanding the biosynthesis of depsidones and their derivatives.
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Affiliation(s)
- Jiafan Yang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, RNAM Center for Marine Microbiology, 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, Beijing 110039, China
| | - Zhenbin Zhou
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, RNAM Center for Marine Microbiology, 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, Beijing 110039, China
| | - Yingying Chen
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Yongxiang Song
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, RNAM Center for Marine Microbiology, 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, Beijing 110039, China
| | - Jianhua Ju
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, RNAM Center for Marine Microbiology, 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, Beijing 110039, China
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Rappleye CA. Targeted gene deletions in the dimorphic fungal pathogen Histoplasma using an optimized episomal CRISPR/Cas9 system. mSphere 2023; 8:e0017823. [PMID: 37389430 PMCID: PMC10449496 DOI: 10.1128/msphere.00178-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 05/22/2023] [Indexed: 07/01/2023] Open
Abstract
The rapid development of CRISPR/CRISPR-associated (Cas) systems has revolutionized the ability to produce genetic mutations in a desired locus, particularly in organisms with low rates of homologous recombination. Histoplasma is an important respiratory and systemic fungal pathogen that has few reverse genetic options. We describe an optimized CRISPR/Cas system for the efficient generation of mutations in desired genes. The limited requirements for CRISPR/Cas, namely a gene-targeting guide RNA (gRNA) and expression of a Cas endonuclease, enabled both the gRNA and the Streptococcus pyogenes Cas9 gene to be expressed from a single episomal vector. The gRNAs are expressed from a strong Pol(II) promoter, a critical parameter for increasing the recovery of mutated genes, and processed into the mature gRNA by ribozymes in the mRNA. Expression of dual-tandem gRNAs facilitates the generation of gene deletions at a good frequency which can be detected by PCR-based screening of pooled isolates resulting in the isolation of marker-less deletion mutants. The CRISPR/Cas system is encoded on an episomal telomeric vector facilitating curing strains of the CRISPR/Cas vector upon generation of the mutant. We demonstrate the successful application of this CRISPR/Cas system in diverse Histoplasma species and applicable for multiple genes. The optimized system shows promise for accelerating reverse genetic studies in Histoplasma spp. IMPORTANCE The ability to eliminate gene product functions is central to understanding molecular mechanisms. In the fungal pathogen Histoplasma, methods to inactivate or deplete gene products are inefficient, which hampers progress in defining Histoplasma's virulence mechanisms. We describe an efficient CRISPR/Cas-based system for generating gene deletions in Histoplasma and show its validation on multiple genes with selectable and non-selectable phenotypes.
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Affiliation(s)
- Chad A. Rappleye
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA
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So LH, Jirakkakul J, Salaipeth L, Toopaang W, Amnuaykanjanasin A. TOR Signaling Tightly Regulated Vegetative Growth, Conidiation, Oxidative Stress Tolerance and Entomopathogenicity in the Fungus Beauveria bassiana. Microorganisms 2023; 11:2129. [PMID: 37763973 PMCID: PMC10537155 DOI: 10.3390/microorganisms11092129] [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: 07/10/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 09/29/2023] Open
Abstract
Beauveria bassiana degenerates after repeated subcultures, demonstrating declined conidiation and insect virulence. The target of rapamycin (TOR) kinase conserved among eukaryotes is the master regulator of cellular physiology and is likely involved in culture degeneration. Indeed, the levels of TOR-associated proteins increase over successive subcultures. Here, CRISPR/Cas9 locus engineering introduced the inducible Tet-On promoter upstream of the TOR kinase 2 gene tor2 in B. bassiana. The mutant PTet-Ontor2 'T41' was verified for the Tet-On integration via PCR analyses and provided a model for evaluating the fungal phenotypes according to the tor2 expression levels, induced by doxycycline (Dox) concentrations. At 0 µg·mL-1 of Dox, T41 had 68% of the wild type's (WT) tor2 expression level, hampered radial growth and relatively lower levels of oxidative stress tolerance, conidiation and virulence against Spodoptera exigua, compared to those under the presence of Dox. A low dose of Dox at 0.1-1 µg·mL-1 induced tor2 upregulation in T41 by up to 91% compared to 0 µg·mL-1 of Dox, resulting in significant increases in radial growth by 8-10% and conidiation by 8-27%. At 20 µg·mL-1 of Dox, which is 132% higher than T41's tor2 expression level at 0 µg·mL-1 of Dox, T41 showed an increased oxidative stress tolerance and a decrease in growth inhibition under iron replete by 62%, but its conidiation significantly dropped by 47% compared to 0 µg·mL-1 of Dox. T41 at 20 µg·mL-1 of Dox had a strikingly increased virulence (1.2 day lower LT50) against S. exigua. The results reflect the crucial roles of TOR kinase in the vegetative growth, conidiation, pathogenicity and oxidative stress tolerance in B. bassiana. Since TOR upregulation is correlated with culture degeneration in multiple subcultures, our data suggest that TOR signaling at relatively low levels plays an important role in growth and development, but at moderate to high levels could contribute to some degenerated phenotypes, e.g., those found in successive subcultures.
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Affiliation(s)
- Lai-Hong So
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Paholyothin Rd., Tambon Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand (W.T.)
- School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok 10140, Thailand; (J.J.); (L.S.)
| | - Jiraporn Jirakkakul
- School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok 10140, Thailand; (J.J.); (L.S.)
| | - Lakha Salaipeth
- School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok 10140, Thailand; (J.J.); (L.S.)
| | - Wachiraporn Toopaang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Paholyothin Rd., Tambon Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand (W.T.)
| | - Alongkorn Amnuaykanjanasin
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Paholyothin Rd., Tambon Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand (W.T.)
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Salazar-Cerezo S, de Vries RP, Garrigues S. Strategies for the Development of Industrial Fungal Producing Strains. J Fungi (Basel) 2023; 9:834. [PMID: 37623605 PMCID: PMC10455633 DOI: 10.3390/jof9080834] [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: 06/12/2023] [Revised: 07/31/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023] Open
Abstract
The use of microorganisms in industry has enabled the (over)production of various compounds (e.g., primary and secondary metabolites, proteins and enzymes) that are relevant for the production of antibiotics, food, beverages, cosmetics, chemicals and biofuels, among others. Industrial strains are commonly obtained by conventional (non-GMO) strain improvement strategies and random screening and selection. However, recombinant DNA technology has made it possible to improve microbial strains by adding, deleting or modifying specific genes. Techniques such as genetic engineering and genome editing are contributing to the development of industrial production strains. Nevertheless, there is still significant room for further strain improvement. In this review, we will focus on classical and recent methods, tools and technologies used for the development of fungal production strains with the potential to be applied at an industrial scale. Additionally, the use of functional genomics, transcriptomics, proteomics and metabolomics together with the implementation of genetic manipulation techniques and expression tools will be discussed.
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Affiliation(s)
- Sonia Salazar-Cerezo
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands (R.P.d.V.)
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands (R.P.d.V.)
| | - Sandra Garrigues
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Catedrático Agustín Escardino Benlloch 7, 46980 Paterna, VLC, Spain
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Carreras-Villaseñor N, Martínez-Rodríguez LA, Ibarra-Laclette E, Monribot-Villanueva JL, Rodríguez-Haas B, Guerrero-Analco JA, Sánchez-Rangel D. The biological relevance of the FspTF transcription factor, homologous of Bqt4, in Fusarium sp. associated with the ambrosia beetle Xylosandrus morigerus. Front Microbiol 2023; 14:1224096. [PMID: 37520351 PMCID: PMC10375492 DOI: 10.3389/fmicb.2023.1224096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 06/22/2023] [Indexed: 08/01/2023] Open
Abstract
Transcription factors in phytopathogenic fungi are key players due to their gene expression regulation leading to fungal growth and pathogenicity. The KilA-N family encompasses transcription factors unique to fungi, and the Bqt4 subfamily is included in it and is poorly understood in filamentous fungi. In this study, we evaluated the role in growth and pathogenesis of the homologous of Bqt4, FspTF, in Fusarium sp. isolated from the ambrosia beetle Xylosandrus morigerus through the characterization of a CRISPR/Cas9 edited strain in Fsptf. The phenotypic analysis revealed that TF65-6, the edited strain, modified its mycelia growth and conidia production, exhibited affectation in mycelia and culture pigmentation, and in the response to certain stress conditions. In addition, the plant infection process was compromised. Untargeted metabolomic and transcriptomic analysis, clearly showed that FspTF may regulate secondary metabolism, transmembrane transport, virulence, and diverse metabolic pathways such as lipid metabolism, and signal transduction. These data highlight for the first time the biological relevance of an orthologue of Bqt4 in Fusarium sp. associated with an ambrosia beetle.
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Affiliation(s)
- Nohemí Carreras-Villaseñor
- Laboratorios de Biología Molecular y Fitopatología, Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
| | - Luis A. Martínez-Rodríguez
- Laboratorios de Biología Molecular y Fitopatología, Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
| | - Enrique Ibarra-Laclette
- Laboratorio de Genómica y Transcriptómica, Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
| | - Juan L. Monribot-Villanueva
- Laboratorio de Química de Productos Naturales, Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
| | - Benjamín Rodríguez-Haas
- Laboratorios de Biología Molecular y Fitopatología, Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
| | - José A. Guerrero-Analco
- Laboratorio de Química de Productos Naturales, Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
| | - Diana Sánchez-Rangel
- Laboratorios de Biología Molecular y Fitopatología, Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
- Investigadora Por Mexico-CONAHCyT, Xalapa, Mexico
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Batth TS, Simonsen JL, Hernández-Rollán C, Brander S, Morth JP, Johansen KS, Nørholm MHH, Hoof JB, Olsen JV. A seven-transmembrane methyltransferase catalysing N-terminal histidine methylation of lytic polysaccharide monooxygenases. Nat Commun 2023; 14:4202. [PMID: 37452022 PMCID: PMC10349129 DOI: 10.1038/s41467-023-39875-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 06/29/2023] [Indexed: 07/18/2023] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are oxidative enzymes that help break down lignocellulose, making them highly attractive for improving biomass utilization in industrial biotechnology. The catalytically essential N-terminal histidine (His1) of LPMOs is post-translationally modified by methylation in filamentous fungi to protect them from auto-oxidative inactivation, however, the responsible methyltransferase enzyme is unknown. Using mass-spectrometry-based quantitative proteomics in combination with systematic CRISPR/Cas9 knockout screening in Aspergillus nidulans, we identify the N-terminal histidine methyltransferase (NHMT) encoded by the gene AN4663. Targeted proteomics confirm that NHMT was solely responsible for His1 methylation of LPMOs. NHMT is predicted to encode a unique seven-transmembrane segment anchoring a soluble methyltransferase domain. Co-localization studies show endoplasmic reticulum residence of NHMT and co-expression in the industrial production yeast Komagataella phaffii with LPMOs results in His1 methylation of the LPMOs. This demonstrates the biotechnological potential of recombinant production of proteins and peptides harbouring this specific post-translational modification.
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Affiliation(s)
- Tanveer S Batth
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen Denmark, Copenhagen, Denmark.
| | - Jonas L Simonsen
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen Denmark, Copenhagen, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Cristina Hernández-Rollán
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Søren Brander
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg, Denmark
| | - Jens Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Katja S Johansen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg, Denmark
| | - Morten H H Nørholm
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - Jakob B Hoof
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - Jesper V Olsen
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen Denmark, Copenhagen, Denmark.
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Yuan G, Czajka JJ, Dai Z, Hu D, Pomraning KR, Hofstad BA, Kim J, Robles AL, Deng S, Magnuson JK. Rapid and robust squashed spore/colony PCR of industrially important fungi. Fungal Biol Biotechnol 2023; 10:15. [PMID: 37422681 DOI: 10.1186/s40694-023-00163-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/18/2023] [Indexed: 07/10/2023] Open
Abstract
BACKGROUND Fungi have been utilized for centuries in medical, agricultural, and industrial applications. Development of systems biology techniques has enabled the design and metabolic engineering of these fungi to produce novel fuels, chemicals, and enzymes from renewable feedstocks. Many genetic tools have been developed for manipulating the genome and creating mutants rapidly. However, screening and confirmation of transformants remain an inefficient step within the design, build, test, and learn cycle in many industrial fungi because extracting fungal genomic DNA is laborious, time-consuming, and involves toxic chemicals. RESULTS In this study we developed a rapid and robust technique called "Squash-PCR" to break open the spores and release fungal genomic DNA as a template for PCR. The efficacy of Squash-PCR was investigated in eleven different filamentous fungal strains. Clean PCR products with high yields were achieved in all tested fungi. Spore age and type of DNA polymerase did not affect the efficiency of Squash-PCR. However, spore concentration was found to be the crucial factor for Squash-PCR in Aspergillus niger, with the dilution of starting material often resulting in higher PCR product yield. We then further evaluated the applicability of the squashing procedure for nine different yeast strains. We found that Squash-PCR can be used to improve the quality and yield of colony PCR in comparison to direct colony PCR in the tested yeast strains. CONCLUSION The developed technique will enhance the efficiency of screening transformants and accelerate genetic engineering in filamentous fungi and yeast.
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Affiliation(s)
- Guoliang Yuan
- Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Jeffrey J Czajka
- Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Ziyu Dai
- Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Dehong Hu
- Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Kyle R Pomraning
- Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Beth A Hofstad
- Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Joonhoon Kim
- Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Ana L Robles
- Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Shuang Deng
- Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA.
| | - Jon K Magnuson
- Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA.
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49
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Joehnk B, Ali N, Voorhies M, Walcott K, Sil A. Recyclable CRISPR/Cas9 mediated gene disruption and deletions in Histoplasma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.05.547774. [PMID: 37461713 PMCID: PMC10350005 DOI: 10.1101/2023.07.05.547774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Targeted gene disruption is challenging in the dimorphic fungal pathogen Histoplasma due to the low frequency of homologous recombination. Transformed DNA is either integrated ectopically into the genome or maintained extra chromosomally by de novo addition of telomeric sequences. Based on a system developed in Blastomyces, we adapted a CRISPR/Cas9 system to facilitate targeted gene disruption in Histoplasma with high efficiency. We express a codon-optimized version of Cas9 as well as guide RNAs from a single ectopic vector carrying a selectable marker. Once the desired mutation is verified, one can screen for isolates that have lost the Cas9 vector by simply removing the selective pressure. Multiple mutations can then be generated in the same strain by retransforming the Cas9 vector carrying different guides. We used this system to disrupt a number of target genes including RYP2 and SRE1 where loss-of-function mutations could be monitored visually by colony morphology or color, respectively. Interestingly, expression of two guide RNAs targeting the 5' and 3' ends of a gene allowed isolation of deletion mutants where the sequence between the guide RNAs was removed from the genome. Whole-genome sequencing showed that the frequency of off-target mutations associated with the Cas9 nuclease was negligible. Finally, we increased the frequency of gene disruption by using an endogenous Histoplasma regulatory sequence to drive guide RNA expression. These tools transform our ability to generate targeted mutations in Histoplasma.
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Affiliation(s)
- Bastian Joehnk
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, USA
| | - Nebat Ali
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, USA
| | - Mark Voorhies
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, USA
| | - Keith Walcott
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, USA
| | - Anita Sil
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA 94158
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Chen Z, Zhang C, Pei L, Qian Q, Lu L. Production of L-Malic Acid by Metabolically Engineered Aspergillus nidulans Based on Efficient CRISPR-Cas9 and Cre- loxP Systems. J Fungi (Basel) 2023; 9:719. [PMID: 37504708 PMCID: PMC10381526 DOI: 10.3390/jof9070719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/29/2023] Open
Abstract
Aspergillus nidulans has been more extensively characterized than other Aspergillus species considering its morphology, physiology, metabolic pathways, and genetic regulation. As it has a rapid growth rate accompanied by simple nutritional requirements and a high tolerance to extreme cultural conditions, A. nidulans is a promising microbial cell factory to biosynthesize various products in industry. However, it remains unclear for whether it is also a suitable host for synthesizing abundant L-malic acid. In this study, we developed a convenient and efficient double-gene-editing system in A. nidulans strain TN02A7 based on the CRISPR-Cas9 and Cre-loxP systems. Using this gene-editing system, we made a L-malic acid-producing strain, ZQ07, derived from TN02A7, by deleting or overexpressing five genes (encoding Pyc, pyruvate carboxylase; OahA, oxaloacetate acetylhydrolase; MdhC, malate dehydrogenase; DctA, C4-dicarboxylic acid transporter; and CexA, citric acid transporter). The L-malic acid yield in ZQ07 increased to approximately 9.6 times higher (up to 30.7 g/L titer) than that of the original unedited strain TN02A7, in which the production of L-malic acid was originally very low. The findings in this study not only demonstrate that A. nidulans could be used as a potential host for biosynthesizing organic acids, but also provide a highly efficient gene-editing strategy in filamentous fungi.
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Affiliation(s)
- Ziqing Chen
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Chi Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Lingling Pei
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Qi Qian
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Ling Lu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
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