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Zhai Z, Zhang M, Yin R, Zhao S, Shen Z, Yang Y, Zhang X, Wang J, Qin Y, Xu D, Zhou L, Lai D. CRISPR/Cas9-assisted gene editing reveals that EgPKS, a polyketide synthase, is required for the biosynthesis of preussomerins in Edenia gomezpompae SV2. World J Microbiol Biotechnol 2025; 41:103. [PMID: 40069470 DOI: 10.1007/s11274-025-04313-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: 01/28/2025] [Accepted: 02/27/2025] [Indexed: 03/29/2025]
Abstract
Edenia gomezpompae, an endophytic fungus derived from plants, produced a diverse array of preussomerins, a type of spirobisnaphthalenes featuring two spiroketal groups, which exhibited significant antibacterial, antifungal, and cytotoxic activities. Structurally, the biosynthesis of preussomerins might be related to the biosynthesis of 1,8-dihydroxynaphthalene (DHN), a precursor of DHN-melanin. However, the absence of efficient gene-editing tools for E. gomezpompae has hindered the biosynthetic study of preussomerins. In this study, we developed a CRISPR/Cas9-based gene editing system for E. gomezpompae SV2 that was isolated from the stem of Setaria viridis, by utilizing the endogenous U6 snRNA promoter to drive sgRNA expression. Using this system, we successfully disrupted the polyketide synthase (PKS)-encoding gene, Egpks, a putative 1,3,6,8-tetrahydroxynaphthalene synthase gene involved in the biosynthesis of DHN-melanin, with an editing efficiency up to 92% and a knockout efficiency of 71% when employing the U6 snRNA-3 promoter. Furthermore, the disrupted mutant (∆Egpks) displayed white hyphae and lost the ability to produce preussomerins. These results provided a foundational tool for genetic manipulation in E. gomezpompae and revealed the role of EgPKS in the biosynthesis of preussomerin-type spirobisnaphthalenes.
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Affiliation(s)
- Ziqi Zhai
- State Key Laboratory of Agricultural and Forestry Biosecurity, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Mengwei Zhang
- State Key Laboratory of Agricultural and Forestry Biosecurity, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Ruya Yin
- State Key Laboratory of Agricultural and Forestry Biosecurity, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Siji Zhao
- State Key Laboratory of Agricultural and Forestry Biosecurity, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Zhen Shen
- State Key Laboratory of Agricultural and Forestry Biosecurity, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Yonglin Yang
- State Key Laboratory of Agricultural and Forestry Biosecurity, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Xuan Zhang
- State Key Laboratory of Agricultural and Forestry Biosecurity, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Jianing Wang
- State Key Laboratory of Agricultural and Forestry Biosecurity, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Yifei Qin
- State Key Laboratory of Agricultural and Forestry Biosecurity, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Dan Xu
- State Key Laboratory of Agricultural and Forestry Biosecurity, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Ligang Zhou
- State Key Laboratory of Agricultural and Forestry Biosecurity, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Daowan Lai
- State Key Laboratory of Agricultural and Forestry Biosecurity, College of Plant Protection, China Agricultural University, Beijing, 100193, China.
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.
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2
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Virgílio MLDS, Quintela ED, Maciel LHR, Goulart GSS, Silva JFAE, Cortes MVDCB. Metarhizium anisopliae engineering mediated by a CRISPR/Cas9 recyclable system. Folia Microbiol (Praha) 2025:10.1007/s12223-025-01249-5. [PMID: 39982596 DOI: 10.1007/s12223-025-01249-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2024] [Accepted: 02/10/2025] [Indexed: 02/22/2025]
Abstract
The advent of CRISPR/Cas technology has revolutionized genome editing, offering simplicity, precision, and cost-effectiveness. While its application in biological control fungi has been limited, including the cosmopolitan fungus Metarhizium anisopliae, recent advancements show promise. However, integrating cas9 and selection-marker genes into fungal genomes poses challenges, including reduced efficiency, toxicity, and off-target effects. Besides, marker-free genetic engineering through a CRISPR recyclable system presents a viable solution, enabling efficient mutant generation without compromising fitness and virulence. This study pioneers the construction of marker-free strains of M. anisopliae using a CRISPR/Cas9 recyclable system. Precise deletion of albA and ku70, alongside gfp cassette insertion, confirms the system efficiency. This innovative approach holds significant potential for facilitating in-depth molecular studies, understanding their ecological roles in agricultural systems, and enhancing biocontrol efficacy against insect pests through genetic improvement.
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Affiliation(s)
| | - Eliane Dias Quintela
- Embrapa Rice & Beans, Brazilian Agricultural Research Corporation, Santo Antônio de Goiás, GO, 75375-000, Brazil
| | | | - Gabriela Souza Silva Goulart
- Embrapa Rice & Beans, Brazilian Agricultural Research Corporation, Santo Antônio de Goiás, GO, 75375-000, Brazil
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3
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Pullen R, Decker SR, Subramanian V, Adler MJ, Tobias AV, Perisin M, Sund CJ, Servinsky MD, Kozlowski MT. Considerations for Domestication of Novel Strains of Filamentous Fungi. ACS Synth Biol 2025; 14:343-362. [PMID: 39883596 PMCID: PMC11852223 DOI: 10.1021/acssynbio.4c00672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2024] [Revised: 01/10/2025] [Accepted: 01/13/2025] [Indexed: 02/01/2025]
Abstract
Fungi, especially filamentous fungi, are a relatively understudied, biotechnologically useful resource with incredible potential for commercial applications. These multicellular eukaryotic organisms have long been exploited for their natural production of useful commodity chemicals and proteins such as enzymes used in starch processing, detergents, food and feed production, pulping and paper making and biofuels production. The ability of filamentous fungi to use a wide range of feedstocks is another key advantage. As chassis organisms, filamentous fungi can express cellular machinery, and metabolic and signal transduction pathways from both prokaryotic and eukaryotic origins. Their genomes abound with novel genetic elements and metabolic processes that can be harnessed for biotechnology applications. Synthetic biology tools are becoming inexpensive, modular, and expansive while systems biology is beginning to provide the level of understanding required to design increasingly complex synthetic systems. This review covers the challenges of working in filamentous fungi and offers a perspective on the approaches needed to exploit fungi as microbial cell factories.
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Affiliation(s)
- Randi
M. Pullen
- DEVCOM
Army Research Laboratory, 2800 Powder Mill Rd., Adelphi, Maryland 20783, United
States
| | - Stephen R. Decker
- National
Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | | | - Meaghan J. Adler
- DEVCOM
Army Research Laboratory, 2800 Powder Mill Rd., Adelphi, Maryland 20783, United
States
| | - Alexander V. Tobias
- DEVCOM
Army Research Laboratory, 2800 Powder Mill Rd., Adelphi, Maryland 20783, United
States
| | - Matthew Perisin
- DEVCOM
Army Research Laboratory, 2800 Powder Mill Rd., Adelphi, Maryland 20783, United
States
| | - Christian J. Sund
- DEVCOM
Army Research Laboratory, 2800 Powder Mill Rd., Adelphi, Maryland 20783, United
States
| | - Matthew D. Servinsky
- DEVCOM
Army Research Laboratory, 2800 Powder Mill Rd., Adelphi, Maryland 20783, United
States
| | - Mark T. Kozlowski
- DEVCOM
Army Research Laboratory, 2800 Powder Mill Rd., Adelphi, Maryland 20783, United
States
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Mascarin GM, Shrestha S, de Carvalho Barros Cortes MV, Ramirez JL, Dunlap CA, Coleman JJ. CRISPR-Cas9-mediated enhancement of Beauveria bassiana virulence with overproduction of oosporein. Fungal Biol Biotechnol 2024; 11:21. [PMID: 39574174 PMCID: PMC11583550 DOI: 10.1186/s40694-024-00190-5] [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: 08/27/2024] [Accepted: 11/11/2024] [Indexed: 11/24/2024] Open
Abstract
Biocontrol agents play a pivotal role in managing pests and contribute to sustainable agriculture. Recent advancements in genetic engineering can facilitate the development of entomopathogenic fungi with desired traits to enhance biocontrol efficacy. In this study, a CRISPR-Cas9 ribonucleoprotein system was utilized to genetically improve the virulence of Beauveria bassiana, a broad-spectrum insect pathogen used in biocontrol of arthropod pests worldwide. CRISPR-Cas9-based disruption of the transcription factor-encoding gene Bbsmr1 led to derepression of the oosporein biosynthetic gene cluster resulting in overproduction of the red-pigmented dibenzoquinone oosporein involved in host immune evasion, thus increasing fungal virulence. Mutants defective for Bbsmr1 displayed a remarkable enhanced insecticidal activity by reducing lethal times and concentrations, while concomitantly presenting negligible or minor pleiotropic effects. In addition, these mutants displayed faster germination on the insect cuticle which correlated with higher density of free-floating blastospores in the hemolymph and accelerated mortality of the host. These findings emphasize the utility of genetic engineering in developing enhanced fungal biocontrol agents with customized phenotypic traits, and provide an efficient and versatile genetic transformation tool for application in other beneficial entomopathogenic fungi.
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Affiliation(s)
- Gabriel Moura Mascarin
- Laboratory of Environmental Microbiology, Embrapa Environment, Brazilian Agricultural Research Corporation, Embrapa Environment, Rodovia SP 340, km 127.5, Jaguariúna, SP, 13918-110, Brazil.
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36849, USA.
| | - Somraj Shrestha
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36849, USA
| | - Marcio Vinícius de Carvalho Barros Cortes
- Laboratory of Agricultural Microbiology, Brazilian Agricultural Research Corporation, Embrapa Rice & Beans, Rodovia GO 462, km 12, Santo Antônio de Goiás, GO, 75375-000, Brazil
| | - Jose Luis Ramirez
- Crop Bioprotection Research Unit, National Center for Agricultural Utilization Research, USDA, Peoria, IL, 61604, USA
| | - Christopher A Dunlap
- Crop Bioprotection Research Unit, National Center for Agricultural Utilization Research, USDA, Peoria, IL, 61604, USA
| | - Jeffrey J Coleman
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36849, USA
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5
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de Miranda RPR, Soares TKDA, Castro DP, Genta FA. General aspects, host interaction, and application of Metarhizium sp. in arthropod pest and vector control. FRONTIERS IN FUNGAL BIOLOGY 2024; 5:1456964. [PMID: 39634290 PMCID: PMC11614621 DOI: 10.3389/ffunb.2024.1456964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Accepted: 10/14/2024] [Indexed: 12/07/2024]
Abstract
The application of microorganisms as bio-control agents against arthropod populations is a need in many countries, especially in tropical, subtropical, and neotropical endemic areas. Several arthropod species became agricultural pests of paramount economic significance, and many methods have been developed for field and urban applications to prevent their, the most common being the application of chemical insecticides. However, the indiscriminate treatment based upon those substances acted as a selective pressure for upcoming resistant phenotype populations. As alternative tools, microorganisms have been prospected as complementary tools for pest and vectorial control, once they act in a more specific pattern against target organisms than chemicals. They are considered environmentally friendly since they have considerably less off-target effects. Entomopathogenic fungi are organisms capable of exerting pathogenesis in many vector species, thus becoming potential tools for biological management. The entomopathogenic fungi Metarhizium sp. have been investigated as a microbiological agent for the control of populations of insects in tropical regions. However, the development of entomopathogenic fungi as control tools depends on physiological studies regarding aspects such as mechanisms of pathogenicity, secreted enzymes, viability, and host-pathogen aspects. The following review briefly narrates current aspects of entomopathogenic fungi, such as physiology, cellular characteristics, host-pathogen interactions, and its previous applications against different insect orders with medical and economic importance. Approaches integrating new isolation, prospection, characterization, delivery strategies, formulations, and molecular and genetic tools will be decisive to elucidate the molecular mechanisms of EPFs and to develop more sustainable alternative pesticides.
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Affiliation(s)
| | | | - Daniele Pereira Castro
- Laboratorio de Bioquímica e Fisiologia de Insetos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Rio de Janeiro, Brazil
| | - Fernando Ariel Genta
- Laboratorio de Bioquímica e Fisiologia de Insetos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Rio de Janeiro, Brazil
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6
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Wang G, Zhang X, Chen B, Peng Y. Construction of an Efficient Agrobacterium tumefaciens-Based Transformation System in the Entomopathogenic fungus Metahizium rileyi. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:21711-21719. [PMID: 39287555 DOI: 10.1021/acs.jafc.4c05535] [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: 09/19/2024]
Abstract
Metarhizium rileyi is a filamentous entomopathogenic fungus that is highly pathogenic to lepidopteran insects. In our study, we constructed an Agrobacterium tumefaciens-mediated transgene system using the hygromycin resistance gene (Hyg R) as a selection marker in M. rileyi through homologous recombination. Binary knockout vectors for two genes (NOR_03501, longevity assurance gene, and NOR_03153, ATP-binding domain protein domain gene) in the M. rileyi strain SZCY201010 were successfully developed. We compared the genetic transformation efficiency using five kinds of asexual spores. The initial genetic transformation rates using a competent blastospore for NOR_03501 and NOR_03153 were 54.35 and 47.19%, respectively. Subsequently, both genes were successfully knocked out, and the transformed fungi were verified by PCR, RT-qPCR, and green fluorescent protein labeling. The biological phenotypes of the two genes were analyzed. The NOR_03501 gene plays a crucial role in carbon source utilization, stress resistance, and cuticle infection of fungal mycelium growth, while the NOR_03153 gene is significant for conidial production, stress resistance, and body wall infection. This study provides a promising tool for gene manipulation in M. rileyi, enhancing research in functional genomics and the exploration of fungal gene resources.
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Affiliation(s)
- Guang Wang
- Yunnan State Key Laboratory of Conservation and Utilization of Biological Resources, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China
| | - Xu Zhang
- Yunnan State Key Laboratory of Conservation and Utilization of Biological Resources, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China
| | - Bin Chen
- Yunnan State Key Laboratory of Conservation and Utilization of Biological Resources, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China
| | - Yuejin Peng
- Yunnan State Key Laboratory of Conservation and Utilization of Biological Resources, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China
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7
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Jain D, Kalia A, Sharma S, Manchanda P. Genome editing tools based improved applications in macrofungi. Mol Biol Rep 2024; 51:873. [PMID: 39080117 DOI: 10.1007/s11033-024-09809-7] [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: 06/11/2024] [Accepted: 07/18/2024] [Indexed: 02/06/2025]
Abstract
Macrofungi commonly referred to as Mushrooms are distributed worldwide and well known for their nutritional, medicinal, and organoleptic properties. Strain improvement in mushrooms is lagging due to paucity of efficient genome modification techniques. Thus, for advanced developments in research and commercial or economical viability and benefit, CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated nuclease 9) emerged as an efficient genome editing tool. The higher efficiency and precision of the desired genetic modification(s) are the most valuable attributes of this recent technology. The present review comprehensively summarizes various conventional methods utilized for strain improvement in mushrooms including hybridization, protoplast fusion, and di-mon mating. Furthermore, the problems associated with these techniques have been discussed besides providing the potential recluses. The significance of CRISPR/Cas9 strategies employed for improvement in various mushroom genera has been deliberated, as these strategies will paves the way forward for obtaining improved strain and effective cultivation methods for enhancing the yield and quality of the fruit bodies.
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Affiliation(s)
- Deepali Jain
- Department of Microbiology, College of Basic Sciences and Humanities, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Anu Kalia
- Electron Microscopy and Nanoscience Laboratory, Department of Soil Science, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, Punjab, India.
| | - Shivani Sharma
- Department of Microbiology, College of Basic Sciences and Humanities, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Pooja Manchanda
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
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8
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Nie H, Zhang Y, Li M, Wang W, Wang Z, Zheng J. Expression of microbial lipase in filamentous fungus Aspergillus niger: a review. 3 Biotech 2024; 14:172. [PMID: 38841267 PMCID: PMC11147998 DOI: 10.1007/s13205-024-03998-5] [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: 01/17/2024] [Accepted: 04/28/2024] [Indexed: 06/07/2024] Open
Abstract
Lipase has high economic importance and is widely used in biodiesel, food, detergents, cosmetics, and pharmaceutical industries. The rapid development of synthetic biology and system biology has not only paved the way for comprehensively understanding the efficient operation mechanism of Aspergillus niger cell factories but also introduced a new technological system for creating and optimizing high-efficiency A. niger cell factories. In this review, all relevant data on microbial lipase enzyme sources and general properties are gathered and updated. The relationship between A. niger strain morphology and protein production is discussed. The safety of A. niger strain is investigated to ensure product safety. The biotechnologies and factors influencing lipase expression in A. niger are summarized. This review focuses on various strategies to improve lipase expression in A. niger. The summary of these methods and the application of the gene editing technology CRISPR/Cas9 system can further improve the efficiency of constructing the engineered lipase-producing A. niger.
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Affiliation(s)
- Hongmei Nie
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
| | - Yueting Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
| | - Mengjiao Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
| | - Weili Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
| | - Zhao Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
| | - Jianyong Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
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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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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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11
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Coca-Ruiz V, Aleu J, Collado IG. Comparing Fungal Sensitivity to Isothiocyanate Products on Different Botrytis spp. PLANTS (BASEL, SWITZERLAND) 2024; 13:756. [PMID: 38592765 PMCID: PMC10974099 DOI: 10.3390/plants13060756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 04/10/2024]
Abstract
Glucosinolates, the main secondary metabolites accumulated in cruciferous flora, have a major impact on fortifying plant immunity against diverse pathogens. Although Botrytis cinerea exhibits varying sensitivity to these compounds, current research has yet to fully understand the intricate mechanisms governing its response to glucosinolates. Different species of the genus Botrytis were exposed to glucosinolate-derived isothiocyanates, revealing that B. fabae, B. deweyae, and B. convolute, species with the mfsG transporter gene (Bcin06g00026) not detected with PCR, were more sensitive to isothiocyanates than Botrytis species containing that gene, such as B. cinerea, B. pseudocinerea, and B. byssoidea. This finding was further corroborated by the inability of species with the mfsG gene not detected with PCR to infect plants with a high concentration of glucosinolate-derived isothiocyanates. These results challenge established correlations, revealing varying aggressiveness on different plant substrates. An expression analysis highlighted the gene's induction in the presence of isothiocyanate, and a bioinformatic investigation identified homologous genes in other Botrytis species. Our study underscored the importance of advanced biotechnology to help understand these proteins and thus offer innovative solutions for agriculture.
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Affiliation(s)
- Víctor Coca-Ruiz
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, 11510 Cádiz, Spain;
- Instituto de Investigación en Biomoléculas (INBIO), Universidad de Cádiz, 11510 Cádiz, Spain
| | - Josefina Aleu
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, 11510 Cádiz, Spain;
- Instituto de Investigación en Biomoléculas (INBIO), Universidad de Cádiz, 11510 Cádiz, Spain
| | - Isidro G. Collado
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, 11510 Cádiz, Spain;
- Instituto de Investigación en Biomoléculas (INBIO), Universidad de Cádiz, 11510 Cádiz, Spain
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12
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Wang X, Ding X, Yuan Z, Jia Z, Fu K, Zhan F, Guo W, Zhou L, Li H, Dai J, Wang Z, Xie Y, Yang X. Analysis of the virulence, infection process, and extracellular enzyme activities of Aspergillus nomius against the Asian corn borer, Ostrinia furnacalis guenée (Lepidoptera: Crambidae). Virulence 2023; 14:2265108. [PMID: 37941402 PMCID: PMC10653701 DOI: 10.1080/21505594.2023.2265108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/25/2023] [Indexed: 11/10/2023] Open
Abstract
The control of Ostrinia furnacalis, a major pest of maize in Xinjiang, is challenging owing to the occurrence of resistant individuals. Entomopathogenic fungi (EPF) are natural insect regulators used as substitutes for synthetic chemical insecticides. The fungus Aspergillus nomius is highly pathogenic to O. furnacalis; however, its virulence characteristics have not been identified. This study aimed to analyse the lethal efficacy, mode of infection on the cuticle, and extracellular enzyme activity of A. nomius against O. furnacalis. We found that the mortality and mycosis of O. furnacalis were dose-dependent when exposed to A. nomius and varied at different life stages. The egg-hatching and adult emergence rates decreased with an increase in conidial suspension. The highest mortality (83.33%, 7 d post-infection [DPI]) and mycosis (74.33%, 7 DPI) and the lowest mortality response (8.52 × 103 conidia mL-1) and median lethal time (4.91 d) occurred in the 3rd instar larvae of O. furnacalis. Scanning electron microscopy indicated that numerous conidia germination and infection structure formation may have contributed to the high pathogenicity of A. nomius against O. furnacalis. There were significant correlations between O. furnacalis mortality and the activities of extracellular protease, lipase, and chitinase of A. nomius. This study revealed the infection process of the highly pathogenic A. nomius against O. furnacalis, providing a theoretical basis and reference for strain improvement and field application of EPF.
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Affiliation(s)
- Xiaowu Wang
- Institute of Microbiology Applications, Xinjiang Academy of Agricultural Sciences, Ürümqi, PR China
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Oasis, Ministry of Agriculture, Ürümqi, PR China
| | - Xinhua Ding
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Oasis, Ministry of Agriculture, Ürümqi, PR China
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Ürümqi, PR China
| | - Zihan Yuan
- Institute of Microbiology Applications, Xinjiang Academy of Agricultural Sciences, Ürümqi, PR China
| | - Zunzun Jia
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Oasis, Ministry of Agriculture, Ürümqi, PR China
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Ürümqi, PR China
| | - Kaiyun Fu
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Oasis, Ministry of Agriculture, Ürümqi, PR China
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Ürümqi, PR China
| | - Faqiang Zhan
- Institute of Microbiology Applications, Xinjiang Academy of Agricultural Sciences, Ürümqi, PR China
| | - Wenchao Guo
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Oasis, Ministry of Agriculture, Ürümqi, PR China
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Ürümqi, PR China
| | - Liuyan Zhou
- Institute of Microbiology Applications, Xinjiang Academy of Agricultural Sciences, Ürümqi, PR China
| | - Haiqiang Li
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Oasis, Ministry of Agriculture, Ürümqi, PR China
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Ürümqi, PR China
| | - Jinping Dai
- Institute of Microbiology Applications, Xinjiang Academy of Agricultural Sciences, Ürümqi, PR China
| | - Zhifang Wang
- Institute of Microbiology Applications, Xinjiang Academy of Agricultural Sciences, Ürümqi, PR China
| | - Yuqing Xie
- Institute of Microbiology Applications, Xinjiang Academy of Agricultural Sciences, Ürümqi, PR China
| | - Xinping Yang
- Institute of Microbiology Applications, Xinjiang Academy of Agricultural Sciences, Ürümqi, PR China
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13
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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: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [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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14
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Proietti S, Falconieri GS, Bertini L, Pascale A, Bizzarri E, Morales-Sanfrutos J, Sabidó E, Ruocco M, Monti MM, Russo A, Dziurka K, Ceci M, Loreto F, Caruso C. Beauveria bassiana rewires molecular mechanisms related to growth and defense in tomato. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4225-4243. [PMID: 37094092 PMCID: PMC10400115 DOI: 10.1093/jxb/erad148] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 04/21/2023] [Indexed: 05/03/2023]
Abstract
Plant roots can exploit beneficial associations with soil-inhabiting microbes, promoting growth and expanding the immune capacity of the host plant. In this work, we aimed to provide new information on changes occurring in tomato interacting with the beneficial fungus Beauveria bassiana. The tomato leaf proteome revealed perturbed molecular pathways during the establishment of the plant-fungus relationship. In the early stages of colonization (5-7 d), proteins related to defense responses to the fungus were down-regulated and proteins related to calcium transport were up-regulated. At later time points (12-19 d after colonization), up-regulation of molecular pathways linked to protein/amino acid turnover and to biosynthesis of energy compounds suggests beneficial interaction enhancing plant growth and development. At the later stage, the profile of leaf hormones and related compounds was also investigated, highlighting up-regulation of those related to plant growth and defense. Finally, B. bassiana colonization was found to improve plant resistance to Botrytis cinerea, impacting plant oxidative damage. Overall, our findings further expand current knowledge on the possible mechanisms underlying the beneficial role of B. bassiana in tomato plants.
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Affiliation(s)
- Silvia Proietti
- Department of Ecological and Biological Sciences, University of Tuscia, largo dell’Università snc, 01100 Viterbo, Italy
| | - Gaia Salvatore Falconieri
- Department of Ecological and Biological Sciences, University of Tuscia, largo dell’Università snc, 01100 Viterbo, Italy
| | - Laura Bertini
- Department of Ecological and Biological Sciences, University of Tuscia, largo dell’Università snc, 01100 Viterbo, Italy
| | - Alberto Pascale
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Elisabetta Bizzarri
- Department of Ecological and Biological Sciences, University of Tuscia, largo dell’Università snc, 01100 Viterbo, Italy
| | - Julia Morales-Sanfrutos
- Proteomics Unit, Centre de Regulació Genòmica, Barcelona Institute of Science and Technology (BIST), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain
- Proteomics Unit, Universitat Pompeu Fabra, Carrer Dr Aiguader 88, 08003 Barcelona, Spain
| | - Eduard Sabidó
- Proteomics Unit, Centre de Regulació Genòmica, Barcelona Institute of Science and Technology (BIST), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain
- Proteomics Unit, Universitat Pompeu Fabra, Carrer Dr Aiguader 88, 08003 Barcelona, Spain
| | - Michelina Ruocco
- Institute for Sustainable Plant Protection (IPSP-CNR), Piazzale Enrico Fermi, 1, 80055 Portici (NA), Italy
| | - Maurilia M Monti
- Institute for Sustainable Plant Protection (IPSP-CNR), Piazzale Enrico Fermi, 1, 80055 Portici (NA), Italy
| | - Assunta Russo
- Institute for Sustainable Plant Protection (IPSP-CNR), Piazzale Enrico Fermi, 1, 80055 Portici (NA), Italy
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici (NA), Italy
| | - Kinga Dziurka
- Department of Biotechnology, The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239 Kraków, Poland
| | - Marcello Ceci
- Department of Ecological and Biological Sciences, University of Tuscia, largo dell’Università snc, 01100 Viterbo, Italy
| | - Francesco Loreto
- Department of Biology, Via Cinthia, University of Naples Federico II, 80126, Naples, Italy
| | - Carla Caruso
- Department of Ecological and Biological Sciences, University of Tuscia, largo dell’Università snc, 01100 Viterbo, Italy
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15
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Zhang Y, Chen S, Yang L, Zhang Q. Application progress of CRISPR/Cas9 genome-editing technology in edible fungi. Front Microbiol 2023; 14:1169884. [PMID: 37303782 PMCID: PMC10248459 DOI: 10.3389/fmicb.2023.1169884] [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: 02/20/2023] [Accepted: 04/26/2023] [Indexed: 06/13/2023] Open
Abstract
Edible fungi are not only delicious but are also rich in nutritional and medicinal value, which is highly sought after by consumers. As the edible fungi industry continues to rapidly advance worldwide, particularly in China, the cultivation of superior and innovative edible fungi strains has become increasingly pivotal. Nevertheless, conventional breeding techniques for edible fungi can be arduous and time-consuming. CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated nuclease 9) is a powerful tool for molecular breeding due to its ability to mediate high-efficiency and high-precision genome modification, which has been successfully applied to many kinds of edible fungi. In this review, we briefly summarized the working mechanism of the CRISPR/Cas9 system and highlighted the application progress of CRISPR/Cas9-mediated genome-editing technology in edible fungi, including Agaricus bisporus, Ganoderma lucidum, Flammulina filiformis, Ustilago maydis, Pleurotus eryngii, Pleurotus ostreatus, Coprinopsis cinerea, Schizophyllum commune, Cordyceps militaris, and Shiraia bambusicola. Additionally, we discussed the limitations and challenges encountered using CRISPR/Cas9 technology in edible fungi and provided potential solutions. Finally, the applications of CRISPR/Cas9 system for molecular breeding of edible fungi in the future are explored.
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16
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Luo N, Li Z, Ling J, Zhao J, Li Y, Yang Y, Mao Z, Xie B, Li H, Jiao Y. Establishment of a CRISPR/Cas9-Mediated Efficient Knockout System of Trichoderma hamatum T21 and Pigment Synthesis PKS Gene Knockout. J Fungi (Basel) 2023; 9:jof9050595. [PMID: 37233306 DOI: 10.3390/jof9050595] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/10/2023] [Accepted: 05/17/2023] [Indexed: 05/27/2023] Open
Abstract
Trichoderma hamatum is a filamentous fungus that serves as a biological control agent for multiple phytopathogens and as an important resource promising for fungicides. However, the lack of adequate knockout technologies has hindered gene function and biocontrol mechanism research of this species. This study obtained a genome assembly of T. hamatum T21, with a 41.4 Mb genome sequence comprising 8170 genes. Based on genomic information, we established a CRISPR/Cas9 system with dual sgRNAs targets and dual screening markers. CRISPR/Cas9 plasmid and donor DNA recombinant plasmid were constructed for disruption of the Thpyr4 and Thpks1 genes. The result indicates the consistency between phenotypic characterization and molecular identification of the knockout strains. The knockout efficiencies of Thpyr4 and Thpks1 were 100% and 89.1%, respectively. Moreover, sequencing revealed fragment deletions between dual sgRNA target sites or GFP gene insertions presented in knockout strains. The situations were caused by different DNA repair mechanisms, nonhomologous end joining (NHEJ), and homologous recombination (HR). Overall, we have successfully constructed an efficient and convenient CRISPR/Cas9 system in T. hamatum for the first time, which has important scientific significance and application value for studies on functional genomics of Trichoderma and other filamentous fungi.
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Affiliation(s)
- Ning Luo
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flower, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zeyu Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flower, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jian Ling
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flower, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianlong Zhao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flower, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yan Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flower, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuhong Yang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flower, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhenchuan Mao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flower, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Bingyan Xie
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flower, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huixia Li
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China
| | - Yang Jiao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flower, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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17
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Zhang C, Teng B, Liu H, Wu C, Wang L, Jin S. Impact of Beauveria bassiana on antioxidant enzyme activities and metabolomic profiles of Spodoptera frugiperda. J Invertebr Pathol 2023; 198:107929. [PMID: 37127135 DOI: 10.1016/j.jip.2023.107929] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 04/20/2023] [Accepted: 04/25/2023] [Indexed: 05/03/2023]
Abstract
Spodoptera frugiperda is a pest that poses serious threat to the production of food and crops. Entopathogenic fungi, represented by Beauveria bassiana, has shown potential for S. frugiperda control. However, the mechanism of this biological control of pathogens is not fully understood, such as how antioxidant enzyme activities and metabolic profiles in S. frugiperda larvae are affected when infected by entomopathogenic fungi. This study assessed the antioxidant enzyme activities and shift in metabolomic profile in the S. frugiperda larvae infected with B.bassiana. The results indicate a pattern of initial increase and subsequent decrease in the activities of superoxide dismutase, catalase, and peroxidase in the B.bassiana-infected larvae. And the enzyme activities at 60 h of infection ended significantly lower than those of the uninfected larvae. A total of 93 differential metabolites were identified in the B.bassiana-infected larvae, of which 41 metabolites were up-regulated and 52 were down-regulated. These metabolites mainly included amino acids, nucleotides, lipids, carbohydrates, and their derivatives. Among the changed metabolites, cystathionine, L-tyrosine, L-dopa, arginine, alpha-ketoglutaric acid, D-sedoheptulose-7-phosphate and citric acid were significantly decreased in B. bassiana-infected larvae. This indicated that the fungal infection might impair the ability of S. frugiperda larvae to cope with oxidative stress, leading to a negative impact of organism fitness. Further analyses of key metabolic pathways reveal that B. bassiana infection might affect purine metabolism, arginine biosynthesis, butanoate metabolism, and phenylalanine metabolism of S. frugiperda larvae. The findings from this study will contribute to our understanding of oxidative stress on immune defense in insects, and offer fundamental support for the biological control of S. frugiperda.
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Affiliation(s)
- Chen Zhang
- College of Life Science, Anhui Agricultural University, Hefei 230036, P. R. China; These authors contributed equally to this work
| | - Bin Teng
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei 230031, P. R. China; These authors contributed equally to this work
| | - Huimin Liu
- College of Life Science, Anhui Agricultural University, Hefei 230036, P. R. China
| | - Chenyuan Wu
- College of Life Science, Anhui Agricultural University, Hefei 230036, P. R. China
| | - Lei Wang
- College of Life Science, Anhui Agricultural University, Hefei 230036, P. R. China
| | - Song Jin
- Department of Civil and Architectural Engineering, University of Wyoming, Laramie, WY 82071, USA.
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18
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Wang Y, Chen H, Ma L, Gong M, Wu Y, Bao D, Zou G. Use of CRISPR-Cas tools to engineer Trichoderma species. Microb Biotechnol 2022; 15:2521-2532. [PMID: 35908288 PMCID: PMC9518982 DOI: 10.1111/1751-7915.14126] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/14/2022] [Accepted: 07/20/2022] [Indexed: 11/27/2022] Open
Abstract
Given their lignocellulose degradability and biocontrol activities, fungi of the ubiquitously distributed genus Trichoderma have multiple industrial and agricultural applications. Genetic manipulation plays a valuable role in tailoring novel engineered strains with enhanced target traits. Nevertheless, as applied to fungi, the classic tools of genetic manipulation tend to be time-consuming and tedious. However, the recent development of the CRISPR-Cas system for gene editing has enabled researchers to achieve genome-wide gene disruptions, gene replacements, and precise editing, and this technology has emerged as a primary focus for novel developments in engineered strains of Trichoderma. Here, we provide a brief overview of the traditional approaches to genetic manipulation, the different strategies employed in establishing CRSIPR-Cas systems, the utilization of these systems to develop engineered strains of Trichoderma for desired applications, and the future trends in biotechnology.
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Affiliation(s)
- Ying Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible FungiShanghai Academy of Agricultural SciencesShanghaiChina
| | - Hongyu Chen
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible FungiShanghai Academy of Agricultural SciencesShanghaiChina
| | - Liang Ma
- Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural SciencesZhejiang A&F UniversityLin'an HangzhouChina
| | - Ming Gong
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible FungiShanghai Academy of Agricultural SciencesShanghaiChina
| | - Yingying Wu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible FungiShanghai Academy of Agricultural SciencesShanghaiChina
| | - Dapeng Bao
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible FungiShanghai Academy of Agricultural SciencesShanghaiChina
| | - Gen Zou
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible FungiShanghai Academy of Agricultural SciencesShanghaiChina
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19
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McCarthy HM, Tarallo M, Mesarich CH, McDougal RL, Bradshaw RE. Targeted Gene Mutations in the Forest Pathogen Dothistroma septosporum Using CRISPR/Cas9. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11081016. [PMID: 35448744 PMCID: PMC9025729 DOI: 10.3390/plants11081016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/04/2022] [Accepted: 04/04/2022] [Indexed: 05/19/2023]
Abstract
Dothistroma needle blight, caused by Dothistroma septosporum, has increased in incidence and severity over the last few decades and is now one of the most important global diseases of pines. Disease resistance breeding could be accelerated by knowledge of pathogen virulence factors and their host targets. However, this is hindered due to inefficient targeted gene disruption in D. septosporum, which is required for virulence gene characterisation. Here we report the first successful application of CRISPR/Cas9 gene editing to a Dothideomycete forest pathogen, D. septosporum. Disruption of the dothistromin pathway regulator gene AflR, with a known phenotype, was performed using nonhomologous end-joining repair with an efficiency of > 90%. Transformants with a range of disruption mutations in AflR were produced. Disruption of Ds74283, a D. septosporum gene encoding a secreted cell death elicitor, was also achieved using CRISPR/Cas9, by using a specific donor DNA repair template to aid selection where the phenotype was unknown. In this case, 100% of screened transformants were identified as disruptants. In establishing CRISPR/Cas9 as a tool for gene editing in D. septosporum, our research could fast track the functional characterisation of candidate virulence factors in D. septosporum and helps set the foundation for development of this technology in other forest pathogens.
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Affiliation(s)
- Hannah M. McCarthy
- BioProtection Aotearoa, School of Natural Sciences, Massey University, Palmerston North 4472, New Zealand; (M.T.); (R.E.B.)
- Correspondence:
| | - Mariana Tarallo
- BioProtection Aotearoa, School of Natural Sciences, Massey University, Palmerston North 4472, New Zealand; (M.T.); (R.E.B.)
| | - Carl H. Mesarich
- BioProtection Aotearoa, School of Agriculture and Environment, Massey University, Palmerston North 4472, New Zealand;
| | - Rebecca L. McDougal
- Scion, New Zealand Forest Research Institute Ltd., Rotorua 3010, New Zealand;
| | - Rosie E. Bradshaw
- BioProtection Aotearoa, School of Natural Sciences, Massey University, Palmerston North 4472, New Zealand; (M.T.); (R.E.B.)
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20
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Dukare A, Mhatre P, Maheshwari HS, Bagul S, Manjunatha BS, Khade Y, Kamble U. Delineation of mechanistic approaches of rhizosphere microorganisms facilitated plant health and resilience under challenging conditions. 3 Biotech 2022; 12:57. [PMID: 35186654 PMCID: PMC8817020 DOI: 10.1007/s13205-022-03115-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 01/12/2022] [Indexed: 12/27/2022] Open
Abstract
Sustainable agriculture demands the balanced use of inorganic, organic, and microbial biofertilizers for enhanced plant productivity and soil fertility. Plant growth-enhancing rhizospheric bacteria can be an excellent biotechnological tool to augment plant productivity in different agricultural setups. We present an overview of microbial mechanisms which directly or indirectly contribute to plant growth, health, and development under highly variable environmental conditions. The rhizosphere microbiomes promote plant growth, suppress pathogens and nematodes, prime plants immunity, and alleviate abiotic stress. The prospective of beneficial rhizobacteria to facilitate plant growth is of primary importance, particularly under abiotic and biotic stresses. Such microbe can promote plant health, tolerate stress, even remediate soil pollutants, and suppress phytopathogens. Providing extra facts and a superior understanding of microbial traits underlying plant growth promotion can stir the development of microbial-based innovative solutions for the betterment of agriculture. Furthermore, the application of novel scientific approaches for facilitating the design of crop-specific microbial biofertilizers is discussed. In this context, we have highlighted the exercise of "multi-omics" methods for assessing the microbiome's impact on plant growth, health, and overall fitness via analyzing biochemical, physiological, and molecular facets. Furthermore, the role of clustered regularly interspaced short palindromic repeats (CRISPR) based genome alteration and nanotechnology for improving the agronomic performance and rhizosphere microbiome is also briefed. In a nutshell, the paper summarizes the recent vital molecular processes that underlie the different beneficial plant-microbe interactions imperative for enhancing plant fitness and resilience under-challenged agriculture.
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Affiliation(s)
- Ajinath Dukare
- ICAR-Central Institute for Research on Cotton Technology (CIRCOT), Mumbai, Maharashtra India
| | - Priyank Mhatre
- ICAR-Central Potato Research Institute (Regional Station), Udhagamandalam, Tamil Nadu India
| | - Hemant S. Maheshwari
- ICAR-Indian Institute of Soybean Research (IISR), Indore, Madhya Pradesh India
- Present Address: Ecophysiology of Plants, Faculty of Science and Engineering, GELIFES-Groningen Institute for Evolutionary Life Sciences, The University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Samadhan Bagul
- ICAR-Directorate of Medicinal and Aromatic Plant Research, Anand, Gujarat India
| | - B. S. Manjunatha
- ICAR-National Institute of Natural Fibre Engineering and Technology, Kolkata, West Bengal India
| | - Yogesh Khade
- ICAR- Directorate of Onion and Garlic Research, Pune, Maharashtra India
| | - Umesh Kamble
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana India
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21
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Development of versatile and efficient genetic tools for the marine-derived fungus Aspergillus terreus RA2905. Curr Genet 2022; 68:153-164. [DOI: 10.1007/s00294-021-01218-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/11/2021] [Accepted: 10/11/2021] [Indexed: 11/26/2022]
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22
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Singh S, Ramakrishna W. Application of CRISPR-Cas9 in plant-plant growth-promoting rhizobacteria interactions for next Green Revolution. 3 Biotech 2021; 11:492. [PMID: 34840925 PMCID: PMC8590643 DOI: 10.1007/s13205-021-03041-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/20/2021] [Indexed: 12/21/2022] Open
Abstract
Agriculture's beginnings resulted in the domestication of numerous plant species as well as the use of natural resources. Food grain production took about 10,000 years to reach a billion tonnes in 1960, however, it took only 40 years to achieve 2 billion tonnes in year 2000. The creation of genetically modified crops, together with the use of enhanced agronomic practices, resulted in this remarkable increase, dubbed the "Green Revolution". Plants and bacteria that interact with each other in nature are co-evolving, according to Red Queen dynamics. Plant microorganisms, also known as plant microbiota, are an essential component of plant life. Plant-microbe (PM) interactions can be beneficial or harmful to hosts, depending on the health impact. The significance of microbiota in plant growth promotion (PGP) and stress resistance is well known. Our understanding of the community composition of the plant microbiome and important driving forces has advanced significantly. As a result, utilising the plant microbiota is a viable strategy for the next Green Revolution for meeting food demand. The utilisation of newer methods to understand essential genetic and molecular components of the multiple PM interactions is required for their application. The use of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas-mediated genome editing (GE) techniques to investigate PM interactions is of tremendous interest. The implementation of GE techniques to boost the ability of microorganisms or plants for agronomic trait development will be enabled by a comprehensive understanding of PM interactions. This review focuses on using GE approaches to investigate the principles of PM interactions, disease resistance, PGP activity, and future implications in agriculture in plants or associated microbiota.
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Affiliation(s)
- Sudiksha Singh
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Ghudda, Bathinda, Punjab 151401 India
| | - Wusirika Ramakrishna
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Ghudda, Bathinda, Punjab 151401 India
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23
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Genome editing for resistance against plant pests and pathogens. Transgenic Res 2021; 30:427-459. [PMID: 34143358 DOI: 10.1007/s11248-021-00262-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 05/27/2021] [Indexed: 12/12/2022]
Abstract
The conventional breeding of crops struggles to keep up with increasing food needs and ever-adapting pests and pathogens. Global climate changes have imposed another layer of complexity to biological systems, increasing the challenge to obtain improved crop cultivars. These dictate the development and application of novel technologies, like genome editing (GE), that assist targeted and fast breeding programs in crops, with enhanced resistance to pests and pathogens. GE does not require crossings, hence avoiding the introduction of undesirable traits through linkage in elite varieties, speeding up the whole breeding process. Additionally, GE technologies can improve plant protection by directly targeting plant susceptibility (S) genes or virulence factors of pests and pathogens, either through the direct edition of the pest genome or by adding the GE machinery to the plant genome or to microorganisms functioning as biocontrol agents (BCAs). Over the years, GE technology has been continuously evolving and more so with the development of CRISPR/Cas. Here we review the latest advancements of GE to improve plant protection, focusing on CRISPR/Cas-based genome edition of crops and pests and pathogens. We discuss how other technologies, such as host-induced gene silencing (HIGS) and the use of BCAs could benefit from CRISPR/Cas to accelerate the development of green strategies to promote a sustainable agriculture in the future.
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Rozhkova AM, Kislitsin VY. CRISPR/Cas Genome Editing in Filamentous Fungi. BIOCHEMISTRY (MOSCOW) 2021; 86:S120-S139. [PMID: 33827404 DOI: 10.1134/s0006297921140091] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The review describes the CRISPR/CAS system and its adaptation for the genome editing in filamentous fungi commonly used for production of enzyme complexes, enzymes, secondary metabolites, and other compounds used in industrial biotechnology and agriculture. In the second part of this review, examples of the CRISPR/CAS technology application for improving properties of the industrial strains of fungi from the Trichoderma, Aspergillus, Penicillium, and other genera are presented. Particular attention is given to the efficiency of genome editing, as well as system optimization for specific industrial producers.
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Affiliation(s)
- Aleksandra M Rozhkova
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia.
| | - Valeriy Yu Kislitsin
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia
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Jiang C, Lv G, Tu Y, Cheng X, Duan Y, Zeng B, He B. Applications of CRISPR/Cas9 in the Synthesis of Secondary Metabolites in Filamentous Fungi. Front Microbiol 2021; 12:638096. [PMID: 33643273 PMCID: PMC7905030 DOI: 10.3389/fmicb.2021.638096] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/18/2021] [Indexed: 12/19/2022] Open
Abstract
Filamentous fungi possess the capacity to produce a wide array of secondary metabolites with diverse biological activities and structures, such as lovastatin and swainsonine. With the advent of the post-genomic era, increasing amounts of cryptic or uncharacterized secondary metabolite biosynthetic gene clusters are continually being discovered. However, owing to the longstanding lack of versatile, comparatively simple, and highly efficient genetic manipulation techniques, the broader exploration of industrially important secondary metabolites has been hampered thus far. With the emergence of CRISPR/Cas9-based genome editing technology, this dilemma may be alleviated, as this advanced technique has revolutionized genetic research and enabled the exploitation and discovery of new bioactive compounds from filamentous fungi. In this review, we introduce the CRISPR/Cas9 system in detail and summarize the latest applications of CRISPR/Cas9-mediated genome editing in filamentous fungi. We also briefly introduce the specific applications of the CRISPR/Cas9 system and CRISPRa in the improvement of secondary metabolite contents and discovery of novel biologically active compounds in filamentous fungi, with specific examples noted. Additionally, we highlight and discuss some of the challenges and deficiencies of using the CRISPR/Cas9-based genome editing technology in research on the biosynthesis of secondary metabolites as well as future application of CRISPR/Cas9 strategy in filamentous fungi are highlighted and discussed.
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Affiliation(s)
- Chunmiao Jiang
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Gongbo Lv
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Yayi Tu
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Xiaojie Cheng
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Yitian Duan
- School of Information, Renmin University of China, Beijing, China
| | - Bin Zeng
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China.,College of Pharmacy, Shenzhen Technology University, Shenzhen, China
| | - Bin He
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
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Arazoe T. CRISPR-based pathogenic fungal genome editing for control of infection and disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 179:161-196. [PMID: 33785176 DOI: 10.1016/bs.pmbts.2020.12.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Fungi play important roles in many aspects of human life, such as in various food, beverage, agricultural, chemical, and pharmaceutical industries. Meanwhile, some fungal species cause several severe diseases in plants, humans and animals. Fungal and fungal-like diseases pose a severe threat to human health, food security, and ecosystem health worldwide. This chapter introduces CRISPR-based genome editing technologies for pathogenic fungi and their application in controlling fungal diseases.
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Affiliation(s)
- Takayuki Arazoe
- Faculty of Science and Technology, Department of Applied Biological Science, Tokyo University of Science, Noda-shi, Chiba, Japan.
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27
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Ullah M, Xia L, Xie S, Sun S. CRISPR/Cas9-based genome engineering: A new breakthrough in the genetic manipulation of filamentous fungi. Biotechnol Appl Biochem 2020; 67:835-851. [PMID: 33179815 DOI: 10.1002/bab.2077] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 10/24/2020] [Indexed: 12/26/2022]
Abstract
Filamentous fungi have several industrial, environmental, and medical applications. However, they are rarely utilized owing to the limited availability of full-genome sequences and genetic manipulation tools. Since the recent discovery of the full-genome sequences for certain industrially important filamentous fungi, CRISPR/Cas9 technology has drawn attention for the efficient development of engineered strains of filamentous fungi. CRISPR/Cas9 genome editing has been successfully applied to diverse filamentous fungi. In this review, we briefly discuss the use of common genetic transformation techniques as well as CRISPR/Cas9-based systems in filamentous fungi. Furthermore, we describe potential limitations and challenges in the practical application of genome engineering of filamentous fungi. Finally, we provide suggestions and highlight future research prospects in the area.
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Affiliation(s)
- Mati Ullah
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lin Xia
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shangxian Xie
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Su Sun
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
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Králová M, Bergougnoux V, Frébort I. CRISPR/Cas9 genome editing in ergot fungus Claviceps purpurea. J Biotechnol 2020; 325:341-354. [PMID: 33053363 DOI: 10.1016/j.jbiotec.2020.09.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/11/2020] [Accepted: 09/30/2020] [Indexed: 02/09/2023]
Abstract
Claviceps purpurea is a filamentous fungus well known as a widespread plant pathogen, but it is also an important ergot alkaloid producer exploited by the pharmaceutic industry. In this work, we demonstrated that CRISPR/Cas9 can be a tool for directed mutagenesis in C. purpurea targeting pyr4 and TrpE genes encoding the orotidine 5'-phosphate decarboxylase involved in pyrimidine biosynthesis and the α-subunit of the anthranilate synthase involved in tryptophan biosynthesis, respectively. After protoplast transformation and single spore isolation, homokaryotic mutants showing uridine or tryptophan auxotrophy were selected. In all cases, insertions or insertions combined with deletions were found mostly 3 bp upstream of the PAM sequence. However, transformation efficiencies of CRISPR/Cas9 and CRISPR/Cas9 mediated homology-directed repair only slightly improved in comparison to homologous recombination-mediated knocking-out of the TrpE gene. Moreover, Trp auxotrophs were non-infectious towards rye plants likely due to a decreased production of the plant hormones auxins, which are synthesized by C. purpurea from indole-3-glycerolphosphate in Trp-dependent and Trp-independent biosynthetic pathways, and help the fungus to colonize the plant host. It was demonstrated that the CRISPR/Cas9 vector containing autonomous replicative sequence AMA1 can be fully removed by further culturing of C. purpurea on non-selective media. This method enables introducing multiple mutations in Claviceps and makes feasible metabolic engineering of industrial strains.
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Affiliation(s)
- Michaela Králová
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Šlechtitelů 27, Olomouc, 783 71, Czech Republic.
| | - Véronique Bergougnoux
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Šlechtitelů 27, Olomouc, 783 71, Czech Republic.
| | - Ivo Frébort
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Šlechtitelů 27, Olomouc, 783 71, Czech Republic.
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29
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Abstract
Flavonoids are known for their numerous biological activities; however, their pharmacological application is limited by poor bioavailability. Glycosides are usually more stable and more soluble in water and in this form, flavonoids are present in nature. Likewise, the presence of the methyl group in the flavonoid skeleton results in facilitated absorption and greater bioavailability. Entomopathogenic filamentous fungi are effective in the biotransformation of flavonoids; they are known especially for efficient glycosylation. In the current study we used strains of Beauveria bassiana KCH J1.5 and Isaria fumosorosea KCH J2 to biotransform flavonoids with a single methyl group. 2′-Hydroxy-5′-methylchalcone was biotransformed by both strains into 2′-hydroxy-5′-methylchalcone 3-O-β-D-(4″-O-methyl)-glucopyranoside. In the culture of B. bassiana KCH J1.5 four products were obtained from 6-methylflavanone: 4′-hydroxy-6-methylflavanone 3′-O-β-D-(4″-O-methyl)-glucopyranoside; 4′-hydroxyflavanone 6-methylene-O-β-D-(4″-O-methyl)-glucopyranoside; 6-hydroxymethylflavanone 3′-O-β-D-(4″-O-methyl)-glucopyranoside and 4′-hydroxy-6-hydroxymethylflavanone 3′-O-β-D-(4″-O-methyl)-glucopyranoside. Biotransformation with I. fumosorosea KCH J2 as a biocatalyst resulted in the formation of 6-methylflavanone 4′-O-β-D-(4″-O-methyl)-glucopyranoside and 2-phenyl-6-methylchromane 4-O-β-D-(4″-O-methyl)-glucopyranoside. All of these flavonoids can be used in biological activity tests and can be useful in studies concerning structure—bioactivity relationships.
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Genetic Reprogramming of the Ergot Alkaloid Pathway of Metarhizium brunneum. Appl Environ Microbiol 2020; 86:AEM.01251-20. [PMID: 32769181 DOI: 10.1128/aem.01251-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 07/30/2020] [Indexed: 12/14/2022] Open
Abstract
Ergot alkaloids are important specialized fungal metabolites that are used to make potent pharmaceuticals for neurological diseases and disorders. Lysergic acid (LA) and dihydrolysergic acid (DHLA) are desirable lead compounds for pharmaceutical semisynthesis but are typically transient intermediates in the ergot alkaloid and dihydroergot alkaloid pathways. Previous work with Neosartorya fumigata demonstrated strategies to produce these compounds as pathway end products, but their percent yield (percentage of molecules in product state as opposed to precursor state) was low. Moreover, ergot alkaloids in N. fumigata are typically retained in the fungus as opposed to being secreted. We used clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated protein 9 (Cas9) and heterologous expression approaches to engineer these compounds in Metarhizium brunneum, representing an alternate expression host from a different lineage of fungi. The relative percent yields of LA (86.9%) and DHLA (72.8%) were much higher than those calculated here for previously engineered strains of N. fumigata (2.6% and 2.0%, respectively). Secretion of these alkaloids also was measured, with averages of 98.4% of LA and 87.5% of DHLA being secreted into the growth medium; both values were significantly higher than those measured for the N. fumigata derivatives (both of which were less than 5.6% secreted). We used a similar approach to engineer a novel dihydroergot alkaloid in M. brunneum and, through high-performance liquid chromatography-mass spectrometry (LC-MS) analyses, provisionally identified it as the dihydrogenated form of lysergic acid α-hydroxyethylamide (dihydro-LAH). The engineering of these strains provides a strategy for producing novel and pharmaceutically important chemicals in a fungus more suitable for their production.IMPORTANCE Ergot alkaloids derived from LA or DHLA are the bases for numerous pharmaceuticals with applications in the treatment of dementia, migraines, hyperprolactinemia, and other conditions. However, extraction of ergot alkaloids from natural sources is inefficient, and their chemical synthesis is expensive. The ability to control and redirect ergot alkaloid synthesis in fungi may allow more efficient production of these important chemicals and facilitate research on novel derivatives. Our results show that Metarhizium brunneum can be engineered to efficiently produce and secrete LA and DHLA and, also, to produce a novel derivative of DHLA not previously found in nature. The engineering of dihydroergot alkaloids, including a novel species, is important because very few natural sources of these compounds are known. Our approach establishes a platform with which to use M. brunneum to study the production of other ergot alkaloids, specifically those classified as lysergic acid amides and dihydroergot alkaloids.
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Li C, Zhou J, Du G, Chen J, Takahashi S, Liu S. Developing Aspergillus niger as a cell factory for food enzyme production. Biotechnol Adv 2020; 44:107630. [PMID: 32919011 DOI: 10.1016/j.biotechadv.2020.107630] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 09/05/2020] [Accepted: 09/05/2020] [Indexed: 02/06/2023]
Abstract
Aspergillus niger has become one of the most important hosts for food enzyme production due to its unique food safety characteristics and excellent protein secretion systems. A series of food enzymes such as glucoamylase have been commercially produced by A. niger strains, making this species a suitable platform for the engineered of strains with improved enzyme production. However, difficulties in genetic manipulations and shortage of expression strategies limit the progress in this regard. Moreover, several mycotoxins have recently been detected in some A. niger strains, which raises the necessity for a regulatory approval process for food enzyme production. With robust strains, processing engineering strategies are also needed for producing the enzymes on a large scale, which is also challenging for A. niger, since its culture is aerobic, and non-Newtonian fluid properties are developed during submerged culture, making mixing and aeration very energy-intensive. In this article, the progress and challenges of developing A. niger for the production of food enzymes are reviewed, including its genetic manipulations, strategies for more efficient production of food enzymes, and elimination of mycotoxins for product safety.
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Affiliation(s)
- Cen Li
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| | - Guocheng Du
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| | - Jian Chen
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| | - Shunji Takahashi
- Natural Product Biosynthesis Research Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Song Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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The polyketide synthase PKS15 has a crucial role in cell wall formation in Beauveria bassiana. Sci Rep 2020; 10:12630. [PMID: 32724143 PMCID: PMC7387532 DOI: 10.1038/s41598-020-69417-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 06/30/2020] [Indexed: 12/13/2022] Open
Abstract
Entomopathogenic fungi utilize specific secondary metabolites to defend against insect immunity, thereby enabling colonization of their specific hosts. We are particularly interested in the polyketide synthesis gene pks15, which is involved in metabolite production, and its role in fungal virulence. Targeted disruption of pks15 followed by genetic complementation with a functional copy of the gene would allow for functional characterization of this secondary metabolite biosynthesis gene. Using a Beauveria bassiana ∆pks15 mutant previously disrupted by a bialophos-resistance (bar) cassette, we report here an in-cis complementation at bar cassette using CRISPR/Cas9 gene editing. A bar-specific short guide RNA was used to target and cause a double-strand break in bar, and a donor DNA carrying a wild-type copy of pks15 was co-transformed with the guide RNA. Isolate G6 of ∆pks15 complemented with pks15 was obtained and verified by PCR, Southern analyses and DNA sequencing. Compared to ∆pks15 which showed a marked reduction in sporulation and insect virulence, the complementation in G6 restored with insect virulence, sporulation and conidial germination to wild-type levels. Atomic force and scanning electron microscopy revealed that G6 and wild-type conidial wall surfaces possessed the characteristic rodlet bundles and rough surface while ∆pks15 walls lacked the bundles and were relatively smoother. Conidia of ∆pks15 were larger and more elongated than that of G6 and the wild type, indicating changes in their cell wall organization. Our data indicate that PKS15 and its metabolite are likely not only important for fungal virulence and asexual reproduction, but also cell wall formation.
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Deng H, Bai Y, Fan TP, Zheng X, Cai Y. Advanced strategy for metabolite exploration in filamentous fungi. Crit Rev Biotechnol 2020; 40:180-198. [PMID: 31906740 DOI: 10.1080/07388551.2019.1709798] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Filamentous fungi comprise an abundance of gene clusters that encode high-value metabolites, whereas affluent gene clusters remain silent during laboratory conditions. Complex cellular metabolism further limits these metabolite yields. Therefore, diverse strategies such as genetic engineering and chemical mutagenesis have been developed to activate these cryptic pathways and improve metabolite productivity. However, lower efficiencies of gene modifications and screen tools delayed the above processes. To address the above issues, this review describes an alternative design-construction evaluation optimization (DCEO) approach. The DCEO tool provides theoretical and practical principles to identify potential pathways, modify endogenous pathways, integrate exogenous pathways, and exploit novel pathways for their diverse metabolites and desirable productivities. This DCEO method also offers different tactics to balance the cellular metabolisms, facilitate the genetic engineering, and exploit the scalable metabolites in filamentous fungi.
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Affiliation(s)
- Huaxiang Deng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.,Center for Synthetic Biochemistry, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen, China
| | - Yajun Bai
- College of Life Sciences, Northwest University, Xi'an, Shanxi, China
| | - Tai-Ping Fan
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Xiaohui Zheng
- College of Life Sciences, Northwest University, Xi'an, Shanxi, China
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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34
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Qiao YM, Yu RL, Zhu P. Advances in targeting and heterologous expression of genes involved in the synthesis of fungal secondary metabolites. RSC Adv 2019; 9:35124-35134. [PMID: 35530690 PMCID: PMC9074735 DOI: 10.1039/c9ra06908a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 10/18/2019] [Indexed: 01/11/2023] Open
Abstract
The revolutionary discovery of penicillin only marks the start of our exploration for valuable fungal natural products. Advanced genome sequencing technologies have translated the fungal genome into a huge reservoir of "recipes" - biosynthetic gene clusters (BGCs) - for biosynthesis. Studying complex fungal genetics demands specific gene manipulation strategies. This review summarizes the current progress in efficient gene targeting in fungal cells and heterologous expression systems for expressing fungal BGCs of fungal secondary metabolites.
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Affiliation(s)
- Yun-Ming Qiao
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biosynthesis of Natural Products, CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College Beijing 100050 China +86-10-63017757 +86-10-63165197
| | - Rui-Lin Yu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biosynthesis of Natural Products, CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College Beijing 100050 China +86-10-63017757 +86-10-63165197
| | - Ping Zhu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biosynthesis of Natural Products, CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences, Peking Union Medical College Beijing 100050 China +86-10-63017757 +86-10-63165197
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35
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Song R, Zhai Q, Sun L, Huang E, Zhang Y, Zhu Y, Guo Q, Tian Y, Zhao B, Lu H. CRISPR/Cas9 genome editing technology in filamentous fungi: progress and perspective. Appl Microbiol Biotechnol 2019; 103:6919-6932. [PMID: 31332488 PMCID: PMC6690858 DOI: 10.1007/s00253-019-10007-w] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/28/2019] [Accepted: 07/01/2019] [Indexed: 12/16/2022]
Abstract
Filamentous fungi play an important role in human health and industrial/agricultural production. With the increasing number of full genomes available for fungal species, the study of filamentous fungi has brought about a wider range of genetic manipulation opportunities. However, the utilization of traditional methods to study fungi is time consuming and laborious. Recent rapid progress and wide application of a versatile genome editing technology, i.e., the CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 (CRISPR-related nuclease 9) system, has revolutionized biological research and has many innovative applications in a wide range of fields showing great promise in research and application of filamentous fungi. In this review, we introduce the CRISPR/Cas9 genome editing technology focusing on its application in research of filamentous fungi and we discuss the general considerations of genome editing using CRISPR/Cas9 system illustrating vector construction, multiple editing strategies, technical consideration of different sizes of homology arms on genome editing efficiency, off-target effects, and different transformation methodologies. In addition, we discuss the challenges encountered using CRISPR/Cas9 technology and give the perspectives of future applications of CRISPR/Cas9 technology for basic research and practical application of filamentous fungi.
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Affiliation(s)
- Runjie Song
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qing Zhai
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850000, Tibet, China
| | - Lu Sun
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Enxia Huang
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yu Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yanli Zhu
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qingyun Guo
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University/Key Laboratory of Agricultural Integrated Pest Management, Qinghai Province/State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, Qinghai, China.
| | - Yanan Tian
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Baoyu Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Hao Lu
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Shelake RM, Pramanik D, Kim JY. Exploration of Plant-Microbe Interactions for Sustainable Agriculture in CRISPR Era. Microorganisms 2019; 7:E269. [PMID: 31426522 PMCID: PMC6723455 DOI: 10.3390/microorganisms7080269] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/08/2019] [Accepted: 08/14/2019] [Indexed: 12/16/2022] Open
Abstract
Plants and microbes are co-evolved and interact with each other in nature. Plant-associated microbes, often referred to as plant microbiota, are an integral part of plant life. Depending on the health effects on hosts, plant-microbe (PM) interactions are either beneficial or harmful. The role of microbiota in plant growth promotion (PGP) and protection against various stresses is well known. Recently, our knowledge of community composition of plant microbiome and significant driving factors have significantly improved. So, the use of plant microbiome is a reliable approach for a next green revolution and to meet the global food demand in sustainable and eco-friendly agriculture. An application of the multifaceted PM interactions needs the use of novel tools to know critical genetic and molecular aspects. Recently discovered clustered regularly interspaced short palindromic repeats (CRISPR)/Cas-mediated genome editing (GE) tools are of great interest to explore PM interactions. A systematic understanding of the PM interactions will enable the application of GE tools to enhance the capacity of microbes or plants for agronomic trait improvement. This review focuses on applying GE techniques in plants or associated microbiota for discovering the fundamentals of the PM interactions, disease resistance, PGP activity, and future implications in agriculture.
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Affiliation(s)
- Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
| | - Dibyajyoti Pramanik
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea.
- Division of Life Science (CK1 Program), Gyeongsang National University, Jinju 660-701, Korea.
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Progress and Challenges: Development and Implementation of CRISPR/Cas9 Technology in Filamentous Fungi. Comput Struct Biotechnol J 2019; 17:761-769. [PMID: 31312414 PMCID: PMC6607083 DOI: 10.1016/j.csbj.2019.06.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/09/2019] [Accepted: 06/11/2019] [Indexed: 12/13/2022] Open
Abstract
Widely distributed in various environmental niches, filamentous fungi play an important role in industry, drug development, and plant/animal health. Manipulation of the genome and the coding sequences are essential for a better understanding of the function of genes and their regulation, but traditional genetic approaches in some filamentous fungi are either inefficient or nonfunctional. The rapid development and wide implementation of CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats /(CRISPR)-associated protein-9 nuclease) technology for various model and non-model organisms has provided the initial framework to adapt this gene editing technology for filamentous fungi. In this review, an overview of the CRISPR/Cas9 tools and strategies that have been developed for different filamentous fungi is presented, including integration of the CAS9 gene into the genome, transient expression of Cas9/sgRNA, the AMA1-based plasmid approach, and the Cas9 RNP method. The various applications of CRISPR/Cas9 technology in filamentous fungi that have been implemented are explored, with particular emphasis on gene disruption/deletion and precise genome modification through gene tagging and alteration in gene regulation. Potential challenges that are confronted when developing a CRISPR/Cas9 system for filamentous fungi are also discussed such as the nuclear localization sequence for the CAS9 gene, potential off-target effects, and highly efficient transformation methods. Overcoming these obstacles may further facilitate wide application of this technology. As a simple, economical, and powerful tool, CRISPR/Cas9 systems have the potential for future implementation into many molecular aspects of filamentous fungi.
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Functional genetic analysis of the leucinostatin biosynthesis transcription regulator lcsL in Purpureocillium lilacinum using CRISPR-Cas9 technology. Appl Microbiol Biotechnol 2019; 103:6187-6194. [PMID: 31175427 DOI: 10.1007/s00253-019-09945-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/22/2019] [Accepted: 05/25/2019] [Indexed: 02/06/2023]
Abstract
Purpureocillium lilacinum is a promising commercial agent for controlling plant-parasitic nematodes and plant pathogens. Leucinostatins are a family of lipopeptides produced by P. lilacinum that are synthesized, modified, and regulated by a gene cluster consisting of 20 genes. Sequence analyses have indicated that lcsL, a gene in the lcs cluster, is a putative bZIP transcription factor. In this study, the CRISPR-Cas9 system was introduced to increase the efficiency of homologous recombination for the disruption of lcsL. The expression of genes in the cluster was significantly reduced in lcsL disruption mutants, and the output of leucinostatins was decreased to undetectable levels. In the lcsL overexpression strain, the expression of genes in the cluster and the yield of leucinostatins were all increased. The antagonism of both the wild type and mutant against Phytophthora infestans was also consistent with the gene expression and the output of leucinostatins. These results indicate that the gene lcsL is crucial for the regulating the synthesis of leucinostatins.
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Integrate CRISPR/Cas9 for protein expression of HLA-B*38:68Q via precise gene editing. Sci Rep 2019; 9:8067. [PMID: 31147565 PMCID: PMC6542842 DOI: 10.1038/s41598-019-44336-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 05/14/2019] [Indexed: 11/16/2022] Open
Abstract
The determination of null- or low-expressed HLA alleles is clinically relevant in both hematopoietic stem cell transplantation and solid organ transplantation. We studied the expression level of a questionable (Q) HLA-B*38:68Q allele, which carries a 9-nucleotide (nt) deletion at codon 230–232 in exon 4 of HLA-B*38:01:01:01 using CRISPR/Cas9 gene editing technology. CRISPR/Cas9 gene editing of HLA-B*38:01:01:01 homozygous EBV B cell line resulted in one HLA-B*38:68Q/B*38:01:01:01 heterozygous and one HLA-B*38:68Q homozygous clone. Flow cytometric analysis of monoclonal anti-Bw4 antibody showed the protein expression of HLA-B*38:01:01:01 in homozygous cells was 2.2 fold higher than HLA-B*38:68Q/B*38:01:01:01 heterozygous cells, and the expression of HLA-B*38:68Q/B*38:01:01:01 heterozygous cells was over 2.0 fold higher than HLA-B*38:68Q homozygous cells. The HLA-B*38:68Q expression was further confirmed using anti-B38 polyclonal antibody. Similarly, the expression of the HLA-B*38:01:01:01 homozygous cells was 1.5 fold higher than that of HLA-B*38:68Q/B*38:01:01:01 heterozygous cells, and the HLA-B*38:68Q/B*38:01:01:01 heterozygous cells was over 1.6 fold higher than that of HLA-B*38:68Q homozygous cells. The treatment of HLA-B*38:68Q homozygous cells with IFN-γ significantly increased its expression. In conclusion, we demonstrate that HLA-B*38:68Q is a low-expressing HLA allele. The CRISPR/Cas9 technology is a useful tool to induce precise gene editing in HLA genes to enable the characterization of HLA gene variants on expression and function.
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Zhang Y, Feng J, Wang P, Xia J, Li X, Zou X. CRISPR/Cas9-mediated efficient genome editing via protoplast-based transformation in yeast-like fungus Aureobasidium pullulans. Gene 2019; 709:8-16. [PMID: 31132514 DOI: 10.1016/j.gene.2019.04.079] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/05/2019] [Accepted: 04/27/2019] [Indexed: 01/30/2023]
Abstract
Aureobasidium pullulans, a yeast-like fungus with strong environmental adaptability, remains a potential host for bio-production of different valuable metabolites. However, its potential application is limited by low-efficient genetic manipulation. In this study, CRISPR/Cas9-mediated genome editing via protoplast-based transformation system was developed. To test CRISPR/Cas9 mediated genomic mutagenesis, the orotidine 5-phosphate decarboxylase (umps) gene was used as a counter-selectable selection marker. By co-transforming of two plasmids harboring cas9 gene and a guide RNA targeting umps, respectively, the CRISPR/Cas9 system could significantly increase frequency of mutation in the targeting site of guide RNA. To further validate that CRISPR/Cas9 stimulated homologous recombination with donor DNA, a color reporter system of beta-glucuronidase (gus) gene was developed for calculating positive mutation rate. The results showed that positive mutation rate with CRISPR/Cas9 system was ~40% significantly higher than only with the donor DNA (~4%). Furthermore, the different posttranscriptional RNA processing schemes were analyzed by compared the effects of flanking gRNA with self-cleaving ribozymes or tRNA. The result demonstrated that gRNA processed by self-cleaving ribozymes achieves higher positive mutant rate. This study provided foundation for a simple and powerful genome editing tool for A. pullulans. Moreover, a counter-selectable selection marker (umps) and a color reporter system (gus) were being developed as genetic parts for strain engineering.
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Affiliation(s)
- Yuan Zhang
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, PR China
| | - Jun Feng
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, PR China
| | - Pan Wang
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, PR China
| | - Jun Xia
- College of Chemistry and Chemical Engineering, Huaiyin Normal University, Huai'an 223300, PR China
| | - Xiaorong Li
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, PR China.
| | - Xiang Zou
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, PR China.
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41
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Schuster M, Kahmann R. CRISPR-Cas9 genome editing approaches in filamentous fungi and oomycetes. Fungal Genet Biol 2019; 130:43-53. [PMID: 31048007 DOI: 10.1016/j.fgb.2019.04.016] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/27/2019] [Accepted: 04/28/2019] [Indexed: 12/26/2022]
Abstract
Due to their biotechnological relevance as well as their importance as disease agents, filamentous fungi and oomycetes have been prime candidates for genetic selection and in vitro manipulation for decades. With the advent of new genome editing technologies such manipulations have reached a new level of speed and sophistication. The CRISPR-Cas9 genome editing technology in particular has revolutionized the ways how desired mutations can be introduced. To date, the CRISPR-Cas9 genome editing system has been established in more than 40 different species of filamentous fungi and oomycetes. In this review we describe the various approaches taken to assure expression of the components necessary for editing and describe the varying strategies used to achieve gene disruptions, gene replacements and precise editing. We discuss potential problems faced when establishing the system, propose ways to circumvent them and suggest future approaches not yet realized in filamentous fungi or oomycetes.
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Affiliation(s)
- Mariana Schuster
- Max Planck Institute for Terrestrial Microbiology, Dept. Organismic Interactions, 35043 Marburg, Germany.
| | - Regine Kahmann
- Max Planck Institute for Terrestrial Microbiology, Dept. Organismic Interactions, 35043 Marburg, Germany.
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42
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Wang J, Lovett B, St. Leger RJ. The secretome and chemistry of Metarhizium; a genus of entomopathogenic fungi. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2018.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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43
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Developments and opportunities in fungal strain engineering for the production of novel enzymes and enzyme cocktails for plant biomass degradation. Biotechnol Adv 2019; 37:107361. [PMID: 30825514 DOI: 10.1016/j.biotechadv.2019.02.017] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 02/11/2019] [Accepted: 02/23/2019] [Indexed: 12/26/2022]
Abstract
Fungal strain engineering is commonly used in many areas of biotechnology, including the production of plant biomass degrading enzymes. Its aim varies from the production of specific enzymes to overall increased enzyme production levels and modification of the composition of the enzyme set that is produced by the fungus. Strain engineering involves a diverse range of methodologies, including classical mutagenesis, genetic engineering and genome editing. In this review, the main approaches for strain engineering of filamentous fungi in the field of plant biomass degradation will be discussed, including recent and not yet implemented methods, such as CRISPR/Cas9 genome editing and adaptive evolution.
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44
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Abstract
This review summarizes the current state of the art of CRISPR/Cas-based genome editing technologies for natural product producers.
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Affiliation(s)
- Yaojun Tong
- The Novo Nordisk Foundation Center for Biosustainability
- Technical University of Denmark
- Denmark
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability
- Technical University of Denmark
- Denmark
| | - Sang Yup Lee
- The Novo Nordisk Foundation Center for Biosustainability
- Technical University of Denmark
- Denmark
- Metabolic and Biomolecular Engineering National Research Laboratory
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program)
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45
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Muñoz IV, Sarrocco S, Malfatti L, Baroncelli R, Vannacci G. CRISPR-Cas for Fungal Genome Editing: A New Tool for the Management of Plant Diseases. FRONTIERS IN PLANT SCIENCE 2019; 10:135. [PMID: 30828340 PMCID: PMC6384228 DOI: 10.3389/fpls.2019.00135] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 01/28/2019] [Indexed: 05/02/2023]
Affiliation(s)
- Isabel Vicente Muñoz
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Sabrina Sarrocco
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
- *Correspondence: Sabrina Sarrocco
| | - Luca Malfatti
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Riccardo Baroncelli
- Spanish-Portuguese Center for Agricultural Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Villamayor, Spain
| | - Giovanni Vannacci
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
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46
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Tong Y, Weber T, Lee SY. CRISPR/Cas-based genome engineering in natural product discovery. Nat Prod Rep 2019; 36:1262-1280. [DOI: 10.1039/c8np00089a] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This review summarizes the current state of the art of CRISPR/Cas-based genome editing technologies for natural product producers.
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Affiliation(s)
- Yaojun Tong
- The Novo Nordisk Foundation Center for Biosustainability
- Technical University of Denmark
- Denmark
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability
- Technical University of Denmark
- Denmark
| | - Sang Yup Lee
- The Novo Nordisk Foundation Center for Biosustainability
- Technical University of Denmark
- Denmark
- Metabolic and Biomolecular Engineering National Research Laboratory
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program)
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47
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Qu S, Wang S. Interaction of entomopathogenic fungi with the host immune system. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 83:96-103. [PMID: 29355579 DOI: 10.1016/j.dci.2018.01.010] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 01/14/2018] [Accepted: 01/15/2018] [Indexed: 06/07/2023]
Abstract
Entomopathogenic fungi can invade wide range of insect hosts in the natural world and have been used as environmentally friendly alternatives to chemical insecticides for pest control. Studies of host-pathogen interactions provide valuable insights into the coevolutionay arms race between fungal pathogens and their hosts. Entomopathogenic fungi have evolved a series of sophisticated strategies to counter insect immune defenses. In response to fungal infection, insect hosts rely on behavior avoidance, physical barrier and innate immune defenses in the fight against invading pathogens. The insect cuticle acts as the first physical barrier against pathogens. It is an inhospitable physiological environment that contains chemicals (e.g., antimicrobial peptides and reactive oxygen species), which inhibit fungal growth. In addition, innate immune responses, including cellular immunity and humoral immunity, play critical roles in preventing fungal infection. In this review, we outline the current state of our knowledge of insect defenses to fungal infection and discuss the strategies by which entomopathogenic fungi counter the host immune system. Increased knowledge regarding the molecular interactions between entomopathogenic fungi and the insect host could provide new strategies for pest management.
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Affiliation(s)
- Shuang Qu
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Sibao Wang
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
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48
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Lovett B, St Leger RJ. Genetically engineering better fungal biopesticides. PEST MANAGEMENT SCIENCE 2018; 74:781-789. [PMID: 28905488 DOI: 10.1002/ps.4734] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 09/08/2017] [Indexed: 06/07/2023]
Abstract
Microbial insect pathogens offer an alternative means of pest control with the potential to wean us off our heavy reliance on chemical pesticides. Insect pathogenic fungi play an important natural role in controlling disease vectors and agricultural pests. Most commercial products employ Ascomycetes in the genera Metarhizium and Beauveria. However, their utilization has been limited by inconsistent field results as a consequence of sensitivity to abiotic stresses and naturally low virulence. Other naturally occurring biocontrol agents also face these hurdles to successful application, but the availability of complete genomes and recombinant DNA technologies have facilitated design of multiple fungal pathogens with enhanced virulence and stress resistance. Many natural and synthetic genes have been inserted into entomopathogen genomes. Some of the biggest gains in virulence have been obtained using genes encoding neurotoxic peptides, peptides that manipulate host physiology and proteases and chitinases that degrade the insect cuticle. Prokaryotes, particularly extremophiles, are useful sources of genes for improving entomopathogen resistance to ultraviolet (UV) radiation. These biological insecticides are environmentally friendly and cost-effective insect pest control options. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Brian Lovett
- Department of Entomology, University of Maryland, College Park, MD, USA
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49
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Pohl C, Mózsik L, Driessen AJM, Bovenberg RAL, Nygård YI. Genome Editing in Penicillium chrysogenum Using Cas9 Ribonucleoprotein Particles. Methods Mol Biol 2018; 1772:213-232. [PMID: 29754231 DOI: 10.1007/978-1-4939-7795-6_12] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Several CRISPR/Cas9 tools have been recently established for precise genome editing in a wide range of filamentous fungi. This genome editing platform offers high flexibility in target selection and the possibility of introducing genetic deletions without the introduction of transgenic sequences . This chapter describes an approach for the transformation of Penicillium chrysogenum protoplasts with preassembled ribonucleoprotein particles (RNPs) consisting of purified Cas9 protein and in vitro transcribed single guide RNA (sgRNA) for the deletion of genome sequences or their replacement with alternative sequences. This method is potentially transferable to all fungal strains where protoplasts can be obtained from.
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Affiliation(s)
- Carsten Pohl
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - László Mózsik
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Arnold J M Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
| | - Roel A L Bovenberg
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- DSM Biotechnology Center, DSM Food Specialties B.V., Delft, The Netherlands
| | - Yvonne I Nygård
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Chalmers University of Technology, Gothenburg, Sweden
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50
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Abstract
As eukaryotes, filamentous fungi share many features with humans, and they produce numerous active metabolites, some of which are toxic. Traditional genetic approaches are generally inefficient, but the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system that has been widely used for basic research on bacteria, mammals and plants offers a simple, fast, versatile technology for systemic research on filamentous fungi. In this review, we summarized the current knowledge on Cas9 and its variants, various selective markers used to screen positive clones, different ways used to detect off-target mutations, and different approaches used to express and transform the CRISPR complex. We also highlight several methods that improve the nuclease specificity and efficiency, and discuss current and potential applications of CRISPR/Cas9 system in filamentous fungi for pathogenesis decoding, confirmation of the gene and pathway, bioenergy process, drug discovery, and chromatin dynamics. We also describe how the synthetic gene circuit of CRISPR/Cas9 systems has been used in the response to various complex environmental signals to redirect metabolite flux and ensure continuous metabolite biosynthesis.
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Affiliation(s)
- Huaxiang Deng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, People's Republic of China
| | - Ruijie Gao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, People's Republic of China
| | - Xiangru Liao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, People's Republic of China.
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, People's Republic of China.
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