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Liu W, An C, Shu X, Meng X, Yao Y, Zhang J, Chen F, Xiang H, Yang S, Gao X, Gao SS. A Dual-Plasmid CRISPR/Cas System for Mycotoxin Elimination in Polykaryotic Industrial Fungi. ACS Synth Biol 2020; 9:2087-2095. [PMID: 32531165 DOI: 10.1021/acssynbio.0c00178] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Mycotoxin contamination causes disease and death in both humans and animals. Monascus Red, produced by Monascus purpureus, is used as a food colorant. However, its application is limited by contamination of the nephrotoxin citrinin, which is also produced by the fungus. Suppressing citrinin production by genetic engineering is difficult in a polykaryotic fungus such as M. purpureus. Hence, we developed a CRISPR/Cas system to delete large genomic fragments in polykaryotic fungi. Protoplast preparation and regeneration were optimized, and a dual-plasmid CRISPR/Cas system was designed to enable the deletion of the 15-kb citrinin biosynthetic gene cluster in M. purpureus industrial strain KL-001. The obtained homokaryotic mutants were stable, and citrinin was unambiguously eliminated. Moreover, the Monascus Red pigment production was increased by 2-5%. Our approach provides a powerful solution to solve this long-standing problem in the food industry and enables engineering of polykaryotic fungi for mycotoxin eliminations.
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Affiliation(s)
- Weiwei Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Chunyan An
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xian Shu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xiangxi Meng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yongpeng Yao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Jun Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Fusheng Chen
- Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100864, PR China
| | - Shuyuan Yang
- Department of Chemical and Biomolecular Engineering and Department of Bioengineering, Rice University, Houston, Texas 77005, United States
| | - Xue Gao
- Department of Chemical and Biomolecular Engineering and Department of Bioengineering, Rice University, Houston, Texas 77005, United States
| | - Shu-Shan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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Xu L, Li G, Jiang D, Chen W. Sclerotinia sclerotiorum: An Evaluation of Virulence Theories. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:311-338. [PMID: 29958073 DOI: 10.1146/annurev-phyto-080417-050052] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Oxalic acid production in Sclerotinia sclerotiorum has long been associated with virulence. Research involving UV-induced, genetically undefined mutants that concomitantly lost oxalate accumulation, sclerotial formation, and pathogenicity supported the conclusion that oxalate is an essential pathogenicity determinant of S. sclerotiorum. However, recent investigations showed that genetically defined mutants that lost oxalic acid production but accumulated fumaric acid could cause disease on many plants and substantiated the conclusion that acidic pH, not oxalic acid per se, is the necessary condition for disease development. Critical evaluation of available evidence showed that the UV-induced mutants harbored previously unrecognized confounding genetic defects in saprophytic growth and pH responsiveness, warranting reevaluation of the conclusions about virulence based on the UV-induced mutants. Furthermore, analyses of the evidence suggested a hypothesis for the existence of an unrecognized regulator responsive to acidic pH. Identifying the unknown pH regulator would offer a new avenue for investigating pH sensing/regulation in S. sclerotiorum and novel targets for intervention in disease control strategies.
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Affiliation(s)
- Liangsheng Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, People's Republic of China
| | - Guoqing Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China
| | - Weidong Chen
- Grain Legume Genetics and Physiology Research Unit, US Department of Agriculture, Agricultural Research Service, Washington State University, Pullman, Washington 99164, USA
- Departments of Plant Pathology and Molecular Plant Sciences Program, Washington State University, Pullman, Washington 99164, USA;
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Wei W, Shu S, Zhu W, Xiong Y, Peng F. The Kinome of Edible and Medicinal Fungus Wolfiporia cocos. Front Microbiol 2016; 7:1495. [PMID: 27708635 PMCID: PMC5030230 DOI: 10.3389/fmicb.2016.01495] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 09/07/2016] [Indexed: 01/10/2023] Open
Abstract
Wolfiporia cocos is an edible and medicinal fungus that grows in association with pine trees, and its dried sclerotium, known as Fuling in China, has been used as a traditional medicine in East Asian countries for centuries. Nearly 10% of the traditional Chinese medicinal preparations contain W. cocos. Currently, the commercial production of Fuling is limited because of the lack of pine-based substrate and paucity of knowledge about the sclerotial development of the fungus. Since protein kinase (PKs) play significant roles in the regulation of growth, development, reproduction, and environmental responses in filamentous fungi, the kinome of W. cocos was analyzed by identifying the PKs genes, studying transcript profiles and assigning PKs to orthologous groups. Of the 10 putative PKs, 11 encode atypical PKs, and 13, 10, 2, 22, and 11 could encoded PKs from the AGC, CAMK, CK, CMGC, STE, and TLK Groups, respectively. The level of transcripts from PK genes associated with sclerotia formation in the mycelium and sclerotium stages were analyzed by qRT-PCR. Based on the functions of the orthologs in Sclerotinia sclerotiorum (a sclerotia-formation fungus) and Saccharomyces cerevisiae, the potential roles of these W. cocos PKs were assigned. To the best of our knowledge, our study is the first identification and functional discussion of the kinome in the edible and medicinal fungus W. cocos. Our study systematically suggests potential roles of W. cocos PKs and provide comprehensive and novel insights into W. cocos sclerotial development and other economically important traits. Additionally, based on our result, genetic engineering can be employed for over expression or interference of some significant PKs genes to promote sclerotial growth and the accumulation of active compounds.
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Affiliation(s)
- Wei Wei
- Institute for Interdisciplinary Research, Jianghan University Wuhan, China
| | - Shaohua Shu
- College of Plant Science and Technology, Huazhong Agricultural University Wuhan, China
| | - Wenjun Zhu
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University Wuhan, China
| | - Ying Xiong
- Hefei Inzyme Information Technology Co., Ltd Wuhan, China
| | - Fang Peng
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University Wuhan, China
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Bashi ZD, Gyawali S, Bekkaoui D, Coutu C, Lee L, Poon J, Rimmer SR, Khachatourians GG, Hegedus DD. The Sclerotinia sclerotiorum Slt2 mitogen-activated protein kinase ortholog, SMK3, is required for infection initiation but not lesion expansion. Can J Microbiol 2016; 62:836-850. [PMID: 27503454 DOI: 10.1139/cjm-2016-0091] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Mitogen-activated protein kinases (MAPKs) play a central role in transferring signals and regulating gene expression in response to extracellular stimuli. An ortholog of the Saccharomyces cerevisiae cell wall integrity MAPK was identified in the phytopathogenic fungus Sclerotinia sclerotiorum. Disruption of the S. sclerotiorum Smk3 gene severely reduced virulence on intact host plant leaves but not on leaves stripped of cuticle wax. This was attributed to alterations in hyphal apical dominance leading to the inability to aggregate and form infection cushions. The mutation also caused loss of the ability to produce sclerotia, increased aerial hyphae formation, and altered hyphal hydrophobicity and cell wall integrity. Mutants had slower radial expansion rates on solid media but more tolerance to elevated temperatures. Loss of the SMK3 cell wall integrity MAPK appears to have impaired the ability of S. sclerotiorum to sense its surrounding environment, leading to misregulation of a variety of functions. Many of the phenotypes were similar to those observed in S. sclerotiorum adenylate cyclase and SMK1 MAPK mutants, suggesting that these signaling pathways co-regulate aspects of fungal growth, physiology, and pathogenicity.
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Affiliation(s)
- Zafer Dallal Bashi
- a Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N OX2, Canada.,b Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Sanjaya Gyawali
- a Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N OX2, Canada
| | - Diana Bekkaoui
- a Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N OX2, Canada
| | - Cathy Coutu
- a Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N OX2, Canada
| | - Leora Lee
- a Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N OX2, Canada
| | - Jenny Poon
- a Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N OX2, Canada
| | - S Roger Rimmer
- a Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N OX2, Canada
| | - George G Khachatourians
- b Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Dwayne D Hegedus
- a Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N OX2, Canada.,b Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
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Hegedus DD, Gerbrandt K, Coutu C. The eukaryotic protein kinase superfamily of the necrotrophic fungal plant pathogen, Sclerotinia sclerotiorum. MOLECULAR PLANT PATHOLOGY 2016; 17:634-647. [PMID: 26395470 PMCID: PMC6638376 DOI: 10.1111/mpp.12321] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Protein kinases have been implicated in the regulation of many processes that guide pathogen development throughout the course of infection. A survey of the Sclerotinia sclerotiorum genome for genes encoding proteins containing the highly conserved eukaryotic protein kinase (ePK) domain, the largest protein kinase superfamily, revealed 92 S. sclerotiorum ePKs. This review examines the composition of the S. sclerotiorum ePKs based on conserved motifs within the ePK domain family, and relates this to orthologues found in other filamentous fungi and yeasts. The ePKs are also discussed in terms of their proposed role(s) in aspects of host pathogenesis, including the coordination of mycelial growth/development and deployment of pathogenicity determinants in response to environmental stimuli, nutrients and stress.
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Affiliation(s)
- Dwayne D Hegedus
- Agriculture and Agri-Food Canada, Saskatoon, SK, Canada, S7N 0X2
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A9
| | - Kelsey Gerbrandt
- Agriculture and Agri-Food Canada, Saskatoon, SK, Canada, S7N 0X2
| | - Cathy Coutu
- Agriculture and Agri-Food Canada, Saskatoon, SK, Canada, S7N 0X2
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Steudler S, Böhmer U, Weber J, Bley T. Biomass measurement by flow cytometry during solid-state fermentation of basidiomycetes. Cytometry A 2014; 87:176-88. [DOI: 10.1002/cyto.a.22592] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 10/24/2014] [Accepted: 10/28/2014] [Indexed: 11/07/2022]
Affiliation(s)
- Susanne Steudler
- Institut für Lebensmittel- und Bioverfahrenstechnik, Technische Universität Dresden; Dresden Germany
| | - Ulrike Böhmer
- Gesellschaft für Wissens- und Technologietransfer-TU Dresden GmbH, (GWT-TUD GmbH); Dresden Germany
| | - Jost Weber
- Institut für Lebensmittel- und Bioverfahrenstechnik, Technische Universität Dresden; Dresden Germany
| | - Thomas Bley
- Institut für Lebensmittel- und Bioverfahrenstechnik, Technische Universität Dresden; Dresden Germany
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Molecular tools for functional genomics in filamentous fungi: recent advances and new strategies. Biotechnol Adv 2013; 31:1562-74. [PMID: 23988676 DOI: 10.1016/j.biotechadv.2013.08.005] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 07/06/2013] [Accepted: 08/05/2013] [Indexed: 11/22/2022]
Abstract
Advances in genetic transformation techniques have made important contributions to molecular genetics. Various molecular tools and strategies have been developed for functional genomic analysis of filamentous fungi since the first DNA transformation was successfully achieved in Neurospora crassa in 1973. Increasing amounts of genomic data regarding filamentous fungi are continuously reported and large-scale functional studies have become common in a wide range of fungal species. In this review, various molecular tools used in filamentous fungi are compared and discussed, including methods for genetic transformation (e.g., protoplast transformation, electroporation, and microinjection), the construction of random mutant libraries (e.g., restriction enzyme mediated integration, transposon arrayed gene knockout, and Agrobacterium tumefaciens mediated transformation), and the analysis of gene function (e.g., RNA interference and transcription activator-like effector nucleases). We also focused on practical strategies that could enhance the efficiency of genetic manipulation in filamentous fungi, such as choosing a proper screening system and marker genes, assembling target-cassettes or vectors effectively, and transforming into strains that are deficient in the nonhomologous end joining pathway. In summary, we present an up-to-date review on the different molecular tools and latest strategies that have been successfully used in functional genomics in filamentous fungi.
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Zhou BJ, Jia PS, Gao F, Guo HS. Molecular characterization and functional analysis of a necrosis- and ethylene-inducing, protein-encoding gene family from Verticillium dahliae. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2012; 25:964-75. [PMID: 22414440 DOI: 10.1094/mpmi-12-11-0319] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Verticillium dahliae Kleb. is a hemibiotrophic, phytopathogenic fungus that causes wilt disease in a wide range of crops, including cotton. Successful host colonization by hemibiotrophic pathogens requires the induction of plant cell death to provide the saprophytic nutrition for the transition from the biotrophic to the necrotrophic stage. In this study, we identified a necrosis-inducing Phytophthora protein (NPP1) domain-containing protein family containing nine genes in a virulent, defoliating isolate of V. dahliae (V592), named the VdNLP genes. Functional analysis demonstrated that only two of these VdNLP genes, VdNLP1 and VdNLP2, encoded proteins that were capable of inducing necrotic lesions and triggering defense responses in Nicotiana benthamiana, Arabidopsis, and cotton plants. Both VdNLP1 and VdNLP2 induced the wilting of cotton seedling cotyledons. However, gene-deletion mutants targeted by VdNLP1, VdNLP2, or both did not affect the pathogenicity of V. dahliae V592 in cotton infection. Similar expression and induction patterns were found for seven of the nine VdNLP transcripts. Through a comparison of the conserved amino acid residues of VdNLP with different necrosis-inducing activities, combined with mutagenesis-based analyses, we identified several novel conserved amino acid residues, in addition to the known conserved heptapeptide GHRHDWE motif and the cysteine residues of the NPP domain-containing protein, that are indispensable for the necrosis-inducing activity of the VdNLP2 protein.
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Affiliation(s)
- Bang-Jun Zhou
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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Frandsen RJN, Frandsen M, Giese H. Targeted gene replacement in fungal pathogens via Agrobacterium tumefaciens- mediated transformation. Methods Mol Biol 2012; 835:17-45. [PMID: 22183645 DOI: 10.1007/978-1-61779-501-5_2] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Genome sequence data on fungal pathogens provide the opportunity to carry out a reverse genetics approach to uncover gene function. Efficient methods for targeted genome modifications such as knockout and in locus over-expression are in high demand. Here we describe two efficient single-step cloning strategies for construction of vectors for Agrobacterium tumefaciens-mediated transformation (ATMT). Targeted genome modifications require integration by a homologous double crossover event, which is achieved by placing target sequences on either side of a selection marker gene in the vector. Protocols are given for two single-step vector construction techniques. The In-Fusion cloning technique is independent of compatible restriction enzyme sites in the vector and the fragment to be cloned. The method can be directly applied to any vector of choice and it is possible to carry out four fragment cloning without the need for subcloning. The cloning efficiency is not always as high as desired, but it still presents an efficient alternative to restriction enzyme and ligase-based cloning systems. The USER technology offers a higher four fragment cloning efficiency than In-Fusion, but depends on specific structures in the binary vector. The available fungal binary vectors adapted for the USER system are described and protocols are provided for vector design and construction. A general protocol for verification of the resulting gene replacement events in the recipient fungal cells is also given. The cloning systems described above are relevant for all transformation vector constructs, but here we describe their application for ATMT compatible binary vectors. Protocols are provided for ATMT exemplified by Fusarium graminearum. For large-scale reverse genetic projects, the USER technology is recommended combined with ATMT.
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Affiliation(s)
- Rasmus John Normand Frandsen
- Department of Systems Biology, Center for Microbial Biotechnology, Technical University of Denmark, Lyngby, Denmark.
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