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Dutta S, Houdinet G, NandaKafle G, Kafle A, Hawkes CV, Garcia K. Agrobacterium tumefaciens-mediated transformation of Nigrospora sp. isolated from switchgrass leaves and antagonistic toward plant pathogens. J Microbiol Methods 2023; 215:106849. [PMID: 37907117 DOI: 10.1016/j.mimet.2023.106849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/25/2023] [Accepted: 10/25/2023] [Indexed: 11/02/2023]
Abstract
Nigrospora is a diverse genus of fungi colonizing plants through endophytic, pathogenic, or saprobic interactions. Endophytic isolates can improve growth and development of host plants, as well as their resistance to microbial pathogens, but exactly how they do so remains poorly understood. Developing a reliable transformation method is crucial to investigate these mechanisms, in particular to identify pivotal genes for specific functions that correlate with specific traits. In this study, we identified eight isolates of Nigrospora sp. internally colonizing the leaves of switchgrass plants cultivated in North Carolina. Using an Agrobacterium tumefaciens-mediated transformation approach with control and GFP-expressing vectors, we report the first successful transformation of two Nigrospora isolates. Finally, we demonstrate that wild-type and transgenic isolates both negatively impact the growth of two plant pathogens in co-culture conditions, Bipolaris maydis and Parastagonospora nodorum, responsible for the Southern Leaf Blight and Septoria Nodorum Blotch diseases, respectively. The GFP-transformed strains developed here can therefore serve as accurate reporters of spatial interactions in future studies of Nigrospora and pathogens in the plant. Finally, the transformation method we describe lays the foundation for further genetic research on the Nigrospora genus to expand our mechanistic understanding of plant-endophyte interactions.
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Affiliation(s)
- Summi Dutta
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA; Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Gabriella Houdinet
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27607, USA
| | - Gitanjali NandaKafle
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Arjun Kafle
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Christine V Hawkes
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27607, USA
| | - Kevin Garcia
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA.
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2
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Abstract
Nematode-trapping fungi (NTF) are the majority of carnivorous microbes to capture nematodes through diverse and sophisticated trapping organs derived from hyphae. They can adopt carnivorous lifestyles in addition to saprophytism to obtain extra-nutrition from nematodes. As a special group of fungi, the NTF are not only excellent model organism for studying lifestyle transition of fungi but also natural resources of exploring biological control of nematodes. However, the carnivorous mechanism of NTF remains poorly understood. Nowadays, the omics studies of NTF have provided numerous genes and pathways that are associated with the phenotypes of carnivorous traits, which need molecular tools to verify. Here, we review the development and progress of gene manipulation tools in NTF, including methodology and strategy of transformation, random gene mutagenesis methods and target gene mutagenesis methods. The principle and practical approach for each method was summarized and discussed, and the basic operational flow for each tool was described. This paper offers a clear reference and instruction for researchers who work on NTF as well as other group of fungi.
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Affiliation(s)
- Shunxian Wang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Science, Nankai University, Tianjin, China
| | - Xingzhong Liu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Science, Nankai University, Tianjin, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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3
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Gao J, Liu H, Zhang Z, Liang Z. Establishment, optimization, and application of genetic technology in Aspergillus spp. Front Microbiol 2023; 14:1141869. [PMID: 37025635 PMCID: PMC10071863 DOI: 10.3389/fmicb.2023.1141869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/27/2023] [Indexed: 04/08/2023] Open
Abstract
Aspergillus is widely distributed in nature and occupies a crucial ecological niche, which has complex and diverse metabolic pathways and can produce a variety of metabolites. With the deepening of genomics exploration, more Aspergillus genomic informations have been elucidated, which not only help us understand the basic mechanism of various life activities, but also further realize the ideal functional transformation. Available genetic engineering tools include homologous recombinant systems, specific nuclease based systems, and RNA techniques, combined with transformation methods, and screening based on selective labeling. Precise editing of target genes can not only prevent and control the production of mycotoxin pollutants, but also realize the construction of economical and efficient fungal cell factories. This paper reviewed the establishment and optimization process of genome technologies, hoping to provide the theoretical basis of experiments, and summarized the recent progress and application in genetic technology, analyzes the challenges and the possibility of future development with regard to Aspergillus.
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Affiliation(s)
- Jing Gao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Huiqing Liu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Zhenzhen Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Zhihong Liang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- The Supervision, Inspection and Testing Center of Genetically Modified Organisms, Ministry of Agriculture, Beijing, China
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- *Correspondence: Zhihong Liang,
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4
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Casado-del Castillo V, MacCabe AP, Orejas M. Agrobacterium tumefaciens-Mediated Transformation of NHEJ Mutant Aspergillus nidulans Conidia: An Efficient Tool for Targeted Gene Recombination Using Selectable Nutritional Markers. J Fungi (Basel) 2021; 7:961. [PMID: 34829246 PMCID: PMC8623315 DOI: 10.3390/jof7110961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 11/17/2022] Open
Abstract
Protoplast transformation for the introduction of recombinant DNA into Aspergillus nidulans is technically demanding and dependant on the availability and batch variability of commercial enzyme preparations. Given the success of Agrobacterium tumefaciens-mediated transformation (ATMT) in diverse pathogenic fungi, we have adapted this method to facilitate transformation of A. nidulans. Using suitably engineered binary vectors, gene-targeted ATMT of A. nidulans non-homologous end-joining (NHEJ) mutant conidia has been carried out for the first time by complementation of a nutritional requirement (uridine/uracil auxotrophy). Site-specific integration in the ΔnkuA host genome occurred at high efficiency. Unlike other transformation techniques, however, cross-feeding of certain nutritional requirements from the bacterium to the fungus was found to occur, thus limiting the choice of auxotrophies available for ATMT. In complementation tests and also for comparative purposes, integration of recombinant cassettes at a specific locus could provide a means to reduce the influence of position effects (chromatin structure) on transgene expression. In this regard, targeted disruption of the wA locus permitted visual identification of transformants carrying site-specific integration events by conidial colour (white), even when auxotrophy selection was compromised due to cross-feeding. The protocol described offers an attractive alternative to the protoplast procedure for obtaining locus-targeted A. nidulans transformants.
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Affiliation(s)
| | - Andrew P. MacCabe
- Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), c/Catedrático Agustín Escardino Benlloch 7, 46980 Paterna, Valencia, Spain; (V.C.-d.C.); (M.O.)
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5
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Hu S, Wang Z, Wang D, Wang J, Hong J. The development of a heterologous gene expression system in thermophilic fungus Thermoascus aurantiacus. 3 Biotech 2021; 11:414. [PMID: 34485007 PMCID: PMC8374019 DOI: 10.1007/s13205-021-02963-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 08/05/2021] [Indexed: 10/20/2022] Open
Abstract
Thermoascus aurantiacus is a thermophilic fungus that belongs to the ascomycetous class and has attracted increasing interest for its ability to produce thermostable cellulolytic enzymes and growth at elevated temperatures. However, studies on this organism have been limited because of the lack of a genetic manipulation system. Here, we developed a polyethylene glycol (PEG)-mediated transformation system for T. aurantiacus based on an orotidine-5'-monophosphate decarboxylase (pyrG)-deficient mutant, with this method achieving a transformation efficiency of 33 ± 3 transformants per microgram of DNA. Intracellular or secretory expression of heterologous proteins, including green fluorescent protein, β-galactosidase and α-amylase, in T. aurantiacus was successful under the inducible endogenous cellobiohydrolase and endoglucanase gene promoter or the constitutive heterologous pyruvate decarboxylase and enolase gene promoter from Trichoderma reesei. To the best of our knowledge, this is the first report on PEG-mediated transformation of T. aurantiacus, which sets the foundation for strain improvement for biotechnological applications and functional genomic studies. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02963-w.
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Affiliation(s)
- Shenglin Hu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 People’s Republic of China
- Hefei National Laboratory for Physical Science At the Microscale, Hefei, Anhui 230026 People’s Republic of China
| | - Zhefan Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 People’s Republic of China
| | - Dongmei Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 People’s Republic of China
| | - Jichao Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 People’s Republic of China
| | - Jiong Hong
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 People’s Republic of China
- Hefei National Laboratory for Physical Science At the Microscale, Hefei, Anhui 230026 People’s Republic of China
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6
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An efficient genetic manipulation protocol for dark septate endophyte Falciphora oryzae. Biotechnol Lett 2021; 43:2045-2052. [PMID: 34390483 DOI: 10.1007/s10529-021-03171-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/05/2021] [Indexed: 10/20/2022]
Abstract
OBJECTIVE To investigate the protoplast preparation and transformation system of endophytic fungus Falciphora oryzae. RESULTS F. oryzae strain obtained higher protoplast yield and effective transformation when treated with enzyme digestion solution containing 0.9 M KCl solution and 10 mg mL-1 glucanase at 30 °C with shaking at 80 rpm for 2-3 h. When the protoplasts were plated on a regenerations-agar medium containing 1 M sucrose, the re-growth rate of protoplasts was the highest. We successfully acquired green fluorescent protein-expressing transformants by transforming the pKD6-GFP vector into protoplasts. Further, the GFP expression in fungal hyphae possessed good stability and intensity during symbiosis in rice roots. CONCLUSIONS This study provided a protoplast transformation system of F. oryzae, creating opportunities for future genetic research in other endophytic fungi.
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7
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Goldman GH. New Opportunities for Modern Fungal Biology. FRONTIERS IN FUNGAL BIOLOGY 2020; 1:596090. [PMID: 37743875 PMCID: PMC10512242 DOI: 10.3389/ffunb.2020.596090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 08/27/2020] [Indexed: 09/26/2023]
Affiliation(s)
- Gustavo Henrique Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
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8
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Lichius A, Ruiz DM, Zeilinger S. Genetic Transformation of Filamentous Fungi: Achievements and Challenges. GRAND CHALLENGES IN FUNGAL BIOTECHNOLOGY 2020. [DOI: 10.1007/978-3-030-29541-7_5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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9
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Inducible promoters and functional genomic approaches for the genetic engineering of filamentous fungi. Appl Microbiol Biotechnol 2018; 102:6357-6372. [PMID: 29860590 PMCID: PMC6061484 DOI: 10.1007/s00253-018-9115-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/17/2018] [Accepted: 05/18/2018] [Indexed: 12/15/2022]
Abstract
In industry, filamentous fungi have a prominent position as producers of economically relevant primary or secondary metabolites. Particularly, the advent of genetic engineering of filamentous fungi has led to a growing number of molecular tools to adopt filamentous fungi for biotechnical applications. Here, we summarize recent developments in fungal biology, where fungal host systems were genetically manipulated for optimal industrial applications. Firstly, available inducible promoter systems depending on carbon sources are mentioned together with various adaptations of the Tet-Off and Tet-On systems for use in different industrial fungal host systems. Subsequently, we summarize representative examples, where diverse expression systems were used for the production of heterologous products, including proteins from mammalian systems. In addition, the progressing usage of genomics and functional genomics data for strain improvement strategies are addressed, for the identification of biosynthesis genes and their related metabolic pathways. Functional genomic data are further used to decipher genomic differences between wild-type and high-production strains, in order to optimize endogenous metabolic pathways that lead to the synthesis of pharmaceutically relevant end products. Lastly, we discuss how molecular data sets can be used to modify products for optimized applications.
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10
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Poyedinok NL, Blume YB. Advances, Problems, and Prospects of Genetic Transformation of Fungi. CYTOL GENET+ 2018. [DOI: 10.3103/s009545271802007x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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Abstract
Transposable elements have colonized the genomes of nearly all organisms, including fungi. Although transposable elements may sometimes provide beneficial functions to their hosts their overall impact is considered deleterious. As a result, the activity of transposable elements needs to be counterbalanced by the host genome defenses. In fungi, the primary genome defense mechanisms include repeat-induced point mutation (RIP) and methylation induced premeiotically, meiotic silencing by unpaired DNA, sex-induced silencing, cosuppression (also known as somatic quelling), and cotranscriptional RNA surveillance. Recent studies of the filamentous fungus Neurospora crassa have shown that the process of repeat recognition for RIP apparently involves interactions between coaligned double-stranded segments of chromosomal DNA. These studies have also shown that RIP can be mediated by the conserved pathway that establishes transcriptional (heterochromatic) silencing of repetitive DNA. In light of these new findings, RIP emerges as a specialized case of the general phenomenon of heterochromatic silencing of repetitive DNA.
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12
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Connolly LR, Erlendson AA, Fargo CM, Jackson KK, Pelker MMG, Mazzola JW, Geisler MS, Freitag M. Application of the Cre/lox System to Construct Auxotrophic Markers for Quantitative Genetic Analyses in Fusarium graminearum. Methods Mol Biol 2018; 1848:235-263. [PMID: 30182239 DOI: 10.1007/978-1-4939-8724-5_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The bacteriophage P1 Cre/lox system has been utilized in diverse fungi for marker recycling and exchange, generation of targeted chromosome translocations, and targeted deletion of interstitial chromosome segments. Here we show the application of this tool in the wheat and maize pathogen, Fusarium graminearum. We explored three different ways to introduce Cre into strains with floxed genes, namely transformation with an episomal or integrative plasmid (pLC28), fusion of protoplasts of strains carrying floxed genes with strains expressing Cre by forcing heterokaryons, and crosses between strains with floxed genes and strains expressing Cre to isolate progeny in which the target genes had been deleted during the cross. We used this system for the construction of strains bearing auxotrophic markers that were generated by gene replacement with positively selectable markers followed by Cre-mediated marker excision. In addition, updated protocols for transformation and crosses for F. graminearum are provided. In combination, strains and tools developed here add to the arsenal of methods that can be used to carry out molecular genetics with F. graminearum.
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Affiliation(s)
- Lanelle R Connolly
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Allyson A Erlendson
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Corinne M Fargo
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Kendra K Jackson
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Morgan M G Pelker
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Jacob W Mazzola
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Mark S Geisler
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA.
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13
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Li D, Tang Y, Lin J, Cai W. Methods for genetic transformation of filamentous fungi. Microb Cell Fact 2017; 16:168. [PMID: 28974205 PMCID: PMC5627406 DOI: 10.1186/s12934-017-0785-7] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 09/26/2017] [Indexed: 12/20/2022] Open
Abstract
Filamentous fungi have been of great interest because of their excellent ability as cell factories to manufacture useful products for human beings. The development of genetic transformation techniques is a precondition that enables scientists to target and modify genes efficiently and may reveal the function of target genes. The method to deliver foreign nucleic acid into cells is the sticking point for fungal genome modification. Up to date, there are some general methods of genetic transformation for fungi, including protoplast-mediated transformation, Agrobacterium-mediated transformation, electroporation, biolistic method and shock-wave-mediated transformation. This article reviews basic protocols and principles of these transformation methods, as well as their advantages and disadvantages.
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Affiliation(s)
- Dandan Li
- Institute of Apply Genomics, Fuzhou University, No.2 Xueyuan Road, Fuzhou, 350108 China
- College of Biological Science and Engineering, Fuzhou University, No.2 Xueyuan Road, Fuzhou, 350108 China
| | - Yu Tang
- Triplex International Biosciences (China) Co. LTD, Xiamen, 361100 China
| | - Jun Lin
- Institute of Apply Genomics, Fuzhou University, No.2 Xueyuan Road, Fuzhou, 350108 China
- School of Basic Medical Sciences, Fujian Medical University, No.1 Xuefubei Road, Fuzhou, 350122 China
- College of Biological Science and Engineering, Fuzhou University, No.2 Xueyuan Road, Fuzhou, 350108 China
| | - Weiwen Cai
- Institute of Apply Genomics, Fuzhou University, No.2 Xueyuan Road, Fuzhou, 350108 China
- College of Biological Science and Engineering, Fuzhou University, No.2 Xueyuan Road, Fuzhou, 350108 China
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14
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Molecular tools for gene manipulation in filamentous fungi. Appl Microbiol Biotechnol 2017; 101:8063-8075. [PMID: 28965220 DOI: 10.1007/s00253-017-8486-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 08/11/2017] [Accepted: 08/13/2017] [Indexed: 10/18/2022]
Abstract
Functional genomics of filamentous fungi has gradually uncovered gene information for constructing 'cell factories' and controlling pathogens. Available gene manipulation methods of filamentous fungi include random integration methods, gene targeting technology, gene editing with artificial nucleases and RNA technology. This review describes random gene integration constructed by restriction enzyme-mediated integration (REMI); Agrobacterium-mediated transformation (AMT); transposon-arrayed gene knockout (TAGKO); gene targeting technology, mainly about homologous recombination; and modern gene editing strategies containing transcription activator-like effector nucleases (TALENs) and a clustered regularly interspaced short palindromic repeat/associated protein system (CRISPR/Cas) developed in filamentous fungi and RNA technology including RNA interference (RNAi) and ribozymes. This review describes historical and modern gene manipulation methods in filamentous fungi and presents the molecular tools available to researchers investigating filamentous fungi. The biggest difference of this review from the previous ones is the addition of successful application and details of the promising gene editing tool CRISPR/Cas9 system in filamentous fungi.
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15
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A simple and efficient method for successful gene silencing of HspA1 in Trametes hirsuta AH28-2. Antonie van Leeuwenhoek 2017; 110:1527-1535. [DOI: 10.1007/s10482-017-0904-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 06/27/2017] [Indexed: 01/13/2023]
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16
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McCluskey K, Baker SE. Diverse data supports the transition of filamentous fungal model organisms into the post-genomics era. Mycology 2017; 8:67-83. [PMID: 30123633 PMCID: PMC6059044 DOI: 10.1080/21501203.2017.1281849] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 01/10/2017] [Indexed: 01/14/2023] Open
Abstract
Filamentous fungi have been important as model organisms since the beginning of modern biological inquiry and have benefitted from open data since the earliest genetic maps were shared. From early origins in simple Mendelian genetics of mating types, parasexual genetics of colony colour, and the foundational demonstration of the segregation of a nutritional requirement, the contribution of research systems utilising filamentous fungi has spanned the biochemical genetics era, through the molecular genetics era, and now are at the very foundation of diverse omics approaches to research and development. Fungal model organisms have come from most major taxonomic groups although Ascomycete filamentous fungi have seen the most major sustained effort. In addition to the published material about filamentous fungi, shared molecular tools have found application in every area of fungal biology. Similarly, shared data has contributed to the success of model systems. The scale of data supporting research with filamentous fungi has grown by 10 to 12 orders of magnitude. From genetic to molecular maps, expression databases, and finally genome resources, the open and collaborative nature of the research communities has assured that the rising tide of data has lifted all of the research systems together.
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Affiliation(s)
- Kevin McCluskey
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Scott E. Baker
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
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17
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Brunson JK, Griffith J, Bowles D, Case ME, Arnold J. lac-1 and lag-1 with ras-1 affect aging and the biological clock in Neurospora crassa. Ecol Evol 2016; 6:8341-8351. [PMID: 28031787 PMCID: PMC5167027 DOI: 10.1002/ece3.2554] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 09/17/2016] [Accepted: 09/22/2016] [Indexed: 12/22/2022] Open
Abstract
Using an automated cell counting technique developed previously (Case et al., Ecology and Evolution 2014; 4: 3494), we explore the lifespan effects of lac‐1, a ceramide synthase gene paralogous to lag‐1 in Neurospora crassa in conjunction with the band bd (ras‐1) gene. We find that the replicative lifespan of a lac‐1KObd double mutants is short, about one race tube cycle, and this double mutant lacks a strong ~21‐hr clock cycle as shown by race tube and fluorometer analysis of fluorescent strains including lac‐1KO. This short replicative lifespan phenotype is contrasted with a very long estimated chronological lifespan for lac‐1KObd double mutants from 247 to 462 days based on our regression analyses on log viability, and for the single mutant lac‐1KO, 161 days. Both of these estimated lifespans are much higher than that of previously studied WT and bd single mutant strains. In a lac‐1 rescue and induction experiment, the expression of lac‐1+ as driven by a quinic acid‐dependent promoter actually decreases the median chronological lifespan of cells down to only 7 days, much lower than the 34‐day median lifespan found in control bd conidia also grown on quinic acid media, which we interpret as an effect of balancing selection acting on ceramide levels based on previous findings from the literature. Prior work has shown phytoceramides can act as a signal for apoptosis in stressed N. crassa cells. To test this hypothesis of balancing selection on phytoceramide levels, we examine the viability of WT, lag‐1KObd, and lac‐1KObd strains following the dual stresses of heat and glycolysis inhibition, along with phytoceramide treatments of different dosages. We find that the phytoceramide dosage–response curve is altered in the lag‐1KObd mutant, but not in the lac‐1KObd mutant. We conclude that phytoceramide production is responsible for the previously reported longevity effects in the lag‐1KObd mutant, but a different ceramide may be responsible for the longevity effect observed in the lac‐1KObd mutant.
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Affiliation(s)
- John K Brunson
- Center for Marine Biotechnology and Biomedicine J. Craig Venter Institute-West Coast Campus University of California San Diego Scripps Institution of Oceanography La Jolla CA USA
| | - James Griffith
- College of Agricultural and Environmental Sciences University of Georgia Athens GA USA; Genetics Department University of Georgia Athens GA USA
| | | | - Mary E Case
- Genetics Department University of Georgia Athens GA USA
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18
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Arras SDM, Fraser JA. Chemical Inhibitors of Non-Homologous End Joining Increase Targeted Construct Integration in Cryptococcus neoformans. PLoS One 2016; 11:e0163049. [PMID: 27643854 PMCID: PMC5028063 DOI: 10.1371/journal.pone.0163049] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 09/01/2016] [Indexed: 11/19/2022] Open
Abstract
The development of a biolistic transformation protocol for Cryptococcus neoformans over 25 years ago ushered in a new era of molecular characterization of virulence in this previously intractable fungal pathogen. However, due to the low rate of homologous recombination in this species, the process of creating targeted gene deletions using biolistic transformation remains inefficient. To overcome the corresponding difficulty achieving molecular genetic modifications, members of the Cryptococcus community have investigated the use of specific genetic backgrounds or construct design strategies aimed at reducing ectopic construct integration via non-homologous end joining (NHEJ). One such approach involves deletion of components of the NHEJ-associated Ku heterodimer. While this strategy increases homologous recombination to nearly 100%, it also restricts strain generation to a ku80Δ genetic background and requires subsequent complex mating procedures to reestablish wild-type DNA repair. In this study, we have investigated the ability of known inhibitors of mammalian NHEJ to transiently phenocopy the C. neoformans Ku deletion strains. Testing of eight candidate inhibitors revealed a range of efficacies in C. neoformans, with the most promising compound (W7) routinely increasing the rate of gene deletion to over 50%. We have successfully employed multiple inhibitors to reproducibly enhance the deletion rate at multiple loci, demonstrating a new, easily applied methodology to expedite acquisition of precise genetic alterations in C. neoformans. Based on this success, we anticipate that the use of these inhibitors will not only become widespread in the Cryptococcus community, but may also find use in other fungal species as well.
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Affiliation(s)
- Samantha D. M. Arras
- Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072 Australia
| | - James A. Fraser
- Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072 Australia
- * E-mail:
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Su X, Schmitz G, Zhang M, Mackie RI, Cann IKO. Heterologous gene expression in filamentous fungi. ADVANCES IN APPLIED MICROBIOLOGY 2016; 81:1-61. [PMID: 22958526 DOI: 10.1016/b978-0-12-394382-8.00001-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Filamentous fungi are critical to production of many commercial enzymes and organic compounds. Fungal-based systems have several advantages over bacterial-based systems for protein production because high-level secretion of enzymes is a common trait of their decomposer lifestyle. Furthermore, in the large-scale production of recombinant proteins of eukaryotic origin, the filamentous fungi become the vehicle of choice due to critical processes shared in gene expression with other eukaryotic organisms. The complexity and relative dearth of understanding of the physiology of filamentous fungi, compared to bacteria, have hindered rapid development of these organisms as highly efficient factories for the production of heterologous proteins. In this review, we highlight several of the known benefits and challenges in using filamentous fungi (particularly Aspergillus spp., Trichoderma reesei, and Neurospora crassa) for the production of proteins, especially heterologous, nonfungal enzymes. We review various techniques commonly employed in recombinant protein production in the filamentous fungi, including transformation methods, selection of gene regulatory elements such as promoters, protein secretion factors such as the signal peptide, and optimization of coding sequence. We provide insights into current models of host genomic defenses such as repeat-induced point mutation and quelling. Furthermore, we examine the regulatory effects of transcript sequences, including introns and untranslated regions, pre-mRNA (messenger RNA) processing, transcript transport, and mRNA stability. We anticipate that this review will become a resource for researchers who aim at advancing the use of these fascinating organisms as protein production factories, for both academic and industrial purposes, and also for scientists with general interest in the biology of the filamentous fungi.
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Affiliation(s)
- Xiaoyun Su
- Energy Biosciences Institute, University of Illinois, Urbana, IL, USA; Institute for Genomic Biology, University of Illinois, Urbana, IL, USA; Equal contribution
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20
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The Renaissance of Neurospora crassa: How a Classical Model System is Used for Applied Research. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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McCluskey K. Boosting Research and Industry by Providing Extensive Resources for Fungal Research. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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22
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Protoplasting, regeneration and transformation of medicinal mushroom Ganoderma multipileum using succinate dehydrogenase mutation gene as a selection marker. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-015-1087-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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23
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24
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Transformation of Lithium Acetate-treated Neurospora crassa. Fungal Biol 2015. [DOI: 10.1007/978-3-319-10142-2_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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25
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Gómez-Lim MA, Ortíz DM, Fernández F, Loske AM. Transformation of Fungi Using Shock Waves. Fungal Biol 2015. [DOI: 10.1007/978-3-319-10142-2_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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26
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Liang L, Li J, Cheng L, Ling J, Luo Z, Bai M, Xie B. A high efficiency gene disruption strategy using a positive–negative split selection marker and electroporation for Fusarium oxysporum. Microbiol Res 2014; 169:835-43. [DOI: 10.1016/j.micres.2014.03.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 02/25/2014] [Accepted: 03/18/2014] [Indexed: 10/25/2022]
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27
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Scazzocchio C. Fungal biology in the post-genomic era. Fungal Biol Biotechnol 2014; 1:7. [PMID: 28955449 PMCID: PMC5611559 DOI: 10.1186/s40694-014-0007-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 09/15/2014] [Indexed: 12/12/2022] Open
Abstract
In this review I give a personal perspective of how fungal biology has changed since I started my Ph. D. in 1963. At that time we were working in the shadow of the birth of molecular biology as an autonomous and reductionistic discipline, embodied in Crick’s central dogma. This first period was methodologically characterised by the fact that we knew what genes were, but we could not access them directly. This radically changed in the 70s-80s when gene cloning, reverse genetics and DNA sequencing become possible. The “next generation” sequencing techniques have produced a further qualitative revolutionary change. The ready access to genomes and transcriptomes of any microbial organism allows old questions to be asked in a radically different way and new questions to be approached. I provide examples chosen somewhat arbitrarily to illustrate some of these changes, from applied aspects to fundamental problems such as the origin of fungal specific genes, the evolutionary history of genes clusters and the realisation of the pervasiveness of horizontal transmission. Finally, I address how the ready availability of genomes and transcriptomes could change the status of model organisms.
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Affiliation(s)
- Claudio Scazzocchio
- Department of Microbiology, Imperial College, London, SW7 2AZ UK.,Institut de Génétique et Microbiologie, CNRS UMR 8621, Université Paris-Sud, Orsay, 91405 France
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Case ME, Griffith J, Dong W, Tigner IL, Gaines K, Jiang JC, Jazwinski SM, Arnold J. The aging biological clock in Neurospora crassa. Ecol Evol 2014; 4:3494-507. [PMID: 25535564 PMCID: PMC4228622 DOI: 10.1002/ece3.1202] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2013] [Accepted: 07/25/2014] [Indexed: 12/22/2022] Open
Abstract
The biological clock affects aging through ras-1 (bd) and lag-1, and these two longevity genes together affect a clock phenotype and the clock oscillator in Neurospora crassa. Using an automated cell-counting technique for measuring conidial longevity, we show that the clock-associated genes lag-1 and ras-1 (bd) are true chronological longevity genes. For example, wild type (WT) has an estimated median life span of 24 days, while the double mutant lag-1, ras-1 (bd) has an estimated median life span of 120 days for macroconidia. We establish the biochemical function of lag-1 by complementing LAG1 and LAC1 in Saccharomyces cerevisiae with lag-1 in N. crassa. Longevity genes can affect the clock as well in that, the double mutant lag-1, ras-1 (bd) can stop the circadian rhythm in asexual reproduction (i.e., banding in race tubes) and lengthen the period of the frequency oscillator to 41 h. In contrast to the ras-1 (bd), lag-1 effects on chronological longevity, we find that this double mutant undergoes replicative senescence (i.e., the loss of replication function with time), unlike WT or the single mutants, lag-1 and ras-1 (bd). These results support the hypothesis that sphingolipid metabolism links aging and the biological clock through a common stress response
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Affiliation(s)
- Mary E Case
- Department of Genetics, University of Georgia Athens, Georgia, 30602
| | - James Griffith
- Department of Genetics, University of Georgia Athens, Georgia, 30602 ; College of Agricultural and Environmental Sciences, University of Georgia Athens, Georgia, 30602
| | - Wubei Dong
- Department of Genetics, University of Georgia Athens, Georgia, 30602
| | - Ira L Tigner
- Department of Genetics, University of Georgia Athens, Georgia, 30602
| | - Kimberly Gaines
- Department of Genetics, University of Georgia Athens, Georgia, 30602
| | - James C Jiang
- Tulane Center for Aging and Department of Medicine, Tulane University Health Sciences Center New Orleans, Louisiana, 70112
| | - S Michal Jazwinski
- Tulane Center for Aging and Department of Medicine, Tulane University Health Sciences Center New Orleans, Louisiana, 70112
| | - Jonathan Arnold
- Department of Genetics, University of Georgia Athens, Georgia, 30602
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30
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Physical methods for genetic transformation of fungi and yeast. Phys Life Rev 2014; 11:184-203. [DOI: 10.1016/j.plrev.2014.01.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 01/21/2014] [Indexed: 01/27/2023]
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31
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A new variant of self-excising β-recombinase/six cassette for repetitive gene deletion and homokaryon purification in Neurospora crassa. J Microbiol Methods 2014; 100:17-23. [DOI: 10.1016/j.mimet.2014.02.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 02/12/2014] [Accepted: 02/12/2014] [Indexed: 11/16/2022]
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32
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Arellano-Carbajal F. Fungi learn how to surf big waves: Comment on "Physical methods for genetic transformation of fungi and yeast" by Ana Leonor Rivera, Denis Magaña-Ortíz, Miguel Gómez-Lim, Francisco Fernández, Achim M. Loske. Phys Life Rev 2014; 11:210-1. [PMID: 24698658 DOI: 10.1016/j.plrev.2014.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 03/11/2014] [Indexed: 10/25/2022]
Affiliation(s)
- Fausto Arellano-Carbajal
- Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Av. de las Ciencias S/N, Juriquilla, Querétaro, Qro., México C.P. 76230, Mexico
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Cartwright GM, Tanaka A, Eaton CJ, Scott B. Formation of arthroconidia during regeneration and selection of transformed Epichloë festucae protoplasts. Fungal Biol 2014; 118:462-71. [PMID: 24863475 DOI: 10.1016/j.funbio.2014.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Revised: 03/05/2014] [Accepted: 03/08/2014] [Indexed: 12/01/2022]
Abstract
Transformation is an essential tool for modern fungal research and has played a fundamental role in gaining insight into gene function. Polyethylene glycol (PEG)-mediated transformation of protoplasts is the most commonly used method for genetic transformation of filamentous fungi. Selectable marker genes, that confer resistance to antibiotics, are generally incorporated with the DNA of interest, allowing transformed cells to grow through the antibiotic overlay. Colonies arising from transformed fungal cells are sub-cultured and further analysed. However, the morphological state of the fungal cells during the transformation procedure has been largely overlooked. We investigated the morphological appearance of transformed fungal cells prior to their emergence through the antibiotic overlay. Hyphae appeared to segment and bulge, reminiscent of arthroconidia, an asexual spore typically produced by segmentation of pre-existing hyphae. Selective expression of eGFP under the control of a spore specific promoter, PcatA, in these cells confirmed their spore-like nature. Reducing the oxygen availability to surface-grown cultures partially recapitulated this morphological form. A GFP fusion to the cell wall integrity MAP kinase MpkA localised to the arthroconidia nuclei suggesting the cell wall integrity signalling pathway modulates cell wall stress responses in arthroconidia. This dramatic morphological change was also observed in transformed Magnaporthe oryzae cells suggesting it may be a more general phenomenon in filamentous fungi. Given the changes in cellular structure and spore-like appearance, these observations may have technical implications for deleting genes involved in these processes in Epichloë festucae and, more broadly, a range of fungal species.
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Affiliation(s)
- Gemma Maree Cartwright
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Aiko Tanaka
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Carla Jane Eaton
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Barry Scott
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand.
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Shao Y, Lei M, Mao Z, Zhou Y, Chen F. Insights into Monascus biology at the genetic level. Appl Microbiol Biotechnol 2014; 98:3911-22. [PMID: 24633442 DOI: 10.1007/s00253-014-5608-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 02/10/2014] [Accepted: 02/10/2014] [Indexed: 12/24/2022]
Abstract
The genus of Monascus was nominated by van Tieghem in 1884, but its fermented product-red mold rice (RMR), namely red yeast rice, has been used as folk medicines, food colorants, and fermentation starters for more than thousands of years in oriental countries. Nowadays, RMR is widely developed as food supplements around the world due to its functional compounds such as monacolin K (MK, also called lovastatin) and γ-aminobutyric acid. But the usage of RMR also incurs controversy resulting from contamination of citrinin (a kind of mycotoxin) produced by some Monascus strains. In the past decade, it has made great progress to Monascus spp. at the genetic level with the application of molecular biology techniques to restrain the citrinin production and increase the yields of MK and pigment in RMR, as well as aid Monascus classification and phylogenesis. Up to now, hundreds of papers about Monascus molecular biology (MMB) have been published in the international primary journals. However, to our knowledge, there is no MMB review issued until now. In this review, current understanding of Monascus spp. from the view of molecular biology will be covered and insights into research areas that need to be further investigated will also be discussed.
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Affiliation(s)
- Yanchun Shao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
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35
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Tudzynski P, Stahl U, Esser K. Transformation to senescence with plasmid like DNA in the ascomycete Podospora anserina. Curr Genet 2013; 2:181-4. [PMID: 24189907 DOI: 10.1007/bf00435683] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/1980] [Indexed: 11/29/2022]
Abstract
In the ascomycete Podospora anserina senescence through strain aging is under nucleo-cytoplasmic control and inducible in juvenile mycelia by an 'infective principle' transferred after cytoplasmic contact via anastomoses. A specific DNA called plasmid-like (pl) DNA, present exclusively in aging mycelia, was found to be identical with this 'infective principle', since it was possible to transform juvenile protoplasts to senescence by using purified p1DNA. Therefore a specific function may be attributed to this ccc DNA. Its direct involvement in a genetically programed senescence is confirmed and its development as a vector for transfer of genetic information in eukaryotes can be undertaken.
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Affiliation(s)
- P Tudzynski
- Lehrstuhl für Allgemeine Botanik, Ruhr-Universität t Bochum, Postfach 102148, D-4630, Bochum, Germany
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36
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Chai R, Zhang G, Sun Q, Zhang M, Zhao S, Qiu L. Liposome-mediated mycelial transformation of filamentous fungi. Fungal Biol 2013; 117:577-83. [PMID: 24012298 DOI: 10.1016/j.funbio.2013.06.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2013] [Revised: 06/17/2013] [Accepted: 06/28/2013] [Indexed: 11/30/2022]
Abstract
Liposome-mediated transformation is common for cells with no cell wall, but has very limited usage in cells with walls, such as bacteria, fungi, and plants. In this study, we developed a procedure to introduce DNA into mycelium of filamentous fungi, Rhizopus nigricans LH 21 and Pleurotus ostreatus TD 300, by liposome-mediation but with no protoplast preparation. The DNA was transformed into R. nigricans via plasmid pEGFP-C1 and into P. ostreatus via 7.2 kb linear DNA. The mycelia were ground in 0.6 M mannitol without any grinding aids or glass powder for 15 min to make mycelial fragments suspension; the suspension was mixed with a mixture of the DNA and Lipofectamine 2000, and placed on ice for 30 min; 100 μL of the transformation solution was plated on potato dextrose agar (PDA) plate and cultivated at 28 °C for transformant screening. The plasmid and the linear DNA were confirmed to be integrated into the host chromosome, proving the success of transformation. The transformation efficiencies were similar to those of electroporation-mediated protoplast transformation (EMPT) of R. nigricans or PEG/CaCl2-mediated protoplast transformation (PMT) of P. ostreatus, respectively. The results showed that our procedure was effective, fast, and simple transformation method for filamentous fungi.
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Affiliation(s)
- Ran Chai
- College of Life Sciences, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China; Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture, 95 Wenhua Road, Zhengzhou 450002, China
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37
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Kumar M, Sharma R, Dua M, Tuteja N, Johri AK. “Electrotransformation” Transformation System for Root Endophytic Fungus Piriformospora indica. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/978-3-642-33802-1_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
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38
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Efficient sequential repetitive gene deletions in Neurospora crassa employing a self-excising β-recombinase/six cassette. J Microbiol Methods 2012; 92:236-43. [PMID: 23246910 DOI: 10.1016/j.mimet.2012.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 12/07/2012] [Accepted: 12/07/2012] [Indexed: 11/20/2022]
Abstract
Despite its long-standing history as a model organism, Neurospora crassa has limited tools for repetitive gene deletions utilizing recyclable self-excising marker systems. Here we describe, for the first time, the functionality of a bacterial recombination system employing β-recombinase acting on six recognition sequences (β-rec/six) in N. crassa, which allowed repetitive site-specific gene deletion and marker recycling. We report generating the mus-51 deletion strain using this system, recycling the marker cassette, and subsequently deleting the global transcriptional regulator gene cre-1.
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Won S, Michkov AV, Krystofova S, Garud AV, Borkovich KA. Genetic and physical interactions between Gα subunits and components of the Gβγ dimer of heterotrimeric G proteins in Neurospora crassa. EUKARYOTIC CELL 2012; 11:1239-48. [PMID: 22903975 PMCID: PMC3485923 DOI: 10.1128/ec.00151-12] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Accepted: 08/07/2012] [Indexed: 11/20/2022]
Abstract
Heterotrimeric G proteins are critical regulators of growth and asexual and sexual development in the filamentous fungus Neurospora crassa. Three Gα subunits (GNA-1, GNA-2, and GNA-3), one Gβ subunit (GNB-1), and one Gγ subunit (GNG-1) have been functionally characterized, but genetic epistasis relationships between Gβ and Gα subunit genes have not been determined. Physical association between GNB-1 and FLAG-tagged GNG-1 has been previously demonstrated by coimmunoprecipitation, but knowledge of the Gα binding partners for the Gβγ dimer is currently lacking. In this study, the three N. crassa Gα subunits are analyzed for genetic epistasis with gnb-1 and for physical interaction with the Gβγ dimer. We created double mutants lacking one Gα gene and gnb-1 and introduced constitutively active, GTPase-deficient alleles for each Gα gene into the Δgnb-1 background. Genetic analysis revealed that gna-3 is epistatic to gnb-1 with regard to negative control of submerged conidiation. gnb-1 is epistatic to gna-2 and gna-3 for aerial hyphal height, while gnb-1 appears to act upstream of gna-1 and gna-2 during aerial conidiation. None of the activated Gα alleles restored female fertility to Δgnb-1 mutants, and the gna-3(Q208L) allele inhibited formation of female reproductive structures, consistent with a need for Gα proteins to cycle through the inactive GDP-bound form for these processes. Coimmunoprecipitation experiments using extracts from the gng-1-FLAG strain demonstrated that the three Gα proteins interact with the Gβγ dimer. The finding that the Gβγ dimer interacts with all three Gα proteins is supported by epistasis between gnb-1 and gna-1, gna-2, and gna-3 for at least one function.
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Affiliation(s)
- Susan Won
- Department of Plant Pathology and Microbiology, Institute for Integrative Genome Biology, University of California-Riverside, CA, USA
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40
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Liu Z, Friesen TL. Polyethylene glycol (PEG)-mediated transformation in filamentous fungal pathogens. Methods Mol Biol 2012; 835:365-75. [PMID: 22183664 DOI: 10.1007/978-1-61779-501-5_21] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Genetic transformation is an essential tool for the modern study of gene function and the genetic improvement of an organism. The genetic transformation of many fungal species is well established and can be carried out by utilizing different transformation methods including electroporation, Agrobacterium, biolistics, or polyethylene glycol (PEG)-mediated transformation. Due to its technical simplicity and common equipment requirements, PEG-mediated transformation is still the most commonly used method for genetic transformation in filamentous fungi. Here, we describe a PEG-based protocol developed for genetic transformation of Stagonospora nodorum, a fungal pathogen of wheat. This protocol is directly applicable to other fungi especially those in the Dothideomycete class of fungi.
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Affiliation(s)
- Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA
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Best practices for fungal germplasm repositories and perspectives on their implementation. Appl Microbiol Biotechnol 2011; 93:975-82. [PMID: 22179706 DOI: 10.1007/s00253-011-3786-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 11/21/2011] [Accepted: 11/22/2011] [Indexed: 10/14/2022]
Abstract
In over 50 years, the Fungal Genetics Stock Center has grown to become a world-recognized biological resource center. Along with this growth comes the development and implementation of myriad practices for the management and curation of a diverse collection of filamentous fungi, yeast, and molecular genetic tools for working with the fungi. These practices include techniques for the testing, manipulation, and preservation of individual fungal isolates as well as for processing of thousands of isolates in parallel. In addition to providing accurate record keeping, an electronic managements system allows the observation of trends in strain distribution and in sample characteristics. Because many ex situ fungal germplasm repositories around the world share similar objectives, best-practice guidelines have been developed by a number of organizations such as the Organization for Economic Cooperation and Development or the International Society for Biological and Environmental Repositories. These best-practice guidelines provide a framework for the successful operation of collections and promote the development and interactions of biological resource centers around the world.
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Park G, Colot HV, Collopy PD, Krystofova S, Crew C, Ringelberg C, Litvinkova L, Altamirano L, Li L, Curilla S, Wang W, Gorrochotegui-Escalante N, Dunlap JC, Borkovich KA. High-throughput production of gene replacement mutants in Neurospora crassa. Methods Mol Biol 2011; 722:179-89. [PMID: 21590421 DOI: 10.1007/978-1-61779-040-9_13] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The model filamentous fungus Neurospora crassa has been the focus of functional genomics studies for the past several years. A high-throughput gene knockout procedure has been developed and used to generate mutants for more than two-thirds of the ∼10,000 annotated N. crassa genes. Yeast recombinational cloning was incorporated as an efficient procedure to produce all knockout cassettes. N. crassa strains with the Δmus-51 or Δmus-52 deletion mutations were used as transformation recipients in order to reduce the incidence of ectopic integration and increase homologous recombination of knockout cassettes into the genome. A 96-well format was used for many steps of the procedure, including fungal transformation, isolation of homokaryons, and verification of mutants. In addition, development of software programs for primer design and restriction enzyme selection facilitated the high-throughput aspects of the overall protocol.
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Affiliation(s)
- Gyungsoon Park
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, USA
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Vollmer SJ, Yanofsky C. Efficient cloning of genes of Neurospora crassa. Proc Natl Acad Sci U S A 2010; 83:4869-73. [PMID: 16593723 PMCID: PMC323844 DOI: 10.1073/pnas.83.13.4869] [Citation(s) in RCA: 379] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have constructed a genomic library of Neurospora crassa DNA in a cosmid vector that contains the dominant selectable marker for benomyl resistance. The library is arranged to permit the rapid cloning of Neurospora genes by either sib-selection or colony-hybridization protocols. Detailed procedures for the uses of the library are described. By use of these procedures, a modest number of unrelated genes have been isolated. The cloning of trp-3, the structural gene for the multifunctional enzyme tryptophan synthetase (tryptophan synthase, EC 4.2.1.20), is reported in detail; its identity was verified by restriction fragment length polymorphism mapping. The strategies described in this paper should be of use in the cloning of any gene of Neurospora, as well as genes of other lower eukaryotes.
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Affiliation(s)
- S J Vollmer
- Department of Biological Sciences, Stanford University, Stanford, CA 94305
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44
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Parsons KA, Chumley FG, Valent B. Genetic transformation of the fungal pathogen responsible for rice blast disease. Proc Natl Acad Sci U S A 2010; 84:4161-5. [PMID: 16593854 PMCID: PMC305044 DOI: 10.1073/pnas.84.12.4161] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The analysis of complex genetic determinants that control the ability of a fungus to colonize its host has been impaired by the lack of sophisticated genetic tools for characterizing important pathogens. We have developed a system for the genetic transformation of Magnaporthe grisea, the causal agent of rice blast disease, to overcome this limitation. A M. grisea arginine auxotroph was shown to contain a mutation (arg3-12) that abolishes ornithine carbamoyltransferase activity. M. grisea strains that contain arg3-12 were used as recipients in transformation experiments with plasmid pMA2, which carries the ArgB(+) gene from Aspergillus nidulans. Stable prototrophic transformants arose at a frequency of about 35 per microgram of plasmid DNA. Integration of single or multiple plasmid copies occurred at a single site in the genome of each transformant; rearrangements were often created during integration. When M. grisea genomic segments were incorporated into pMA2, the presence of any one of five different M. grisea segments did not greatly affect the efficiency of transformation. Integration via homologous recombination occurred when the donor plasmid was linearized by cleaving at a unique restriction site within the M. grisea segment.
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Affiliation(s)
- K A Parsons
- E. I. du Pont de Nemours & Company, Central Research and Development Department, Experimental Station, E402/2208, Wilmington, DE 19898
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Gold MH, Cheng TM, Alic M. Formation, Fusion, and Regeneration of Protoplasts from Wild-Type and Auxotrophic Strains of the White Rot Basidiomycete Phanerochaete chrysosporium. Appl Environ Microbiol 2010; 46:260-3. [PMID: 16346345 PMCID: PMC239297 DOI: 10.1128/aem.46.1.260-263.1983] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A preparation of two commercial enzymes was used to liberate protoplasts from 16-h-old mycelium of Phanerochaete chrysosporium. Regeneration frequencies of up to 5% were attained when the protoplasts were plated in a medium containing 10% sorbose and 3% agar. Fusion of protoplasts from different auxotrophic strains in polyethylene glycol-Ca produced heterokaryons. Separation of the heterokaryons into their constituent homokaryotic strains could be effected through protoplast release and formation of colonies on regeneration agar.
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Affiliation(s)
- M H Gold
- Department of Chemistry and Biochemical Sciences, Oregon Graduate Center, Beaverton, Oregon 97006
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Abstract
Genetic transformation is a key technology in modern fungal research. Most commonly, protoplasts are transformed using the polyethylene glycol-mediated transformation protocols. Because protoplasts are generated by treatment of mycelia with a crude enzyme preparation, the results tend to be inconsistent. Furthermore, some species cannot be transformed by this method. Electroporation (EP) and Agrobacterium tumefaciens-mediated transformation (AMT) are two alternative methods. These methods allow the transformation of spores or mycelia, they are simple to perform and provide consistent results. In this chapter, we describe EP and AMT protocols for the fungus Colletotrichum gloeosporioides f. sp. aeschynomene (C. gloeosporioides). These protocols can be used as baseline for the calibration of similar transformation protocols in other species.
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Affiliation(s)
- Anna Minz
- Department of Plant Sciences, Tel-Aviv University, Tel Aviv, Israel
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Yamada T, Makimura K, Satoh K, Umeda Y, Ishihara Y, Abe S. Agrobacterium tumefaciens-mediated transformation of the dermatophyte, Trichophyton mentagrophytes: an efficient tool for gene transfer. Med Mycol 2010; 47:485-94. [PMID: 18951290 DOI: 10.1080/13693780802322240] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Agrobacterium tumefaciens-mediated transformation (ATMT) was used to facilitate gene transfer into the clinically important dermatophyte, Trichophyton mentagrophytes (teleomorph: Arthroderma vanbreuseghemii). A binary vector containing a hygromycin B resistance cassette was introduced into A. tumefaciens, and the resultant strain was co-cultivated with fungal small conidia. Transformation yielded a large number of hygromycin B-resistant transformants. Hybridization analysis showed that most of the transformants harboured a single copy of T-DNA randomly integrated into the genome. Transformation frequency was increased to more than 200 per 10(7) conidia by optimizing the co-cultivation time and temperature. ATMT was then used for targeted gene disruption mediated by homologous recombination. Using a PCR-based strategy, we isolated the areA/nit-2-like nitrogen regulatory gene (tnr:Trichophytonnitrogen regulator) from T. mentagrophytes. A binary vector containing two regions of the tnr locus flanking the hygromycin B resistance cassette was constructed and introduced into T. mentagrophytesvia ATMT. Transformants with disruption of the areA/nit-2-like gene (tnr) were obtained in three of four independent disruption experiments, most of which showed homologous recombination via double crossover without additional ectopic integration of the disruption construct.
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Affiliation(s)
- Tsuyoshi Yamada
- Teikyo University Institute of Medical Mycology, Teikyo University, Hachioji, Tokyo, Japan
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Affiliation(s)
- Scott E Baker
- Chemical and Biological Process Development Group, Energy and Environment Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, PO Box 999, MSIN P8-60, Richland, WA 99352, USA.
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Abstract
The protoplast method for the transformation of filamentous fungi is described in detail, as is the Restriction Enzyme-Mediated Integration (REMI) procedure for introducing tagged mutations into the fungal genome. A split marker method for generating PCR fragments for targeted integration and deletion of genes of interest is also detailed.
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Affiliation(s)
- B Gillian Turgeon
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY, USA
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