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Gene complementation strategies for filamentous fungi biotechnology. Process Biochem 2023. [DOI: 10.1016/j.procbio.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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2
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Roux I, Chooi YH. Cre/ lox-Mediated Chromosomal Integration of Biosynthetic Gene Clusters for Heterologous Expression in Aspergillus nidulans. ACS Synth Biol 2022; 11:1186-1195. [PMID: 35168324 DOI: 10.1021/acssynbio.1c00458] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Building strains of filamentous fungi for stable long-term heterologous expression of large biosynthetic pathways is limited by the low transformation efficiency or genetic stability of current methods. Here, we developed a system for targeted chromosomal integration of large biosynthetic gene clusters in Aspergillus nidulans based on site-specific recombinase-mediated cassette exchange. We built A. nidulans strains harboring a chromosomal landing pad for Cre/lox-mediated recombination and demonstrated efficient targeted integration of a 21 kb DNA fragment in a single step. We further evaluated the integration at two loci by analyzing the expression of a fluorescent reporter and the production of a heterologous polyketide metabolite. We compared chromosomal expression at those landing loci to episomal AMA1-based expression, which also shed light on uncharacterized aspects of episomal expression in filamentous fungi. This is the first demonstration of site-specific recombinase-mediated integration in filamentous fungi, setting the foundations for the further development of this tool.
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Affiliation(s)
- Indra Roux
- School of Molecular Sciences, University of Western Australia, Perth, Western Australia 6009, Australia
| | - Yit-Heng Chooi
- School of Molecular Sciences, University of Western Australia, Perth, Western Australia 6009, Australia
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3
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de la Torre A, Jurca M, Hoffmann K, Schmitz L, Heimel K, Kämper J, Pérez-Martín J. Robust Cre recombinase activity in the biotrophic smut fungus Ustilago maydis enables efficient conditional null mutants in planta. Genetics 2022; 220:iyab152. [PMID: 34849846 PMCID: PMC8733456 DOI: 10.1093/genetics/iyab152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/10/2021] [Indexed: 11/12/2022] Open
Abstract
Site-specific recombinases have been used in higher eukaryotes, especially in animals, for a broad range of applications, including chromosomal translocations, large deletions, site-specific integration, and tissue-specific as well as conditional knock-outs. The application of site-specific recombination has also been demonstrated in simple eukaryotes like fungi and protozoa. However, its use in fungal research, especially in phytopathogenic fungi, has often been limited to "recycle" the marker genes used in transformation experiments. We show that Cre recombinase can be used for conditional gene deletions in the phytopathogenic fungus Ustilago maydis. Conditional gene knock-outs can be generated via the transcriptional control of the recombinase by U. maydis promoters specifically activated during the biotrophic phase of fungal growth, enabling gene deletions at defined developmental stages inside the plant tissue. Also, we show that a tamoxifen-activated Cre-recombinase allows the tight control necessary for the induced deletion of essential genes by the addition of tamoxifen. These tools will be helpful to address the function of genes under both axenic and in planta conditions for the U. maydis-maize pathosystem and should pave the way for similar approaches in other plant pathosystems.
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Affiliation(s)
| | - Matteo Jurca
- Department of Genetics, Karlsruhe Institute of Technology, Institute for Applied Biosciences, 76131 Karlsruhe, Germany
| | - Kai Hoffmann
- Department of Genetics, Karlsruhe Institute of Technology, Institute for Applied Biosciences, 76131 Karlsruhe, Germany
| | - Lara Schmitz
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen 37073, Germany
| | - Kai Heimel
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen 37073, Germany
| | - Jörg Kämper
- Department of Genetics, Karlsruhe Institute of Technology, Institute for Applied Biosciences, 76131 Karlsruhe, Germany
| | - José Pérez-Martín
- Instituto de Biología Funcional y Genómica (CSIC), Salamanca 37007, Spain
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4
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Arnesen JA, Hoof JB, Kildegaard HF, Borodina I. Genome Editing of Eukarya. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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5
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Miao Y, Xia Y, Kong Y, Zhu H, Mei H, Li P, Feng H, Xun W, Xu Z, Zhang N, Liu D, Shen Q, Zhang R. Overcoming diverse homologous recombinations and single chimeric guide RNA competitive inhibition enhances Cas9-based cyclical multiple genes coediting in filamentous fungi. Environ Microbiol 2021; 23:2937-2954. [PMID: 33754479 DOI: 10.1111/1462-2920.15477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 03/18/2021] [Indexed: 12/26/2022]
Abstract
Deciphering the complex cellular behaviours and advancing the biotechnology applications of filamentous fungi increase the requirement for genetically manipulating a large number of target genes. The current strategies cannot cyclically coedit multiple genes simultaneously. In this study, we firstly revealed the existence of diverse homologous recombination (HR) types in marker-free editing of filamentous fungi, and then, demonstrated that sgRNA efficiency-mediated competitive inhibition resulted in the low integration of multiple genetic sites during coediting, which are the two major obstacles to limit the efficiency of cyclically coediting of multiple genes. To overcome these obstacles, we developed a biased cutting strategy by Cas9 to greatly enhance the desired HR type and applied a new selection marker labelling strategy for multiple donor DNAs, in which only the donor DNA with the lowest sgRNA efficiency was labelled. Combined with these strategies, we successfully developed a convenient method for cyclically coediting multiple genes in different filamentous fungi. In addition, diverse HRs resulted in a useful and convenient one-step approach for gene functional study combining both gene disruption and complementation. This research provided both a useful one-step approach for gene functional study and an efficient strategy for cyclically coediting multiple genes in filamentous fungi.
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Affiliation(s)
- Youzhi Miao
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanwei Xia
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanqiong Kong
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Han Zhu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huiling Mei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Pan Li
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Haichao Feng
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weibing Xun
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhihui Xu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Nan Zhang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dongyang Liu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruifu Zhang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Liu Q, Zhang Y, Li F, Li J, Sun W, Tian C. Upgrading of efficient and scalable CRISPR-Cas-mediated technology for genetic engineering in thermophilic fungus Myceliophthora thermophila. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:293. [PMID: 31890021 PMCID: PMC6927189 DOI: 10.1186/s13068-019-1637-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 12/12/2019] [Indexed: 06/01/2023]
Abstract
BACKGROUND Thermophilic filamentous fungus Myceliophthora thermophila has great capacity for biomass degradation and is an attractive system for direct production of enzymes and chemicals from plant biomass. Its industrial importance inspired us to develop genome editing tools to speed up the genetic engineering of this fungus. First-generation CRISPR-Cas9 technology was developed in 2017 and, since then, some progress has been made in thermophilic fungi genetic engineering, but a number of limitations remain. They include the need for complex independent expression cassettes for targeting multiplex genomic loci and the limited number of available selectable marker genes. RESULTS In this study, we developed an Acidaminococcus sp. Cas12a-based CRISPR system for efficient multiplex genome editing, using a single-array approach in M. thermophila. These CRISPR-Cas12a cassettes worked well for simultaneous multiple gene deletions/insertions. We also developed a new simple approach for marker recycling that relied on the novel cleavage activity of the CRISPR-Cas12a system to make DNA breaks in selected markers. We demonstrated its performance by targeting nine genes involved in the cellulase production pathway in M. thermophila via three transformation rounds, using two selectable markers neo and bar. We obtained the nonuple mutant M9 in which protein productivity and lignocellulase activity were 9.0- and 18.5-fold higher than in the wild type. We conducted a parallel investigation using our transient CRISPR-Cas9 system and found the two technologies were complementary. Together we called them CRISPR-Cas-assisted marker recycling technology (Camr technology). CONCLUSIONS Our study described new approaches (Camr technology) that allow easy and efficient marker recycling and iterative stacking of traits in the same thermophilic fungus strain either, using the newly established CRISPR-Cas12a system or the established CRISPR-Cas9 system. This Camr technology will be a versatile and efficient tool for engineering, theoretically, an unlimited number of genes in fungi. We expect this advance to accelerate biotechnology-oriented engineering processes in fungi.
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Affiliation(s)
- Qian Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Yongli Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Fangya Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Jingen Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Wenliang Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Chaoguang Tian
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
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7
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Genome editing of different strains of Aureobasidium melanogenum using an efficient Cre/loxp site-specific recombination system. Fungal Biol 2019; 123:723-731. [DOI: 10.1016/j.funbio.2019.06.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/31/2019] [Accepted: 06/03/2019] [Indexed: 01/19/2023]
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8
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Kjærbølling I, Mortensen UH, Vesth T, Andersen MR. Strategies to establish the link between biosynthetic gene clusters and secondary metabolites. Fungal Genet Biol 2019; 130:107-121. [DOI: 10.1016/j.fgb.2019.06.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 05/26/2019] [Accepted: 06/02/2019] [Indexed: 01/01/2023]
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9
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Development of a Cre-loxP-based genetic system in Aspergillus niger ATCC1015 and its application to construction of efficient organic acid-producing cell factories. Appl Microbiol Biotechnol 2019; 103:8105-8114. [DOI: 10.1007/s00253-019-10054-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 07/08/2019] [Accepted: 07/26/2019] [Indexed: 02/06/2023]
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10
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Cell surface display of proteins on filamentous fungi. Appl Microbiol Biotechnol 2019; 103:6949-6972. [PMID: 31359105 DOI: 10.1007/s00253-019-10026-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 07/11/2019] [Accepted: 07/15/2019] [Indexed: 12/14/2022]
Abstract
Protein display approaches have been useful to endow the cell surface of yeasts with new catalytic activities so that they can act as enhanced whole-cell biocatalysts. Despite their biotechnological potential, protein display technologies remain poorly developed for filamentous fungi. The lignocellulolytic character of some of them coupled to the cell surface biosynthesis of valuable molecules by a single or a cascade of several displayed enzymes is an appealing prospect. Cell surface protein display consists in the co-translational fusion of a functional protein (passenger) to an anchor one, usually a cell-wall-resident protein. The abundance, spacing, and local environment of the displayed enzymes-determined by the relationship of the anchor protein with the structure and dynamics of the engineered cell wall-are factors that influence the performance of display-based biocatalysts. The development of protein display strategies in filamentous fungi could be based on the field advances in yeasts; however, the unique composition, structure, and biology of filamentous fungi cell walls require the customization of the approach to those microorganisms. In this prospective review, the cellular bases, the design principles, and the available tools to foster the development of cell surface protein display technologies in filamentous fungi are discussed.
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11
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Strategies for gene disruption and expression in filamentous fungi. Appl Microbiol Biotechnol 2019; 103:6041-6059. [DOI: 10.1007/s00253-019-09953-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/24/2019] [Accepted: 05/28/2019] [Indexed: 02/02/2023]
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12
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Twaruschek K, Spörhase P, Michlmayr H, Wiesenberger G, Adam G. New Plasmids for Fusarium Transformation Allowing Positive-Negative Selection and Efficient Cre- loxP Mediated Marker Recycling. Front Microbiol 2018; 9:1954. [PMID: 30258410 PMCID: PMC6143793 DOI: 10.3389/fmicb.2018.01954] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/02/2018] [Indexed: 11/14/2022] Open
Abstract
In filamentous fungi such as Fusarium graminearum, disruption of multiple genes of interest in the same strain (e.g., to test for redundant gene function) is a difficult task due to the limited availability of reliable selection markers. We have created a series of transformation vectors that allow antibiotic-based selection of transformants and subsequent negative selection for marker removal using thymidine kinase fusions combined with the Cre-loxP system. The fusion genes contain commonly used C-terminal drug resistance markers, either nptII (G418), nat1 (nourseothricin), or hph (hygromycin B). These resistance genes are fused to the sequence encoding Herpes simplex virus thymidine kinase (HSVtk). Despite the presence of the 1 kb HSVtk gene (about ∼30% increase in total marker size), there is only a slight reduction in transformation efficiency on a molar basis. The fusion genes expressed under the Trichoderma pyruvate kinase (PKI) promoter also confer antibiotic resistance in Escherichia coli, allowing straightforward construction of disruption plasmids. For removal of the loxP flanked resistance cassettes, protoplasts of transformants are directly treated with purified Cre recombinase protein. Loss of the HSVtk containing cassette is selected by restoration of resistance to 5-fluoro-2-deoxyuridine (FdU). As a proof of principle, we demonstrated the efficiency of the HSVtk-based marker removal in Fusarium by reversing the disruption phenotype of the gene responsible for production of the red pigment aurofusarin. We first disrupted the FgPKS12 gene via integration of the loxP-flanked HSVtk-nptII cassette into the promoter or the first intron, thereby generating transformants with a white mycelium phenotype. Using Cre recombinase and FdU, the selection marker was subsequently removed, and the resulting transformants regained red pigmentation despite the remaining loxP site. We also found that it is possible to remove several unselected loxP-flanked cassettes with a single Cre protein treatment, as long as one of them contains a negative selectable HSVtk cassette. The negative selection system can also be used to introduce allele swaps into strains without leaving marker sequences, by first disrupting the gene of interest and then complementing the deletion in situ with genomic DNA containing a different allele.
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Affiliation(s)
| | | | | | - Gerlinde Wiesenberger
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
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13
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Fang X, Qu Y. Metabolic Engineering of Fungal Strains for Efficient Production of Cellulolytic Enzymes. FUNGAL CELLULOLYTIC ENZYMES 2018:27-41. [PMCID: PMC7120360 DOI: 10.1007/978-981-13-0749-2_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Filamentous fungi are widely used for production of cellulase and other cellulolytic enzymes. Metabolic engineering of filamentous fungal strains has been applied to improve enzyme production, and rapid progress has been made in the recent years. In this chapter, genetic tools and methods to develop superior enzyme producers are summarized, which includes establishment of genetic modification systems, selection and redesign of promoters, and metabolic engineering using either native transcription factors or artificial ones. In addition, enhancement of cellulase production through morphology engineering was also discussed. Emerging tools including CRISPR-Cas9-based genome editing and synthetic biology are highlighted, which are speeding up mechanisms elucidation and strain development, and will further facilitate economic cellulolytic enzyme production.
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Affiliation(s)
- Xu Fang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong China
| | - Yinbo Qu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong China
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14
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Sgolastra F, Kuksin CA, Gonzalez-Perez G, Minter LM, Tew GN. Enhanced TAT-Cre Protein Transduction for Efficient Gene Recombination in T cells. ACS APPLIED BIO MATERIALS 2018; 1:444-451. [PMID: 35016365 DOI: 10.1021/acsabm.8b00153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Genetic manipulation has increased our understanding of gene function and led to the discovery of new therapeutic targets. Cre/LoxP DNA recombination is widely used for genetic studies in mammalian cells. The direct delivery of Cre recombinase fused to protein transduction domains (PTDs), such as TAT, has been described as a valid alternative to the conditional, site-specific Cre expression in transgenic mice. However, efficiently conveying proteins into live cells, especially primary T cells, remains a major challenge. In this study, we show that one of our recently developed PTDs synthetic mimic greatly enhances the cellular uptake of the TAT-Cre fusion protein, enabling significantly smaller amounts of the protein to be used. We used this technique in primary mouse T cells to successfully delete, ex vivo, two essential genes involved in regulating T cell activation, Notch1 and Rbpjκ. Ex vivo gene deletion resulted in substantial protein reduction, comparable to that obtained in vivo when Cre-expressing Notch1-floxed (MxCre±Notch1fl/fl) mice were treated with polyinosinic-polycytidylic acid (polyl/C), but in considerably less time, and without altering normal cell physiology. These results highlight several key advantages that include the ability to use less expensive protein (TAT-Cre), a major reduction in total experimental time and labor, and fewer side effects on the treated cells. This method should offer new opportunities for immunological studies, especially in the context of identifying novel therapeutic targets.
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15
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Targeted cloning of a large gene cluster from Lecanicillium genome by Cre/ loxP based method. J Microbiol Methods 2018; 150:47-54. [DOI: 10.1016/j.mimet.2018.05.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 05/22/2018] [Accepted: 05/22/2018] [Indexed: 11/21/2022]
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16
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Hasan H, Abd Rahim MH, Campbell L, Carter D, Abbas A, Montoya A. Overexpression of acetyl-CoA carboxylase in Aspergillus terreus to increase lovastatin production. N Biotechnol 2018; 44:64-71. [PMID: 29727712 DOI: 10.1016/j.nbt.2018.04.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 04/30/2018] [Accepted: 04/30/2018] [Indexed: 02/08/2023]
Abstract
The present work describes the application of homologous recombination techniques in a wild-type Aspergillus terreus (ATCC 20542) strain to increase the flow of precursors towards the lovastatin biosynthesis pathway. A new strain was generated to overexpress acetyl-CoA carboxylase (ACCase) by replacing the native ACCase promoter with a strong constitutive PadhA promoter from Aspergillus nidulans. Glycerol and a mixture of lactose and glycerol were used independently as the carbon feedstock to determine the degree of response by the A. terreus strains towards the production of acetyl-CoA, and malonyl-CoA. The new strain increased the levels of malonyl-CoA and acetyl-CoA by 240% and 14%, respectively, compared to the wild-type strain. As a result, lovastatin production was increased by 40% and (+)-geodin was decreased by 31% using the new strain. This study shows for the first time that the metabolism of Aspergillus terreus can be manipulated to attain higher levels of precursors and valuable secondary metabolites.
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Affiliation(s)
- Hanan Hasan
- University of Sydney, School of Chemical and Biomolecular Engineering, Australia; Universiti Putra Malaysia, Faculty of Food Science and Technology, Malaysia
| | - Muhammad Hafiz Abd Rahim
- University of Sydney, School of Chemical and Biomolecular Engineering, Australia; Universiti Putra Malaysia, Faculty of Food Science and Technology, Malaysia
| | - Leona Campbell
- University of Sydney, School of Life and Environmental Sciences, Australia
| | - Dee Carter
- University of Sydney, School of Life and Environmental Sciences, Australia
| | - Ali Abbas
- University of Sydney, School of Chemical and Biomolecular Engineering, Australia
| | - Alejandro Montoya
- University of Sydney, School of Chemical and Biomolecular Engineering, Australia.
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17
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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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18
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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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Zhang S, Ban A, Ebara N, Mizutani O, Tanaka M, Shintani T, Gomi K. Self-excising Cre/mutant lox marker recycling system for multiple gene integrations and consecutive gene deletions in Aspergillus oryzae. J Biosci Bioeng 2017; 123:403-411. [DOI: 10.1016/j.jbiosc.2016.11.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 11/01/2016] [Accepted: 11/02/2016] [Indexed: 01/29/2023]
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Fiedler MRM, Gensheimer T, Kubisch C, Meyer V. HisB as novel selection marker for gene targeting approaches in Aspergillus niger. BMC Microbiol 2017; 17:57. [PMID: 28274204 PMCID: PMC5343542 DOI: 10.1186/s12866-017-0960-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 02/17/2017] [Indexed: 01/06/2023] Open
Abstract
Background For Aspergillus niger, a broad set of auxotrophic and dominant resistance markers is available. However, only few offer targeted modification of a gene of interest into or at a genomic locus of choice, which hampers functional genomics studies. We thus aimed to extend the available set by generating a histidine auxotrophic strain with a characterized hisB locus for targeted gene integration and deletion in A. niger. Results A histidine-auxotrophic strain was established via disruption of the A. niger hisB gene by using the counterselectable pyrG marker. After curing, a hisB-, pyrG- strain was obtained, which served as recipient strain for further studies. We show here that both hisB orthologs from A. nidulans and A. niger can be used to reestablish histidine prototrophy in this recipient strain. Whereas the hisB gene from A. nidulans was suitable for efficient gene targeting at different loci in A. niger, the hisB gene from A. niger allowed efficient integration of a Tet-on driven luciferase reporter construct at the endogenous non-functional hisB locus. Subsequent analysis of the luciferase activity revealed that the hisB locus is tight under non-inducing conditions and allows even higher luciferase expression levels compared to the pyrG integration locus. Conclusion Taken together, we provide here an alternative selection marker for A. niger, hisB, which allows efficient homologous integration rates as well as high expression levels which compare favorably to the well-established pyrG selection marker. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-0960-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Markus R M Fiedler
- Institute of Biotechnology, Department of Applied and Molecular Microbiology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355, Berlin, Germany
| | - Tarek Gensheimer
- Institute of Biotechnology, Department of Applied and Molecular Microbiology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355, Berlin, Germany
| | - Christin Kubisch
- Institute of Biotechnology, Department of Applied and Molecular Microbiology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355, Berlin, Germany
| | - Vera Meyer
- Institute of Biotechnology, Department of Applied and Molecular Microbiology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355, Berlin, Germany.
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Huang X, Chen M, Li J, Lu X. Establishing an efficient gene-targeting system in an itaconic-acid producing Aspergillus terreus strain. Biotechnol Lett 2016; 38:1603-10. [DOI: 10.1007/s10529-016-2143-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 05/26/2016] [Indexed: 12/24/2022]
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Jiang B, Zhang R, Feng D, Wang F, Liu K, Jiang Y, Niu K, Yuan Q, Wang M, Wang H, Zhang Y, Fang X. A Tet-on and Cre-loxP Based Genetic Engineering System for Convenient Recycling of Selection Markers in Penicillium oxalicum. Front Microbiol 2016; 7:485. [PMID: 27148179 PMCID: PMC4828452 DOI: 10.3389/fmicb.2016.00485] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 03/23/2016] [Indexed: 01/15/2023] Open
Abstract
The lack of selective markers has been a key problem preventing multistep genetic engineering in filamentous fungi, particularly for industrial species such as the lignocellulose degrading Penicillium oxalicum JUA10-1(formerly named as Penicillium decumbens). To resolve this problem, we constructed a genetic manipulation system taking advantage of two established genetic systems: the Cre-loxP system and Tet-on system in P. oxalicum JUA10-1. This system is efficient and convenient. The expression of Cre recombinase was activated by doxycycline since it was controlled by Tet-on system. Using this system, two genes, ligD and bglI, were sequentially disrupted by loxP flanked ptrA. The successful application of this procedure will provide a useful tool for genetic engineering in filamentous fungi. This system will also play an important role in improving the productivity of interesting products and minimizing by-product when fermented by filamentous fungi.
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Affiliation(s)
- Baojie Jiang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
| | - Ruiqin Zhang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
| | - Dan Feng
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
| | - Fangzhong Wang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
| | - Kuimei Liu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
| | - Yi Jiang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
| | - Kangle Niu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
| | - Quanquan Yuan
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
| | - Mingyu Wang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
| | - Hailong Wang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong UniversityJinan, China; State Key Laboratory of Microbial Technology, School of Life Science, Shandong University-Helmholtz Institute of Biotechnology, Shandong UniversityJinan, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong UniversityJinan, China; State Key Laboratory of Microbial Technology, School of Life Science, Shandong University-Helmholtz Institute of Biotechnology, Shandong UniversityJinan, China
| | - Xu Fang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University Jinan, China
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Light-inducible genetic engineering and control of non-homologous end-joining in industrial eukaryotic microorganisms: LML 3.0 and OFN 1.0. Sci Rep 2016; 6:20761. [PMID: 26857594 PMCID: PMC4746737 DOI: 10.1038/srep20761] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 01/07/2016] [Indexed: 01/20/2023] Open
Abstract
Filamentous fungi play important roles in the production of plant cell-wall degrading enzymes. In recent years, homologous recombinant technologies have contributed significantly to improved enzymes production and system design of genetically manipulated strains. When introducing multiple gene deletions, we need a robust and convenient way to control selectable marker genes, especially when only a limited number of markers are available in filamentous fungi. Integration after transformation is predominantly nonhomologous in most fungi other than yeast. Fungal strains deficient in the non-homologous end-joining (NHEJ) pathway have limitations associated with gene function analyses despite they are excellent recipient strains for gene targets. We describe strategies and methods to address these challenges above and leverage the power of resilient NHEJ deficiency strains. We have established a foolproof light-inducible platform for one-step unmarked genetic modification in industrial eukaryotic microorganisms designated as 'LML 3.0', and an on-off control protocol of NHEJ pathway called 'OFN 1.0', using a synthetic light-switchable transactivation to control Cre recombinase-based excision and inversion. The methods provide a one-step strategy to sequentially modify genes without introducing selectable markers and NHEJ-deficiency. The strategies can be used to manipulate many biological processes in a wide range of eukaryotic cells.
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24
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Chen L, Wei D, Zhang Q, Yu X, Wang Y, Zhu X. Orotidine 5′-phosphate decarboxylase-based reusable in situ genetic editing system: Development and application in taxol-producingPestalotiopsis microspora. Eng Life Sci 2015. [DOI: 10.1002/elsc.201400220] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Longfei Chen
- State Key Program of Microbiology and Department of Microbiology; College of Life Sciences; Nankai University; Tianjin China
| | - Dongsheng Wei
- State Key Program of Microbiology and Department of Microbiology; College of Life Sciences; Nankai University; Tianjin China
| | - Qian Zhang
- State Key Program of Microbiology and Department of Microbiology; College of Life Sciences; Nankai University; Tianjin China
| | - Xi Yu
- State Key Program of Microbiology and Department of Microbiology; College of Life Sciences; Nankai University; Tianjin China
| | - Yu Wang
- State Key Program of Microbiology and Department of Microbiology; College of Life Sciences; Nankai University; Tianjin China
| | - Xudong Zhu
- State Key Program of Microbiology and Department of Microbiology; College of Life Sciences; Nankai University; Tianjin China
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25
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26
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A Recyclable and Bidirectionally Selectable Marker System for Transformation of Trichoderma. Fungal Biol 2015. [DOI: 10.1007/978-3-319-10503-1_14] [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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27
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Cre-loxP-based system for removal and reuse of selection markers in Ashbya gossypii targeted engineering. Fungal Genet Biol 2014; 68:1-8. [DOI: 10.1016/j.fgb.2014.04.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 04/18/2014] [Accepted: 04/21/2014] [Indexed: 01/13/2023]
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28
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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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29
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Genetic surgery in fungi: employing site-specific recombinases for genome manipulation. Appl Microbiol Biotechnol 2014; 98:1971-82. [DOI: 10.1007/s00253-013-5480-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 12/16/2013] [Accepted: 12/17/2013] [Indexed: 12/21/2022]
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30
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Hegemann JH, Heick SB, Pöhlmann J, Langen MM, Fleig U. Targeted gene deletion in Saccharomyces cerevisiae and Schizosaccharomyces pombe. Methods Mol Biol 2014; 1163:45-73. [PMID: 24841299 DOI: 10.1007/978-1-4939-0799-1_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Gene deletion is an important element in the functional characterization of gene and protein function. Efficient tools for gene deletion have been developed in the model yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, all of which rely on the replacement of the endogenous gene of interest with a selectable marker gene by homologous recombination. In order to minimize incidental recombination events between DNA sequences within the marker gene and a chromosomal sequence, gene deletion cassettes consisting entirely of heterologous DNA sequences are preferred. The gene deletion cassettes, which are composed of the marker gene flanked by short DNA segments homologous to the chromosomal sequences lying to the left and right of the gene to be deleted, are generated by PCR and mediate highly efficient one-step gene deletion events. Incorporation of loxP sites flanking the marker gene allows Cre recombinase-mediated rescue, so that the marker can be reused for the next gene deletion. This is particularly useful for the characterization of gene families in S. cerevisiae. The one-step gene deletion method is not limited to the elimination of individual genes, but can also be used for the removal of chromosomal segments exceeding 100 kbp in length. Here we describe a comprehensive set of gene deletion cassettes and outline their use in S. cerevisiae and S. pombe.
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Affiliation(s)
- Johannes H Hegemann
- Lehrstuhl für Funktionelle Genomforschung der Mikroorganismen, Heinrich-Heine-Universität, Gebäude 25.02.U1.23, Universitätsstr.1, Düsseldorf, 40225, Germany,
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31
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Zhang DX, Lu HL, Liao X, St Leger RJ, Nuss DL. Simple and efficient recycling of fungal selectable marker genes with the Cre-loxP recombination system via anastomosis. Fungal Genet Biol 2013; 61:1-8. [PMID: 24007936 DOI: 10.1016/j.fgb.2013.08.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 08/20/2013] [Accepted: 08/21/2013] [Indexed: 10/26/2022]
Abstract
Reverse-genetics analysis has played a significant role in advancing fungal biology, but is limited by the number of available selectable marker genes (SMGs). The Cre-loxP recombination system has been adapted for use in filamentous fungi to overcome this limitation. Expression of the Cre recombinase results in excision of an integrated SMG that is flanked by loxP sites, allowing a subsequent round of transformation with the same SMG. However, current protocols for regulated expression or presentation of Cre require multiple time-consuming steps. During efforts to disrupt four different RNA-dependent RNA polymerase genes in a single strain of the chestnut blight fungus Cryphonectria parasitica, we tested whether Cre could successfully excise loxP-flanked SMGs when provided in trans via anastomosis. Stable Cre-producing donor strains were constructed by transformation of wild-type C. parasitica strain EP155 with the Cre-coding domain under the control of a constitutive promoter. Excision of multiple loxP-flanked SMGs was efficiently achieved by simply pairing the Cre-donor strain and the loxP-flanked SMGs-transformed recipient strain and recovering mycelia from the margin of the recipient colony near the anastomosis zone. This method was shown to be as efficient as and much less time consuming than excision by transformation-mediated expression of Cre. It also allows unlimited recycling of loxP-flanked SMGs and the generation of disruption mutant strains that are free of any foreign gene. The successful application of this method to Metarhizium robertsii suggests potential use for optimizing reverse-genetics analysis in a broad range of filamentous fungi.
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Affiliation(s)
- Dong-Xiu Zhang
- Institute for Bioscience and Biotechnology Research, Department of Cell Biology and Molecular Genetics, University of Maryland, Rockville, MD 20850, United States
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32
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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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33
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Amich J, Krappmann S. Deciphering metabolic traits of the fungal pathogen Aspergillus fumigatus: redundancy vs. essentiality. Front Microbiol 2012; 3:414. [PMID: 23264772 PMCID: PMC3525513 DOI: 10.3389/fmicb.2012.00414] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 11/15/2012] [Indexed: 11/13/2022] Open
Abstract
Incidence rates of infections caused by environmental opportunistic fungi have risen over recent decades. Aspergillus species have emerged as serious threat for the immunecompromised, and detailed knowledge about virulence-determining traits is crucial for drug target identification. As a prime saprobe, A. fumigatus has evolved to efficiently adapt to various stresses and to sustain nutritional supply by osmotrophy, which is characterized by extracellular substrate digestion followed by efficient uptake of breakdown products that are then fed into the fungal primary metabolism. These intrinsic metabolic features are believed to be related with its virulence ability. The plethora of genes that encode underlying effectors has hampered their in-depth analysis with respect to pathogenesis. Recent developments in Aspergillus molecular biology allow conditional gene expression or comprehensive targeting of gene families to cope with redundancy. Furthermore, identification of essential genes that are intrinsically connected to virulence opens accurate perspectives for novel targets in antifungal therapy.
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Affiliation(s)
- Jorge Amich
- Research Center for Infectious Diseases, Julius-Maximilians-Universität Würzburg Würzburg, Germany
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34
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Segato F, Damásio ARL, Gonçalves TA, de Lucas RC, Squina FM, Decker SR, Prade RA. High-yield secretion of multiple client proteins in Aspergillus. Enzyme Microb Technol 2012; 51:100-6. [PMID: 22664194 DOI: 10.1016/j.enzmictec.2012.04.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 03/27/2012] [Accepted: 04/24/2012] [Indexed: 10/28/2022]
Abstract
Production of pure and high-yield client proteins is an important technology that addresses the need for industrial applications of enzymes as well as scientific experiments in protein chemistry and crystallization. Fungi are utilized in industrial protein production because of their ability to secrete large quantities of proteins. In this study, we engineered a high-expression-secretion vector, pEXPYR that directs proteins towards the extracellular medium in two Aspergillii host strains, examine the effect of maltose-induced over-expression and protein secretion as well as time and pH-dependent protein stability in the medium. We describe five client proteins representing a core set of hemicellulose degrading enzymes that accumulated up to 50-100 mg/L of protein. Using a recyclable genetic marker that allows serial insertion of multiple genes, simultaneous hyper-secretion of three client proteins in a single host strain was accomplished.
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Affiliation(s)
- Fernando Segato
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
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35
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Modified Cre-loxP recombination in Aspergillus oryzae by direct introduction of Cre recombinase for marker gene rescue. Appl Environ Microbiol 2012; 78:4126-33. [PMID: 22504800 DOI: 10.1128/aem.00080-12] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Marker rescue is an important molecular technique that enables sequential gene deletions. The Cre-loxP recombination system has been used for marker gene rescue in various organisms, including aspergilli. However, this system requires many time-consuming steps, including construction of a Cre expression plasmid, introduction of the plasmid, and Cre expression in the transformant. To circumvent this laborious process, we investigated a method wherein Cre could be directly introduced into Aspergillus oryzae protoplasts on carrier DNA such as a fragment or plasmid. In this study, we define the carrier DNA (Cre carrier) as a carrier for the Cre enzyme. A mixture of commercial Cre and nucleic acids (e.g., pUG6 plasmid) was introduced into A. oryzae protoplasts using a modified protoplast-polyethylene glycol method, resulting in the deletion of a selectable marker gene flanked by loxP sites. By using this method, we readily constructed a marker gene-rescued strain lacking ligD to optimize homologous recombination. Furthermore, we succeeded in integrative recombination at a loxP site in A. oryzae. Thus, we developed a simple method to use the Cre-loxP recombination system in A. oryzae by direct introduction of Cre into protoplasts using DNA as a carrier for the enzyme.
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36
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Transformation system for Hypocrea jecorina (Trichoderma reesei) that favors homologous integration and employs reusable bidirectionally selectable markers. Appl Environ Microbiol 2010; 77:114-21. [PMID: 21075888 DOI: 10.1128/aem.02100-10] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hypocrea jecorina is an industrially important filamentous fungus due to its effective production of hydrolytic enzymes. It has received increasing interest because of its ability to convert lignocellulosic biomass to monomeric sugars, which can be converted into biofuels or platform chemicals. Genetic engineering of strains is a highly important means of meeting the requirements of tailor-made applications. Therefore, we report the development of a transformation system that allows highly efficient gene targeting by using a tmus53 (human LIG4 homolog) deletion strain. Moreover, it permits the unlimited reuse of the same marker by employing a Cre/loxP-based excision system. Both marker insertion and marker excision can be positively selected for by combining resistance to hygromycin B and loss of sensitivity to fluoroacetamide. Finally, the marker pyr4, also positively selectable for insertion and loss, can be used to remove the cre gene.
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Khrunyk Y, Münch K, Schipper K, Lupas AN, Kahmann R. The use of FLP-mediated recombination for the functional analysis of an effector gene family in the biotrophic smut fungus Ustilago maydis. THE NEW PHYTOLOGIST 2010; 187:957-968. [PMID: 20673282 DOI: 10.1111/j.1469-8137.2010.03413.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
*In the Ustilago maydis genome, several novel secreted effector proteins are encoded by gene families. Because of the limited number of selectable markers, the ability to carry out sequential gene deletions has limited the analysis of effector gene families that may have redundant functions. *Here, we established an inducible FLP-mediated recombination system in U. maydis that allows repeated rounds of gene deletion using a single selectable marker (Hyg(R)). To avoid genome rearrangements via FRT sites remaining in the genome after excision, different mutated FRT sites were introduced. *The FLP-mediated selectable marker-removal technique was successfully applied to delete a family of 11 effector genes (eff1) using five sequential rounds of recombination. We showed that expression of all 11 genes is up-regulated during the biotrophic phase. Strains carrying deletions of 9 or all 11 genes showed a significant reduction in virulence, and this phenotype could be partially complemented by the introduction of different members from the gene family, demonstrating redundancy. *The establishment of the FLP/FRT system in a plant pathogenic fungus paves the way for analyzing multigene families with redundant functions.
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Affiliation(s)
- Yuliya Khrunyk
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany
| | - Karin Münch
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany
| | - Kerstin Schipper
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany
| | - Andrei N Lupas
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstr. 35, D-72076 Tübingen, Germany
| | - Regine Kahmann
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany
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Validation of a self-excising marker in the human pathogen Aspergillus fumigatus by employing the beta-rec/six site-specific recombination system. Appl Environ Microbiol 2010; 76:6313-7. [PMID: 20656854 DOI: 10.1128/aem.00882-10] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recyclable markers based on site-specific recombination allow repetitive gene targeting in filamentous fungi. Here we describe for the first time functionality of the bacterial recombination system employing beta serine recombinase acting on six recognition sequences (beta-rec/six) in a fungal host, the human pathogen Aspergillus fumigatus, and its use in establishing a self-excising resistance marker cassette for serial gene replacement.
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39
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Expression and export: recombinant protein production systems for Aspergillus. Appl Microbiol Biotechnol 2010; 87:1255-70. [DOI: 10.1007/s00253-010-2672-6] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Revised: 05/07/2010] [Accepted: 05/08/2010] [Indexed: 11/26/2022]
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Application of the Saccharomyces cerevisiae FLP/FRT recombination system in filamentous fungi for marker recycling and construction of knockout strains devoid of heterologous genes. Appl Environ Microbiol 2010; 76:4664-74. [PMID: 20472720 DOI: 10.1128/aem.00670-10] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To overcome the limited availability of antibiotic resistance markers in filamentous fungi, we adapted the FLP/FRT recombination system from the yeast Saccharomyces cerevisiae for marker recycling. We tested this system in the penicillin producer Penicillium chrysogenum using different experimental approaches. In a two-step application, we first integrated ectopically a nourseothricin resistance cassette flanked by the FRT sequences in direct repeat orientation (FRT-nat1 cassette) into a P. chrysogenum recipient. In the second step, the gene for the native yeast FLP recombinase, and in parallel, a codon-optimized P. chrysogenum flp (Pcflp) recombinase gene, were transferred into the P. chrysogenum strain carrying the FRT-nat1 cassette. The corresponding transformants were analyzed by PCR, growth tests, and sequencing to verify successful recombination events. Our analysis of several single- and multicopy transformants showed that only when the codon-optimized recombinase was present could a fully functional recombination system be generated in P. chrysogenum. As a proof of application of this system, we constructed a DeltaPcku70 knockout strain devoid of any heterologous genes. To further improve the FLP/FRT system, we produced a flipper cassette carrying the FRT sites as well as the Pcflp gene together with a resistance marker. This cassette allows the controlled expression of the recombinase gene for one-step marker excision. Moreover, the applicability of the optimized FLP/FRT recombination system in other fungi was further demonstrated by marker recycling in the ascomycete Sordaria macrospora. Here, we discuss the application of the optimized FLP/FRT recombination system as a molecular tool for the genetic manipulation of filamentous fungi.
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Tools for fungal proteomics: multifunctional neurospora vectors for gene replacement, protein expression and protein purification. Genetics 2009; 182:11-23. [PMID: 19171944 DOI: 10.1534/genetics.108.098707] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The completion of genome-sequencing projects for a number of fungi set the stage for detailed investigations of proteins. We report the generation of versatile expression vectors for detection and isolation of proteins and protein complexes in the filamentous fungus Neurospora crassa. The vectors, which can be adapted for other fungi, contain C- or N-terminal FLAG, HA, Myc, GFP, or HAT-FLAG epitope tags with a flexible poly-glycine linker and include sequences for targeting to the his-3 locus in Neurospora. To introduce mutations at native loci, we also made a series of knock-in vectors containing epitope tags followed by the selectable marker hph (resulting in hygromycin resistance) flanked by two loxP sites. We adapted the Cre/loxP system for Neurospora, allowing the selectable marker hph to be excised by introduction of Cre recombinase into a strain containing a knock-in cassette. Additionally, a protein purification method was developed on the basis of the HAT-FLAG tandem affinity tag system, which was used to purify HETEROCHROMATIN PROTEIN 1 (HP1) and associated proteins from Neurospora. As expected on the basis of yeast two-hybrid and co-immunoprecipitation (Co-IP) experiments, the Neurospora DNA methyltransferase DIM-2 was found in a complex with HP1. Features of the new vectors allowed for verification of an interaction between HP1 and DIM-2 in vivo by Co-IP assays on proteins expressed either from their native loci or from the his-3 locus.
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Maruyama JI, Kitamoto K. Multiple gene disruptions by marker recycling with highly efficient gene-targeting background (DeltaligD) in Aspergillus oryzae. Biotechnol Lett 2008; 30:1811-7. [PMID: 18574559 DOI: 10.1007/s10529-008-9763-9] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Revised: 05/16/2008] [Accepted: 05/30/2008] [Indexed: 12/20/2022]
Abstract
Previously we reported that double disruption of the proteinase genes (tppA and pepE) improved heterologous protein production by Aspergillus oryzae (Jin et al. Appl Microbiol Biotechnol 76:1059-1068, 2007). Since A. oryzae has 134 protease genes, the number of auxotrophy in a single host is limited for multiple disruptions of many protease genes. In order to rapidly perform multiple gene disruptions in A. oryzae, we generated the marker recycling system in highly efficient gene-targeting background. A. oryzae ligD gene homologous to Neurospora crassa mus-53 gene involved in nonhomologous chromosomal integration was disrupted, followed by disruption of the pyrG gene for uridine/uracil auxotroph. We further performed successive rounds of gene disruption (tppA and pepE) by the pyrG marker with high gene-targeting efficiency allowed by the DeltaligD background. After each disruption process the pyrG marker was excised by the direct repeats consisting of ~300 bp upstream flanking region of the target gene, resulting in no residual ectopic/foreign DNA fragments in the genome. Consequently, we succeeded to breed the double proteinase gene disruptant (DeltatppA DeltapepE) applicable to further sequential gene disruptions in A. oryzae.
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Affiliation(s)
- Jun-Ichi Maruyama
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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