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Toffaletti DL, Tenor JL, Perfect JR. Biolistic Transformation of Cryptococcus neoformans. Methods Mol Biol 2024; 2775:59-79. [PMID: 38758311 DOI: 10.1007/978-1-0716-3722-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Biolistic transformation of Cryptococcus neoformans is used as a molecular tool to genetically alter or delete targeted genes. The DNA is introduced into the yeast on DNA-coated gold beads by a helium shock wave produced using a biolistic particle system. The procedure often involves insertion of a dominant selectable marker into the desired site by homologous recombination. To increase the likelihood of homologous recombination, large fragments of overlapping DNA are used. The two most used dominant selectable markers are nourseothricin and Geneticin. With the need to generate multiple gene deletions in the same strain, there are recyclable marker systems, such as the bacteriophage P1 Cre-loxP system or CRISPR that provide additional useful molecular tools. While newer strategies exist to generate deletions and introduce markers and other gene modifications, biolistic transformation has remained a viable tool to facilitate the construction of genetically modified yeast strains. This chapter provides a working protocol on how to delete and restore a gene in C. neoformans.
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Affiliation(s)
- Dena L Toffaletti
- Duke University School of Medicine, Department of Medicine, Division of Infectious Diseases, Durham, NC, USA
| | - Jennifer L Tenor
- Duke University School of Medicine, Department of Medicine, Division of Infectious Diseases, Durham, NC, USA
| | - John R Perfect
- Duke University School of Medicine, Department of Medicine, Division of Infectious Diseases, Durham, NC, USA.
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2
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Development of versatile and efficient genetic tools for the marine-derived fungus Aspergillus terreus RA2905. Curr Genet 2022; 68:153-164. [DOI: 10.1007/s00294-021-01218-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/11/2021] [Accepted: 10/11/2021] [Indexed: 11/26/2022]
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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 2021; 220:6371959. [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] [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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Xu X, Zhong H, Liu W, Tao Y. Extension of Genetic Marker List Using Unnatural Amino Acid System: An Efficient Genomic Modification Strategy in Escherichia coli. Front Bioeng Biotechnol 2020; 8:145. [PMID: 32411679 PMCID: PMC7198746 DOI: 10.3389/fbioe.2020.00145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/12/2020] [Indexed: 11/24/2022] Open
Abstract
Genetic manipulations including chromosome engineering are essential techniques used to restructure cell metabolism. Lambda/Red (λ/Red)-mediated recombination is the most commonly applied approach for chromosomal modulation in Escherichia coli. However, the efficiency of this method is significantly hampered by the laborious removal of the selectable markers. To overcome the problem, the integration helper plasmid was constructed, pSBC1a-CtR, which contains Red recombinase, Cre recombinase, and exogenous orthogonal aminoacyl-transfer RNA (tRNA) synthetase/tRNA pairs, allows an unnatural amino acid (UAA) to be genetically encoded at the defined site of the antibiotic resistance gene-encoded protein. When UAAs are not in the culture medium, there was no expression in the antibiotic resistance gene-encoded protein. Accordingly, the next procedure of antibiotic gene excising is not needed. To verify this method, poxB gene was knocked out successfully. Furthermore, sequential deletion of three target genes (galR, ptsG, and pgi) was able to generate neurosporene-producing strain marked by high growth rate. Thus, the site-specific incorporation UAA mutagenesis system were used to control and expand the use of conditional selectable marker, and the technique is used to facilitate a rapid continuous genome editing in Escherichia coli.
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Affiliation(s)
- Xinyi Xu
- Engineering Research Center of Molecular and & Neuroimaging, Ministry of Education, School of Life Sciences and Technology, Xidian University, Xi'an, China.,Chinese Academy of Sciences Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | | | - Weifeng Liu
- Chinese Academy of Sciences Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yong Tao
- Chinese Academy of Sciences Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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5
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Zhao Y, Wang Y, Upadhyay S, Xue C, Lin X. Activation of Meiotic Genes Mediates Ploidy Reduction during Cryptococcal Infection. Curr Biol 2020; 30:1387-1396.e5. [PMID: 32109388 DOI: 10.1016/j.cub.2020.01.081] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 12/04/2019] [Accepted: 01/28/2020] [Indexed: 12/23/2022]
Abstract
Cryptococcus neoformans is a global human fungal pathogen that causes fatal meningoencephalitis in mostly immunocompromised individuals. During pulmonary infection, cryptococcal cells form large polyploid cells that exhibit increased resistance to host immune attack and are proposed to contribute to the latency of cryptococcal infection. These polyploid titan cells can generate haploid and aneuploid progeny that may result in systemic infection. What triggers cryptococcal polyploidization and how ploidy reduction is achieved remain open questions. Here, we discovered that Cryptococcus cells polyploidize in response to genotoxic stresses that cause DNA double-strand breaks. Intriguingly, meiosis-specific genes are activated in C. neoformans and contribute to ploidy reduction, both in vitro and during infection in mice. Cryptococcal cells that activated their meiotic genes in mice were resistant to specific genotoxic stress compared to sister cells recovered from the same host tissue but without activation of meiotic genes. Our findings support the idea that meiotic genes, in addition to their conventional roles in classic sexual reproduction, contribute to adaptation of eukaryotic cells that undergo dramatic genome changes in response to genotoxic stress. The discovery has additional implications for evolution of sexual reproduction and the paradox of the presence of meiotic machinery in asexual species. Finally, our findings in this eukaryotic microbe mirror the revolutionary discoveries of the polyploidization and meiosis-like ploidy reduction process in cancer cells, suggesting that the reversible ploidy change itself could provide a general mechanism for rejuvenation to promote individual survival in response to stress.
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Affiliation(s)
- Youbao Zhao
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Yina Wang
- Public Health Research Institute Center, New Jersey Medical School - Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Srijana Upadhyay
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Chaoyang Xue
- Public Health Research Institute Center, New Jersey Medical School - Rutgers, The State University of New Jersey, Newark, NJ 07103, USA.
| | - Xiaorong Lin
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA; Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.
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So YS, Lee DG, Idnurm A, Ianiri G, Bahn YS. The TOR Pathway Plays Pleiotropic Roles in Growth and Stress Responses of the Fungal Pathogen Cryptococcus neoformans. Genetics 2019; 212:1241-1258. [PMID: 31175227 PMCID: PMC6707454 DOI: 10.1534/genetics.119.302191] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/02/2019] [Indexed: 11/18/2022] Open
Abstract
The target of rapamycin (TOR) pathway is an evolutionarily conserved signal transduction system that governs a plethora of eukaryotic biological processes, but its role in Cryptococcus neoformans remains elusive. In this study, we investigated the TOR pathway by functionally characterizing two Tor-like kinases, Tor1 and Tlk1, in C. neoformans We successfully deleted TLK1, but not TOR1TLK1 deletion did not result in any evident in vitro phenotypes, suggesting that Tlk1 is dispensable for the growth of C. neoformans We demonstrated that Tor1, but not Tlk1, is essential and the target of rapamycin by constructing and analyzing conditionally regulated strains and sporulation analysis of heterozygous mutants in the diploid strain background. To further analyze the Tor1 function, we constructed constitutive TOR1 overexpression strains. Tor1 negatively regulated thermotolerance and the DNA damage response, which are two important virulence factors of C. neoformansTOR1 overexpression reduced Mpk1 phosphorylation, which is required for cell wall integrity and thermoresistance, and Rad53 phosphorylation, which governs the DNA damage response pathway. Tor1 is localized to the cytoplasm, but enriched in the vacuole membrane. Phosphoproteomics and transcriptomics revealed that Tor1 regulates a variety of biological processes, including metabolic processes, cytoskeleton organization, ribosome biogenesis, and stress response. TOR inhibition by rapamycin caused actin depolarization in a Tor1-dependent manner. Finally, screening rapamycin-sensitive and -resistant kinase and transcription factor mutants revealed that the TOR pathway may crosstalk with a number of stress signaling pathways. In conclusion, our study demonstrates that a single Tor1 kinase plays pleiotropic roles in C. neoformans.
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Affiliation(s)
- Yee-Seul So
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Dong-Gi Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Alexander Idnurm
- School of BioSciences, The University of Melbourne, Victoria 3010, Australia
| | - Giuseppe Ianiri
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710
| | - Yong-Sun Bahn
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
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7
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amdS as a dominant recyclable marker in Cryptococcus neoformans. Fungal Genet Biol 2019; 131:103241. [PMID: 31220607 DOI: 10.1016/j.fgb.2019.103241] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/13/2019] [Accepted: 06/13/2019] [Indexed: 02/04/2023]
Abstract
While the fungal pathogen Cryptoccocus neoformans is a leading cause of death in immunocompromised individuals, the molecular toolkit currently available to study this important pathogen is extremely limited. To enable an unprecedented level of control over manipulation of the genome, we have developed a dominant recyclable marker by expanding on the classic studies of the amdS gene by Michael J. Hynes and John Pateman. The ascomycete Aspergillus nidulans employs the acetamidase AmdS to hydrolyse acetamide to ammonium and acetate, which serve as a nitrogen and carbon source, respectively. Acetamidase activity has never been reported in the Basidiomycota. Here we have successfully demonstrated that acetamide can be utilized as a good nitrogen source in C. neoformans heterologously expressing amdS and that this activity does not influence virulence, enabling it to be used as a basic dominant selectable marker. The expression of this gene in C. neoformans also causes sensitivity to fluoroacetamide, permitting counterselection. Taking advantage of this toxicity we have modified our basic marker to create a comprehensive series of powerful and reliable tools to successfully delete multiple genes in the one strain, generate markerless strains with modifications such as fluorescent protein fusions at native genomic loci, and establish whether a gene is essential in C. neoformans.
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8
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Selectable marker recycling in the nonconventional yeast Xanthophyllomyces dendrorhous by transient expression of Cre on a genetically unstable vector. Appl Microbiol Biotechnol 2018; 103:963-971. [DOI: 10.1007/s00253-018-9496-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/29/2018] [Accepted: 10/29/2018] [Indexed: 10/27/2022]
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9
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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: 11] [Impact Index Per Article: 1.8] [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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10
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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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Cairns TC, Studholme DJ, Talbot NJ, Haynes K. New and Improved Techniques for the Study of Pathogenic Fungi. Trends Microbiol 2015; 24:35-50. [PMID: 26549580 DOI: 10.1016/j.tim.2015.09.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Revised: 09/29/2015] [Accepted: 09/30/2015] [Indexed: 02/05/2023]
Abstract
Fungal pathogens pose serious threats to human, plant, and ecosystem health. Improved diagnostics and antifungal strategies are therefore urgently required. Here, we review recent developments in online bioinformatic tools and associated interactive data archives, which enable sophisticated comparative genomics and functional analysis of fungal pathogens in silico. Additionally, we highlight cutting-edge experimental techniques, including conditional expression systems, recyclable markers, RNA interference, genome editing, compound screens, infection models, and robotic automation, which are promising to revolutionize the study of both human and plant pathogenic fungi. These novel techniques will allow vital knowledge gaps to be addressed with regard to the evolution of virulence, host-pathogen interactions and antifungal drug therapies in both the clinic and agriculture. This, in turn, will enable delivery of improved diagnosis and durable disease-control strategies.
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Affiliation(s)
- Timothy C Cairns
- Institut für Biotechnologie, Technische Universität Berlin, Gustav-Meyer Allee 22, Berlin, Germany.
| | | | | | - Ken Haynes
- Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
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12
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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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13
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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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14
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Srikanta D, Santiago-Tirado FH, Doering TL. Cryptococcus neoformans: historical curiosity to modern pathogen. Yeast 2014; 31:47-60. [PMID: 24375706 PMCID: PMC3938112 DOI: 10.1002/yea.2997] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 12/06/2013] [Accepted: 12/10/2013] [Indexed: 12/22/2022] Open
Abstract
The importance of the Basidiomycete Cryptococcus neoformans to human health has stimulated its development as an experimental model for both basic physiology and pathogenesis. We briefly review the history of this fascinating and versatile fungus, some notable aspects of its biology that contribute to virulence, and current tools available for its study.
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Affiliation(s)
- Deepa. Srikanta
- Department of Molecular Microbiology, Washington University School of Medicine
| | | | - Tamara L. Doering
- Department of Molecular Microbiology, Washington University School of Medicine
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15
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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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16
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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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Dong J, Wang G, Zhang C, Tan H, Sun X, Wu M, Xiao D. A two-step integration method for seamless gene deletion in baker's yeast. Anal Biochem 2013; 439:30-6. [PMID: 23597844 DOI: 10.1016/j.ab.2013.04.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 04/04/2013] [Accepted: 04/06/2013] [Indexed: 11/19/2022]
Abstract
In this study, we developed a seamless gene deletion method through a two-step integration protocol to construct an industrial baker's yeast with NTH1 deletion. A fusion fragment consisted of the upstream sequence, and the downstream sequence of NTH1 was subcloned into an integrating plasmid containing a URA3 counter-selection marker for excision of unwanted DNA. The plasmid was integrated into the genomic NTH1 locus of recipient baker's yeast, leading to tandem repeats of the upstream flank and the downstream flank. Pop-out of the URA3 marker occurs by integration recombination between either the downstream flank repeats or the upstream flank repeats. Integration recombination between the repeats results in NTH1 deletion without any heterologous DNA and reversion to a wild-type strain. The desired deletion occurred with a frequency of approximately 10(-5). Polymerase chain reaction verification and sequence analysis confirmed the NTH1 disruption and the absence of integrated plasmid sequences in the genome of the selected strain. In addition, the mutant with NTH1 deletion exhibits a higher trehalose accumulation and consequently displays a higher viability of yeast cells after freezing. Thus, this method proposes a protocol to construct mutant yeast without leaving behind any heterologous DNA sequences and will facilitate the genetic engineering of any yeast.
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Affiliation(s)
- Jian Dong
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
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Hegemann JH, Heick SB. Delete and repeat: a comprehensive toolkit for sequential gene knockout in the budding yeast Saccharomyces cerevisiae. Methods Mol Biol 2011; 765:189-206. [PMID: 21815094 DOI: 10.1007/978-1-61779-197-0_12] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Gene inactivation is an essential step in the molecular dissection of gene function. In the yeast Saccharomyces cerevisiae, many tools for gene disruption are available. Gene disruption cassettes comprising completely heterologous marker genes flanked by short DNA segments homologous to the regions to the left and right of the gene to be deleted mediate highly efficient one-step gene disruption events. Routinely, in more than 50% of analyzed clones, the marker cassette is integrated in the targeted location. The inclusion of loxP sites flanking the disruption marker gene allows sequence-specific Cre recombinase-mediated marker rescue so that the marker can be reused to disrupt another gene. Here, we describe a comprehensive toolbox for multiple gene disruptions comprising a set of seven heterologous marker genes including four dominant resistance markers for gene disruption, plus a set of Cre expression plasmids carrying eight different selection markers, four of them dominant.
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Affiliation(s)
- Johannes H Hegemann
- Heinrich-Heine-Universität, Lehrstuhl für Funktionelle Genomforschung der Mikroorganismen, Düsseldorf, Germany.
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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: 116] [Impact Index Per Article: 8.3] [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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Current awareness on yeast. Yeast 2010. [DOI: 10.1002/yea.1719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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