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Kobercová E, Srba M, Fischer L. Sulfadiazine and phosphinothricin selection systems optimised for the transformation of tobacco BY-2 cells. Plant Cell Rep 2023; 42:535-548. [PMID: 36609768 DOI: 10.1007/s00299-022-02975-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
We extended the applicability of the BY-2 cell line as a model by introducing two new selection systems. Our protocol provides guidelines for optimising Basta selection in other recalcitrant models. Tobacco BY-2 cell line is the most commonly used cytological model in plant research. It is uniform, can be simply treated by chemicals, synchronised and easily transformed. However, only a few selection systems are available that complicate advanced studies using multiple stacked transgenes and extensive gene editing. In our work, we adopted for BY-2 cell line two other selection systems: sulfadiazine and phosphinothricin (PPT, an active ingredient of Basta herbicide). We show that sulfadiazine can be used in a wide range of concentrations. It is suitable for co-transformation and subsequent double selection with kanamycin or hygromycin, which are standardly used for BY-2 transformation. We also have domesticated the sulfadiazine resistance for the user-friendly GoldenBraid cloning system. Compared to sulfadiazine, establishing selection on phosphinothricin was considerably more challenging. It did not work in any concentration of PPT with standardly cultured cells. Since the selection is based on blocking glutamine synthetase and consequent ammonium toxicity and deficiency of assimilated nitrogen, we tried to manipulate nitrogen availability. We found that the PPT selection reliably works only with nitrogen-starved cells with reduced nitrate reserves that are selected on a medium without ammonium nitrate. Both these adjustments prevent the release of large amounts of ammonium, which can toxify the entire culture in the case of standardly cultured cells. Since high nitrogen reserves can be a common feature of in vitro cultures grown on MS media, nitrogen starvation could be a key step in establishing phosphinothricin resistance in other plant models.
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Affiliation(s)
- Eliška Kobercová
- Department of Experimental Plant Biology, Charles University Faculty of Science, Viničná 5, Prague 2, Czech Republic
| | - Miroslav Srba
- Department of Experimental Plant Biology, Charles University Faculty of Science, Viničná 5, Prague 2, Czech Republic
| | - Lukáš Fischer
- Department of Experimental Plant Biology, Charles University Faculty of Science, Viničná 5, Prague 2, Czech Republic.
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Qin L, Li A, Tan K, Guo S, Chen Y, Wang F, Wong KH. Universal plasmids to facilitate gene deletion and gene tagging in filamentous fungi. Fungal Genet Biol 2019; 125:28-35. [PMID: 30641126 DOI: 10.1016/j.fgb.2019.01.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 01/03/2019] [Accepted: 01/09/2019] [Indexed: 10/27/2022]
Abstract
Gene manipulation is an important routine technique and its efficiency is often a rate-limiting step in research. To facilitate gene manipulation in filamentous fungi, we adapted the S. cerevisiae Gene Deletion and Gene Tagging plasmid collections to include additional selectable markers that make the useful resources applicable to other fungi. Three markers for auxotrophic selection in Aspergillus and related species (the riboB, pyroA and pyrG genes of Aspergillus fumigatus) and a dominant selectable marker for glufosinate resistance (the Bar gene from Streptomyces hygroscopicus) were introduced to the collections. A total of fifty-six plasmids were constructed for all combinations between the four new markers and thirteen epitope tags (viz., 3xHA, 13xMYC, 3xFLAG, FLAG, MYC, T7, HIS, Strep, S, HSV, VSV-G, V5 and GFP). The selectable marker and epitope tag cassettes are positioned between two universal sequences in the plasmids, and therefore, can be amplified by PCR using the same pair of primers. With these plasmids, we have also established a simple and efficient procedure for making gene deletion and gene tagging transformation DNA constructs. The procedure, along with the universal flanking sequences, allows quick and easy interchange of selectable marker and epitope cassettes in transformation DNA constructs for different selection and/or tagging. To demonstrate utility and efficiency of the system, we simultaneously performed C-terminal tagging of HapB - a subunit of the highly conserved Aspergillus nidulans CCAAT binding complex that plays important transcriptional regulatory roles - using ten different epitopes in order to identify those neutral to HapB function in vivo. It is expected that the expanded plasmid collections coupled with the simple construction strategy would facilitate gene manipulation in many fungal species.
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Affiliation(s)
- Longguang Qin
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau
| | - Ang Li
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau
| | - Kaeling Tan
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau; Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau
| | - Shuhui Guo
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau
| | - Yingying Chen
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau
| | - Fang Wang
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau
| | - Koon Ho Wong
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau; Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau.
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Oliva Chávez AS, Herron MJ, Nelson CM, Felsheim RF, Oliver JD, Burkhardt NY, Kurtti TJ, Munderloh UG. Mutational analysis of gene function in the Anaplasmataceae: Challenges and perspectives. Ticks Tick Borne Dis 2018; 10:482-494. [PMID: 30466964 DOI: 10.1016/j.ttbdis.2018.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 08/13/2018] [Accepted: 11/09/2018] [Indexed: 01/10/2023]
Abstract
Mutational analysis is an efficient approach to identifying microbial gene function. Until recently, lack of an effective tool for Anaplasmataceae yielding reproducible results has created an obstacle to functional genomics, because surrogate systems, e.g., ectopic gene expression and analysis in E. coli, may not provide accurate answers. We chose to focus on a method for high-throughput generation of mutants via random mutagenesis as opposed to targeted gene inactivation. In our search for a suitable mutagenesis tool, we considered attributes of the Himar1 transposase system, i.e., random insertion into AT dinucleotide sites, which are abundant in Anaplasmataceae, and lack of requirement for specific host factors. We chose the Anaplasma marginale tr promoter, and the clinically irrelevant antibiotic spectinomycin for selection, and in addition successfully implemented non-antibiotic selection using an herbicide resistance gene. These constructs function reasonably well in Anaplasma phagocytophilum harvested from human promyelocyte HL-60 cells or Ixodes scapularis tick cells. We describe protocols developed in our laboratory, and discuss what likely makes them successful. What makes Anaplasmataceae electroporation competent is unknown and manipulating electroporation conditions has not improved mutational efficiency. A concerted effort is needed to resolve remaining problems that are inherent to the obligate intracellular bacteria. Finally, using this approach, we describe the discovery and characterization of a putative secreted effector necessary for Ap survival in HL-60 cells.
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Affiliation(s)
- Adela S Oliva Chávez
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Michael J Herron
- Department of Entomology, University of Minnesota, St. Paul, MN, USA
| | - Curtis M Nelson
- Department of Entomology, University of Minnesota, St. Paul, MN, USA
| | | | - Jonathan D Oliver
- School of Public Health, Division of Environmental Health Sciences, University of Minnesota, Minneapolis, MN, USA
| | | | - Timothy J Kurtti
- Department of Entomology, University of Minnesota, St. Paul, MN, USA
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Dohn JW, Grubbs AW, Oakley CE, Oakley BR. New multi-marker strains and complementing genes for Aspergillus nidulans molecular biology. Fungal Genet Biol 2018; 111:1-6. [PMID: 29309843 DOI: 10.1016/j.fgb.2018.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 01/03/2018] [Accepted: 01/04/2018] [Indexed: 11/15/2022]
Abstract
Technical advances in Aspergillus nidulans enable relatively easy deletion of genomic sequences, insertion of sequences into the genome and alteration of genomic sequences. To extend the power of this system we wished to create strains with several selectable markers in a common genetic background to facilitate multiple, sequential transformations. We have developed an approach, using the recycling of the pyrG selectable marker, that has allowed us to create new deletions of the biA, pabaA, choA, and lysB genes. We have deleted these genes in a strain that carries the commonly used pyrG89, riboB2, and pyroA4 mutations as well as a deletion of the sterigmatocystin gene cluster and a deletion of the nkuA gene, which greatly reduces heterologous integration of transforming sequences. The new deletions are fully, easily and cheaply supplementable. We have created a strain that carries seven selectable markers as well as strains that carry subsets of these markers. We have identified the homologous genes from Aspergillus terreus, cloned them and used them as selectable markers to transform our new strains. The newly created strains transform well and the new deletion alleles appear to be complemented fully by the A. terreus genes. In addition, we have used deep sequencing data to determine the sequence alterations of the venerable and frequently used pyrG89, riboB2 and pyroA4 alleles and we have reannotated the choA gene.
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Affiliation(s)
- James W Dohn
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
| | - Alexander W Grubbs
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
| | - C Elizabeth Oakley
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
| | - Berl R Oakley
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA.
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Abstract
Efficient and site-specific alteration of the genome is key to decoding and altering the genomic information of an organism. Over the last couple of years, the RNA-guided Cas9 nucleases derived from the prokaryotic type 2 CRISPR (clustered regularly interspaced short palindromic repeats) systems have drastically improved our ability to engineer the genomes of a variety of organisms including Toxoplasma gondii. In this chapter, we describe detailed protocols for using the CRISPR/Cas9 system adapted from Streptococcus pyogenes to perform efficient genetic manipulations in T. gondii such as gene disruption, gene tagging and genetic complementation. The technical details of the strategy, including CRISPR plasmid construction, target construct generation, parasite transfection and positive clone identification are also provided. These methods are easy to customize to any gene of interest (GOI) and will greatly accelerate studies on this important pathogen.
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Affiliation(s)
- Bang Shen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Kevin Brown
- Department of Molecular Microbiology, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO, 63110, USA
| | - Shaojun Long
- Department of Molecular Microbiology, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO, 63110, USA
| | - L David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO, 63110, USA.
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Kilaru S, Steinberg G. Yeast recombination-based cloning as an efficient way of constructing vectors for Zymoseptoria tritici. Fungal Genet Biol 2016; 79:76-83. [PMID: 26092792 PMCID: PMC4502459 DOI: 10.1016/j.fgb.2015.03.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 03/13/2015] [Accepted: 03/21/2015] [Indexed: 11/28/2022]
Abstract
Yeast recombination-based cloning (YRBC) is a reliable and inexpensive way of generating plasmids. We provide 4 vectors for YRBC that a cover different resistance genes. Using this technique promises rapid generation of molecular tools to study Z. tritici.
Many pathogenic fungi are genetically tractable. Analysis of their cellular organization and invasion mechanisms underpinning virulence determinants profits from exploiting such molecular tools as fluorescent fusion proteins or conditional mutant protein alleles. Generation of these tools requires efficient cloning methods, as vector construction is often a rate-limiting step. Here, we introduce an efficient yeast recombination-based cloning (YRBC) method to construct vectors for the fungus Zymoseptoria tritici. This method is of low cost and avoids dependency on the availability of restriction enzyme sites in the DNA sequence, as needed in more conventional restriction/ligation-based cloning procedures. Furthermore, YRBC avoids modification of the DNA of interest, indeed this potential risk limits the use of site-specific recombination systems, such as Gateway cloning. Instead, in YRBC, multiple DNA fragments, with 30 bp overlap sequences, are transformed into Saccharomyces cerevisiae, whereupon homologous recombination generates the vector in a single step. Here, we provide a detailed experimental protocol and four vectors, each encoding a different dominant selectable marker cassette, that enable YRBC of constructs to be used in the wheat pathogen Z. tritici.
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Affiliation(s)
- S Kilaru
- School of Biosciences, University of Exeter, Exeter EX4 4QD, UK.
| | - G Steinberg
- School of Biosciences, University of Exeter, Exeter EX4 4QD, UK
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