1
|
Kan M, Huang T, Zhao P. Artificial chromosome technology and its potential application in plants. FRONTIERS IN PLANT SCIENCE 2022; 13:970943. [PMID: 36186059 PMCID: PMC9519882 DOI: 10.3389/fpls.2022.970943] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
Plant genetic engineering and transgenic technology are powerful ways to study the function of genes and improve crop yield and quality in the past few years. However, only a few genes could be transformed by most available genetic engineering and transgenic technologies, so changes still need to be made to meet the demands for high throughput studies, such as investigating the whole genetic pathway of crop traits and avoiding undesirable genes simultaneously in the next generation. Plant artificial chromosome (PAC) technology provides a carrier which allows us to assemble multiple and specific genes to produce a variety of products by minichromosome. However, PAC technology also have limitations that may hinder its further development and application. In this review, we will introduce the current state of PACs technology from PACs formation, factors on PACs formation, problems and potential solutions of PACs and exogenous gene(s) integration.
Collapse
Affiliation(s)
- Manman Kan
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Tengbo Huang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
| | - Panpan Zhao
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
| |
Collapse
|
2
|
Abstract
Conventional methods of DNA sequence insertion into plants, using Agrobacterium-mediated transformation or microprojectile bombardment, result in the integration of the DNA at random sites in the genome. These plants may exhibit altered agronomic traits as a consequence of disruption or silencing of genes that serve a critical function. Also, genes of interest inserted at random sites are often not expressed at the desired level. For these reasons, targeted DNA insertion at suitable genomic sites in plants is a desirable alternative. In this paper we review approaches of targeted DNA insertion in plant genomes, discuss current technical challenges, and describe promising applications of targeted DNA insertion for crop genetic improvement.
Collapse
|
3
|
Anand A, Wu E, Li Z, TeRonde S, Arling M, Lenderts B, Mutti JS, Gordon‐Kamm W, Jones TJ, Chilcoat ND. High efficiency Agrobacterium-mediated site-specific gene integration in maize utilizing the FLP-FRT recombination system. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1636-1645. [PMID: 30706638 PMCID: PMC6662307 DOI: 10.1111/pbi.13089] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 01/23/2019] [Accepted: 01/27/2019] [Indexed: 05/20/2023]
Abstract
An efficient Agrobacterium-mediated site-specific integration (SSI) technology using the flipase/flipase recognition target (FLP/FRT) system in elite maize inbred lines is described. The system allows precise integration of a single copy of a donor DNA flanked by heterologous FRT sites into a predefined recombinant target line (RTL) containing the corresponding heterologous FRT sites. A promoter-trap system consisting of a pre-integrated promoter followed by an FRT site enables efficient selection of events. The efficiency of this system is dependent on several factors including Agrobacterium tumefaciens strain, expression of morphogenic genes Babyboom (Bbm) and Wuschel2 (Wus2) and choice of heterologous FRT pairs. Of the Agrobacterium strains tested, strain AGL1 resulted in higher transformation frequency than strain LBA4404 THY- (0.27% vs. 0.05%; per cent of infected embryos producing events). The addition of morphogenic genes increased transformation frequency (2.65% in AGL1; 0.65% in LBA4404 THY-). Following further optimization, including the choice of FRT pairs, a method was developed that achieved 19%-22.5% transformation frequency. Importantly, >50% of T0 transformants contain the desired full-length site-specific insertion. The frequencies reported here establish a new benchmark for generating targeted quality events compatible with commercial product development.
Collapse
Affiliation(s)
- Ajith Anand
- Agricultural Division of Dow DuPontCorteva Agriscience™JohnstonIAUSA
| | - Emily Wu
- Agricultural Division of Dow DuPontCorteva Agriscience™JohnstonIAUSA
| | - Zhi Li
- Agricultural Division of Dow DuPontCorteva Agriscience™JohnstonIAUSA
| | - Sue TeRonde
- Agricultural Division of Dow DuPontCorteva Agriscience™JohnstonIAUSA
| | - Maren Arling
- Agricultural Division of Dow DuPontCorteva Agriscience™JohnstonIAUSA
| | - Brian Lenderts
- Agricultural Division of Dow DuPontCorteva Agriscience™JohnstonIAUSA
| | - Jasdeep S. Mutti
- Agricultural Division of Dow DuPontCorteva Agriscience™JohnstonIAUSA
| | | | - Todd J. Jones
- Agricultural Division of Dow DuPontCorteva Agriscience™JohnstonIAUSA
| | | |
Collapse
|
4
|
Sardesai N, Subramanyam S. Agrobacterium: A Genome-Editing Tool-Delivery System. Curr Top Microbiol Immunol 2018; 418:463-488. [PMID: 30043343 DOI: 10.1007/82_2018_101] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
With the rapidly increasing global population, it will be extremely challenging to provide food to the world without increasing food production by at least 70% over the next 30 years. As we reach the limits of expanding arable land, the responsibility of meeting this production goal will rely on increasing yields. Traditional plant breeding practices will not be able to realistically meet these expectations, thrusting plant biotechnology into the limelight to fulfill these needs. Better varieties will need to be developed faster and with the least amount of regulatory hurdles. With the need to add, delete, and substitute genes into existing genomes, the field of genome editing and gene targeting is now rapidly developing with numerous new technologies coming to the forefront. Agrobacterium-mediated crop transformation has been the most utilized method to generate transgenic varieties that are better yielding, have new traits, and are disease and pathogen resistant. Genome-editing technologies rely on the creation of double-strand breaks (DSBs) in the genomic DNA of target species to facilitate gene disruption, addition, or replacement through either non-homologous end joining or homology-dependent repair mechanisms. DSBs can be introduced through the use of zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), or clustered regularly interspersed short palindromic repeats (CRISPR)/Cas nucleases, among others. Agrobacterium strains have been employed to deliver the reagents for genome editing to the specific target cells. Understanding the biology of transformation from the perspective not only of Agrobacterium, but also of the host, from processing of T-DNA to its integration in the host genome, has resulted in a wealth of information that has been used to engineer Agrobacterium strains having increased virulence. As more technologies are being developed, that will help overcome issues of Agrobacterium host range and random integration of DNA, combined with highly sequence-specific nucleases, a robust crop genome-editing toolkit finally seems attainable.
Collapse
Affiliation(s)
- Nagesh Sardesai
- Corteva Agriscience™, Agriculture Division of DowDuPont, 8305 NW 62nd Avenue, Johnston, IA, USA.
| | - Subhashree Subramanyam
- Department of Agronomy, Purdue University, 915 W State Street, West Lafayette, IN, 47907, USA
| |
Collapse
|
5
|
Advancing Agrobacterium-Based Crop Transformation and Genome Modification Technology for Agricultural Biotechnology. Curr Top Microbiol Immunol 2018; 418:489-507. [PMID: 29959543 DOI: 10.1007/82_2018_97] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The last decade has seen significant strides in Agrobacterium-mediated plant transformation technology. This has not only expanded the number of crop species that can be transformed by Agrobacterium, but has also made it possible to routinely transform several recalcitrant crop species including cereals (e.g., maize, sorghum, and wheat). However, the technology is limited by the random nature of DNA insertions, genotype dependency, low frequency of quality events, and variation in gene expression arising from genomic insertion sites. A majority of these deficiencies have now been addressed by improving the frequency of quality events, developing genotype-independent transformation capability in maize, developing an Agrobacterium-based site-specific integration technology for precise gene targeting, and adopting Agrobacterium-delivered CRISPR-Cas genes for gene editing. These improved transformation technologies are discussed in detail in this chapter.
Collapse
|
6
|
Cardi T, Neal Stewart C. Progress of targeted genome modification approaches in higher plants. PLANT CELL REPORTS 2016; 35:1401-16. [PMID: 27025856 DOI: 10.1007/s00299-016-1975-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 03/21/2016] [Indexed: 05/07/2023]
Abstract
Transgene integration in plants is based on illegitimate recombination between non-homologous sequences. The low control of integration site and number of (trans/cis)gene copies might have negative consequences on the expression of transferred genes and their insertion within endogenous coding sequences. The first experiments conducted to use precise homologous recombination for gene integration commenced soon after the first demonstration that transgenic plants could be produced. Modern transgene targeting categories used in plant biology are: (a) homologous recombination-dependent gene targeting; (b) recombinase-mediated site-specific gene integration; (c) oligonucleotide-directed mutagenesis; (d) nuclease-mediated site-specific genome modifications. New tools enable precise gene replacement or stacking with exogenous sequences and targeted mutagenesis of endogeneous sequences. The possibility to engineer chimeric designer nucleases, which are able to target virtually any genomic site, and use them for inducing double-strand breaks in host DNA create new opportunities for both applied plant breeding and functional genomics. CRISPR is the most recent technology available for precise genome editing. Its rapid adoption in biological research is based on its inherent simplicity and efficacy. Its utilization, however, depends on available sequence information, especially for genome-wide analysis. We will review the approaches used for genome modification, specifically those for affecting gene integration and modification in higher plants. For each approach, the advantages and limitations will be noted. We also will speculate on how their actual commercial development and implementation in plant breeding will be affected by governmental regulations.
Collapse
Affiliation(s)
- Teodoro Cardi
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Centro di Ricerca per l'Orticoltura, Via Cavalleggeri 25, 84098, Pontecagnano, Italy.
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| |
Collapse
|
7
|
Schneider K, Schiermeyer A, Dolls A, Koch N, Herwartz D, Kirchhoff J, Fischer R, Russell SM, Cao Z, Corbin DR, Sastry-Dent L, Ainley WM, Webb SR, Schinkel H, Schillberg S. Targeted gene exchange in plant cells mediated by a zinc finger nuclease double cut. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1151-60. [PMID: 26426390 DOI: 10.1111/pbi.12483] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 08/21/2015] [Accepted: 09/03/2015] [Indexed: 06/05/2023]
Abstract
Genome modification by homology-directed repair (HDR) is an attractive tool for the controlled genetic manipulation of plants. Here, we report the HDR-mediated gene exchange of expression cassettes in tobacco BY-2 cells using a designed zinc finger nuclease (ZFN). The target contained a 7-kb fragment flanked by two ZFN cutting sites. That fragment was replaced with a 4-kb donor cassette, which integrates gene markers for selection (kanamycin resistance) and for scoring targeting (red fluorescent protein, RFP). Candidates resulting from cassette exchange were identified by molecular analysis of calli generated by transformation via direct DNA delivery. The precision of HDR-mediated donor integration was evaluated by Southern blot analysis, sequencing of the integration locus and analysis of RFP fluorescence by flow cytometry. Screening of 1326 kanamycin-resistant calli yielded 18 HDR events, 16 of which had a perfect cassette exchange at the insert junction and 13 of which produced functional RFP. Our results demonstrate that ZFN-based HDR can be used for high frequency, precise, targeted exchange of fragments of sizes that are commercially relevant in plants.
Collapse
Affiliation(s)
- Katja Schneider
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Andreas Schiermeyer
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Anja Dolls
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Natalie Koch
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Denise Herwartz
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Janina Kirchhoff
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Rainer Fischer
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | | | - Zehui Cao
- Dow AgroSciences LLC, Indianapolis, IN, USA
| | | | | | | | | | - Helga Schinkel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Stefan Schillberg
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| |
Collapse
|
8
|
Srivastava V, Thomson J. Gene stacking by recombinases. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:471-82. [PMID: 26332944 DOI: 10.1111/pbi.12459] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 07/24/2015] [Accepted: 07/28/2015] [Indexed: 05/09/2023]
Abstract
Efficient methods of stacking genes into plant genomes are needed to expedite transfer of multigenic traits to crop varieties of diverse ecosystems. Over two decades of research has identified several DNA recombinases that carryout efficient cis and trans recombination between the recombination sites artificially introduced into the plant chromosome. The specificity and efficiency of recombinases make them extremely attractive for genome engineering. In plant biotechnology, recombinases have mostly been used for removing selectable marker genes and have rarely been extended to more complex applications. The reversibility of recombination, a property of the tyrosine family of recombinases, does not lend itself to gene stacking approaches that involve rounds of transformation for integrating genes into the engineered sites. However, recent developments in the field of recombinases have overcome these challenges and paved the way for gene stacking. Some of the key advancements include the application of unidirectional recombination systems, modification of recombination sites and transgene site modifications to allow repeated site-specific integrations into the selected site. Gene stacking is relevant to agriculturally important crops, many of which are difficult to transform; therefore, development of high-efficiency gene stacking systems will be important for its application on agronomically important crops, and their elite varieties. Recombinases, by virtue of their specificity and efficiency in plant cells, emerge as powerful tools for a variety of applications including gene stacking.
Collapse
Affiliation(s)
- Vibha Srivastava
- Department of Crop, Soil & Environmental Science, University of Arkansas, Fayetteville, AR, USA
| | | |
Collapse
|
9
|
Li R, Han Z, Hou L, Kaur G, Yin Q, Ow DW. Method for Biolistic Site-Specific Integration in Plants Catalyzed by Bxb1 Integrase. Methods Mol Biol 2016; 1469:15-30. [PMID: 27557683 DOI: 10.1007/978-1-4939-4931-1_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Crop improvement is a never ending process. With a transgenesis approach, it is not inconceivable to envision a continuous addition of new transgenes to existing cultivars. Previously, we described a recombinase-directed gene stacking method in tobacco (Hou et al., Mol Plant 7:1756-1765, 2014). Being able to stack DNA to a previous location ensures that the number of genetic loci does not increase with each new round of transgene addition. Whereas the previous demonstration was conducted through polyethylene glycol to mediate uptake of DNA into tobacco protoplasts, we now describe protocols for using biolistic transformation to stack DNA in tobacco and rice.
Collapse
Affiliation(s)
- Ruyu Li
- Plant Gene Engineering Center, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Guangzhou, 510650, China
| | - Zhiguo Han
- Plant Gene Engineering Center, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Guangzhou, 510650, China
| | - Lili Hou
- Plant Gene Engineering Center, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Gurminder Kaur
- Plant Gene Engineering Center, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qian Yin
- Plant Gene Engineering Center, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, China
| | - David W Ow
- Plant Gene Engineering Center, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Guangzhou, 510650, China.
| |
Collapse
|
10
|
Voziyanova E, Anderson RP, Shah R, Li F, Voziyanov Y. Efficient Genome Manipulation by Variants of Site-Specific Recombinases R and TD. J Mol Biol 2015; 428:990-1003. [PMID: 26555749 DOI: 10.1016/j.jmb.2015.11.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Revised: 10/17/2015] [Accepted: 11/02/2015] [Indexed: 10/22/2022]
Abstract
Genome engineering benefits from the availability of DNA modifying enzymes that have different target specificities and have optimized performance in different cell types. This variety of site-specific enzymes can be used to develop complex genome engineering applications at multiple loci. Although eight yeast site-specific tyrosine recombinases are known, only Flp is actively used in genome engineering. To expand the pool of the yeast site-specific tyrosine recombinases capable of mediating genome manipulations in mammalian cells, we engineered and analyzed variants of two tyrosine recombinases: R and TD. The activity of the evolved variants, unlike the activity of the native R and TD recombinases, is suitable for genome engineering in Escherichia coli and mammalian cells. Unexpectedly, we found that R recombinase benefits from the shortening of its C-terminus. We also found that the activity of wild-type R can be modulated by its non-consensus "head" sequence but this modulation became not apparent in the evolved R variants. The engineered recombinase variants were found to be active in all recombination reactions tested: excision, integration, and dual recombinase-mediated cassette exchange. The analysis of the latter reaction catalyzed by the R/TD recombinase pair shows that the condition supporting the most efficient replacement reaction favors efficient TD-mediated integration reaction while favoring efficient R-mediated integration and deletion reactions.
Collapse
Affiliation(s)
- Eugenia Voziyanova
- School of Biosciences, Louisiana Tech University, 1 Adams Boulevard, Ruston, LA 71272, USA
| | - Rachelle P Anderson
- School of Biosciences, Louisiana Tech University, 1 Adams Boulevard, Ruston, LA 71272, USA
| | - Riddhi Shah
- School of Biosciences, Louisiana Tech University, 1 Adams Boulevard, Ruston, LA 71272, USA
| | - Feng Li
- School of Biosciences, Louisiana Tech University, 1 Adams Boulevard, Ruston, LA 71272, USA
| | - Yuri Voziyanov
- School of Biosciences, Louisiana Tech University, 1 Adams Boulevard, Ruston, LA 71272, USA.
| |
Collapse
|
11
|
Nandy S, Zhao S, Pathak BP, Manoharan M, Srivastava V. Gene stacking in plant cell using recombinases for gene integration and nucleases for marker gene deletion. BMC Biotechnol 2015; 15:93. [PMID: 26452472 PMCID: PMC4600305 DOI: 10.1186/s12896-015-0212-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/01/2015] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Practical approaches for multigene transformation and gene stacking are extremely important for engineering complex traits and adding new traits in transgenic crops. Trait deployment by gene stacking would greatly simplify downstream plant breeding and trait introgression into cultivars. Gene stacking into pre-determined genomic sites depends on mechanisms of targeted DNA integration and recycling of selectable marker genes. Targeted integrations into chromosomal breaks, created by nucleases, require large transformation efforts. Recombinases such as Cre-lox, on the other hand, efficiently drive site-specific integrations in plants. However, the reversibility of Cre-lox recombination, due to the incorporation of two cis-positioned lox sites, presents a major bottleneck in its application in gene stacking. Here, we describe a strategy of resolving this bottleneck through excision of one of the cis-positioned lox, embedded in the marker gene, by nuclease activity. METHODS All transgenic lines were developed by particle bombardment of rice callus with plasmid constructs. Standard molecular approach was used for building the constructs. Transgene loci were analyzed by PCR, Southern hybridization, and DNA sequencing. RESULTS We developed a highly efficient gene stacking method by utilizing powerful recombinases such as Cre-lox and FLP-FRT, for site-specific gene integrations, and nucleases for marker gene excisions. We generated Cre-mediated site-specific integration locus in rice and showed excision of marker gene by I-SceI at ~20 % efficiency, seamlessly connecting genes in the locus. Next, we showed ZFN could be used for marker excision, and the locus can be targeted again by recombinases. Hence, we extended the power of recombinases to gene stacking application in plants. Finally, we show that heat-inducible I-SceI is also suitable for marker excision, and therefore could serve as an important tool in streamlining this gene stacking platform. CONCLUSIONS A practical approach for gene stacking in plant cell was developed that allows targeted gene insertions through rounds of transformation, a method needed for introducing new traits into transgenic lines for their rapid deployment in the field. By using Cre-lox, a powerful site-specific recombination system, this method greatly improves gene stacking efficiency, and through the application of nucleases develops marker-free, seamless stack of genes at pre-determined chromosomal sites.
Collapse
Affiliation(s)
- Soumen Nandy
- Department of Crop, Soil & Environmental Science, 115 Plant Science Building, University of Arkansas, Fayetteville, AR, 72701, USA.
| | - Shan Zhao
- Department of Crop, Soil & Environmental Science, 115 Plant Science Building, University of Arkansas, Fayetteville, AR, 72701, USA.
| | - Bhuvan P Pathak
- Department of Crop, Soil & Environmental Science, 115 Plant Science Building, University of Arkansas, Fayetteville, AR, 72701, USA.
| | - Muthusamy Manoharan
- Department of Agriculture, 144 Woodard Hall, University of Arkansas at Pine Bluff, Pine Bluff, AR, 71601, USA.
| | - Vibha Srivastava
- Department of Crop, Soil & Environmental Science, 115 Plant Science Building, University of Arkansas, Fayetteville, AR, 72701, USA.
| |
Collapse
|
12
|
Ebinuma H, Nakahama K, Nanto K. Enrichments of gene replacement events by Agrobacterium-mediated recombinase-mediated cassette exchange. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2015; 35:82. [PMID: 25705118 PMCID: PMC4329185 DOI: 10.1007/s11032-015-0215-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 08/22/2014] [Indexed: 05/09/2023]
Abstract
We report recombinase-mediated cassette exchange (RMCE), which can permit integration of transgenes into pre-defined chromosomal loci with no co-expressed marker gene by using Agrobacterium-mediated transformation. Transgenic tobacco plants which have a single copy of negative marker genes (codA) at target loci in heterozygous and homozygous conditions were used for gene exchange by the RMCE method. By negative selection, we were able to obtain five heterozygous and four homozygous transgenic plants in which the genes were exchanged from 64 leaf segments of heterozygous and homozygous target plants, respectively. Except for one transgenic plant with an extra copy, the other eight plants had only a single copy of marker-free transgenes, and no footprint of random integrated copies was detected in half of the eight plants. The RMCE re-transformation frequencies were calculated as 6.25 % per explant and were approximately the same as the average percentage of intact single-copy transformation events for standard tobacco Agrobacterium-mediated transformation.
Collapse
Affiliation(s)
- Hiroyasu Ebinuma
- Faculty of Textile Science and Technology, Shinshu University, 3-15-1, Tokida, Ueda, Nagano, 386-8567 Japan
| | - Katsuhiko Nakahama
- Agri-Biotechnology Research Laboratory, Nippon Paper Industries Co. Ltd., 5-21-1, Oji, Kita-ku, Tokyo, 114-0002 Japan
| | - Kazuya Nanto
- Agri-Biotechnology Research Laboratory, Nippon Paper Industries Co. Ltd., 5-21-1, Oji, Kita-ku, Tokyo, 114-0002 Japan
| |
Collapse
|
13
|
Nandy S, Srivastava V. Marker-free site-specific gene integration in rice based on the use of two recombination systems. PLANT BIOTECHNOLOGY JOURNAL 2012; 10:904-12. [PMID: 22686401 DOI: 10.1111/j.1467-7652.2012.00715.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Transgene integration mediated by heterologous site-specific recombination (SSR) systems into the dedicated genomic sites has been demonstrated in a few different plant species. This approach of plant transformation generates a precise site-specific integration (SSI) structure consisting of a single copy of the transgene construct. As a result, stable transgene expression correlated with promoter strength and gene copy number is observed among independent transgenic lines and faithfully transmitted through subsequent generations. Site-specific integration approaches use selectable marker genes, removal of which is necessary for the implementation of this approach as a biotechnology application. As SSR systems are also excellent tools for excising marker genes from transgene locus, a molecular strategy involving gene integration followed by marker excision, each mediated by a distinct recombination system, was earlier proposed. Experimental validation of this approach is the focus of this work. Using FLPe-FRT system for site-specific gene integration and heat-inducible Cre-lox for marker gene excision, marker-free SSI lines were developed in the first generation itself. More importantly, progeny derived from these lines inherited the marker-free locus, indicating efficient germinal transmission. Finally, as the transgene expression from SSI locus was not altered upon marker excision, this method is suitable for streamlining the production of marker-free SSI lines.
Collapse
Affiliation(s)
- Soumen Nandy
- Department of Crop, Soil & Environmental Sciences, University of Arkansas, Fayetteville, AR, USA
| | | |
Collapse
|
14
|
Thomson JG, Chan R, Smith J, Thilmony R, Yau YY, Wang Y, Ow DW. The Bxb1 recombination system demonstrates heritable transmission of site-specific excision in Arabidopsis. BMC Biotechnol 2012; 12:9. [PMID: 22436504 PMCID: PMC3341217 DOI: 10.1186/1472-6750-12-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 03/21/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The mycobacteriophage large serine recombinase Bxb1 catalyzes site-specific recombination between its corresponding attP and attB recognition sites. Previously, we and others have shown that Bxb1 has catalytic activity in various eukaryotic species including Nicotiana tabacum, Schizosaccharomyces pombe, insects and mammalian cells. RESULTS In this work, the Bxb1 recombinase gene was transformed and constitutively expressed in Arabidopsis thaliana plants harboring a chromosomally integrated attP and attB-flanked target sequence. The Bxb1 recombinase successfully excised the target sequence in a conservative manner and the resulting recombination event was heritably transmitted to subsequent generations in the absence of the recombinase transgene. In addition, we also show that Bxb1 recombinase expressing plants can be manually crossed with att-flanked target transgenic plants to generate excised progeny. CONCLUSION The Bxb1 large serine recombinase performs site-specific recombination in Arabidopsis thaliana germinal tissue, producing stable lines free of unwanted DNA. The precise site-specific deletion produced by Bxb1 in planta demonstrates that this enzyme can be a useful tool for the genetic engineering of plants without selectable marker transgenes or other undesirable exogenous sequences.
Collapse
Affiliation(s)
- James G Thomson
- Crop Improvement and Utilization Research Unit, Western Regional Research Center, USDA-ARS, 800 Buchanan Street, Albany, CA 94710, USA.
| | | | | | | | | | | | | |
Collapse
|
15
|
Anderson RP, Voziyanova E, Voziyanov Y. Flp and Cre expressed from Flp-2A-Cre and Flp-IRES-Cre transcription units mediate the highest level of dual recombinase-mediated cassette exchange. Nucleic Acids Res 2012; 40:e62. [PMID: 22270085 PMCID: PMC3333864 DOI: 10.1093/nar/gks027] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Recombinase-mediated cassette exchange (RMCE) is a powerful tool for unidirectional integration of DNA fragments of interest into a pre-determined genome locale. In this report, we examined how the efficiency of dual RMCE catalyzed by Flp and Cre depends on the nature of transcription units that express the recombinases. The following recombinase transcription units were analyzed: (i) Flp and Cre genes expressed as individual transcription units located on different vectors, (ii) Flp and Cre genes expressed as individual transcription units located on the same vector, (iii) Flp and Cre genes expressed from a single promoter and separated by internal ribosome entry sequence and (iv) Flp and Cre coding sequences separated by the 2A peptide and expressed as a single gene. We found that the highest level of dual RMCE (35-45% of the transfected cells) can be achieved when Flp and Cre recombinases are expressed as Flp-2A-Cre and Flp-IRES-Cre transcription units. In contrast, the lowest level of dual RMCE (∼1% of the transfected cells) is achieved when Flp and Cre are expressed as individual transcription units. The analysis shows that it is the relative Flp-to-Cre ratio that critically affects the efficiency of dual RMCE. Our results will be helpful for maximizing the efficiency of dual RMCE aimed to engineer and re-engineer genomes.
Collapse
Affiliation(s)
- Rachelle P Anderson
- School of Biosciences, Louisiana Tech University, 1 Adams Blvd., Ruston, LA 71272, USA
| | | | | |
Collapse
|
16
|
Ebinuma H, Nanto K, Kasahara S, Komamine A. Marker-free gene targeting by recombinase-mediated cassette exchange. Methods Mol Biol 2012; 847:379-90. [PMID: 22351023 DOI: 10.1007/978-1-61779-558-9_30] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Repeated gene targeting by recombinase-mediated cassette exchange (RMCE) is an efficient tool for the study of gene function and regulation because of the high predictability and repeatability of gene expression. We have developed the site-directed integration (SDI) vector system for Agrobacterium-mediated transformation to precisely integrate a single copy of a desired gene into a predefined chromosomal locus in the absence of any coexpressed selection marker gene (Nanto et al. Plant Biotechnol J 3:203-214, 2005; Nanto and Ebinuma Transgenic Res 17:337-344, 2008; Nanto et al. Plant Cell Rep 28:777-785, 2009; Ebinuma and Nanto (2009) Marker-free targeted transformation, in Molecular techniques in crop improvement (2nd Edition). (Jain, S. M. and Brar, D. S. eds.), Springer Netherlands, pp. 527-543; Ebinuma and Nanto in preparation). The SDI vector system consists of a target vector to introduce the target cassette and an exchange vector to reintroduce the exchange cassette for gene replacement. We describe the molecular design and experimental protocol that can efficiently enrich RMCE events through the removal of randomly integrated copies and select clean marker-free targeted transgenic plants by using a negative marker.
Collapse
|
17
|
Ow DW. Recombinase-mediated gene stacking as a transformation operating system. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2011; 53:512-9. [PMID: 21676171 DOI: 10.1111/j.1744-7909.2011.01061.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The current method for combining transgenes into a genome is through the assortment of independent loci, a classical operating system compatible with transgenic traits created by different developers, at different times and/or through different transformation techniques. However, as the number of transgenic loci increases over time, increasingly larger populations are needed to find the rare individual with the desired assortment of transgenic loci along with the non-transgenic elite traits. Introducing a transgene directly into a field cultivar would bypass the need to introgress the engineered trait. However, this necessitates separate transformations into numerous field cultivars, along with the characterization and regulatory approval of each independent transformation event. Reducing the number of segregating transgenic loci could be achieved if multiple traits are introduced at the same time, a preferred option if each of the many traits is new or requires re-engineering. If re-engineering of previously introduced traits is not needed, then appending a new trait to an existing locus would be a rational strategy. The insertion of new DNA at a known locus can be accomplished by site-specific integration, through a host-dependent homology-based process, or a heterologous site-specific recombination system. Here, we discuss gene stacking through the use of site-specific recombinases.
Collapse
Affiliation(s)
- David W Ow
- South China Botanical Garden, Guangzhou 510650, China.
| |
Collapse
|
18
|
Husaini AM, Rashid Z, Mir RUR, Aquil B. Approaches for gene targeting and targeted gene expression in plants. ACTA ACUST UNITED AC 2011; 2:150-62. [PMID: 22179193 DOI: 10.4161/gmcr.2.3.18605] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Transgenic science and technology are fundamental to state-of-the-art plant molecular genetics and crop improvement. The new generation of technology endeavors to introduce genes 'stably' into 'site-specific' locations and in 'single copy' without the integration of extraneous vector 'backbone' sequences or selectable markers and with a 'predictable and consistent' expression. Several similar strategies and technologies, which can push the development of 'smart' genetically modified plants with desirable attributes, as well as enhance their consumer acceptability, are discussed in this review.
Collapse
Affiliation(s)
- Amjad Masood Husaini
- Division of Plant Breeding and Genetics; Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir; Shalimar, India.
| | | | | | | |
Collapse
|
19
|
Wang Y, Yau YY, Perkins-Balding D, Thomson JG. Recombinase technology: applications and possibilities. PLANT CELL REPORTS 2011; 30:267-85. [PMID: 20972794 PMCID: PMC3036822 DOI: 10.1007/s00299-010-0938-1] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 10/06/2010] [Accepted: 10/08/2010] [Indexed: 05/02/2023]
Abstract
The use of recombinases for genomic engineering is no longer a new technology. In fact, this technology has entered its third decade since the initial discovery that recombinases function in heterologous systems (Sauer in Mol Cell Biol 7(6):2087-2096, 1987). The random insertion of a transgene into a plant genome by traditional methods generates unpredictable expression patterns. This feature of transgenesis makes screening for functional lines with predictable expression labor intensive and time consuming. Furthermore, an antibiotic resistance gene is often left in the final product and the potential escape of such resistance markers into the environment and their potential consumption raises consumer concern. The use of site-specific recombination technology in plant genome manipulation has been demonstrated to effectively resolve complex transgene insertions to single copy, remove unwanted DNA, and precisely insert DNA into known genomic target sites. Recombinases have also been demonstrated capable of site-specific recombination within non-nuclear targets, such as the plastid genome of tobacco. Here, we review multiple uses of site-specific recombination and their application toward plant genomic engineering. We also provide alternative strategies for the combined use of multiple site-specific recombinase systems for genome engineering to precisely insert transgenes into a pre-determined locus, and removal of unwanted selectable marker genes.
Collapse
Affiliation(s)
- Yueju Wang
- Department of Natural Sciences, Northeastern State University, Broken Arrow, OK 74014 USA
| | - Yuan-Yeu Yau
- Department of Plant and Microbial Biology, Plant Gene Expression Center, USDA-ARS, University of California-Berkeley, 800 Buchanan St., Albany, CA 94710 USA
| | | | - James G. Thomson
- Crop Improvement and Utilization Unit, USDA-ARS WRRC, 800 Buchanan St., Albany, CA 94710 USA
| |
Collapse
|
20
|
Yau YY, Wang Y, Thomson JG, Ow DW. Method for Bxb1-mediated site-specific integration in planta. Methods Mol Biol 2011; 701:147-66. [PMID: 21181529 DOI: 10.1007/978-1-61737-957-4_8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Gene targeting in plants through homologous recombination has been sparsely reported, although notable breakthroughs have been achieved in recent years. In particular, the use of zinc finger nucleases to promote homologous end joining has revived the promise that homologous gene targeting could someday become practical for plant genetic engineering. An alternative and complementary approach that has progressed steadily over the years has been recombinase-mediated site-specific integration. In this approach, a first recombination site is introduced into the genome to serve as a target for inserting subsequent DNA. Here, we describe the method for generating the chromosomal target and the subsequent insertion of new DNA into the chromosomal target by Bxb1-mediated site-specific integration. This method would permit the comparison of different molecular constructs at the same genomic locations.
Collapse
Affiliation(s)
- Yuan-Yeu Yau
- Plant Gene Expression Center, USDA-ARS & Plant & Microbial Biology, University of California-Berkeley, Albany, CA, USA
| | | | | | | |
Collapse
|
21
|
Li Z, Moon BP, Xing A, Liu ZB, McCardell RP, Damude HG, Falco SC. Stacking multiple transgenes at a selected genomic site via repeated recombinase-mediated DNA cassette exchanges. PLANT PHYSIOLOGY 2010; 154:622-31. [PMID: 20720171 PMCID: PMC2949048 DOI: 10.1104/pp.110.160093] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Accepted: 08/18/2010] [Indexed: 05/18/2023]
Abstract
Recombinase-mediated DNA cassette exchange (RMCE) has been successfully used to insert transgenes at previously characterized genomic sites in plants. Following the same strategy, groups of transgenes can be stacked to the same site through multiple rounds of RMCE. A gene-silencing cassette, designed to simultaneously silence soybean (Glycine max) genes fatty acid ω-6 desaturase 2 (FAD2) and acyl-acyl carrier protein thioesterase 2 (FATB) to improve oleic acid content, was first inserted by RMCE at a precharacterized genomic site in soybean. Selected transgenic events were subsequently retransformed with the second DNA construct containing a Yarrowia lipolytica diacylglycerol acyltransferase gene (DGAT1) to increase oil content by the enhancement of triacylglycerol biosynthesis and three other genes, a Corynebacterium glutamicum dihydrodipicolinate synthetase gene (DHPS), a barley (Hordeum vulgare) high-lysine protein gene (BHL8), and a truncated soybean cysteine synthase gene (CGS), to improve the contents of the essential amino acids lysine and methionine. Molecular characterization confirmed that the second RMCE successfully stacked the four overexpression cassettes to the previously integrated FAD2-FATB gene-silencing cassette. Phenotypic analyses indicated that all the transgenes expressed expected phenotypes.
Collapse
Affiliation(s)
- Zhongsen Li
- DuPont Agricultural Biotechnology, Experimental Station E353, Wilmington, Delaware 19880, USA.
| | | | | | | | | | | | | |
Collapse
|
22
|
Fladung M, Becker D. Targeted integration and removal of transgenes in hybrid aspen (Populus tremula L. x P. tremuloides Michx.) using site-specific recombination systems. PLANT BIOLOGY (STUTTGART, GERMANY) 2010; 12:334-340. [PMID: 20398239 DOI: 10.1111/j.1438-8677.2009.00293.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Two site-specific recombination systems, Cre/lox and FLP/FRT, were tested for marker gene removal and targeted gene transfer in a model tree system. A hybrid aspen clone (Populus tremula x Populus tremuloides) was co-transformed with plasmids containing either the FLP or the Cre recombinase, both under control of a heat-inducible promoter (HSP, Gmhsp17.5-E from soybean) flanked by the two recognition sites (FRT or lox). Molecular investigations of heat-shock treated Cre or FLP transgenic lines indicate excision of inserts between the two recognition sites. Further, a site-specific recombination at the FRT sites leading to targeted integration of a fragment could be demonstrated for the FLP/FRT system. Transgenic aspen carrying two constructs (each with different genes between the FRT sites) revealed (i) excision of both fragments between the FRT sites, and (ii) targeted integration of the fragment from the second construct exactly at the former position of the fragment in the first construct. These results indicate the usefulness of the two site-specific recombination systems in the tree species Populus. Combining both site-specific recombination systems, a strategy is suggested for targeted transgene transfer and removal of antibiotic marker genes.
Collapse
Affiliation(s)
- M Fladung
- Johann Heinrich von Thünen-Institut, Federal Research Institute for Rural Areas, Forestry and Fisheries, Institute of Forest Genetics, Grosshansdorf, Germany.
| | | |
Collapse
|
23
|
Thomson JG, Chan R, Thilmony R, Yau YY, Ow DW. PhiC31 recombination system demonstrates heritable germinal transmission of site-specific excision from the Arabidopsis genome. BMC Biotechnol 2010; 10:17. [PMID: 20178628 PMCID: PMC2837860 DOI: 10.1186/1472-6750-10-17] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Accepted: 02/23/2010] [Indexed: 11/10/2022] Open
Abstract
Background The large serine recombinase phiC31 from broad host range Streptomyces temperate phage, catalyzes the site-specific recombination of two recognition sites that differ in sequence, typically known as attachment sites attB and attP. Previously, we characterized the phiC31 catalytic activity and modes of action in the fission yeast Schizosaccharomyces pombe. Results In this work, the phiC31 recombinase gene was placed under the control of the Arabidopsis OXS3 promoter and introduced into Arabidopsis harboring a chromosomally integrated attB and attP-flanked target sequence. The phiC31 recombinase excised the attB and attP-flanked DNA, and the excision event was detected in subsequent generations in the absence of the phiC31 gene, indicating germinal transmission was possible. We further verified that the genomic excision was conservative and that introduction of a functional recombinase can be achieved through secondary transformation as well as manual crossing. Conclusion The phiC31 system performs site-specific recombination in germinal tissue, a prerequisite for generating stable lines with unwanted DNA removed. The precise site-specific deletion by phiC31 in planta demonstrates that the recombinase can be used to remove selectable markers or other introduced transgenes that are no longer desired and therefore can be a useful tool for genome engineering in plants.
Collapse
Affiliation(s)
- James G Thomson
- Crop Improvement and Utilization Research Unit, Western Regional Research Center, USDA-ARS, 800 Buchanan Street, Albany, CA 94710, USA.
| | | | | | | | | |
Collapse
|
24
|
Li Z, Xing A, Moon BP, McCardell RP, Mills K, Falco SC. Site-specific integration of transgenes in soybean via recombinase-mediated DNA cassette exchange. PLANT PHYSIOLOGY 2009; 151:1087-95. [PMID: 19429604 PMCID: PMC2773068 DOI: 10.1104/pp.109.137612] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Accepted: 05/05/2009] [Indexed: 05/02/2023]
Abstract
A targeting method to insert genes at a previously characterized genetic locus to make plant transformation and transgene expression predictable is highly desirable for plant biotechnology. We report the successful targeting of transgenes to predefined soybean (Glycine max) genome sites using the yeast FLP-FRT recombination system. First, a target DNA containing a pair of incompatible FRT sites flanking a selection gene was introduced in soybean by standard biolistic transformation. Transgenic events containing a single copy of the target were retransformed with a donor DNA, which contained the same pair of FRT sites flanking a different selection gene, and a FLP expression DNA. Precise DNA cassette exchange was achieved between the target and donor DNA via recombinase-mediated cassette exchange, so that the donor DNA was introduced at the locus previously occupied by the target DNA. The introduced donor genes expressed normally and segregated according to Mendelian laws.
Collapse
Affiliation(s)
- Zhongsen Li
- DuPont/Pioneer Crop Genetics, Experimental Station, Wilmington, Delaware 19880, USA.
| | | | | | | | | | | |
Collapse
|
25
|
Gudynaite-Savitch L, Johnson DA, Miki BLA. Strategies to mitigate transgene-promoter interactions. PLANT BIOTECHNOLOGY JOURNAL 2009; 7:472-485. [PMID: 19490507 DOI: 10.1111/j.1467-7652.2009.00416.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The expression pattern of tissue-specific promoters in transgenes can be influenced by promoter/enhancer elements employed for the expression of selectable marker genes or elements found in DNA flanking the insertion site. We have developed an analytical system in Arabidopsis thaliana to investigate strategies useful in blocking or reducing nonspecific interactions. These experiments confirm that the DNA configuration and the insertion of spacer DNA aid in the appropriate expression of tissue-specific promoters. It is also demonstrated that the novel tobacco cryptic promoter (tCUP), when used to replace the cauliflower mosaic virus (CaMV) 35S promoter/enhancer, does not show nonspecific interactions. Furthermore, it is shown that insulators isolated from yeast and animals may have potential application in plants. Our results may allow the design of strategies that, individually or in combination, can be used to minimize nonspecific interactions and to design vectors for individual tissue-specific promoters.
Collapse
|
26
|
Nanto K, Sato K, Katayama Y, Ebinuma H. Expression of a transgene exchanged by the recombinase-mediated cassette exchange (RMCE) method in plants. PLANT CELL REPORTS 2009; 28:777-85. [PMID: 19241079 DOI: 10.1007/s00299-009-0683-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2008] [Revised: 01/31/2009] [Accepted: 02/04/2009] [Indexed: 05/09/2023]
Abstract
We developed a site-directed integration (SDI) system for Agrobacterium-mediated transformation to precisely integrate a single copy of a desired gene into a predefined target locus by recombinase-mediated cassette exchange (RMCE). We produced site-specific transgenic tobacco plants from four target lines and examined expression of the transgene in T1 site-specific transgenic tobacco plants, which were obtained by backcrossing. We found that site-specific transgenic plants from the same target lines showed approximately the same level of expression of the transgene. Moreover, we demonstrated that site-specific transgenic plants showed much less variability of transgene expression than random-integration transgenic plants. Interestingly, transgenes in the same direction at the same target locus showed the same level of activity, but transgenes in different directions showed different levels of activity. The expression levels of transgene did not correlate with those of the target gene. Our results showed that the SDI system could benefit the precise comparisons between different gene constructs, the characterization of different chromosomal regions and the cost-effective screening of reliable transgenic plants.
Collapse
Affiliation(s)
- Kazuya Nanto
- Forestly Science Laboratory, Nippon Paper Industries Co., Ltd, Kita-ku, Tokyo, Japan
| | | | | | | |
Collapse
|
27
|
Miki B, Abdeen A, Manabe Y, MacDonald P. Selectable marker genes and unintended changes to the plant transcriptome. PLANT BIOTECHNOLOGY JOURNAL 2009; 7:211-8. [PMID: 19261135 DOI: 10.1111/j.1467-7652.2009.00400.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The intended effect of a selectable marker gene is to confer a novel trait that allows for the selection and recovery of transgenic plants. Unintended effects may also occur as a result of interactions between the selectable marker gene or its regulatory elements and genetic elements at the site of insertion. These are called position effects. Other unintended effects may occur if the selectable marker gene has a range of pleiotropic effects related to the functional and regulatory domains within the coding region or the regulatory elements used to drive expression. Both pleiotropic and position effects may generate unpredictable events depending on the process used for transgenesis and the state of knowledge associated with the selectable marker gene. Although some selectable marker genes, such as the neomycin phosphotransferase type II gene (nptII), have no pleiotropic effects on the transcriptomes of transgenic plants, others, such as the bialaphos resistance gene (bar), have pleiotropic effects. These must be clearly understood and accounted for when evaluating the expression patterns conferred by other co-transforming transgenes under study. The number and kinds of selectable marker genes are large. A detailed understanding of their unintended effects is needed to develop transgenic strategies that will minimize or eliminate unintended and unpredictable changes to plants with newly inserted genes.
Collapse
Affiliation(s)
- Brian Miki
- Eastern Cereals and Oilseeds Research Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada K1A 0C6.
| | | | | | | |
Collapse
|
28
|
Djukanovic V, Lenderts B, Bidney D, Lyznik LA. A Cre::FLP fusion protein recombines FRT or loxP sites in transgenic maize plants. PLANT BIOTECHNOLOGY JOURNAL 2008; 6:770-781. [PMID: 18627532 DOI: 10.1111/j.1467-7652.2008.00357.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The coding sequences of Cre (site-specific recombinase from bacteriophage P1) and FLP (yeast 2-microm plasmid site-specific recombinase) were fused in frame to produce a novel, dual-function, site-specific recombinase gene. Transgenic maize plants containing the Cre::FLP fusion expression vector were crossed to transgenic plants containing either the loxP or FRT excision substrate. Complete and precise excisions of chromosomal fragments flanked by the respective target sites were observed in the F1 and F2 progeny plants. The episomal DNA recombination products were frequently lost. Non-recombined FRT substrates found in the F1 plants were recovered in the F2 generation after the Cre::FLP gene segregated out. They produced the recombination products in the F3 generation when crossed back to the FLP-expressing plants. These observations may indicate that the efficiency of site-specific recombination is affected by the plant developmental stage, with site-specific recombination being more prevalent in developing embryos. The Cre::FLP fusion protein was also tested for excisions catalysed by Cre. Excisions were identified in the F1 plants and verified in the F2 plants by polymerase chain reaction and Southern blotting. Both components of the fusion protein (FLP and Cre) were functional and acted with similar efficiency. The crossing strategy proved to be suitable for the genetic engineering of maize using the FLP or Cre site-specific recombination system.
Collapse
Affiliation(s)
- Vesna Djukanovic
- Pioneer Hi-Bred International, A DuPont Business, Research Center, 7300 NW 62nd Avenue, Johnston, IA 50131-1004, USA
| | | | | | | |
Collapse
|
29
|
Louwerse JD, van Lier MCM, van der Steen DM, de Vlaam CMT, Hooykaas PJJ, Vergunst AC. Stable recombinase-mediated cassette exchange in Arabidopsis using Agrobacterium tumefaciens. PLANT PHYSIOLOGY 2007; 145:1282-93. [PMID: 17921337 PMCID: PMC2151714 DOI: 10.1104/pp.107.108092] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2007] [Accepted: 09/27/2007] [Indexed: 05/02/2023]
Abstract
Site-specific integration is an attractive method for the improvement of current transformation technologies aimed at the production of stable transgenic plants. Here, we present a Cre-based targeting strategy in Arabidopsis (Arabidopsis thaliana) using recombinase-mediated cassette exchange (RMCE) of transferred DNA (T-DNA) delivered by Agrobacterium tumefaciens. The rationale for effective RMCE is the precise exchange of a genomic and a replacement cassette both flanked by two heterospecific lox sites that are incompatible with each other to prevent unwanted cassette deletion. We designed a strategy in which the coding region of a loxP/lox5171-flanked bialaphos resistance (bar) gene is exchanged for a loxP/lox5171-flanked T-DNA replacement cassette containing the neomycin phosphotransferase (nptII) coding region via loxP/loxP and lox5171/lox5171 directed recombination. The bar gene is driven by the strong 35S promoter, which is located outside the target cassette. This placement ensures preferential selection of RMCE events and not random integration events by expression of nptII from this same promoter. Using root transformation, during which Cre was provided on a cotransformed T-DNA, 50 kanamycin-resistant calli were selected. Forty-four percent contained a correctly exchanged cassette based on PCR analysis, indicating the stringency of the selection system. This was confirmed for the offspring of five analyzed events by Southern-blot analysis. In four of the five analyzed RMCE events, there were no additional T-DNA insertions or they easily segregated, resulting in high-efficiency single-copy RMCE events. Our approach enables simple and efficient selection of targeting events using the advantages of Agrobacterium-mediated transformation.
Collapse
Affiliation(s)
- Jeanine D Louwerse
- Institute of Biology, Clusius Laboratory, Leiden University, 2333 AL Leiden, The Netherlands
| | | | | | | | | | | |
Collapse
|
30
|
Nanto K, Ebinuma H. Marker-free site-specific integration plants. Transgenic Res 2007; 17:337-44. [PMID: 17588210 DOI: 10.1007/s11248-007-9106-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2006] [Accepted: 05/15/2007] [Indexed: 10/23/2022]
Abstract
Recently, site-specific recombination methods in plants have been developed to delete selection markers to produce marker-free transgenic plants or to integrate the transgene into a pre-determined genomic location to produce site-specific transgenic plants. However, these methods have been developed independently, and although the strategies of producing marker-free site-specific integration plants have been discussed, the concept has not been demonstrated. In the present study, we combined two approaches to site-specific recombination and demonstrated the concepts for removing the marker after site-specific integration for producing marker-free site-specific transgenic plants.
Collapse
Affiliation(s)
- Kazuya Nanto
- Forestry Science Research Laboratory, Nippon Paper Industries Co., Ltd., 5-21-1, Oji, Kita-ku, Tokyo 114-0002, Japan
| | | |
Collapse
|
31
|
Chawla R, Ariza-Nieto M, Wilson AJ, Moore SK, Srivastava V. Transgene expression produced by biolistic-mediated, site-specific gene integration is consistently inherited by the subsequent generations. PLANT BIOTECHNOLOGY JOURNAL 2006; 4:209-18. [PMID: 17177797 DOI: 10.1111/j.1467-7652.2005.00173.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The efficient production of stable transgenic plants is important for both crop improvement and functional genomics. Site-specific integration of foreign genes into a designated genomic position is an attractive tool for minimizing expression variability between transgenic lines. Here, we studied the utility of a Cre-mediated, site-specific integration approach, facilitated by particle bombardment, for streamlining the production of stable transgenic plants, using rice as a model species. Using this method, we generated 18 different transgenic lines containing a precise integration of a single copy of beta-glucuronidase gene (gusA) into a designated genomic location. Eleven of these lines contained no illegitimate integration in the background (single-copy lines), and seven contained illegitimate integrations in addition to the site-specific integration (multicopy lines). We monitored gusA expression in these lines up to three to four successive generations. Each of the single-copy lines expressed the gusA gene at consistent levels and nearly doubled the expression level in the homozygous state. In contrast, multicopy lines displayed expression variation and gene silencing. In about half of the multicopy lines, however, expression of the site-specific integration locus could be reactivated and stabilized on segregation of the illegitimate integrations, whereas, in the remaining half, expression could not be restored, as they contained genetically linked illegitimate integrations. This study demonstrates that biolistic-mediated, site-specific gene integration is an efficient and reliable tool for streamlining the production of stable transgenic plants.
Collapse
Affiliation(s)
- Rekha Chawla
- Department of Crop, Soil & Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | | | | | | | | |
Collapse
|