1
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Gudeta DD, Foley SL. Versatile allelic replacement and self-excising integrative vectors for plasmid genome mutation and complementation. Microbiol Spectr 2024; 12:e0338723. [PMID: 37991378 PMCID: PMC10782977 DOI: 10.1128/spectrum.03387-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 10/23/2023] [Indexed: 11/23/2023] Open
Abstract
IMPORTANCE In spite of the dissemination of multidrug-resistant plasmids among Gram-negative pathogens, including those carrying virulence genes, vector tools for studying plasmid-born genes are lacking. The allelic replacement vectors can be used to generate plasmid or chromosomal mutations including markless point mutations. This is the first report describing a self-excising integrative vector that can be used as a stable single-copy complementing tool to study medically important pathogens including in vivo studies without the need for antibiotic selection. Overall, our newly developed vectors can be applied for the assessment of the function of plasmid-encoded genes by specifically creating mutations, moving large operons between plasmids and to/from the chromosome, and complementing phenotypes associated with gene mutation. Furthermore, the vectors express chromophores for the detection of target gene modification or colony isolation, avoiding time-consuming screening procedures.
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Affiliation(s)
- Dereje D. Gudeta
- Division of Microbiology, National Center for Toxicological Research, Jefferson, Arkansas, USA
| | - Steven L. Foley
- Division of Microbiology, National Center for Toxicological Research, Jefferson, Arkansas, USA
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2
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Singh C, Kumar R, Sehgal H, Bhati S, Singhal T, Gayacharan, Nimmy MS, Yadav R, Gupta SK, Abdallah NA, Hamwieh A, Kumar R. Unclasping potentials of genomics and gene editing in chickpea to fight climate change and global hunger threat. Front Genet 2023; 14:1085024. [PMID: 37144131 PMCID: PMC10153629 DOI: 10.3389/fgene.2023.1085024] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/24/2023] [Indexed: 09/09/2023] Open
Abstract
Genomics and genome editing promise enormous opportunities for crop improvement and elementary research. Precise modification in the specific targeted location of a genome has profited over the unplanned insertional events which are generally accomplished employing unadventurous means of genetic modifications. The advent of new genome editing procedures viz; zinc finger nucleases (ZFNs), homing endonucleases, transcription activator like effector nucleases (TALENs), Base Editors (BEs), and Primer Editors (PEs) enable molecular scientists to modulate gene expressions or create novel genes with high precision and efficiency. However, all these techniques are exorbitant and tedious since their prerequisites are difficult processes that necessitate protein engineering. Contrary to first generation genome modifying methods, CRISPR/Cas9 is simple to construct, and clones can hypothetically target several locations in the genome with different guide RNAs. Following the model of the application in crop with the help of the CRISPR/Cas9 module, various customized Cas9 cassettes have been cast off to advance mark discrimination and diminish random cuts. The present study discusses the progression in genome editing apparatuses, and their applications in chickpea crop development, scientific limitations, and future perspectives for biofortifying cytokinin dehydrogenase, nitrate reductase, superoxide dismutase to induce drought resistance, heat tolerance and higher yield in chickpea to encounter global climate change, hunger and nutritional threats.
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Affiliation(s)
- Charul Singh
- USBT, Guru Govind Singh Indraprastha University, Delhi, India
| | - Ramesh Kumar
- Department of Biochemistry, University of Allahabad Prayagraj, Prayagraj, India
| | - Hansa Sehgal
- Department of Biological Sciences, Birla Institute of Technology and Sciences, Pilani, India
| | - Sharmista Bhati
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
| | - Tripti Singhal
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Gayacharan
- Division of Germplasm Evaluation, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - M. S. Nimmy
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | | | | | | | - Aladdin Hamwieh
- The International Center for Agricultural Research in the Dry Areas (ICARDA), Cairo, Egypt
| | - Rajendra Kumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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3
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Guiziou S, Maranas CJ, Chu JC, Nemhauser JL. An integrase toolbox to record gene-expression during plant development. Nat Commun 2023; 14:1844. [PMID: 37012288 PMCID: PMC10070421 DOI: 10.1038/s41467-023-37607-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 03/23/2023] [Indexed: 04/05/2023] Open
Abstract
There are many open questions about the mechanisms that coordinate the dynamic, multicellular behaviors required for organogenesis. Synthetic circuits that can record in vivo signaling networks have been critical in elucidating animal development. Here, we report on the transfer of this technology to plants using orthogonal serine integrases to mediate site-specific and irreversible DNA recombination visualized by switching between fluorescent reporters. When combined with promoters expressed during lateral root initiation, integrases amplify reporter signal and permanently mark all descendants. In addition, we present a suite of methods to tune the threshold for integrase switching, including: RNA/protein degradation tags, a nuclear localization signal, and a split-intein system. These tools improve the robustness of integrase-mediated switching with different promoters and the stability of switching behavior over multiple generations. Although each promoter requires tuning for optimal performance, this integrase toolbox can be used to build history-dependent circuits to decode the order of expression during organogenesis in many contexts.
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Affiliation(s)
- Sarah Guiziou
- Department of Biology, University of Washington, Seattle, WA, 98195, USA
| | | | - Jonah C Chu
- Department of Biology, University of Washington, Seattle, WA, 98195, USA
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4
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Wang F, Ji YT, Tian C, Wang YC, Xu S, Wang RY, Yang QQ, Zhao P, Xia QY. An inducible constitutive expression system in Bombyx mori mediated by phiC31 integrase. INSECT SCIENCE 2021; 28:1277-1289. [PMID: 32803790 DOI: 10.1111/1744-7917.12866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 08/05/2020] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
Inducible gene-expression systems play important roles in gene functional assays in the post-genome era. Streptomyces phage-derived phiC31 integrase, which mediates an irreversible site-specific cassette exchange between the phage attachment site (attP) and the bacterial attachment site (attB), provides a promising option for the construction of a controllable gene-expression system. Here, we report a phiC31 integrase-mediated promoter flip system (FLIP) for the inducible expression of target genes in silkworm (Bombyx mori). First, we constructed a FLIP reporter system, in which a BmAct4 promoter with enhanced translational efficiency was flanked by the attB and attP sites in a head-to-head orientation and further linked in a reverse orientation to a DsRed reporter gene. The coexpression of a C-terminal modified phiC31-NLS integrase carrying a simian virus 40 (SV40) nuclear localization signal (NLS) effectively flipped the BmAct4 promoter through an attB/attP exchange, thereby activating the downstream expression of DsRed in a silkworm embryo-derived cell line, BmE. Subsequently, the FLIP system, together with a system continuously expressing the phiC31-NLS integrase, was used to construct binary transgenic silkworm lines. Hybridization between FLIP and phiC31-NLS transgenic silkworm lines resulted in the successful flipping of the BmAct4 promoter, with an approximately 39% heritable transformation efficiency in silkworm offspring, leading to the constitutive and high-level expression of DsRed in silkworms, which accounted for approximately 0.81% of the silkworm pupal weight. Our successful development of the FLIP system offers an effective alternative for manipulating gene expression in silkworms and other lepidopteran species.
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Affiliation(s)
- Feng Wang
- State Key Laboratory of Silkworm Genome Biology, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Biological Science Research Center, Southwest University, Chongqing, China
| | - Yan-Ting Ji
- State Key Laboratory of Silkworm Genome Biology, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Biological Science Research Center, Southwest University, Chongqing, China
| | - Chi Tian
- State Key Laboratory of Silkworm Genome Biology, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Biological Science Research Center, Southwest University, Chongqing, China
| | - Yuan-Cheng Wang
- State Key Laboratory of Silkworm Genome Biology, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Biological Science Research Center, Southwest University, Chongqing, China
| | - Shen Xu
- State Key Laboratory of Silkworm Genome Biology, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Biological Science Research Center, Southwest University, Chongqing, China
| | - Ri-Yuan Wang
- State Key Laboratory of Silkworm Genome Biology, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Biological Science Research Center, Southwest University, Chongqing, China
| | - Qian-Qian Yang
- State Key Laboratory of Silkworm Genome Biology, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Biological Science Research Center, Southwest University, Chongqing, China
| | - Ping Zhao
- State Key Laboratory of Silkworm Genome Biology, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Biological Science Research Center, Southwest University, Chongqing, China
| | - Qing-You Xia
- State Key Laboratory of Silkworm Genome Biology, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Biological Science Research Center, Southwest University, Chongqing, China
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5
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Čermák T. Sequence modification on demand: search and replace tools for precise gene editing in plants. Transgenic Res 2021; 30:353-379. [PMID: 34086167 DOI: 10.1007/s11248-021-00253-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 04/05/2021] [Indexed: 12/26/2022]
Abstract
Until recently, our ability to generate allelic diversity in plants was limited to introduction of variants from domesticated and wild species by breeding via uncontrolled recombination or the use of chemical and physical mutagens-processes that are lengthy and costly or lack specificity, respectively. Gene editing provides a faster and more precise way to create new variation, although its application in plants has been dominated by the creation of short insertion and deletion mutations leading to loss of gene function, mostly due to the dependence of editing outcomes on DNA repair pathway choices intrinsic to higher eukaryotes. Other types of edits such as point mutations and precise and pre-designed targeted sequence insertions have rarely been implemented, despite providing means to modulate the expression of target genes or to engineer the function and stability of their protein products. Several advancements have been developed in recent years to facilitate custom editing by regulation of repair pathway choices or by taking advantage of alternative types of DNA repair. We have seen the advent of novel gene editing tools that are independent of DNA double-strand break repair, and methods completely independent of host DNA repair processes are being increasingly explored. With the aim to provide a comprehensive review of the state-of-the-art methodology for allele replacement in plants, I discuss the adoption of these improvements for plant genome engineering.
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6
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Gomide MS, Sales TT, Barros LRC, Limia CG, de Oliveira MA, Florentino LH, Barros LMG, Robledo ML, José GPC, Almeida MSM, Lima RN, Rehen SK, Lacorte C, Melo EO, Murad AM, Bonamino MH, Coelho CM, Rech E. Genetic switches designed for eukaryotic cells and controlled by serine integrases. Commun Biol 2020; 3:255. [PMID: 32444777 PMCID: PMC7244727 DOI: 10.1038/s42003-020-0971-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 04/28/2020] [Indexed: 11/16/2022] Open
Abstract
Recently, new serine integrases have been identified, increasing the possibility of scaling up genomic modulation tools. Here, we describe the use of unidirectional genetic switches to evaluate the functionality of six serine integrases in different eukaryotic systems: the HEK 293T cell lineage, bovine fibroblasts and plant protoplasts. Moreover, integrase activity was also tested in human cell types of therapeutic interest: peripheral blood mononuclear cells (PBMCs), neural stem cells (NSCs) and undifferentiated embryonic stem (ES) cells. The switches were composed of plasmids designed to flip two different genetic parts driven by serine integrases. Cell-based assays were evaluated by measurement of EGFP fluorescence and by molecular analysis of attL/attR sites formation after integrase functionality. Our results demonstrate that all the integrases were capable of inverting the targeted DNA sequences, exhibiting distinct performances based on the cell type or the switchable genetic sequence. These results should support the development of tunable genetic circuits to regulate eukaryotic gene expression.
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Affiliation(s)
- Mayna S Gomide
- Brazilian Agriculture Research Corporation - Embrapa - Genetic Resources and Biotechnology - CENARGEN, Brasília, 70770917, DF, Brazil
- Department of Cell Biology, Institute of Biological Science, University of Brasília, Brasília, 70910900, DF, Brazil
- School of Medicine, Federal University of Juiz de Fora, Juiz de Fora, 36036900, MG, Brazil
| | - Thais T Sales
- Brazilian Agriculture Research Corporation - Embrapa - Genetic Resources and Biotechnology - CENARGEN, Brasília, 70770917, DF, Brazil
- Department of Cell Biology, Institute of Biological Science, University of Brasília, Brasília, 70910900, DF, Brazil
| | - Luciana R C Barros
- Molecular Carcinogenesis Program, Research Coordination, National Cancer Institute (INCA), Rio de Janeiro, 20231050, RJ, Brazil
| | - Cintia G Limia
- Molecular Carcinogenesis Program, Research Coordination, National Cancer Institute (INCA), Rio de Janeiro, 20231050, RJ, Brazil
| | - Marco A de Oliveira
- Brazilian Agriculture Research Corporation - Embrapa - Genetic Resources and Biotechnology - CENARGEN, Brasília, 70770917, DF, Brazil
- Department of Cell Biology, Institute of Biological Science, University of Brasília, Brasília, 70910900, DF, Brazil
| | - Lilian H Florentino
- Brazilian Agriculture Research Corporation - Embrapa - Genetic Resources and Biotechnology - CENARGEN, Brasília, 70770917, DF, Brazil
| | - Leila M G Barros
- Brazilian Agriculture Research Corporation - Embrapa - Genetic Resources and Biotechnology - CENARGEN, Brasília, 70770917, DF, Brazil
| | - Maria L Robledo
- Molecular Carcinogenesis Program, Research Coordination, National Cancer Institute (INCA), Rio de Janeiro, 20231050, RJ, Brazil
| | - Gustavo P C José
- Brazilian Agriculture Research Corporation - Embrapa - Genetic Resources and Biotechnology - CENARGEN, Brasília, 70770917, DF, Brazil
| | - Mariana S M Almeida
- Brazilian Agriculture Research Corporation - Embrapa - Genetic Resources and Biotechnology - CENARGEN, Brasília, 70770917, DF, Brazil
| | - Rayane N Lima
- Brazilian Agriculture Research Corporation - Embrapa - Genetic Resources and Biotechnology - CENARGEN, Brasília, 70770917, DF, Brazil
| | - Stevens K Rehen
- D'Or Institute for Research and Education (IDOR), Rio de Janeiro, 22281100, RJ, Brazil
- Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, 21941902, RJ, Brazil
| | - Cristiano Lacorte
- Brazilian Agriculture Research Corporation - Embrapa - Genetic Resources and Biotechnology - CENARGEN, Brasília, 70770917, DF, Brazil
| | - Eduardo O Melo
- Brazilian Agriculture Research Corporation - Embrapa - Genetic Resources and Biotechnology - CENARGEN, Brasília, 70770917, DF, Brazil
- Graduation Program in Biotechnology, Federal University of Tocantins, Gurupi, 77402970, TO, Brazil
| | - André M Murad
- Brazilian Agriculture Research Corporation - Embrapa - Genetic Resources and Biotechnology - CENARGEN, Brasília, 70770917, DF, Brazil
| | - Martín H Bonamino
- Molecular Carcinogenesis Program, Research Coordination, National Cancer Institute (INCA), Rio de Janeiro, 20231050, RJ, Brazil.
- Vice-Presidency of Research and Biological Collections (VPPCB), FIOCRUZ - Oswaldo Cruz Foundation Institute, Rio de Janeiro, 21040900, RJ, Brazil.
| | - Cintia M Coelho
- Department of Genetic and Morphology, Institute of Biological Science, University of Brasília, Brasília, 70910900, DF, Brazil.
| | - Elibio Rech
- Brazilian Agriculture Research Corporation - Embrapa - Genetic Resources and Biotechnology - CENARGEN, Brasília, 70770917, DF, Brazil.
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7
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Leydon AR, Gala HP, Guiziou S, Nemhauser JL. Engineering Synthetic Signaling in Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:767-788. [PMID: 32092279 DOI: 10.1146/annurev-arplant-081519-035852] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Synthetic signaling is a branch of synthetic biology that aims to understand native genetic regulatory mechanisms and to use these insights to engineer interventions and devices that achieve specified design parameters. Applying synthetic signaling approaches to plants offers the promise of mitigating the worst effects of climate change and providing a means to engineer crops for entirely novel environments, such as those in space travel. The ability to engineer new traits using synthetic signaling methods will require standardized libraries of biological parts and methods to assemble them; the decoupling of complex processes into simpler subsystems; and mathematical models that can accelerate the design-build-test-learn cycle. The field of plant synthetic signaling is relatively new, but it is poised for rapid advancement. Translation from the laboratory to the field is likely to be slowed, however, by the lack of constructive dialogue between researchers and other stakeholders.
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Affiliation(s)
- Alexander R Leydon
- Department of Biology, University of Washington, Seattle, Washington 98195, USA; , , ,
| | - Hardik P Gala
- Department of Biology, University of Washington, Seattle, Washington 98195, USA; , , ,
| | - Sarah Guiziou
- Department of Biology, University of Washington, Seattle, Washington 98195, USA; , , ,
| | - Jennifer L Nemhauser
- Department of Biology, University of Washington, Seattle, Washington 98195, USA; , , ,
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8
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Markina NM, Kotlobay AA, Tsarkova AS. Heterologous Metabolic Pathways: Strategies for Optimal Expression in Eukaryotic Hosts. Acta Naturae 2020; 12:28-39. [PMID: 32742725 PMCID: PMC7385092 DOI: 10.32607/actanaturae.10966] [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: 04/15/2020] [Accepted: 04/29/2020] [Indexed: 11/20/2022] Open
Abstract
Heterologous pathways are linked series of biochemical reactions occurring in a host organism after the introduction of foreign genes. Incorporation of metabolic pathways into host organisms is a major strategy used to increase the production of valuable secondary metabolites. Unfortunately, simple introduction of the pathway genes into the heterologous host in most cases does not result in successful heterologous expression. Extensive modification of heterologous genes and the corresponding enzymes on many different levels is required to achieve high target metabolite production rates. This review summarizes the essential techniques used to create heterologous biochemical pathways, with a focus on the key challenges arising in the process and the major strategies for overcoming them.
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Affiliation(s)
- N. M. Markina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
- Planta LLC, Moscow, 121205 Russia
| | - A. A. Kotlobay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
| | - A. S. Tsarkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
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9
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Ruiz Y, Ramos PL, Soto J, Rodríguez M, Carlos N, Reyes A, Callard D, Sánchez Y, Pujol M, Fuentes A. The M4 insulator, the TM2 matrix attachment region, and the double copy of the heavy chain gene contribute to the enhanced accumulation of the PHB-01 antibody in tobacco plants. Transgenic Res 2020; 29:171-186. [PMID: 31919795 DOI: 10.1007/s11248-019-00187-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 12/31/2019] [Indexed: 11/24/2022]
Abstract
The expression of recombinant proteins in plants is a valuable alternative to bioreactors using mammalian cell systems. Ease of scaling, and their inability to host human pathogens, enhance the use of plants to generate complex therapeutic products such as monoclonal antibodies. However, stably transformed plants expressing antibodies normally have a poor accumulation of these proteins that probably arise from the negative positional effects of their flanking chromatin. The induction of boundaries between the transgenes and the surrounding DNA using matrix attachment regions (MAR) and insulator elements may minimize these effects. With the PHB-01 antibody as a model, we demonstrated that the insertion of DNA elements, the TM2 (MAR) and M4 insulator, flanking the transcriptional cassettes that encode the light and heavy chains of the PHB-01 antibody, increased the protein accumulation that remained stable in the first plant progeny. The M4 insulator had a stronger effect than the TM2, with over a twofold increase compared to the standard construction. This effect was probably associated with an enhancer-promoter interference. Moreover, transgenic plants harboring two transcriptional units encoding for the PHB-01 heavy chain combined with both TM2 and M4 elements enhanced the accumulation of the antibody. In summary, the M4 combined with a double transcriptional unit of the heavy chain may be a suitable strategy for potentiating PHB-01 production in tobacco plants.
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Affiliation(s)
- Yoslaine Ruiz
- Plant Biotechnology Department, Center for Genetic Engineering and Biotechnology, Cuba, Ave. 31/158 and 190, Playa, P.O. Box 6162, 10600, Havana, Cuba.
| | - Pedro Luis Ramos
- Plant Biotechnology Department, Center for Genetic Engineering and Biotechnology, Cuba, Ave. 31/158 and 190, Playa, P.O. Box 6162, 10600, Havana, Cuba
- Department of Phytopathology and Plant Biochemistry, Instituto Biologico, São Paulo, Brazil
| | - Jeny Soto
- Plant Biotechnology Department, Center for Genetic Engineering and Biotechnology, Cuba, Ave. 31/158 and 190, Playa, P.O. Box 6162, 10600, Havana, Cuba
- Comparative Pathology Department, University of Miami, Miami, USA
| | - Meilyn Rodríguez
- Plant Biotechnology Department, Center for Genetic Engineering and Biotechnology, Cuba, Ave. 31/158 and 190, Playa, P.O. Box 6162, 10600, Havana, Cuba
| | - Natacha Carlos
- Plant Biotechnology Department, Center for Genetic Engineering and Biotechnology, Cuba, Ave. 31/158 and 190, Playa, P.O. Box 6162, 10600, Havana, Cuba
| | - Aneisi Reyes
- Plant Biotechnology Department, Center for Genetic Engineering and Biotechnology, Cuba, Ave. 31/158 and 190, Playa, P.O. Box 6162, 10600, Havana, Cuba
| | - Danay Callard
- Plant Biotechnology Department, Center for Genetic Engineering and Biotechnology, Cuba, Ave. 31/158 and 190, Playa, P.O. Box 6162, 10600, Havana, Cuba
| | - Yadira Sánchez
- Plant Biotechnology Department, Center for Genetic Engineering and Biotechnology, Cuba, Ave. 31/158 and 190, Playa, P.O. Box 6162, 10600, Havana, Cuba
| | - Merardo Pujol
- Plant Biotechnology Department, Center for Genetic Engineering and Biotechnology, Cuba, Ave. 31/158 and 190, Playa, P.O. Box 6162, 10600, Havana, Cuba
| | - Alejandro Fuentes
- Plant Biotechnology Department, Center for Genetic Engineering and Biotechnology, Cuba, Ave. 31/158 and 190, Playa, P.O. Box 6162, 10600, Havana, Cuba.
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10
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Cody JP, Graham ND, Zhao C, Swyers NC, Birchler JA. Site-specific recombinase genome engineering toolkit in maize. PLANT DIRECT 2020; 4:e00209. [PMID: 32166212 PMCID: PMC7061458 DOI: 10.1002/pld3.209] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/08/2020] [Accepted: 02/18/2020] [Indexed: 05/20/2023]
Abstract
Site-specific recombinase enzymes function in heterologous cellular environments to initiate strand-switching reactions between unique DNA sequences termed recombinase binding sites. Depending on binding site position and orientation, reactions result in integrations, excisions, or inversions of targeted DNA sequences in a precise and predictable manner. Here, we established five different stable recombinase expression lines in maize through Agrobacterium-mediated transformation of T-DNA molecules that contain coding sequences for Cre, R, FLPe, phiC31 Integrase, and phiC31 excisionase. Through the bombardment of recombinase activated DsRed transient expression constructs, we have determined that all five recombinases are functional in maize plants. These recombinase expression lines could be utilized for a variety of genetic engineering applications, including selectable marker removal, targeted transgene integration into predetermined locations, and gene stacking.
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Affiliation(s)
- Jon P. Cody
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
| | | | - Changzeng Zhao
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
| | - Nathan C. Swyers
- Division of Biological SciencesUniversity of MissouriColumbiaMOUSA
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11
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Wang X, Deng Z, Liu T. Marker‐Free System Using Ribosomal Promoters Enhanced Xylose/Glucose Isomerase Production inStreptomyces rubiginosus. Biotechnol J 2019; 14:e1900114. [DOI: 10.1002/biot.201900114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/05/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Xiaojie Wang
- State Key Laboratory of Microbial Metabolism, School of Life Science and BiotechnologyShanghai Jiao Tong UniversityShanghai 200030 P. R. China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Science and BiotechnologyShanghai Jiao Tong UniversityShanghai 200030 P. R. China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan 430071 P. R. China
- Hubei Engineering Laboratory for Synthetic MicrobiologyWuhan Institute of BiotechnologyWuhan 430075 P. R. China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan 430071 P. R. China
- Hubei Engineering Laboratory for Synthetic MicrobiologyWuhan Institute of BiotechnologyWuhan 430075 P. R. China
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12
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Haussmann IU, Ustaoglu P, Brauer U, Hemani Y, Dix TC, Soller M. Plasmid-based gap-repair recombineered transgenes reveal a central role for introns in mutually exclusive alternative splicing in Down Syndrome Cell Adhesion Molecule exon 4. Nucleic Acids Res 2019; 47:1389-1403. [PMID: 30541104 PMCID: PMC6379703 DOI: 10.1093/nar/gky1254] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/22/2018] [Accepted: 12/03/2018] [Indexed: 12/18/2022] Open
Abstract
Alternative splicing is a key feature of human genes, yet studying its regulation is often complicated by large introns. The Down Syndrome Cell Adhesion Molecule (Dscam) gene from Drosophila is one of the most complex genes generating vast molecular diversity by mutually exclusive alternative splicing. To resolve how alternative splicing in Dscam is regulated, we first developed plasmid-based UAS reporter genes for the Dscam variable exon 4 cluster and show that its alternative splicing is recapitulated by GAL4-mediated expression in neurons. We then developed gap-repair recombineering to very efficiently manipulate these large reporter plasmids in Escherichia coli using restriction enzymes or sgRNA/Cas9 DNA scission to capitalize on the many benefits of plasmids in phiC31 integrase-mediated transgenesis. Using these novel tools, we show that inclusion of Dscam exon 4 variables differs little in development and individual flies, and is robustly determined by sequences harbored in variable exons. We further show that introns drive selection of both proximal and distal variable exons. Since exon 4 cluster introns lack conserved sequences that could mediate robust long-range base-pairing to bring exons into proximity for splicing, our data argue for a central role of introns in mutually exclusive alternative splicing of Dscam exon 4 cluster.
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Affiliation(s)
- Irmgard U Haussmann
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.,School of Life Science, CSELS, Coventry University, Coventry CV1 5FB, UK
| | - Pinar Ustaoglu
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Ulrike Brauer
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Yash Hemani
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Thomas C Dix
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Matthias Soller
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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13
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Sekhavati MH, Hosseini SM, Tahmoorespur M, Ghaedi K, Jafarpour F, Hajian M, Dormiani K, Nasr-Esfahani MH. PhiC31-based Site-Specific Transgenesis System for Production of Transgenic Bovine Embryos by Somatic Cell Nuclear Transfer and Intracytoplasmic Sperm Injection. CELL JOURNAL 2018; 20:98-107. [PMID: 29308625 PMCID: PMC5759686 DOI: 10.22074/cellj.2018.4385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 03/01/2017] [Indexed: 01/10/2023]
Abstract
OBJECTIVES The Streptomyces phage phiC31 integrase offers a sequence-specific method of transgenesis with a robust long-term gene expression. PhiC31 has been successfully developed in a variety of tissues and organs for purpose of in vivo gene therapy. The objective of the present experiment was to evaluate PhiC31-based site-specific transgenesis system for production of transgenic bovine embryos by somatic cell nuclear transfer and intracytoplasmic sperm injection. MATERIALS AND METHODS In this experimental study, the application of phiC31 integrase system was evaluated for generating transgenic bovine embryos by somatic cell nuclear transfer (SCNT) and sperm mediated gene transfer (SMGT) approaches. RESULTS PhiC31 integrase mRNA and protein was produced in vitro and their functionality was confirmed. Seven phiC31 recognizable bovine pseudo attachment sites of phage (attP) sites were considered for evaluation of site specific recombination. The accuracy of these sites was validated in phic31 targeted bovine fibroblasts using polymerase chain reaction (PCR) and sequencing. The efficiency and site-specificity of phiC31 integrase system was also confirmed in generated transgenic bovine embryo which successfully obtained using SCNT and SMGT technique. CONCLUSIONS The results showed that both SMGT and SCNT-derived embryos were enhanced green fluorescent protein (EGFP) positive and phiC31 integrase could recombine the reporter gene in a site specific manner. These results demonstrate that attP site can be used as a proper location to conduct site directed transgenesis in both mammalian cells and embryos in phiC31 integrase system when even combinaed to SCNT and intracytoplasmic sperm injection (ICSI) method.
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Affiliation(s)
| | - Sayed Morteza Hosseini
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | | | - Kamran Ghaedi
- Department of Biology, Facualty of Sciences, Uneversity of Isfahan, Isfahan, Iran
- Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Farnoosh Jafarpour
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Mehdi Hajian
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Kyanoosh Dormiani
- Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Mohammad Hossain Nasr-Esfahani
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.
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14
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Abstract
When constructing transgenic cell lines via plasmid DNA integration, precise targeting to a desired genomic location is advantageous. It is also often advantageous to remove the bacterial backbone, since bacterial elements can lead to the epigenetic silencing of neighboring DNA. The least cumbersome method to remove the plasmid backbone is recombinase-mediated cassette exchange (RMCE). RMCE is accomplished by arranging recombinase sites in the genome and in a donor plasmid such that a recombinase can both integrate the donor plasmid and excise its bacterial backbone. When a single recombinase is used for RMCE, recombination between undesired pairings of the sites can lead to a significant number of unwanted cell lines. To reduce the frequency with which these side products occur, several variants of RMCE that increase desired outcomes have been developed. Nevertheless, an important feature lacking from these improved RMCE methods is that none have fully utilized the recombinases that have been demonstrated to be the most robust and stringent at performing genomic integration in plants and animals, i.e., the phiC31 and Bxb1 phage integrases. To address this need, we have developed an RMCE protocol using these two serine integrases that we call dual integrase cassette exchange (DICE). Our DICE system provides a means to achieve high-precision DNA integration at a desired location and is especially well suited for repeated recombination into the same locus. In this chapter, we provide our most current protocols for using DICE in feeder-free human-induced pluripotent stem cells .
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Affiliation(s)
- Alfonso P Farruggio
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Alway Building, M316, Stanford, CA, 94305-5120, USA
| | - Mital S Bhakta
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Alway Building, M316, Stanford, CA, 94305-5120, USA
| | - Michele P Calos
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Alway Building, M316, Stanford, CA, 94305-5120, USA.
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15
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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: 15] [Impact Index Per Article: 1.9] [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.
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Affiliation(s)
- Vibha Srivastava
- Department of Crop, Soil & Environmental Science, University of Arkansas, Fayetteville, AR, USA
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16
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HAMZEH S, MOTALLEBI M, ZAMANI MR. Efficient seed-specifically regulated autoexcision of marker gene (nptII) with inducible expression of interest gene in transgenic Nicotiana tabacum. Turk J Biol 2016. [DOI: 10.3906/biy-1408-32] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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17
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Haghighat-Khah RE, Scaife S, Martins S, St John O, Matzen KJ, Morrison N, Alphey L. Site-specific cassette exchange systems in the Aedes aegypti mosquito and the Plutella xylostella moth. PLoS One 2015; 10:e0121097. [PMID: 25830287 PMCID: PMC4382291 DOI: 10.1371/journal.pone.0121097] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 02/09/2015] [Indexed: 12/02/2022] Open
Abstract
Genetically engineered insects are being evaluated as potential tools to decrease the economic and public health burden of mosquitoes and agricultural pest insects. Here we describe a new tool for the reliable and targeted genome manipulation of pest insects for research and field release using recombinase mediated cassette exchange (RMCE) mechanisms. We successfully demonstrated the established ΦC31-RMCE method in the yellow fever mosquito, Aedes aegypti, which is the first report of RMCE in mosquitoes. A new variant of this RMCE system, called iRMCE, combines the ΦC31-att integration system and Cre or FLP-mediated excision to remove extraneous sequences introduced as part of the site-specific integration process. Complete iRMCE was achieved in two important insect pests, Aedes aegypti and the diamondback moth, Plutella xylostella, demonstrating the transferability of the system across a wide phylogenetic range of insect pests.
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Affiliation(s)
- Roya Elaine Haghighat-Khah
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Oxitec Limited, Oxford, United Kingdom
| | | | - Sara Martins
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Oxitec Limited, Oxford, United Kingdom
| | - Oliver St John
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Oxitec Limited, Oxford, United Kingdom
| | | | | | - Luke Alphey
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Oxitec Limited, Oxford, United Kingdom
- * E-mail: (LA); (KJM)
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18
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Fogg PCM, Colloms S, Rosser S, Stark M, Smith MCM. New applications for phage integrases. J Mol Biol 2014; 426:2703-16. [PMID: 24857859 PMCID: PMC4111918 DOI: 10.1016/j.jmb.2014.05.014] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/09/2014] [Accepted: 05/16/2014] [Indexed: 11/28/2022]
Abstract
Within the last 25 years, bacteriophage integrases have rapidly risen to prominence as genetic tools for a wide range of applications from basic cloning to genome engineering. Serine integrases such as that from ϕC31 and its relatives have found an especially wide range of applications within diverse micro-organisms right through to multi-cellular eukaryotes. Here, we review the mechanisms of the two major families of integrases, the tyrosine and serine integrases, and the advantages and disadvantages of each type as they are applied in genome engineering and synthetic biology. In particular, we focus on the new areas of metabolic pathway construction and optimization, biocomputing, heterologous expression and multiplexed assembly techniques. Integrases are versatile and efficient tools that can be used in conjunction with the various extant molecular biology tools to streamline the synthetic biology production line. Phage integrases are site-specific recombinases that mediate controlled and precise DNA integration and excision. The serine integrases, such as ϕC31 integrase, can be used for efficient recombination in heterologous hosts as they use short recombination substrates, they are directional and they do not require host factors. Both serine and tyrosine integrases, such as λ integrase, are versatile tools for DNA cloning and assembly in vivo and in vitro. Controlled expression of orthologous serine integrases and their cognate recombination directionality factors can be used to generate living biocomputers. Serine integrases are increasingly being exploited for synthetic biology applications.
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Affiliation(s)
- Paul C M Fogg
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Sean Colloms
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Bower Building, Glasgow G12 8QQ, UK
| | - Susan Rosser
- School of Biological Sciences, University of Edinburgh, King's Building, Edinburgh EH9 3JR, UK
| | - Marshall Stark
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Bower Building, Glasgow G12 8QQ, UK
| | - Margaret C M Smith
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK.
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19
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20
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Shao M, Kumar S, Thomson JG. Precise excision of plastid DNA by the large serine recombinase Bxb1. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:322-9. [PMID: 24261912 DOI: 10.1111/pbi.12139] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 09/12/2013] [Accepted: 10/03/2013] [Indexed: 05/08/2023]
Abstract
Marker genes are essential for the selection and identification of rarely occurring transformation events generated in biotechnology. This includes plastid transformation, which requires that multiple copies of the modified chloroplast genome be present to obtain genetically stable transplastomic plants. However, the marker gene becomes dispensable when homoplastomic plants are obtained. Here, we demonstrate the precise excision of attP- and attB-flanked DNA from the plastid genome mediated by the large serine recombinase Bxb1. We transformed the tobacco plastid genome with the pTCH-PB vector containing a stuffer fragment of DNA flanked by directly oriented nonhomologous attP and attB recombinase recognition sites. In the absence of the Bxb1 recombinase, the transformed plastid genomes were stable and heritable. Nuclear-transformed transgenic tobacco plants expressing a plastid-targeted Bxb1 recombinase were crossed with transplastomic pTCH-PB plants, and the T₁ hybrids exhibited efficient excision of the target sequence. The Bxb1-att system should prove to be a useful tool for site-specifically manipulating the plastid genome and generating marker-free transplastomic plants.
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Affiliation(s)
- Min Shao
- Department of Plant Sciences, UC Davis, Davis, CA, USA
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21
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Long D, Zhao A, Xu L, Lu W, Guo Q, Zhang Y, Xiang Z. In vivo site-specific integration of transgene in silkworm via PhiC31 integrase-mediated cassette exchange. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2013; 43:997-1008. [PMID: 23974010 DOI: 10.1016/j.ibmb.2013.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 07/24/2013] [Accepted: 08/07/2013] [Indexed: 06/02/2023]
Abstract
Current techniques for genetic engineering of the silkworm Bombyx mori genome utilize transposable elements, which result in positional effects and insertional mutagenesis through random insertion of exogenous DNA. New methods for introducing transgenes at specific positions are therefore needed to overcome the limitations of transposon-based strategies. Although site-specific recombination systems have proven powerful tools for genome manipulation in many organisms, their use has not yet been well established for the integration of transgenes in the silkworm. We describe a method for integrating target genes at pre-defined chromosomal sites in the silkworm via phiC31/att site-specific recombination system-mediated cassette exchange. Successful recombinase-mediated cassette exchange (RMCE) was observed in the two transgenic target strains with an estimated transformation efficiency of 3.84-7.01%. Our results suggest that RMCE events between chromosomal attP/attP target sites and incoming attB/attB sites were more frequent than those in the reciprocal direction. This is the first report of in vivo RMCE via phiC31 integrase in the silkworm, and thus represents a key step toward establishing genome manipulation technologies in silkworms and other lepidopteran species.
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Affiliation(s)
- Dingpei Long
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, BeiBei, Chongqing 400716, China
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22
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Magnusdottir A, Vidarsson H, Björnsson JM, Örvar BL. Barley grains for the production of endotoxin-free growth factors. Trends Biotechnol 2013; 31:572-80. [DOI: 10.1016/j.tibtech.2013.06.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 06/11/2013] [Accepted: 06/12/2013] [Indexed: 02/07/2023]
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23
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Kirchmaier S, Höckendorf B, Möller EK, Bornhorst D, Spitz F, Wittbrodt J. Efficient site-specific transgenesis and enhancer activity tests in medaka using PhiC31 integrase. Development 2013; 140:4287-95. [PMID: 24048591 PMCID: PMC3809364 DOI: 10.1242/dev.096081] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Established transgenesis methods for fish model systems allow efficient genomic integration of transgenes. However, thus far a way of controlling copy number and integration sites has not been available, leading to variable transgene expression caused by position effects. The integration of transgenes at predefined genomic positions enables the direct comparison of different transgenes, thereby improving time and cost efficiency. Here, we report an efficient PhiC31-based site-specific transgenesis system for medaka. This system includes features that allow the pre-selection of successfully targeted integrations early on in the injected generation. Pre-selected embryos transmit the correctly integrated transgene through the germline with high efficiency. The landing site design enables a variety of applications, such as reporter and enhancer switch, in addition to the integration of any insert. Importantly, this allows assaying of enhancer activity in a site-specific manner without requiring germline transmission, thus speeding up large-scale analyses of regulatory elements.
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Affiliation(s)
- Stephan Kirchmaier
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
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24
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De Paepe A, De Buck S, Nolf J, Van Lerberge E, Depicker A. Site-specific T-DNA integration in Arabidopsis thaliana mediated by the combined action of CRE recombinase and ϕC31 integrase. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 75:172-184. [PMID: 23574114 DOI: 10.1111/tpj.12202] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 04/04/2013] [Accepted: 04/08/2013] [Indexed: 06/02/2023]
Abstract
Random T-DNA integration into the plant host genome can be problematic for a variety of reasons, including potentially variable transgene expression as a result of different integration positions and multiple T-DNA copies, the risk of mutating the host genome and the difficulty of stacking well-defined traits. Therefore, recombination systems have been proposed to integrate the T-DNA at a pre-selected site in the host genome. Here, we demonstrate the capacity of the ϕC31 integrase (INT) for efficient targeted T-DNA integration. Moreover, we show that the iterative site-specific integration system (ISSI), which combines the activities of the CRE recombinase and INT, enables the targeting of genes to a pre-selected site with the concomitant removal of the resident selectable marker. To begin, plants expressing both the CRE and INT recombinase and containing the target attP site were constructed. These plants were supertransformed with a T-DNA vector harboring the loxP site, the attB sites, a selectable marker and an expression cassette encoding a reporter protein. Three out of the 35 transformants obtained (9%) showed transgenerational site-specific integration (SSI) of this T-DNA and removal of the resident selectable marker, as demonstrated by PCR, Southern blot and segregation analysis. In conclusion, our results show the applicability of the ISSI system for precise and targeted Agrobacterium-mediated integration, allowing the serial integration of transgenic DNA sequences in plants.
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Affiliation(s)
- Annelies De Paepe
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Sylvie De Buck
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Jonah Nolf
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Els Van Lerberge
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Ann Depicker
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
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