1
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Van Duyne GD, Landy A. Bacteriophage lambda site-specific recombination. Mol Microbiol 2024; 121:895-911. [PMID: 38372210 PMCID: PMC11096046 DOI: 10.1111/mmi.15241] [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: 08/29/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/20/2024]
Abstract
The site-specific recombination pathway of bacteriophage λ encompasses isoenergetic but highly directional and tightly regulated integrative and excisive reactions that integrate and excise the vial chromosome into and out of the bacterial chromosome. The reactions require 240 bp of phage DNA and 21 bp of bacterial DNA comprising 16 protein binding sites that are differentially used in each pathway by the phage-encoded Int and Xis proteins and the host-encoded integration host factor and factor for inversion stimulation proteins. Structures of higher-order protein-DNA complexes of the four-way Holliday junction recombination intermediates provided clarifying insights into the mechanisms, directionality, and regulation of these two pathways, which are tightly linked to the physiology of the bacterial host cell. Here we review our current understanding of the mechanisms responsible for regulating and executing λ site-specific recombination, with an emphasis on key studies completed over the last decade.
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Affiliation(s)
- Gregory D Van Duyne
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Arthur Landy
- Department of Molecular Biology, Cell Biology, and Biochemistry, Warren Alpert Medical School, Brown University, Providence, Rhode Island, USA
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2
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Sun C, Lei Y, Li B, Gao Q, Li Y, Cao W, Yang C, Li H, Wang Z, Li Y, Wang Y, Liu J, Zhao KT, Gao C. Precise integration of large DNA sequences in plant genomes using PrimeRoot editors. Nat Biotechnol 2024; 42:316-327. [PMID: 37095350 DOI: 10.1038/s41587-023-01769-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/28/2023] [Indexed: 04/26/2023]
Abstract
A technique for chromosomal insertion of large DNA segments is much needed in plant breeding and synthetic biology to facilitate the introduction of desired agronomic traits and signaling and metabolic pathways. Here we describe PrimeRoot, a genome editing approach to generate targeted precise large DNA insertions in plants. Third-generation PrimeRoot editors employ optimized prime editing guide RNA designs, an enhanced plant prime editor and superior recombinases to enable precise large DNA insertions of up to 11.1 kilobases into plant genomes. We demonstrate the use of PrimeRoot to accurately introduce gene regulatory elements in rice. In this study, we also integrated a gene cassette comprising PigmR, which confers rice blast resistance driven by an Act1 promoter, into a predicted genomic safe harbor site of Kitaake rice and obtain edited plants harboring the expected insertion with an efficiency of 6.3%. We found that these rice plants have increased blast resistance. These results establish PrimeRoot as a promising approach to precisely insert large segments of DNA in plants.
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Affiliation(s)
- Chao Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuan Lei
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Boshu Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qiang Gao
- Qi Biodesign, Life Science Park, Beijing, China
| | - Yunjia Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wen Cao
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory for Monitoring and Green Management of Crop Pests, China Agricultural University, Beijing, China
| | - Chao Yang
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory for Monitoring and Green Management of Crop Pests, China Agricultural University, Beijing, China
| | - Hongchao Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Zhiwei Wang
- Qi Biodesign, Life Science Park, Beijing, China
| | - Yan Li
- Qi Biodesign, Life Science Park, Beijing, China
| | - Yanpeng Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jun Liu
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory for Monitoring and Green Management of Crop Pests, China Agricultural University, Beijing, China
| | | | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
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3
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Tkachenko AA, Borshchevskaya LN, Sineoky SP, Gordeeva TL. CRISPR/Cas9-Mediated Genome Editing of the Komagataella phaffii to Obtain a Phytase-Producer Markerless Strain. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1338-1346. [PMID: 37770400 DOI: 10.1134/s0006297923090134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 04/19/2023] [Accepted: 05/19/2023] [Indexed: 09/30/2023]
Abstract
Using CRISPR/Cas9 system, the recipient strains K. phaffii VKPM Y-5013 (His- phenotype) and K. phaffii VKPM Y-5014 (Leu- phenotype) were derived from the K. phaffii VKPM Y-4287 strain, which has a high expression potential. Based on the developed recipient strains, markerless producers of heterologous proteins could be obtained. Efficiency of the gene inactivation with different variants of sgRNA ranged from 65 to 98% and from 15 to 72% for the HIS4 and LEU2 genes, respectively. The recipient strains retained growth characteristics of the parent strain and exhibited high expression potential, as estimated by the production of heterologous phytase from Citrobacter gillenii. Average productivity of the transformants based on the K. phaffii VKPM Y-5013 and K. phaffii VKPM Y-5014 strains was 2.1 and 2.0 times higher than productivity of the transformants of the commercial K. phaffii GS115 strain. Method for sequential integration of genetic material into genome of the K. phaffii VKPM Y-5013 strain was proposed. A highly effective multicopy markerless strain producing C. gillenii phytase was obtained.
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Affiliation(s)
- Artur A Tkachenko
- National Research Center "Kurchatov Institute", Moscow, 117545, Russia.
| | | | - Sergey P Sineoky
- National Research Center "Kurchatov Institute", Moscow, 117545, Russia
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4
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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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5
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Abstract
The advent of clustered regularly interspaced short palindromic repeat (CRISPR) genome editing, coupled with advances in computing and imaging capabilities, has initiated a new era in which genetic diseases and individual disease susceptibilities are both predictable and actionable. Likewise, genes responsible for plant traits can be identified and altered quickly, transforming the pace of agricultural research and plant breeding. In this Review, we discuss the current state of CRISPR-mediated genetic manipulation in human cells, animals, and plants along with relevant successes and challenges and present a roadmap for the future of this technology.
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Affiliation(s)
- Joy Y Wang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Jennifer A Doudna
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA.,Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA.,Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
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6
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Zhang Q, Azarin SM, Sarkar CA. Model-guided engineering of DNA sequences with predictable site-specific recombination rates. Nat Commun 2022; 13:4152. [PMID: 35858965 PMCID: PMC9300676 DOI: 10.1038/s41467-022-31538-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 06/22/2022] [Indexed: 11/09/2022] Open
Abstract
Site-specific recombination (SSR) is an important tool in synthetic biology, but its applications are limited by the inability to predictably tune SSR reaction rates. Facile rate manipulation could be achieved by modifying the DNA substrate sequence; however, this approach lacks rational design principles. Here, we develop an integrated experimental and computational method to engineer the DNA attachment sequence attP for predictably modulating the inversion reaction mediated by the recombinase Bxb1. After developing a qPCR method to measure SSR reaction rate, we design, select, and sequence attP libraries to inform a machine-learning model that computes Bxb1 inversion rate as a function of attP sequence. We use this model to predict reaction rates of attP variants in vitro and demonstrate their utility in gene circuit design in Escherichia coli. Our high-throughput, model-guided approach for rationally tuning SSR reaction rates enhances our understanding of recombinase function and expands the synthetic biology toolbox.
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Affiliation(s)
- Qiuge Zhang
- grid.17635.360000000419368657Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455 USA
| | - Samira M. Azarin
- grid.17635.360000000419368657Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455 USA
| | - Casim A. Sarkar
- grid.17635.360000000419368657Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455 USA
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7
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Ganguly J, Martin-Pascual M, Montiel González D, Bulut A, Vermeulen B, Tjalma I, Vidaki A, van Kranenburg R. Breaking the Restriction Barriers and Applying CRISPRi as a Gene Silencing Tool in Pseudoclostridium thermosuccinogenes. Microorganisms 2022; 10:microorganisms10040698. [PMID: 35456750 PMCID: PMC9044749 DOI: 10.3390/microorganisms10040698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 12/10/2022] Open
Abstract
Pseudoclostridium thermosuccinogenes is a thermophilic bacterium capable of producing succinate from lignocellulosic-derived sugars and has the potential to be exploited as a platform organism. However, exploitation of P. thermosuccinogenes has been limited partly due to the genetic inaccessibility and lack of genome engineering tools. In this study, we established the genetic accessibility for P. thermosuccinogenes DSM 5809. By overcoming restriction barriers, transformation efficiencies of 102 CFU/µg plasmid DNA were achieved. To this end, the plasmid DNA was methylated in vivo when transformed into an engineered E. coli HST04 strain expressing three native methylation systems of the thermophile. This protocol was used to introduce a ThermodCas9-based CRISPRi tool targeting the gene encoding malic enzyme in P. thermosuccinogenes, demonstrating the principle of gene silencing. This resulted in 75% downregulation of its expression and had an impact on the strain’s fermentation profile. Although the details of the functioning of the restriction modification systems require further study, in vivo methylation can already be applied to improve transformation efficiency of P. thermosuccinogenes. Making use of the ThermodCas9-based CRISPRi, this is the first example demonstrating that genetic engineering in P. thermosuccinogenes is feasible and establishing the way for metabolic engineering of this bacterium.
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Affiliation(s)
| | - Maria Martin-Pascual
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands; (M.M.-P.); (B.V.); (I.T.)
| | - Diego Montiel González
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands; (D.M.G.); (A.V.)
| | - Alkan Bulut
- Fontys University of Applied Sciences, 5612 AR Eindhoven, The Netherlands;
| | - Bram Vermeulen
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands; (M.M.-P.); (B.V.); (I.T.)
| | - Ivo Tjalma
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands; (M.M.-P.); (B.V.); (I.T.)
| | - Athina Vidaki
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands; (D.M.G.); (A.V.)
| | - Richard van Kranenburg
- Corbion, 4206 AC Gorinchem, The Netherlands;
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands; (M.M.-P.); (B.V.); (I.T.)
- Correspondence:
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8
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Shen Y, Luchetti A, Fernandes G, Do Heo W, Silva AJ. The emergence of molecular systems neuroscience. Mol Brain 2022; 15:7. [PMID: 34983613 PMCID: PMC8728933 DOI: 10.1186/s13041-021-00885-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/03/2021] [Indexed: 12/18/2022] Open
Abstract
Systems neuroscience is focused on how ensemble properties in the brain, such as the activity of neuronal circuits, gives rise to internal brain states and behavior. Many of the studies in this field have traditionally involved electrophysiological recordings and computational approaches that attempt to decode how the brain transforms inputs into functional outputs. More recently, systems neuroscience has received an infusion of approaches and techniques that allow the manipulation (e.g., optogenetics, chemogenetics) and imaging (e.g., two-photon imaging, head mounted fluorescent microscopes) of neurons, neurocircuits, their inputs and outputs. Here, we will review novel approaches that allow the manipulation and imaging of specific molecular mechanisms in specific cells (not just neurons), cell ensembles and brain regions. These molecular approaches, with the specificity and temporal resolution appropriate for systems studies, promise to infuse the field with novel ideas, emphases and directions, and are motivating the emergence of a molecularly oriented systems neuroscience, a new discipline that studies how the spatial and temporal patterns of molecular systems modulate circuits and brain networks, and consequently shape the properties of brain states and behavior.
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Affiliation(s)
- Yang Shen
- Departments of Neurobiology, Psychiatry and Biobehavioral Sciences, and Psychology, Integrative Center for Learning and Memory, and Brain Research Institute, UCLA, Los Angeles, CA, USA
| | - Alessandro Luchetti
- Departments of Neurobiology, Psychiatry and Biobehavioral Sciences, and Psychology, Integrative Center for Learning and Memory, and Brain Research Institute, UCLA, Los Angeles, CA, USA
| | - Giselle Fernandes
- Departments of Neurobiology, Psychiatry and Biobehavioral Sciences, and Psychology, Integrative Center for Learning and Memory, and Brain Research Institute, UCLA, Los Angeles, CA, USA
| | - Won Do Heo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Alcino J Silva
- Departments of Neurobiology, Psychiatry and Biobehavioral Sciences, and Psychology, Integrative Center for Learning and Memory, and Brain Research Institute, UCLA, Los Angeles, CA, USA.
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9
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Chao G, Travis C, Church G. Measurement of large serine integrase enzymatic characteristics in HEK293 cells reveals variability and influence on downstream reporter expression. FEBS J 2021; 288:6410-6427. [PMID: 34043859 DOI: 10.1111/febs.16037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/20/2021] [Accepted: 05/25/2021] [Indexed: 11/30/2022]
Abstract
Large serine integrases (LSIs) offer tremendous potential for rapid genetic engineering as well as building biological systems capable of responding to stimuli and integrating information. Currently, there is no unified metric for directly measuring the enzymatic characteristics of LSI function, which hinders evaluation of their suitability to specific applications. Here, we present an experimental protocol for recording DNA recombination in HEK293 cells in real-time through fluorophore expression and software which fits the kinetic data to a model tailored to LSI recombination dynamics. Our model captures the activity of LSIs as three parameters: expression level (Kexp ), catalytic rate (kcat ), and substrate affinity (Kd ). The expression level and catalytic rate for phiC31 and Bxb1 varied greatly, suggesting disparate routes to high recombination efficiencies. Moreover, the expression level and substrate affinity jointly impacted downstream reporter expression, potentially by obstructing transcriptional machinery. We validated these observations by swapping between promoters and mutating key recombinase residues and DNA recognition sites to individually modulate each parameter. Our model for identifying key LSI parameters in cellulo provides insight into selecting the optimal recombinase for various applications as well as for guiding the engineering of improved LSIs.
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Affiliation(s)
- George Chao
- Genetics Department, Harvard Medical School, Boston, MA, USA
| | - Clair Travis
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - George Church
- Genetics Department, Harvard Medical School, Boston, MA, USA
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10
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Abe K, Takahashi T, Sato T. Extreme C-terminal element of SprA serine integrase is a potential component of the "molecular toggle switch" which controls the recombination and its directionality. Mol Microbiol 2020; 115:1110-1121. [PMID: 33244797 DOI: 10.1111/mmi.14654] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 10/26/2020] [Accepted: 11/21/2020] [Indexed: 12/11/2022]
Abstract
In Bacillus subtilis, a sporulation-related gene, spsM, is disrupted by SPβ prophage, but reconstituted during sporulation through SPβ excision. The spsM reconstitution is catalyzed by a site-specific DNA recombinase, SprA, and its cognate recombination directionality factor, SprB. SprB interacts with SprA, directing the SprA-mediated recombination reaction from integration to excision; however, the details of the directionality control remains unclear. Here, we demonstrate the importance of the extreme C-terminal region (ECT) of SprA in the DNA recombination and directionality control. We created a series of SprA C-terminal deletants and examined their DNA-binding and recombination activities. Deletions in the ECT caused a loss of integration and excision activity, the magnitudes of which positively correlated with the deletion size. Gel shift study revealed that the loss of the integration activity was attributable to the failure of synaptic complex formation. The excision deficiency was caused by defective interaction with SprB. Moreover, alanine scanning analysis revealed that Phe532 is essential to interact with SprB. SprAF532A , therefore, showed almost no excision activity, while retaining the integration activity. Collectively, these results suggest that the ECT plays the crucial roles in the interaction of SprA with SprB and possibly in the directional control of the recombination.
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Affiliation(s)
- Kimihiro Abe
- Research Center of Micro-Nano Technology, Hosei University, Koganei, Japan
| | - Takumi Takahashi
- Department of Frontier Bioscience, Hosei University, Koganei, Japan
| | - Tsutomu Sato
- Research Center of Micro-Nano Technology, Hosei University, Koganei, Japan.,Department of Frontier Bioscience, Hosei University, Koganei, Japan
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11
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Yang X, Medford JI, Markel K, Shih PM, De Paoli HC, Trinh CT, McCormick AJ, Ployet R, Hussey SG, Myburg AA, Jensen PE, Hassan MM, Zhang J, Muchero W, Kalluri UC, Yin H, Zhuo R, Abraham PE, Chen JG, Weston DJ, Yang Y, Liu D, Li Y, Labbe J, Yang B, Lee JH, Cottingham RW, Martin S, Lu M, Tschaplinski TJ, Yuan G, Lu H, Ranjan P, Mitchell JC, Wullschleger SD, Tuskan GA. Plant Biosystems Design Research Roadmap 1.0. BIODESIGN RESEARCH 2020; 2020:8051764. [PMID: 37849899 PMCID: PMC10521729 DOI: 10.34133/2020/8051764] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 10/30/2020] [Indexed: 10/19/2023] Open
Abstract
Human life intimately depends on plants for food, biomaterials, health, energy, and a sustainable environment. Various plants have been genetically improved mostly through breeding, along with limited modification via genetic engineering, yet they are still not able to meet the ever-increasing needs, in terms of both quantity and quality, resulting from the rapid increase in world population and expected standards of living. A step change that may address these challenges would be to expand the potential of plants using biosystems design approaches. This represents a shift in plant science research from relatively simple trial-and-error approaches to innovative strategies based on predictive models of biological systems. Plant biosystems design seeks to accelerate plant genetic improvement using genome editing and genetic circuit engineering or create novel plant systems through de novo synthesis of plant genomes. From this perspective, we present a comprehensive roadmap of plant biosystems design covering theories, principles, and technical methods, along with potential applications in basic and applied plant biology research. We highlight current challenges, future opportunities, and research priorities, along with a framework for international collaboration, towards rapid advancement of this emerging interdisciplinary area of research. Finally, we discuss the importance of social responsibility in utilizing plant biosystems design and suggest strategies for improving public perception, trust, and acceptance.
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Affiliation(s)
- Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - June I. Medford
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Kasey Markel
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
| | - Patrick M. Shih
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
| | - Henrique C. De Paoli
- Department of Biodesign, Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Cong T. Trinh
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Alistair J. McCormick
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Raphael Ployet
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Steven G. Hussey
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Alexander A. Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Poul Erik Jensen
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, DK-1858, Frederiksberg, Copenhagen, Denmark
| | - Md Mahmudul Hassan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin Zhang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Udaya C. Kalluri
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Hengfu Yin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Renying Zhuo
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Paul E. Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - David J. Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Yinong Yang
- Department of Plant Pathology and Environmental Microbiology and the Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Degao Liu
- Department of Genetics, Cell Biology and Development, Center for Precision Plant Genomics and Center for Genome Engineering, University of Minnesota, Saint Paul, MN 55108, USA
| | - Yi Li
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT 06269, USA
| | - Jessy Labbe
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Bing Yang
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Jun Hyung Lee
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | | | - Stanton Martin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Mengzhu Lu
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Haiwei Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Priya Ranjan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Julie C. Mitchell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Stan D. Wullschleger
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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12
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Site-Specific Recombination with Inverted Target Sites: A Cautionary Tale of Dicentric and Acentric Chromosomes. Genetics 2020; 215:923-930. [PMID: 32586890 DOI: 10.1534/genetics.120.303394] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 06/22/2020] [Indexed: 11/18/2022] Open
Abstract
Site-specific recombinases are widely used tools for analysis of genetics, development, and cell biology, and many schemes have been devised to alter gene expression by recombinase-mediated DNA rearrangements. Because the FRT and lox target sites for the commonly used FLP and Cre recombinases are asymmetrical, and must pair in the same direction to recombine, construct design must take into account orientation of the target sites. Both direct and inverted configurations have been used. However, the outcome of recombination between target sites on sister chromatids is frequently overlooked. This is especially consequential with inverted target sites, where exchange between oppositely oriented target sites on sisters will produce dicentric and acentric chromosomes. By using constructs that have inverted target sites in Drosophila melanogaster and in mice, we show here that dicentric chromosomes are produced in the presence of recombinase, and that the frequency of this event is quite high. The negative effects on cell viability and behavior can be significant, and should be considered when using such constructs.
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13
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Hotton SK, Kammerzell M, Chan R, Hernandez BT, Young HA, Tobias C, McKeon T, Brichta J, Thomson NJ, Thomson JG. Phenotypic Examination of Camelina sativa (L.) Crantz Accessions from the USDA-ARS National Genetics Resource Program. PLANTS (BASEL, SWITZERLAND) 2020; 9:E642. [PMID: 32438618 PMCID: PMC7286027 DOI: 10.3390/plants9050642] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/04/2020] [Accepted: 05/11/2020] [Indexed: 12/19/2022]
Abstract
Camelina sativa (L.) Crntz. is a hardy self-pollinated oilseed plant that belongs to the Brassicaceae family; widely grown throughout the northern hemisphere until the 1940s for production of vegetable oil but was later displaced by higher-yielding rapeseed and sunflower crops. However, interest in camelina as an alternative oil source has been renewed due to its high oil content that is rich in polyunsaturated fatty acids, antioxidants as well as its ability to grow on marginal lands with minimal requirements. For this reason, our group decided to screen the existing (2011) National Genetic Resources Program (NGRP) center collection of camelina for its genetic diversity and provide a phenotypic evaluation of the cultivars available. Properties evaluated include seed and oil traits, developmental and mature morphologies, as well as chromosome content. Selectable marker genes were also evaluated for potential use in biotech manipulation. Data is provided in a raw uncompiled format to allow other researchers to analyze the unbiased information for their own studies. Our evaluation has determined that the NGRP collection has a wide range of genetic potential for both breeding and biotechnological manipulation purposes. Accessions were identified within the NGRP collection that appear to have desirable seed harvest weight (5.06 g/plant) and oil content (44.1%). Other cultivars were identified as having fatty acid characteristics that may be suitable for meal and/or food use, such as low (<2%) erucic acid content, which is often considered for healthy consumption and ranged from a high of 4.79% to a low of 1.83%. Descriptive statistics are provided for a breadth of traits from 41 accessions, as well as raw data, and key seed traits are further explored. Data presented is available for public use.
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Affiliation(s)
| | | | - Ron Chan
- Crop Improvement and Genetics, USDA-ARS-WRRC, Albany, CA 94710, USA; (R.C.); (C.T.); (T.M.); (J.B.)
| | - Bryan T. Hernandez
- Department of Plant Sciences, University of California, Davis, CA 95616, USA;
| | | | - Christian Tobias
- Crop Improvement and Genetics, USDA-ARS-WRRC, Albany, CA 94710, USA; (R.C.); (C.T.); (T.M.); (J.B.)
| | - Thomas McKeon
- Crop Improvement and Genetics, USDA-ARS-WRRC, Albany, CA 94710, USA; (R.C.); (C.T.); (T.M.); (J.B.)
| | - Jenny Brichta
- Crop Improvement and Genetics, USDA-ARS-WRRC, Albany, CA 94710, USA; (R.C.); (C.T.); (T.M.); (J.B.)
| | | | - James G. Thomson
- Crop Improvement and Genetics, USDA-ARS-WRRC, Albany, CA 94710, USA; (R.C.); (C.T.); (T.M.); (J.B.)
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14
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Bernabé-Orts JM, Quijano-Rubio A, Vazquez-Vilar M, Mancheño-Bonillo J, Moles-Casas V, Selma S, Gianoglio S, Granell A, Orzaez D. A memory switch for plant synthetic biology based on the phage ϕC31 integration system. Nucleic Acids Res 2020; 48:3379-3394. [PMID: 32083668 PMCID: PMC7102980 DOI: 10.1093/nar/gkaa104] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 02/07/2020] [Accepted: 02/10/2020] [Indexed: 02/07/2023] Open
Abstract
Synthetic biology has advanced from the setup of basic genetic devices to the design of increasingly complex gene circuits to provide organisms with new functions. While many bacterial, fungal and mammalian unicellular chassis have been extensively engineered, this progress has been delayed in plants due to the lack of reliable DNA parts and devices that enable precise control over these new synthetic functions. In particular, memory switches based on DNA site-specific recombination have been the tool of choice to build long-term and stable synthetic memory in other organisms, because they enable a shift between two alternative states registering the information at the DNA level. Here we report a memory switch for whole plants based on the bacteriophage ϕC31 site-specific integrase. The switch was built as a modular device made of standard DNA parts, designed to control the transcriptional state (on or off) of two genes of interest by alternative inversion of a central DNA regulatory element. The state of the switch can be externally operated by action of the ϕC31 integrase (Int), and its recombination directionality factor (RDF). The kinetics, memory, and reversibility of the switch were extensively characterized in Nicotiana benthamiana plants.
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Affiliation(s)
- Joan Miquel Bernabé-Orts
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). CSIC - Universidad Politécnica de Valencia. Camino de Vera s/n, 46022 Valencia, Spain
| | - Alfredo Quijano-Rubio
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). CSIC - Universidad Politécnica de Valencia. Camino de Vera s/n, 46022 Valencia, Spain
| | - Marta Vazquez-Vilar
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). CSIC - Universidad Politécnica de Valencia. Camino de Vera s/n, 46022 Valencia, Spain
| | - Javier Mancheño-Bonillo
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). CSIC - Universidad Politécnica de Valencia. Camino de Vera s/n, 46022 Valencia, Spain
| | - Victor Moles-Casas
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). CSIC - Universidad Politécnica de Valencia. Camino de Vera s/n, 46022 Valencia, Spain
| | - Sara Selma
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). CSIC - Universidad Politécnica de Valencia. Camino de Vera s/n, 46022 Valencia, Spain
| | - Silvia Gianoglio
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). CSIC - Universidad Politécnica de Valencia. Camino de Vera s/n, 46022 Valencia, Spain
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). CSIC - Universidad Politécnica de Valencia. Camino de Vera s/n, 46022 Valencia, Spain
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). CSIC - Universidad Politécnica de Valencia. Camino de Vera s/n, 46022 Valencia, Spain
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15
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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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16
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Saleeba C, Dempsey B, Le S, Goodchild A, McMullan S. A Student's Guide to Neural Circuit Tracing. Front Neurosci 2019; 13:897. [PMID: 31507369 PMCID: PMC6718611 DOI: 10.3389/fnins.2019.00897] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/12/2019] [Indexed: 12/17/2022] Open
Abstract
The mammalian nervous system is comprised of a seemingly infinitely complex network of specialized synaptic connections that coordinate the flow of information through it. The field of connectomics seeks to map the structure that underlies brain function at resolutions that range from the ultrastructural, which examines the organization of individual synapses that impinge upon a neuron, to the macroscopic, which examines gross connectivity between large brain regions. At the mesoscopic level, distant and local connections between neuronal populations are identified, providing insights into circuit-level architecture. Although neural tract tracing techniques have been available to experimental neuroscientists for many decades, considerable methodological advances have been made in the last 20 years due to synergies between the fields of molecular biology, virology, microscopy, computer science and genetics. As a consequence, investigators now enjoy an unprecedented toolbox of reagents that can be directed against selected subpopulations of neurons to identify their efferent and afferent connectomes. Unfortunately, the intersectional nature of this progress presents newcomers to the field with a daunting array of technologies that have emerged from disciplines they may not be familiar with. This review outlines the current state of mesoscale connectomic approaches, from data collection to analysis, written for the novice to this field. A brief history of neuroanatomy is followed by an assessment of the techniques used by contemporary neuroscientists to resolve mesoscale organization, such as conventional and viral tracers, and methods of selecting for sub-populations of neurons. We consider some weaknesses and bottlenecks of the most widely used approaches for the analysis and dissemination of tracing data and explore the trajectories that rapidly developing neuroanatomy technologies are likely to take.
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Affiliation(s)
- Christine Saleeba
- Neurobiology of Vital Systems Node, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
- The School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, United Kingdom
| | - Bowen Dempsey
- CNRS, Hindbrain Integrative Neurobiology Laboratory, Neuroscience Paris-Saclay Institute (Neuro-PSI), Université Paris-Saclay, Gif-sur-Yvette, France
| | - Sheng Le
- Neurobiology of Vital Systems Node, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ann Goodchild
- Neurobiology of Vital Systems Node, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Simon McMullan
- Neurobiology of Vital Systems Node, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
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17
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McCue KF, Gardner E, Chan R, Thilmony R, Thomson J. Transgene stacking in potato using the GAANTRY system. BMC Res Notes 2019; 12:457. [PMID: 31345264 PMCID: PMC6659271 DOI: 10.1186/s13104-019-4493-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 07/17/2019] [Indexed: 01/12/2023] Open
Abstract
OBJECTIVE GAANTRY (Gene Assembly in Agrobacterium by Nucleic acid Transfer using Recombinase technologY) is a flexible and effective system for stably stacking multiple genes within an Agrobacterium virulence plasmid Transfer-DNA (T-DNA). We examined the ability of the GAANTRY Agrobacterium rhizogenes ArPORT1 '10-stack' strain to generate transgenic potato plants. RESULTS The 28.5 kilobase 10-stack T-DNA, was introduced into Lenape potato plants with a 32% transformation efficiency. Molecular and phenotypic characterization confirmed that six of the seven tested independent transgenic lines carried the entire desired construct, demonstrating that the GAANTRY 10-stack strain can be used can be used in a tissue culture-based callus transformation method to efficiently generate transgenic potato plants. Analysis using droplet digital PCR showed that most of the characterized events carry one or two copies of the 10-stack transgenes and that 'backbone' DNA from outside of the T-DNA was absent in the transgenic plants. These results demonstrate that the GAANTRY system efficiently generates high quality transgenic potato plants with a large construct of stacked transgenes.
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Affiliation(s)
- Kent F McCue
- Crop Improvement and Genetics, Western Regional Research Center, USDA-ARS, Albany, CA, USA
| | - Ethan Gardner
- Crop Improvement and Genetics, Western Regional Research Center, USDA-ARS, Albany, CA, USA
| | - Ronald Chan
- Crop Improvement and Genetics, Western Regional Research Center, USDA-ARS, Albany, CA, USA
| | - Roger Thilmony
- Crop Improvement and Genetics, Western Regional Research Center, USDA-ARS, Albany, CA, USA
| | - James Thomson
- Crop Improvement and Genetics, Western Regional Research Center, USDA-ARS, Albany, CA, USA.
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18
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Rozov SM, Deineko EV. Strategies for Optimizing Recombinant Protein Synthesis in Plant Cells: Classical Approaches and New Directions. Mol Biol 2019. [DOI: 10.1134/s0026893319020146] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Du D, Jin R, Guo J, Zhang F. Construction of Marker-Free Genetically Modified Maize Using a Heat-Inducible Auto-Excision Vector. Genes (Basel) 2019; 10:genes10050374. [PMID: 31108922 PMCID: PMC6562874 DOI: 10.3390/genes10050374] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/10/2019] [Accepted: 05/13/2019] [Indexed: 11/30/2022] Open
Abstract
Gene modification is a promising tool for plant breeding, and gradual application from the laboratory to the field. Selectable marker genes (SMG) are required in the transformation process to simplify the identification of transgenic plants; however, it is more desirable to obtain transgenic plants without selection markers. Transgene integration mediated by site-specific recombination (SSR) systems into the dedicated genomic sites has been demonstrated in a few different plant species. Here, we present an auto-elimination vector system that uses a heat-inducible Cre to eliminate the selectable marker from transgenic maize, without the need for repeated transformation or sexual crossing. The vector combines an inducible site-specific recombinase (hsp70::Cre) that allows for the precise elimination of the selectable marker gene egfp upon heating. This marker gene is used for the initial positive selection of transgenic tissue. The egfp also functions as a visual marker to demonstrate the effectiveness of the heat-inducible Cre. A second marker gene for anthocyanin pigmentation (Rsc) is located outside of the region eliminated by Cre and is used for the identification of transgenic offspring in future generations. Using the heat-inducible auto-excision vector, marker-free transgenic maize plants were obtained in a precisely controlled genetic modification process. Genetic and molecular analyses indicated that the inducible auto-excision system was tightly controlled, with highly efficient DNA excision, and provided a highly reliable method to generate marker-free transgenic maize.
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Affiliation(s)
- Dengxiang Du
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Ruchang Jin
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jinjie Guo
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Fangdong Zhang
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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20
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Dual-targeting by CRISPR/Cas9 leads to efficient point mutagenesis but only rare targeted deletions in the rice genome. 3 Biotech 2019; 9:158. [PMID: 30944805 PMCID: PMC6439133 DOI: 10.1007/s13205-019-1690-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 03/20/2019] [Indexed: 11/05/2022] Open
Abstract
The present study investigated the efficiency of CRISPR/Cas9 in creating genomic deletions as the basis of its application in removing selection marker genes or the intergenic regions. Three loci, representing a transgene and two rice genes, were targeted at two sites each, in separate experiments, and the deletion of the defined fragments was investigated by PCR and sequencing. Genomic deletions were found at a low rate among the transformed callus lines that could be isolated, cultured, and regenerated into plants harboring the deletion. However, randomly regenerated plants showed mixed genomic effects, and generally did not harbor heritable genomic deletions. To determine whether point mutations occurred at each targeted site, a total of 114 plants consisting of primary transgenic lines and their progeny were analyzed. Ninety-three plants showed targeting, 60 of which were targeted at both sites. The presence of point mutations at both sites was correlated with the guide RNA efficiency. In summary, genomic deletions through dual-targeting by the paired-guide RNAs were generally observed in callus, while de novo point mutations at one or both sites occurred at high rates in transgenic plants and their progeny, generating a variety of insertion–deletions or single-nucleotide variations. In this study, point mutations were exceedingly favored over genomic deletions; therefore, for the recovery of plant lines harboring targeted deletions, identifying early transformed clones harboring the deletions, and isolating them for plant regeneration is recommended.
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Timerbaev V, Mitiouchkina T, Pushin A, Dolgov S. Production of Marker-Free Apple Plants Expressing the Supersweet Protein Gene Driven by Plant Promoter. FRONTIERS IN PLANT SCIENCE 2019; 10:388. [PMID: 30984230 PMCID: PMC6449483 DOI: 10.3389/fpls.2019.00388] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 03/13/2019] [Indexed: 05/30/2023]
Abstract
The presence of antibiotic resistance and other marker genes in genetically modified plants causes concern in society because of perceived risks for the environment and human health. The creation of transgenic plants that do not contain foreign genetic material, especially that of bacterial and viral origin, largely alleviates the tension and makes the plants potentially more attractive for consumers. To produce marker-free transgenic apple plants, we used the pMF1 vector, which combines Zygosaccharomyces rouxii recombinaseR and a CodA-nptII bifunctional selectable gene. The thaumatin II gene from the tropical plant Thaumatococcus daniellii, which is under the control of the plant E8 gene (a predominantly fruit-specific promoter) and rbsS3A terminator, was taken as the gene of interest for modification of the fruit taste and enhancing its sweetness. Exploitation of this gene in our laboratory has allowed enhancing the sweetness, as well as improving the taste characteristics, of fruits and vegetables of plants such as strawberry, carrot, tomato and pear. We have obtained three independent transgenic apple lines that have been analyzed by PCR and Southern blot analyses for the presence of T-DNA sequences. Two of them contained a partial sequence of the T-DNA. With one line containing the full insert we then used a delayed strategy for the selection of marker-free plants. After induction of recombinase activity in leaf explants on selective media with 5-fluorocytosine (5-FC) we obtained more than 30 sublines, most of which lost their resistance to kanamycin. Most of the apple sublines showed the expression of the supersweet protein gene in a wide range of levels as detected by RNA accumulation. The plants from the group with the highest transcript level were propagated and grafted onto dwarf rootstocks for early fruit production for future estimates of protein levels and organoleptic analyses. Thus, we developed a protocol that allowed the production of marker-free apple plants expressing the supersweet protein.
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Affiliation(s)
- Vadim Timerbaev
- Laboratory of Expression Systems and Modification of the Plant Genome “Biotron”, Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Russia
- Laboratory of Plant Bioengineering, Nikita Botanical Gardens – National Scientific Center, Russian Academy of Sciences, Yalta, Russia
- Laboratory of Plant Genetic Engineering, All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana Mitiouchkina
- Laboratory of Expression Systems and Modification of the Plant Genome “Biotron”, Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Russia
- Laboratory of Plant Bioengineering, Nikita Botanical Gardens – National Scientific Center, Russian Academy of Sciences, Yalta, Russia
- Laboratory of Plant Genetic Engineering, All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander Pushin
- Laboratory of Expression Systems and Modification of the Plant Genome “Biotron”, Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Russia
- Laboratory of Plant Genetic Engineering, All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Sergey Dolgov
- Laboratory of Expression Systems and Modification of the Plant Genome “Biotron”, Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Russia
- Laboratory of Plant Bioengineering, Nikita Botanical Gardens – National Scientific Center, Russian Academy of Sciences, Yalta, Russia
- Laboratory of Plant Genetic Engineering, All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, Russia
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Collier R, Thomson JG, Thilmony R. A versatile and robust Agrobacterium-based gene stacking system generates high-quality transgenic Arabidopsis plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:573-583. [PMID: 29901840 DOI: 10.1111/tpj.13992] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/15/2018] [Accepted: 05/18/2018] [Indexed: 05/20/2023]
Abstract
Biotechnology provides a means for the rapid genetic improvement of plants. Although single genes have been important in engineering herbicide and pest tolerance traits in crops, future improvements of complex traits like yield and nutritional quality will likely require the introduction of multiple genes. This research reports a system (GAANTRY; Gene Assembly in Agrobacterium by Nucleic acid Transfer using Recombinase technologY) for the flexible, in vivo stacking of multiple genes within an Agrobacterium virulence plasmid Transfer-DNA (T-DNA). The GAANTRY system utilizes in vivo transient expression of unidirectional site-specific recombinases and an alternating selection scheme to sequentially assemble multiple genes into a single transformation construct. To demonstrate GAANTRY's capabilities, 10 cargo sequences were sequentially stacked together to produce a 28.5-kbp T-DNA, which was used to generate hundreds of transgenic events. Approximately 90% of the events identified using a dual antibiotic selection screen exhibited all of the introduced traits. A total of 68% of the tested lines carried a single copy of the selection marker transgene located near the T-DNA left border, and only 8% contained sequence from outside the T-DNA. The GAANTRY system can be modified to easily accommodate any method of DNA assembly and generate high-quality transgenic plants, making it a powerful, yet simple to use tool for plant genetic engineering.
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Affiliation(s)
- Ray Collier
- United States Department of Agriculture-Agriculture Research Service, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA, 94710, USA
| | - James G Thomson
- United States Department of Agriculture-Agriculture Research Service, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA, 94710, USA
| | - Roger Thilmony
- United States Department of Agriculture-Agriculture Research Service, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA, 94710, USA
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Shao M, Blechl A, Thomson JG. Small serine recombination systems ParA-MRS and CinH-RS2 perform precise excision of plastid DNA. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1577-1589. [PMID: 28421718 PMCID: PMC5698047 DOI: 10.1111/pbi.12740] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 03/23/2017] [Accepted: 03/24/2017] [Indexed: 06/07/2023]
Abstract
Selectable marker genes (SMGs) are necessary for selection of transgenic plants. However, once stable transformants have been identified, the marker gene is no longer needed. In this study, we demonstrate the use of the small serine recombination systems, ParA-MRS and CinH-RS2, to precisely excise a marker gene from the plastid genome of tobacco. Transplastomic plants transformed with the pTCH-MRS and pTCH-RS2 vectors, containing the visual reporter gene DsRed flanked by directly oriented MRS and RS2 recognition sites, respectively, were crossed with nuclear-genome transformed tobacco plants expressing plastid-targeted ParA and CinH recombinases, respectively. One hundred per cent of both types of F1 hybrids exhibited excision of the DsRed marker gene. PCR and Southern blot analyses of DNA from F2 plants showed that approximately 30% (CinH-RS2) or 40% (ParA-MRS) had lost the recombinase genes by segregation. The postexcision transformed plastid genomes were stable and the excision events heritable. The ParA-MRS and CinH-RS2 recombination systems will be useful tools for site-specific manipulation of the plastid genome and for generating marker-free plants, an essential step for reuse of SMG and for addressing concerns about the presence of antibiotic resistance genes in transgenic plants.
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Affiliation(s)
- Min Shao
- UC Davis Department of Plant SciencesDavisCAUSA
| | - Ann Blechl
- USDA‐WRRC‐ARS Crop Improvement and Genetics Research UnitAlbanyCAUSA
| | - James G. Thomson
- USDA‐WRRC‐ARS Crop Improvement and Genetics Research UnitAlbanyCAUSA
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Zhang M, Coaker G. Harnessing Effector-Triggered Immunity for Durable Disease Resistance. PHYTOPATHOLOGY 2017; 107:912-919. [PMID: 28430023 PMCID: PMC5810938 DOI: 10.1094/phyto-03-17-0086-rvw] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Genetic control of plant diseases has traditionally included the deployment of single immune receptors with nucleotide-binding leucine-rich repeat (NLR) domain architecture. These NLRs recognize corresponding pathogen effector proteins inside plant cells, resulting in effector-triggered immunity (ETI). Although ETI triggers robust resistance, deployment of single NLRs can be rapidly overcome by pathogen populations within a single or a few growing seasons. In order to generate more durable disease resistance against devastating plant pathogens, a multitiered strategy that incorporates stacked NLRs combined with other sources of disease resistance is necessary. New genetic and genomic technologies have enabled advancements in identifying conserved pathogen effectors, isolating NLR repertoires from diverse plants, and editing plant genomes to enhance resistance. Significant advancements have also been made in understanding plant immune perception at the receptor level, which has promise for engineering new sources of resistance. Here, we discuss how to utilize recent scientific advancements in a multilayered strategy for developing more durable disease resistance.
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Affiliation(s)
- Meixiang Zhang
- First and second authors: Department of Plant Pathology, University of California, Davis 95616; and first author: Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Gitta Coaker
- First and second authors: Department of Plant Pathology, University of California, Davis 95616; and first author: Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
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Collier R, Dasgupta K, Xing YP, Hernandez BT, Shao M, Rohozinski D, Kovak E, Lin J, de Oliveira MLP, Stover E, McCue KF, Harmon FG, Blechl A, Thomson JG, Thilmony R. Accurate measurement of transgene copy number in crop plants using droplet digital PCR. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:1014-1025. [PMID: 28231382 DOI: 10.1111/tpj.13517] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/14/2017] [Accepted: 02/15/2017] [Indexed: 05/22/2023]
Abstract
Genetic transformation is a powerful means for the improvement of crop plants, but requires labor- and resource-intensive methods. An efficient method for identifying single-copy transgene insertion events from a population of independent transgenic lines is desirable. Currently, transgene copy number is estimated by either Southern blot hybridization analyses or quantitative polymerase chain reaction (qPCR) experiments. Southern hybridization is a convincing and reliable method, but it also is expensive, time-consuming and often requires a large amount of genomic DNA and radioactively labeled probes. Alternatively, qPCR requires less DNA and is potentially simpler to perform, but its results can lack the accuracy and precision needed to confidently distinguish between one- and two-copy events in transgenic plants with large genomes. To address this need, we developed a droplet digital PCR-based method for transgene copy number measurement in an array of crops: rice, citrus, potato, maize, tomato and wheat. The method utilizes specific primers to amplify target transgenes, and endogenous reference genes in a single duplexed reaction containing thousands of droplets. Endpoint amplicon production in the droplets is detected and quantified using sequence-specific fluorescently labeled probes. The results demonstrate that this approach can generate confident copy number measurements in independent transgenic lines in these crop species. This method and the compendium of probes and primers will be a useful resource for the plant research community, enabling the simple and accurate determination of transgene copy number in these six important crop species.
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Affiliation(s)
- Ray Collier
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, USDA-ARS, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Kasturi Dasgupta
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Yan-Ping Xing
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, USDA-ARS, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Bryan Tarape Hernandez
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Min Shao
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Dominica Rohozinski
- Plant Gene Expression Center, USDA-ARS, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Emma Kovak
- Plant Gene Expression Center, USDA-ARS, 800 Buchanan Street, Albany, CA, 94710, USA
- Department of Plant & Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Jeanie Lin
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, USDA-ARS, 800 Buchanan Street, Albany, CA, 94710, USA
| | | | - Ed Stover
- USDA-ARS Subtropical Insects and Horticulture Research Unit, Fort Pierce, FL, 34945, USA
| | - Kent F McCue
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, USDA-ARS, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Frank G Harmon
- Plant Gene Expression Center, USDA-ARS, 800 Buchanan Street, Albany, CA, 94710, USA
- Department of Plant & Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Ann Blechl
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, USDA-ARS, 800 Buchanan Street, Albany, CA, 94710, USA
| | - James G Thomson
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, USDA-ARS, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Roger Thilmony
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, USDA-ARS, 800 Buchanan Street, Albany, CA, 94710, USA
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Baltes NJ, Gil-Humanes J, Voytas DF. Genome Engineering and Agriculture: Opportunities and Challenges. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2017; 149:1-26. [PMID: 28712492 PMCID: PMC8409219 DOI: 10.1016/bs.pmbts.2017.03.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In recent years, plant biotechnology has witnessed unprecedented technological change. Advances in high-throughput sequencing technologies have provided insight into the location and structure of functional elements within plant DNA. At the same time, improvements in genome engineering tools have enabled unprecedented control over genetic material. These technologies, combined with a growing understanding of plant systems biology, will irrevocably alter the way we create new crop varieties. As the first wave of genome-edited products emerge, we are just getting a glimpse of the immense opportunities the technology provides. We are also seeing its challenges and limitations. It is clear that genome editing will play an increased role in crop improvement and will help us to achieve food security in the coming decades; however, certain challenges and limitations must be overcome to realize the technology's full potential.
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Dasgupta K, Thilmony R, Stover E, Oliveira ML, Thomson J. Novel R2R3-MYB transcription factors from Prunus americana regulate differential patterns of anthocyanin accumulation in tobacco and citrus. GM CROPS & FOOD 2017; 8:85-105. [PMID: 28051907 PMCID: PMC5443614 DOI: 10.1080/21645698.2016.1267897] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 11/22/2016] [Accepted: 11/28/2016] [Indexed: 11/17/2022]
Abstract
The level of anthocyanins in plants vary widely among cultivars, developmental stages and environmental stimuli. Previous studies have reported that the expression of various MYBs regulate anthocyanin pigmentation during growth and development. Here we examine the activity of 3 novel R2R3-MYB transcription factor (TF) genes, PamMybA.1, PamMybA.3 and PamMybA.5 from Prunus americana. The anthocyanin accumulation patterns mediated by CaMV double35S promoter (db35Sp) controlled expression of the TFs in transgenic tobacco were compared with citrus-MoroMybA, Arabidopsis-AtMybA1 and grapevine-VvMybA1 transgenics during their entire growth cycles. The db35Sp-PamMybA.1 and db35Sp-PamMybA.5 constructs induced high levels of anthocyanin accumulation in both transformed tobacco calli and the regenerated plants. The red/purple color pigmentation induced in the PamMybA.1 and PamMybA.5 lines was not uniformly distributed, but appeared as patches in the leaves, whereas the flowers showed intense uniform pigmentation similar to the VvMybA1 expressing lines. MoroMybA and AtMybA1 showed more uniform pink coloration in both vegetative and reproductive tissues. Plant morphology, anthocyanin content, seed viability, and transgene inheritance were examined for the PamMybA.5 transgenic plants and compared with the controls. We conclude that these TFs alone are sufficient for activating anthocyanin production in plants and may be used as visible reporter genes for plant transformation. Evaluating these TFs in a heterologous crop species such as citrus further validated that these genes can be useful for the metabolic engineering of anthocyanin production and cultivar enhancement.
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Affiliation(s)
- Kasturi Dasgupta
- Department of Plant Sciences, UC Davis, Davis, CA, USA
- Crop Improvement and Genetics Research Unit, Western Regional Research Center, USDA-ARS, Albany, CA, USA
| | - Roger Thilmony
- Crop Improvement and Genetics Research Unit, Western Regional Research Center, USDA-ARS, Albany, CA, USA
| | - Ed Stover
- USDA-ARS Subtropical Insects and Horticulture Research Unit, Fort Pierce, FL, USA
| | - Maria Luiza Oliveira
- USDA-ARS Subtropical Insects and Horticulture Research Unit, Fort Pierce, FL, USA
| | - James Thomson
- Crop Improvement and Genetics Research Unit, Western Regional Research Center, USDA-ARS, Albany, CA, USA
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Tomimatsu K, Kokura K, Nishida T, Yoshimura Y, Kazuki Y, Narita M, Oshimura M, Ohbayashi T. Multiple expression cassette exchange via TP901-1, R4, and Bxb1 integrase systems on a mouse artificial chromosome. FEBS Open Bio 2017; 7:306-317. [PMID: 28286726 PMCID: PMC5337897 DOI: 10.1002/2211-5463.12169] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/17/2016] [Accepted: 11/24/2016] [Indexed: 01/21/2023] Open
Abstract
The site-specific excision of a target DNA sequence for genetic knockout or lineage tracing is a powerful tool for investigating biological systems. Currently, site-specific recombinases (SSRs), such as Cre or Flp recombination target cassettes, have been successfully excised or inverted by a single SSR to regulate transgene expression. However, the use of a single SSR might restrict the complex control of gene expression. This study investigated the potential for expanding the multiple regulation of transgenes using three different integrase systems (TP901-1, R4, and Bxb1). We designed three excision cassettes that expressed luciferase, where the luciferase expression could be exchanged to a fluorescent protein by site-specific recombination. Individual cassettes that could be regulated independently by a different integrase were connected in tandem and inserted into a mouse artificial chromosome (MAC) vector in Chinese hamster ovary cells. The transient expression of an integrase caused the targeted luciferase activity to be lost and fluorescence was activated. Additionally, the integrase system enabled the specific excision of targeted DNA sequences without cross-reaction with the other recombination targets. These results suggest that the combined use of these integrase systems in a defined locus on a MAC vector permits the multiple regulation of transgene expression and might contribute to genomic or cell engineering.
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Affiliation(s)
- Kosuke Tomimatsu
- Research Center for Bioscience and TechnologyTottori UniversityYonagoJapan
- Japan Society for the Promotion of ScienceTokyoJapan
| | - Kenji Kokura
- Chromosome Engineering Research CenterTottori UniversityYonagoJapan
- Division of Human Genome ScienceDepartment of Molecular and Cellular BiologySchool of Life SciencesFaculty of MedicineTottori UniversityYonagoJapan
| | - Tadashi Nishida
- Research Center for Bioscience and TechnologyTottori UniversityYonagoJapan
| | - Yuki Yoshimura
- Department of Biomedical ScienceInstitute of Regenerative Medicine and BiofunctionGraduate School of Medical SciencesTottori UniversityYonagoJapan
- Central Institute for Experimental AnimalsKawasakiJapan
| | - Yasuhiro Kazuki
- Chromosome Engineering Research CenterTottori UniversityYonagoJapan
- Department of Biomedical ScienceInstitute of Regenerative Medicine and BiofunctionGraduate School of Medical SciencesTottori UniversityYonagoJapan
| | - Masashi Narita
- Cancer Research UK Cambridge InstituteLi Ka Shing CentreUniversity of CambridgeUK
| | - Mitsuo Oshimura
- Chromosome Engineering Research CenterTottori UniversityYonagoJapan
- Department of Biomedical ScienceInstitute of Regenerative Medicine and BiofunctionGraduate School of Medical SciencesTottori UniversityYonagoJapan
| | - Tetsuya Ohbayashi
- Research Center for Bioscience and TechnologyTottori UniversityYonagoJapan
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Cardi T, D’Agostino N, Tripodi P. Genetic Transformation and Genomic Resources for Next-Generation Precise Genome Engineering in Vegetable Crops. FRONTIERS IN PLANT SCIENCE 2017; 8:241. [PMID: 28275380 PMCID: PMC5319998 DOI: 10.3389/fpls.2017.00241] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/08/2017] [Indexed: 05/22/2023]
Abstract
In the frame of modern agriculture facing the predicted increase of population and general environmental changes, the securement of high quality food remains a major challenge to deal with. Vegetable crops include a large number of species, characterized by multiple geographical origins, large genetic variability and diverse reproductive features. Due to their nutritional value, they have an important place in human diet. In recent years, many crop genomes have been sequenced permitting the identification of genes and superior alleles associated with desirable traits. Furthermore, innovative biotechnological approaches allow to take a step forward towards the development of new improved cultivars harboring precise genome modifications. Sequence-based knowledge coupled with advanced biotechnologies is supporting the widespread application of new plant breeding techniques to enhance the success in modification and transfer of useful alleles into target varieties. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 system, zinc-finger nucleases, and transcription activator-like effector nucleases represent the main methods available for plant genome engineering through targeted modifications. Such technologies, however, require efficient transformation protocols as well as extensive genomic resources and accurate knowledge before they can be efficiently exploited in practical breeding programs. In this review, we revise the state of the art in relation to availability of such scientific and technological resources in various groups of vegetables, describe genome editing results obtained so far and discuss the implications for future applications.
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Affiliation(s)
- Teodoro Cardi
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA), Centro di ricerca per l’orticoltura, Pontecagnano FaianoItaly
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30
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Abstract
We describe a non-DNA-based system for delivering Cre recombinase protein into maize tissue using gold-plated mesoporous silica nanoparticle (Au-MSN). Cre protein is first loaded into the pores of Au-MSNs and then delivered using the biolistic method to immature embryos of a maize line (Lox-corn), which harbors loxP sites flanking a selection and a reporter gene. The release of the Cre recombinase protein inside the plant cell leads to recombination at the loxP sites, eliminating both genes. Visual screening is used to identify recombination events, which can be regenerated to mature and fertile plants. Using the experimental procedures and conditions described here, as high as 20% of bombarded embryos can produce regenerable recombinant callus events. This nanomaterial-mediated, DNA-free methodology has potential to become an effective tool for plant genome editing.
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Affiliation(s)
- Susana Martin-Ortigosa
- Department of Agronomy, Iowa State University, Ames, IA, 50011-1010, USA
- Center for Plant Transformation, Plant Sciences Institute, Iowa State University, Ames, IA, 50011-1010, USA
- KWS SAAT SE, Einbeck, 37555, Germany
| | - Brian G Trewyn
- Department of Chemistry, Iowa State University, Ames, IA, 50011-3111, USA
- U.S. Department of Energy, Ames Laboratory, Iowa State University, Ames, IA, 50011-3111, USA
- Department of Chemistry, Colorado School of Mines, Golden, CO, 80401, USA
| | - Kan Wang
- Department of Agronomy, Iowa State University, Ames, IA, 50011-1010, USA.
- Center for Plant Transformation, Plant Sciences Institute, Iowa State University, Ames, IA, 50011-1010, USA.
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31
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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.
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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
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Meinke G, Bohm A, Hauber J, Pisabarro MT, Buchholz F. Cre Recombinase and Other Tyrosine Recombinases. Chem Rev 2016; 116:12785-12820. [PMID: 27163859 DOI: 10.1021/acs.chemrev.6b00077] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Tyrosine-type site-specific recombinases (T-SSRs) have opened new avenues for the predictable modification of genomes as they enable precise genome editing in heterologous hosts. These enzymes are ubiquitous in eubacteria, prevalent in archaea and temperate phages, present in certain yeast strains, but barely found in higher eukaryotes. As tools they find increasing use for the generation and systematic modification of genomes in a plethora of organisms. If applied in host organisms, they enable precise DNA cleavage and ligation without the gain or loss of nucleotides. Criteria directing the choice of the most appropriate T-SSR system for genetic engineering include that, whenever possible, the recombinase should act independent of cofactors and that the target sequences should be long enough to be unique in a given genome. This review is focused on recent advancements in our mechanistic understanding of simple T-SSRs and their application in developmental and synthetic biology, as well as in biomedical research.
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Affiliation(s)
- Gretchen Meinke
- Department of Developmental, Molecular & Chemical Biology, Tufts University School of Medicine , Boston, Massachusetts 02111, United States
| | - Andrew Bohm
- Department of Developmental, Molecular & Chemical Biology, Tufts University School of Medicine , Boston, Massachusetts 02111, United States
| | - Joachim Hauber
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology , 20251 Hamburg, Germany
| | | | - Frank Buchholz
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus TU Dresden , 01307 Dresden, Germany
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Abstract
The use of Cre recombinase to carry out conditional mutagenesis of transgenes and insert DNA cassettes into eukaryotic chromosomes is widespread. In addition to the numerous in vivo and in vitro applications that have been reported since Cre was first shown to function in yeast and mammalian cells nearly 30 years ago, the Cre-loxP system has also played an important role in understanding the mechanism of recombination by the tyrosine recombinase family of site-specific recombinases. The simplicity of this system, requiring only a single recombinase enzyme and short recombination sequences for robust activity in a variety of contexts, has been an important factor in both cases. This review discusses advances in the Cre recombinase field that have occurred over the past 12 years since the publication of Mobile DNA II. The focus is on those recent contributions that have provided new mechanistic insights into the reaction. Also discussed are modifications of Cre and/or the loxP sequence that have led to improvements in genome engineering applications.
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Schook LB, Rund L, Begnini KR, Remião MH, Seixas FK, Collares T. Emerging Technologies to Create Inducible and Genetically Defined Porcine Cancer Models. Front Genet 2016; 7:28. [PMID: 26973698 PMCID: PMC4770043 DOI: 10.3389/fgene.2016.00028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 02/13/2016] [Indexed: 12/26/2022] Open
Abstract
There is an emerging need for new animal models that address unmet translational cancer research requirements. Transgenic porcine models provide an exceptional opportunity due to their genetic, anatomic, and physiological similarities with humans. Due to recent advances in the sequencing of domestic animal genomes and the development of new organism cloning technologies, it is now very feasible to utilize pigs as a malleable species, with similar anatomic and physiological features with humans, in which to develop cancer models. In this review, we discuss genetic modification technologies successfully used to produce porcine biomedical models, in particular the Cre-loxP System as well as major advances and perspectives the CRISPR/Cas9 System. Recent advancements in porcine tumor modeling and genome editing will bring porcine models to the forefront of translational cancer research.
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Affiliation(s)
- Lawrence B Schook
- University of Illinois Cancer Center, University of Illinois at ChicagoChicago, IL, USA; Department of Animal Sciences, University of Illinois at Urbana-ChampaignChampaign, IL, USA
| | - Laurie Rund
- Department of Animal Sciences, University of Illinois at Urbana-Champaign Champaign, IL, USA
| | - Karine R Begnini
- Postgraduate Program in Biotechnology, Biotechnology Unit, Technology Development Center, Federal University of Pelotas Pelotas, Brazil
| | - Mariana H Remião
- Postgraduate Program in Biotechnology, Biotechnology Unit, Technology Development Center, Federal University of Pelotas Pelotas, Brazil
| | - Fabiana K Seixas
- Postgraduate Program in Biotechnology, Biotechnology Unit, Technology Development Center, Federal University of Pelotas Pelotas, Brazil
| | - Tiago Collares
- Postgraduate Program in Biotechnology, Biotechnology Unit, Technology Development Center, Federal University of Pelotas Pelotas, Brazil
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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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Manzoni R, Urrios A, Velazquez-Garcia S, de Nadal E, Posas F. Synthetic biology: insights into biological computation. Integr Biol (Camb) 2016; 8:518-32. [DOI: 10.1039/c5ib00274e] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Synthetic biology attempts to rationally engineer biological systems in order to perform desired functions. Our increasing understanding of biological systems guides this rational design, while the huge background in electronics for building circuits defines the methodology.
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Affiliation(s)
- Romilde Manzoni
- Cell Signaling Research Group
- Departament de Ciències Experimentals i de la Salut
- Universitat Pompeu Fabra (UPF)
- E-08003 Barcelona
- Spain
| | - Arturo Urrios
- Cell Signaling Research Group
- Departament de Ciències Experimentals i de la Salut
- Universitat Pompeu Fabra (UPF)
- E-08003 Barcelona
- Spain
| | - Silvia Velazquez-Garcia
- Cell Signaling Research Group
- Departament de Ciències Experimentals i de la Salut
- Universitat Pompeu Fabra (UPF)
- E-08003 Barcelona
- Spain
| | - Eulàlia de Nadal
- Cell Signaling Research Group
- Departament de Ciències Experimentals i de la Salut
- Universitat Pompeu Fabra (UPF)
- E-08003 Barcelona
- Spain
| | - Francesc Posas
- Cell Signaling Research Group
- Departament de Ciències Experimentals i de la Salut
- Universitat Pompeu Fabra (UPF)
- E-08003 Barcelona
- Spain
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37
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Czarnecki O, Bryan AC, Jawdy SS, Yang X, Cheng ZM, Chen JG, Tuskan GA. Simultaneous knockdown of six non-family genes using a single synthetic RNAi fragment in Arabidopsis thaliana. PLANT METHODS 2016; 12:16. [PMID: 26889205 PMCID: PMC4756541 DOI: 10.1186/s13007-016-0116-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/08/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND Genetic engineering of plants that results in successful establishment of new biochemical or regulatory pathways requires stable introduction of one or more genes into the plant genome. It might also be necessary to down-regulate or turn off expression of endogenous genes in order to reduce activity of competing pathways. An established way to knockdown gene expression in plants is expressing a hairpin-RNAi construct, eventually leading to degradation of a specifically targeted mRNA. Knockdown of multiple genes that do not share homologous sequences is still challenging and involves either sophisticated cloning strategies to create vectors with different serial expression constructs or multiple transformation events that is often restricted by a lack of available transformation markers. RESULTS Synthetic RNAi fragments were assembled in yeast carrying homologous sequences to six or seven non-family genes and introduced into pAGRIKOLA. Transformation of Arabidopsis thaliana and subsequent expression analysis of targeted genes proved efficient knockdown of all target genes. CONCLUSIONS We present a simple and cost-effective method to create constructs to simultaneously knockdown multiple non-family genes or genes that do not share sequence homology. The presented method can be applied in plant and animal synthetic biology as well as traditional plant and animal genetic engineering.
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Affiliation(s)
- Olaf Czarnecki
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA ; KWS SAAT SE, Grimsehlstraße 31, 37555 Einbeck, Germany
| | - Anthony C Bryan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Sara S Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Zong-Ming Cheng
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
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Noman A, Aqeel M, He S. CRISPR-Cas9: Tool for Qualitative and Quantitative Plant Genome Editing. FRONTIERS IN PLANT SCIENCE 2016; 7:1740. [PMID: 27917188 PMCID: PMC5116475 DOI: 10.3389/fpls.2016.01740] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 11/04/2016] [Indexed: 05/07/2023]
Abstract
Recent developments in genome editing techniques have aroused substantial excitement among agricultural scientists. These techniques offer new opportunities for developing improved plant lines with addition of important traits or removal of undesirable traits. Increased adoption of genome editing has been geared by swiftly developing Clustered regularly interspaced short palindromic repeats (CRISPR). This is appearing as driving force for innovative utilization in diverse branches of plant biology. CRISPR-Cas9 mediated genome editing is being used for rapid, easy and efficient alteration of genes among diverse plant species. With approximate completion of conceptual work about CRISPR-Cas9, plant scientists are applying this genome editing tool for crop attributes enhancement. The capability of this system for performing targeted and efficient modifications in genome sequence as well as gene expression will certainly spur novel developments not only in model plants but in crop and ornamental plants as well. Additionally, due to non-involvement of foreign DNA, this technique may help alleviating regulatory issues associated with genetically modified plants. We expect that prevailing challenges in plant science like genomic region manipulation, crop specific vectors etc. will be addressed along with sustained growth of this genome editing tool. In this review, recent progress of CRISPR-Cas9 technology in plants has been summarized and discussed. We reviewed significance of CRISPR-Cas9 for specific and non-traditional aspects of plant life. It also covers strengths of this technique in comparison with other genome editing techniques, e.g., Zinc finger nucleases, Transcription activator-like effector nucleases and potential challenges in coming decades have been described.
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Affiliation(s)
- Ali Noman
- College of Crop Science, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Muhammad Aqeel
- Department of Botany, University of AgricultureFaisalabad, Pakistan
| | - Shuilin He
- College of Crop Science, Fujian Agriculture and Forestry UniversityFuzhou, China
- National Education Minister Key Laboratory for Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry UniversityFuzhou, China
- *Correspondence: Shuilin He,
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Sekan AS, Isayenkov SV, Blume YB. Development of marker-free transformants by site-specific recombinases. CYTOL GENET+ 2015. [DOI: 10.3103/s0095452715060080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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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.
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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.
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Shao M, Michno JM, Hotton SK, Blechl A, Thomson J. A bacterial gene codA encoding cytosine deaminase is an effective conditional negative selectable marker in Glycine max. PLANT CELL REPORTS 2015; 34:1707-16. [PMID: 26082433 DOI: 10.1007/s00299-015-1818-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 05/22/2015] [Accepted: 06/01/2015] [Indexed: 06/04/2023]
Abstract
KEY MESSAGE Research describes the practical application of the codA negative selection marker in Soybean. Conditions are given for codA selection at both the shooting and rooting stages of regeneration. Conditional negative selection is a powerful technique whereby the absence of a gene product allows survival in otherwise lethal conditions. In plants, the Escherichia coli gene codA has been employed as a negative selection marker. Our research demonstrates that codA can be used as a negative selection marker in soybean, Glycine max. Like most plants, soybean does not contain cytosine deaminase activity and we show here that wild-type seedlings are not affected by inclusion of 5-FC in growth media. In contrast, transgenic G. max plants expressing codA and grown in the presence of more than 200 μg/mL 5-FC exhibit reductions in hypocotyl and taproot lengths, and severe suppression of lateral root development. We also demonstrate a novel negative selection-rooting assay in which codA-expressing aerial tissues or shoot cuttings are inhibited for root formation in media containing 5-FC. Taken together these techniques allow screening during either the regeneration or rooting phase of tissue culture.
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Affiliation(s)
- Min Shao
- Department of Plant Sciences, University of California-Davis, Davis, CA, 95616, USA
| | - Jean-Michel Michno
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Sara K Hotton
- Department of Plant Sciences, University of California-Davis, Davis, CA, 95616, USA
| | - Ann Blechl
- Western Regional Research Center, USDA-ARS Crop Improvement and Genetics, Albany, CA, 94710, USA
| | - James Thomson
- Western Regional Research Center, USDA-ARS Crop Improvement and Genetics, Albany, CA, 94710, USA.
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Experimental approaches to investigate effector translocation into host cells in the Ustilago maydis/maize pathosystem. Eur J Cell Biol 2015; 94:349-58. [PMID: 26118724 DOI: 10.1016/j.ejcb.2015.06.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The fungus Ustilago maydis is a pathogen that establishes a biotrophic interaction with Zea mays. The interaction with the plant host is largely governed by more than 300 novel, secreted protein effectors, of which only four have been functionally characterized. Prerequisite to examine effector function is to know where effectors reside after secretion. Effectors can remain in the extracellular space, i.e. the plant apoplast (apoplastic effectors), or can cross the plant plasma membrane and exert their function inside the host cell (cytoplasmic effectors). The U. maydis effectors lack conserved motifs in their primary sequences that could allow a classification of the effectome into apoplastic/cytoplasmic effectors. This represents a significant obstacle in functional effector characterization. Here we describe our attempts to establish a system for effector classification into apoplastic and cytoplasmic members, using U. maydis for effector delivery.
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de Oliveira MLP, Stover E, Thomson JG. The codA gene as a negative selection marker in Citrus. SPRINGERPLUS 2015; 4:264. [PMID: 26090311 PMCID: PMC4469690 DOI: 10.1186/s40064-015-1047-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/16/2015] [Indexed: 11/14/2022]
Abstract
The use of positive selectable marker genes is widespread in plant genetic transformation allowing transgenic cells to grow while repressing non-transgenic cells. Negative selectable markers, on the contrary, allow the repression or ablation of transgenic cells. The codA gene of Escherichia coli encodes cytosine deaminase that hydrolyzes 5-fluorocytosine (5-FC) into the cytotoxic compound 5 fluorouracil. We tested the transgenic expression of the bacterial codA gene in citrus as a conditional negative selection marker, with the goal of selecting against plant tissues in which a transgenic cassette has not been successfully removed. We developed transgenic citrus lines containing the selection cassette, codA::nptII, driven by double enhanced CaMV35S promoter, verified by Southern blot analysis, RT-PCR, DsRed expression and subjected these transgenic lines to a 5-FC sensitivity assay. We found that, while non-transgenic citrus were unaffected by the presence of 5-FC, all of the transformed lines displayed symptoms of toxicity, indicating that the codA gene could be used as a negative selectable marker in Citrus, for post-transformation detection of the removal of undesired sequences.
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Affiliation(s)
| | - Ed Stover
- USDA-ARS Subtropical Insects and Horticulture Research Unit, Fort Pierce, FL 34945 USA
| | - James G Thomson
- USDA-ARS Crop Improvement and Utilization Research Unit, Albany, CA 94710 USA
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Bosch P, Forcato DO, Alustiza FE, Alessio AP, Fili AE, Olmos Nicotra MF, Liaudat AC, Rodríguez N, Talluri TR, Kues WA. Exogenous enzymes upgrade transgenesis and genetic engineering of farm animals. Cell Mol Life Sci 2015; 72:1907-29. [PMID: 25636347 PMCID: PMC11114025 DOI: 10.1007/s00018-015-1842-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 01/15/2015] [Accepted: 01/16/2015] [Indexed: 01/14/2023]
Abstract
Transgenic farm animals are attractive alternative mammalian models to rodents for the study of developmental, genetic, reproductive and disease-related biological questions, as well for the production of recombinant proteins, or the assessment of xenotransplants for human patients. Until recently, the ability to generate transgenic farm animals relied on methods of passive transgenesis. In recent years, significant improvements have been made to introduce and apply active techniques of transgenesis and genetic engineering in these species. These new approaches dramatically enhance the ease and speed with which livestock species can be genetically modified, and allow to performing precise genetic modifications. This paper provides a synopsis of enzyme-mediated genetic engineering in livestock species covering the early attempts employing naturally occurring DNA-modifying proteins to recent approaches working with tailored enzymatic systems.
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Affiliation(s)
- Pablo Bosch
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Fco-Qcas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba Republic of Argentina
| | - Diego O. Forcato
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Fco-Qcas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba Republic of Argentina
| | - Fabrisio E. Alustiza
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Fco-Qcas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba Republic of Argentina
| | - Ana P. Alessio
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Fco-Qcas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba Republic of Argentina
| | - Alejandro E. Fili
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Fco-Qcas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba Republic of Argentina
| | - María F. Olmos Nicotra
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Fco-Qcas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba Republic of Argentina
| | - Ana C. Liaudat
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Fco-Qcas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba Republic of Argentina
| | - Nancy Rodríguez
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Fco-Qcas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba Republic of Argentina
| | - Thirumala R. Talluri
- Friedrich-Loeffler-Institute, Institute of Farm Animal Genetics, Biotechnology, 31535 Neustadt, Germany
| | - Wilfried A. Kues
- Friedrich-Loeffler-Institute, Institute of Farm Animal Genetics, Biotechnology, 31535 Neustadt, Germany
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Abdallah NA, Prakash CS, McHughen AG. Genome editing for crop improvement: Challenges and opportunities. GM CROPS & FOOD 2015; 6:183-205. [PMID: 26930114 PMCID: PMC5033222 DOI: 10.1080/21645698.2015.1129937] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Genome or gene editing includes several new techniques to help scientists precisely modify genome sequences. The techniques also enables us to alter the regulation of gene expression patterns in a pre-determined region and facilitates novel insights into the functional genomics of an organism. Emergence of genome editing has brought considerable excitement especially among agricultural scientists because of its simplicity, precision and power as it offers new opportunities to develop improved crop varieties with clear-cut addition of valuable traits or removal of undesirable traits. Research is underway to improve crop varieties with higher yields, strengthen stress tolerance, disease and pest resistance, decrease input costs, and increase nutritional value. Genome editing encompasses a wide variety of tools using either a site-specific recombinase (SSR) or a site-specific nuclease (SSN) system. Both systems require recognition of a known sequence. The SSN system generates single or double strand DNA breaks and activates endogenous DNA repair pathways. SSR technology, such as Cre/loxP and Flp/FRT mediated systems, are able to knockdown or knock-in genes in the genome of eukaryotes, depending on the orientation of the specific sites (loxP, FLP, etc.) flanking the target site. There are 4 main classes of SSN developed to cleave genomic sequences, mega-nucleases (homing endonuclease), zinc finger nucleases (ZFNs), transcriptional activator-like effector nucleases (TALENs), and the CRISPR/Cas nuclease system (clustered regularly interspaced short palindromic repeat/CRISPR-associated protein). The recombinase mediated genome engineering depends on recombinase (sub-) family and target-site and induces high frequencies of homologous recombination. Improving crops with gene editing provides a range of options: by altering only a few nucleotides from billions found in the genomes of living cells, altering the full allele or by inserting a new gene in a targeted region of the genome. Due to its precision, gene editing is more precise than either conventional crop breeding methods or standard genetic engineering methods. Thus this technology is a very powerful tool that can be used toward securing the world's food supply. In addition to improving the nutritional value of crops, it is the most effective way to produce crops that can resist pests and thrive in tough climates. There are 3 types of modifications produced by genome editing; Type I includes altering a few nucleotides, Type II involves replacing an allele with a pre-existing one and Type III allows for the insertion of new gene(s) in predetermined regions in the genome. Because most genome-editing techniques can leave behind traces of DNA alterations evident in a small number of nucleotides, crops created through gene editing could avoid the stringent regulation procedures commonly associated with GM crop development. For this reason many scientists believe plants improved with the more precise gene editing techniques will be more acceptable to the public than transgenic plants. With genome editing comes the promise of new crops being developed more rapidly with a very low risk of off-target effects. It can be performed in any laboratory with any crop, even those that have complex genomes and are not easily bred using conventional methods.
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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.
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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
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Gao X, Zhou J, Li J, Zou X, Zhao J, Li Q, Xia R, Yang R, Wang D, Zuo Z, Tu J, Tao Y, Chen X, Xie Q, Zhu Z, Qu S. Efficient generation of marker-free transgenic rice plants using an improved transposon-mediated transgene reintegration strategy. PLANT PHYSIOLOGY 2015; 167:11-24. [PMID: 25371551 PMCID: PMC4280998 DOI: 10.1104/pp.114.246173] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 11/02/2014] [Indexed: 05/27/2023]
Abstract
Marker-free transgenic plants can be developed through transposon-mediated transgene reintegration, which allows intact transgene insertion with defined boundaries and requires only a few primary transformants. In this study, we improved the selection strategy and validated that the maize (Zea mays) Activator/Dissociation (Ds) transposable element can be routinely used to generate marker-free transgenic plants. A Ds-based gene of interest was linked to green fluorescent protein in transfer DNA (T-DNA), and a green fluorescent protein-aided counterselection against T-DNA was used together with polymerase chain reaction (PCR)-based positive selection for the gene of interest to screen marker-free progeny. To test the efficacy of this strategy, we cloned the Bacillus thuringiensis (Bt) δ-endotoxin gene into the Ds elements and transformed transposon vectors into rice (Oryza sativa) cultivars via Agrobacterium tumefaciens. PCR assays of the transposon empty donor site exhibited transposition in somatic cells in 60.5% to 100% of the rice transformants. Marker-free (T-DNA-free) transgenic rice plants derived from unlinked germinal transposition were obtained from the T1 generation of 26.1% of the primary transformants. Individual marker-free transgenic rice lines were subjected to thermal asymmetric interlaced-PCR to determine Ds(Bt) reintegration positions, reverse transcription-PCR and enzyme-linked immunosorbent assay to detect Bt expression levels, and bioassays to confirm resistance against the striped stem borer Chilo suppressalis. Overall, we efficiently generated marker-free transgenic plants with optimized transgene insertion and expression. The transposon-mediated marker-free platform established in this study can be used in rice and possibly in other important crops.
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Affiliation(s)
- Xiaoqing Gao
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jie Zhou
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jun Li
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiaowei Zou
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jianhua Zhao
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Qingliang Li
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ran Xia
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ruifang Yang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Dekai Wang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zhaoxue Zuo
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jumin Tu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yuezhi Tao
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiaoyun Chen
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Qi Xie
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zengrong Zhu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shaohong Qu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control and Institute of Virology and Biotechnology (X.G., J.Zho., J.L., X.Z., J.Zha., Y.T., S.Q.), Institute of Crop Science and Nuclear Technology Utilization (D.W.), and Institute of Quality Standards for Agricultural Products (X.C.), Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China;Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., R.X., Q.X.); andInstitute of Crop Science (R.Y., J.T.) and Institute of Insect Sciences (Z.Zu., Z.Zh.), Zhejiang University, Hangzhou, Zhejiang 310058, China
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Yu B, Wages JM, Larrick JW. Antibody-membrane switch (AMS) technology for facile cell line development. Protein Eng Des Sel 2014; 27:309-15. [DOI: 10.1093/protein/gzu039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Somleva MN, Xu CA, Ryan KP, Thilmony R, Peoples O, Snell KD, Thomson J. Transgene autoexcision in switchgrass pollen mediated by the Bxb1 recombinase. BMC Biotechnol 2014; 14:79. [PMID: 25148894 PMCID: PMC4148497 DOI: 10.1186/1472-6750-14-79] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 08/18/2014] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Switchgrass (Panicum virgatum L.) has a great potential as a platform for the production of biobased plastics, chemicals and energy mainly because of its high biomass yield on marginal land and low agricultural inputs. During the last decade, there has been increased interest in the genetic improvement of this crop through transgenic approaches. Since switchgrass, like most perennial grasses, is exclusively cross pollinating and poorly domesticated, preventing the dispersal of transgenic pollen into the environment is a critical requisite for the commercial deployment of this important biomass crop. In this study, the feasibility of controlling pollen-mediated gene flow in transgenic switchgrass using the large serine site-specific recombinase Bxb1 has been investigated. RESULTS A novel approach utilizing co-transformation of two separate vectors was used to test the functionality of the Bxb1/att recombination system in switchgrass. In addition, two promoters with high pollen-specific activity were identified and thoroughly characterized prior to their introduction into a test vector explicitly designed for both autoexcision and quantitative analyses of recombination events. Our strategy for developmentally programmed precise excision of the recombinase and marker genes in switchgrass pollen resulted in the generation of transgene-excised progeny. The autoexcision efficiencies were in the range of 22-42% depending on the transformation event and assay used. CONCLUSION The results presented here mark an important milestone towards the establishment of a reliable biocontainment system for switchgrass which will facilitate the development of this crop as a biorefinery feedstock through advanced biotechnological approaches.
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Affiliation(s)
| | - Chang Ai Xu
- Metabolix, Inc., 21 Erie St., Cambridge, MA 02139, USA
| | - Kieran P Ryan
- Metabolix, Inc., 21 Erie St., Cambridge, MA 02139, USA
| | | | | | | | - James Thomson
- USDA-ARS-CIU, 800 Buchanan St., Albany, CA 94710, USA
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