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Thomson G, Dickinson L, Jacob Y. Genomic consequences associated with Agrobacterium-mediated transformation of plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:342-363. [PMID: 37831618 PMCID: PMC10841553 DOI: 10.1111/tpj.16496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/22/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023]
Abstract
Attenuated strains of the naturally occurring plant pathogen Agrobacterium tumefaciens can transfer virtually any DNA sequence of interest to model plants and crops. This has made Agrobacterium-mediated transformation (AMT) one of the most commonly used tools in agricultural biotechnology. Understanding AMT, and its functional consequences, is of fundamental importance given that it sits at the intersection of many fundamental fields of study, including plant-microbe interactions, DNA repair/genome stability, and epigenetic regulation of gene expression. Despite extensive research and use of AMT over the last 40 years, the extent of genomic disruption associated with integrating exogenous DNA into plant genomes using this method remains underappreciated. However, new technologies like long-read sequencing make this disruption more apparent, complementing previous findings from multiple research groups that have tackled this question in the past. In this review, we cover progress on the molecular mechanisms involved in Agrobacterium-mediated DNA integration into plant genomes. We also discuss localized mutations at the site of insertion and describe the structure of these DNA insertions, which can range from single copy insertions to large concatemers, consisting of complex DNA originating from different sources. Finally, we discuss the prevalence of large-scale genomic rearrangements associated with the integration of DNA during AMT with examples. Understanding the intended and unintended effects of AMT on genome stability is critical to all plant researchers who use this methodology to generate new genetic variants.
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Affiliation(s)
- Geoffrey Thomson
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; New Haven, Connecticut 06511, USA
| | - Lauren Dickinson
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; New Haven, Connecticut 06511, USA
| | - Yannick Jacob
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; New Haven, Connecticut 06511, USA
- Yale Cancer Center, Yale School of Medicine; New Haven, Connecticut 06511, USA
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Neelakandan AK, Kabahuma M, Yang Q, Lopez M, Wisser RJ, Balint-Kurti P, Lauter N. Characterization of integration sites and transfer DNA structures in Agrobacterium-mediated transgenic events of maize inbred B104. G3 (BETHESDA, MD.) 2023; 13:jkad166. [PMID: 37523773 PMCID: PMC10542558 DOI: 10.1093/g3journal/jkad166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/17/2023] [Accepted: 07/20/2023] [Indexed: 08/02/2023]
Abstract
In maize, the community-standard transformant line B104 is a useful model for dissecting features of transfer DNA (T-DNA) integration due to its compatibility with Agrobacterium-mediated transformation and the availability of its genome sequence. Knowledge of transgene integration sites permits the analysis of the genomic environment that governs the strength of gene expression and phenotypic effects due to the disruption of an endogenous gene or regulatory element. In this study, we optimized a fusion primer and nested integrated PCR (FPNI-PCR) technique for T-DNA detection in maize to characterize the integration sites of 89 T-DNA insertions in 81 transformant lines. T-DNA insertions preferentially occurred in gene-rich regions and regions distant from centromeres. Integration junctions with and without microhomologous sequences as well as junctions with de novo sequences were detected. Sequence analysis of integration junctions indicated that T-DNA was incorporated via the error-prone repair pathways of nonhomologous (predominantly) and microhomology-mediated (minor) end-joining. This report provides a quantitative assessment of Agrobacterium-mediated T-DNA integration in maize with respect to insertion site features, the genomic distribution of T-DNA incorporation, and the mechanisms of integration. It also demonstrates the utility of the FPNI-PCR technique, which can be adapted to any species of interest.
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Affiliation(s)
| | - Mercy Kabahuma
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
- Interdisciplinary Genetics and Genomics Graduate Program, Iowa State University, Ames, IA 50011, USA
| | - Qin Yang
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling 712100, China
| | - Miriam Lopez
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011, USA
| | - Randall J Wisser
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
- Laboratoire d’Ecophysiologie des Plantes sous Stress Environmentaux, INRAE, University of Montpellier, L’Institut Agro, Montpellier 34000, France
| | - Peter Balint-Kurti
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
- Plant Science Research Unit, USDA-ARS, Raleigh, NC 27695, USA
| | - Nick Lauter
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
- Interdisciplinary Genetics and Genomics Graduate Program, Iowa State University, Ames, IA 50011, USA
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011, USA
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The Structure of T-DNA Insertions in Transgenic Tobacco Plants Producing Bovine Interferon-Gamma. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12020761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Many of the most modern drugs are of a protein nature and are synthesized by transgenic producer organisms. Bacteria, yeast, or animal cell cultures are commonly used, but plants have a number of advantages—minimal biomass unit cost, animal safety (plants are not attacked by mammalian pathogens), the agricultural scale of production, and the ability to produce complex proteins. A disadvantage of plants may be an unstable level of transgene expression, which depends on the transgene structure and its insertion site. We analyzed the structure of T-DNA inserts in transgenic tobacco plants (Nicotiana tabacum L.) belonging to two lines obtained using the same genetic construct but demonstrating different biological activities of the recombinant protein (bovine interferon-gamma). We found that, in one case, T-DNA was integrated into genomic DNA in the region of centromeric repeats, and in the other, into a transcriptionally active region of the genome. It was also found that in one case, the insert has a clustered structure and consists of three copies. Thus, the structure of T-DNA inserts in both lines is not optimal (the optimal structure includes a single copy of the insert located in the active region of the genome). It is desirable to carry out such studies at the early stages of transgenic plants selection.
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Gong W, Zhou Y, Wang R, Wei X, Zhang L, Dai Y, Zhu Z. Analysis of T-DNA integration events in transgenic rice. JOURNAL OF PLANT PHYSIOLOGY 2021; 266:153527. [PMID: 34563791 DOI: 10.1016/j.jplph.2021.153527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/13/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Agrobacterium-mediated plant transformation has been widely used for introducing transgene(s) into a plant genome and plant breeding. However, our understanding of T-DNA integration into rice genome remains limited relative to that in the model dicot Arabidopsis. To better elucidate the T-DNA integration into the rice genome, we investigated extensively the T-DNA ends and their flanking rice genomic sequences from two transgenic rice plants carrying Cowpea Trypsin Inhibitor (CpTI)-derived gene Signal-CpTI-KDEL (SCK) and Bacillus thuringiensis (BT) gene, respectively, by TAIL-PCR method. Analysis of the junction sequences between the T-DNA ends and rice genome DNA indicated that there were three joining patterns of microhomology, filler DNA sequences, and exact joining, and both the T-DNA ends tend to adopt identical manner to join the rice genome. After T-DNA integration, there were several variations of rice genomic sequences, including small deletions at the integration sites, superfluous DNA inserted between T-DNA and genome, and translocation of genomic DNA in the flanking regions. The translocation block could be from a noncontiguous region in the same chromosome or different chromosomes at the integration sites, and the originating position of the translocated block resulted in comparable deletion based on a cut/paste mechanism rather than a replication mechanism. Our study may lead to a better understand of T-DNA integration mechanism and facilitate functional genomic studies and further crop improvement.
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Affiliation(s)
- Wankui Gong
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China.
| | - Yun Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Rui Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China; Public Health Emergency Center, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
| | - Xiaoli Wei
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Lei Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yan Dai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Zhen Zhu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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The Mechanism of T-DNA Integration: Some Major Unresolved Questions. Curr Top Microbiol Immunol 2018; 418:287-317. [DOI: 10.1007/82_2018_98] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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